RProtoBuf/0000755000175100001440000000000013037462513012156 5ustar hornikusersRProtoBuf/TODO0000644000175100001440000000673512440004312012643 0ustar hornikusersCurrent TODO list: o Finish improved vignette / R Journal writeup. o Push some type coercion hacks done in RProtoBuf upstream to Rcpp (Rcpp:as types should work on character strings representing numbers, especially for int64s since we don't otherwise have a way to represent 64-bit integers in base R). o Add more packages that depend on or enhance RProtoBuf. o Improve exception handling to prevent cases where an Rcpp exception crashes the interactive R instance. o Investigate Rcpp Modules support for some classes. Murray is not personally super enthusiastic about this one, as I think it may require non trivial changes to Rcpp and/or result in losing some of the user-friendliness we've crafted in the explicit RcppExported function entry points. Still, it could be explored and may result in significantly fewer lines of code if successful. o Add a FAQ and other documentation / examples. o Add more unit tests. o Explore removing the CLONE() in extractors.cpp. This makes for unusual semantics for any mutable methods of sub-messages. For example, clear(), setExtension(), and probably also update() ( but "$<-" on sub-messages is not a problem, it seems). More details below. o What should we do when we unload the package? Any additional resources to free that is not currently done? o finalizers [murray: what is needed here?] o Clean up formatting / whitespace of R code. The C++ code is now kept consistent through clang-format and a new emacs directory level config in pkg/src, and the style guide notes in the STYLE file on R-Forge. o Thoroughly audit extensions support and other deeply nested types support to ensure everything is implemented as expected. Stuff I think belongs in additional packages that depend on RProtoBuf, rather than inside RProtoBuf directly: o http-powered rpc implementation o More as.Message methods --- Detailed Notes ---- 8. CLONE() --[ examples from Murray illustrating the problem ]-- library(RProtoBuf) InitGoogle() if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto",package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } test <- new(protobuf_unittest.TestAllTypes) test$optional_foreign_message <- new(protobuf_unittest.ForeignMessage, c=3) # Example 1: test$optional_foreign_message$c test$optional_foreign_message$clear() test$optional_foreign_message$c # didn't clear test$optional_foreign_message$c # Example 2: foo <- new(protobuf_unittest.ForeignMessage, c=3) foo$c foo$clear() foo$c # did clear foo$c # Example 3: baz <- test$optional_foreign_message baz$c baz$c <- 4 test$optional_foreign_message$c # still 3, but would be 4 if we removed the CLONE(). Example 1 is currently I think very confusing semantically for users of RProtoBuf with nested messages and I would like to fix that case. Example 2 works correctly now and would not be affected by this change. Example 3 would change behavior and could cause problems for users. Would need to be clearly announced in the NEWS file and to our user list. --[ Romain's thoughts ]-- `$<-` is the task of setMessageField: https://github.com/RProtoBuf/RProtoBuf/blob/master/R/00classes.R#L197 https://github.com/RProtoBuf/RProtoBuf/blob/master/src/mutators.cpp#L377 For "$" we could perhaps move to some sort of copy on change semantics (similar to what R does), instead of what we use currently which is more like copy on access. RProtoBuf/inst/0000755000175100001440000000000013005251424013123 5ustar hornikusersRProtoBuf/inst/examples/0000755000175100001440000000000012440004312014733 5ustar hornikusersRProtoBuf/inst/examples/addressbook.pb0000644000175100001440000000017512440004312017561 0ustar hornikusers < Romain Francoisromain@r-enthusiasts.com" +33(0)... = Dirk Eddelbuetteledd@debian.org" +01..." +01...RProtoBuf/inst/CITATION0000644000175100001440000000513512740556466014307 0ustar hornikusers## JSS publication bibentry(bibtype = "Article", title = "{RProtoBuf}: Efficient Cross-Language Data Serialization in {R}", author = c(person(given = "Dirk", family = "Eddelbuettel", email = "edd@debian.org"), person(given = "Murray", family = "Stokely", email = "murray@stokely.org"), person(given = "Jeroen", family = "Ooms", email = "jeroen.ooms@stat.ucla.edu")), journal = "Journal of Statistical Software", year = "2016", volume = "71", number = "2", pages = "1--24", doi = "10.18637/jss.v071.i02", header = "To cite RProtoBuf in publications use:", textVersion = paste("Dirk Eddelbuettel, Murray Stokely, Jeroen Ooms (2016).", "RProtoBuf: Efficient Cross-Language Data Serialization in R.", "Journal of Statistical Software, 71(2), 1-24.", "doi:10.18637/jss.v071.i02") ) # Also include the normal auto-generated RProtoBuf citation() # citation(auto=meta) RProtoBuf/inst/python/0000755000175100001440000000000012440004312014436 5ustar hornikusersRProtoBuf/inst/python/writemsg.R0000644000175100001440000000071312440004312016423 0ustar hornikusers#simple R script to serialize some R objects library(RProtoBuf) #some vectors serialize_pb(c(1,2,pi, NA,NaN,Inf,-Inf), "double.msg") serialize_pb(c(1L, 2L, NA), "integer.msg") serialize_pb(c(TRUE, FALSE, NA), "logical.msg") serialize_pb(c("foo", "bar", NA), "character.msg") serialize_pb(charToRaw("This is a test"), "raw.msg") #lists serialize_pb(list(foo=c(1,2,pi), bar=TRUE, baz="blabla", zoo=NULL), "list.msg") serialize_pb(iris[1:3,], "dataframe.msg") RProtoBuf/inst/python/runtest.sh0000755000175100001440000000040112440004312016474 0ustar hornikusers#!/bin/sh #write some PB data with R Rscript writemsg.R #compile proto file cp -f ../proto/rexp.proto . protoc rexp.proto --python_out=. rm rexp.proto #read with python and print python readmsg.py #cleanup tmp files rm rexp_pb2.py rexp_pb2.pyc rm *.msg RProtoBuf/inst/python/readmsg.py0000644000175100001440000000051212440004312016430 0ustar hornikusers#!/usr/bin/env python # # Simple test script to read a serialized message in python # import rexp_pb2; import glob; messages = glob.glob("*.msg"); for myfile in messages: print("Reading message " + myfile + " ...") f = open(myfile, 'rb') msg = rexp_pb2.REXP(); msg.ParseFromString(f.read()) f.close(); print(msg) del msg RProtoBuf/inst/NEWS.Rd0000644000175100001440000003374513037406310014203 0ustar hornikusers\name{NEWS} \title{News for Package \pkg{RProtoBuf}} \newcommand{\ghpr}{\href{https://github.com/eddelbuettel/rprotobuf/pull/#1}{##1}} \newcommand{\ghit}{\href{https://github.com/eddelbuettel/rprotobuf/issues/#1}{##1}} \section{Changes in RProtoBuf version 0.4.8 (2017-01-17)}{ \itemize{ \item Windows builds now use the proto3 library as well (PR \ghpr{21} fixing \ghit{20}) } } \section{Changes in RProtoBuf version 0.4.7 (2016-10-27)}{ \itemize{ \item At the request of CRAN, two documentation instances referring to the Omegehat repository were updated to \url{http://omegahat.net} } } \section{Changes in RProtoBuf version 0.4.6 (2016-09-08)}{ \itemize{ \item Support for serializing zero-length objects was added (PR \ghpr{18} addressing \ghit{13}) \item S4 objects are natively encoded (also PR \ghpr{18}) \item The vignette based on the JSS paper no longer uses a macro available only with the R-devel version of jss.cls, and hence builds on all R versions } } \section{Changes in RProtoBuf version 0.4.5 (2016-08-29)}{ \itemize{ \item Support for version 3 of the Protcol Buffers API \item Added 'syntax = "proto2";' to all proto files (PR \ghpr{17}) \item Updated Travis CI script to test against both versions 2 and 3 using custom-built .deb packages of version 3 (PR \ghpr{16}) \item Improved build system with support for custom CXXFLAGS (Craig Radcliffe in PR \ghpr{15}) } } \section{Changes in RProtoBuf version 0.4.4 (2016-07-10)}{ \itemize{ \item New vignette based on JSS publication (v71 i02) \item Some documentation enhancements were made, as well as other minor cleanups to file modes and operations \item Unit-test vignette no longer writes to \code{/tmp} per CRAN request \item The new Windows toolchain (based on g++ 4.9.*) is supported } } \section{Changes in RProtoBuf version 0.4.3 (2015-08-25)}{ \itemize{ \item Declare additional imports from \pkg{methods} in \code{NAMESPACE}. \item Travis CI tests now run faster as all CRAN dependencies are installed as binaries. \item The \code{tools/winlibs.R} script now tests for R (< 3.3.0) before calling the (soon-to-be phased out) \code{setInternet2()} function. \item Several small edits were made to \code{DESCRIPTION} to clarify library dependencies, provide additonal references and conform to now-current R packaging standards. } } \section{Changes in RProtoBuf version 0.4.2 (2014-12-10)}{ \itemize{ \item Address changes suggested by anonymous reviewers for our Journal of Statistical Software submission. \item Make \code{Descriptor} and \code{EnumDescriptor} objects subsettable with "\code{[[}". \item Add \code{length()} method for \code{Descriptor} objects. \item Add \code{names()} method for \code{Message}, \code{Descriptor}, and \code{EnumDescriptor} objects. \item Clarify order of returned list for descriptor objects in \code{as.list} documentation. \item Correct the definition of \code{as.list} for \code{EnumDescriptors} to return a proper list instead of a named vector. \item Update the default print methods to use \code{cat()} with \code{fill=TRUE} instead of \code{show()} to eliminate the confusing \code{[1]} since the classes in \pkg{RProtoBuf} are not vectorized. \item Add support for serializing function, language, and environment objects by falling back to R's native serialization with \code{serialize_pb} and \code{unserialize_pb} to make it easy to serialize into a Protocol Buffer all of the more than 100 datasets which come with R. \item Use \code{normalizePath} instead of creating a temporary file with \code{file.create} when getting absolute path names. \item Add unit tests for all of the above. } } \section{Changes in RProtoBuf version 0.4.1 (2014-03-25)}{ \itemize{ \item Document and add a test for the deprecated group functionality. \item Add a \code{CITATION} file pointing to the arXiv.org preprint. \item Fix a bug in the \code{show} method for \code{EnumDescriptor} types. \item Import all top-level enums from imported \code{.proto} files. \item Removed duplicate enum value type from the unit tests that caused problems with the most recent libprotobuf-2.5. (without option allow_alias). } } \section{Changes in RProtoBuf version 0.4.0 (2014-01-14)}{ \itemize{ \item Changes to support CRAN builds for MS Windows. \item Added functions \code{serialize_pb}, \code{unserialize_pb}, and \code{can_serialize_pb} plus documentation from Jeroen Ooms RProtoBufUtils package. \item New dir \code{inst/python} with some Python examples. \item Added Jeroen Ooms as author. \item Vignettes have been converted to the R 3.0.0 or later use of external vignette builders, no longer need a \code{Makefile} \item Added missing methods to dollar completion list for Message, Descriptor, EnumValueDescriptor, and FileDescriptor classes. \item Add missing export for \code{.DollarNames} EnumValueDescriptor to allow completion on that class. \item Add more than 15 additional pages to the main Intro vignette documenting better all of the S4 classes implemented by RProtoBuf, updating the type mapping tables to take into account 64-bit support, and documenting advanced features such as Extensions. \item Added better error checking in EnumDescriptors to catch the case when wrong types are provided. \item Updated the FileDescriptor \code{name()} method to accept a boolean for full paths just like the generic \code{name()} method. \item Correct a bug that incorrectly dispatched \code{as.character()} when \code{as.list()} was called on Descriptor objects. \item Update FileDescriptor \code{$} dispatch to work properly for the names of fields defined in the FileDescriptor, instead of just returning \code{NULL} even for types returned by \code{$} completion. \item Added a reservation for extension fields in the example tutorial.Person schema. \item Support setting int32 fields with character representations and raise an R-level \code{stop()} error if the provided string can not be parsed as a 32-bit integer, rather than crashing the R instance. \item Update the project TODO file. \item Add better documentation and tests for all of the above. \item Corrected the handling of uint32 and fixed32 types in protocol buffers to ensure that they work with numbers as large as 2^32 - 1, which is larger than an integer can hold in R since R does not have an unsigned integer class. These values are stored as doubles internally now to avoid losing precision. \item Added unit tests to verify behavior of RProtoBuf with extreme values for uint32 types. \item Removed old exception handling code and instead rely on the more modern Rcpp::stop method maintained in Rcpp. \item Add better error messages when setting a repeated field of messages to inform the user which element index was of the wrong type and what the expected type was. \item Add an optional 'partial' argument to readASCII allowing uninitialized message fragments to be read in. \item (internal) Added const qualifiers in more places throughout the C++ code for type safety. \item (internal) Standardize coding conventions of the C++ files and run them through clang-format for consistency. A STYLE file has been submitted to R-Forge with details about the coding standards and how they are enforced with Emacs and clang-format. \item Applied changes suggested by Kevin Ushey to the \code{S4} class handling to support both the currently released \CRANpkg{Rcpp} as well as the currently pending next version. } } \section{Changes in RProtoBuf version 0.3.2 (2013-12-15)}{ \itemize{ \item Fixed a bug that erroneously prevented users from setting raw byte fields in protocol buffers under certain circumstances. \item Give a user friendly error message when seting an extension to a message of the wrong type instead of causing a C++ check failure that terminates the Rsession. \item Change object table lookup slightly to allow users to use the \code{<<-} operator in code using \pkg{RProtoBuf} without hitting a \code{stop()} error in the lookup routine. \item Add missing \code{enum_type} method and improve show method for EnumValueDescriptors. \item Improve documentation and tests for all of the above. \item Rewrote \code{tests/} script calling \CRANpkg{RUnit} tests } } \section{Changes in RProtoBuf version 0.3.1 (2013-09-13)}{ \itemize{ \item Added support for setting and getting 64-bit integer types as character strings of decimal integers to work around R's lack of native 64-bit integer types. \item Added better error handling, documentation, and tests to the extensions support (getExtension and setExtension). \item Add support to P for returning extension descriptors. \item Improved error messages to include field names when invalid fields are specified to protocol buffer messages with new, update, etc. \item Improved configure to detect and pass -std=c++0x if it is available to enable long long 64-bit integer support in Rcpp. \item Improved configure in the case when pkg-config is not available or does not know about the google protocol buffer includes. \item Replaced newly deprecated Rcpp macros with a simplified macro functionality to avoid warnings on the latest development version of Rcpp. } } \section{Changes in RProtoBuf version 0.3 (2013-07-13)}{ \itemize{ \item Added support for Protocol Buffer extensions through the new getExtension and setExtension methods for Message objects, and added top-level extensions to the descriptor pool. \item Added more user-friendly \code{show()} methods for Messages, Descriptors, and other RProtoBuf objects. A common source of confusion on the mailing lists is to confuse Messages and Descriptors. The new \code{show()} methods succinctly display more information about e.g. the number of set fields in a message to make it a little clearer to users what type of object they are working with. \item Added has method for EnumDescriptor objects to test existance of a named constant in an enumeration, and fix a bug in the length method for these objects. \item Added a number method for EnumValueDescriptor objects to return the number of a named enumeration constant directly. \item Improved documentation and unit tests. } } \section{Changes in RProtoBuf version 0.2.6 (2012-10-04)}{ \itemize{ \item Applied several more patches by Murray to \itemize{ \item correct '_' and '__' mismatches in wrapper calls \item update a few manual pages for style, and add examples \item fix a bug where NAs were silently treated as TRUE for logical/bool types \item fix a bug that caused crashes when adding vectors to optional fields \item fix bugs in readASCII that returned empty protocol buffers when the file or connection could not be opened \item distinguish between non-existant and not-set fieldswith has() by returning NULL in the former case. \item fix a bug that caused non-deterministic behavior when setting a repeated message field in a protobuf to a single Message. \item add unit tests for all of the above. } \item Added Murray to Authors: field in DESCRIPTION \item Removed old and unconvincing example on RProtoBuf for storage and serialization in an imagined HighFrequencyFinance context } } \section{Changes in RProtoBuf version 0.2.5 (2012-08-08)}{ \itemize{ \item Applied patches by Murray to \itemize{ \item correctly deal with nested Protocol Buffer definitions, and also add new unit test for this \item test a a protocol buffer for missing required fields before serializing it, also add a unit test \item add a small stylistic fix and examples to the 'add.Rd' manual page } \item Moved inst/doc/ to vignettes/ per newer CRAN Policy } } \section{Changes in RProtoBuf version 0.2.4 (2012-05-15)}{ \itemize{ \item Applied several patches kindly supplied by Murray Stokely to \itemize{ \item properly work with repeated strings \item correct C++ function naming in a few instances \item add an example of ascii export/import of messages } \item Suppport g++-4.7 and stricter #include file checking by adding unistd \item Made small improvements to the startup code } } \section{Changes in RProtoBuf version 0.2.3 (2011-04-12)}{ \itemize{ \item Protect UINT64 and INT64 with '#ifdef RCPP_HAS_LONG_LONG' which itself is valid with either g++ <= 4.4, or newer versions if the -std=c++0x is used \item The documentation Makefile now uses the $R_HOME environment variable \item The documentation Makefile no longer calls clean in the all target } } \section{Changes in RProtoBuf version 0.2.2 (2011-01-11)}{ \itemize{ \item Applied two patches by Murray Stokely which \itemize{ \item correct a typo preventing some functions from being called, \item add bounds checking in call to google protobuf library, \item add a new name method \item add a tiny unit test for the above \item add more graceful error handling \item add support for import patterns other than .proto$, \item add simple reading file that does not exist (exception) test \item add simple repeated field unit test } } } \section{Changes in RProtoBuf version 0.2.1 (2010-10-18)}{ \itemize{ \item Support for raw bytes added thanks to a patch by Koert Kuipers } } \section{Changes in RProtoBuf version 0.2.0 (2010-09-10)}{ \itemize{ \item Second release with numerous internal changes made possible by changes in Rcpp } } \section{Changes in RProtoBuf version 0.1-0 (2010-02-01)}{ \itemize{ \item Initial CRAN release } } RProtoBuf/inst/THANKS0000644000175100001440000000021212440004312014023 0ustar hornikusers In alphabetical order: Koert Kuipers for a patch adding raw byte support Murray Stokely for several patches and helpful discussions RProtoBuf/inst/doc/0000755000175100001440000000000013037407201013671 5ustar hornikusersRProtoBuf/inst/doc/RProtoBuf-unitTests.pdf0000644000175100001440000024513413037407201020257 0ustar hornikusers%PDF-1.5 % 5 0 obj << /Length 581 /Filter /FlateDecode >> stream xWn0 +tE(ٖv,(0lӶ8E4.dh#-s1 eɐ-^hn0^E0:Qn DʃZ|#?M2Z˷i'oڢȍCbK.]Y1*)оT@+o󈗊7c6Hex-iT(:fXq5.j*펋!z#=[*\{\/DK8ϐU6wS3G!ݖo3MS⣯01őujPM)ɣ)벨j;PއXuxۓ븳3:z1enEP!2j(,1nD䇱!IɆpU+8l zRӤ-W8E7hqK}99_c 3ٍGRѱA\(Q.Tk^'A endstream endobj 17 0 obj << /Length 726 /Filter /FlateDecode >> stream x]o0"!$v OCjxBoCt[2ؿZ@ꇓuJ&Gwd&D%HI'1"3xz?4,5,4|ӰװҰps<(Cu \[  *Kͥ9pNbZiEZ4 5$wv@86{pƾKdnh@hWc>n 4f3<Ct5\-h߾Jz'>Ax}SCqW]+m'&0HYh` X/.Π5Wa{]W]h7Olr7&Y)Gwe:@60ᩈp<(*}bTԷLӫs9L2KR* ')cõ.7@v#ѹ(d_hA;\eAB :* 18\s3\ CPlr%I! 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Many formats commonly used to import and export data between different programs or systems, such as CSV or JSON, are verbose, inefficient, not type-safe, or tied to a specific programming language. Protocol Buffers are a popular method of serializing structured data between applications -- while remaining independent of programming languages or operating systems. They offer a unique combination of features, performance, and maturity that seems particularly well suited for data-driven applications and numerical computing. The \pkg{RProtoBuf} package provides a complete interface to Protocol Buffers from the \proglang{R} environment for statistical computing. This paper outlines the general class of data serialization requirements for statistical computing, describes the implementation of the \pkg{RProtoBuf} package, and illustrates its use with example applications in large-scale data collection pipelines and web services. } \Keywords{\proglang{R}, \pkg{Rcpp}, Protocol Buffers, serialization, cross-platform} \Plainkeywords{R, Rcpp, Protocol Buffers, serialization, cross-platform} \Volume{71} \Issue{2} \Month{July} \Year{2016} \Submitdate{2014-02-05} \Acceptdate{2015-04-13} %\DOI{10.18637/jss.v071.i02} %% The address of (at least) one author should be given %% in the following format: \Address{ Dirk Eddelbuettel \\ Debian Project \\ River Forest, IL, United States of America\\ E-mail: \email{edd@debian.org}\\ URL: \url{http://dirk.eddelbuettel.com/}\\ Murray Stokely\\ Google, Inc.\\ 1600 Amphitheatre Parkway\\ Mountain View, CA, United States of America\\ E-mail: \email{murray@stokely.org}\\ URL: \url{http://www.stokely.org/}\\ Jeroen Ooms\\ UCLA Department of Statistics\\ University of California, Los Angeles\\ Los Angeles, CA, United States of America\\ E-mail: \email{jeroen.ooms@stat.ucla.edu}\\ URL: \url{https://jeroenooms.github.io/} } %% It is also possible to add a telephone and fax number %% before the e-mail in the following format: %% Telephone: +43/512/507-7103 %% Fax: +43/512/507-2851 %% for those who use Sweave please include the following line (with % symbols): %% need no \usepackage{Sweave.sty} %% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% <>= library(RProtoBuf) rprotobuf.version <- packageDescription("RProtoBuf")$Version rprotobuf.date <- packageDescription("RProtoBuf")$Date now.date <- strftime(Sys.Date(), "%B %d, %Y") @ \begin{document} \SweaveOpts{concordance=FALSE,prefix.string=figures/fig} %% include your article here, just as usual %% Note that you should use the \pkg{}, \proglang{} and \code{} commands. % We don't want a left margin for Sinput or Soutput for our table 1. %\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=0em} %\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=0em} %\DefineVerbatimEnvironment{Scode}{Verbatim}{xleftmargin=2em} % Setting the topsep to 0 reduces spacing from input to output and % improves table 1. \fvset{listparameters={\setlength{\topsep}{0pt}}} \renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}} %% DE: I tend to have wider option(width=...) so this %% guarantees better line breaks <>= ## cf http://www.jstatsoft.org/style#q12 options(prompt = "R> ", continue = "+ ", width = 70, useFancyQuotes = FALSE, digits = 4) @ \maketitle \section{Introduction} Modern data collection and analysis pipelines increasingly involve collections of decoupled components in order to better manage software complexity through reusability, modularity, and fault isolation \citep{Wegiel:2010:CTT:1932682.1869479}. These pipelines are frequently built using different programming languages for the different phases of data analysis -- collection, cleaning, modeling, analysis, post-processing, and presentation -- in order to take advantage of the unique combination of performance, speed of development, and library support offered by different environments and languages. Each stage of such a data analysis pipeline may produce intermediate results that need to be stored in a file, or sent over the network for further processing. Given these requirements, how do we safely and efficiently share intermediate results between different applications, possibly written in different languages, and possibly running on different computer systems? In computer programming, \emph{serialization} is the process of translating data structures, variables, and session states into a format that can be stored or transmitted and then later reconstructed in the original form \citep{clinec++}. Programming languages such as \proglang{R} \citep{r}, \proglang{Julia} \citep{julia}, \proglang{Java}, and \proglang{Python} \citep{python} include built-in support for serialization, but the default formats are usually language-specific and thereby lock the user into a single environment. Data analysts and researchers often use character-separated text formats such as CSV \citep{shafranovich2005common} to export and import data. However, anyone who has ever used CSV files will have noticed that this method has many limitations: It is restricted to tabular data, lacks type-safety, and has limited precision for numeric values. Moreover, ambiguities in the format itself frequently cause problems. For example, conventions on which characters are used as separator or decimal point vary by country. \emph{Extensible markup language} (XML) is a well-established and widely-supported format with the ability to define just about any arbitrarily complex schema \citep{nolan2013xml}. However, it pays for this complexity with comparatively large and verbose messages, and added complexity at the parsing side (these problems are somewhat mitigated by the availability of mature libraries and parsers). Because XML is text-based and has no native notion of numeric types or arrays, it is usually not a very practical format to store numeric data sets as they appear in statistical applications. A more modern format is \emph{\proglang{JavaScript} object notation} (JSON), which is derived from the object literals of \proglang{JavaScript}, and already widely-used on the world wide web. Several \proglang{R} packages implement functions to parse and generate JSON data from \proglang{R} objects \citep{rjson,RJSONIO,jsonlite}. JSON natively supports arrays and four primitive types: numbers, strings, booleans, and null. However, as it also is a text-based format, numbers are stored in human-readable decimal notation which is inefficient and leads to loss of type (double versus integer) and precision. A number of binary formats based on JSON have been proposed that reduce the parsing cost and improve efficiency, but these formats are not widely supported. Furthermore, such formats lack a separate schema for the serialized data and thus still duplicate field names with each message sent over the network or stored in a file. Once the data serialization needs of an application become complex enough, developers typically benefit from the use of an \emph{interface description language}, or \emph{IDL}. IDLs like Protocol Buffers \citep{protobuf}, Apache Thrift \citep{Apache:Thrift}, and Apache Avro \citep{Apache:Avro} provide a compact well-documented schema for cross-language data structures and efficient binary interchange formats. Since the schema is provided separately from the data, the data can be efficiently encoded to minimize storage costs when compared with simple ``schema-less'' binary interchange formats. %Many sources compare data serialization formats %and show Protocol Buffers perform favorably to the alternatives; see %\citet{Sumaray:2012:CDS:2184751.2184810} for one such comparison. Protocol Buffers perform well in the comparison of such formats by \citet{Sumaray:2012:CDS:2184751.2184810}. This paper describes an \proglang{R} interface to Protocol Buffers, and is organized as follows. Section~\ref{sec:protobuf} provides a general high-level overview of Protocol Buffers as well as a basic motivation for their use. Section~\ref{sec:rprotobuf-basic} describes the interactive \proglang{R} interface provided by the \pkg{RProtoBuf} package, and introduces the two main abstractions: \emph{Messages} and \emph{Descriptors}. Section~\ref{sec:rprotobuf-classes} details the implementation of the main \proglang{S}4 classes and methods. Section~\ref{sec:types} describes the challenges of type coercion between \proglang{R} and other languages. Section~\ref{sec:evaluation} introduces a general \proglang{R} language schema for serializing arbitrary \proglang{R} objects and compares it to the serialization capabilities built directly into \proglang{R}. Sections~\ref{sec:mapreduce} and \ref{sec:opencpu} provide real-world use cases of \pkg{RProtoBuf} in MapReduce and web service environments, respectively, before Section~\ref{sec:summary} concludes. \makeatletter \if@nojss This vignette corresponds to the paper published in the \textsl{Journal of Statistical Software}. For citations, please see the output of \proglang{R} function \texttt{citation("RProtoBuf")}. This version corresponds to \pkg{RProtoBuf} version \Sexpr{rprotobuf.version} and was typeset on \Sexpr{now.date}. \fi \makeatother \section{Protocol Buffers} \label{sec:protobuf} Protocol Buffers are a modern, language-neutral, platform-neutral, extensible mechanism for sharing and storing structured data. Some of their features, particularly in the context of data analysis, are: % \begin{itemize} \item \emph{Portable}: Enable users to send and receive data between applications as well as different computers or operating systems. \item \emph{Efficient}: Data is serialized into a compact binary representation for transmission or storage. \item \emph{Extensible}: New fields can be added to Protocol Buffer schemas in a forward-compatible way that does not break older applications. \item \emph{Stable}: Protocol Buffers have been in wide use for over a decade. \end{itemize} % \begin{figure}[t!] \centering \includegraphics[width=0.9\textwidth]{protobuf-distributed-system-crop.pdf} \caption{Example usage of Protocol Buffers.} \label{fig:protobuf-distributed-usecase} \end{figure} % Figure~\ref{fig:protobuf-distributed-usecase} illustrates an example communication work flow with Protocol Buffers and an interactive \proglang{R} session. Common use cases include populating a request remote-procedure call (RPC) Protocol Buffer in \proglang{R} that is then serialized and sent over the network to a remote server. The server deserializes the message, acts on the request, and responds with a new Protocol Buffer over the network. The key difference to, say, a request to an \pkg{Rserve} \citep{Urbanek:2003:Rserve,CRAN:Rserve} instance is that the remote server may be implemented in any language. %, with no dependence on \proglang{R}. While traditional IDLs have at times been criticized for code bloat and complexity, Protocol Buffers are based on a simple list and records model that is flexible and easy to use. The schema for structured Protocol Buffer data is defined in \code{.proto} files, which may contain one or more message types. Each message type has one or more fields. A field is specified with a unique number (called a \emph{tag number}), a name, a value type, and a field rule specifying whether the field is optional, required, or repeated. The supported value types are numbers, enumerations, booleans, strings, raw bytes, or other nested message types. The \code{.proto} file syntax for defining the structure of Protocol Buffer data is described comprehensively on Google Code at \url{http://code.google.com/apis/protocolbuffers/docs/proto.html}. Table~\ref{tab:proto} shows an example \code{.proto} file that defines the \code{tutorial.Person} type\footnote{The compound name \code{tutorial.Person} in \proglang{R} is derived from the name of the message (\emph{Person}) and the name of the package defined at the top of the \code{.proto} file in which it is defined (\emph{tutorial}).}. The \proglang{R} code in the right column shows an example of creating a new message of this type and populating its fields. \noindent \begin{table}[t!] \begin{tabular}{p{0.45\textwidth}p{0.5\textwidth}} \toprule Schema : \code{addressbook.proto} & Example \proglang{R} session\\ \cmidrule{1-2} \begin{minipage}{.40\textwidth} \vspace{2mm} \begin{example} package tutorial; message Person { required string name = 1; required int32 id = 2; optional string email = 3; enum PhoneType { MOBILE = 0; HOME = 1; WORK = 2; } message PhoneNumber { required string number = 1; optional PhoneType type = 2; } repeated PhoneNumber phone = 4; } \end{example} \vspace{2mm} \end{minipage} & \begin{minipage}{.55\textwidth} <>= library("RProtoBuf") p <- new(tutorial.Person, id=1, name="Dirk") p$name p$name <- "Murray" cat(as.character(p)) serialize(p, NULL) class(p) @ \end{minipage} \\ \bottomrule \end{tabular} \caption{The schema representation from a \code{.proto} file for the \code{tutorial.Person} class (left) and simple \proglang{R} code for creating an object of this class and accessing its fields (right).} \label{tab:proto} \end{table} For added speed and efficiency, the \proglang{C++}, \proglang{Java}, and \proglang{Python} bindings to Protocol Buffers are used with a compiler that translates a Protocol Buffer schema description file (ending in \code{.proto}) into language-specific classes that can be used to create, read, write, and manipulate Protocol Buffer messages. The \proglang{R} interface, in contrast, uses a reflection-based API that makes some operations slightly slower but which is much more convenient for interactive data analysis. All messages in \proglang{R} have a single class structure, but different accessor methods are created at runtime based on the named fields of the specified message type, as described in the next section. \section{Basic usage: Messages and descriptors} \label{sec:rprotobuf-basic} This section describes how to use the \proglang{R} API to create and manipulate Protocol Buffer messages in \proglang{R}, and how to read and write the binary representation of the message (often called the \emph{payload}) to files and arbitrary binary \proglang{R} connections. The two fundamental building blocks of Protocol Buffers are \emph{Messages} and \emph{Descriptors}. Messages provide a common abstract encapsulation of structured data fields of the type specified in a Message Descriptor. Message Descriptors are defined in \code{.proto} files and define a schema for a particular named class of messages. \subsection[Importing Message Descriptors from .proto files]{Importing Message Descriptors from \code{.proto} files} To create or parse a Protocol Buffer message, one must first read in the Message Descriptor (\emph{message type}) from a \code{.proto} file. A small number of message types are imported when the package is first loaded, including the \code{tutorial.Person} type we saw in the last section. All other types must be imported from \code{.proto} files using the \code{readProtoFiles} function, which can either import a single file, all files in a directory, or every \code{.proto} file provided by a particular \proglang{R} package. After importing proto files, the corresponding Message Descriptors are available by name from the \code{RProtoBuf:DescriptorPool} environment in the \proglang{R} search path. This environment is implemented with the user-defined tables framework from the \pkg{RObjectTables} package available from the OmegaHat project \citep{RObjectTables}. Instead of being associated with a static hash table, this environment dynamically queries the in-memory database of loaded descriptors during normal variable lookup. This allows new descriptors to be parsed from \code{.proto} files and added to the global namespace.\footnote{Note that there is a significant performance overhead with this \pkg{RObjectTables} implementation. Because the table is on the search path and is not cacheable, lookups of symbols that are behind it in the search path cannot be added to the global object cache, and \proglang{R} must perform an expensive lookup through all of the attached environments and the Protocol Buffer definitions to find common symbols (most notably those in base) from the global environment. Fortunately, proper use of namespaces and package imports reduces the impact of this for code in packages.} \subsection*{Creating, accessing, and modifying messages.} New messages are created with the \code{new} function which accepts a Message Descriptor and optionally a list of ``name = value'' pairs to set in the message. %The objects contained in the special environment are %descriptors for their associated message types. Descriptors will be %discussed in detail in another part of this document, but for the %purpose of this section, descriptors are just used with the \code{new} %function to create messages. <<>>= p <- new(tutorial.Person, name = "Murray", id = 1) @ % \subsection*{Access and modify fields of a message} Once the message is created, its fields can be queried and modified using the dollar operator of \proglang{R}, making Protocol Buffer messages seem like lists. <<>>= p$name p$id p$email <- "murray@stokely.org" @ As opposed to \proglang{R} lists, no partial matching is performed and the name must be given entirely. The \verb|[[| operator can also be used to query and set fields of a message, supplying either their name or their tag number: <<>>= p[["name"]] <- "Murray Stokely" p[[ 2 ]] <- 3 p[["email"]] @ Protocol Buffers include a 64-bit integer type, but \proglang{R} lacks native 64-bit integer support. A workaround is available and described in Section~\ref{sec:int64} for working with large integer values. \subsection*{Printing, reading, and writing Messages} % \textbf{Printing, Reading, and Writing Messages} Protocol Buffer messages and descriptors implement \code{show} methods that provide basic information about the message: <<>>= p @ %For additional information, such as for debugging purposes, The \code{as.character} method provides a more complete ASCII representation of the contents of a message. <<>>= writeLines(as.character(p)) @ % \subsection{Serializing messages} A primary benefit of Protocol Buffers is an efficient binary wire-format representation. The \code{serialize} method is implemented for Protocol Buffer messages to serialize a message into a sequence of bytes (raw vector) that represents the message. The raw bytes can then be parsed back into the original message safely as long as the message type is known and its descriptor is available. <<>>= serialize(p, NULL) @ The same method can be used to serialize messages to files or arbitrary binary connections: <<>>= tf1 <- tempfile() serialize(p, tf1) readBin(tf1, raw(0), 500) @ %\subsection{Parsing messages} The \pkg{RProtoBuf} package defines the \code{read} and \code{readASCII} functions to read messages from files, raw vectors, or arbitrary connections. \code{read} expects to read the message payload from binary files or connections and \code{readASCII} parses the human-readable ASCII output that is created with \code{as.character}. The binary representation of the message does not contain information that can be used to dynamically infer the message type, so we have to provide this information to the \code{read} function in the form of a descriptor: <<>>= msg <- read(tutorial.Person, tf1) writeLines(as.character(msg)) @ The \code{input} argument of \code{read} can also be a binary readable \proglang{R} connection, such as a binary file connection, or a raw vector of serialized bytes. \section{Under the hood: S4 classes and methods} \label{sec:rprotobuf-classes} The \pkg{RProtoBuf} package uses the \proglang{S}4 system to store information about descriptors and messages. Each \proglang{R} object contains an external pointer to an object managed by the \pkg{protobuf} \proglang{C++} library, and the \proglang{R} objects make calls into more than 100 \proglang{C++} functions that provide the glue code between the \proglang{R} language classes and the underlying \proglang{C++} classes. \proglang{S}4 objects are immutable, and so the methods that modify field values of a message return a new copy of the object with \proglang{R}'s usual functional copy on modify semantics\footnote{\pkg{RProtoBuf} was designed and implemented before Reference Classes were introduced to offer a new class system with mutable objects. If \pkg{RProtoBuf} were implemented today Reference Classes would almost certainly be a better design choice than \proglang{S}4 classes.}. Using the \proglang{S}4 system allows the package to dispatch methods that are not generic in the \proglang{S}3 sense, such as \code{new} and \code{serialize}. The \pkg{Rcpp} package \citep{eddelbuettel2011rcpp,eddelbuettel2013seamless} is used to facilitate this integration of the \proglang{R} and \proglang{C++} code for these objects. Each method is wrapped individually which allows us to add user-friendly custom error handling, type coercion, and performance improvements at the cost of a more verbose implementation. The \pkg{RProtoBuf} package in many ways motivated the development of \pkg{Rcpp} Modules \citep{eddelbuettel2013exposing}, which provide a more concise way of wrapping \proglang{C++} functions and classes in a single entity. Since \pkg{RProtoBuf} users are most often switching between two or more different languages as part of a larger data analysis pipeline, both generic function and message passing OO style calling conventions are supported: \begin{itemize} \item The functional dispatch mechanism of the the form \verb|method(object, arguments)| (common to \proglang{R}). \item The message passing object-oriented notation of the form \verb|object$method(arguments)|. \end{itemize} Additionally, \pkg{RProtoBuf} supports tab completion for all classes. Completion possibilities include method names for all classes, plus \emph{dynamic dispatch} on names or types specific to a given object. This functionality is implemented with the \code{.DollarNames} S3 generic function defined in the \pkg{utils} package that is included with \proglang{R} \citep{r}. Table~\ref{class-summary-table} lists the six primary message and descriptor classes in \pkg{RProtoBuf}. The package documentation provides a complete description of the slots and methods for each class. % [bp] \begin{table}[t!] \centering \begin{tabular}{lccl} \hline Class & Slots & Methods & Dynamic dispatch\\ \hline `\code{Message}' & 2 & 20 & yes (field names)\\ `\code{Descriptor}' & 2 & 16 & yes (field names, enum types, nested types)\\ `\code{FieldDescriptor}' & 4 & 18 & no\\ `\code{EnumDescriptor}' & 4 & 11 & yes (enum constant names)\\ `\code{EnumValueDescriptor}' & 3 & \phantom{1}6 & no\\ `\code{FileDescriptor}' & 3 & \phantom{1}6 & yes (message/field definitions)\\ \hline \end{tabular} \caption{\label{class-summary-table}Overview of class, slot, method and dispatch relationships.} \end{table} \subsection{Messages} The `\code{Message}' \proglang{S}4 class represents Protocol Buffer messages and is the core abstraction of \pkg{RProtoBuf}. Each `\code{Message}' contains a pointer to a `\code{Descriptor}' which defines the schema of the data defined in the message, as well as a number of `\code{FieldDescriptor}'s for the individual fields of the message. <<>>= new(tutorial.Person) @ \subsection{Descriptors} Descriptors describe the type of a message. This includes what fields a message contains and what the types of those fields are. Message descriptors are represented in \proglang{R} by the `\code{Descriptor}' \proglang{S}4 class. The class contains the slots \code{pointer} and \code{type}. Similarly to messages, the \verb|$| operator can be used to retrieve descriptors that are contained in the descriptor, or invoke methods. When \pkg{RProtoBuf} is first loaded it calls \code{readProtoFiles} which reads in the example file \code{addressbook.proto} included with the package. The \code{tutorial.Person} descriptor and all other descriptors defined in the loaded \code{.proto} files are then available on the search path\footnote{This explains why the example in Table~\ref{tab:proto} lacked an explicit call to \code{readProtoFiles}.}. \subsubsection*{Field descriptors} \label{subsec-field-descriptor} <<>>= tutorial.Person$email tutorial.Person$email$is_required() tutorial.Person$email$type() tutorial.Person$email$as.character() class(tutorial.Person$email) @ \subsubsection*{Enum and EnumValue descriptors} \label{subsec-enum-descriptor} The \code{EnumDescriptor} type contains information about what values a type defines, while the \code{EnumValueDescriptor} describes an individual enum constant of a particular type. The \verb|$| operator can be used to retrieve the value of enum constants contained in the EnumDescriptor, or to invoke methods. <<>>= tutorial.Person$PhoneType tutorial.Person$PhoneType$WORK class(tutorial.Person$PhoneType) tutorial.Person$PhoneType$value(1) tutorial.Person$PhoneType$value(name="HOME") tutorial.Person$PhoneType$value(number=1) class(tutorial.Person$PhoneType$value(1)) @ \subsubsection*{File descriptors} \label{subsec-file-descriptor} The class `\code{FileDescriptor}' represents file descriptors in \proglang{R}. The \verb|$| operator can be used to retrieve named fields defined in the `\code{FileDescriptor}', or to invoke methods. % < < > > = % f <- tutorial.Person$fileDescriptor() % f % f$Person % @ \begin{Schunk} \begin{Sinput} R> f <- tutorial.Person$fileDescriptor() R> f \end{Sinput} \begin{Soutput} file descriptor for package tutorial \ (/usr/local/lib/R/site-library/RProtoBuf/proto/addressbook.proto) \end{Soutput} \begin{Sinput} R> f$Person \end{Sinput} \begin{Soutput} descriptor for type 'tutorial.Person' \end{Soutput} \end{Schunk} \section{Type coercion} \label{sec:types} One of the benefits of using an interface definition language (IDL) like Protocol Buffers is that it provides a highly portable basic type system. This permits different language and hardware implementations to map to the most appropriate type in different environments. Table~\ref{table-get-types} details the correspondence between the field type and the type of data that is retrieved by \verb|$| and \verb|[[| extractors. Three types in particular need further attention due to specific differences in the \proglang{R} language: booleans, unsigned integers, and 64-bit integers. \begin{table}[t!] \centering \begin{small} \begin{tabular}{lp{5cm}p{5.5cm}} \toprule Field type & \proglang{R} type (non repeated) & \proglang{R} type (repeated) \\ \cmidrule(r){2-3} double & \code{double} vector & \code{double} vector \\ float & \code{double} vector & \code{double} vector \\[3mm] uint32 & \code{double} vector & \code{double} vector \\ fixed32 & \code{double} vector & \code{double} vector \\[3mm] int32 & \code{integer} vector & \code{integer} vector \\ sint32 & \code{integer} vector & \code{integer} vector \\ sfixed32 & \code{integer} vector & \code{integer} vector \\[3mm] int64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ uint64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ sint64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ fixed64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ sfixed64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\[3mm] bool & \code{logical} vector & \code{logical} vector \\[3mm] string & \code{character} vector & \code{character} vector \\ bytes & \code{character} vector & \code{character} vector \\[3mm] enum & \code{integer} vector & \code{integer} vector \\[3mm] message & \code{S4} object of class \code{Message} & \code{list} of \code{S4} objects of class \code{Message} \\ \bottomrule \end{tabular} \end{small} \caption{\label{table-get-types}Correspondence between field type and \proglang{R} type retrieved by the extractors. \proglang{R} lacks native 64-bit integers, so the \code{RProtoBuf.int64AsString} option is available to return large integers as characters to avoid losing precision; see Section~\ref{sec:int64} below. All but the \code{Message} type can be represented in vectors of one or more elements; for the latter a list is used.} \end{table} \subsection{Booleans} \proglang{R} booleans can accept three values: \code{TRUE}, \code{FALSE}, and \code{NA}. However, most other languages, including the Protocol Buffer schema, only accept \code{TRUE} or \code{FALSE}. This means that we simply can not store \proglang{R} logical vectors that include all three possible values as booleans. The library will refuse to store \code{NA}s in Protocol Buffer boolean fields, and users must instead choose another type (such as enum or integer) capable of storing three distinct values. <>= if (!exists("JSSPaper.Example1", "RProtoBuf:DescriptorPool")) { readProtoFiles(file="proto/int64.proto") } @ % We want a cleaner error message here. \begin{CodeChunk} \begin{CodeInput} R> a <- new(JSSPaper.Example1) R> a$optional_bool <- TRUE R> a$optional_bool <- FALSE R> a$optional_bool <- NA \end{CodeInput} \begin{CodeOutput} Error: NA boolean values can not be stored in bool Protocol Buffer fields \end{CodeOutput} \end{CodeChunk} \subsection{Unsigned integers} \proglang{R} lacks a native unsigned integer type. Values between $2^{31}$ and $2^{32} - 1$ read from unsigned integer Protocol Buffer fields must be stored as doubles in \proglang{R}. <<>>= as.integer(2^31-1) as.integer(2^31 - 1) + as.integer(1) 2^31 class(2^31) @ \subsection{64-bit integers} \label{sec:int64} \proglang{R} also does not support the native 64-bit integer type. Numeric vectors with integer values greater or equal to $2^{31}$ can only be stored as floating-point double precision variables. This conversion incurs a loss of precision, and \proglang{R} loses the ability to distinguish between some distinct integer variables: <<>>= 2^53 == (2^53 + 1) @ Most modern languages do have support for 64-bit integer values, which becomes problematic when \pkg{RProtoBuf} is used to exchange data with a system that requires this integer type. To work around this, \pkg{RProtoBuf} allows users to get and set 64-bit integer values by specifying them as character strings. On 64-bit platforms, character strings representing large decimal numbers will be coerced to \code{int64} during assignment to 64-bit Protocol Buffer types to work around the lack of native 64-bit types in \proglang{R} itself. The values are stored as distinct \code{int64} values in memory. But when accessed from \proglang{R} language code, they will be coerced into numeric (floating-point) values. If the full 64-bit precision is required, the \code{RProtoBuf.int64AsString} option can be set to \code{TRUE} to return \code{int64} values from messages as character strings. Such character values are useful because they can accurately be used as unique identifiers, and can easily be passed to \proglang{R} packages such as \pkg{int64} \citep{int64} or \pkg{bit64} \citep{bit64} which represent 64-bit integers in \proglang{R}. \section[Converting R data structures into Protocol Buffers]{Converting \proglang{R} data structures into Protocol Buffers} \label{sec:evaluation} The previous sections discussed functionality in the \pkg{RProtoBuf} package for creating, manipulating, parsing, and serializing Protocol Buffer messages of a defined schema. This is useful when there are pre-existing systems with defined schemas or significant software components written in other languages that need to be accessed from within \proglang{R}. The package also provides methods for converting arbitrary \proglang{R} data structures into Protocol Buffers and vice versa with a universal \proglang{R} object schema. The \code{serialize\_pb} and \code{unserialize\_pb} functions serialize arbitrary \proglang{R} objects into a universal Protocol Buffer message: <<>>= msg <- serialize_pb(iris, NULL) identical(iris, unserialize_pb(msg)) @ In order to accomplish this, \pkg{RProtoBuf} uses the same catch-all \code{proto} schema used by \pkg{RHIPE} for exchanging \proglang{R} data with Hadoop \citep{rhipe}. This schema, which we will refer to as \code{rexp.proto}, is printed in %appendix \ref{rexp.proto}. the appendix. The Protocol Buffer messages generated by \pkg{RProtoBuf} and \pkg{RHIPE} are naturally compatible between the two systems because they use the same schema. This shows the power of using a schema-based cross-platform format such as Protocol Buffers: interoperability is achieved without effort or close coordination. The \code{rexp.proto} schema natively supports all main \proglang{R} storage types holding \emph{data}. These include \code{NULL}, \code{list} and vectors of type \code{logical}, \code{character}, \code{double}, \code{integer}, and \code{complex}. In addition, every type can contain a named set of attributes, as is the case in \proglang{R}. The storage types \code{function}, \code{language}, and \code{environment} are specific to \proglang{R} and have no equivalent native type in Protocol Buffers. These three types are supported by first serializing with \code{base::serialize} in \proglang{R} and then stored in a raw bytes field. \subsection[Evaluation: Serializing R data sets]{Evaluation: Serializing \proglang{R} data sets} \label{sec:compression} <>= datasets <- as.data.frame(data(package="datasets")$results) datasets$name <- sub("\\s+.*$", "", datasets$Item) n <- nrow(datasets) @ This section evaluates the effectiveness of serializing arbitrary \proglang{R} data structures into Protocol Buffers. We use the \Sexpr{n} standard data sets included in the \pkg{datasets} package included with \proglang{R} as our evaluation data. These data sets include data frames, matrices, time series, tables, lists, and some more exotic data classes. For each data set, we compare how many bytes are used to store the data set using four different methods: \begin{itemize} \item normal \proglang{R} serialization \citep{serialization}, \item \proglang{R} serialization followed by gzip, \item normal Protocol Buffer serialization, and \item Protocol Buffer serialization followed by gzip. \end{itemize} <>= datasets$object.size <- unname(sapply(datasets$name, function(x) object.size(eval(as.name(x))))) datasets$R.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize(eval(as.name(x)), NULL)))) datasets$R.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize(eval(as.name(x)), NULL)))) datasets$R.serialize.size.gz <- unname(sapply(datasets$name, function(x) length(memCompress(serialize(eval(as.name(x)), NULL), "gzip")))) datasets$RProtoBuf.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize_pb(eval(as.name(x)), NULL)))) datasets$RProtoBuf.serialize.size.gz <- unname(sapply(datasets$name, function(x) length(memCompress(serialize_pb(eval(as.name(x)), NULL), "gzip")))) clean.df <- data.frame(dataset=datasets$name, object.size=datasets$object.size, "serialized"=datasets$R.serialize.size, "gzipped serialized"=datasets$R.serialize.size.gz, "RProtoBuf"=datasets$RProtoBuf.serialize.size, "gzipped RProtoBuf"=datasets$RProtoBuf.serialize.size.gz, "ratio.serialized" = datasets$R.serialize.size / datasets$object.size, "ratio.rprotobuf" = datasets$RProtoBuf.serialize.size / datasets$object.size, "ratio.serialized.gz" = datasets$R.serialize.size.gz / datasets$object.size, "ratio.rprotobuf.gz" = datasets$RProtoBuf.serialize.size.gz / datasets$object.size, "savings.serialized" = 1-(datasets$R.serialize.size / datasets$object.size), "savings.rprotobuf" = 1-(datasets$RProtoBuf.serialize.size / datasets$object.size), "savings.serialized.gz" = 1-(datasets$R.serialize.size.gz / datasets$object.size), "savings.rprotobuf.gz" = 1-(datasets$RProtoBuf.serialize.size.gz / datasets$object.size), check.names=FALSE) all.df<-data.frame(dataset="TOTAL", object.size=sum(datasets$object.size), "serialized"=sum(datasets$R.serialize.size), "gzipped serialized"=sum(datasets$R.serialize.size.gz), "RProtoBuf"=sum(datasets$RProtoBuf.serialize.size), "gzipped RProtoBuf"=sum(datasets$RProtoBuf.serialize.size.gz), "ratio.serialized" = sum(datasets$R.serialize.size) / sum(datasets$object.size), "ratio.rprotobuf" = sum(datasets$RProtoBuf.serialize.size) / sum(datasets$object.size), "ratio.serialized.gz" = sum(datasets$R.serialize.size.gz) / sum(datasets$object.size), "ratio.rprotobuf.gz" = sum(datasets$RProtoBuf.serialize.size.gz) / sum(datasets$object.size), "savings.serialized" = 1-(sum(datasets$R.serialize.size) / sum(datasets$object.size)), "savings.rprotobuf" = 1-(sum(datasets$RProtoBuf.serialize.size) / sum(datasets$object.size)), "savings.serialized.gz" = 1-(sum(datasets$R.serialize.size.gz) / sum(datasets$object.size)), "savings.rprotobuf.gz" = 1-(sum(datasets$RProtoBuf.serialize.size.gz) / sum(datasets$object.size)), check.names=FALSE) clean.df<-rbind(clean.df, all.df) @ Figure~\ref{fig:compression} shows the space savings $\left(1 - \frac{\textrm{Compressed Size}}{\textrm{Uncompressed Size}}\right)$ for each of the data sets using each of these four methods. The associated table shows the exact data sizes for some outliers and the aggregate of all 104 data sets. Note that Protocol Buffer serialization results in slightly smaller byte streams compared to native \proglang{R} serialization in most cases (red dots), but this difference disappears if the results are compressed with gzip (blue triangles). % Sizes are comparable but Protocol Buffers provide simple getters and % setters in multiple languages instead of requiring other programs to % parse the \proglang{R} serialization % format. % \citep{serialization}. The \code{crimtab} dataset of anthropometry measurements of British prisoners \citep{garson1900metric} and the \code{airquality} dataset of air quality measurements in New York show the greatest difference in the space savings when using Protocol Buffers compared to \proglang{R} native serialization. The \code{crimtab} dataset is a 42 $\times$ 22 table of integers, most equal to 0, and the \code{airquality} dataset is a data frame of 154 observations of 1 numeric and 5 integer variables. In both data sets, the large number of small integer values can be very efficiently encoded by the \emph{Varint} integer encoding scheme used by Protocol Buffers which use a variable number of bytes for each value. The other extreme is represented by the \code{faithful} dataset of waiting time and eruptions of the Old Faithful geyser in Yellowstone National Park, Wyoming, USA \citep{azzalini1990look}. This dataset is a data frame with 272 observations of 2 numeric variables. The \proglang{R} native serialization of repeated numeric values is more space-efficient, resulting in a slightly smaller object size compared to the serialized Protocol Buffer equivalent. This evaluation shows that the \code{rexp.proto} universal \proglang{R} object schema included in \pkg{RProtoBuf} does not in general provide any significant saving in file size compared to the normal serialization mechanism in \proglang{R}. % redundant: which is seen as equally compact. The benefits of \pkg{RProtoBuf} accrue more naturally in applications where multiple programming languages are involved, or when a more concise application-specific schema has been defined. The example in the next section satisfies both of these conditions. \begin{figure}[t!] \begin{center} <>= old.mar<-par("mar") new.mar<-old.mar new.mar[3]<-0 new.mar[4]<-0 my.cex<-1.3 par("mar"=new.mar) plot(clean.df$savings.serialized, clean.df$savings.rprotobuf, pch=1, col="red", las=1, xlab="Serialization Space Savings", ylab="Protocol Buffer Space Savings", xlim=c(0,1),ylim=c(0,1),cex.lab=my.cex, cex.axis=my.cex) points(clean.df$savings.serialized.gz, clean.df$savings.rprotobuf.gz,pch=2, col="blue") # grey dotted diagonal abline(a=0,b=1, col="grey",lty=2,lwd=3) # find point furthest off the X axis. clean.df$savings.diff <- clean.df$savings.serialized - clean.df$savings.rprotobuf clean.df$savings.diff.gz <- clean.df$savings.serialized.gz - clean.df$savings.rprotobuf.gz # The one to label. tmp.df <- clean.df[which(clean.df$savings.diff == min(clean.df$savings.diff)),] # This minimum means most to the left of our line, so pos=2 is label to the left text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=2, cex=my.cex) # Some gziped version # text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=2, cex=my.cex) # Second one is also an outlier tmp.df <- clean.df[which(clean.df$savings.diff == sort(clean.df$savings.diff)[2]),] # This minimum means most to the left of our line, so pos=2 is label to the left text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=2, cex=my.cex) #text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=my.cex) tmp.df <- clean.df[which(clean.df$savings.diff == max(clean.df$savings.diff)),] # This minimum means most to the right of the diagonal, so pos=4 is label to the right # Only show the gziped one. #text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=4, cex=my.cex) text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=4, cex=my.cex) #outlier.dfs <- clean.df[c(which(clean.df$savings.diff == min(clean.df$savings.diff)), legend("topleft", c("Raw", "Gzip Compressed"), pch=1:2, col=c("red", "blue"), cex=my.cex) #interesting.df <- clean.df[unique(c(which(clean.df$savings.diff == min(clean.df$savings.diff)), # which(clean.df$savings.diff == max(clean.df$savings.diff)), # which(clean.df$savings.diff.gz == max(clean.df$savings.diff.gz)), # which(clean.df$dataset == "TOTAL"))),c("dataset", "object.size", "serialized", "gzipped serialized", "RProtoBuf", "gzipped RProtoBuf", "savings.serialized", "savings.serialized.gz", "savings.rprotobuf", "savings.rprotobuf.gz")] interesting.df <- clean.df[as.character(clean.df[,1]) %in% c("crimtab", "airquality", "faithful", "TOTAL"), c("dataset", "object.size", "serialized", "gzipped serialized", "RProtoBuf", "gzipped RProtoBuf", "savings.serialized", "savings.serialized.gz", "savings.rprotobuf", "savings.rprotobuf.gz")] interesting.df <- interesting.df[c(2,1,3,4),] # Print without .00 in xtable interesting.df$object.size <- as.integer(interesting.df$object.size) par("mar"=old.mar) @ \includegraphics[width=0.45\textwidth]{figures/fig-SER} % latex table generated in R 3.0.2 by xtable 1.7-0 package % Wed Nov 26 15:31:30 2014 % updated to R 3.3.1 on Sun Jul 10 17:29:41 CDT 2016 %\begin{table}[ht] %\begin{center} \begin{tabular}{rlrrrrr} \hline Data set & \code{object.size} & \multicolumn{2}{c}{\proglang{R} serialization} & \multicolumn{2}{c}{\pkg{RProtoBuf} serialization} \\ & & default & gzipped & default & gzipped \\ \hline \code{crimtab} & 7,936 & 4,641 (41.5\%) & 714 (91.0\%) & 1,655 (79.1\%) & 576 (92.7\%)\\ \code{airquality} & 5,496 & 4,551 (17.2\%) & 1,242 (77.4\%) & 2,874 (47.7\%) & 1,294 (76.4\%)\\ \code{faithful} & 5,136 & 4,543 (11.5\%) & 1,339 (73.9\%) & 4,936 \phantom{0}(3.9\%) & 1,776 (65.4\%)\\ \hline All & 609,024 & 463,833 (24\%) & 139,814 (77\%) & 436,746 (28\%) & 142,783 (77\%)\\ \hline \end{tabular} \end{center} \caption{(Top) Relative space savings of Protocol Buffers and native \proglang{R} serialization over the raw object sizes of each of the 104 data sets in the \pkg{datasets} package. Points to the left of the dashed $y=x$ line represent datasets that are more efficiently encoded with Protocol Buffers. (Bottom) Absolute space savings of three outlier datasets and the aggregate performance of all datasets. R version 3.3.1 was used for both the figure and the table. } \label{fig:compression} \end{figure} \section{Application: Distributed data collection with MapReduce} \label{sec:mapreduce} Protocol Buffers are used extensively at Google for almost all RPC protocols, and to store structured information on a variety of persistent storage systems \citep{dean2009designs}. Since the initial release in 2010, hundreds of Google's statisticians and software engineers use the \pkg{RProtoBuf} package on a daily basis to interact with these systems from within \proglang{R}. The current section illustrates the power of Protocol Buffers to collect and manage large structured data in one language before analyzing it in \proglang{R}. Our example uses MapReduce \citep{dean2008mapreduce}, which has emerged in the last decade as a popular design pattern to facilitate parallel processing of big data using distributed computing clusters. Big data sets in fields such as particle physics and information processing are often stored in binned (histogram) form in order to reduce storage requirements \citep{scott2009multivariate}. Because analysis over such large data sets may involve very rare phenomenon or deal with highly skewed data sets or inflexible raw data storage systems, unbiased sampling is often not feasible. In these situations, MapReduce and binning may be combined as a pre-processing step for a wide range of statistical and scientific analyses \citep{blocker2013}. There are two common patterns for generating histograms of large data sets in a single pass with MapReduce. In the first method, each mapper task generates a histogram over a subset of the data that it has been assigned, serializes this histogram and sends it to one or more reducer tasks which merge the intermediate histograms from the mappers. In the second method, illustrated in Figure~\ref{fig:mr-histogram-pattern1}, each mapper rounds a data point to a bucket width and outputs that bucket as a key and '1' as a value. Reducers count how many times each key occurs and outputs a histogram to a data store. \begin{figure}[t!] \begin{center} \includegraphics[width=0.9\textwidth]{figures/histogram-mapreduce-diag1.pdf} \end{center} \caption{Diagram of MapReduce histogram generation pattern.} \label{fig:mr-histogram-pattern1} \end{figure} In both methods, the mapper tasks must choose identical bucket boundaries in advance if we are to construct the histogram in a single pass, even though they are analyzing disjoint parts of the input set that may cover different ranges. All distributed tasks involved in the pre-processing as well as any downstream data analysis tasks must share a schema of the histogram representation to coordinate effectively. The \pkg{HistogramTools} package \citep{histogramtools} enhances \pkg{RProtoBuf} by providing a concise schema for \proglang{R} histogram objects: \begin{example} package HistogramTools; message HistogramState { repeated double breaks = 1; repeated int32 counts = 2; optional string name = 3; } \end{example} This \code{HistogramState} message type is designed to be helpful if some of the Map or Reduce tasks are written in \proglang{R}, or if those components are written in other languages and only the resulting output histograms need to be manipulated in \proglang{R}. \subsection[A simple single-machine example for Python to R serialization]{A simple single-machine example for \proglang{Python} to \proglang{R} serialization} To create \code{HistogramState} messages in \proglang{Python} for later consumption by \proglang{R}, we first compile the \code{histogram.proto} descriptor into a python module using the \code{protoc} compiler: \begin{verbatim} protoc histogram.proto --python_out=. \end{verbatim} This generates a Python module called \code{histogram\_pb2.py}, containing both the descriptor information as well as methods to read and manipulate the histogram message data. The following simple Python script uses this generated module to create a histogram (to which breakpoints and binned data are added), and writes out the Protocol Buffer representation to a file: \begin{Code} from histogram_pb2 import HistogramState; hist = HistogramState() hist.counts.extend([2, 6, 2, 4, 6]) hist.breaks.extend(range(6)) hist.name="Example Histogram Created in Python" outfile = open("/tmp/hist.pb", "wb") outfile.write(hist.SerializeToString()) outfile.close() \end{Code} The Protocol Buffer created from this \proglang{Python} script can then be read into \proglang{R} and converted to a native \proglang{R} histogram object for plotting. The code below first attaches the \pkg{HistogramTools} package which imports \pkg{RProtoBuf}. Then reads all of the \code{.proto} descriptor definitions provided by \pkg{HistogramTools} and adds them to the environment as described in Section~\ref{sec:rprotobuf-basic}. Next the serialized Protocol Buffer is parsed using the \code{HistogramTools.HistogramState} schema. Finally the Protocol Buffer representation of the histogram is converted to a native \proglang{R} histogram object with \code{as.histogram} and passes the result to \code{plot} (see Figure~\ref{figure}). \lstdefinelanguage{jss} {sensitive=false, morecomment=[l]{R>}} \lstset{language=jss, basicstyle=\ttfamily, numbers=left, numberstyle=\tiny, stepnumber=2, numbersep=5pt, columns=fullflexible, keepspaces=true, showstringspaces=false, commentstyle=\textsl} %\begin{Code} \begin{lstlisting} R> library("HistogramTools") R> readProtoFiles(package="HistogramTools") R> hist <- HistogramTools.HistogramState$read("/tmp/hist.pb") R> hist [1] "message of type 'HistogramTools.HistogramState' with 3 fields set" R> plot(as.histogram(hist), main="") \end{lstlisting} %\end{Code} %% DEdd 2016-07-10 Taking a shortcut here an showing a prepared %% HistogramTools chart to not depend on HistogramTools %% on Travis CI etc \begin{center} <>= require(HistogramTools) readProtoFiles(package="HistogramTools") hist <- HistogramTools.HistogramState$read("proto/hist.pb") plot(as.histogram(hist), main="") @ \includegraphics[width=0.45\textwidth]{figures/HistogramTools} \end{center} This simple example uses a constant histogram generated in \proglang{Python} to illustrate the serialization concepts without requiring the reader to be familiar with the interface of any particular MapReduce implementation. In practice, using Protocol Buffers to pass histograms between another programming language and \proglang{R} would provide a much greater benefit in a distributed context. For example, a first-class data type to represent histograms would prevent individual histograms from being split up and would allow the use of combiners on Map workers to process large data sets more efficiently than simply passing around lists of counts and buckets. One of the authors has used this design pattern with \proglang{C++} MapReduces over very large data sets to write out histogram protocol buffers for several large-scale studies of distributed storage systems \citep{sciencecloud,janus}. \section{Application: Data interchange in web services} \label{sec:opencpu} The previous section described an application where data from a program written in another language was saved to persistent storage and then read into \proglang{R} for further analysis. This section describes another common use case where Protocol Buffers are used as the interchange format for client-server communication. Network protocols such as HTTP provide mechanisms for client-server communication, i.e., how to initiate requests, authenticate, send messages, etc. However, network protocols generally do not regulate the \emph{content} of messages: they allow transfer of any media type, such as web pages, static files or multimedia content. When designing systems where various components require exchange of specific data structures, we need something on top of the network protocol that prescribes how these structures are to be represented in messages (buffers) on the network. Protocol Buffers solve this problem by providing a cross-platform method for serializing arbitrary structures into well defined messages, which can then be exchanged using any protocol. \subsection[Interacting with R through HTTPS and Protocol Buffers]{Interacting with \proglang{R} through HTTPS and Protocol Buffers} One example of a system that supports Protocol Buffers to interact with \proglang{R} is OpenCPU \citep{opencpu}. OpenCPU is a framework for embedded statistical computation and reproducible research based on \proglang{R} and \LaTeX. It exposes a HTTP(S) API to access and manipulate \proglang{R} objects and execute remote \proglang{R} function calls. Clients do not need to understand or generate any \proglang{R} code: HTTP requests are automatically mapped to function calls, and arguments/return values can be posted/retrieved using several data interchange formats, such as Protocol Buffers. OpenCPU uses the \code{rexp.proto} descriptor and the \code{serialize\_pb} and \code{unserialize\_pb} functions described in Section~\ref{sec:evaluation} to convert between \proglang{R} objects and Protocol Buffer messages. \subsection[HTTP GET: Retrieving an R object]{HTTP GET: Retrieving an \proglang{R} object} The \code{HTTP GET} method is used to read a resource from OpenCPU. For example, to access the data set \code{Animals} from the package \code{MASS}, a client performs the following HTTP request: \begin{verbatim} GET https://demo.ocpu.io/MASS/data/Animals/pb \end{verbatim} The postfix \code{/pb} in the URL tells the server to send this object in the form of a Protocol Buffer message. % Alternative formats include \code{/json}, \code{/csv}, \code{/rds} and others. If the request is successful, OpenCPU returns the serialized object with HTTP status code 200 and HTTP response header \code{Content-Type: application/x-protobuf}. The latter is the conventional MIME type that formally notifies the client to interpret the response as a Protocol Buffer. Because both HTTP and Protocol Buffers have libraries available for many languages, clients can be implemented in just a few lines of code. Below is example code for both \proglang{R} and Python that retrieves an \proglang{R} data set encoded as a Protocol Buffer message from OpenCPU. In \proglang{R}, we use the HTTP client from the \code{httr} package \citep{httr}. In this example we download a data set which is part of the base \proglang{R} distribution, so we can verify that the object was transferred without loss of information. <>= library("RProtoBuf") library("httr") req <- GET('https://demo.ocpu.io/MASS/data/Animals/pb') output <- unserialize_pb(req$content) identical(output, MASS::Animals) @ Similarly, to retrieve the same data set in a \proglang{Python} client, we first compile the \code{rexp.proto} descriptor into a python module using the \code{protoc} compiler: \begin{verbatim} protoc rexp.proto --python_out=. \end{verbatim} This generates \proglang{Python} module called \code{rexp\_pb2.py}, containing both the descriptor information as well as methods to read and manipulate the \proglang{R} object message. We use the HTTP client from the \code{urllib2} module in our example to retrieve the encoded Protocol Buffer from the remote server then parse and print it from \proglang{Python}. \begin{verbatim} import urllib2 from rexp_pb2 import REXP req = urllib2.Request('https://demo.ocpu.io/MASS/data/Animals/pb') res = urllib2.urlopen(req) msg = REXP() msg.ParseFromString(res.read()) print(msg) \end{verbatim} The \code{msg} object contains all data from the \code{Animals} data set. From here we can easily extract the desired fields for further use in \proglang{Python}. \subsection[HTTP POST: Calling an R function]{HTTP POST: Calling an \proglang{R} function} The previous example used a simple \code{HTTP GET} method to retrieve an \proglang{R} object from a remote service (\pkg{OpenCPU}) encoded as a Protocol Buffer. In many cases simple \code{HTTP GET} methods are insufficient, and a more complete RPC system may need to create compact Protocol Buffers for each request to send to the remote server in addition to parsing the response Protocol Buffers. The \pkg{OpenCPU} framework allows us to do arbitrary \proglang{R} function calls from within any programming language by encoding the arguments in the request Protocol Buffer. The following example \proglang{R} client code performs the remote function call \code{stats::rnorm(n = 42, mean = 100)}. The function arguments (in this case \code{n} and \code{mean}) as well as the return value (a vector with 42 random numbers) are transferred using Protocol Buffer messages. RPC in \pkg{OpenCPU} works like the \code{do.call} function in \proglang{R}, hence all arguments are contained within a list. <>= library("httr") library("RProtoBuf") args <- list(n=42, mean=100) payload <- serialize_pb(args, NULL) req <- POST ( url = "https://demo.ocpu.io/stats/R/rnorm/pb", body = payload, add_headers ( "Content-Type" = "application/x-protobuf" ) ) output <- unserialize_pb(req$content) print(output) @ The \pkg{OpenCPU} server basically performs the following steps to process the above RPC request: <>= fnargs <- unserialize_pb(inputmsg) val <- do.call(stats::rnorm, fnargs) outputmsg <- serialize_pb(val) @ \section{Summary} \label{sec:summary} Over the past decade, many formats for interoperable data exchange have become available, each with its unique features, strengths and weaknesses. Text based formats such as CSV and JSON are easy to use, and will likely remain popular among statisticians for many years to come. However, in the context of increasingly complex analysis stacks and applications involving distributed computing as well as mixed language analysis pipelines, choosing a more sophisticated data interchange format may reap considerable benefits. %Protocol Buffers is itself not a protocol. %Forward-compatibility is one of the features. No need to re-iterate those The Protocol Buffers standard and library offer a unique combination of features, performance, and maturity, that seems particularly well suited for data-driven applications and numerical computing. The \pkg{RProtoBuf} package builds on the Protocol Buffers \proglang{C++} library, and extends the \proglang{R} system with the ability to create, read, write, parse, and manipulate Protocol Buffer messages. \pkg{RProtoBuf} has been used extensively inside Google for the past five years by statisticians, analysts, and software engineers. At the time of this writing there are over 300 active users of \pkg{RProtoBuf} using it to read data from and otherwise interact with distributed systems written in \proglang{C++}, \proglang{Java}, \proglang{Python}, and other languages. We hope that making Protocol Buffers available to the \proglang{R} community will contribute to better software integration and allow for building even more advanced applications and analysis pipelines with \proglang{R}. \section*{Acknowledgments} The first versions of \pkg{RProtoBuf} were written during 2009--2010. Very significant contributions, both in code and design, were made by Romain Fran\c{c}ois whose continued influence on design and code is greatly appreciated. Several features of the package reflect the design of the \pkg{rJava} package by Simon Urbanek \citep{rjava}. The user-defined table mechanism, implemented by Duncan Temple Lang for the purpose of the \pkg{RObjectTables} package, allows for the dynamic symbol lookup. Kenton Varda was generous with his time in reviewing code and explaining obscure Protocol Buffer semantics. Karl Millar and Tim Hesterberg were very helpful in reviewing code and offering suggestions. Saptarshi Guha's work on \pkg{RHIPE} and implementation of a universal message type for \proglang{R} language objects allowed us to add the \code{serialize_pb} and \code{unserialize_pb} methods for turning arbitrary \proglang{R} objects into Protocol Buffers without a specialized pre-defined schema. Feedback from two anonymous referees greatly improved both the presentation of this paper and the package contents. \bibliography{RProtoBuf-paper} \begin{appendix} \section[The rexp.proto schema descriptor]{The \code{rexp.proto} schema descriptor} \label{rexp.proto} Below a print of the \code{rexp.proto} schema (originally designed by \citealt{rhipe}) that is included with the \pkg{RProtoBuf} package and used by \code{serialize\_pb} and \code{unserialize\_pb}. \begin{verbatim} package rexp; message REXP { enum RClass { STRING = 0; RAW = 1; REAL = 2; COMPLEX = 3; INTEGER = 4; LIST = 5; LOGICAL = 6; NULLTYPE = 7; LANGUAGE = 8; ENVIRONMENT = 9; FUNCTION = 10; } enum RBOOLEAN { F=0; T=1; NA=2; } required RClass rclass = 1; repeated double realValue = 2 [packed=true]; repeated sint32 intValue = 3 [packed=true]; repeated RBOOLEAN booleanValue = 4; repeated STRING stringValue = 5; optional bytes rawValue = 6; repeated CMPLX complexValue = 7; repeated REXP rexpValue = 8; repeated string attrName = 11; repeated REXP attrValue = 12; optional bytes languageValue = 13; optional bytes environmentValue = 14; optional bytes functionValue = 15; } message STRING { optional string strval = 1; optional bool isNA = 2 [default=false]; } message CMPLX { optional double real = 1 [default=0]; required double imag = 2; } \end{verbatim} \end{appendix} \end{document} RProtoBuf/inst/doc/RProtoBuf-intro.Rnw0000644000175100001440000021004013037407201017371 0ustar hornikusers\documentclass[11pt]{article} %\VignetteIndexEntry{RProtoBuf-intro} %\VignetteEngine{highlight::highlight} %\VignetteKeywords{RProtoBuf, Protocol Buffers, package} %\VignetteDepends{RProtoBuf} \usepackage{url} \usepackage{color} \usepackage[colorlinks]{hyperref} \definecolor{link}{rgb}{0,0,0.3} \hypersetup{ colorlinks,% citecolor=link,% filecolor=link,% linkcolor=link,% urlcolor=link } \setlength{\oddsidemargin}{0pt} \setlength{\textwidth}{17cm} % uh-oh, I use letter :) \setcounter{tocdepth}{2} \usepackage{microtype} %% cf http://www.khirevich.com/latex/microtype/ \usepackage[T1]{fontenc} %% cf http://www.khirevich.com/latex/font/ \usepackage[bitstream-charter]{mathdesign} %% cf http://www.khirevich.com/latex/font/ <>= library("RProtoBuf") options("width"=65) rpb.version <- packageDescription("RProtoBuf")$Version prettyDate <- format(Sys.Date(), "%B %e, %Y") @ % closing $ needed here \author{Romain Fran\c{c}ois \and Dirk Eddelbuettel \and Murray Stokely} \title{RProtoBuf: An R API for Protocol Buffers} \date{Version \Sexpr{rpb.version} as of \Sexpr{prettyDate}} \begin{document} \maketitle \abstract{ \noindent \textsl{Protocol Buffers} is a software project by Google that is used extensively internally and also released under an Open Source license. It provides a way of encoding structured data in an efficient yet extensible format. Google formally supports APIs for C++, Java and Python. This vignette describes version \Sexpr{rpb.version} of the \texttt{RProtoBuf} package which brings support for protocol buffer messages to R. } \tableofcontents \section{Protocol Buffers} Protocol buffers are a language-neutral, platform-neutral, extensible way of serializing structured data for use in communications protocols, data storage, and more. Protocol Buffers offer key features such as an efficient data interchange format that is both language- and operating system-agnostic yet uses a lightweight and highly performant encoding, object serialization and de-serialization as well data and configuration management. Protocol buffers are also forward compatible: updates to the \texttt{proto} files do not break programs built against the previous specification. While benchmarks are not available, Google states on the project page that in comparison to XML, protocol buffers are at the same time \textsl{simpler}, between three to ten times \textsl{smaller}, between twenty and one hundred times \textsl{faster}, as well as less ambiguous and easier to program. The protocol buffers code is released under an open-source (BSD) license. The protocol buffer project (\url{http://code.google.com/p/protobuf/}) contains a C++ library and a set of runtime libraries and compilers for C++, Java and Python. With these languages, the workflow follows standard practice of so-called Interface Description Languages (IDL) (c.f. \href{http://en.wikipedia.org/wiki/Interface_description_language}{Wikipedia on IDL}). This consists of compiling a protocol buffer description file (ending in \texttt{.proto}) into language specific classes that can be used to create, read, write and manipulate protocol buffer messages. In other words, given the 'proto' description file, code is automatically generated for the chosen target language(s). The project page contains a tutorial for each of these officially supported languages: \url{http://code.google.com/apis/protocolbuffers/docs/tutorials.html} Besides the officially supported C++, Java and Python implementations, several projects have been created to support protocol buffers for many languages. The list of known languages to support protocol buffers is compiled as part of the project page: \url{http://code.google.com/p/protobuf/wiki/ThirdPartyAddOns} The protocol buffer project page contains a comprehensive description of the language: \url{http://code.google.com/apis/protocolbuffers/docs/proto.html} \section{Basic use: Protocol Buffers and R} This section describes how to use the R API to create and manipulate protocol buffer messages in R, and how to read and write the binary \emph{payload} of the messages to files and arbitrary binary R connections. \subsection{Importing proto files dynamically} In contrast to the other languages (Java, C++, Python) that are officially supported by Google, the implementation used by the \texttt{RProtoBuf} package does not rely on the \texttt{protoc} compiler (with the exception of the two functions discussed in the previous section). This means that no initial step of statically compiling the proto file into C++ code that is then accessed by R code is necessary. Instead, \texttt{proto} files are parsed and processed \textsl{at runtime} by the protobuf C++ library---which is much more appropriate for a dynamic language. The \texttt{readProtoFiles} function allows importing \texttt{proto} files in several ways. <<>>= args( readProtoFiles ) @ Using the \texttt{file} argument, one can specify one or several file paths that ought to be proto files. <<>>= proto.dir <- system.file( "proto", package = "RProtoBuf" ) proto.file <- file.path( proto.dir, "addressbook.proto" ) <>= readProtoFiles( proto.file ) @ With the \texttt{dir} argument, which is ignored if the \texttt{file} is supplied, all files matching the \texttt{.proto} extension will be imported. <<>>= dir( proto.dir, pattern = "\\.proto$", full.names = TRUE ) <>= readProtoFiles( dir = proto.dir ) @ Finally, with the \texttt{package} argument (ignored if \texttt{file} or \texttt{dir} is supplied), the function will import all \texttt{.proto} files that are located in the \texttt{proto} sub-directory of the given package. A typical use for this argument is in the \texttt{.onLoad} function of a package. <>= readProtoFiles( package = "RProtoBuf" ) @ Once the proto files are imported, all message descriptors are are available in the R search path in the \texttt{RProtoBuf:DescriptorPool} special environment. The underlying mechanism used here is described in more detail in section~\ref{sec-lookup}. <<>>= ls( "RProtoBuf:DescriptorPool" ) @ \subsection{Creating a message} The objects contained in the special environment are descriptors for their associated message types. Descriptors will be discussed in detail in another part of this document, but for the purpose of this section, descriptors are just used with the \texttt{new} function to create messages. <<>>= p <- new( tutorial.Person, name = "Romain", id = 1 ) @ \subsection{Access and modify fields of a message} Once the message is created, its fields can be queried and modified using the dollar operator of R, making protocol buffer messages seem like lists. <<>>= p$name p$id p$email <- "francoisromain@free.fr" @ However, as opposed to R lists, no partial matching is performed and the name must be given entirely. The \verb|[[| operator can also be used to query and set fields of a mesages, supplying either their name or their tag number : <<>>= p[["name"]] <- "Romain Francois" p[[ 2 ]] <- 3 p[[ "email" ]] @ Protocol buffers include a 64-bit integer type, but R lacks native 64-bit integer support. A workaround is available and described in Section~\ref{sec:int64} for working with large integer values. % TODO(mstokely): Document extensions here. % There are none in addressbook.proto though. \subsection{Display messages} Protocol buffer messages and descriptors implement \texttt{show} methods that provide basic information about the message : <<>>= p @ For additional information, such as for debugging purposes, the \texttt{as.character} method provides a more complete ASCII representation of the contents of a message. <<>>= writeLines( as.character( p ) ) @ \subsection{Serializing messages} However, the main focus of protocol buffer messages is efficiency. Therefore, messages are transported as a sequence of bytes. The \texttt{serialize} method is implemented for protocol buffer messages to serialize a message into the sequence of bytes (raw vector in R speech) that represents the message. <<>>= serialize( p, NULL ) @ The same method can also be used to serialize messages to files : <<>>= tf1 <- tempfile() tf1 serialize( p, tf1 ) readBin( tf1, raw(0), 500 ) @ Or to arbitrary binary connections: <<>>= tf2 <- tempfile() con <- file( tf2, open = "wb" ) serialize( p, con ) close( con ) readBin( tf2, raw(0), 500 ) @ \texttt{serialize} can also be used in a more traditionnal object oriented fashion using the dollar operator : <<>>= # serialize to a file p$serialize( tf1 ) # serialize to a binary connection con <- file( tf2, open = "wb" ) p$serialize( con ) close( con ) @ \subsection{Parsing messages} The \texttt{RProtoBuf} package defines the \texttt{read} function to read messages from files, raw vector (the message payload) and arbitrary binary connections. <<>>= args( read ) @ The binary representation of the message (often called the payload) does not contain information that can be used to dynamically infer the message type, so we have to provide this information to the \texttt{read} function in the form of a descriptor : <<>>= message <- read( tutorial.Person, tf1 ) writeLines( as.character( message ) ) @ The \texttt{input} argument of \texttt{read} can also be a binary readable R connection, such as a binary file connection: <<>>= con <- file( tf2, open = "rb" ) message <- read( tutorial.Person, con ) close( con ) writeLines( as.character( message ) ) @ Finally, the payload of the message can be used : <<>>= # reading the raw vector payload of the message payload <- readBin( tf1, raw(0), 5000 ) message <- read( tutorial.Person, payload ) @ \texttt{read} can also be used as a pseudo method of the descriptor object : <<>>= # reading from a file message <- tutorial.Person$read( tf1 ) # reading from a binary connection con <- file( tf2, open = "rb" ) message <- tutorial.Person$read( con ) close( con ) # read from the payload message <- tutorial.Person$read( payload ) @ \section{Classes, Methods and Pseudo Methods} The \texttt{RProtoBuf} package uses the S4 system to store information about descriptors and messages, but the information stored in the R object is very minimal and mainly consists of an external pointer to a C++ variable that is managed by the \texttt{proto} C++ library. <<>>= str( p ) @ Using the S4 system allows the \texttt{RProtoBuf} package to dispatch methods that are not generic in the S3 sense, such as \texttt{new} and \texttt{serialize}. The \texttt{RProtoBuf} package combines the \emph{R typical} dispatch of the form \verb|method( object, arguments)| and the more traditional object oriented notation \verb|object$method(arguments)|. \subsection{messages} Messages are represented in R using the \texttt{Message} S4 class. The class contains the slots \texttt{pointer} and \texttt{type} as described on the Table~\ref{Message-class-table}. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & external pointer to the \texttt{Message} object of the C++ proto library. Documentation for the \texttt{Message} class is available from the protocol buffer project page: \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.message.html#Message} \\ \hline \texttt{type} & fully qualified path of the message. For example a \texttt{Person} message has its \texttt{type} slot set to \texttt{tutorial.Person} \\ \hline \end{tabular} \caption{\label{Message-class-table}Description of slots for the \texttt{Message} S4 class} \end{table} Although the \texttt{RProtoBuf} package uses the S4 system, the \verb|@| operator is very rarely used. Fields of the message are retrieved or modified using the \verb|$| or \verb|[[| operators as seen on the previous section, and pseudo-methods can also be called using the \verb|$| operator. Table~\ref{Message-methods-table} describes the methods defined for the \texttt{Message} class : \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{has} & \ref{Message-method-has} & Indicates if a message has a given field. \\ \texttt{clone} & \ref{Message-method-clone} & Creates a clone of the message \\ \texttt{isInitialized} & \ref{Message-method-isInitialized} & Indicates if a message has all its required fields set\\ \texttt{serialize} & \ref{Message-method-serialize} & serialize a message to a file or a binary connection or retrieve the message payload as a raw vector\\ \texttt{clear} & \ref{Message-method-clear} & Clear one or several fields of a message, or the entire message\\ \texttt{size} & \ref{Message-method-size} & The number of elements in a message field\\ \texttt{bytesize} & \ref{Message-method-bytesize} & The number of bytes the message would take once serialized\\ \hline \texttt{swap} & \ref{Message-method-swap} & swap elements of a repeated field of a message\\ \texttt{set} & \ref{Message-method-set} & set elements of a repeated field\\ \texttt{fetch} & \ref{Message-method-fetch} & fetch elements of a repeated field\\ \texttt{setExtension} & \ref{Message-method-setExtension} & set an extension of a message\\ \texttt{getExtension} & \ref{Message-method-getExtension} & get the value of an extension of a message\\ \texttt{add} & \ref{Message-method-add} & add elements to a repeated field \\ \hline \texttt{str} & \ref{Message-method-str} & the R structure of the message\\ \texttt{as.character} & \ref{Message-method-ascharacter} & character representation of a message\\ \texttt{toString} & \ref{Message-method-toString} & character representation of a message (same as \texttt{as.character}) \\ \texttt{as.list} & \ref{Message-method-aslist} & converts message to a named R list\\ \texttt{update} & \ref{Message-method-update} & updates several fields of a message at once\\ \texttt{descriptor} & \ref{Message-method-descriptor} & get the descriptor of the message type of this message\\ \texttt{fileDescriptor} & \ref{Message-method-fileDescriptor} & get the file descriptor of this message's descriptor\\ \hline \end{tabular} \end{small} \caption{\label{Message-methods-table}Description of methods for the \texttt{Message} S4 class} \end{table} \subsubsection{Retrieve fields} \label{Message-method-getfield} The \verb|$| and \verb|[[| operators allow extraction of a field data. <>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2, phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$name message$email message[[ "phone" ]] # using the tag number message[[ 2 ]] # id @ Neither \verb|$| nor \verb|[[| support partial matching of names. The \verb|$| is also used to call methods on the message, and the \verb|[[| operator can use the tag number of the field. Table~\ref{table-get-types} details correspondance between the field type and the type of data that is retrieved by \verb|$| and \verb|[[|. \begin{table}[h] \centering \begin{small} \begin{tabular}{|c|p{5cm}p{5cm}|} \hline field type & R type (non repeated) & R type (repeated) \\ \hline \hline double & \texttt{double} vector & \texttt{double} vector \\ float & \texttt{double} vector & \texttt{double} vector \\ \hline uint32 & \texttt{double} vector & \texttt{double} vector \\ fixed32 & \texttt{double} vector & \texttt{double} vector \\ \hline int32 & \texttt{integer} vector & \texttt{integer} vector \\ sint32 & \texttt{integer} vector & \texttt{integer} vector \\ sfixed32 & \texttt{integer} vector & \texttt{integer} vector \\ \hline int64 & \texttt{integer} or \texttt{character} vector \footnotemark & \texttt{integer} or \texttt{character} vector \\ uint64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ sint64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ fixed64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ sfixed64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ \hline bool & \texttt{logical} vector & \texttt{logical} vector \\ \hline string & \texttt{character} vector & \texttt{character} vector \\ bytes & \texttt{character} vector & \texttt{character} vector \\ \hline enum & \texttt{integer} vector & \texttt{integer} vector \\ \hline message & \texttt{S4} object of class \texttt{Message} & \texttt{list} of \texttt{S4} objects of class \texttt{Message} \\ \hline \end{tabular} \end{small} \caption{\label{table-get-types}Correspondance between field type and R type retrieved by the extractors. \footnotesize{1. R lacks native 64-bit integers, so the \texttt{RProtoBuf.int64AsString} option is available to return large integers as characters to avoid losing precision. This option is described in Section~\ref{sec:int64}}. R also lacks an unsigned integer type.} \end{table} \subsubsection{Modify fields} \label{Message-method-setfield} The \verb|$<-| and \verb|[[<-| operators are implemented for \texttt{Message} objects to set the value of a field. The R data is coerced to match the type of the message field. <<>>= message <- new( tutorial.Person, name = "foo", id = 2 ) message$email <- "foo@bar.com" message[[ "id" ]] <- 2 message[[ 1 ]] <- "foobar" writeLines( message$as.character() ) @ Table~\ref{table-message-field-setters} describes the R types that are allowed in the right hand side depending on the target type of the field. \begin{table}[h] \centering \begin{small} \begin{tabular}{|p{5cm}|p{7cm}|} \hline internal type & allowed R types \\ \hline \hline \texttt{double}, \texttt{float} & \texttt{integer}, \texttt{raw}, \texttt{double}, \texttt{logical} \\ \hline \texttt{int32}, \texttt{int64}, \texttt{uint32}, \texttt{uint64}, \texttt{sint32}, \texttt{sint64}, \texttt{fixed32}, \texttt{fixed64}, \texttt{sfixed32}, \texttt{sfixed64} & \texttt{integer}, \texttt{raw}, \texttt{double}, \texttt{logical}, \texttt{character} \\ \hline \texttt{bool} & \texttt{integer}, \texttt{raw}, \texttt{double}, \texttt{logical} \\ \hline \texttt{bytes}, \texttt{string} & \texttt{character} \\ \hline \texttt{enum} & \texttt{integer}, \texttt{double}, \texttt{raw}, \texttt{character} \\ \hline \texttt{message}, \texttt{group} & \texttt{S4}, of class \texttt{Message} of the appropriate message type, or a \texttt{list} of \texttt{S4} objects of class \texttt{Message} of the appropriate message type.\\ \hline \end{tabular} \end{small} \caption{\label{table-message-field-setters}Allowed R types depending on internal field types. } \end{table} \subsubsection{Message\$has method} \label{Message-method-has} The \texttt{has} method indicates if a field of a message is set. For repeated fields, the field is considered set if there is at least on object in the array. For non-repeated fields, the field is considered set if it has been initialized. The \texttt{has} method is a thin wrapper around the \texttt{HasField} and \texttt{FieldSize} methods of the \texttt{google::protobuf::Reflection} C++ class. <<>>= message <- new( tutorial.Person, name = "foo" ) message$has( "name" ) message$has( "id" ) message$has( "phone" ) @ \subsubsection{Message\$clone method} \label{Message-method-clone} The \texttt{clone} function creates a new message that is a clone of the message. This function is a wrapper around the methods \texttt{New} and \texttt{CopyFrom} of the \texttt{google::protobuf::Message} C++ class. <<>>= m1 <- new( tutorial.Person, name = "foo" ) m2 <- m1$clone( ) m2$email <- "foo@bar.com" writeLines( as.character( m1 ) ) writeLines( as.character( m2 ) ) @ \subsubsection{Message\$isInitialized method} \label{Message-method-isInitialized} The \texttt{isInitialized} method quickly checks if all required fields have values set. This is a thin wrapper around the \texttt{IsInitialized} method of the \texttt{google::protobuf::Message} C++ class. <<>>= message <- new( tutorial.Person, name = "foo" ) message$isInitialized() message$id <- 2 message$isInitialized() @ \subsubsection{Message\$serialize method} \label{Message-method-serialize} The \texttt{serialize} method can be used to serialize the message as a sequence of bytes into a file or a binary connection. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) tf1 <- tempfile( ) tf1 message$serialize( tf1 ) tf2 <- tempfile( ) tf2 con <- file( tf2, open = "wb" ) message$serialize( con ) close( con ) @ The files \Sexpr{basename(tf1)} and \Sexpr{basename(tf2)} both contain the message payload as a sequence of bytes. The \texttt{readBin} function can be used to read the files as a raw vector in R: <<>>= readBin( tf1, raw(0), 500 ) readBin( tf2, raw(0), 500 ) @ The \texttt{serialize} method can also be used to directly retrieve the payload of the message as a raw vector: <<>>= message$serialize(NULL) @ \subsubsection{Message\$clear method} \label{Message-method-clear} The \texttt{clear} method can be used to clear all fields of a message when used with no argument, or a given field. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( as.character( message ) ) message$clear() writeLines( as.character( message ) ) message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$clear( "id" ) writeLines( as.character( message ) ) @ The \texttt{clear} method is a thin wrapper around the \texttt{Clear} method of the \texttt{google::protobuf::Message} C++ class. \subsubsection{Message\$size method} \label{Message-method-size} The \texttt{size} method is used to query the number of objects in a repeated field of a message : <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$size( "phone" ) size( message, "phone" ) @ The \texttt{size} method is a thin wrapper around the \texttt{FieldSize} method of the \texttt{google::protobuf::Reflection} C++ class. \subsubsection{Message\$bytesize method} \label{Message-method-bytesize} The \texttt{bytesize} method retrieves the number of bytes the message would take once serialized. This is a thin wrapper around the \texttt{ByteSize} method of the \texttt{google::protobuf::Message} C++ class. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$bytesize() bytesize( message ) length( message$serialize( NULL ) ) @ \subsubsection{Message\$swap method} \label{Message-method-swap} The \texttt{swap} method can be used to swap elements of a repeated field. <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$swap( "phone", 1, 2 ) writeLines( as.character( message$phone[[1]] ) ) writeLines( as.character( message$phone[[2]] ) ) swap( message, "phone", 1, 2 ) writeLines( as.character( message$phone[[1]] ) ) writeLines( as.character( message$phone[[2]] ) ) @ \subsubsection{Message\$set method} \label{Message-method-set} The \texttt{set} method can be used to set values of a repeated field. <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) number <- new( tutorial.Person.PhoneNumber, number = "+33(0)---", type = "WORK" ) message$set( "phone", 1, number ) writeLines( as.character( message ) ) @ \subsubsection{Message\$fetch method} \label{Message-method-fetch} The \texttt{fetch} method can be used to get values of a repeated field. <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$fetch( "phone", 1 ) @ \subsubsection{Message\$setExtension method} \label{Message-method-setExtension} The \texttt{setExtension} method can be used to set an extension field of the Message. <>= if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } ## Test setting a singular extensions. test <- new(protobuf_unittest.TestAllExtensions) test$setExtension(protobuf_unittest.optional_int32_extension, as.integer(1)) @ \subsubsection{Message\$getExtension method} \label{Message-method-getExtension} The \texttt{getExtension} method can be used to get values of an extension. <>= test$getExtension(protobuf_unittest.optional_int32_extension) @ \subsubsection{Message\$add method} \label{Message-method-add} The \texttt{add} method can be used to add values to a repeated field. <>= message <- new( tutorial.Person, name = "foo") phone <- new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ) message$add( "phone", phone ) writeLines( message$toString() ) @ \subsubsection{Message\$str method} \label{Message-method-str} The \texttt{str} method gives the R structure of the message. This is rarely useful. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$str() str( message ) @ \subsubsection{Message\$as.character method} \label{Message-method-ascharacter} The \texttt{as.character} method gives the debug string of the message. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( message$as.character() ) writeLines( as.character( message ) ) @ \subsubsection{Message\$toString method} \label{Message-method-toString} \texttt{toString} currently is an alias to the \texttt{as.character} function. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( message$toString() ) writeLines( toString( message ) ) @ \subsubsection{Message\$as.list method} \label{Message-method-aslist} The \texttt{as.list} method converts the message to an named R list <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) as.list( message ) @ The names of the list are the names of the declared fields of the message type, and the content is the same as can be extracted with the \verb|$| operator described in section~\ref{Message-method-getfield}. \subsubsection{Message\$update method} \label{Message-method-update} The \texttt{update} method can be used to update several fields of a message at once. <>= message <- new( tutorial.Person ) update( message, name = "foo", id = 2, email = "foo@bar.com" ) writeLines( message$as.character() ) @ \subsubsection{Message\$descriptor method} \label{Message-method-descriptor} The \texttt{descriptor} method retrieves the descriptor of a message. See section~\ref{subsec-descriptor} for more information about message type descriptors. <<>>= message <- new( tutorial.Person ) message$descriptor() descriptor( message ) @ \subsubsection{Message\$fileDescriptor method} \label{Message-method-fileDescriptor} The \texttt{fileDescriptor} method retrieves the file descriptor of the descriptor associated with a message. See section~\ref{subsec-fileDescriptor} for more information about file descriptors. <<>>= message <- new( tutorial.Person ) message$fileDescriptor() fileDescriptor( message ) @ \subsection{message descriptors} \label{subsec-descriptor} Message descriptors are represented in R with the \emph{Descriptor} S4 class. The class contains the slots \texttt{pointer} and \texttt{type} : \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & external pointer to the \texttt{Descriptor} object of the C++ proto library. Documentation for the \texttt{Descriptor} class is available from the protocol buffer project page: \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.descriptor.html#Descriptor} \\ \hline \texttt{type} & fully qualified path of the message type. \\ \hline \end{tabular} \caption{\label{Descriptor-class-table}Description of slots for the \texttt{Descriptor} S4 class} \end{table} Similarly to messages, the \verb|$| operator can be used to extract information from the descriptor, or invoke pseudo-methods. Table~\ref{Descriptor-methods-table} describes the methods defined for the \texttt{Descriptor} class : \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{Method} & \textbf{Section} & \textbf{Description} \\ \hline \hline \texttt{new} & \ref{Descriptor-method-new} & Creates a prototype of a message described by this descriptor.\\ \texttt{read} & \ref{Descriptor-method-read} & Reads a message from a file or binary connection.\\ \texttt{readASCII} & \ref{Descriptor-method-readASCII} & Read a message in ASCII format from a file or text connection.\\ \hline \texttt{name} & \ref{Descriptor-method-name} & Retrieve the name of the message type associated with this descriptor.\\ \texttt{as.character} & \ref{Descriptor-method-ascharacter} & character representation of a descriptor\\ \texttt{toString} & \ref{Descriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}) \\ \texttt{as.list} & \ref{Descriptor-method-aslist} & return a named list of the field, enum, and nested descriptors included in this descriptor.\\ \texttt{asMessage} & \ref{Descriptor-method-asmessage} & return DescriptorProto message. \\ \hline \texttt{fileDescriptor} & \ref{Descriptor-method-filedescriptor} & Retrieve the file descriptor of this descriptor.\\ \texttt{containing\_type} & \ref{Descriptor-method-containingtype} & Retrieve the descriptor describing the message type containing this descriptor.\\ \texttt{field\_count} & \ref{Descriptor-method-fieldcount} & Return the number of fields in this descriptor.\\ \texttt{field} & \ref{Descriptor-method-field} & Return the descriptor for the specified field in this descriptor.\\ \texttt{nested\_type\_count} & \ref{Descriptor-method-nestedtypecount} & The number of nested types in this descriptor.\\ \texttt{nested\_type} & \ref{Descriptor-method-nestedtype} & Return the descriptor for the specified nested type in this descriptor.\\ \texttt{enum\_type\_count} & \ref{Descriptor-method-enumtypecount} & The number of enum types in this descriptor.\\ \texttt{enum\_type} & \ref{Descriptor-method-enumtype} & Return the descriptor for the specified enum type in this descriptor.\\ \hline \end{tabular} \end{small} \caption{\label{Descriptor-methods-table}Description of methods for the \texttt{Descriptor} S4 class} \end{table} \subsubsection{Extracting descriptors} The \verb|$| operator, when used on a descriptor object retrieves descriptors that are contained in the descriptor. This can be a field descriptor (see section~\ref{subsec-field-descriptor} ), an enum descriptor (see section~\ref{subsec-enum-descriptor}) or a descriptor for a nested type <<>>= # field descriptor tutorial.Person$email # enum descriptor tutorial.Person$PhoneType # nested type descriptor tutorial.Person$PhoneNumber # same as tutorial.Person.PhoneNumber @ \subsubsection{The new method} \label{Descriptor-method-new} The \texttt{new} method creates a prototype of a message described by the descriptor. <<>>= tutorial.Person$new( ) new( tutorial.Person ) @ Passing additional arguments to the method allows to directlt set the fields of the message at construction time. <<>>= tutorial.Person$new( email = "foo@bar.com" ) # same as update( tutorial.Person$new( ), email = "foo@bar.com" ) @ \subsubsection{The read method} \label{Descriptor-method-read} The \texttt{read} method is used to read a message from a file or a binary connection. <<>>= # start by serializing a message message <- new( tutorial.Person.PhoneNumber, type = "HOME", number = "+33(0)...." ) tf <- tempfile() serialize( message, tf ) # now read back the message m <- tutorial.Person.PhoneNumber$read( tf ) writeLines( as.character( m ) ) m <- read( tutorial.Person.PhoneNumber, tf ) writeLines( as.character( m ) ) @ \subsubsection{The readASCII method} \label{Descriptor-method-readASCII} The \texttt{readASCII} method is used to read a message from a text file or a character vector. <<>>= # start by generating the ASCII representation of a message text <- as.character(new(tutorial.Person, id=1, name="Murray")) text # Then read the ascii representation in as a new message object. msg <- tutorial.Person$readASCII(text) @ \subsubsection{The toString method} \label{Descriptor-method-tostring} \texttt{toString} currently is an alias to the \texttt{as.character} function. \subsubsection{The as.character method} \label{Descriptor-method-ascharacter} \texttt{as.character} prints the text representation of the descriptor as it would be specified in the \texttt{.proto} file. <<>>= desc <- tutorial.Person writeLines( desc$toString() ) writeLines( toString( desc ) ) writeLines( as.character(tutorial.Person) ) @ \subsubsection{as.list} \label{Descriptor-method-aslist} The \texttt{as.list} method returns a named list of the field, enum, and nested descriptors included in this descriptor. <<>>= tutorial.Person$as.list() @ \subsubsection{asMessage} \label{Descriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.DescriptorProto} of the Descriptor. <<>>= tutorial.Person$asMessage() @ \subsubsection{The fileDescriptor method} \label{Descriptor-method-filedescriptor} The \texttt{fileDescriptor} method retrieves the file descriptor of the descriptor. See section~\ref{subsec-fileDescriptor} for more information about file descriptors. <<>>= desc <- tutorial.Person desc$fileDescriptor() fileDescriptor( desc ) @ \subsubsection{The name method} \label{Descriptor-method-name} The \texttt{name} method can be used to retrieve the name of the message type associated with the descriptor. <<>>= # simple name tutorial.Person$name() # name including scope tutorial.Person$name(full = TRUE) @ \subsubsection{The containing\_type method} \label{Descriptor-method-containingtype} The \texttt{containing\_type} method retrieves the descriptor describing the message type containing this descriptor. <<>>= tutorial.Person$containing_type() tutorial.Person$PhoneNumber$containing_type() @ \subsubsection{The field\_count method} \label{Descriptor-method-fieldcount} Tme \texttt{field\_count} method retrieves the number of fields in this descriptor. <<>>= tutorial.Person$field_count() @ \subsubsection{The field method} \label{Descriptor-method-field} The \texttt{field} method returns the descriptor for the specified field in this descriptor. <<>>= tutorial.Person$field(1) @ \subsubsection{The nested\_type\_count method} \label{Descriptor-method-nestedtypecount} The \texttt{nested\_type\_count} method returns the number of nested types in this descriptor. <<>>= tutorial.Person$nested_type_count() @ \subsubsection{The nested\_type method} \label{Descriptor-method-nestedtype} The \texttt{nested\_type} method return the descriptor for the specified nested type in this descriptor. <<>>= tutorial.Person$nested_type(1) @ \subsubsection{The enum\_type\_count method} \label{Descriptor-method-enumtypecount} The \texttt{enum\_type\_count} method returns the number of enum types in this descriptor. <<>>= tutorial.Person$enum_type_count() @ \subsubsection{The enum\_type method} \label{Descriptor-method-enumtype} The \texttt{enum\_type} method returns the descriptor for the specified enum type in this descriptor. <<>>= tutorial.Person$enum_type(1) @ \subsection{field descriptors} \label{subsec-field-descriptor} The class \emph{FieldDescriptor} represents field descriptor in R. This is a wrapper S4 class around the \texttt{google::protobuf::FieldDescriptor} C++ class. Table~\ref{fielddescriptor-methods-table} describes the methods defined for the \texttt{FieldDescriptor} class. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & External pointer to the \texttt{FieldDescriptor} C++ variable \\ \hline \texttt{name} & simple name of the field \\ \hline \texttt{full\_name} & fully qualified name of the field \\ \hline \texttt{type} & name of the message type where the field is declared \\ \hline \end{tabular} \caption{\label{FieldDescriptor-class-table}Description of slots for the \texttt{FieldDescriptor} S4 class} \end{table} \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{as.character} & \ref{fielddescriptor-method-ascharacter} & character representation of a descriptor\\ \texttt{toString} & \ref{fielddescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}) \\ \texttt{asMessage} & \ref{fielddescriptor-method-asmessage} & return FieldDescriptorProto message. \\ \texttt{name} & \ref{fielddescriptor-method-name} & Return the name of the field descriptor.\\ \texttt{fileDescriptor} & \ref{fielddescriptor-method-filedescriptor} & Return the fileDescriptor where this field is defined.\\ \texttt{containing\_type} & \ref{fielddescriptor-method-containingtype} & Return the containing descriptor of this field.\\ \texttt{is\_extension} & \ref{fielddescriptor-method-isextension} & Return TRUE if this field is an extension.\\ \texttt{number} & \ref{fielddescriptor-method-number} & Gets the declared tag number of the field.\\ \texttt{type} & \ref{fielddescriptor-method-type} & Gets the type of the field.\\ \texttt{cpp\_type} & \ref{fielddescriptor-method-cpptype} & Gets the C++ type of the field.\\ \texttt{label} & \ref{fielddescriptor-method-label} & Gets the label of a field (optional, required, or repeated).\\ \texttt{is\_repeated} & \ref{fielddescriptor-method-isrepeated} & Return TRUE if this field is repeated.\\ \texttt{is\_required} & \ref{fielddescriptor-method-isrequired} & Return TRUE if this field is required.\\ \texttt{is\_optional} & \ref{fielddescriptor-method-isoptional} & Return TRUE if this field is optional.\\ \texttt{has\_default\_value} & \ref{fielddescriptor-method-hasdefaultvalue} & Return TRUE if this field has a default value.\\ \texttt{default\_value} & \ref{fielddescriptor-method-defaultvalue} & Return the default value.\\ \texttt{message\_type} & \ref{fielddescriptor-method-messagetype} & Return the message type if this is a message type field.\\ \texttt{enum\_type} & \ref{fielddescriptor-method-enumtype} & Return the enum type if this is an enum type field.\\ \hline \end{tabular} \end{small} \caption{\label{fielddescriptor-methods-table}Description of methods for the \texttt{FieldDescriptor} S4 class} \end{table} \subsubsection{as.character} \label{fielddescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the field descriptor. <<>>= writeLines( as.character( tutorial.Person$PhoneNumber ) ) @ \subsubsection{toString} \label{fielddescriptor-method-tostring} \texttt{toString} is an alias of \texttt{as.character}. <<>>= writeLines( tutorial.Person.PhoneNumber$toString() ) @ \subsubsection{asMessage} \label{fielddescriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.FieldDescriptorProto} of the FieldDescriptor. <<>>= tutorial.Person$id$asMessage() writeLines(as.character(tutorial.Person$id$asMessage())) @ \subsubsection{name} \label{fielddescriptor-method-name} The \texttt{name} method can be used to retrieve the name of the field descriptor. <<>>= # simple name. name( tutorial.Person$id ) # name including scope. name( tutorial.Person$id, full=TRUE ) @ \subsubsection{fileDescriptor} \label{fielddescriptor-method-filedescriptor} The \texttt{fileDescriptor} method can be used to retrieve the file descriptor of the field descriptor. <<>>= fileDescriptor(tutorial.Person$id) tutorial.Person$id$fileDescriptor() @ \subsubsection{containing\_type} \label{fielddescriptor-method-containingtype} The \texttt{containing\_type} method can be used to retrieve the descriptor for the message type that contains this descriptor. <<>>= containing_type(tutorial.Person$id) tutorial.Person$id$containing_type() @ \subsubsection{is\_extension} \label{fielddescriptor-method-isextension} The \texttt{is\_extension} method returns TRUE if this field is an extension. % TODO(ms): cross reference to a to be written section on extensions. <<>>= is_extension( tutorial.Person$id ) tutorial.Person$id$is_extension() @ \subsubsection{number} \label{fielddescriptor-method-number} The \texttt{number} method returns the declared tag number of this field. <<>>= number( tutorial.Person$id ) tutorial.Person$id$number() @ \subsubsection{type} \label{fielddescriptor-method-type} The \texttt{type} method can be used to retrieve the type of the field descriptor. <<>>= type( tutorial.Person$id ) tutorial.Person$id$type() @ \subsubsection{cpp\_type} \label{fielddescriptor-method-cpptype} The \texttt{cpp\_type} method can be used to retrieve the C++ type of the field descriptor. <<>>= cpp_type( tutorial.Person$id ) tutorial.Person$id$cpp_type() @ \subsubsection{label} \label{fielddescriptor-method-label} Gets the label of a field (optional, required, or repeated). The \texttt{label} method returns the label of a field (optional, required, or repeated). By defualt it returns a number value, but the optional \texttt{as.string} argument can be provided to return a human readable string representation. <<>>= label( tutorial.Person$id ) label( tutorial.Person$id , TRUE) tutorial.Person$id$label(TRUE) @ \subsubsection{is\_repeated} \label{fielddescriptor-method-isrepeated} The \texttt{is\_repeated} method returns TRUE if this field is repeated. <<>>= is_repeated( tutorial.Person$id ) tutorial.Person$id$is_repeated() @ \subsubsection{is\_required} \label{fielddescriptor-method-isrequired} The \texttt{is\_required} method returns TRUE if this field is required. <<>>= is_required( tutorial.Person$id ) tutorial.Person$id$is_required() @ \subsubsection{is\_optional} \label{fielddescriptor-method-isoptional} The \texttt{is\_optional} method returns TRUE if this field is optional. <<>>= is_optional( tutorial.Person$id ) tutorial.Person$id$is_optional() @ \subsubsection{has\_default\_value} \label{fielddescriptor-method-hasdefaultvalue} The \texttt{has\_default\_value} method returns TRUE if this field has a default value. <<>>= has_default_value(tutorial.Person$PhoneNumber$type) has_default_value(tutorial.Person$PhoneNumber$number) @ \subsubsection{default\_value} \label{fielddescriptor-method-defaultvalue} The \texttt{default\_value} method returns the default value of a field. <<>>= default_value( tutorial.Person$PhoneNumber$type ) default_value( tutorial.Person$PhoneNumber$number ) @ \subsubsection{message\_type} \label{fielddescriptor-method-messagetype} The \texttt{message\_type} method returns the message type if this is a message type field. <<>>= message_type(tutorial.Person$phone) tutorial.Person$phone$message_type() @ \subsubsection{enum\_type} \label{fielddescriptor-method-enumtype} The \texttt{enum\_type} method returns the enum type if this is an enum type field. <<>>= enum_type(tutorial.Person$PhoneNumber$type) @ \subsection{enum descriptors} \label{subsec-enum-descriptor} The class \emph{EnumDescriptor} is an R wrapper class around the C++ class \texttt{google::protobuf::EnumDescriptor}. Table~\ref{enumdescriptor-methods-table} describes the methods defined for the \texttt{EnumDescriptor} class. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & External pointer to the \texttt{EnumDescriptor} C++ variable \\ \hline \texttt{name} & simple name of the enum \\ \hline \texttt{full\_name} & fully qualified name of the enum \\ \hline \texttt{type} & name of the message type where the enum is declared \\ \hline \end{tabular} \caption{\label{EnumDescriptor-class-table}Description of slots for the \texttt{EnumDescriptor} S4 class} \end{table} \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{as.list} & \ref{enumdescriptor-method-aslist} & return a named integer vector with the values of the enum and their names.\\ \texttt{as.character} & \ref{enumdescriptor-method-ascharacter} & character representation of a descriptor\\ \texttt{toString} & \ref{enumdescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}) \\ \texttt{asMessage} & \ref{enumdescriptor-method-asmessage} & return EnumDescriptorProto message. \\ \texttt{name} & \ref{enumdescriptor-method-name} & Return the name of the enum descriptor.\\ \texttt{fileDescriptor} & \ref{enumdescriptor-method-filedescriptor} & Return the fileDescriptor where this field is defined.\\ \texttt{containing\_type} & \ref{enumdescriptor-method-containingtype} & Return the containing descriptor of this field.\\ \texttt{length} & \ref{enumdescriptor-method-length} & Return the number of constants in this enum.\\ \texttt{has} & \ref{enumdescriptor-method-has} & Return TRUE if this enum contains the specified named constant string.\\ \texttt{value\_count} & \ref{enumdescriptor-method-valuecount} & Return the number of constants in this enum (same as \texttt{length}).\\ \texttt{value} & \ref{enumdescriptor-method-value} & Return the EnumValueDescriptor of an enum value of specified index, name, or number.\\ \hline \end{tabular} \end{small} \caption{\label{enumdescriptor-methods-table}Description of methods for the \texttt{EnumDescriptor} S4 class} \end{table} \subsubsection{Extracting descriptors} The \verb|$| operator, when used on a EnumDescriptor object retrieves EnumValueDescriptors that are contained in the descriptor. <<>>= tutorial.Person$PhoneType$WORK name(tutorial.Person$PhoneType$value(number=2)) @ \subsubsection{as.list} \label{enumdescriptor-method-aslist} The \texttt{as.list} method creates a named R integer vector that captures the values of the enum and their names. <<>>= as.list( tutorial.Person$PhoneType ) @ \subsubsection{as.character} \label{enumdescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the enum type. <<>>= writeLines( as.character( tutorial.Person$PhoneType ) ) @ \subsubsection{toString} \label{enumdescriptor-method-tostring} The \texttt{toString} method brings the debug string of the enum type. <<>>= writeLines( toString( tutorial.Person$PhoneType ) ) @ \subsubsection{asMessage} \label{enumdescriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.EnumDescriptorProto} of the EnumDescriptor. <<>>= tutorial.Person$PhoneType$asMessage() writeLines(as.character(tutorial.Person$PhoneType$asMessage())) @ \subsubsection{name} \label{enumdescriptor-method-name} The \texttt{name} method can be used to retrieve the name of the enum descriptor. <<>>= # simple name. name( tutorial.Person$PhoneType ) # name including scope. name( tutorial.Person$PhoneType, full=TRUE ) @ \subsubsection{fileDescriptor} \label{enumdescriptor-method-filedescriptor} The \texttt{fileDescriptor} method can be used to retrieve the file descriptor of the enum descriptor. <<>>= fileDescriptor(tutorial.Person$PhoneType) tutorial.Person$PhoneType$fileDescriptor() @ \subsubsection{containing\_type} \label{enumdescriptor-method-containingtype} The \texttt{containing\_type} method can be used to retrieve the descriptor for the message type that contains this enum descriptor. <<>>= tutorial.Person$PhoneType$containing_type() @ \subsubsection{length} \label{enumdescriptor-method-length} The \texttt{length} method returns the number of constants in this enum. <<>>= length(tutorial.Person$PhoneType) tutorial.Person$PhoneType$length() @ \subsubsection{has} \label{enumdescriptor-method-has} The \texttt{has} method returns TRUE if this enum contains the specified named constant string. <<>>= tutorial.Person$PhoneType$has("WORK") tutorial.Person$PhoneType$has("nonexistant") @ \subsubsection{value\_count} \label{enumdescriptor-method-valuecount} The \texttt{value\_count} method returnst he number of constants in this enum. %TODO(ms): Duplicate of length, just like tostring/as.character. <<>>= value_count(tutorial.Person$PhoneType) tutorial.Person$PhoneType$value_count() @ \subsubsection{value} \label{enumdescriptor-method-value} The \texttt{value} method extracts an EnumValueDescriptor. Exactly one argument of 'index', 'number', or 'name' must be specified to identify which constant is desired. <<>>= tutorial.Person$PhoneType$value(1) tutorial.Person$PhoneType$value(name="HOME") tutorial.Person$PhoneType$value(number=1) @ \subsection{enum value descriptors} \label{subsec-EnumValueDescriptor} The class \emph{EnumValueDescriptor} is an R wrapper class around the C++ class \texttt{google::protobuf::EnumValueDescriptor}. Table~\ref{enumvaluedescriptor-methods-table} describes the methods defined for the \texttt{EnumValueDescriptor} class. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & External pointer to the \texttt{EnumValueDescriptor} C++ variable \\ \hline \texttt{name} & simple name of the enum value \\ \hline \texttt{full\_name} & fully qualified name of the enum value \\ \hline \end{tabular} \caption{\label{EnumValueDescriptor-class-table}Description of slots for the \texttt{EnumValueDescriptor} S4 class} \end{table} \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{number} & \ref{enumvaluedescriptor-method-number} & return the number of this EnumValueDescriptor. \\ \texttt{name} & \ref{enumvaluedescriptor-method-name} & Return the name of the enum value descriptor.\\ \texttt{enum\_type} & \ref{enumvaluedescriptor-method-enumtype} & return the EnumDescriptor type of this EnumValueDescriptor. \\ \texttt{as.character} & \ref{enumvaluedescriptor-method-ascharacter} & character representation of a descriptor. \\ \texttt{toString} & \ref{enumvaluedescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}). \\ \texttt{asMessage} & \ref{enumvaluedescriptor-method-asmessage} & return EnumValueDescriptorProto message. \\ \hline \end{tabular} \end{small} \caption{\label{enumvaluedescriptor-methods-table}Description of methods for the \texttt{EnumValueDescriptor} S4 class} \end{table} \subsubsection{number} \label{enumvaluedescriptor-method-number} The \texttt{number} method can be used to retrieve the number of the enum value descriptor. <<>>= number( tutorial.Person$PhoneType$value(number=2) ) @ \subsubsection{name} \label{enumvaluedescriptor-method-name} The \texttt{name} method can be used to retrieve the name of the enum value descriptor. <<>>= # simple name. name( tutorial.Person$PhoneType$value(number=2) ) # name including scope. name( tutorial.Person$PhoneType$value(number=2), full=TRUE ) @ \subsubsection{enum\_type} \label{enumvaluedescriptor-method-enumtype} The \texttt{enum\_type} method can be used to retrieve the EnumDescriptor of the enum value descriptor. <<>>= enum_type( tutorial.Person$PhoneType$value(number=2) ) @ \subsubsection{as.character} \label{enumvaluedescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the enum value type. <<>>= writeLines( as.character( tutorial.Person$PhoneType$value(number=2) ) ) @ \subsubsection{toString} \label{enumvaluedescriptor-method-tostring} The \texttt{toString} method brings the debug string of the enum value type. <<>>= writeLines( toString( tutorial.Person$PhoneType$value(number=2) ) ) @ \subsubsection{asMessage} \label{enumvaluedescriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.EnumValueDescriptorProto} of the EnumValueDescriptor. <<>>= tutorial.Person$PhoneType$value(number=2)$asMessage() writeLines(as.character(tutorial.Person$PhoneType$value(number=2)$asMessage())) @ \subsection{file descriptors} \label{subsec-fileDescriptor} File descriptors describe a whole \texttt{.proto} file and are represented in R with the \emph{FileDescriptor} S4 class. The class contains the slots \texttt{pointer}, \texttt{filename}, and \texttt{package} : \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & external pointer to the \texttt{FileDescriptor} object of the C++ proto library. Documentation for the \texttt{FileDescriptor} class is available from the protocol buffer project page: \url{http://developers.google.com/protocol-buffers/docs/reference/cpp/google.protobuf.descriptor.html#FileDescriptor} \\ \hline \texttt{filename} & fully qualified pathname of the \texttt{.proto} file.\\ \hline \texttt{package} & package name defined in this \texttt{.proto} file.\\ \hline \end{tabular} \caption{\label{FileDescriptor-class-table}Description of slots for the \texttt{FileDescriptor} S4 class} \end{table} Similarly to messages, the \verb|$| operator can be used to extract fields from the file descriptor (in this case, types defined in the file), or invoke pseuso-methods. Table~\ref{filedescriptor-methods-table} describes the methods defined for the \texttt{FileDescriptor} class. <<>>= f <- tutorial.Person$fileDescriptor() f f$Person @ \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{name} & \ref{filedescriptor-method-name} & Return the filename for this FileDescriptorProto.\\ \texttt{package} & \ref{filedescriptor-method-package} & Return the file-level package name specified in this FileDescriptorProto.\\ \texttt{as.character} & \ref{filedescriptor-method-ascharacter} & character representation of a descriptor. \\ \texttt{toString} & \ref{filedescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}). \\ \texttt{asMessage} & \ref{filedescriptor-method-asmessage} & return FileDescriptorProto message. \\ \texttt{as.list} & \ref{filedescriptor-method-aslist} & return named list of descriptors defined in this file descriptor.\\ \hline \end{tabular} \end{small} \caption{\label{filedescriptor-methods-table}Description of methods for the \texttt{FileDescriptor} S4 class} \end{table} \subsubsection{as.character} \label{filedescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the file descriptor. <<>>= writeLines( as.character(fileDescriptor(tutorial.Person)) ) @ \subsubsection{toString} \label{filedescriptor-method-tostring} \texttt{toString} is an alias of \texttt{as.character}. <<>>= writeLines( fileDescriptor(tutorial.Person)$toString() ) @ \subsubsection{asMessage} \label{filedescriptor-method-asmessage} The \texttt{asMessage} method returns a protocol buffer message representation of the file descriptor. <<>>= asMessage(tutorial.Person$fileDescriptor()) writeLines( as.character(asMessage(tutorial.Person$fileDescriptor())) ) @ \subsubsection{as.list} \label{filedescriptor-method-aslist} The \texttt{as.list} method creates a named R list that contains the descriptors defined in this file descriptor. <<>>= as.list( tutorial.Person$fileDescriptor() ) @ \subsubsection{name} \label{filedescriptor-method-name} The \texttt{name} method can be used to retrieve the file name associated with the file descriptor. The optional boolean argument can be specified if full pathnames are desired. <<>>= name( tutorial.Person$fileDescriptor() ) tutorial.Person$fileDescriptor()$name(TRUE) @ \subsubsection{package} \label{filedescriptor-method-package} The \texttt{package} method can be used to retrieve the package scope associated with this file descriptor. <<>>= tutorial.Person$fileDescriptor()$package() @ \subsection{service descriptors} \label{subsec-ServiceDescriptor} Not fully implemented. Needs to be connected to a concrete RPC implementation. The Google Protocol Buffers C++ open-source library does not include an RPC implementation, but this can be connected easily to others. \subsection{method descriptors} \label{subsec-MethodDescriptor} Not fully implemented. Needs to be connected to a concrete RPC implementation. The Google Protocol Buffers C++ open-source library does not include an RPC implementation, but this can be connected easily to others. \section{Utilities} \subsection{coercing objects to messages} The \texttt{asMessage} function uses the standard coercion mechanism of the \texttt{as} method, and so can be used as a shorthand : <<>>= # coerce a message type descriptor to a message # asMessage( tutorial.Person ) # coerce a enum descriptor asMessage( tutorial.Person.PhoneType ) # coerce a field descriptor asMessage( tutorial.Person$email ) # coerce a file descriptor asMessage( fileDescriptor( tutorial.Person ) ) @ \subsection{completion} The \texttt{RProtoBuf} package implements the \texttt{.DollarNames} S3 generic function (defined in the \texttt{utils} package) for all classes. Completion possibilities include pseudo method names for all classes, plus : \begin{itemize} \item field names for messages \item field names, enum types, nested types for message type descriptors \item names for enum descriptors \item names for top-level extensions \item message names for file descriptors \end{itemize} In the unlikely event that there is a user-defined field of exactly the same name as one of the pseudo methods, the user-defined field shall take precedence for completion purposes by design, since the method name can always be invoked directly. \subsection{with and within} The S3 generic \texttt{with} function is implemented for class \texttt{Message}, allowing to evaluate an R expression in an environment that allows to retrieve and set fields of a message simply using their names. <<>>= message <- new( tutorial.Person, email = "foo@bar.com" ) with( message, { # set the id field id <- 2 # set the name field from the email field name <- gsub( "[@]", " ", email ) sprintf( "%d [%s] : %s", id, email, name ) } ) @ The difference between \texttt{with} and \texttt{within} is the value that is returned. For \texttt{with} returns the result of the R expression, for \texttt{within} the message is returned. In both cases, the message is modified because \texttt{RProtoBuf} works by reference. \subsection{identical} The \texttt{identical} method is implemented to compare two messages. <<>>= m1 <- new( tutorial.Person, email = "foo@bar.com", id = 2 ) m2 <- update( new( tutorial.Person) , email = "foo@bar.com", id = 2 ) identical( m1, m2 ) @ The \verb|==| operator can be used as an alias to \texttt{identical}. <<>>= m1 == m2 m1 != m2 @ Alternatively, the \texttt{all.equal} function can be used, allowing a tolerance when comparing \texttt{float} or \texttt{double} values. \subsection{merge} \texttt{merge} can be used to merge two messages of the same type. <<>>= m1 <- new( tutorial.Person, name = "foobar" ) m2 <- new( tutorial.Person, email = "foo@bar.com" ) m3 <- merge( m1, m2 ) writeLines( as.character( m3 ) ) @ \subsection{P} The \texttt{P} function is an alternative way to retrieve a message descriptor using its type name. It is not often used because of the lookup mechanism described in section~\ref{sec-lookup}. <<>>= P("tutorial.Person") new( P("tutorial.Person") ) # but we can do this instead tutorial.Person new( tutorial.Person ) @ \section{Advanced Features} \subsection{Extensions} \label{sec-extensions} Extensions allow you to declare a range of field numbers in a message that are available for extension types. This allows others to declare new fields for a given message type possibly in their own \texttt{.proto} files without having to edit the original file. See \url{https://developers.google.com/protocol-buffers/docs/proto#extensions}. Notice that the last line of the \texttt{Person} message schema in \texttt{addressbook.proto} is the following line : \begin{verbatim} extensions 100 to 199; \end{verbatim} This specifies that other users in other .proto files can use tag numbers between 100 and 199 for extention types of this message. For example, the following file \texttt{extend.proto}: <>= extend.proto <- tempfile() writeLines(c( paste0('import "', name(tutorial.Person$fileDescriptor(), TRUE), '";'), "package tutorial;", paste0("extend Person {\n optional string nationality = 100;\n}")), extend.proto) @ <>= writeLines(readLines(extend.proto)) @ After importing this new \texttt{.proto} file with an extension defined, we can get or set the value of this extension in Messages of type \texttt{Person}. <<>>= library(RProtoBuf) readProtoFiles(extend.proto) person <- new(tutorial.Person, id=1, name="Murray") person person$setExtension(P("tutorial.nationality"), "USA") cat(as.character(person)) person$getExtension(P("tutorial.nationality")) @ The character output of this message places the extension type in brackets to differentiate it from other fields in the message, and so we know we need to use the \texttt{getExtension} method rather than a '\$' field extractor to get the value. \subsection{Descriptor lookup} \label{sec-lookup} The \texttt{RProtoBuf} package uses the user defined tables framework that is defined as part of the \texttt{RObjectTables} package available from the OmegaHat project. The feature allows \texttt{RProtoBuf} to install the special environment \emph{RProtoBuf:DescriptorPool} in the R search path. The environment is special in that, instead of being associated with a static hash table, it is dynamically queried by R as part of R's usual variable lookup. In other words, it means that when the R interpreter looks for a binding to a symbol (foo) in its search path, it asks to our package if it knows the binding "foo", this is then implemented by the \texttt{RProtoBuf} package by calling an internal method of the \texttt{protobuf} C++ library. \subsection{64-bit integer issues} \label{sec:int64} R does not have native 64-bit integer support. Instead, R treats large integers as doubles which have limited precision. For example, it loses the ability to distinguish some distinct integers: <<>>= 2^53 == (2^53 + 1) @ Protocol Buffers are frequently used to pass data between different systems, however, and most other systems these days have support for 64-bit integers. To work around this, RProtoBuf allows users to get and set 64-bit integer types by treating them as characters when running on a platform with a 64-bit long long type available. <>= if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } @ If we try to set an int64 field in R to double values, we lose precision: % We comment out the raw Sweave here because it doesn't work on 32-bit % platforms but it is important to illustrate what the user is missing % out on so we hard code the output from a platform with 64-bit long % long type. % % <<>>= % test <- new(protobuf_unittest.TestAllTypes) % test$repeated_int64 <- c(2^53, 2^53+1) % length(unique(test$repeated_int64)) % @ \begin{Schunk} \begin{Sinput} > test <- new(protobuf_unittest.TestAllTypes) > test$repeated_int64 <- c(2^53, 2^53+1) > length(unique(test$repeated_int64)) \end{Sinput} \begin{Soutput} [1] 1 \end{Soutput} \end{Schunk} However, we can specify the values as character strings so that the C++ library on which RProtoBuf is based can store a true 64-bit integer representation of the data. % <<>>= % test$repeated_int64 <- c("9007199254740992", "9007199254740993") % @ \begin{Schunk} \begin{Sinput} > test$repeated_int64 <- c("9007199254740992", "9007199254740993") \end{Sinput} \end{Schunk} When reading the value back into R, numeric types are returned by default, but when the full precision is required a character value will be returned if the \texttt{RProtoBuf.int64AsString} option is set to \texttt{TRUE}. % TODO: the if statement prevents us from seeing line by line % output inside the block (E.g. the output of test$repeated_int64). % This reduces the usefulness of this example when we are on a 64-bit % platform. E.g. only the final ``2'' is returned. % <>= % options("RProtoBuf.int64AsString" = FALSE) % test$repeated_int64 % length(unique(test$repeated_int64)) % options("RProtoBuf.int64AsString" = TRUE) % test$repeated_int64 % length(unique(test$repeated_int64)) %@ \begin{Schunk} \begin{Sinput} > options("RProtoBuf.int64AsString" = FALSE) \end{Sinput} \begin{Soutput} $RProtoBuf.int64AsString [1] FALSE \end{Soutput} \begin{Sinput} > test$repeated_int64 \end{Sinput} \begin{Soutput} [1] 9.007199e+15 9.007199e+15 \end{Soutput} \begin{Sinput} > length(unique(test$repeated_int64)) \end{Sinput} \begin{Soutput} [1] 1 \end{Soutput} \begin{Sinput} > options("RProtoBuf.int64AsString" = TRUE) \end{Sinput} \begin{Soutput} $RProtoBuf.int64AsString [1] FALSE \end{Soutput} \begin{Sinput} > test$repeated_int64 \end{Sinput} \begin{Soutput} [1] "9007199254740992" "9007199254740993" \end{Soutput} \begin{Sinput} > length(unique(test$repeated_int64)) \end{Sinput} \begin{Soutput} [1] 2 \end{Soutput} \end{Schunk} <>= options("RProtoBuf.int64AsString" = FALSE) @ \subsection{Deprecated Feature: Protocol Buffer Groups} \label{sec:groups} Groups are a deprecated feature that offered another way to nest information in message definitions. For example, the \texttt{TestAllTypes} message type in \texttt{unittest.proto} includes an OptionalGroup type: \begin{verbatim} optional group OptionalGroup = 16 { optional int32 a = 17; } \end{verbatim} And although the feature is deprecated, it can be used with RProtoBuf: <>= test <- new(protobuf_unittest.TestAllTypes) test$optionalgroup$a <- 3 test$optionalgroup$a cat(as.character(test)) @ Note that groups simply combine a nested message type and a field into a single declaration. The field type is OptionalGroup in this example, and the field name is converted to lower-case 'optionalgroup' so as not to conflict with the type name. \section{Other approaches} Saptarshi Guha wrote another package that deals with integration of protocol buffer messages with R, taking a different angle : serializing any R object as a message, based on a single catch-all \texttt{proto} file. Saptarshi's package is available at \url{http://ml.stat.purdue.edu/rhipe/doc/html/ProtoBuffers.html}. Jeroen Ooms took a similar approach influenced by Saptarshi in his \texttt{RProtoBufUtils} package. Unlike Saptarshi's package, RProtoBufUtils depends on RProtoBuf for underlying message operations. This package is available at \url{https://github.com/jeroenooms/RProtoBufUtils}. % Phillip Yelland wrote another implementation, currently proprietary, % that has significant speed advantages when querying fields from a % large number of protocol buffers, but is less user friendly for the % basic cases documented here. \section{Plans for future releases} Protocol buffers have a mechanism for remote procedure calls (rpc) that is not yet used by \texttt{RProtoBuf}, but we may one day take advantage of this by writing a protocol buffer message R server, and client code as well, probably based on the functionality of the \texttt{Rserve} package. Extensions have been implemented in RProtoBuf and have been extensively used and tested, but they are not currently described in this vignette. Additional examples and documentation are needed for extensions. % \section{Troubleshouting} \section{Acknowledgments} % protobuf ? % saptarshi ? Some of the design of the package is based on the design of the \texttt{rJava} package by Simon Urbanek (dispatch on new, S4 class structures using external pointers, etc ...). We'd like to thank Simon for his indirect involvment on \texttt{RProtoBuf}. The user defined table mechanism, implemented by Duncan Temple Lang for the purpose of the \texttt{RObjectTables} package allowed the dynamic symbol lookup (see section~\ref{sec-lookup}). Many thanks to Duncan for this amazing feature. \end{document} RProtoBuf/inst/doc/RProtoBuf-intro.pdf0000644000175100001440000060233713037407201017412 0ustar hornikusers%PDF-1.5 % 156 0 obj << /Length 1295 /Filter /FlateDecode >> stream xYYoF~ϯ#D۽H-%ÊZl(RT,-#WN6b/roUD7OS$D%LBM02-y]iy2'dʵ/p89eU㤿? \KW7f>F^ݔq"AݔM̓׵-? 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invisible(sapply(c("txt", "html"), function(ext) { # fname <- sprintf("unitTests-results/%s-unitTests.%s", pkg, ext) # file.copy(fname, "/tmp", overwrite=TRUE) # })) #} @ \section*{Test Results} \begin{verbatim} <>= results <- sprintf("unitTests-results/%s-unitTests.txt", pkg) if (file.exists(results)) { writeLines(readLines(results)) } else{ writeLines("Unit test results not available") } @ \end{verbatim} \end{document} RProtoBuf/inst/doc/RProtoBuf-unitTests.R0000644000175100001440000000332113037407201017675 0ustar hornikusers### R code from vignette source 'RProtoBuf-unitTests.Rnw' ################################################### ### code chunk number 1: RProtoBuf-unitTests.Rnw:9-13 ################################################### require(RProtoBuf) prettyVersion <- packageDescription("RProtoBuf")$Version prettyDate <- format(Sys.Date(), "%B %e, %Y") library(RUnit) ################################################### ### code chunk number 2: unitTesting ################################################### pkg <- "RProtoBuf" if (file.exists("unitTests-results")) unlink("unitTests-results", recursive = TRUE) dir.create("unitTests-results") pathRcppTests <<- system.file("unitTests", package = pkg) path <- system.file("unitTests", package=pkg) testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path) tests <- runTestSuite(testSuite) err <- getErrors(tests) if (err$nFail > 0) cat(sprintf("unit test problems: %d failures", err$nFail)) if (err$nErr > 0) cat(sprintf("unit test problems: %d errors", err$nErr)) printHTMLProtocol(tests, fileName=sprintf("unitTests-results/%s-unitTests.html", pkg)) printTextProtocol(tests, fileName=sprintf("unitTests-results/%s-unitTests.txt" , pkg)) #if (file.exists("/tmp")) { # 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rprotobuf.date <- packageDescription("RProtoBuf")$Date now.date <- strftime(Sys.Date(), "%B %d, %Y") ################################################### ### code chunk number 2: RProtoBuf-paper.Rnw:126-132 ################################################### ## cf http://www.jstatsoft.org/style#q12 options(prompt = "R> ", continue = "+ ", width = 70, useFancyQuotes = FALSE, digits = 4) ################################################### ### code chunk number 3: RProtoBuf-paper.Rnw:326-334 ################################################### library("RProtoBuf") p <- new(tutorial.Person, id=1, name="Dirk") p$name p$name <- "Murray" cat(as.character(p)) serialize(p, NULL) class(p) ################################################### ### code chunk number 4: RProtoBuf-paper.Rnw:414-415 ################################################### p <- new(tutorial.Person, name = "Murray", id = 1) ################################################### ### code chunk number 5: RProtoBuf-paper.Rnw:424-427 ################################################### p$name p$id p$email <- "murray@stokely.org" ################################################### ### code chunk number 6: RProtoBuf-paper.Rnw:435-438 ################################################### p[["name"]] <- "Murray Stokely" p[[ 2 ]] <- 3 p[["email"]] ################################################### ### code chunk number 7: RProtoBuf-paper.Rnw:452-453 ################################################### p ################################################### ### code chunk number 8: RProtoBuf-paper.Rnw:460-461 ################################################### writeLines(as.character(p)) ################################################### ### code chunk number 9: RProtoBuf-paper.Rnw:474-475 ################################################### serialize(p, NULL) ################################################### ### code chunk number 10: RProtoBuf-paper.Rnw:480-483 ################################################### tf1 <- tempfile() serialize(p, tf1) readBin(tf1, raw(0), 500) ################################################### ### code chunk number 11: RProtoBuf-paper.Rnw:500-502 ################################################### msg <- read(tutorial.Person, tf1) writeLines(as.character(msg)) ################################################### ### code chunk number 12: RProtoBuf-paper.Rnw:592-593 ################################################### new(tutorial.Person) ################################################### ### code chunk number 13: RProtoBuf-paper.Rnw:617-622 ################################################### tutorial.Person$email tutorial.Person$email$is_required() tutorial.Person$email$type() tutorial.Person$email$as.character() class(tutorial.Person$email) ################################################### ### code chunk number 14: RProtoBuf-paper.Rnw:634-641 ################################################### tutorial.Person$PhoneType tutorial.Person$PhoneType$WORK class(tutorial.Person$PhoneType) tutorial.Person$PhoneType$value(1) tutorial.Person$PhoneType$value(name="HOME") tutorial.Person$PhoneType$value(number=1) class(tutorial.Person$PhoneType$value(1)) ################################################### ### code chunk number 15: RProtoBuf-paper.Rnw:737-740 ################################################### if (!exists("JSSPaper.Example1", "RProtoBuf:DescriptorPool")) { readProtoFiles(file="proto/int64.proto") } ################################################### ### code chunk number 16: RProtoBuf-paper.Rnw:762-766 ################################################### as.integer(2^31-1) as.integer(2^31 - 1) + as.integer(1) 2^31 class(2^31) ################################################### ### code chunk number 17: RProtoBuf-paper.Rnw:778-779 ################################################### 2^53 == (2^53 + 1) ################################################### ### code chunk number 18: RProtoBuf-paper.Rnw:816-818 ################################################### msg <- serialize_pb(iris, NULL) identical(iris, unserialize_pb(msg)) ################################################### ### code chunk number 19: RProtoBuf-paper.Rnw:846-849 ################################################### datasets <- as.data.frame(data(package="datasets")$results) datasets$name <- sub("\\s+.*$", "", datasets$Item) n <- nrow(datasets) ################################################### ### code chunk number 20: RProtoBuf-paper.Rnw:867-910 ################################################### datasets$object.size <- unname(sapply(datasets$name, function(x) object.size(eval(as.name(x))))) datasets$R.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize(eval(as.name(x)), NULL)))) datasets$R.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize(eval(as.name(x)), NULL)))) datasets$R.serialize.size.gz <- unname(sapply(datasets$name, function(x) length(memCompress(serialize(eval(as.name(x)), NULL), "gzip")))) datasets$RProtoBuf.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize_pb(eval(as.name(x)), NULL)))) datasets$RProtoBuf.serialize.size.gz <- unname(sapply(datasets$name, function(x) length(memCompress(serialize_pb(eval(as.name(x)), NULL), "gzip")))) clean.df <- data.frame(dataset=datasets$name, object.size=datasets$object.size, "serialized"=datasets$R.serialize.size, "gzipped serialized"=datasets$R.serialize.size.gz, "RProtoBuf"=datasets$RProtoBuf.serialize.size, "gzipped RProtoBuf"=datasets$RProtoBuf.serialize.size.gz, "ratio.serialized" = datasets$R.serialize.size / datasets$object.size, "ratio.rprotobuf" = datasets$RProtoBuf.serialize.size / datasets$object.size, "ratio.serialized.gz" = datasets$R.serialize.size.gz / datasets$object.size, "ratio.rprotobuf.gz" = datasets$RProtoBuf.serialize.size.gz / datasets$object.size, "savings.serialized" = 1-(datasets$R.serialize.size / datasets$object.size), "savings.rprotobuf" = 1-(datasets$RProtoBuf.serialize.size / datasets$object.size), "savings.serialized.gz" = 1-(datasets$R.serialize.size.gz / datasets$object.size), "savings.rprotobuf.gz" = 1-(datasets$RProtoBuf.serialize.size.gz / datasets$object.size), check.names=FALSE) all.df<-data.frame(dataset="TOTAL", object.size=sum(datasets$object.size), "serialized"=sum(datasets$R.serialize.size), "gzipped serialized"=sum(datasets$R.serialize.size.gz), "RProtoBuf"=sum(datasets$RProtoBuf.serialize.size), "gzipped RProtoBuf"=sum(datasets$RProtoBuf.serialize.size.gz), "ratio.serialized" = sum(datasets$R.serialize.size) / sum(datasets$object.size), "ratio.rprotobuf" = sum(datasets$RProtoBuf.serialize.size) / sum(datasets$object.size), "ratio.serialized.gz" = sum(datasets$R.serialize.size.gz) / sum(datasets$object.size), "ratio.rprotobuf.gz" = sum(datasets$RProtoBuf.serialize.size.gz) / sum(datasets$object.size), "savings.serialized" = 1-(sum(datasets$R.serialize.size) / sum(datasets$object.size)), "savings.rprotobuf" = 1-(sum(datasets$RProtoBuf.serialize.size) / sum(datasets$object.size)), "savings.serialized.gz" = 1-(sum(datasets$R.serialize.size.gz) / sum(datasets$object.size)), "savings.rprotobuf.gz" = 1-(sum(datasets$RProtoBuf.serialize.size.gz) / sum(datasets$object.size)), check.names=FALSE) clean.df<-rbind(clean.df, all.df) ################################################### ### code chunk number 21: SER ################################################### old.mar<-par("mar") new.mar<-old.mar new.mar[3]<-0 new.mar[4]<-0 my.cex<-1.3 par("mar"=new.mar) plot(clean.df$savings.serialized, clean.df$savings.rprotobuf, pch=1, col="red", las=1, xlab="Serialization Space Savings", ylab="Protocol Buffer Space Savings", xlim=c(0,1),ylim=c(0,1),cex.lab=my.cex, cex.axis=my.cex) points(clean.df$savings.serialized.gz, clean.df$savings.rprotobuf.gz,pch=2, col="blue") # grey dotted diagonal abline(a=0,b=1, col="grey",lty=2,lwd=3) # find point furthest off the X axis. clean.df$savings.diff <- clean.df$savings.serialized - clean.df$savings.rprotobuf clean.df$savings.diff.gz <- clean.df$savings.serialized.gz - clean.df$savings.rprotobuf.gz # The one to label. tmp.df <- clean.df[which(clean.df$savings.diff == min(clean.df$savings.diff)),] # This minimum means most to the left of our line, so pos=2 is label to the left text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=2, cex=my.cex) # Some gziped version # text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=2, cex=my.cex) # Second one is also an outlier tmp.df <- clean.df[which(clean.df$savings.diff == sort(clean.df$savings.diff)[2]),] # This minimum means most to the left of our line, so pos=2 is label to the left text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=2, cex=my.cex) #text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=my.cex) tmp.df <- clean.df[which(clean.df$savings.diff == max(clean.df$savings.diff)),] # This minimum means most to the right of the diagonal, so pos=4 is label to the right # Only show the gziped one. #text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=4, cex=my.cex) text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=4, cex=my.cex) #outlier.dfs <- clean.df[c(which(clean.df$savings.diff == min(clean.df$savings.diff)), legend("topleft", c("Raw", "Gzip Compressed"), pch=1:2, col=c("red", "blue"), cex=my.cex) #interesting.df <- clean.df[unique(c(which(clean.df$savings.diff == min(clean.df$savings.diff)), # which(clean.df$savings.diff == max(clean.df$savings.diff)), # which(clean.df$savings.diff.gz == max(clean.df$savings.diff.gz)), # which(clean.df$dataset == "TOTAL"))),c("dataset", "object.size", "serialized", "gzipped serialized", "RProtoBuf", "gzipped RProtoBuf", "savings.serialized", "savings.serialized.gz", "savings.rprotobuf", "savings.rprotobuf.gz")] interesting.df <- clean.df[as.character(clean.df[,1]) %in% c("crimtab", "airquality", "faithful", "TOTAL"), c("dataset", "object.size", "serialized", "gzipped serialized", "RProtoBuf", "gzipped RProtoBuf", "savings.serialized", "savings.serialized.gz", "savings.rprotobuf", "savings.rprotobuf.gz")] interesting.df <- interesting.df[c(2,1,3,4),] # Print without .00 in xtable interesting.df$object.size <- as.integer(interesting.df$object.size) par("mar"=old.mar) ################################################### ### code chunk number 22: RProtoBuf-paper.Rnw:1174-1178 (eval = FALSE) ################################################### ## require(HistogramTools) ## readProtoFiles(package="HistogramTools") ## hist <- HistogramTools.HistogramState$read("proto/hist.pb") ## plot(as.histogram(hist), main="") ################################################### ### code chunk number 23: RProtoBuf-paper.Rnw:1265-1272 (eval = FALSE) ################################################### ## library("RProtoBuf") ## library("httr") ## ## req <- GET('https://demo.ocpu.io/MASS/data/Animals/pb') ## output <- unserialize_pb(req$content) ## ## identical(output, MASS::Animals) ################################################### ### code chunk number 24: RProtoBuf-paper.Rnw:1324-1340 (eval = FALSE) ################################################### ## library("httr") ## library("RProtoBuf") ## ## args <- list(n=42, mean=100) ## payload <- serialize_pb(args, NULL) ## ## req <- POST ( ## url = "https://demo.ocpu.io/stats/R/rnorm/pb", ## body = payload, ## add_headers ( ## "Content-Type" = "application/x-protobuf" ## ) ## ) ## ## output <- unserialize_pb(req$content) ## print(output) ################################################### ### code chunk number 25: RProtoBuf-paper.Rnw:1344-1347 (eval = FALSE) ################################################### ## fnargs <- unserialize_pb(inputmsg) ## val <- do.call(stats::rnorm, fnargs) ## outputmsg <- serialize_pb(val) RProtoBuf/inst/doc/RProtoBuf-quickref.Rnw0000644000175100001440000000774613037407201020070 0ustar hornikusers\documentclass[10pt,twocolumn,a4paper]{article} %\VignetteIndexEntry{RProtoBuf-quickref} %\VignetteEngine{highlight::highlight} %\VignetteKeywords{RProtoBuf, Protocol Buffers, package} %\VignetteDepends{RProtoBuf} \setlength{\hoffset}{-0.8in} \setlength{\voffset}{-0.8in} \setlength{\marginparwidth}{0pt} \setlength{\marginparsep}{0pt} \setlength{\oddsidemargin}{0pt} \setlength{\headheight}{0pt} \setlength{\topmargin}{0pt} \setlength{\headsep}{0pt} \setlength{\footskip}{0pt} \setlength{\textheight}{27cm} \setlength{\textwidth}{20cm} \usepackage[colorlinks]{hyperref} \usepackage{microtype} %% cf http://www.khirevich.com/latex/microtype/ \usepackage[T1]{fontenc} %% cf http://www.khirevich.com/latex/font/ \usepackage[bitstream-charter]{mathdesign} %% cf http://www.khirevich.com/latex/font/ <>= options(width= 50) library("RProtoBuf") rpb.version <- packageDescription("RProtoBuf")$Version @ % closing $ needed here \author{Romain Fran\c{c}ois \and Dirk Eddelbuettel \and Murray Stokely} \title{RProtoBuf \Sexpr{rpb.version}: Quick Reference Guide} \begin{document} \maketitle \thispagestyle{empty} \paragraph{example proto file} <>= ab.proto <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) writeLines( readLines( ab.proto ) ) @ \paragraph{read proto description files} <>= readProtoFiles( "somefile.proto" ) readProtoFiles( dir = somedir ) readProtoFiles( package = AnRPackage ) @ \paragraph{create a message} <>= message <- new( tutorial.Person, id = 0, name = "Romain Francois", email = "francoisromain@free.fr" ) @ \paragraph{serialize a message to a file or binary connection} <>= # to a file tf1 <- tempfile() message$serialize( tf1 ) # to a binary connection tf2 <- tempfile(); con <- file( tf2, open = "wb" ) message$serialize( con ) close(con) # retrieve the payload message$serialize( NULL ) @ \paragraph{read a message from a file or binary connection} <>= # from a file tutorial.Person$read( tf1 ) # from a connection con <- file( tf2, open = "rb" ) tutorial.Person$read( con ) <>= close( con ) @ \paragraph{Get/Set fields} <>= email <- message$email message$id <- 2 message[[ "name" ]] <- "Romain" id <- message[[ 2 ]] # tag number for 'id' @ \paragraph{Message methods} \begin{center} \begin{small} \begin{tabular}{cp{7cm}} \hline \texttt{has} & Indicates if a message has a given field. \\ \texttt{clone} & Creates a clone of the message \\ \texttt{isInitialized} & Indicates if a message has all its required fields set\\ \texttt{serialize} & serialize a message to a file or a binary connection or retrieve the message payload as a raw vector\\ \texttt{clear} & Clear one or several fields of a message, or the entire message\\ \texttt{size} & The number of elements in a message field\\ \texttt{bytesize} & The number of bytes the message would take once serialized\\ \hline \texttt{swap} & swap elements of a repeated field of a message\\ \texttt{set} & set elements of a repeated field\\ \texttt{fetch} & fetch elements of a repeated field\\ \texttt{add} & add elements to a repeated field \\ \hline \texttt{str} & the R structure of the message\\ \texttt{as.character} & character representation of a message\\ \texttt{toString} & character representation of a message (same as \texttt{as.character}) \\ \texttt{update} & updates several fields of a message at once\\ \texttt{descriptor} & get the descriptor of the message type of this message\\ \hline \end{tabular} \end{small} \end{center} <<>>= writeLines( message$toString() ) @ \paragraph{More info} \begin{center} \begin{small} \begin{tabular}{cp{7cm}} full vignette & \verb|vignette( "RProtoBuf")| \\ protobuf & \url{http://code.google.com/p/protobuf/} \\ RProtoBuf & \url{http://r-forge.r-project.org/projects/rprotobuf/}\\ mailing list & \url{https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rprotobuf-yada} \\ \end{tabular} \end{small} \end{center} \end{document} RProtoBuf/inst/doc/RProtoBuf-quickref.R0000644000175100001440000000461513037407201017513 0ustar hornikusers### R code from vignette source 'RProtoBuf-quickref.Rnw' ################################################### ### code chunk number 1: RProtoBuf-quickref.Rnw:26-29 ################################################### options(width= 50) library("RProtoBuf") rpb.version <- packageDescription("RProtoBuf")$Version ################################################### ### code chunk number 2: RProtoBuf-quickref.Rnw:42-45 ################################################### ab.proto <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) writeLines( readLines( ab.proto ) ) ################################################### ### code chunk number 3: RProtoBuf-quickref.Rnw:50-53 (eval = FALSE) ################################################### ## readProtoFiles( "somefile.proto" ) ## readProtoFiles( dir = somedir ) ## readProtoFiles( package = AnRPackage ) ################################################### ### code chunk number 4: RProtoBuf-quickref.Rnw:58-61 ################################################### message <- new( tutorial.Person, id = 0, name = "Romain Francois", email = "francoisromain@free.fr" ) ################################################### ### code chunk number 5: RProtoBuf-quickref.Rnw:66-77 ################################################### # to a file tf1 <- tempfile() message$serialize( tf1 ) # to a binary connection tf2 <- tempfile(); con <- file( tf2, open = "wb" ) message$serialize( con ) close(con) # retrieve the payload message$serialize( NULL ) ################################################### ### code chunk number 6: RProtoBuf-quickref.Rnw:82-87 ################################################### # from a file tutorial.Person$read( tf1 ) # from a connection con <- file( tf2, open = "rb" ) tutorial.Person$read( con ) ################################################### ### code chunk number 7: RProtoBuf-quickref.Rnw:88-89 ################################################### close( con ) ################################################### ### code chunk number 8: RProtoBuf-quickref.Rnw:94-98 ################################################### email <- message$email message$id <- 2 message[[ "name" ]] <- "Romain" id <- message[[ 2 ]] # tag number for 'id' ################################################### ### code chunk number 9: RProtoBuf-quickref.Rnw:130-131 ################################################### writeLines( message$toString() ) RProtoBuf/inst/doc/RProtoBuf-quickref.pdf0000644000175100001440000023530413037407201020064 0ustar hornikusers%PDF-1.5 % 8 0 obj << /Length 3139 /Filter /FlateDecode >> stream xo۸B0` ְ(JTv]{K3쇴8(j[$' ǏG%[s(E4ŏHq-g珞Q/)FeNs>v.Y=[MNN0:vӓSV蓪>;!q2Id1JTU:NN>y0PLsA"= B~Nj=aq2\%e*[}}Jfbj{ 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CCbhBT|{uL׏Wz٫oz߼a[I?[ endstream endobj startxref 80187 %%EOF RProtoBuf/inst/doc/RProtoBuf-intro.R0000644000175100001440000007725013037407201017042 0ustar hornikusers### R code from vignette source 'RProtoBuf-intro.Rnw' ################################################### ### code chunk number 1: RProtoBuf-intro.Rnw:26-30 ################################################### library("RProtoBuf") options("width"=65) rpb.version <- packageDescription("RProtoBuf")$Version prettyDate <- format(Sys.Date(), "%B %e, %Y") ################################################### ### code chunk number 2: RProtoBuf-intro.Rnw:120-121 ################################################### args( readProtoFiles ) ################################################### ### code chunk number 3: RProtoBuf-intro.Rnw:127-129 ################################################### proto.dir <- system.file( "proto", package = "RProtoBuf" ) proto.file <- file.path( proto.dir, "addressbook.proto" ) ################################################### ### code chunk number 4: RProtoBuf-intro.Rnw:130-131 (eval = FALSE) ################################################### ## readProtoFiles( proto.file ) ################################################### ### code chunk number 5: RProtoBuf-intro.Rnw:138-139 ################################################### dir( proto.dir, pattern = "\\.proto$", full.names = TRUE ) ################################################### ### code chunk number 6: RProtoBuf-intro.Rnw:140-141 (eval = FALSE) ################################################### ## readProtoFiles( dir = proto.dir ) ################################################### ### code chunk number 7: RProtoBuf-intro.Rnw:151-152 (eval = FALSE) ################################################### ## readProtoFiles( package = "RProtoBuf" ) ################################################### ### code chunk number 8: RProtoBuf-intro.Rnw:160-161 ################################################### ls( "RProtoBuf:DescriptorPool" ) ################################################### ### code chunk number 9: RProtoBuf-intro.Rnw:173-174 ################################################### p <- new( tutorial.Person, name = "Romain", id = 1 ) ################################################### ### code chunk number 10: RProtoBuf-intro.Rnw:183-186 ################################################### p$name p$id p$email <- "francoisromain@free.fr" ################################################### ### code chunk number 11: RProtoBuf-intro.Rnw:195-198 ################################################### p[["name"]] <- "Romain Francois" p[[ 2 ]] <- 3 p[[ "email" ]] ################################################### ### code chunk number 12: RProtoBuf-intro.Rnw:213-214 ################################################### p ################################################### ### code chunk number 13: RProtoBuf-intro.Rnw:221-222 ################################################### writeLines( as.character( p ) ) ################################################### ### code chunk number 14: RProtoBuf-intro.Rnw:233-234 ################################################### serialize( p, NULL ) ################################################### ### code chunk number 15: RProtoBuf-intro.Rnw:239-243 ################################################### tf1 <- tempfile() tf1 serialize( p, tf1 ) readBin( tf1, raw(0), 500 ) ################################################### ### code chunk number 16: RProtoBuf-intro.Rnw:248-253 ################################################### tf2 <- tempfile() con <- file( tf2, open = "wb" ) serialize( p, con ) close( con ) readBin( tf2, raw(0), 500 ) ################################################### ### code chunk number 17: RProtoBuf-intro.Rnw:259-265 ################################################### # serialize to a file p$serialize( tf1 ) # serialize to a binary connection con <- file( tf2, open = "wb" ) p$serialize( con ) close( con ) ################################################### ### code chunk number 18: RProtoBuf-intro.Rnw:275-276 ################################################### args( read ) ################################################### ### code chunk number 19: RProtoBuf-intro.Rnw:285-287 ################################################### message <- read( tutorial.Person, tf1 ) writeLines( as.character( message ) ) ################################################### ### code chunk number 20: RProtoBuf-intro.Rnw:293-297 ################################################### con <- file( tf2, open = "rb" ) message <- read( tutorial.Person, con ) close( con ) writeLines( as.character( message ) ) ################################################### ### code chunk number 21: RProtoBuf-intro.Rnw:302-305 ################################################### # reading the raw vector payload of the message payload <- readBin( tf1, raw(0), 5000 ) message <- read( tutorial.Person, payload ) ################################################### ### code chunk number 22: RProtoBuf-intro.Rnw:312-320 ################################################### # reading from a file message <- tutorial.Person$read( tf1 ) # reading from a binary connection con <- file( tf2, open = "rb" ) message <- tutorial.Person$read( con ) close( con ) # read from the payload message <- tutorial.Person$read( payload ) ################################################### ### code chunk number 23: RProtoBuf-intro.Rnw:331-332 ################################################### str( p ) ################################################### ### code chunk number 24: RProtoBuf-intro.Rnw:416-427 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2, phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$name message$email message[[ "phone" ]] # using the tag number message[[ 2 ]] # id ################################################### ### code chunk number 25: RProtoBuf-intro.Rnw:489-495 ################################################### message <- new( tutorial.Person, name = "foo", id = 2 ) message$email <- "foo@bar.com" message[[ "id" ]] <- 2 message[[ 1 ]] <- "foobar" writeLines( message$as.character() ) ################################################### ### code chunk number 26: RProtoBuf-intro.Rnw:544-548 ################################################### message <- new( tutorial.Person, name = "foo" ) message$has( "name" ) message$has( "id" ) message$has( "phone" ) ################################################### ### code chunk number 27: RProtoBuf-intro.Rnw:558-563 ################################################### m1 <- new( tutorial.Person, name = "foo" ) m2 <- m1$clone( ) m2$email <- "foo@bar.com" writeLines( as.character( m1 ) ) writeLines( as.character( m2 ) ) ################################################### ### code chunk number 28: RProtoBuf-intro.Rnw:574-578 ################################################### message <- new( tutorial.Person, name = "foo" ) message$isInitialized() message$id <- 2 message$isInitialized() ################################################### ### code chunk number 29: RProtoBuf-intro.Rnw:587-597 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) tf1 <- tempfile( ) tf1 message$serialize( tf1 ) tf2 <- tempfile( ) tf2 con <- file( tf2, open = "wb" ) message$serialize( con ) close( con ) ################################################### ### code chunk number 30: RProtoBuf-intro.Rnw:604-606 ################################################### readBin( tf1, raw(0), 500 ) readBin( tf2, raw(0), 500 ) ################################################### ### code chunk number 31: RProtoBuf-intro.Rnw:612-613 ################################################### message$serialize(NULL) ################################################### ### code chunk number 32: RProtoBuf-intro.Rnw:622-630 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( as.character( message ) ) message$clear() writeLines( as.character( message ) ) message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$clear( "id" ) writeLines( as.character( message ) ) ################################################### ### code chunk number 33: RProtoBuf-intro.Rnw:643-650 ################################################### message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$size( "phone" ) size( message, "phone" ) ################################################### ### code chunk number 34: RProtoBuf-intro.Rnw:664-668 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$bytesize() bytesize( message ) length( message$serialize( NULL ) ) ################################################### ### code chunk number 35: RProtoBuf-intro.Rnw:677-689 ################################################### message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$swap( "phone", 1, 2 ) writeLines( as.character( message$phone[[1]] ) ) writeLines( as.character( message$phone[[2]] ) ) swap( message, "phone", 1, 2 ) writeLines( as.character( message$phone[[1]] ) ) writeLines( as.character( message$phone[[2]] ) ) ################################################### ### code chunk number 36: RProtoBuf-intro.Rnw:699-708 ################################################### message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) number <- new( tutorial.Person.PhoneNumber, number = "+33(0)---", type = "WORK" ) message$set( "phone", 1, number ) writeLines( as.character( message ) ) ################################################### ### code chunk number 37: RProtoBuf-intro.Rnw:717-723 ################################################### message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$fetch( "phone", 1 ) ################################################### ### code chunk number 38: RProtoBuf-intro.Rnw:732-744 ################################################### if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } ## Test setting a singular extensions. test <- new(protobuf_unittest.TestAllExtensions) test$setExtension(protobuf_unittest.optional_int32_extension, as.integer(1)) ################################################### ### code chunk number 39: RProtoBuf-intro.Rnw:753-754 ################################################### test$getExtension(protobuf_unittest.optional_int32_extension) ################################################### ### code chunk number 40: RProtoBuf-intro.Rnw:762-767 ################################################### message <- new( tutorial.Person, name = "foo") phone <- new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ) message$add( "phone", phone ) writeLines( message$toString() ) ################################################### ### code chunk number 41: RProtoBuf-intro.Rnw:776-779 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$str() str( message ) ################################################### ### code chunk number 42: RProtoBuf-intro.Rnw:787-790 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( message$as.character() ) writeLines( as.character( message ) ) ################################################### ### code chunk number 43: RProtoBuf-intro.Rnw:798-801 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( message$toString() ) writeLines( toString( message ) ) ################################################### ### code chunk number 44: RProtoBuf-intro.Rnw:809-811 ################################################### message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) as.list( message ) ################################################### ### code chunk number 45: RProtoBuf-intro.Rnw:825-831 ################################################### message <- new( tutorial.Person ) update( message, name = "foo", id = 2, email = "foo@bar.com" ) writeLines( message$as.character() ) ################################################### ### code chunk number 46: RProtoBuf-intro.Rnw:841-844 ################################################### message <- new( tutorial.Person ) message$descriptor() descriptor( message ) ################################################### ### code chunk number 47: RProtoBuf-intro.Rnw:855-858 ################################################### message <- new( tutorial.Person ) message$fileDescriptor() fileDescriptor( message ) ################################################### ### code chunk number 48: RProtoBuf-intro.Rnw:937-947 ################################################### # field descriptor tutorial.Person$email # enum descriptor tutorial.Person$PhoneType # nested type descriptor tutorial.Person$PhoneNumber # same as tutorial.Person.PhoneNumber ################################################### ### code chunk number 49: RProtoBuf-intro.Rnw:956-958 ################################################### tutorial.Person$new( ) new( tutorial.Person ) ################################################### ### code chunk number 50: RProtoBuf-intro.Rnw:964-968 ################################################### tutorial.Person$new( email = "foo@bar.com" ) # same as update( tutorial.Person$new( ), email = "foo@bar.com" ) ################################################### ### code chunk number 51: RProtoBuf-intro.Rnw:977-989 ################################################### # start by serializing a message message <- new( tutorial.Person.PhoneNumber, type = "HOME", number = "+33(0)...." ) tf <- tempfile() serialize( message, tf ) # now read back the message m <- tutorial.Person.PhoneNumber$read( tf ) writeLines( as.character( m ) ) m <- read( tutorial.Person.PhoneNumber, tf ) writeLines( as.character( m ) ) ################################################### ### code chunk number 52: RProtoBuf-intro.Rnw:999-1004 ################################################### # start by generating the ASCII representation of a message text <- as.character(new(tutorial.Person, id=1, name="Murray")) text # Then read the ascii representation in as a new message object. msg <- tutorial.Person$readASCII(text) ################################################### ### code chunk number 53: RProtoBuf-intro.Rnw:1019-1023 ################################################### desc <- tutorial.Person writeLines( desc$toString() ) writeLines( toString( desc ) ) writeLines( as.character(tutorial.Person) ) ################################################### ### code chunk number 54: RProtoBuf-intro.Rnw:1032-1033 ################################################### tutorial.Person$as.list() ################################################### ### code chunk number 55: RProtoBuf-intro.Rnw:1042-1043 ################################################### tutorial.Person$asMessage() ################################################### ### code chunk number 56: RProtoBuf-intro.Rnw:1053-1056 ################################################### desc <- tutorial.Person desc$fileDescriptor() fileDescriptor( desc ) ################################################### ### code chunk number 57: RProtoBuf-intro.Rnw:1065-1069 ################################################### # simple name tutorial.Person$name() # name including scope tutorial.Person$name(full = TRUE) ################################################### ### code chunk number 58: RProtoBuf-intro.Rnw:1078-1080 ################################################### tutorial.Person$containing_type() tutorial.Person$PhoneNumber$containing_type() ################################################### ### code chunk number 59: RProtoBuf-intro.Rnw:1089-1090 ################################################### tutorial.Person$field_count() ################################################### ### code chunk number 60: RProtoBuf-intro.Rnw:1099-1100 ################################################### tutorial.Person$field(1) ################################################### ### code chunk number 61: RProtoBuf-intro.Rnw:1109-1110 ################################################### tutorial.Person$nested_type_count() ################################################### ### code chunk number 62: RProtoBuf-intro.Rnw:1119-1120 ################################################### tutorial.Person$nested_type(1) ################################################### ### code chunk number 63: RProtoBuf-intro.Rnw:1129-1130 ################################################### tutorial.Person$enum_type_count() ################################################### ### code chunk number 64: RProtoBuf-intro.Rnw:1139-1140 ################################################### tutorial.Person$enum_type(1) ################################################### ### code chunk number 65: RProtoBuf-intro.Rnw:1213-1214 ################################################### writeLines( as.character( tutorial.Person$PhoneNumber ) ) ################################################### ### code chunk number 66: RProtoBuf-intro.Rnw:1222-1223 ################################################### writeLines( tutorial.Person.PhoneNumber$toString() ) ################################################### ### code chunk number 67: RProtoBuf-intro.Rnw:1232-1234 ################################################### tutorial.Person$id$asMessage() writeLines(as.character(tutorial.Person$id$asMessage())) ################################################### ### code chunk number 68: RProtoBuf-intro.Rnw:1243-1247 ################################################### # simple name. name( tutorial.Person$id ) # name including scope. name( tutorial.Person$id, full=TRUE ) ################################################### ### code chunk number 69: RProtoBuf-intro.Rnw:1256-1258 ################################################### fileDescriptor(tutorial.Person$id) tutorial.Person$id$fileDescriptor() ################################################### ### code chunk number 70: RProtoBuf-intro.Rnw:1267-1269 ################################################### containing_type(tutorial.Person$id) tutorial.Person$id$containing_type() ################################################### ### code chunk number 71: RProtoBuf-intro.Rnw:1279-1281 ################################################### is_extension( tutorial.Person$id ) tutorial.Person$id$is_extension() ################################################### ### code chunk number 72: RProtoBuf-intro.Rnw:1289-1291 ################################################### number( tutorial.Person$id ) tutorial.Person$id$number() ################################################### ### code chunk number 73: RProtoBuf-intro.Rnw:1300-1302 ################################################### type( tutorial.Person$id ) tutorial.Person$id$type() ################################################### ### code chunk number 74: RProtoBuf-intro.Rnw:1310-1312 ################################################### cpp_type( tutorial.Person$id ) tutorial.Person$id$cpp_type() ################################################### ### code chunk number 75: RProtoBuf-intro.Rnw:1324-1327 ################################################### label( tutorial.Person$id ) label( tutorial.Person$id , TRUE) tutorial.Person$id$label(TRUE) ################################################### ### code chunk number 76: RProtoBuf-intro.Rnw:1334-1336 ################################################### is_repeated( tutorial.Person$id ) tutorial.Person$id$is_repeated() ################################################### ### code chunk number 77: RProtoBuf-intro.Rnw:1344-1346 ################################################### is_required( tutorial.Person$id ) tutorial.Person$id$is_required() ################################################### ### code chunk number 78: RProtoBuf-intro.Rnw:1354-1356 ################################################### is_optional( tutorial.Person$id ) tutorial.Person$id$is_optional() ################################################### ### code chunk number 79: RProtoBuf-intro.Rnw:1365-1367 ################################################### has_default_value(tutorial.Person$PhoneNumber$type) has_default_value(tutorial.Person$PhoneNumber$number) ################################################### ### code chunk number 80: RProtoBuf-intro.Rnw:1375-1377 ################################################### default_value( tutorial.Person$PhoneNumber$type ) default_value( tutorial.Person$PhoneNumber$number ) ################################################### ### code chunk number 81: RProtoBuf-intro.Rnw:1386-1388 ################################################### message_type(tutorial.Person$phone) tutorial.Person$phone$message_type() ################################################### ### code chunk number 82: RProtoBuf-intro.Rnw:1395-1396 ################################################### enum_type(tutorial.Person$PhoneNumber$type) ################################################### ### code chunk number 83: RProtoBuf-intro.Rnw:1468-1470 ################################################### tutorial.Person$PhoneType$WORK name(tutorial.Person$PhoneType$value(number=2)) ################################################### ### code chunk number 84: RProtoBuf-intro.Rnw:1479-1480 ################################################### as.list( tutorial.Person$PhoneType ) ################################################### ### code chunk number 85: RProtoBuf-intro.Rnw:1488-1489 ################################################### writeLines( as.character( tutorial.Person$PhoneType ) ) ################################################### ### code chunk number 86: RProtoBuf-intro.Rnw:1497-1498 ################################################### writeLines( toString( tutorial.Person$PhoneType ) ) ################################################### ### code chunk number 87: RProtoBuf-intro.Rnw:1507-1509 ################################################### tutorial.Person$PhoneType$asMessage() writeLines(as.character(tutorial.Person$PhoneType$asMessage())) ################################################### ### code chunk number 88: RProtoBuf-intro.Rnw:1518-1522 ################################################### # simple name. name( tutorial.Person$PhoneType ) # name including scope. name( tutorial.Person$PhoneType, full=TRUE ) ################################################### ### code chunk number 89: RProtoBuf-intro.Rnw:1531-1533 ################################################### fileDescriptor(tutorial.Person$PhoneType) tutorial.Person$PhoneType$fileDescriptor() ################################################### ### code chunk number 90: RProtoBuf-intro.Rnw:1542-1543 ################################################### tutorial.Person$PhoneType$containing_type() ################################################### ### code chunk number 91: RProtoBuf-intro.Rnw:1551-1553 ################################################### length(tutorial.Person$PhoneType) tutorial.Person$PhoneType$length() ################################################### ### code chunk number 92: RProtoBuf-intro.Rnw:1562-1564 ################################################### tutorial.Person$PhoneType$has("WORK") tutorial.Person$PhoneType$has("nonexistant") ################################################### ### code chunk number 93: RProtoBuf-intro.Rnw:1573-1575 ################################################### value_count(tutorial.Person$PhoneType) tutorial.Person$PhoneType$value_count() ################################################### ### code chunk number 94: RProtoBuf-intro.Rnw:1585-1588 ################################################### tutorial.Person$PhoneType$value(1) tutorial.Person$PhoneType$value(name="HOME") tutorial.Person$PhoneType$value(number=1) ################################################### ### code chunk number 95: RProtoBuf-intro.Rnw:1647-1648 ################################################### number( tutorial.Person$PhoneType$value(number=2) ) ################################################### ### code chunk number 96: RProtoBuf-intro.Rnw:1657-1661 ################################################### # simple name. name( tutorial.Person$PhoneType$value(number=2) ) # name including scope. name( tutorial.Person$PhoneType$value(number=2), full=TRUE ) ################################################### ### code chunk number 97: RProtoBuf-intro.Rnw:1670-1671 ################################################### enum_type( tutorial.Person$PhoneType$value(number=2) ) ################################################### ### code chunk number 98: RProtoBuf-intro.Rnw:1680-1681 ################################################### writeLines( as.character( tutorial.Person$PhoneType$value(number=2) ) ) ################################################### ### code chunk number 99: RProtoBuf-intro.Rnw:1690-1691 ################################################### writeLines( toString( tutorial.Person$PhoneType$value(number=2) ) ) ################################################### ### code chunk number 100: RProtoBuf-intro.Rnw:1700-1702 ################################################### tutorial.Person$PhoneType$value(number=2)$asMessage() writeLines(as.character(tutorial.Person$PhoneType$value(number=2)$asMessage())) ################################################### ### code chunk number 101: RProtoBuf-intro.Rnw:1736-1739 ################################################### f <- tutorial.Person$fileDescriptor() f f$Person ################################################### ### code chunk number 102: RProtoBuf-intro.Rnw:1771-1772 ################################################### writeLines( as.character(fileDescriptor(tutorial.Person)) ) ################################################### ### code chunk number 103: RProtoBuf-intro.Rnw:1780-1781 ################################################### writeLines( fileDescriptor(tutorial.Person)$toString() ) ################################################### ### code chunk number 104: RProtoBuf-intro.Rnw:1789-1791 ################################################### asMessage(tutorial.Person$fileDescriptor()) writeLines( as.character(asMessage(tutorial.Person$fileDescriptor())) ) ################################################### ### code chunk number 105: RProtoBuf-intro.Rnw:1799-1800 ################################################### as.list( tutorial.Person$fileDescriptor() ) ################################################### ### code chunk number 106: RProtoBuf-intro.Rnw:1810-1812 ################################################### name( tutorial.Person$fileDescriptor() ) tutorial.Person$fileDescriptor()$name(TRUE) ################################################### ### code chunk number 107: RProtoBuf-intro.Rnw:1821-1822 ################################################### tutorial.Person$fileDescriptor()$package() ################################################### ### code chunk number 108: RProtoBuf-intro.Rnw:1848-1860 ################################################### # coerce a message type descriptor to a message # asMessage( tutorial.Person ) # coerce a enum descriptor asMessage( tutorial.Person.PhoneType ) # coerce a field descriptor asMessage( tutorial.Person$email ) # coerce a file descriptor asMessage( fileDescriptor( tutorial.Person ) ) ################################################### ### code chunk number 109: RProtoBuf-intro.Rnw:1891-1901 ################################################### message <- new( tutorial.Person, email = "foo@bar.com" ) with( message, { # set the id field id <- 2 # set the name field from the email field name <- gsub( "[@]", " ", email ) sprintf( "%d [%s] : %s", id, email, name ) } ) ################################################### ### code chunk number 110: RProtoBuf-intro.Rnw:1913-1916 ################################################### m1 <- new( tutorial.Person, email = "foo@bar.com", id = 2 ) m2 <- update( new( tutorial.Person) , email = "foo@bar.com", id = 2 ) identical( m1, m2 ) ################################################### ### code chunk number 111: RProtoBuf-intro.Rnw:1921-1923 ################################################### m1 == m2 m1 != m2 ################################################### ### code chunk number 112: RProtoBuf-intro.Rnw:1933-1937 ################################################### m1 <- new( tutorial.Person, name = "foobar" ) m2 <- new( tutorial.Person, email = "foo@bar.com" ) m3 <- merge( m1, m2 ) writeLines( as.character( m3 ) ) ################################################### ### code chunk number 113: RProtoBuf-intro.Rnw:1946-1952 ################################################### P("tutorial.Person") new( P("tutorial.Person") ) # but we can do this instead tutorial.Person new( tutorial.Person ) ################################################### ### code chunk number 114: RProtoBuf-intro.Rnw:1977-1984 ################################################### extend.proto <- tempfile() writeLines(c( paste0('import "', name(tutorial.Person$fileDescriptor(), TRUE), '";'), "package tutorial;", paste0("extend Person {\n optional string nationality = 100;\n}")), extend.proto) ################################################### ### code chunk number 115: RProtoBuf-intro.Rnw:1987-1988 ################################################### writeLines(readLines(extend.proto)) ################################################### ### code chunk number 116: RProtoBuf-intro.Rnw:1995-2002 ################################################### library(RProtoBuf) readProtoFiles(extend.proto) person <- new(tutorial.Person, id=1, name="Murray") person person$setExtension(P("tutorial.nationality"), "USA") cat(as.character(person)) person$getExtension(P("tutorial.nationality")) ################################################### ### code chunk number 117: RProtoBuf-intro.Rnw:2034-2035 ################################################### 2^53 == (2^53 + 1) ################################################### ### code chunk number 118: RProtoBuf-intro.Rnw:2044-2051 ################################################### if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } ################################################### ### code chunk number 119: RProtoBuf-intro.Rnw:2150-2151 ################################################### options("RProtoBuf.int64AsString" = FALSE) ################################################### ### code chunk number 120: RProtoBuf-intro.Rnw:2170-2174 ################################################### test <- new(protobuf_unittest.TestAllTypes) test$optionalgroup$a <- 3 test$optionalgroup$a cat(as.character(test)) RProtoBuf/inst/opencpu/0000755000175100001440000000000012440004312014566 5ustar hornikusersRProtoBuf/inst/opencpu/ocpu-rpc.py0000644000175100001440000000206012440004312016666 0ustar hornikusers#!/usr/bin/env python # Jeroen Ooms # # HTTPS+ProtoBuf RPC POC using OpenCPU # The call below maps to: do.call(stats::rnorm, list(n=42, mean=100)) import urllib2; from rexp_pb2 import *; #create the post payload, i.e. list(n=42, mean=100) payload = REXP( rclass = 5, rexpValue = [ REXP(rclass = 2, realValue = [42]), REXP(rclass = 2, realValue = [100]) ], attrName = [ "names" ], attrValue = [ REXP(rclass = 0, stringValue = [STRING(strval="n"), STRING(strval="mean")]) ] ); #HTTP POST req = urllib2.Request( 'https://public.opencpu.org/ocpu/library/stats/R/rnorm/pb', data = payload.SerializeToString(), headers = { 'Content-type': 'application/x-protobuf' } ); res = urllib2.urlopen(req); #parse output pb msg = REXP(); msg.ParseFromString(res.read()); #the return value is a double vector in this case print(msg.realValue); ##### To debug: #f = open("payload.msg", "wb") #f.write(payload.SerializeToString()) #f.close() # # Then do in R do: # library(RProtoBuf) # payload <- unserialize_pb("payload.msg") # do.call(stats::rnorm, payload)RProtoBuf/inst/opencpu/ocpu-rpc.R0000644000175100001440000000116112440004312016440 0ustar hornikusers# Jeroen Ooms # # HTTPS+ProtoBuf RPC POC using OpenCPU # The call below maps to: do.call(stats::rnorm, list(n=42, mean=100)) # !! This requires httr (>= 0.2.99). Version 0.2 has a bug. # library(devtools) # install_github("httr") # Actual code library(RProtoBuf) library(httr) args <- list(n=42, mean=100) payload <- serialize_pb(args, NULL) req <- POST ( url = "https://public.opencpu.org/ocpu/library/stats/R/rnorm/pb", body = payload, add_headers( "Content-Type" = "application/x-protobuf" ) ) #This is the output of stats::rnorm(n=42, mean=100) output <- unserialize_pb(req$content) print(length(output)) RProtoBuf/inst/opencpu/ocpu-getdata.R0000644000175100001440000000044212440004312017266 0ustar hornikusers# Jeroen Ooms # # HTTPS+ProtoBuf RPC POC using OpenCPU # Script below downloads MASS::Animals using protobuf library(RProtoBuf) library(httr) req <- GET ('https://public.opencpu.org/ocpu/library/MASS/data/Animals/pb') output <- unserialize_pb(req$content) identical(output, MASS::Animals) RProtoBuf/inst/opencpu/ocpu-getdata.py0000644000175100001440000000065212440004312017520 0ustar hornikusers#!/usr/bin/env python # Jeroen Ooms # # HTTPS+ProtoBuf RPC POC using OpenCPU # Script below downloads MASS::Animals using protobuf import urllib2; from rexp_pb2 import *; #HTTP GET req = urllib2.Request('https://public.opencpu.org/ocpu/library/MASS/data/Animals/pb'); res = urllib2.urlopen(req); #parse output pb msg = REXP(); msg.ParseFromString(res.read()); #the return value is a double vector in this case print(msg); RProtoBuf/inst/opencpu/readme.txt0000644000175100001440000000017312440004312016565 0ustar hornikusersThese scripts illustrate how protocol buffers can be used as a data interchange format or as the basis of an RPC protocol. RProtoBuf/inst/opencpu/rexp_pb2.py0000644000175100001440000002350412440004312016665 0ustar hornikusers# Generated by the protocol buffer compiler. DO NOT EDIT! from google.protobuf import descriptor from google.protobuf import message from google.protobuf import reflection from google.protobuf import descriptor_pb2 # @@protoc_insertion_point(imports) DESCRIPTOR = descriptor.FileDescriptor( name='rexp.proto', package='rexp', serialized_pb='\n\nrexp.proto\x12\x04rexp\"\xb3\x03\n\x04REXP\x12!\n\x06rclass\x18\x01 \x02(\x0e\x32\x11.rexp.REXP.RClass\x12\x15\n\trealValue\x18\x02 \x03(\x01\x42\x02\x10\x01\x12\x14\n\x08intValue\x18\x03 \x03(\x11\x42\x02\x10\x01\x12)\n\x0c\x62ooleanValue\x18\x04 \x03(\x0e\x32\x13.rexp.REXP.RBOOLEAN\x12!\n\x0bstringValue\x18\x05 \x03(\x0b\x32\x0c.rexp.STRING\x12\x10\n\x08rawValue\x18\x06 \x01(\x0c\x12!\n\x0c\x63omplexValue\x18\x07 \x03(\x0b\x32\x0b.rexp.CMPLX\x12\x1d\n\trexpValue\x18\x08 \x03(\x0b\x32\n.rexp.REXP\x12\x10\n\x08\x61ttrName\x18\x0b \x03(\t\x12\x1d\n\tattrValue\x18\x0c \x03(\x0b\x32\n.rexp.REXP\"f\n\x06RClass\x12\n\n\x06STRING\x10\x00\x12\x07\n\x03RAW\x10\x01\x12\x08\n\x04REAL\x10\x02\x12\x0b\n\x07\x43OMPLEX\x10\x03\x12\x0b\n\x07INTEGER\x10\x04\x12\x08\n\x04LIST\x10\x05\x12\x0b\n\x07LOGICAL\x10\x06\x12\x0c\n\x08NULLTYPE\x10\x07\" \n\x08RBOOLEAN\x12\x05\n\x01\x46\x10\x00\x12\x05\n\x01T\x10\x01\x12\x06\n\x02NA\x10\x02\"-\n\x06STRING\x12\x0e\n\x06strval\x18\x01 \x01(\t\x12\x13\n\x04isNA\x18\x02 \x01(\x08:\x05\x66\x61lse\"&\n\x05\x43MPLX\x12\x0f\n\x04real\x18\x01 \x01(\x01:\x01\x30\x12\x0c\n\x04imag\x18\x02 \x02(\x01\x32(\n\x04ocpu\x12 \n\x06\x64oCall\x12\n.rexp.REXP\x1a\n.rexp.REXP') _REXP_RCLASS = descriptor.EnumDescriptor( name='RClass', full_name='rexp.REXP.RClass', filename=None, file=DESCRIPTOR, values=[ descriptor.EnumValueDescriptor( name='STRING', index=0, number=0, options=None, type=None), descriptor.EnumValueDescriptor( name='RAW', index=1, number=1, options=None, type=None), descriptor.EnumValueDescriptor( name='REAL', index=2, number=2, options=None, type=None), descriptor.EnumValueDescriptor( name='COMPLEX', index=3, number=3, options=None, type=None), descriptor.EnumValueDescriptor( name='INTEGER', index=4, number=4, options=None, type=None), descriptor.EnumValueDescriptor( name='LIST', index=5, number=5, options=None, type=None), descriptor.EnumValueDescriptor( name='LOGICAL', index=6, number=6, options=None, type=None), descriptor.EnumValueDescriptor( name='NULLTYPE', index=7, number=7, options=None, type=None), ], containing_type=None, options=None, serialized_start=320, serialized_end=422, ) _REXP_RBOOLEAN = descriptor.EnumDescriptor( name='RBOOLEAN', full_name='rexp.REXP.RBOOLEAN', filename=None, file=DESCRIPTOR, values=[ descriptor.EnumValueDescriptor( name='F', index=0, number=0, options=None, type=None), descriptor.EnumValueDescriptor( name='T', index=1, number=1, options=None, type=None), descriptor.EnumValueDescriptor( name='NA', index=2, number=2, options=None, type=None), ], containing_type=None, options=None, serialized_start=424, serialized_end=456, ) _REXP = descriptor.Descriptor( name='REXP', full_name='rexp.REXP', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ descriptor.FieldDescriptor( name='rclass', full_name='rexp.REXP.rclass', index=0, number=1, type=14, cpp_type=8, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='realValue', full_name='rexp.REXP.realValue', index=1, number=2, type=1, cpp_type=5, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')), descriptor.FieldDescriptor( name='intValue', full_name='rexp.REXP.intValue', index=2, number=3, type=17, cpp_type=1, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')), descriptor.FieldDescriptor( name='booleanValue', full_name='rexp.REXP.booleanValue', index=3, number=4, type=14, cpp_type=8, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='stringValue', full_name='rexp.REXP.stringValue', index=4, number=5, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='rawValue', full_name='rexp.REXP.rawValue', index=5, number=6, type=12, cpp_type=9, label=1, has_default_value=False, default_value="", message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='complexValue', full_name='rexp.REXP.complexValue', index=6, number=7, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='rexpValue', full_name='rexp.REXP.rexpValue', index=7, number=8, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='attrName', full_name='rexp.REXP.attrName', index=8, number=11, type=9, cpp_type=9, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='attrValue', full_name='rexp.REXP.attrValue', index=9, number=12, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ _REXP_RCLASS, _REXP_RBOOLEAN, ], options=None, is_extendable=False, extension_ranges=[], serialized_start=21, serialized_end=456, ) _STRING = descriptor.Descriptor( name='STRING', full_name='rexp.STRING', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ descriptor.FieldDescriptor( name='strval', full_name='rexp.STRING.strval', index=0, number=1, type=9, cpp_type=9, label=1, has_default_value=False, default_value=unicode("", "utf-8"), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='isNA', full_name='rexp.STRING.isNA', index=1, number=2, type=8, cpp_type=7, label=1, has_default_value=True, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, extension_ranges=[], serialized_start=458, serialized_end=503, ) _CMPLX = descriptor.Descriptor( name='CMPLX', full_name='rexp.CMPLX', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ descriptor.FieldDescriptor( name='real', full_name='rexp.CMPLX.real', index=0, number=1, type=1, cpp_type=5, label=1, has_default_value=True, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), descriptor.FieldDescriptor( name='imag', full_name='rexp.CMPLX.imag', index=1, number=2, type=1, cpp_type=5, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, extension_ranges=[], serialized_start=505, serialized_end=543, ) _REXP.fields_by_name['rclass'].enum_type = _REXP_RCLASS _REXP.fields_by_name['booleanValue'].enum_type = _REXP_RBOOLEAN _REXP.fields_by_name['stringValue'].message_type = _STRING _REXP.fields_by_name['complexValue'].message_type = _CMPLX _REXP.fields_by_name['rexpValue'].message_type = _REXP _REXP.fields_by_name['attrValue'].message_type = _REXP _REXP_RCLASS.containing_type = _REXP; _REXP_RBOOLEAN.containing_type = _REXP; DESCRIPTOR.message_types_by_name['REXP'] = _REXP DESCRIPTOR.message_types_by_name['STRING'] = _STRING DESCRIPTOR.message_types_by_name['CMPLX'] = _CMPLX class REXP(message.Message): __metaclass__ = reflection.GeneratedProtocolMessageType DESCRIPTOR = _REXP # @@protoc_insertion_point(class_scope:rexp.REXP) class STRING(message.Message): __metaclass__ = reflection.GeneratedProtocolMessageType DESCRIPTOR = _STRING # @@protoc_insertion_point(class_scope:rexp.STRING) class CMPLX(message.Message): __metaclass__ = reflection.GeneratedProtocolMessageType DESCRIPTOR = _CMPLX # @@protoc_insertion_point(class_scope:rexp.CMPLX) # @@protoc_insertion_point(module_scope) RProtoBuf/inst/unitTests/0000755000175100001440000000000013037201575015134 5ustar hornikusersRProtoBuf/inst/unitTests/runit.FieldDescriptor.R0000644000175100001440000000633412566711213021510 0ustar hornikusers# Copyright 2012 Google Inc. # Author: Murray Stokely # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # this is executed before each test function .setUp <- function(){ if( !exists("tutorial.Person", "RProtoBuf:DescriptorPool")) { protofile <- system.file("proto", "addressbook.proto", package = "RProtoBuf" ) readProtoFiles(file = protofile) } } test.FieldDescriptor.class <- function() { Person <- P( "tutorial.Person") ## field descriptor object checkTrue(!is.null(Person$email), msg="non-null email") ## debug string checkTrue(nchar(as.character( Person$email )) > 1, msg="non-empty email") ## default values checkTrue(!has_default_value(Person$id), msg="no default for id") checkTrue(has_default_value(Person$PhoneNumber$type), msg="default for phone") checkEquals(default_value(Person$PhoneNumber$type), 1, msg="check default for phone type") checkEquals(default_value(Person$id), 0, msg="check default for person id") ## Get the types of field descriptors checkEquals(type(Person$id), TYPE_INT32, msg="type int32") checkEquals(type(Person$id, TRUE), "TYPE_INT32", msg="type int32 as char") checkEquals(cpp_type(Person$email), CPPTYPE_STRING, msg="cpptype string") checkEquals(cpp_type(Person$email, TRUE), "CPPTYPE_STRING", msg="cpptype string as char") ## Get the label of a field descriptor checkEquals(label(Person$id), LABEL_REQUIRED, msg="label required") checkEquals(label(Person$id, TRUE), "LABEL_REQUIRED", msg="label required as char") checkEquals(label(Person$email), LABEL_OPTIONAL, msg="label optional") checkEquals(label(Person$email, TRUE), "LABEL_OPTIONAL", msg="label optional as char") ## Test if a field is optional checkTrue(is_required(Person$id), msg="id is required") checkTrue(!is_optional(Person$id), msg="id is not optional") checkTrue(!is_repeated(Person$id), msg="id is not repeated") checkTrue(!is_required(Person$email), msg="email is not required") checkTrue(is_optional(Person$email), msg="email is optional") checkTrue(!is_repeated(Person$email), msg="email is not repeated") ## Return the class of a message field checkTrue(inherits(message_type(Person$phone), "Descriptor"), msg="inherits Descriptor") ## Containing type of a field is the message descriptor checkTrue(inherits(Person$id$containing_type(), "Descriptor"), msg="inherits containing type Descriptor") ## No containing type for the top-level message descriptor. checkTrue(is.null(Person$containing_type()), msg="no containing typw") } RProtoBuf/inst/unitTests/runit.int32.R0000644000175100001440000000373512440004312017351 0ustar hornikusers# Copyright 2013 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.int32 <- function() { if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } a <- new(protobuf_unittest.TestAllTypes) a$repeated_int32 <- 1 # Verify we can set character strings a$repeated_int32 <- c("9007", "9008") checkEquals(length(a$repeated_int32), 2) # Verify we can't set any garbage string to a repeated int32. checkException(a$repeated_int32 <-c("invalid", "invalid")) checkException(a$repeated_int32 <-c("33-")) a$optional_int32 <- 1 a$optional_int32 <- "2" checkEquals(a$optional_int32, 2) # Verify we can't set any garbage string to an optional int32. checkException(a$optional_int32 <- "invalid") a$optional_uint32 <- 10000 a$optional_uint32 <- "200000" checkEquals(a$optional_uint32, 200000) # Verify we can't set any garbage string to an optional uint32. checkException(a$optional_uint32 <- "invalid") a$repeated_uint32 <- c("9007", "9008") checkEquals(length(a$repeated_uint32), 2) } RProtoBuf/inst/unitTests/runit.addressbook.R0000644000175100001440000000773312754736105020740 0ustar hornikusers ## created as ## demo(addressbook) ## creates 'book' ## serialize(book, "/tmp/addressbook.pb") # this is executed before each test function -- but somehow does not work .setUp <- function() { file <- system.file( "examples", "addressbook.pb", package = "RProtoBuf" ) book <- read( tutorial.AddressBook, file ) assign("book", book, globalenv()) } test.size <- function() { checkEquals(book$size("person"), 2, msg="Number of persons") checkEquals(bytesize(book), 125, msg="Bytes in book") checkEquals(bytesize(book$person[[1]]), 60, msg="Bytes of first person message") } test.fileDescriptor <- function() { checkEquals(name(book$fileDescriptor()), "addressbook.proto") } test.personOne <- function() { checkEquals(book$person[[1]]$name, "Romain Francois", msg="First person name") checkEquals(book$person[[2]]$name, "Dirk Eddelbuettel", msg="First person name") checkEquals(book$person[[1]]$id, 1, msg="First person id") checkEquals(book$person[[2]]$id, 2, msg="First person id") checkEquals(book$person[[1]]$email, "romain@r-enthusiasts.com", msg="First person email") checkEquals(book$person[[2]]$email, "edd@debian.org", msg="Second person email") checkEquals(length(book$person[[1]]$phone), 1, msg="First person phones") checkEquals(length(book$person[[2]]$phone), 2, msg="Second person phones") checkEquals(book$person[[1]]$phone[[1]]$number, "+33(0)...", msg="First person phone number") checkEquals(book$person[[2]]$phone[[1]]$number, "+01...", msg="Second person phone number") checkEquals(book$person[[2]]$phone[[1]]$type, 0, msg="Second person phone number") } test.ascii <- function() { # Output in text format to a temporary file out.file <- tempfile() writeLines( as.character(book), file(out.file)) # Verify that we can read back in the message from a text file. book2 <- readASCII( tutorial.AddressBook, file(out.file, "rb")) checkEquals(as.character(book), as.character(book2) ) # Verify that we can read in messages from unopened connections. book3 <- readASCII( tutorial.AddressBook, file(out.file)) checkEquals(as.character(book), as.character(book3) ) # Verify that we get an exception if we try to read from a text connection. # (better than silently getting an empty proto.) book4 <- checkException( readASCII( tutorial.AddressBook, file(out.file, "rt"))) ## # Test does not work on windows because of chmod ## if(!grepl("mingw", R.Version()$platform)){ ## # Verify that we get an exception if the file is not readable. ## old.mode <- file.info(out.file)[["mode"]] ## Sys.chmod(out.file, "0000") ## book5 <- checkException( readASCII( tutorial.AddressBook, file(out.file, "rb"))) ## # Set the permissions back to ensure the file is cleaned up properly. ## Sys.chmod(out.file, old.mode) ## } # Verify that we get an exception if the file is not parseable. out.file2 <- tempfile() writeLines("jibberish", file(out.file2)) book6 <- checkException( readASCII( tutorial.AddressBook, file(out.file2))) # Verify that we get an exception if we forget the file() and thus treat the # path as a protobuf string. checkException( readASCII( tutorial.AddressBook, out.file2)) incomplete.msg <- new(tutorial.Person, name="Murray", email="murray@stokely.org") tmp.file <- tempfile() writeLines(as.character(incomplete.msg), file(tmp.file)) checkTrue(!incomplete.msg$isInitialized()) # Verify we normally get an exception if we try to read an incomplete ASCII protocol buffer checkException( tutorial.Person$readASCII(file(tmp.file))) # Verify we can however read it if we set partial=TRUE. new.msg <- tutorial.Person$readASCII(file(tmp.file), TRUE) checkEquals(incomplete.msg$name, new.msg$name) } RProtoBuf/inst/unitTests/runit.extremevalues.R0000644000175100001440000000352112440004312021274 0ustar hornikusers# Copyright 2013 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.uint32 <- function() { if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } foo <- new(protobuf_unittest.TestAllTypes) foo$optional_uint32 <- 2^32 - 1 foo$repeated_uint32 <- c(foo$optional_uint32, foo$optional_uint32) checkEquals(as.character(foo$optional_uint32), "4294967295") checkEquals(foo$optional_uint32, foo$repeated_uint32[[1]]) foo$add("repeated_uint32", c(2^32 - 1, 2^32 - 1)) checkEquals(length(unique(foo$repeated_uint32)), 1) # fixed32 are a more efficient representation of uint32 foo$optional_fixed32 <- 2^32 - 1 foo$repeated_fixed32 <- c(foo$optional_fixed32, foo$optional_fixed32) checkEquals(as.character(foo$optional_fixed32), "4294967295") checkEquals(foo$optional_fixed32, foo$repeated_fixed32[[1]]) } RProtoBuf/inst/unitTests/runit.serialize_pb.R0000644000175100001440000000247512762053206021077 0ustar hornikusers#Jeroen Ooms test.serialize_pb <- function() { #verify that rexp.proto is loaded RProtoBuf:::pb(rexp.REXP) #serialize a nested list x <- list(foo=cars, bar=Titanic) checkEquals(unserialize_pb(serialize_pb(x, NULL)), x) #a bit of everything, copied from jsonlite package set.seed('123') myobject <- list( mynull = NULL, mycomplex = lapply(eigen(matrix(-rnorm(9),3)), round, 3), mymatrix = round(matrix(rnorm(9), 3),3), myint = as.integer(c(1,2,3)), mydf = cars, mylist = list(foo='bar', 123, NA, NULL, list('test')), mylogical = c(TRUE,FALSE,NA), mychar = c('foo', NA, 'bar'), myemptychar = character(0), somemissings = c(1,2,NA,NaN,5, Inf, 7 -Inf, 9, NA), myrawvec = charToRaw('This is a test'), myS4 = asS4("test") ); checkEquals(unserialize_pb(serialize_pb(myobject, NULL)), myobject) } test.serialize_pb.alldatasets <- function() { datasets <- as.data.frame(data(package="datasets")$results) datasets$name <- sub("\\s+.*$", "", datasets$Item) encoded.datasets <- sapply(datasets$name, function(x) serialize_pb(get(x), NULL)) unserialized.datasets <- sapply(encoded.datasets, unserialize_pb) checkTrue(all(sapply(names(unserialized.datasets), function(name) identical(get(name), unserialized.datasets[[name]])))) } RProtoBuf/inst/unitTests/runit.serialize.R0000644000175100001440000000654612566711213020422 0ustar hornikusers# -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- # Copyright 2012 Google Inc. All Rights Reserved. # Author: Murray Stokely # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # this is executed before each test function .setUp <- function() { if (!exists("tutorial.Person", "RProtoBuf:DescriptorPool")) { protofile <- system.file("proto", "addressbook.proto", package = "RProtoBuf") readProtoFiles(file = protofile) } } test.arrayinputstream <- function() { # Note: This class is experimental, and some parts of the design # may need to change, but this works now. stream <- ArrayInputStream(as.raw(0:10)) checkEquals(stream$ReadRaw(5), as.raw(0:4)) stringstream <- ArrayInputStream(as.raw(c(0x74, 0x65, 0x73, 0x74, 0x69, 0x6e, 0x67))) checkEquals(stringstream$ReadString(as.integer(7)), "testing") intstream <- ArrayInputStream(as.raw(c(0x9e, 0xa7, 0x05))) checkEquals(intstream$ReadVarint32(), 86942) } test.encoding <- function() { if (!exists("protobuf_encoding_test.Test1", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "encoding.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } # Encoding examples from: # https://developers.google.com/protocol-buffers/docs/encoding test1 <- new(protobuf_encoding_test.Test1) test1$a <- 150 checkIdentical(test1$serialize(NULL), as.raw(c(0x08,0x96,0x01))) test2 <- new(protobuf_encoding_test.Test2) test2$b <- "testing" checkIdentical(test2$serialize(NULL), as.raw(c(0x12, 0x07, 0x74, 0x65, 0x73, 0x74, 0x69, 0x6e, 0x67))) test3 <- new(protobuf_encoding_test.Test3) test3$c$a <- 150 checkIdentical(test3$serialize(NULL), as.raw(c(0x1a, 0x03, 0x08, 0x96, 0x01))) test4 <- new(protobuf_encoding_test.Test4) test4$d <- c(3, 270, 86942) checkIdentical(test4$serialize(NULL), as.raw(c(0x22, 0x06, 0x03, 0x8e, 0x02, 0x9e, 0xa7, 0x05))) } test.serialize <- function() { person <- new(tutorial.Person) checkTrue(!person$isInitialized()) checkException(serialize(person, NULL), "Uninitialized object should fail to serialize.") person$id <- 1 checkException(serialize(person, NULL), "Uninitialized object should fail to serialize.") person$name <- "Murray" checkTrue(person$isInitialized()) checkTrue(length(serialize(person, NULL)) > 1) } RProtoBuf/inst/unitTests/data/0000755000175100001440000000000013037201575016045 5ustar hornikusersRProtoBuf/inst/unitTests/data/nested.proto0000644000175100001440000000024012754736105020417 0ustar hornikusers// mark as Protocol Buffers v2 format syntax = "proto2"; message NestedInner { required int32 x = 1; } message NestedOuter { required NestedInner b = 1; } RProtoBuf/inst/unitTests/data/int64.ascii0000644000175100001440000000010212440004312017777 0ustar hornikusersrepeated_int64: 9007199254740992 repeated_int64: 9007199254740993 RProtoBuf/inst/unitTests/data/unittest.proto0000644000175100001440000005037312754736105021030 0ustar hornikusers// Protocol Buffers - Google's data interchange format // Copyright 2008 Google Inc. All rights reserved. // http://code.google.com/p/protobuf/ // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above // copyright notice, this list of conditions and the following disclaimer // in the documentation and/or other materials provided with the // distribution. // * Neither the name of Google Inc. nor the names of its // contributors may be used to endorse or promote products derived from // this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // Author: kenton@google.com (Kenton Varda) // Based on original Protocol Buffers design by // Sanjay Ghemawat, Jeff Dean, and others. // // A proto file we will use for unit testing. // mark as Protocol Buffers v2 format syntax = "proto2"; // (Romain Francois) The only thing I have changed in this // file is this import directive. RProtoBuf will import // the extra file from the directory in which this file is import "unittest_import.proto"; // We don't put this in a package within proto2 because we need to make sure // that the generated code doesn't depend on being in the proto2 namespace. // In test_util.h we do "using namespace unittest = protobuf_unittest". package protobuf_unittest; // Protos optimized for SPEED use a strict superset of the generated code // of equivalent ones optimized for CODE_SIZE, so we should optimize all our // tests for speed unless explicitly testing code size optimization. option optimize_for = SPEED; option java_outer_classname = "UnittestProto"; // This proto includes every type of field in both singular and repeated // forms. message TestAllTypes { message NestedMessage { // The field name "b" fails to compile in proto1 because it conflicts with // a local variable named "b" in one of the generated methods. Doh. // This file needs to compile in proto1 to test backwards-compatibility. optional int32 bb = 1; } enum NestedEnum { FOO = 1; BAR = 2; BAZ = 3; } // Singular optional int32 optional_int32 = 1; optional int64 optional_int64 = 2; optional uint32 optional_uint32 = 3; optional uint64 optional_uint64 = 4; optional sint32 optional_sint32 = 5; optional sint64 optional_sint64 = 6; optional fixed32 optional_fixed32 = 7; optional fixed64 optional_fixed64 = 8; optional sfixed32 optional_sfixed32 = 9; optional sfixed64 optional_sfixed64 = 10; optional float optional_float = 11; optional double optional_double = 12; optional bool optional_bool = 13; optional string optional_string = 14; optional bytes optional_bytes = 15; optional group OptionalGroup = 16 { optional int32 a = 17; } optional NestedMessage optional_nested_message = 18; optional ForeignMessage optional_foreign_message = 19; optional protobuf_unittest_import.ImportMessage optional_import_message = 20; optional NestedEnum optional_nested_enum = 21; optional ForeignEnum optional_foreign_enum = 22; optional protobuf_unittest_import.ImportEnum optional_import_enum = 23; optional string optional_string_piece = 24 [ctype=STRING_PIECE]; optional string optional_cord = 25 [ctype=CORD]; // Repeated repeated int32 repeated_int32 = 31; repeated int64 repeated_int64 = 32; repeated uint32 repeated_uint32 = 33; repeated uint64 repeated_uint64 = 34; repeated sint32 repeated_sint32 = 35; repeated sint64 repeated_sint64 = 36; repeated fixed32 repeated_fixed32 = 37; repeated fixed64 repeated_fixed64 = 38; repeated sfixed32 repeated_sfixed32 = 39; repeated sfixed64 repeated_sfixed64 = 40; repeated float repeated_float = 41; repeated double repeated_double = 42; repeated bool repeated_bool = 43; repeated string repeated_string = 44; repeated bytes repeated_bytes = 45; repeated group RepeatedGroup = 46 { optional int32 a = 47; } repeated NestedMessage repeated_nested_message = 48; repeated ForeignMessage repeated_foreign_message = 49; repeated protobuf_unittest_import.ImportMessage repeated_import_message = 50; repeated NestedEnum repeated_nested_enum = 51; repeated ForeignEnum repeated_foreign_enum = 52; repeated protobuf_unittest_import.ImportEnum repeated_import_enum = 53; repeated string repeated_string_piece = 54 [ctype=STRING_PIECE]; repeated string repeated_cord = 55 [ctype=CORD]; // Singular with defaults optional int32 default_int32 = 61 [default = 41 ]; optional int64 default_int64 = 62 [default = 42 ]; optional uint32 default_uint32 = 63 [default = 43 ]; optional uint64 default_uint64 = 64 [default = 44 ]; optional sint32 default_sint32 = 65 [default = -45 ]; optional sint64 default_sint64 = 66 [default = 46 ]; optional fixed32 default_fixed32 = 67 [default = 47 ]; optional fixed64 default_fixed64 = 68 [default = 48 ]; optional sfixed32 default_sfixed32 = 69 [default = 49 ]; optional sfixed64 default_sfixed64 = 70 [default = -50 ]; optional float default_float = 71 [default = 51.5 ]; optional double default_double = 72 [default = 52e3 ]; optional bool default_bool = 73 [default = true ]; optional string default_string = 74 [default = "hello"]; optional bytes default_bytes = 75 [default = "world"]; optional NestedEnum default_nested_enum = 81 [default = BAR ]; optional ForeignEnum default_foreign_enum = 82 [default = FOREIGN_BAR]; optional protobuf_unittest_import.ImportEnum default_import_enum = 83 [default = IMPORT_BAR]; optional string default_string_piece = 84 [ctype=STRING_PIECE,default="abc"]; optional string default_cord = 85 [ctype=CORD,default="123"]; } // Define these after TestAllTypes to make sure the compiler can handle // that. message ForeignMessage { optional int32 c = 1; } enum ForeignEnum { FOREIGN_FOO = 4; FOREIGN_BAR = 5; FOREIGN_BAZ = 6; } message TestAllExtensions { extensions 1 to max; } extend TestAllExtensions { // Singular optional int32 optional_int32_extension = 1; optional int64 optional_int64_extension = 2; optional uint32 optional_uint32_extension = 3; optional uint64 optional_uint64_extension = 4; optional sint32 optional_sint32_extension = 5; optional sint64 optional_sint64_extension = 6; optional fixed32 optional_fixed32_extension = 7; optional fixed64 optional_fixed64_extension = 8; optional sfixed32 optional_sfixed32_extension = 9; optional sfixed64 optional_sfixed64_extension = 10; optional float optional_float_extension = 11; optional double optional_double_extension = 12; optional bool optional_bool_extension = 13; optional string optional_string_extension = 14; optional bytes optional_bytes_extension = 15; optional group OptionalGroup_extension = 16 { optional int32 a = 17; } optional TestAllTypes.NestedMessage optional_nested_message_extension = 18; optional ForeignMessage optional_foreign_message_extension = 19; optional protobuf_unittest_import.ImportMessage optional_import_message_extension = 20; optional TestAllTypes.NestedEnum optional_nested_enum_extension = 21; optional ForeignEnum optional_foreign_enum_extension = 22; optional protobuf_unittest_import.ImportEnum optional_import_enum_extension = 23; optional string optional_string_piece_extension = 24 [ctype=STRING_PIECE]; optional string optional_cord_extension = 25 [ctype=CORD]; // Repeated repeated int32 repeated_int32_extension = 31; repeated int64 repeated_int64_extension = 32; repeated uint32 repeated_uint32_extension = 33; repeated uint64 repeated_uint64_extension = 34; repeated sint32 repeated_sint32_extension = 35; repeated sint64 repeated_sint64_extension = 36; repeated fixed32 repeated_fixed32_extension = 37; repeated fixed64 repeated_fixed64_extension = 38; repeated sfixed32 repeated_sfixed32_extension = 39; repeated sfixed64 repeated_sfixed64_extension = 40; repeated float repeated_float_extension = 41; repeated double repeated_double_extension = 42; repeated bool repeated_bool_extension = 43; repeated string repeated_string_extension = 44; repeated bytes repeated_bytes_extension = 45; repeated group RepeatedGroup_extension = 46 { optional int32 a = 47; } repeated TestAllTypes.NestedMessage repeated_nested_message_extension = 48; repeated ForeignMessage repeated_foreign_message_extension = 49; repeated protobuf_unittest_import.ImportMessage repeated_import_message_extension = 50; repeated TestAllTypes.NestedEnum repeated_nested_enum_extension = 51; repeated ForeignEnum repeated_foreign_enum_extension = 52; repeated protobuf_unittest_import.ImportEnum repeated_import_enum_extension = 53; repeated string repeated_string_piece_extension = 54 [ctype=STRING_PIECE]; repeated string repeated_cord_extension = 55 [ctype=CORD]; // Singular with defaults optional int32 default_int32_extension = 61 [default = 41 ]; optional int64 default_int64_extension = 62 [default = 42 ]; optional uint32 default_uint32_extension = 63 [default = 43 ]; optional uint64 default_uint64_extension = 64 [default = 44 ]; optional sint32 default_sint32_extension = 65 [default = -45 ]; optional sint64 default_sint64_extension = 66 [default = 46 ]; optional fixed32 default_fixed32_extension = 67 [default = 47 ]; optional fixed64 default_fixed64_extension = 68 [default = 48 ]; optional sfixed32 default_sfixed32_extension = 69 [default = 49 ]; optional sfixed64 default_sfixed64_extension = 70 [default = -50 ]; optional float default_float_extension = 71 [default = 51.5 ]; optional double default_double_extension = 72 [default = 52e3 ]; optional bool default_bool_extension = 73 [default = true ]; optional string default_string_extension = 74 [default = "hello"]; optional bytes default_bytes_extension = 75 [default = "world"]; optional TestAllTypes.NestedEnum default_nested_enum_extension = 81 [default = BAR]; optional ForeignEnum default_foreign_enum_extension = 82 [default = FOREIGN_BAR]; optional protobuf_unittest_import.ImportEnum default_import_enum_extension = 83 [default = IMPORT_BAR]; optional string default_string_piece_extension = 84 [ctype=STRING_PIECE, default="abc"]; optional string default_cord_extension = 85 [ctype=CORD, default="123"]; } message TestNestedExtension { extend TestAllExtensions { // Check for bug where string extensions declared in tested scope did not // compile. optional string test = 1002 [default="test"]; } } // We have separate messages for testing required fields because it's // annoying to have to fill in required fields in TestProto in order to // do anything with it. Note that we don't need to test every type of // required filed because the code output is basically identical to // optional fields for all types. message TestRequired { required int32 a = 1; optional int32 dummy2 = 2; required int32 b = 3; extend TestAllExtensions { optional TestRequired single = 1000; repeated TestRequired multi = 1001; } // Pad the field count to 32 so that we can test that IsInitialized() // properly checks multiple elements of has_bits_. optional int32 dummy4 = 4; optional int32 dummy5 = 5; optional int32 dummy6 = 6; optional int32 dummy7 = 7; optional int32 dummy8 = 8; optional int32 dummy9 = 9; optional int32 dummy10 = 10; optional int32 dummy11 = 11; optional int32 dummy12 = 12; optional int32 dummy13 = 13; optional int32 dummy14 = 14; optional int32 dummy15 = 15; optional int32 dummy16 = 16; optional int32 dummy17 = 17; optional int32 dummy18 = 18; optional int32 dummy19 = 19; optional int32 dummy20 = 20; optional int32 dummy21 = 21; optional int32 dummy22 = 22; optional int32 dummy23 = 23; optional int32 dummy24 = 24; optional int32 dummy25 = 25; optional int32 dummy26 = 26; optional int32 dummy27 = 27; optional int32 dummy28 = 28; optional int32 dummy29 = 29; optional int32 dummy30 = 30; optional int32 dummy31 = 31; optional int32 dummy32 = 32; required int32 c = 33; } message TestRequiredForeign { optional TestRequired optional_message = 1; repeated TestRequired repeated_message = 2; optional int32 dummy = 3; } // Test that we can use NestedMessage from outside TestAllTypes. message TestForeignNested { optional TestAllTypes.NestedMessage foreign_nested = 1; } // TestEmptyMessage is used to test unknown field support. message TestEmptyMessage { } // Like above, but declare all field numbers as potential extensions. No // actual extensions should ever be defined for this type. message TestEmptyMessageWithExtensions { extensions 1 to max; } // Test that really large tag numbers don't break anything. message TestReallyLargeTagNumber { // The largest possible tag number is 2^28 - 1, since the wire format uses // three bits to communicate wire type. optional int32 a = 1; optional int32 bb = 268435455; } message TestRecursiveMessage { optional TestRecursiveMessage a = 1; optional int32 i = 2; } // Test that mutual recursion works. message TestMutualRecursionA { optional TestMutualRecursionB bb = 1; } message TestMutualRecursionB { optional TestMutualRecursionA a = 1; optional int32 optional_int32 = 2; } // Test that groups have disjoint field numbers from their siblings and // parents. This is NOT possible in proto1; only proto2. When outputting // proto1, the dup fields should be dropped. message TestDupFieldNumber { optional int32 a = 1; optional group Foo = 2 { optional int32 a = 1; } optional group Bar = 3 { optional int32 a = 1; } } // Needed for a Python test. message TestNestedMessageHasBits { message NestedMessage { repeated int32 nestedmessage_repeated_int32 = 1; repeated ForeignMessage nestedmessage_repeated_foreignmessage = 2; } optional NestedMessage optional_nested_message = 1; } // mstokely commented this out, it breaks with libprotobuf-2.5. // // Test an enum that has multiple values with the same number. // enum TestEnumWithDupValue { // FOO1 = 1; // BAR1 = 2; // BAZ = 3; // FOO2 = 1; // BAR2 = 2; //} // Test an enum with large, unordered values. enum TestSparseEnum { SPARSE_A = 123; SPARSE_B = 62374; SPARSE_C = 12589234; SPARSE_D = -15; SPARSE_E = -53452; SPARSE_F = 0; SPARSE_G = 2; } // Test message with CamelCase field names. This violates Protocol Buffer // standard style. message TestCamelCaseFieldNames { optional int32 PrimitiveField = 1; optional string StringField = 2; optional ForeignEnum EnumField = 3; optional ForeignMessage MessageField = 4; optional string StringPieceField = 5 [ctype=STRING_PIECE]; optional string CordField = 6 [ctype=CORD]; repeated int32 RepeatedPrimitiveField = 7; repeated string RepeatedStringField = 8; repeated ForeignEnum RepeatedEnumField = 9; repeated ForeignMessage RepeatedMessageField = 10; repeated string RepeatedStringPieceField = 11 [ctype=STRING_PIECE]; repeated string RepeatedCordField = 12 [ctype=CORD]; } // We list fields out of order, to ensure that we're using field number and not // field index to determine serialization order. message TestFieldOrderings { optional string my_string = 11; extensions 2 to 10; optional int64 my_int = 1; extensions 12 to 100; optional float my_float = 101; } extend TestFieldOrderings { optional string my_extension_string = 50; optional int32 my_extension_int = 5; } message TestExtremeDefaultValues { optional bytes escaped_bytes = 1 [default = "\0\001\a\b\f\n\r\t\v\\\'\"\xfe"]; optional uint32 large_uint32 = 2 [default = 0xFFFFFFFF]; optional uint64 large_uint64 = 3 [default = 0xFFFFFFFFFFFFFFFF]; optional int32 small_int32 = 4 [default = -0x7FFFFFFF]; optional int64 small_int64 = 5 [default = -0x7FFFFFFFFFFFFFFF]; // The default value here is UTF-8 for "\u1234". (We could also just type // the UTF-8 text directly into this text file rather than escape it, but // lots of people use editors that would be confused by this.) optional string utf8_string = 6 [default = "\341\210\264"]; // Tests for single-precision floating-point values. optional float zero_float = 7 [default = 0]; optional float one_float = 8 [default = 1]; optional float small_float = 9 [default = 1.5]; optional float negative_one_float = 10 [default = -1]; optional float negative_float = 11 [default = -1.5]; // Using exponents optional float large_float = 12 [default = 2E8]; optional float small_negative_float = 13 [default = -8e-28]; } // Test String and Bytes: string is for valid UTF-8 strings message OneString { optional string data = 1; } message OneBytes { optional bytes data = 1; } // Test messages for packed fields message TestPackedTypes { repeated int32 packed_int32 = 90 [packed = true]; repeated int64 packed_int64 = 91 [packed = true]; repeated uint32 packed_uint32 = 92 [packed = true]; repeated uint64 packed_uint64 = 93 [packed = true]; repeated sint32 packed_sint32 = 94 [packed = true]; repeated sint64 packed_sint64 = 95 [packed = true]; repeated fixed32 packed_fixed32 = 96 [packed = true]; repeated fixed64 packed_fixed64 = 97 [packed = true]; repeated sfixed32 packed_sfixed32 = 98 [packed = true]; repeated sfixed64 packed_sfixed64 = 99 [packed = true]; repeated float packed_float = 100 [packed = true]; repeated double packed_double = 101 [packed = true]; repeated bool packed_bool = 102 [packed = true]; repeated ForeignEnum packed_enum = 103 [packed = true]; } message TestPackedExtensions { extensions 1 to max; } extend TestPackedExtensions { repeated int32 packed_int32_extension = 90 [packed = true]; repeated int64 packed_int64_extension = 91 [packed = true]; repeated uint32 packed_uint32_extension = 92 [packed = true]; repeated uint64 packed_uint64_extension = 93 [packed = true]; repeated sint32 packed_sint32_extension = 94 [packed = true]; repeated sint64 packed_sint64_extension = 95 [packed = true]; repeated fixed32 packed_fixed32_extension = 96 [packed = true]; repeated fixed64 packed_fixed64_extension = 97 [packed = true]; repeated sfixed32 packed_sfixed32_extension = 98 [packed = true]; repeated sfixed64 packed_sfixed64_extension = 99 [packed = true]; repeated float packed_float_extension = 100 [packed = true]; repeated double packed_double_extension = 101 [packed = true]; repeated bool packed_bool_extension = 102 [packed = true]; repeated ForeignEnum packed_enum_extension = 103 [packed = true]; } // Test that RPC services work. message FooRequest {} message FooResponse {} service TestService { rpc Foo(FooRequest) returns (FooResponse); rpc Bar(BarRequest) returns (BarResponse); } message BarRequest {} message BarResponse {} RProtoBuf/inst/unitTests/data/unittest_import.proto0000644000175100001440000000473612754736105022424 0ustar hornikusers// Protocol Buffers - Google's data interchange format // Copyright 2008 Google Inc. All rights reserved. // http://code.google.com/p/protobuf/ // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above // copyright notice, this list of conditions and the following disclaimer // in the documentation and/or other materials provided with the // distribution. // * Neither the name of Google Inc. nor the names of its // contributors may be used to endorse or promote products derived from // this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // Author: kenton@google.com (Kenton Varda) // Based on original Protocol Buffers design by // Sanjay Ghemawat, Jeff Dean, and others. // // A proto file which is imported by unittest.proto to test importing. // mark as Protocol Buffers v2 format syntax = "proto2"; // We don't put this in a package within proto2 because we need to make sure // that the generated code doesn't depend on being in the proto2 namespace. // In test_util.h we do // "using namespace unittest_import = protobuf_unittest_import". package protobuf_unittest_import; option optimize_for = SPEED; // Excercise the java_package option. option java_package = "com.google.protobuf.test"; // Do not set a java_outer_classname here to verify that Proto2 works without // one. message ImportMessage { optional int32 d = 1; } enum ImportEnum { IMPORT_FOO = 7; IMPORT_BAR = 8; IMPORT_BAZ = 9; } RProtoBuf/inst/unitTests/data/bytes.proto0000644000175100001440000000040312754736105020264 0ustar hornikusers// mark as Protocol Buffers v2 format syntax = "proto2"; option optimize_for = SPEED; option java_outer_classname = "BytesProto"; message TestBytes { required bytes req = 1; optional bytes opt = 2 [default = "hello world"]; repeated bytes rep = 3; } RProtoBuf/inst/unitTests/data/proto3.proto0000644000175100001440000000017113037201575020357 0ustar hornikusers syntax = "proto3"; message SearchRequest { string query = 1; int32 page_number = 2; int32 result_per_page = 3; } RProtoBuf/inst/unitTests/data/encoding.proto0000644000175100001440000000054412754736105020732 0ustar hornikusers// mark as Protocol Buffers v2 format syntax = "proto2"; // Examples from: // https://developers.google.com/protocol-buffers/docs/encoding package protobuf_encoding_test; message Test1 { required int32 a = 1; } message Test2 { required string b = 2; } message Test3 { required Test1 c = 3; } message Test4 { repeated int32 d = 4 [packed=true]; } RProtoBuf/inst/unitTests/runit.messages.R0000644000175100001440000000400212440004312020205 0ustar hornikusers# Copyright 2013 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.message <- function() { if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } a <- new(protobuf_unittest.TestAllTypes) a$optionalgroup$a <- 3 checkEquals(a$optionalgroup$a, 3) a$repeated_nested_message <- list( new(protobuf_unittest.TestAllTypes.NestedMessage, bb=3), new(protobuf_unittest.TestAllTypes.NestedMessage, bb=4)) checkEquals(a$repeated_nested_message[[1]]$bb, 3) checkEquals(a$repeated_nested_message[[2]]$bb, 4) checkException(a$repeated_nested_message <- list( new(protobuf_unittest.ForeignMessage, c=1), new(protobuf_unittest.TestAllTypes.NestedMessage, bb=4))) checkException(a$repeated_nested_message <- list( new(protobuf_unittest.TestAllTypes.NestedMessage, bb=4), new(protobuf_unittest.ForeignMessage, c=1))) checkException(a$repeated_nested_message <- list( new(protobuf_unittest.TestAllTypes.NestedMessage, bb=4), 3)) checkException(a$repeated_nested_message <- list( new(protobuf_unittest.TestAllTypes.NestedMessage, bb=4), "foo")) } RProtoBuf/inst/unitTests/runit.bool.R0000644000175100001440000000352012440004312017335 0ustar hornikusers# Copyright 2013 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.bool <- function() { if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } a <- new(protobuf_unittest.TestAllTypes) a$optional_bool <- TRUE a$optional_bool <- FALSE # Verify we can not set a protocol buffer bool to NA. checkException(a$optional_bool <- NA) # Verify we can set character strings a$repeated_bool <- c(TRUE, FALSE, TRUE) checkEquals(length(unique(a$repeated_bool)), 2) # Verify we can't set any garbage string to a bool. checkException(a$optional_bool <- "100") checkException(a$optional_bool <- "invalid") # Verify we can't set any garbage string to a repeated bool. checkException(a$repeated_bool <-c("invalid", "invalid")) checkException(a$repeated_bool <-c("33-")) # Verify we can set NA checkException(a$repeated_bool <- c(TRUE, FALSE, TRUE, NA)) } RProtoBuf/inst/unitTests/runit.import.R0000644000175100001440000000170712440004312017721 0ustar hornikusers# Copyright 2011 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.import <- function() { # Verify that we get a graceful error rather than a segfault. checkException(readProtoFiles("/etc/hosts")) } test.assign.in.global <- function() { xx.undef <<- 3 checkEquals(xx.undef, 3) } RProtoBuf/inst/unitTests/runit.enums.R0000644000175100001440000000475512440004312017544 0ustar hornikusers# Copyright 2011 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.enums <- function() { ProtoFormat <- P("tutorial.Person") # value(..) returns an EnumValueDescriptor object checkEquals(name(value(ProtoFormat$PhoneType, index=1)), "MOBILE") checkEquals(name(value(ProtoFormat$PhoneType, index=1), TRUE), "tutorial.Person.MOBILE") checkEquals(number(value(ProtoFormat$PhoneType, index=1)), 0) checkTrue(inherits(enum_type(value(ProtoFormat$PhoneType, index=1)), "EnumDescriptor")) checkTrue(inherits(asMessage(value(ProtoFormat$PhoneType, index=1)), "Message")) # Now check the '$' interfaces checkEquals(name(value(ProtoFormat$PhoneType, index=1)), value(ProtoFormat$PhoneType, index=1)$name()) checkEquals(number(value(ProtoFormat$PhoneType, index=1)), value(ProtoFormat$PhoneType, index=1)$number()) checkEquals(name(value(ProtoFormat$PhoneType, index=2)), "HOME") checkEquals(length(ProtoFormat$PhoneType), 3) checkTrue(has(ProtoFormat$PhoneType, "WORK")) checkTrue(!has(ProtoFormat$PhoneType, "NONEXISTANT")) # Verify we can subset the EnumDescriptor class checkEquals(ProtoFormat$PhoneType[["WORK"]], 2) checkEquals(ProtoFormat$PhoneType[["MOBILE"]], 0) # Verify that invalid indices are returned as NULL. checkTrue(is.null(value(ProtoFormat$PhoneType, index=900))) # Verify that we import top-level enums from .proto files. if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } checkTrue(inherits(P("protobuf_unittest.ForeignEnum"), "EnumDescriptor")) } RProtoBuf/inst/unitTests/runit.descriptors.R0000644000175100001440000000241212440004312020742 0ustar hornikusers# Copyright 2014 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.descriptor <- function() { checkTrue(inherits(tutorial.Person$email, "FieldDescriptor")) checkTrue(inherits(tutorial.Person[["email"]], "FieldDescriptor")) checkTrue(inherits(tutorial.Person[[1]], "FieldDescriptor")) # Currently, the $ extractor for fields returns NULL for invalid reference # stop() probably better. checkEquals(tutorial.Person$nonexistantfoobarbaz, NULL) # But we raise an error with invalid indices with '[['. checkException(tutorial.Person[[909]]) checkException(tutorial.Person[["nonexistantfoobarbaz"]]) } RProtoBuf/inst/unitTests/runit.int64.R0000644000175100001440000000544112442165432017367 0ustar hornikusers# Copyright 2013 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.int64 <- function() { # Preserve option. old.optval <- options("RProtoBuf.int64AsString") on.exit(options(old.optval)) if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } if (.Machine$sizeof.longlong < 8) { warning("Can't test 64-bit int type on platform with sizeof(long long) < 8") return() } if (is.na(Rcpp:::capabilities()["long long"]) || Rcpp:::capabilities()["long long"] != TRUE) { warning("Can't test 64-bit int type without RCPP_LONG_LONG support.") return() } a <- new(protobuf_unittest.TestAllTypes) a$repeated_int64 <- 1 # Now just test that we can use add to set int64 fields. a$add("repeated_int64", 2:10) checkEquals(length(a$repeated_int64), 10) # Verify we can set character strings of large 64-bit ints a$repeated_int64 <- c("9007199254740992", "9007199254740993") checkEquals(length(a$repeated_int64), 2) # Verify we can't set any garbage string to a repeated int64. checkException(a$repeated_int64 <-c("invalid", "invalid")) a$optional_int64 <- 1 a$optional_int64 <- "2" checkEquals(a$optional_int64, 2) # Verify we can't set any garbage string to an optional int64. checkException(a$optional_int64 <- "invalid") a <- protobuf_unittest.TestAllTypes$readASCII( file(system.file("unitTests", "data", "int64.ascii", package="RProtoBuf"))) # And can read them in OK from an ASCII file. checkEquals(length(a$repeated_int64), 2) # By default, when they are read as numerics, only 1 unique value checkEquals(length(unique(a$repeated_int64)), 1) options("RProtoBuf.int64AsString" = TRUE) # But we can see they are different if we treat them as strings. checkEquals(length(unique(a$repeated_int64)), 2) } RProtoBuf/inst/unitTests/runit.proto3.R0000644000175100001440000000307313037201575017650 0ustar hornikusers## rprotobuf.h: R/C++ interface class library ## ## Copyright (C) 2017 - Dirk Eddelbuettel ## ## This file is part of RProtoBuf. ## ## RProtoBuf is free software: you can redistribute it and/or modify it ## under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 2 of the License, or ## (at your option) any later version. ## ## RProtoBuf is distributed in the hope that it will be useful, but ## WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with RProtoBuf. If not, see . ## The Travis CI tests use both proto2 and proto3, so we need to condition against ## running this one with proto2 where it cannot pass we impose a proto3 file isProto3 <- (RProtoBuf:::getProtobufLibVersion() >= 3000000) if (isProto3) { .setUp <- function(){ if( !exists("SearchRequest", "RProtoBuf:DescriptorPool")) { unitest.proto.file <- system.file("unitTests", "data", "proto3.proto", package="RProtoBuf") readProtoFiles(file = unitest.proto.file) } } test.proto3 <- function() { q <- new(SearchRequest, query="abc", page_number=42L, result_per_page=77L) checkEquals(q$query, "abc", msg="proto3 string") checkEquals(q$page_number, 42L, msg="proto3 int") checkEquals(q$result_per_page, 77L, msg="proto3 int again") } } RProtoBuf/inst/unitTests/runTests.R0000644000175100001440000000354612440004312017101 0ustar hornikuserspkg <- "RProtoBuf" if(require("RUnit", quietly = TRUE)) { library(package=pkg, character.only = TRUE) if(!(exists("path") && file.exists(path))) path <- system.file("unitTests", package = pkg) ## --- Testing --- ## Define tests testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs = path) if(interactive()) { cat("Now have RUnit Test Suite 'testSuite' for package '", pkg, "' :\n", sep='') str(testSuite) cat('', "Consider doing", "\t tests <- runTestSuite(testSuite)", "\nand later", "\t printTextProtocol(tests)", '', sep="\n") } else { ## run from shell / Rscript / R CMD Batch / ... ## Run tests <- runTestSuite(testSuite) if(file.access(path, 02) != 0) { ## cannot write to path -> use writable one tdir <- tempfile(paste(pkg, "unitTests", sep="_")) dir.create(tdir) pathReport <- file.path(tdir, "report") cat("RUnit reports are written into ", tdir, "/report.(txt|html)", sep = "") } else { pathReport <- file.path(path, "report") } ## Print results # printTextProtocol(tests) printTextProtocol(tests, fileName=paste(pathReport, ".txt", sep="")) ## Print HTML version to a file ## printHTMLProtocol has problems on Mac OS X if (Sys.info()["sysname"] != "Darwin") printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) ## stop() if there are any failures i.e. FALSE to unit test. ## This will cause R CMD check to return error and stop if(getErrors(tests)$nFail > 0) { stop("one of the unit tests failed") } } } else { cat("R package 'RUnit' cannot be loaded -- no unit tests run\n", "for package", pkg,"\n") } RProtoBuf/inst/unitTests/runit.extensions.R0000644000175100001440000000770312440004312020610 0ustar hornikusers# Copyright 2013 Google Inc. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. test.extension <- function() { if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } checkTrue(inherits(protobuf_unittest.optional_uint32_extension, "FieldDescriptor")) # Verify we can pull in other extensions with P() checkTrue(inherits(P("protobuf_unittest.optional_uint32_extension"), "FieldDescriptor")) ## Test setting and getting singular extensions. test <- new(protobuf_unittest.TestAllExtensions) test$setExtension(protobuf_unittest.optional_int32_extension, as.integer(1)) checkEquals(test$getExtension(protobuf_unittest.optional_int32_extension), as.integer(1)) ## Unset extensions should return NULL. checkEquals(test$getExtension(protobuf_unittest.optional_double_extension), NULL) ## Test setting and getting repeated extensions. checkEquals(test$getExtension(protobuf_unittest.repeated_int32_extension), NULL) test$setExtension(protobuf_unittest.repeated_int32_extension, 1:10) checkEquals(test$getExtension(protobuf_unittest.repeated_int32_extension), 1:10) ## Test nested extensions. checkEquals(test$getExtension(protobuf_unittest.TestNestedExtension.test), NULL) test$setExtension(protobuf_unittest.TestNestedExtension.test, "foo") checkEquals(test$getExtension(protobuf_unittest.TestNestedExtension.test), "foo") ## Test setting and getting enums. test$setExtension(protobuf_unittest.optional_nested_enum_extension, protobuf_unittest.TestAllTypes.NestedEnum$BAR) ## Test foreign message extensions foo <- new(protobuf_unittest.ForeignMessage) foo$c <- 3 test$setExtension(protobuf_unittest.optional_foreign_message_extension, foo) checkEquals(test$getExtension(protobuf_unittest.optional_foreign_message_extension)$c, 3) # This causes an Rcpp exception, but not an R stop error as of my # version of Rcpp, so we can't checkError unfortunately, but we # can at least make sure it doesn't crash R. # TODO(edd): Commented out now # test$setExtension(protobuf_unittest.optional_nested_enum_extension, 9) ## Test nested message extensions. tmp <- new( protobuf_unittest.TestAllTypes.NestedMessage ) tmp$bb <- 3 test$setExtension(protobuf_unittest.optional_nested_message_extension, tmp) checkEquals(test$getExtension(protobuf_unittest.optional_nested_message_extension)$bb, 3) ## Check that we do something sensible if invalid field descriptors are passed checkException(test$getExtension(protobuf_unittest.TestAllExtensions)) checkException(test$setExtension(protobuf_unittest.TestAllExtensions, 3)) ## Check that we don't CHECK fail in C++, but instead give a reasonable ## error message if incorrect extensions types are provided. checkException(test$getExtension(protobuf_unittest.my_extension_string)) } RProtoBuf/inst/unitTests/runit.golden.message.R0000644000175100001440000001272012440004312021277 0ustar hornikusers # this is executed before each test function .setUp <- function(){ if( ! exists( "protobuf_unittest_import.TestAllTypes", "RProtoBuf:DescriptorPool" ) ){ unitest.proto.file <- system.file( "unitTests", "data", "unittest.proto", package = "RProtoBuf" ) readProtoFiles( file = unitest.proto.file ) } } .tearDown <- function(){} test.import <- function(){ checkTrue( exists( "protobuf_unittest_import.ImportMessage", "RProtoBuf:DescriptorPool" ) , msg = "exists( protobuf_unittest_import.ImportMessage ) " ) checkTrue( exists( "protobuf_unittest_import.ImportEnum", "RProtoBuf:DescriptorPool" ) , msg = "exists( protobuf_unittest_import.ImportEnum ) " ) checkEquals( names(as.list( protobuf_unittest_import.ImportMessage)), "d", msg = "names( protobuf_unittest_import.ImportMessage ) == 'd'" ) import_enum <- as.list(protobuf_unittest_import.ImportEnum ) checkTrue( all( c("IMPORT_FOO", "IMPORT_BAR", "IMPORT_BAZ") %in% names(import_enum) ), msg = "expected names for 'protobuf_unittest_import.ImportEnum'" ) checkEquals( unlist(unname(import_enum)), 7:9, msg = "expected values for 'protobuf_unittest_import.ImportEnum' " ) } test.readProtoFile <- function(){ checkTrue( exists( "protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool" ), msg = "exists( protobuf_unittest_import.TestAllTypes ) " ) checkTrue( exists( "protobuf_unittest.TestAllTypes.NestedMessage", "RProtoBuf:DescriptorPool" ), msg = "exists( protobuf_unittest_import.TestAllTypes.NestedMessage ) " ) checkTrue( exists( "protobuf_unittest.TestAllTypes.NestedEnum", "RProtoBuf:DescriptorPool" ), msg = "exists( protobuf_unittest_import.TestAllTypes.NestedEnum ) " ) checkTrue( exists( "protobuf_unittest.TestAllTypes.OptionalGroup", "RProtoBuf:DescriptorPool" ) , msg = "exists( protobuf_unittest.TestAllTypes.OptionalGroup ) " ) types <- c("int32", "int64", "uint32", "uint64", "sint32", "sint64", "fixed32", "fixed64", "sfixed32", "sfixed64", "float", "double", "bool", "string", "bytes" ) fieldnames <- names( as.list( protobuf_unittest.TestAllTypes ) ) prefixes <- c("optional", "default", "repeated" ) for( prefix in prefixes ){ for( type in types ){ checkTrue( sprintf( "%s_%s", prefix, type ) %in% fieldnames, msg = sprintf( "%s_%s in field names", prefix, type ) ) } checkTrue( sprintf("%s_foreign_enum" , prefix ) %in% fieldnames, msg = sprintf( "%s_foreign_enum in field names" , prefix ) ) checkTrue( sprintf("%s_import_enum" , prefix ) %in% fieldnames, msg = sprintf( "%s_import_enum in field names" , prefix ) ) } checkTrue( exists( "protobuf_unittest.ForeignMessage", "RProtoBuf:DescriptorPool" ) , msg = "exists( protobuf_unittest.ForeignMessage ) " ) checkEquals( names(as.list(protobuf_unittest.ForeignMessage)), "c" ) checkTrue( exists( "protobuf_unittest.ForeignEnum", "RProtoBuf:DescriptorPool" ) , msg = "exists( protobuf_unittest.ForeignEnum ) " ) foreign_enum <- as.list( protobuf_unittest.ForeignEnum ) checkEquals( length(foreign_enum), 3L, msg = "length( protobuf_unittest.ForeignEnum ) == 3" ) checkTrue( all( c("FOREIGN_FOO", "FOREIGN_BAR", "FOREIGN_BAZ") %in% names( foreign_enum ) ), msg = "expected names for enum `protobuf_unittest.ForeignEnum`" ) checkEquals( unlist(unname(as.list(protobuf_unittest.ForeignEnum))), 4:6, msg = "expected values for enum `protobuf_unittest.ForeignEnum`" ) } # Early versions of RProtoBuf did not support repeated messages properly. test.repeatedFields <- function(){ test <- new(protobuf_unittest.TestAllTypes) test$add("repeated_int32", c(1:5)) checkEquals(test$repeated_int32, c(1:5)) test$repeated_int32 <- 1 checkEquals(test$repeated_int32, 1) # Prior to RProtoBuf v0.2.5, this was not handled properly. test.2 <- new(protobuf_unittest.TestAllTypes, repeated_string=c("foo", "bar")) checkEquals(test.2$repeated_string, c("foo", "bar")) # Versions of RProtoBuf <= 0.2.5 had non-deterministic behavior due to a # memory management bug when setting a repeated field to a # non-vector type (e.g. a Message). test$repeated_foreign_message <- list(new(protobuf_unittest.ForeignMessage, c = 1), new(protobuf_unittest.ForeignMessage, c = 2)) checkEquals(length(test$repeated_foreign_message), 2) test$repeated_foreign_message <- new(protobuf_unittest.ForeignMessage, c = 3) checkEquals(length(test$repeated_foreign_message), 1) } test.repeated.bools <- function() { test <- new(protobuf_unittest.TestAllTypes) test$add("repeated_bool", c(TRUE, FALSE)) checkEquals(test$repeated_bool, c(TRUE, FALSE)) test$add("repeated_bool", as.integer(c(TRUE, FALSE))) test$add("repeated_bool", as.numeric(c(TRUE, FALSE))) checkEquals(test$repeated_bool, rep(c(TRUE, FALSE), 3)) # Verify that we don't silently cast NA into TRUE or FALSE. checkException(test$add("repeated_bool"), c(TRUE, FALSE, NA)) } # Versions of RProtoBuf <= 0.2.5 would terminate the R instance with unhandled Rcpp exceptions. test.invalidAssignments <- function(){ test <- new(protobuf_unittest.TestAllTypes) checkException(test$optional_int32 <- 1:10) } # Versions of RProtoBuf <= 0.2.5 did not distinguish between non-existant # and not-set fields with has(). test.has <- function(){ test <- new(protobuf_unittest.TestAllTypes) test$add("repeated_int32", c(1:5)) checkTrue( has(test, "repeated_int32")) checkTrue( test$has("repeated_int32")) checkTrue( is.null(test$has("nonexistant"))) checkTrue( !test$has("optional_int32")) } RProtoBuf/inst/unitTests/runit.bytes.R0000644000175100001440000000211112707407313017541 0ustar hornikusers .setUp <- function(){ if( ! exists( "TestBytes", "RProtoBuf:DescriptorPool" ) ){ unitest.proto.file <- system.file( "unitTests", "data", "bytes.proto", package = "RProtoBuf" ) readProtoFiles(file = unitest.proto.file) } } test.all <- function() { test <- new(TestBytes, req = "abc", rep = list(charToRaw("def"), raw(10))) checkEquals(rawToChar(test$req), "abc") test$req <- charToRaw("abc") checkEquals(rawToChar(test$req), "abc") checkEquals(rawToChar(test$opt), "hello world") checkEquals(test$rep, list(charToRaw("def"), raw(10))) test$rep[[3]]=charToRaw("ghi") checkEquals(test$rep, list(charToRaw("def"), raw(10), charToRaw("ghi"))) ser <- serialize(test, NULL) test1 <- read(TestBytes, ser) checkEquals(rawToChar(test1$req), "abc") checkEquals(rawToChar(test1$opt), "hello world") checkEquals(test1$rep, list(charToRaw("def"), raw(10), charToRaw("ghi"))) # Test raw(10) can be set to a single req field. test$req <- raw(10) checkEquals(length(test$req), 10) checkTrue(all(test$req == raw(10))) } RProtoBuf/inst/unitTests/runit.nested.R0000644000175100001440000000122112440004312017660 0ustar hornikusers.setUp <- function(){ if( ! exists( "NestedOuter", "RProtoBuf:DescriptorPool" ) ) { ## None of the messages in unittest.proto is exactly right to tickle this bug. unitest.proto.file <- system.file( "unitTests", "data", "nested.proto", package = "RProtoBuf" ) readProtoFiles(file = unitest.proto.file) } } # RProtoBuf before v0.2.5 had a bug whereby uninitialized memory was read and used # to determine whether or not to update a nested message field in new() / update(). test.nested <- function() { for (i in 1:1000) { q <- new(NestedOuter, b=new(NestedInner, x=1)) checkTrue(q$isInitialized()) } } RProtoBuf/inst/proto/0000755000175100001440000000000012754736105014304 5ustar hornikusersRProtoBuf/inst/proto/rexp.proto0000644000175100001440000000243512754736105016353 0ustar hornikusers// Originally written by Saptarshi Guha for RHIPE (http://www.rhipe.org) // Released under Apache License 2.0, and reused with permission here // Extended in November 2014 with new types to support encoding // language, environment, and function types from R. // mark as Protocol Buffers v2 format syntax = "proto2"; package rexp; option java_package = "org.godhuli.rhipe"; option java_outer_classname = "REXPProtos"; // TODO(mstokely): Refine this using the new protobuf 2.6 oneof field // for unions. message REXP { enum RClass { STRING = 0; RAW = 1; REAL = 2; COMPLEX = 3; INTEGER = 4; LIST = 5; LOGICAL = 6; NULLTYPE = 7; NATIVE = 8; } enum RBOOLEAN { F=0; T=1; NA=2; } required RClass rclass = 1; repeated double realValue = 2 [packed=true]; repeated sint32 intValue = 3 [packed=true]; repeated RBOOLEAN booleanValue = 4; repeated STRING stringValue = 5; optional bytes rawValue = 6; repeated CMPLX complexValue = 7; repeated REXP rexpValue = 8; repeated string attrName = 11; repeated REXP attrValue = 12; optional bytes nativeValue = 13; } message STRING { optional string strval = 1; optional bool isNA = 2 [default=false]; } message CMPLX { optional double real = 1 [default=0]; required double imag = 2; } RProtoBuf/inst/proto/addressbook.proto0000644000175100001440000000117412754736105017674 0ustar hornikusers// mark as Protocol Buffers v2 format syntax = "proto2"; package tutorial; option java_package = "com.example.tutorial"; option java_outer_classname = "AddressBookProtos"; message Person { required string name = 1; required int32 id = 2; optional string email = 3; enum PhoneType { MOBILE = 0; HOME = 1; WORK = 2; } message PhoneNumber { required string number = 1; optional PhoneType type = 2 [default = HOME]; } repeated PhoneNumber phone = 4; extensions 100 to 199; } message AddressBook { repeated Person person = 1; } service EchoService { rpc Echo (Person) returns (Person); } RProtoBuf/inst/proto/helloworld.proto0000644000175100001440000000054012754736105017543 0ustar hornikusers// mark as Protocol Buffers v2 format syntax = "proto2"; package rprotobuf; option java_package = "org.rproject.rprotobuf"; option java_outer_classname = "HelloWorld"; message HelloWorldRequest{} message HelloWorldResponse{ required string message = 1; } service HelloWorldService{ rpc HelloWorld(HelloWorldRequest) returns(HelloWorldResponse); } RProtoBuf/tests/0000755000175100001440000000000012522170720013312 5ustar hornikusersRProtoBuf/tests/runUnitTests.R0000644000175100001440000000232712440004312016120 0ustar hornikusers ## doRUnit.R --- Run RUnit tests ## ## with credits to package fUtilities in RMetrics ## which credits Gregor Gojanc's example in CRAN package 'gdata' ## as per the R Wiki http://wiki.r-project.org/rwiki/doku.php?id=developers:runit ## and changed further by Martin Maechler ## and more changes by Murray Stokely in HistogramTools ## ## Dirk Eddelbuettel, Dec 2013 stopifnot(require("RUnit", quietly=TRUE)) stopifnot(require("RProtoBuf", quietly=TRUE)) # path <- system.file("unitTests", package = pkg) # stopifnot(file.exists(path), file.info(path.expand(path))$isdir) # source(file.path(path, "runTests.R"), echo = TRUE) ## Set a seed to make the test deterministic set.seed(42) ## Define tests testSuite <- defineTestSuite(name="RProtoBuf Unit Tests", dirs=system.file("unitTests", package = "RProtoBuf"), testFuncRegexp = "^[Tt]est.+") ## Run tests tests <- runTestSuite(testSuite) ## Print results printTextProtocol(tests) ## Return success or failure to R CMD CHECK if (getErrors(tests)$nFail > 0) { stop("TEST FAILED!") } if (getErrors(tests)$nErr > 0) { stop("TEST HAD ERRORS!") } if (getErrors(tests)$nTestFunc < 1) { stop("NO TEST FUNCTIONS RUN!") } RProtoBuf/src/0000755000175100001440000000000013037407202012737 5ustar hornikusersRProtoBuf/src/ZeroCopyOutputStreamWrapper.cpp0000644000175100001440000000137313037407202021157 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" namespace rprotobuf { ZeroCopyOutputStreamWrapper::ZeroCopyOutputStreamWrapper(GPB::io::ZeroCopyOutputStream* stream) : stream(stream) { coded_stream = new GPB::io::CodedOutputStream(stream); } ZeroCopyOutputStreamWrapper::~ZeroCopyOutputStreamWrapper() { try { /* first clear the coded stream */ delete coded_stream; /* then the stream itself */ delete stream; } catch (...) { } } GPB::io::ZeroCopyOutputStream* ZeroCopyOutputStreamWrapper::get_stream() { return stream; } GPB::io::CodedOutputStream* ZeroCopyOutputStreamWrapper::get_coded_stream() { return coded_stream; } } // namespace rprotobuf RProtoBuf/src/wrapper_ServiceDescriptor.cpp0000644000175100001440000000635513037407202020653 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(ServiceDescriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(length), GPB::ServiceDescriptor, method_count) RPB_XP_METHOD_0(METHOD(method_count), GPB::ServiceDescriptor, method_count) RPB_XP_METHOD_0(METHOD(as_character), GPB::ServiceDescriptor, DebugString) RPB_XP_METHOD_CAST_1(METHOD(getMethodByIndex), GPB::ServiceDescriptor, method, S4_MethodDescriptor) RPB_XP_METHOD_CAST_1(METHOD(getMethodByName), GPB::ServiceDescriptor, FindMethodByName, S4_MethodDescriptor) RPB_FUNCTION_1(Rcpp::CharacterVector, METHOD(getMethodNames), Rcpp::XPtr desc) { int nmeths = desc->method_count(); Rcpp::CharacterVector res(nmeths); for (int i = 0; i < nmeths; i++) { res[i] = desc->method(i)->name(); } return res; } /** * @param xp (GPB::ServiceDescriptor*) external pointer * @return the descriptor as an R list */ RPB_FUNCTION_1(Rcpp::List, METHOD(as_list), Rcpp::XPtr desc) { int n = desc->method_count(); Rcpp::CharacterVector names(n); Rcpp::List res(n); for (int i = 0; i < n; i++) { const GPB::MethodDescriptor* met = desc->method(i); res[i] = S4_MethodDescriptor(met); names[i] = met->name(); } res.names() = names; return res; } RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::ServiceDescriptorProto* message = new GPB::ServiceDescriptorProto(); d->CopyTo(message); return S4_Message(message); } RPB_FUNCTION_1(S4_FileDescriptor, METHOD(fileDescriptor), Rcpp::XPtr desc) { return S4_FileDescriptor(desc->file()); } RPB_FUNCTION_2(std::string, METHOD(name), Rcpp::XPtr d, bool full) { return full ? d->full_name() : d->name(); } /** * extract a method descriptor from a service descriptor using its * name or position * * @param pointer (GPB::ServiceDescriptor*) external pointer * @param name name or position of the method */ SEXP get_service_method(SEXP pointer, SEXP name) { /* grab the Message pointer */ Rcpp::XPtr desc(pointer); GPB::MethodDescriptor* method_desc = static_cast(0); switch (TYPEOF(name)) { case STRSXP: { /* what we are looking for */ const char* what = CHAR(STRING_ELT(name, 0)); /* the method descriptor */ method_desc = (GPB::MethodDescriptor*)desc->FindMethodByName(what); break; } case REALSXP: { /* the method descriptor */ method_desc = (GPB::MethodDescriptor*)desc->method((int)REAL(name)[0]); break; } case INTSXP: { /* the method descriptor */ method_desc = (GPB::MethodDescriptor*)desc->method(INTEGER(name)[0]); break; } } if (!method_desc) { Rcpp::stop("could not get MethodDescriptor"); } return S4_MethodDescriptor(method_desc); } #undef METHOD } // namespace rprotobuf RProtoBuf/src/wrapper_Descriptor.cpp0000644000175100001440000002131113037407202017317 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(Descriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(as_character), GPB::Descriptor, DebugString) RPB_XP_METHOD_0(METHOD(field_count), GPB::Descriptor, field_count) RPB_XP_METHOD_0(METHOD(nested_type_count), GPB::Descriptor, nested_type_count) RPB_XP_METHOD_0(METHOD(enum_type_count), GPB::Descriptor, enum_type_count) RPB_XP_METHOD_CAST_0(METHOD(containing_type), GPB::Descriptor, containing_type, S4_Descriptor) /** * returns the names of the members contained in the descriptor * (nested types, enums, fields) * * @param xp external pointer to a Descriptor * * @return member names, as an R character vector (STRSXP) */ RPB_FUNCTION_1(Rcpp::CharacterVector, METHOD(getMemberNames), Rcpp::XPtr desc) { int nfields = desc->field_count(); int ntypes = desc->nested_type_count(); int nenums = desc->enum_type_count(); Rcpp::CharacterVector res(nfields + ntypes + nenums); int j = 0; for (int i = 0; i < nfields; i++, j++) { res[j] = desc->field(i)->name(); } for (int i = 0; i < ntypes; i++, j++) { res[j] = desc->nested_type(i)->name(); } for (int i = 0; i < nenums; i++, j++) { res[j] = desc->enum_type(i)->name(); } return (res); } /** * @param xp external pointer to a Descriptor * @return the descriptor as an R list */ RPB_FUNCTION_1(Rcpp::List, METHOD(as_list), Rcpp::XPtr desc) { int nfields = desc->field_count(); int ntypes = desc->nested_type_count(); int nenums = desc->enum_type_count(); int n = nfields + ntypes + nenums; Rcpp::CharacterVector names(n); Rcpp::List res(n); int cnt = 0; for (int i = 0; i < nfields; cnt++, i++) { const GPB::FieldDescriptor* fd = desc->field(i); res[cnt] = S4_FieldDescriptor(fd); names[cnt] = fd->name(); } for (int i = 0; i < ntypes; cnt++, i++) { const GPB::Descriptor* d = desc->nested_type(i); res[cnt] = S4_Descriptor(d); names[cnt] = d->name(); } for (int i = 0; i < nenums; cnt++, i++) { const GPB::EnumDescriptor* ed = desc->enum_type(i); res[cnt] = S4_EnumDescriptor(ed); names[cnt] = ed->name(); } res.names() = names; return res; } RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::DescriptorProto* message = new GPB::DescriptorProto(); d->CopyTo(message); return message; } RPB_FUNCTION_2(S4_FieldDescriptor, METHOD(field), Rcpp::XPtr d, int i) { return d->field(i); } RPB_FUNCTION_2(S4_FieldDescriptor, METHOD(FindFieldByNumber), Rcpp::XPtr d, int num) { return d->FindFieldByNumber(num); } RPB_FUNCTION_2(S4_FieldDescriptor, METHOD(FindFieldByName), Rcpp::XPtr d, std::string nam) { return d->FindFieldByName(nam); } RPB_FUNCTION_2(S4_Descriptor, METHOD(nested_type), Rcpp::XPtr d, int i) { return d->nested_type(i); } RPB_FUNCTION_2(S4_Descriptor, METHOD(FindNestedTypeByName), Rcpp::XPtr d, std::string nam) { return d->FindNestedTypeByName(nam); } RPB_FUNCTION_2(S4_EnumDescriptor, METHOD(enum_type), Rcpp::XPtr d, int i) { return d->enum_type(i); } // FIXME: two methods cant have the same name // RPB_FUNCTION_2( S4_EnumDescriptor, METHOD(enum_type), // Rcpp::XPtr d, std::string name){ // return d->FindEnumTypeByName( i ) ; // } RPB_FUNCTION_1(S4_FileDescriptor, METHOD(fileDescriptor), Rcpp::XPtr desc) { return S4_FileDescriptor(desc->file()); } RPB_FUNCTION_2(std::string, METHOD(name), Rcpp::XPtr d, bool full) { return full ? d->full_name() : d->name(); } RPB_FUNCTION_2(S4_Message, METHOD(readMessageFromFile), Rcpp::XPtr desc, std::string filename) { /* open the file to read in binary mode */ int file = open(filename.c_str(), O_RDONLY | O_BINARY); /* create a prototype of the message we are going to read */ GPB::Message* message = PROTOTYPE(desc); if (!message) { throw std::range_error("could not call factory->GetPrototype(desc)->New()"); } /* read the message from the file */ // TODO(mstokely): Check return value! message->ParsePartialFromFileDescriptor(file); close(file); return (S4_Message(message)); } RPB_FUNCTION_2(S4_Message, METHOD(readMessageFromConnection), Rcpp::XPtr desc, int conn_id) { RconnectionCopyingInputStream wrapper(conn_id); GPB::io::CopyingInputStreamAdaptor stream(&wrapper); GPB::io::CodedInputStream coded_stream(&stream); /* create a prototype of the message we are going to read */ GPB::Message* message = PROTOTYPE(desc); if (!message) { throw std::range_error("could not call factory->GetPrototype(desc)->New()"); } // TODO(mstokely): Check return value! message->ParsePartialFromCodedStream(&coded_stream); S4_Message res(message); return res; } RPB_FUNCTION_2(S4_Message, METHOD(readMessageFromRawVector), Rcpp::XPtr desc, Rcpp::RawVector raw) { GPB::io::ArrayInputStream ais((void*)raw.begin(), raw.size()); GPB::io::CodedInputStream stream(&ais); GPB::Message* message = PROTOTYPE(desc); if (!message) { throw std::range_error("could not call factory->GetPrototype(desc)->New()"); } message->MergePartialFromCodedStream(&stream); return (S4_Message(message)); } RPB_FUNCTION_3(S4_Message, METHOD(readASCIIFromString), Rcpp::XPtr desc, std::string input, bool partial) { GPB::Message* message = PROTOTYPE(desc); if (partial) { // Allow partial messages where object is not fully initialized GPB::TextFormat::Parser parser; parser.AllowPartialMessage(partial); if (parser.ParseFromString(input, message)) { return (S4_Message(message)); } else { throw std::range_error("Could not parse ASCII protocol buffer from text string."); } } else { // Default parser requires fully initialized ascii messages. if (GPB::TextFormat::ParseFromString(input, message)) { return (S4_Message(message)); } else { throw std::range_error("Could not parse ASCII protocol buffer from text string." " Consider setting partial=TRUE"); } } } RPB_FUNCTION_3(S4_Message, METHOD(readASCIIFromConnection), Rcpp::XPtr desc, int conn_id, bool partial) { RconnectionCopyingInputStream wrapper(conn_id); GPB::io::CopyingInputStreamAdaptor stream(&wrapper); /* create a prototype of the message we are going to read */ GPB::Message* message = PROTOTYPE(desc); if (!message) { throw std::range_error("could not call factory->GetPrototype(desc)->New()"); } if (partial) { // Allow partial messages where object is not fully initialized GPB::TextFormat::Parser parser; parser.AllowPartialMessage(partial); if (!parser.Parse(&stream, message)) { throw std::range_error("Could not parse ASCII protocol buffer."); } } else { // Default parser requires fully initialized ascii messages. if (!GPB::TextFormat::Parse(&stream, message)) { throw std::range_error("Could not parse ASCII protocol buffer."); } } if (wrapper.Failure()) { throw std::range_error("Could not read ASCII protocol buffer."); } return (S4_Message(message)); } RcppExport SEXP Descriptor_getField(SEXP pointer, SEXP name) { GPB::FieldDescriptor* field_desc = (GPB::FieldDescriptor*)0; BEGIN_RCPP std::string error_message = "could not get FieldDescriptor for field"; SEXP retVal = R_NilValue; switch (TYPEOF(name)) { case CHARSXP: case STRSXP: // This tries to get the field by name for various types of descriptors. retVal = do_dollar_Descriptor(pointer, name); if (retVal == R_NilValue) { error_message = "Unknown field"; } else { return retVal; } break; default: { error_message = "Invalid type for get field extractor."; break; } } if (!field_desc) { Rcpp::stop(error_message.c_str()); } return S4_FieldDescriptor(field_desc); VOID_END_RCPP return S4_FieldDescriptor(field_desc); } #undef METHOD } // namespace rprotobuf RProtoBuf/src/streams.cpp0000644000175100001440000002157313037407202015131 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "ConnectionInputStream.h" #include "ConnectionOutputStream.h" namespace rprotobuf { void ZeroCopyInputStreamWrapper_finalizer(SEXP xp) { delete (ZeroCopyInputStreamWrapper*)XPP(xp); } void ZeroCopyOutputStreamWrapper_finalizer(SEXP xp) { delete (ZeroCopyOutputStreamWrapper*)XPP(xp); } // {{{ input streams // {{{ FileInputStream SEXP FileInputStream_new(SEXP filename, SEXP block_size, SEXP close_on_delete) { BEGIN_RCPP NEW_S4_OBJECT("FileInputStream"); int fd = open(CHAR(STRING_ELT(filename, 0)), O_RDONLY | O_BINARY); GPB::io::FileInputStream* stream = new GPB::io::FileInputStream(fd, INTEGER(block_size)[0]); stream->SetCloseOnDelete(LOGICAL(close_on_delete)[0]); ZeroCopyInputStreamWrapper* wrapper = new ZeroCopyInputStreamWrapper(stream); SEXP ptr = PROTECT(R_MakeExternalPtr((void*)wrapper, R_NilValue, R_NilValue)); R_RegisterCFinalizerEx(ptr, ZeroCopyInputStreamWrapper_finalizer, _FALSE_); SET_SLOT(oo, Rf_install("pointer"), ptr); UNPROTECT(2); /* oo, ptr */ return oo; END_RCPP } SEXP FileInputStream_GetErrno(SEXP xp) { BEGIN_RCPP GPB::io::FileInputStream* stream = GET_FIS(xp); return Rf_ScalarInteger(stream->GetErrno()); END_RCPP } SEXP FileInputStream_SetCloseOnDelete(SEXP xp, SEXP close) { BEGIN_RCPP GPB::io::FileInputStream* stream = GET_FIS(xp); stream->SetCloseOnDelete(LOGICAL(close)); return R_NilValue; END_RCPP } SEXP FileInputStream_Close(SEXP xp) { BEGIN_RCPP GPB::io::FileInputStream* stream = GET_FIS(xp); bool res = stream->Close(); return Rf_ScalarLogical(res ? _TRUE_ : _FALSE_); END_RCPP } // }}} // {{{ ConnectionInputStream SEXP ConnectionInputStream_new(SEXP con, SEXP was_open) { BEGIN_RCPP NEW_S4_OBJECT("ConnectionInputStream"); ConnectionInputStream* stream = new ConnectionInputStream(con, (bool)LOGICAL(was_open)[0]); ZeroCopyInputStreamWrapper* wrapper = new ZeroCopyInputStreamWrapper(stream); SEXP ptr = PROTECT(R_MakeExternalPtr((void*)wrapper, R_NilValue, con)); R_RegisterCFinalizerEx(ptr, ZeroCopyInputStreamWrapper_finalizer, _FALSE_); SET_SLOT(oo, Rf_install("pointer"), ptr); UNPROTECT(2); /* oo, ptr */ return oo; END_RCPP } // }}} // }}} // {{{ output streams // {{{ ZeroCopyOutputStream SEXP ZeroCopyOutputStream_Next(SEXP xp, SEXP payload) { BEGIN_RCPP GPB::io::ZeroCopyOutputStream* stream = GET_ZCOS(xp); void* out; int s = LENGTH(payload); bool res = stream->Next(&out, &s); if (!res) { Rcpp_error("cannot write to stream"); } memcpy(out, RAW(payload), s); return Rf_ScalarInteger(s); END_RCPP } SEXP ZeroCopyOutputStream_ByteCount(SEXP xp) { BEGIN_RCPP GPB::io::ZeroCopyOutputStream* stream = GET_ZCOS(xp); return (Rf_ScalarReal((double)stream->ByteCount())); END_RCPP } SEXP ZeroCopyOutputStream_BackUp(SEXP xp, SEXP count) { BEGIN_RCPP GPB::io::ZeroCopyOutputStream* stream = GET_ZCOS(xp); int s = GET_int(count, 0); stream->BackUp(s); return R_NilValue; END_RCPP } // }}} // {{{ ArrayOutputStream // }}} // {{{ FileOutputStream SEXP FileOutputStream_new(SEXP filename, SEXP block_size, SEXP close_on_delete) { BEGIN_RCPP NEW_S4_OBJECT("FileOutputStream"); int fd = open(CHAR(STRING_ELT(filename, 0)), O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666); GPB::io::FileOutputStream* stream = new GPB::io::FileOutputStream(fd, INTEGER(block_size)[0]); stream->SetCloseOnDelete(LOGICAL(close_on_delete)[0]); ZeroCopyOutputStreamWrapper* wrapper = new ZeroCopyOutputStreamWrapper(stream); SEXP ptr = PROTECT(R_MakeExternalPtr((void*)wrapper, R_NilValue, R_NilValue)); R_RegisterCFinalizerEx(ptr, ZeroCopyOutputStreamWrapper_finalizer, _FALSE_); SET_SLOT(oo, Rf_install("pointer"), ptr); UNPROTECT(2); /* oo, ptr */ return oo; END_RCPP } SEXP FileOutputStream_Flush(SEXP xp) { BEGIN_RCPP GPB::io::FileOutputStream* stream = GET_FOS(xp); bool res = stream->Flush(); return Rf_ScalarLogical(res ? _TRUE_ : _FALSE_); END_RCPP } SEXP FileOutputStream_Close(SEXP xp) { BEGIN_RCPP GPB::io::FileOutputStream* stream = GET_FOS(xp); bool res = stream->Close(); return Rf_ScalarLogical(res ? _TRUE_ : _FALSE_); END_RCPP } SEXP FileOutputStream_GetErrno(SEXP xp) { BEGIN_RCPP GPB::io::FileOutputStream* stream = GET_FOS(xp); return Rf_ScalarInteger(stream->GetErrno()); END_RCPP } SEXP FileOutputStream_SetCloseOnDelete(SEXP xp, SEXP close) { BEGIN_RCPP GPB::io::FileOutputStream* stream = GET_FOS(xp); stream->SetCloseOnDelete(LOGICAL(close)); return R_NilValue; END_RCPP } // }}} // {{{ ConnectionOutputStream SEXP ConnectionOutputStream_new(SEXP con, SEXP was_open) { BEGIN_RCPP NEW_S4_OBJECT("ConnectionOutputStream"); ConnectionOutputStream* stream = new ConnectionOutputStream(con, (bool)LOGICAL(was_open)[0]); ZeroCopyOutputStreamWrapper* wrapper = new ZeroCopyOutputStreamWrapper(stream); /* we keep the R connection protected as long as the external pointer is kept out of GC */ SEXP ptr = PROTECT(R_MakeExternalPtr((void*)wrapper, R_NilValue, con)); R_RegisterCFinalizerEx(ptr, ZeroCopyOutputStreamWrapper_finalizer, _FALSE_); SET_SLOT(oo, Rf_install("pointer"), ptr); UNPROTECT(2); /* oo, ptr */ return oo; END_RCPP } // }}} // }}} // {{{ Read*** functions using CodedInputStream SEXP ZeroCopyInputStream_ReadRaw(SEXP xp, SEXP size) { BEGIN_RCPP GPB::io::CodedInputStream* coded_stream = GET_CIS(xp); int s = INTEGER(size)[0]; SEXP payload = PROTECT(Rf_allocVector(RAWSXP, s)); if (!coded_stream->ReadRaw(RAW(payload), s)) Rcpp_error("error reading raw bytes"); UNPROTECT(1); /* payload */ return payload; END_RCPP } SEXP ZeroCopyInputStream_ReadString(SEXP xp, SEXP size) { BEGIN_RCPP GPB::io::CodedInputStream* coded_stream = GET_CIS(xp); int s = INTEGER(size)[0]; std::string buffer(""); if (!coded_stream->ReadString(&buffer, s)) Rcpp_error("error reading string"); return Rf_mkString(buffer.c_str()); END_RCPP } SEXP ZeroCopyInputStream_ReadVarint32(SEXP xp) { BEGIN_RCPP GPB::io::CodedInputStream* coded_stream = GET_CIS(xp); uint32 res = 0; if (!coded_stream->ReadVarint32(&res)) Rcpp_error("error reading varint32"); return Rf_ScalarInteger(res); END_RCPP } SEXP ZeroCopyInputStream_ReadLittleEndian32(SEXP xp) { BEGIN_RCPP GPB::io::CodedInputStream* coded_stream = GET_CIS(xp); uint32 res = 0; if (!coded_stream->ReadVarint32(&res)) Rcpp_error("error reading little endian int32"); return Rf_ScalarInteger(res); END_RCPP } SEXP ZeroCopyInputStream_ReadLittleEndian64(SEXP xp) { BEGIN_RCPP GPB::io::CodedInputStream* coded_stream = GET_CIS(xp); uint64 res = 0; if (!coded_stream->ReadVarint64(&res)) Rcpp_error("error reading little endian int32"); return Rf_ScalarReal((double)res); END_RCPP } SEXP ZeroCopyInputStream_ReadVarint64(SEXP xp) { BEGIN_RCPP GPB::io::CodedInputStream* coded_stream = GET_CIS(xp); uint64 res = 0; if (!coded_stream->ReadVarint64(&res)) Rcpp_error("error reading varint64"); return Rf_ScalarReal((double)res); END_RCPP } // }}} // {{{ Write*** functions using CodedOuputStream SEXP ZeroCopyOutputStream_WriteRaw(SEXP xp, SEXP payload) { BEGIN_RCPP GPB::io::CodedOutputStream* stream = GET_COS(xp); stream->WriteRaw(RAW(payload), LENGTH(payload)); return R_NilValue; END_RCPP } SEXP ZeroCopyOutputStream_WriteString(SEXP xp, SEXP payload) { BEGIN_RCPP if (LENGTH(payload) > 1) { Rf_warning("only the first element is used"); } if (LENGTH(payload) == 0) { Rcpp_error("need at least one element"); } GPB::io::CodedOutputStream* stream = GET_COS(xp); stream->WriteString(CHAR(STRING_ELT(payload, 0))); return R_NilValue; END_RCPP } SEXP ZeroCopyOutputStream_WriteLittleEndian32(SEXP xp, SEXP payload) { BEGIN_RCPP GPB::io::CodedOutputStream* stream = GET_COS(xp); stream->WriteLittleEndian32(GET_int32(payload, 0)); return R_NilValue; END_RCPP } SEXP ZeroCopyOutputStream_WriteLittleEndian64(SEXP xp, SEXP payload) { BEGIN_RCPP GPB::io::CodedOutputStream* stream = GET_COS(xp); stream->WriteLittleEndian64(GET_int64(payload, 0)); return R_NilValue; END_RCPP } SEXP ZeroCopyOutputStream_WriteVarint32(SEXP xp, SEXP payload) { BEGIN_RCPP GPB::io::CodedOutputStream* stream = GET_COS(xp); stream->WriteVarint32(GET_int32(payload, 0)); return R_NilValue; END_RCPP } SEXP ZeroCopyOutputStream_WriteVarint64(SEXP xp, SEXP payload) { BEGIN_RCPP GPB::io::CodedOutputStream* stream = GET_COS(xp); stream->WriteVarint64(GET_int64(payload, 0)); return R_NilValue; END_RCPP } // }}} } // namespace rprotobuf RProtoBuf/src/ConnectionCopyingOutputStream.cpp0000644000175100001440000000107113037407202021467 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "ConnectionCopyingOutputStream.h" namespace rprotobuf { ConnectionCopyingOutputStream::ConnectionCopyingOutputStream(SEXP con) : con(con), writeBin("writeBin") {} bool ConnectionCopyingOutputStream::Write(const void* buffer, int size) { /* we need to take care of error handling */ Rcpp::RawVector payload(size); memcpy(payload.begin(), buffer, size); writeBin(payload, con); return true; } } RProtoBuf/src/wrapper_FieldDescriptor.cpp0000644000175100001440000000724713037407202020277 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- // Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #include "rprotobuf.h" #include "fieldtypes.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(FieldDescriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(as_character), GPB::FieldDescriptor, DebugString) RPB_XP_METHOD_0(METHOD(is_extension), GPB::FieldDescriptor, is_extension) RPB_XP_METHOD_0(METHOD(number), GPB::FieldDescriptor, number) RPB_XP_METHOD_0(METHOD(type), GPB::FieldDescriptor, type) RPB_XP_METHOD_0(METHOD(cpp_type), GPB::FieldDescriptor, cpp_type) RPB_XP_METHOD_0(METHOD(label), GPB::FieldDescriptor, label) RPB_XP_METHOD_0(METHOD(is_repeated), GPB::FieldDescriptor, is_repeated) RPB_XP_METHOD_0(METHOD(is_optional), GPB::FieldDescriptor, is_optional) RPB_XP_METHOD_0(METHOD(is_required), GPB::FieldDescriptor, is_required) RPB_XP_METHOD_0(METHOD(has_default_value), GPB::FieldDescriptor, has_default_value) RPB_FUNCTION_1(S4_Descriptor, METHOD(containing_type), Rcpp::XPtr d) { return S4_Descriptor(d->containing_type()); } #define RPB_HANDLE_CASE(__CPP__, __LC__) \ case CPPTYPE_##__CPP__: { \ return Rcpp::wrap(d->default_value_##__LC__()); \ } RPB_FUNCTION_1(SEXP, METHOD(default_value), Rcpp::XPtr d) { switch (d->cpp_type()) { RPB_HANDLE_CASE(INT32, int32) RPB_HANDLE_CASE(UINT32, uint32) #ifdef RCPP_HAS_LONG_LONG_TYPES RPB_HANDLE_CASE(INT64, int64) RPB_HANDLE_CASE(UINT64, uint64) #endif RPB_HANDLE_CASE(DOUBLE, double) RPB_HANDLE_CASE(FLOAT, float) RPB_HANDLE_CASE(BOOL, bool) RPB_HANDLE_CASE(STRING, string) case CPPTYPE_ENUM: { return Rf_ScalarInteger(d->default_value_enum()->number()); } default: break; } return R_NilValue; } RPB_FUNCTION_1(S4_Descriptor, METHOD(message_type), Rcpp::XPtr d) { if (d->cpp_type() != CPPTYPE_MESSAGE) { throw Rcpp::not_compatible("not a message type field"); } return S4_Descriptor(d->message_type()); } RPB_FUNCTION_1(S4_EnumDescriptor, METHOD(enum_type), Rcpp::XPtr d) { if (d->cpp_type() != CPPTYPE_ENUM) { Rcpp::stop("not an enum type field"); } return S4_EnumDescriptor(d->enum_type()); } RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::FieldDescriptorProto* message = new GPB::FieldDescriptorProto(); d->CopyTo(message); return S4_Message(message); } RPB_FUNCTION_1(S4_FileDescriptor, METHOD(fileDescriptor), Rcpp::XPtr desc) { return S4_FileDescriptor(desc->file()); } RPB_FUNCTION_2(std::string, METHOD(name), Rcpp::XPtr d, bool full) { return full ? d->full_name() : d->name(); } #undef RPB_HANDLE_CASE #undef METHOD } // namespace rprotobuf RProtoBuf/src/ConnectionCopyingInputStream.cpp0000644000175100001440000000134713037407202021274 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "ConnectionCopyingInputStream.h" namespace rprotobuf { ConnectionCopyingInputStream::ConnectionCopyingInputStream(SEXP con) : con(con), readBin("readBin") {} /** * call readBin to read size bytes from R * * @param buffer buffer to fill with at most size bytes * @param size maximum number of bytes * * @return the number of bytes actually read */ int ConnectionCopyingInputStream::Read(void* buffer, int size) { /* TODO: error handling */ Rcpp::RawVector res = readBin(con, Rcpp::RawVector(0), size); memcpy(buffer, res.begin(), res.size()); return res.size(); } } RProtoBuf/src/DescriptorPoolLookup.cpp0000644000175100001440000000677713037407202017626 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- // DescriptorPoolLookup.cpp: R/C++ interface class library // // Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #include "rprotobuf.h" #include "DescriptorPoolLookup.h" namespace rprotobuf { void DescriptorPoolLookup::add(const std::string& element) { elements.insert(element); } bool DescriptorPoolLookup::contains(const std::string& element) { return elements.find(element) != elements.end(); } SEXP DescriptorPoolLookup::getElements() { return Rcpp::wrap(elements); } std::set DescriptorPoolLookup::elements; RWarningErrorCollector DescriptorPoolLookup::error_collector; RSourceTree DescriptorPoolLookup::source_tree; GPB::compiler::Importer DescriptorPoolLookup::importer(&source_tree, &error_collector); GPB::DynamicMessageFactory DescriptorPoolLookup::message_factory(importer.pool()); /** * Add descriptors from a proto file to the descriptor pool. * * Specifically, message types, extensions, and enums are added. * Services are not added because they are not really used in RProtoBuf. * * @param files A character vector of .proto files to import. * @param dirs A character vector of directories to import from. * @throws Rcpp::exception if a file can't be loaded (uncaught). */ void DescriptorPoolLookup::importProtoFiles(SEXP files, SEXP dirs) { source_tree.addDirectories(dirs); int n = LENGTH(files); for (int j = 0; j < n; j++) { const GPB::FileDescriptor* file_desc = importer.Import(CHAR(STRING_ELT(files, j))); if (!file_desc) { std::string message = std::string("Could not load proto file '") + CHAR(STRING_ELT(files, j)) + "'\n"; Rcpp_error(message.c_str()); } // add top level messages from the file. int ntypes = file_desc->message_type_count(); for (int i = 0; i < ntypes; i++) { const GPB::Descriptor* desc = file_desc->message_type(i); add(desc->full_name()); /* should we bother recursing ? */ } // add top level extensions int nexts = file_desc->extension_count(); for (int i = 0; i < nexts; i++) { const GPB::FieldDescriptor* field_desc = file_desc->extension(i); add(field_desc->full_name()); } // add top level enums. int nenums = file_desc->enum_type_count(); for (int i = 0; i < nenums; i++) { const GPB::EnumDescriptor* enum_desc = file_desc->enum_type(i); add(enum_desc->full_name()); } } // source_tree.removeDirectories( dirs ) ; } const GPB::DescriptorPool* DescriptorPoolLookup::pool() { return importer.pool(); } const GPB::DynamicMessageFactory* DescriptorPoolLookup::factory() { return &message_factory; } } // namespace rprotobuf RProtoBuf/src/DescriptorPoolLookup.h0000644000175100001440000000156213037407202017256 0ustar hornikusers#ifndef RPROTOBUF_DescriptorPoolLookup_H #define RPROTOBUF_DescriptorPoolLookup_H #include /* For set */ #include /* For string */ #include "RSourceTree.h" #include "RWarningErrorCollector.h" namespace rprotobuf { class DescriptorPoolLookup { public: static void add(const std::string& element); static bool contains(const std::string& element); static SEXP getElements(); static void importProtoFiles(SEXP files, SEXP cwd); static const GPB::DescriptorPool* pool(); static const GPB::DynamicMessageFactory* factory(); private: static std::set elements; static RWarningErrorCollector error_collector; static RSourceTree source_tree; static GPB::compiler::Importer importer; static GPB::DynamicMessageFactory message_factory; }; } // namespace rprotobuf #endif RProtoBuf/src/lookup.cpp0000644000175100001440000001654713037407202014771 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "DescriptorPoolLookup.h" /* This uses the mechanism of the RObjectTables package see: http://www.omegahat.net/RObjectTables/ */ namespace rprotobuf { /** * Returns the R_UnboundValue */ SEXP R_getUnboundValue() { return (R_UnboundValue); } /** * @param name potential message type * @param canCache Can R cache this object * @param tb object table * * @return _TRUE_ if there is a message of the given type in the DescriptorPool */ Rboolean rProtoBufTable_exists(const char *const name, Rboolean *canCache, R_ObjectTable *tb) { #ifdef LOOKUP_DEBUG Rprintf(" >> rProtoBufTable_exists\n"); #endif if (tb->active == _FALSE_) return (_FALSE_); tb->active = _FALSE_; Rboolean val = _FALSE_; if (DescriptorPoolLookup::contains(name)) { /* first check the cache */ val = _TRUE_; } else { /* try the generated pool */ const GPB::DescriptorPool *pool = GPB::DescriptorPool::generated_pool(); if (pool->FindMessageTypeByName(name) || pool->FindEnumTypeByName(name) || pool->FindServiceByName(name) || pool->FindMethodByName(name) || pool->FindExtensionByName(name)) { DescriptorPoolLookup::add(name); val = _TRUE_; } else { /* try the runtime pool */ pool = DescriptorPoolLookup::pool(); if (pool->FindMessageTypeByName(name) || pool->FindEnumTypeByName(name) || pool->FindServiceByName(name) || pool->FindMethodByName(name) || pool->FindExtensionByName(name)) { DescriptorPoolLookup::add(name); val = _TRUE_; } } } tb->active = _TRUE_; return (val); } SEXP findSomething(const GPB::DescriptorPool *pool, const char *const name) { const GPB::Descriptor *desc = pool->FindMessageTypeByName(name); std::string name_string(name); if (desc) { /* message */ DescriptorPoolLookup::add(name_string); return S4_Descriptor(desc); } else { const GPB::EnumDescriptor *enum_desc = pool->FindEnumTypeByName(name_string); if (enum_desc) { /* enum */ DescriptorPoolLookup::add(name_string); return S4_EnumDescriptor(enum_desc); } else { const GPB::FieldDescriptor *extension_desc = pool->FindExtensionByName(name_string); if (extension_desc) { /* extension */ DescriptorPoolLookup::add(name_string); return S4_FieldDescriptor(extension_desc); } else { const GPB::ServiceDescriptor *service_desc = pool->FindServiceByName(name_string); if (service_desc) { DescriptorPoolLookup::add(name_string); return S4_ServiceDescriptor(service_desc); } else { const GPB::MethodDescriptor *method_desc = pool->FindMethodByName(name_string); if (method_desc) { DescriptorPoolLookup::add(name_string); return S4_MethodDescriptor(method_desc); } } } } } return R_NilValue; } /** * Returns a new "Descriptor" if there is such a message type * in the descriptor pool. NULL otherwise * * @param name message type name (without package path) * @param canCache * @param tb lookup table */ SEXP rProtoBufTable_get(const char *const name, Rboolean *canCache, R_ObjectTable *tb) { #ifdef LOOKUP_DEBUG Rprintf(" >> rProtoBufTable_get\n"); #endif if (tb->active == _FALSE_) return (R_UnboundValue); tb->active = _FALSE_; SEXP res_generated; SEXP res_runtime; int np = 0; /* first try the generated pool */ const GPB::DescriptorPool *pool = GPB::DescriptorPool::generated_pool(); res_generated = PROTECT(findSomething(pool, name)); np++; if (res_generated == R_NilValue) { /* try the runtime pool */ pool = DescriptorPoolLookup::pool(); res_runtime = PROTECT(findSomething(pool, name)); np++; } tb->active = _TRUE_; SEXP res = PROTECT((np == 2) ? res_runtime : res_generated); UNPROTECT(np + 1); if (res != R_NilValue) return res; return R_getUnboundValue(); // -Wall } /** * Does nothing. Not applicable */ int rProtoBufTable_remove(const char *const unused_name, R_ObjectTable *unused_tb) { #ifdef LOOKUP_DEBUG Rprintf(" >> rProtoBufTable_remove( %s) \n", unused_name); #endif Rf_error("cannot remove from protobuf descriptor pool"); return (0); // make -Wall happy } /** * Indicates if R can cache the variable name. * Currently allways return _FALSE_ * * @param name message type name * @param tb lookup table * @return allways _FALSE_ (for now) */ Rboolean rProtoBufTable_canCache(const char *const unused_name, R_ObjectTable *unused_tb) { #ifdef LOOKUP_DEBUG Rprintf(" >> rProtoBufTable_canCache\n"); #endif return (_FALSE_); } /** * Previously this function returned a stop() error, but this has side * effects such as preventing users from using '<<-' operator in any * scripts that include RProtoBuf. So instead, we now simply return * NULL to indicate assign is not possible on this lookup table * without giving such a hard error. */ SEXP rProtoBufTable_assign(const char *const unused_name, SEXP unused_value, R_ObjectTable *unused_tb) { #ifdef LOOKUP_DEBUG Rprintf(" >> rProtoBufTable_assign( %s ) \n", unused_name); #endif return (R_NilValue); // make -Wall happy } /** * Returns the list of classes known to be included in the * packages. * * @param tb lookup table */ SEXP rProtoBufTable_objects(R_ObjectTable *tb) { #ifdef LOOKUP_DEBUG Rprintf(" >> rProtoBufTable_objects\n"); #endif tb->active = _FALSE_; SEXP objects = PROTECT(DescriptorPoolLookup::getElements()); tb->active = _TRUE_; UNPROTECT(1); /* objects */ return (objects); } RcppExport SEXP newProtocolBufferLookup(SEXP possexp) { BEGIN_RCPP #ifdef LOOKUP_DEBUG Rprintf("\n"); #endif R_ObjectTable *tb; SEXP val, klass; tb = (R_ObjectTable *)malloc(sizeof(R_ObjectTable)); if (!tb) throw Rcpp::exception("cannot allocate space for an internal R object table"); tb->type = RPROTOBUF_LOOKUP; /* FIXME: not sure what this should be */ tb->cachedNames = NULL; tb->privateData = (void *)0; tb->exists = rProtoBufTable_exists; tb->get = rProtoBufTable_get; tb->remove = rProtoBufTable_remove; tb->assign = rProtoBufTable_assign; tb->objects = rProtoBufTable_objects; tb->canCache = rProtoBufTable_canCache; tb->onAttach = NULL; tb->onDetach = NULL; PROTECT(val = R_MakeExternalPtr(tb, Rf_install("UserDefinedDatabase"), R_NilValue)); PROTECT(klass = Rf_mkString("UserDefinedDatabase")); Rf_setAttrib(val, R_ClassSymbol, klass); UNPROTECT(2); /* val, klass */ #ifdef LOOKUP_DEBUG Rprintf("\n"); #endif Rcpp::Function fun("attach"); int pos = Rcpp::as(possexp); fun(val, Rcpp::Named("pos") = pos, Rcpp::Named("name") = "RProtoBuf:DescriptorPool"); // TODO(mstokely): Somewhere we should deallocate tb? If package is unattached? return (val); END_RCPP } } // namespace rprotobuf RProtoBuf/src/RconnectionCopyingInputStream.h0000644000175100001440000000065713037407202021126 0ustar hornikusers#ifndef RPROTOBUF_RconnectionCopyingInputStream_H #define RPROTOBUF_RconnectionCopyingInputStream_H namespace rprotobuf { class RconnectionCopyingInputStream : public GPB::io::CopyingInputStream { public: RconnectionCopyingInputStream(int id); int Read(void* buffer, int size); bool Failure() const { return (failure); } private: int connection_id; bool failure; }; } // namespace rprotobuf #endif RProtoBuf/src/RSourceTree.h0000644000175100001440000000100313037407202015304 0ustar hornikusers#ifndef RPROTOBUF_RSourceTree_H #define RPROTOBUF_RSourceTree_H namespace rprotobuf { class RSourceTree : public GPB::compiler::SourceTree { public: RSourceTree(); GPB::io::ZeroCopyInputStream* Open(const std::string& filename); void addDirectory(const std::string& directory); void addDirectories(SEXP dirs); void removeDirectory(const std::string& directory); void removeDirectories(SEXP dirs); private: std::set directories; }; } // namespace rprotobuf #endif RProtoBuf/src/wrapper_MethodDescriptor.cpp0000644000175100001440000000365313037407202020471 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(MethodDescriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(as_character), GPB::MethodDescriptor, DebugString) RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::MethodDescriptorProto* message = new GPB::MethodDescriptorProto(); d->CopyTo(message); return S4_Message(message); } RPB_FUNCTION_1(S4_FileDescriptor, METHOD(fileDescriptor), Rcpp::XPtr desc) { return S4_FileDescriptor(desc->service()->file()); } RPB_FUNCTION_1(S4_Descriptor, METHOD(input_type), Rcpp::XPtr method) { return method->input_type(); } RPB_FUNCTION_1(S4_Descriptor, METHOD(output_type), Rcpp::XPtr method) { return method->output_type(); } RPB_FUNCTION_1(S4_Message, get_method_input_prototype, Rcpp::XPtr method) { const GPB::Descriptor* desc = method->input_type(); return S4_Message(PROTOTYPE(desc)); } RPB_FUNCTION_1(S4_Message, get_method_output_prototype, Rcpp::XPtr method) { const GPB::Descriptor* desc = method->output_type(); return S4_Message(PROTOTYPE(desc)); } RPB_FUNCTION_2(bool, valid_input_message, Rcpp::XPtr method, Rcpp::XPtr message) { return message->GetDescriptor() == method->input_type(); } RPB_FUNCTION_2(bool, valid_output_message, Rcpp::XPtr method, Rcpp::XPtr message) { return message->GetDescriptor() == method->output_type(); } RPB_FUNCTION_2(std::string, METHOD(name), Rcpp::XPtr d, bool full) { return full ? d->full_name() : d->name(); } #undef METHOD } // namespace rprotobuf RProtoBuf/src/wrapper_EnumValueDescriptor.cpp0000644000175100001440000000343213037407202021145 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- // wrapper_EnumValueDescriptor.h: R/C++ interface class library // // Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(EnumValueDescriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(as_character), GPB::EnumValueDescriptor, DebugString) RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::EnumValueDescriptorProto* message = new GPB::EnumValueDescriptorProto(); d->CopyTo(message); return S4_Message(message); } RPB_FUNCTION_2(std::string, METHOD(name), Rcpp::XPtr d, bool full) { return full ? d->full_name() : d->name(); } RPB_FUNCTION_1(int, METHOD(number), Rcpp::XPtr d) { return d->number(); } RPB_FUNCTION_1(S4_EnumDescriptor, METHOD(enum_type), Rcpp::XPtr d) { return S4_EnumDescriptor(d->type()); } #undef METHOD } // namespace rprotobuf RProtoBuf/src/fieldtypes.h0000644000175100001440000000307513037407202015265 0ustar hornikusers#ifndef FIELD_TYPES_H #define FIELD_TYPES_H using namespace google::protobuf; #define TYPE_DOUBLE FieldDescriptor::TYPE_DOUBLE #define TYPE_FLOAT FieldDescriptor::TYPE_FLOAT #define TYPE_INT64 FieldDescriptor::TYPE_INT64 #define TYPE_UINT64 FieldDescriptor::TYPE_UINT64 #define TYPE_INT32 FieldDescriptor::TYPE_INT32 #define TYPE_FIXED64 FieldDescriptor::TYPE_FIXED64 #define TYPE_FIXED32 FieldDescriptor::TYPE_FIXED32 #define TYPE_BOOL FieldDescriptor::TYPE_BOOL #define TYPE_STRING FieldDescriptor::TYPE_STRING #define TYPE_GROUP FieldDescriptor::TYPE_GROUP #define TYPE_MESSAGE FieldDescriptor::TYPE_MESSAGE #define TYPE_BYTES FieldDescriptor::TYPE_BYTES #define TYPE_UINT32 FieldDescriptor::TYPE_UINT32 #define TYPE_ENUM FieldDescriptor::TYPE_ENUM #define TYPE_SFIXED32 FieldDescriptor::TYPE_SFIXED32 #define TYPE_SFIXED64 FieldDescriptor::TYPE_SFIXED64 #define TYPE_SINT32 FieldDescriptor::TYPE_SINT32 #define TYPE_SINT64 FieldDescriptor::TYPE_SINT64 #define MAX_TYPE FieldDescriptor::MAX_TYPE #define CPPTYPE_INT32 FieldDescriptor::CPPTYPE_INT32 #define CPPTYPE_INT64 FieldDescriptor::CPPTYPE_INT64 #define CPPTYPE_UINT32 FieldDescriptor::CPPTYPE_UINT32 #define CPPTYPE_UINT64 FieldDescriptor::CPPTYPE_UINT64 #define CPPTYPE_DOUBLE FieldDescriptor::CPPTYPE_DOUBLE #define CPPTYPE_FLOAT FieldDescriptor::CPPTYPE_FLOAT #define CPPTYPE_BOOL FieldDescriptor::CPPTYPE_BOOL #define CPPTYPE_ENUM FieldDescriptor::CPPTYPE_ENUM #define CPPTYPE_STRING FieldDescriptor::CPPTYPE_STRING #define CPPTYPE_MESSAGE FieldDescriptor::CPPTYPE_MESSAGE #define MAX_CPPTYPE FieldDescriptor::MAX_CPPTYPE #endif RProtoBuf/src/extractors.cpp0000644000175100001440000001665013037407202015651 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- // Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #include "rprotobuf.h" #include "fieldtypes.h" #include "Rcppsupport.h" namespace rprotobuf { const char* kIntStringOptionName = "RProtoBuf.int64AsString"; bool UseStringsForInt64() { static const SEXP option_name = Rf_install(kIntStringOptionName); return (Rf_asLogical(Rf_GetOption1(option_name))); } // Rcpp::wrap silently coerces 64-bit integers to numerics // which drop precision for values between 2^53 - 2^64. // So, if an option is set, we return as a character string. template SEXP Int64AsSEXP(ValueType value) { BEGIN_RCPP if (UseStringsForInt64()) { std::stringstream ss; if ((ss << value).fail()) { // This should not happen, its a bug in the code. std::string message = std::string("Error converting int64 to string, unset ") + kIntStringOptionName + " option."; Rcpp::stop(message.c_str()); } return Rcpp::CharacterVector(ss.str()); } else { return Rcpp::wrap(value); } END_RCPP } /** * extract a field from a message * * @param pointer external pointer to a message * @param name name of the field * * @return the field called "name" of the message if the * message has the field, otherwise an error is generated */ RcppExport SEXP getMessageField(SEXP pointer, SEXP name) { RPB_DEBUG_BEGIN("getMessageField") PRINT_DEBUG_INFO("pointer", pointer); PRINT_DEBUG_INFO("name", name); /* grab the Message pointer */ Rcpp::XPtr message(pointer); GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, name); RPB_DEBUG_END("getMessageField"); return (extractFieldAsSEXP(message, field_desc)); } RcppExport SEXP extractFieldAsSEXP(const Rcpp::XPtr& message, const GPB::FieldDescriptor* fieldDesc) { BEGIN_RCPP const Reflection* ref = message->GetReflection(); if (fieldDesc->is_repeated()) { switch (GPB::FieldDescriptor::TypeToCppType(fieldDesc->type())) { #undef HANDLE_REPEATED_FIELD #define HANDLE_REPEATED_FIELD(TYPE, DATATYPE) \ case TYPE: \ return Rcpp::wrap(RepeatedFieldImporter(ref, *message, fieldDesc)); HANDLE_REPEATED_FIELD(CPPTYPE_INT32, GPB::int32) HANDLE_REPEATED_FIELD(CPPTYPE_DOUBLE, double) HANDLE_REPEATED_FIELD(CPPTYPE_FLOAT, float) HANDLE_REPEATED_FIELD(CPPTYPE_BOOL, bool) HANDLE_REPEATED_FIELD(CPPTYPE_ENUM, enum_field) HANDLE_REPEATED_FIELD(CPPTYPE_MESSAGE, message_field) // TODO(mstokely): Rcpp doesn't handle uint32 properly as of 2013/12 // See // https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1360&group_id=155&atid=637 case CPPTYPE_UINT32: return Rcpp::wrap(UInt32RepeatedFieldImporter(ref, *message, fieldDesc)); #ifdef RCPP_HAS_LONG_LONG_TYPES // We can't handle these the same way, because Rcpp::wrap silently // casts int64s to doubles which may cause us to lose precision. case CPPTYPE_INT64: if (UseStringsForInt64()) { return Rcpp::wrap(Int64AsStringRepeatedFieldImporter(ref, *message, fieldDesc)); } else { return Rcpp::wrap(RepeatedFieldImporter(ref, *message, fieldDesc)); } case CPPTYPE_UINT64: if (UseStringsForInt64()) { return Rcpp::wrap( UInt64AsStringRepeatedFieldImporter(ref, *message, fieldDesc)); } else { return Rcpp::wrap(RepeatedFieldImporter(ref, *message, fieldDesc)); } #endif #undef HANDLE_REPEATED_FIELD case CPPTYPE_STRING: if (fieldDesc->type() == TYPE_STRING) { return Rcpp::wrap(RepeatedFieldImporter(ref, *message, fieldDesc)); } else if (fieldDesc->type() == TYPE_BYTES) { int field_size = ref->FieldSize(*message, fieldDesc); Rcpp::List res(field_size); for (int i = 0; i < field_size; i++) { std::string s = ref->GetRepeatedString(*message, fieldDesc, i); res[i] = Rcpp::wrap(std::vector(s.begin(), s.end())); } return res; } else { Rcpp::stop("unknown field type with CPP_TYPE STRING"); } default: Rcpp::stop("Unsupported type"); } } else { switch (GPB::FieldDescriptor::TypeToCppType(fieldDesc->type())) { #undef HANDLE_SINGLE_FIELD #define HANDLE_SINGLE_FIELD(CPPTYPE, SUFFIX) \ case CPPTYPE: \ return Rcpp::wrap(ref->Get##SUFFIX(*message, fieldDesc)); HANDLE_SINGLE_FIELD(CPPTYPE_INT32, Int32) HANDLE_SINGLE_FIELD(CPPTYPE_DOUBLE, Double) HANDLE_SINGLE_FIELD(CPPTYPE_FLOAT, Float) HANDLE_SINGLE_FIELD(CPPTYPE_BOOL, Bool) // TODO(mstokely): Rcpp doesn't handle uint32 properly as of 2013/12 // See // https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1360&group_id=155&atid=637 case CPPTYPE_UINT32: return Rcpp::wrap(double(ref->GetUInt32(*message, fieldDesc))); #ifdef RCPP_HAS_LONG_LONG_TYPES // Handle these types separately since Rcpp::wrap doesn't // do the right thing. case CPPTYPE_INT64: return Int64AsSEXP(ref->GetInt64(*message, fieldDesc)); case CPPTYPE_UINT64: return Int64AsSEXP(ref->GetUInt64(*message, fieldDesc)); #endif #undef HANDLE_SINGLE_FIELD case CPPTYPE_STRING: if (fieldDesc->type() == TYPE_STRING) { return Rcpp::wrap(ref->GetString(*message, fieldDesc)); } else if (fieldDesc->type() == TYPE_BYTES) { std::string s = ref->GetString(*message, fieldDesc); return Rcpp::wrap(std::vector(s.begin(), s.end())); } else { Rcpp::stop("unknown field type with CPP_TYPE STRING"); } case CPPTYPE_ENUM: return Rcpp::wrap(ref->GetEnum(*message, fieldDesc)->number()); case CPPTYPE_MESSAGE: return S4_Message(CLONE(&ref->GetMessage(*message, fieldDesc))); default: Rcpp::stop("Unsupported type"); } } END_RCPP } } // namespace rprotobuf RProtoBuf/src/Rcppsupport.h0000644000175100001440000001465313037407202015462 0ustar hornikusers// rprotobuf.h: support for using Rcpp // // Copyright (C) 2010 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #ifndef RPROTOBUF__RCPPSUPPORT__H #define RPROTOBUF__RCPPSUPPORT__H #include /* for stringstream, basic_ostream */ #include /* for string */ #include "rprotobuf.h" namespace rprotobuf { /* support for Rcpp::wrap protobuf repeated fields, this essentially uses the same macro trick as in protobuf, but reversed */ struct enum_field{}; struct message_field{}; class Int64AsStringRepeatedFieldImporter { public: // Probably want to convert to strings here. typedef std::string r_import_type; Int64AsStringRepeatedFieldImporter(const GPB::Reflection* ref_ , const GPB::Message& message_, const GPB::FieldDescriptor* field_) : ref(ref_), message(message_), field(field_) {} inline int size() const { return ref->FieldSize(message, field); } inline std::string get(int i) const { std::stringstream stream; int64 val = ref->GetRepeatedInt64(message, field, i); stream << val; return stream.str(); } private: const GPB::Reflection* ref; const GPB::Message& message; const GPB::FieldDescriptor* field; }; class UInt64AsStringRepeatedFieldImporter { public: // Probably want to convert to strings here. typedef std::string r_import_type; UInt64AsStringRepeatedFieldImporter(const GPB::Reflection* ref_, const GPB::Message& message_, const GPB::FieldDescriptor* field_) : ref(ref_), message(message_), field(field_) {} inline int size() const { return ref->FieldSize(message, field) ; } inline std::string get(int i) const { std::stringstream stream; uint64 val = ref->GetRepeatedUInt64(message, field, i); stream << val; return stream.str(); } private: const GPB::Reflection* ref; const GPB::Message& message; const GPB::FieldDescriptor* field; }; // TODO(mstokely): Rcpp doesn't handle uint32 properly as of 2013/12 // See https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1360&group_id=155&atid=637 class UInt32RepeatedFieldImporter { public: // Represent as doubles, since R doesn't have uint32s. typedef double r_import_type; UInt32RepeatedFieldImporter(const GPB::Reflection* ref_ , const GPB::Message& message_, const GPB::FieldDescriptor* field_) : ref(ref_), message(message_), field(field_) {} inline int size() const { return ref->FieldSize(message, field); } inline double get(int i) const { return double(ref->GetRepeatedUInt32(message, field, i)); } private: const GPB::Reflection* ref; const GPB::Message& message; const GPB::FieldDescriptor* field; }; template class RepeatedFieldImporter{} ; #undef GENERATE__FIELD__IMPORTER__DECL #define GENERATE__FIELD__IMPORTER__DECL(__TYPE__, __CAMEL__) \ template<> class RepeatedFieldImporter<__TYPE__> { \ public: \ typedef __TYPE__ r_import_type; \ RepeatedFieldImporter( \ const GPB::Reflection* ref_, \ const GPB::Message& message_, \ const GPB::FieldDescriptor* field_): \ ref(ref_), message(message_), field(field_) {} \ inline int size() const { \ return ref->FieldSize( message, field ); \ } \ inline __TYPE__ get(int i) const { \ return ref->GetRepeated##__CAMEL__(message, field, i); \ } \ private: \ const GPB::Reflection* ref; \ const GPB::Message& message; \ const GPB::FieldDescriptor* field; \ }; GENERATE__FIELD__IMPORTER__DECL(GPB::int32, Int32) GENERATE__FIELD__IMPORTER__DECL(GPB::uint32, UInt32) GENERATE__FIELD__IMPORTER__DECL(GPB::int64, Int64) GENERATE__FIELD__IMPORTER__DECL(GPB::uint64, UInt64) GENERATE__FIELD__IMPORTER__DECL(float, Float) GENERATE__FIELD__IMPORTER__DECL(double, Double) GENERATE__FIELD__IMPORTER__DECL(bool, Bool) GENERATE__FIELD__IMPORTER__DECL(std::string, String) #undef GENERATE__FIELD__IMPORTER__DECL template<> class RepeatedFieldImporter{ public: typedef int r_import_type ; RepeatedFieldImporter( const GPB::Reflection* ref_, const GPB::Message& message_, const GPB::FieldDescriptor* field_): ref(ref_), message(message_), field(field_) {}; inline int size() const { return ref->FieldSize( message, field ); } inline int get(int i) const { return ref->GetRepeatedEnum(message, field, i)->number(); } private: const GPB::Reflection* ref; const GPB::Message& message; const GPB::FieldDescriptor* field; } ; template<> class RepeatedFieldImporter{ public: typedef message_field r_import_type ; RepeatedFieldImporter( const GPB::Reflection* ref_ , const GPB::Message& message_, const GPB::FieldDescriptor* field_): ref(ref_), message(message_), field(field_) {}; inline int size() const { return ref->FieldSize( message, field ); } inline SEXP wrap(int i) const { return S4_Message(CLONE(&ref->GetRepeatedMessage(message, field, i))); } private: const GPB::Reflection* ref; const GPB::Message& message; const GPB::FieldDescriptor* field; }; } // namespace rprotobuf #endif RProtoBuf/src/wrapper_ZeroCopyInputStream.cpp0000644000175100001440000000251213037407202021151 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" namespace rprotobuf { SEXP ZeroCopyInputStream_Next(SEXP xp) { BEGIN_RCPP GPB::io::ZeroCopyInputStream* stream = GET_ZCIS(xp); int s = 0; const void* in; bool res = stream->Next(&in, &s); Rcpp::RawVector result; if (!res) { throw std::range_error("cannot read from stream"); } else { result.assign(reinterpret_cast(in), reinterpret_cast(in) + s); } return result; END_RCPP } SEXP ZeroCopyInputStream_BackUp(SEXP xp, SEXP size) { BEGIN_RCPP GPB::io::ZeroCopyInputStream* stream = GET_ZCIS(xp); int s = GET_int(size, 0); if (s <= 0) { Rf_error("can only BackUp with positive numbers"); } stream->BackUp(s); return R_NilValue; END_RCPP } SEXP ZeroCopyInputStream_Skip(SEXP xp, SEXP size) { BEGIN_RCPP GPB::io::ZeroCopyInputStream* stream = GET_ZCIS(xp); int s = GET_int(size, 0); bool res = stream->Skip(s); return (Rf_ScalarLogical(res ? _TRUE_ : _FALSE_)); END_RCPP } SEXP ZeroCopyInputStream_ByteCount(SEXP xp) { BEGIN_RCPP GPB::io::ZeroCopyInputStream* stream = GET_ZCIS(xp); return (Rf_ScalarReal((double)stream->ByteCount())); END_RCPP } } RProtoBuf/src/RWarningErrorCollector.cpp0000644000175100001440000000073013037407202020053 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RWarningErrorCollector.h" namespace rprotobuf { void RWarningErrorCollector::AddError(const std::string& filename, int line, int column, const std::string& message) { Rprintf("%s:%d:%d:%s\n", filename.c_str(), line + 1, column + 1, message.c_str()); } } // namespace rprotobuf RProtoBuf/src/wrapper_EnumDescriptor.cpp0000644000175100001440000001043313037407202020147 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- // wrapper_EnumDescriptor.cpp: R/C++ interface class library // // Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(EnumDescriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(as_character), GPB::EnumDescriptor, DebugString) RPB_XP_METHOD_0(METHOD(length), GPB::EnumDescriptor, value_count) RPB_XP_METHOD_0(METHOD(value_count), GPB::EnumDescriptor, value_count) RPB_FUNCTION_1(S4_Descriptor, METHOD(containing_type), Rcpp::XPtr d) { return S4_Descriptor(d->containing_type()); } RPB_FUNCTION_2(SEXP, METHOD(getValueByIndex), Rcpp::XPtr d, int index) { if ((index >= 0) && (index < d->value_count())) { return S4_EnumValueDescriptor(d->value(index)); } else { return R_NilValue; } } RPB_FUNCTION_2(SEXP, METHOD(getValueByNumber), Rcpp::XPtr d, int i) { const GPB::EnumValueDescriptor* descriptor = d->FindValueByNumber(i); if (descriptor) return S4_EnumValueDescriptor(descriptor); return R_NilValue; } RPB_FUNCTION_2(SEXP, METHOD(getValueByName), Rcpp::XPtr d, std::string name) { const GPB::EnumValueDescriptor* descriptor = d->FindValueByName(name); if (descriptor) return S4_EnumValueDescriptor(descriptor); return R_NilValue; } RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::EnumDescriptorProto* message = new GPB::EnumDescriptorProto(); d->CopyTo(message); return S4_Message(message); } /** * Get the value of the enum called name * * @param xp external pointer to an EnumDescriptor * @param name the name of the enum * * @param the value associated with the name */ RPB_FUNCTION_2(int, get_value_of_enum, Rcpp::XPtr d, std::string name) { const GPB::EnumValueDescriptor* evd = d->FindValueByName(name); if (!evd) { /* or maybe it should just be NA */ Rcpp::stop("cannot get the value"); } return evd->number(); } /** * Does enum have value named 'name'? * * @param xp external pointer to an EnumDescriptor * @param name the name of the enum * @return logical */ RPB_FUNCTION_2(bool, has_enum_name, Rcpp::XPtr d, std::string name) { const GPB::EnumValueDescriptor* evd = d->FindValueByName(name); return (evd != NULL); } /** * @param xp external pointer to a Descriptor * @return the descriptor as an R list */ RPB_FUNCTION_1(Rcpp::List, METHOD(as_list), Rcpp::XPtr d) { int n = d->value_count(); Rcpp::CharacterVector names(n); Rcpp::List res(n); for (int i = 0; i < n; i++) { const GPB::EnumValueDescriptor* value_d = d->value(i); res[i] = value_d->number(); names[i] = value_d->name(); } res.names() = names; return res; } RPB_FUNCTION_1(Rcpp::CharacterVector, METHOD(getConstantNames), Rcpp::XPtr d) { int n = d->value_count(); Rcpp::CharacterVector res(n); for (int i = 0; i < n; i++) { res[i] = d->value(i)->name(); } return res; } RPB_FUNCTION_1(S4_FileDescriptor, METHOD(fileDescriptor), Rcpp::XPtr desc) { return S4_FileDescriptor(desc->file()); } RPB_FUNCTION_2(std::string, METHOD(name), Rcpp::XPtr d, bool full) { return full ? d->full_name() : d->name(); } #undef METHOD } // namespace rprotobuf RProtoBuf/src/rprotobuf.h0000644000175100001440000002225013037407202015133 0ustar hornikusers// rprotobuf.h: R/C++ interface class library // // Copyright (C) 2009-2012 Dirk Eddelbuettel and Romain Francois // Copyright (C) 2012-2013 Dirk Eddelbuettel, Romain Francois and Murray Stokely // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #ifndef RPROTOBUF_H #define RPROTOBUF_H // TODO(mstokely): should we check if this header is available? #include #include // for strerror #include // g++-4.7 wants this #include // for string // O_BINARY does not exist on Unix/Linux, since there is no distinction // between text mode and binary mode files there, but if we ever got // this code running on Windows this would be needed. #ifndef O_BINARY #define O_BINARY 0 #endif #include #include #include #include #include #include #include #include #include namespace GPB = google::protobuf; #define R_NO_REMAP /* we need to read and write to connections */ #define NEED_CONNECTION_PSTREAMS #include RCPP_ENUM_TRAITS(GPB::FieldDescriptor::Label) RCPP_ENUM_TRAITS(GPB::FieldDescriptor::CppType) RCPP_ENUM_TRAITS(GPB::FieldDescriptor::Type) // RCPP_TRAITS(GPB::int64,REALSXP) // RCPP_TRAITS(GPB::uint64,REALSXP) #include #include #include /* uncomment for debugging */ // #define RPB_DEBUG #ifdef RPB_DEBUG #define RPB_DEBUG_BEGIN(__WHAT__) Rprintf("<" #__WHAT__ ">\n"); #define RPB_DEBUG_END(__WHAT__) Rprintf("\n"); #else #define RPB_DEBUG_BEGIN(__WHAT__) #define RPB_DEBUG_END(__WHAT__) #endif // #define FIN_DBG(ptr, CLAZZ) // #define FIN_DBG(ptr, CLAZZ) Rprintf( "RProtoBuf finalizing %s (%p)\n", CLAZZ, // ptr ) #ifdef RPB_DEBUG #define PRINT_DEBUG_INFO(name, o) \ Rprintf(" %s [%d] = ", name, TYPEOF(o)); \ Rf_PrintValue(o); #else #define PRINT_DEBUG_INFO(name, o) #endif #define RPROTOBUF_LOOKUP 24 // #define LOOKUP_DEBUG /* FIXME : quick hack because just using TRUE and FALSE did not work in * lookup.cpp */ #define _TRUE_ (Rboolean) TRUE #define _FALSE_ (Rboolean) FALSE #define GET_MESSAGE_POINTER_FROM_XP(xp) (GPB::Message*) EXTPTR_PTR(xp) #define GET_MESSAGE_POINTER_FROM_S4(m) \ (GPB::Message*) EXTPTR_PTR(GET_SLOT(m, Rf_install("pointer"))) #define GET_DESCRIPTOR_POINTER_FROM_XP(xp) (GPB::Descriptor*) EXTPTR_PTR(xp) #define GET_DESCRIPTOR_POINTER_FROM_S4(m) \ (GPB::Descriptor*) EXTPTR_PTR(GET_SLOT(m, Rf_install("pointer"))) #define GET_FIELD_DESCRIPTOR_POINTER_FROM_XP(xp) (GPB::FieldDescriptor*) EXTPTR_PTR(xp) #define GET_FIELD_DESCRIPTOR_POINTER_FROM_S4(m) \ (GPB::FieldDescriptor*) EXTPTR_PTR(GET_SLOT(m, Rf_install("pointer"))) #define GET_ENUM_VALUE_DESCRIPTOR_POINTER_FROM_XP(xp) (GPB::EnumValueDescriptor*) EXTPTR_PTR(xp) #define GET_ENUM_VALUE_DESCRIPTOR_POINTER_FROM_S4(m) \ (GPB::EnumValueDescriptor*) EXTPTR_PTR(GET_SLOT(m, Rf_install("pointer"))) #define COPYSTRING(s) s #define THROW_SOCKET_ERROR(message) Rf_error("%s : %s", message, strerror(sockerrno)) #define XPP EXTPTR_PTR #define NEW_S4_OBJECT(CLAZZ) \ SEXP oo = PROTECT(NEW_OBJECT(MAKE_CLASS(CLAZZ))); \ if (!Rf_inherits(oo, CLAZZ)) Rcpp::stop(CLAZZ); namespace rprotobuf { typedef GPB::int32 int32; typedef GPB::uint32 uint32; typedef GPB::int64 int64; typedef GPB::uint64 uint64; /* in rprotobuf.cpp */ GPB::Message* PROTOTYPE(const GPB::Descriptor*); GPB::Message* CLONE(const GPB::Message*); RcppExport SEXP do_dollar_Descriptor(SEXP, SEXP); RcppExport SEXP newProtoMessage(SEXP); RcppExport SEXP getProtobufDescriptor(SEXP); RcppExport SEXP getExtensionDescriptor(SEXP); RcppExport SEXP readProtoFiles(SEXP, SEXP); RcppExport Rboolean isMessage(SEXP, const char*); RcppExport GPB::FieldDescriptor* getFieldDescriptor(const GPB::Message*, SEXP); /* in extractors.cpp */ RcppExport SEXP getMessageField(SEXP, SEXP); RcppExport SEXP extractFieldAsSEXP(const Rcpp::XPtr&, const GPB::FieldDescriptor*); /* in lookup.cpp */ RcppExport SEXP newProtocolBufferLookup(SEXP); /* in mutators.cpp */ RcppExport SEXP setMessageField(SEXP, SEXP, SEXP); int GET_int(SEXP, int); double GET_double(SEXP, int); float GET_float(SEXP, int); int32 GET_int32(SEXP, R_xlen_t); int64 GET_int64(SEXP, R_xlen_t); uint32 GET_uint32(SEXP, R_xlen_t); uint64 GET_uint64(SEXP, R_xlen_t); bool GET_bool(SEXP, R_xlen_t); std::string GET_stdstring(SEXP, R_xlen_t); std::string GET_bytes(SEXP, R_xlen_t); void CHECK_values_for_enum(const GPB::FieldDescriptor*, SEXP); void CHECK_messages(const GPB::FieldDescriptor*, SEXP); /* in wrapper_ServiceDescriptor.cpp */ RcppExport SEXP ServiceDescriptor_length(SEXP); RcppExport SEXP ServiceDescriptor_method_count(SEXP); RcppExport SEXP ServiceDescriptor_getMethodByIndex(SEXP, SEXP); RcppExport SEXP ServiceDescriptor_getMethodByName(SEXP, SEXP); /* in streams.cpp */ void ZeroCopyInputStreamWrapper_finalizer(SEXP); void ZeroCopyOutputStreamWrapper_finalizer(SEXP); RcppExport SEXP ZeroCopyInputStream_Next(SEXP); RcppExport SEXP ZeroCopyInputStream_BackUp(SEXP, SEXP); RcppExport SEXP ZeroCopyInputStream_ByteCount(SEXP); RcppExport SEXP ZeroCopyInputStream_Skip(SEXP, SEXP); RcppExport SEXP ZeroCopyInputStream_ReadRaw(SEXP, SEXP); RcppExport SEXP ZeroCopyInputStream_ReadString(SEXP, SEXP); RcppExport SEXP ZeroCopyInputStream_ReadVarint32(SEXP); RcppExport SEXP ZeroCopyInputStream_ReadVarint64(SEXP); RcppExport SEXP ZeroCopyInputStream_ReadLittleEndian32(SEXP); RcppExport SEXP ZeroCopyInputStream_ReadLittleEndian64(SEXP); RcppExport SEXP ZeroCopyOutputStream_Next(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_BackUp(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_ByteCount(SEXP); RcppExport SEXP ZeroCopyOutputStream_WriteRaw(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_WriteString(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_WriteLittleEndian32(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_WriteLittleEndian64(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_WriteVarint32(SEXP, SEXP); RcppExport SEXP ZeroCopyOutputStream_WriteVarint64(SEXP, SEXP); RcppExport SEXP FileOutputStream_new(SEXP, SEXP, SEXP); RcppExport SEXP FileOutputStream_Close(SEXP); RcppExport SEXP FileOutputStream_Flush(SEXP); RcppExport SEXP FileOutputStream_GetErrno(SEXP); RcppExport SEXP FileOutputStream_SetCloseOnDelete(SEXP, SEXP); RcppExport SEXP FileInputStream_new(SEXP, SEXP, SEXP); RcppExport SEXP FileInputStream_Close(SEXP); RcppExport SEXP FileInputStream_GetErrno(SEXP); RcppExport SEXP FileInputStream_SetCloseOnDelete(SEXP, SEXP); RcppExport SEXP ConnectionInputStream_new(SEXP, SEXP); RcppExport SEXP ConnectionOutputStream_new(SEXP, SEXP); /** * simple class that wraps together a ZeroCopyOutputStream * and its associated CodedOutputStream. Since we don't expose * CodedOutputStream at the R level, this allows to keep only one such * object with each ZeroCopyOutputStream */ class ZeroCopyOutputStreamWrapper { public: ZeroCopyOutputStreamWrapper(GPB::io::ZeroCopyOutputStream* stream); ~ZeroCopyOutputStreamWrapper(); GPB::io::ZeroCopyOutputStream* get_stream(); GPB::io::CodedOutputStream* get_coded_stream(); private: GPB::io::ZeroCopyOutputStream* stream; GPB::io::CodedOutputStream* coded_stream; }; /** * simple class that wraps together a ZeroCopyInputStream * and its associated CodedInputStream. Since we don't expose * CodedInputStream at the R level, this allows to keep only one such * object with each zero copy input stream */ class ZeroCopyInputStreamWrapper { public: ZeroCopyInputStreamWrapper(GPB::io::ZeroCopyInputStream* stream); ~ZeroCopyInputStreamWrapper(); GPB::io::ZeroCopyInputStream* get_stream(); GPB::io::CodedInputStream* get_coded_stream(); private: GPB::io::ZeroCopyInputStream* stream; GPB::io::CodedInputStream* coded_stream; }; } // namespace rprotobuf #include "S4_classes.h" #include "RconnectionCopyingInputStream.h" #define GET_ZCIS(xp) ((ZeroCopyInputStreamWrapper*)XPP(xp))->get_stream() #define GET_CIS(xp) ((ZeroCopyInputStreamWrapper*)XPP(xp))->get_coded_stream() #define GET_FIS(xp) (GPB::io::FileInputStream*)((ZeroCopyInputStreamWrapper*)XPP(xp))->get_stream() #define GET_ZCOS(xp) ((ZeroCopyOutputStreamWrapper*)XPP(xp))->get_stream() #define GET_COS(xp) ((ZeroCopyOutputStreamWrapper*)XPP(xp))->get_coded_stream() #define GET_FOS(xp) \ (GPB::io::FileOutputStream*)((ZeroCopyOutputStreamWrapper*)XPP(xp))->get_stream() #endif RProtoBuf/src/S4_classes.h0000644000175100001440000001701113037407202015113 0ustar hornikusers// S4_classes.h: R/C++ interface class library // // Copyright (C) 2010 - 2014 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #ifndef RPROTOBUF_S4CLASSES_H #define RPROTOBUF_S4CLASSES_H //1. Place using Rcpp::S4; somewhere in the top of S4_classes.h in the //src directory (so S4 is looked up in the right place), //2. Replace setSEXP with set__, and asSexp with get__. namespace rprotobuf { // deal with Rcpp API changes #if defined(RCPP_VERSION) && RCPP_VERSION <= Rcpp_Version(0,10,6) #define SetSexp setSEXP #define AsSexp asSexp #else #define SetSexp set__ #define AsSexp get__ #endif using Rcpp::S4; class ZeroCopyInputStreamWrapper; class ZeroCopyOutputStreamWrapper; class S4_EnumValueDescriptor : public Rcpp::S4 { public: S4_EnumValueDescriptor(const GPB::EnumValueDescriptor* d) : S4("EnumValueDescriptor") { slot("pointer") = Rcpp::XPtr( const_cast(d), false); if (d) { slot("name") = d->name(); slot("full_name") = d->full_name(); } else { slot("name") = Rcpp::StringVector(0); slot("full_name") = Rcpp::StringVector(0); } } S4_EnumValueDescriptor(const S4_EnumValueDescriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_EnumValueDescriptor& operator=(const S4_EnumValueDescriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_Descriptor : public Rcpp::S4 { public: S4_Descriptor(const GPB::Descriptor* d) : S4("Descriptor") { slot("pointer") = Rcpp::XPtr(const_cast(d), false); if (!d) { slot("type") = Rcpp::StringVector(0); } else { slot("type") = d->full_name(); } } S4_Descriptor(const S4_Descriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_Descriptor& operator=(const S4_Descriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_FileDescriptor : public Rcpp::S4 { public: S4_FileDescriptor(const GPB::FileDescriptor* d) : S4("FileDescriptor") { slot("pointer") = Rcpp::XPtr(const_cast(d), false); if (!d) { slot("package") = Rcpp::StringVector(0); slot("filename") = Rcpp::StringVector(0); } else { slot("package") = d->package(); slot("filename") = d->name(); } } S4_FileDescriptor(const S4_FileDescriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_FileDescriptor& operator=(const S4_FileDescriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_FieldDescriptor : public Rcpp::S4 { public: S4_FieldDescriptor(const GPB::FieldDescriptor* d) : S4("FieldDescriptor") { slot("pointer") = Rcpp::XPtr(const_cast(d), false); slot("name") = d->name(); slot("full_name") = d->full_name(); slot("type") = d->containing_type()->full_name(); } S4_FieldDescriptor(const S4_FieldDescriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_FieldDescriptor& operator=(const S4_FieldDescriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_ServiceDescriptor : public Rcpp::S4 { public: S4_ServiceDescriptor(const GPB::ServiceDescriptor* d) : S4("ServiceDescriptor") { slot("pointer") = Rcpp::XPtr(const_cast(d), false); } S4_ServiceDescriptor(const S4_ServiceDescriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_ServiceDescriptor& operator=(const S4_ServiceDescriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_MethodDescriptor : public Rcpp::S4 { public: S4_MethodDescriptor(const GPB::MethodDescriptor* d) : S4("MethodDescriptor") { slot("pointer") = Rcpp::XPtr(const_cast(d), false); } S4_MethodDescriptor(const S4_MethodDescriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_MethodDescriptor& operator=(const S4_MethodDescriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_EnumDescriptor : public Rcpp::S4 { public: S4_EnumDescriptor(const GPB::EnumDescriptor* d) : S4("EnumDescriptor") { slot("pointer") = Rcpp::XPtr(const_cast(d), false); slot("type") = Rcpp::StringVector(0); if (d) { slot("name") = d->name(); slot("full_name") = d->full_name(); const GPB::Descriptor* type_desc = d->containing_type(); if (type_desc) { slot("type") = type_desc->full_name(); } } else { slot("name") = Rcpp::StringVector(0); slot("full_name") = Rcpp::StringVector(0); } } S4_EnumDescriptor(const S4_EnumDescriptor& other) : S4() { SetSexp(other.AsSexp()); } S4_EnumDescriptor& operator=(const S4_EnumDescriptor& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_Message : public Rcpp::S4 { public: S4_Message(const GPB::Message* d) : S4("Message") { slot("pointer") = Rcpp::XPtr(const_cast(d), true); slot("type") = d->GetDescriptor()->full_name(); } S4_Message(const S4_Message& other) : S4() { SetSexp(other.AsSexp()); } S4_Message& operator=(const S4_Message& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_ArrayOutputStream : public Rcpp::S4 { public: S4_ArrayOutputStream(int size, int block_size) : S4("ArrayOutputStream") { Rcpp::RawVector payload(size); GPB::io::ArrayOutputStream* stream = new GPB::io::ArrayOutputStream(payload.begin(), size, block_size); Rcpp::XPtr wrapper(new ZeroCopyOutputStreamWrapper(stream), true, R_NilValue, payload); slot("pointer") = wrapper; } S4_ArrayOutputStream(const S4_ArrayOutputStream& other) { SetSexp(other.AsSexp()); } S4_ArrayOutputStream& operator=(const S4_ArrayOutputStream& other) { SetSexp(other.AsSexp()); return *this; } }; class S4_ArrayInputStream : public Rcpp::S4 { public: S4_ArrayInputStream(Rcpp::RawVector payload, int block_size) : S4("ArrayInputStream") { GPB::io::ArrayInputStream* stream = new GPB::io::ArrayInputStream(payload.begin(), payload.size(), block_size); Rcpp::XPtr wrapper( new ZeroCopyInputStreamWrapper(stream), true, R_NilValue, payload); slot("pointer") = wrapper; } }; #undef SetSexp #undef AsSexp } // namespace rprotobuf #endif RProtoBuf/src/RconnectionCopyingInputStream.cpp0000644000175100001440000000217213037407202021453 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RconnectionCopyingInputStream.h" namespace rprotobuf { /* N.B. connection must be opened in binary mode due to call * to readBin below. */ RconnectionCopyingInputStream::RconnectionCopyingInputStream(int id) : connection_id(id), failure(false) {} /** * call readBin to read size bytes from R * * @param buffer buffer to fill with at most size bytes * @param size maximum number of bytes * * @return the number of bytes actually read */ int RconnectionCopyingInputStream::Read(void* buffer, int size) { Rcpp::Language call("readBin", connection_id, Rcpp::RawVector(0), size); Rcpp::RawVector res; try { res = call.eval(); } catch (...) { /* Failed to read anything from the connection, * could have been permissions, or connection opened * in the wrong type, etc. */ failure = true; return -1; } int len = res.size(); memcpy(buffer, reinterpret_cast(res.begin()), len); return len; } } RProtoBuf/src/rprotobuf.cpp0000644000175100001440000002030613037407202015466 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "DescriptorPoolLookup.h" #include "RcppMacros.h" namespace rprotobuf { GPB::Message* PROTOTYPE(const GPB::Descriptor* desc) { RPB_DEBUG_BEGIN("PROTOTYPE") #ifdef RPB_DEBUG Rprintf("desc = %d\n", desc); #endif /* first try the runtime factory */ GPB::Message* m = (GPB::Message*)((GPB::DynamicMessageFactory*)DescriptorPoolLookup::factory()) ->GetPrototype(desc) ->New(); #ifdef RPB_DEBUG Rprintf("generated factory = %d\n", m); #endif if (!m) { /* then the dynamic runtime factory */ m = (GPB::Message*)GPB::MessageFactory::generated_factory()->GetPrototype(desc)->New(); #ifdef RPB_DEBUG Rprintf("runtime factory = %d\n", m); #endif } RPB_DEBUG_END("PROTOTYPE") return m; } GPB::Message* CLONE(const GPB::Message* origin) { RPB_DEBUG_BEGIN("CLONE") const GPB::Descriptor* desc = origin->GetDescriptor(); GPB::Message* sheep = PROTOTYPE(desc); sheep->CopyFrom(*origin); RPB_DEBUG_END("CLONE") return sheep; } /** * read a proto file and cache the message definitions it contains * * @param file proto file name */ RcppExport SEXP readProtoFiles(SEXP file, SEXP dirs) { BEGIN_RCPP DescriptorPoolLookup::importProtoFiles(file, dirs); return R_NilValue; END_RCPP } /** * get the descriptor associated with a message type * * @param type message type * * @return an S4 object of class Descriptor, or NULL if the type * is unknown */ RcppExport SEXP getProtobufDescriptor(SEXP type) { #ifdef RPB_DEBUG Rprintf("\n type = "); Rf_PrintValue(type); #endif const char* typeName = CHAR(STRING_ELT(type, 0)); /* first try the generated pool */ const GPB::DescriptorPool* pool = GPB::DescriptorPool::generated_pool(); const GPB::Descriptor* desc = pool->FindMessageTypeByName(typeName); if (!desc) { /* then try the "runtime" pool" */ pool = DescriptorPoolLookup::pool(); desc = pool->FindMessageTypeByName(typeName); if (!desc) { /* unlucky */ return R_NilValue; } } return (S4_Descriptor(desc)); } /** * get the descriptor associated with an extension * * @param type message type * * @return an S4 object of class FieldDescriptor, or NULL if the type * is unknown */ RcppExport SEXP getExtensionDescriptor(SEXP type) { #ifdef RPB_DEBUG Rprintf("\n type = "); Rf_PrintValue(type); #endif const char* typeName = CHAR(STRING_ELT(type, 0)); /* first try the generated pool */ const GPB::DescriptorPool* pool = GPB::DescriptorPool::generated_pool(); const GPB::FieldDescriptor* desc = pool->FindExtensionByName(typeName); if (!desc) { /* then try the "runtime" pool" */ pool = DescriptorPoolLookup::pool(); desc = pool->FindExtensionByName(typeName); if (!desc) { /* unlucky */ return R_NilValue; } } return (S4_FieldDescriptor(desc)); } /** * get the descriptor associated with an enum * * @param type message type * * @return an S4 object of class EnumDescriptor, or NULL if the type * is unknown */ RcppExport SEXP getEnumDescriptor(SEXP type) { #ifdef RPB_DEBUG Rprintf("\n type = "); Rf_PrintValue(type); #endif const char* typeName = CHAR(STRING_ELT(type, 0)); /* first try the generated pool */ const GPB::DescriptorPool* pool = GPB::DescriptorPool::generated_pool(); const GPB::EnumDescriptor* desc = pool->FindEnumTypeByName(typeName); if (!desc) { /* then try the "runtime" pool" */ pool = DescriptorPoolLookup::pool(); desc = pool->FindEnumTypeByName(typeName); if (!desc) { /* unlucky */ return R_NilValue; } } return (S4_EnumDescriptor(desc)); } /** * make a new protobuf message * * @param descriptor a "Descriptor" R object */ SEXP newProtoMessage(SEXP descriptor) { BEGIN_RCPP RPB_DEBUG_BEGIN("newProtoMessage") #ifdef RPB_DEBUG /* FIXME: the message type, we don't really need that*/ SEXP type = GET_SLOT(descriptor, Rf_install("type")); #endif /* the pointer to the c++ descriptor object */ GPB::Descriptor* desc = GET_DESCRIPTOR_POINTER_FROM_S4(descriptor); #ifdef RPB_DEBUG Rprintf("desc = %d\n", desc); PRINT_DEBUG_INFO("type", type); #endif /* grab the Message from the factory */ const GPB::Message* message = PROTOTYPE(desc); if (!message) { Rcpp_error("could not call factory->GetPrototype(desc)->New()"); } RPB_DEBUG_END("newProtoMessage") return (S4_Message(message)); END_RCPP } /** * dollar extractor for Descriptor objects * it may return a Field descriptor or a nested type descriptor * * @param pointer external pointer to a google::protobuf::Descriptor object * @param name name of the thing to extract */ RcppExport SEXP do_dollar_Descriptor(SEXP pointer, SEXP name) { const char* what = CHAR(STRING_ELT(name, 0)); GPB::Descriptor* desc = (GPB::Descriptor*)EXTPTR_PTR(pointer); // trying fields first : if (desc->field_count()) { const GPB::FieldDescriptor* fd = desc->FindFieldByName(what); if (fd) { return (S4_FieldDescriptor(fd)); } } // now trying nested types if (desc->nested_type_count()) { const GPB::Descriptor* d = desc->FindNestedTypeByName(what); if (d) { return (S4_Descriptor(d)); } } // now for enum types if (desc->enum_type_count()) { const GPB::EnumDescriptor* ed = desc->FindEnumTypeByName(what); if (ed) { return (S4_EnumDescriptor(ed)); } } // TODO: extensions (later) // give up // TODO: should this be unbound instead return (R_NilValue); } /** * * @param m potentially a message * @param target the expected type * * @return TRUE if m is a a message of the given type */ Rboolean isMessage(SEXP m, const char* target) { RPB_DEBUG_BEGIN("isMessage") if (TYPEOF(m) != S4SXP || !Rf_inherits(m, "Message")) return _FALSE_; GPB::Message* message = (GPB::Message*)EXTPTR_PTR(GET_SLOT(m, Rf_install("pointer"))); const char* type = message->GetDescriptor()->full_name().c_str(); RPB_DEBUG_END("isMessage") if (strcmp(type, target)) { return _FALSE_; } return _TRUE_; } RcppExport GPB::FieldDescriptor* getFieldDescriptor(const GPB::Message* message, SEXP name) { GPB::FieldDescriptor* field_desc = (GPB::FieldDescriptor*)0; BEGIN_RCPP const GPB::Descriptor* desc = message->GetDescriptor(); std::string error_message = "could not get FieldDescriptor for field"; switch (TYPEOF(name)) { case S4SXP: { if (Rf_inherits(name, "FieldDescriptor")) { field_desc = GET_FIELD_DESCRIPTOR_POINTER_FROM_S4(name); } else { Rcpp::stop("S4 class is not a FieldDescriptor"); } break; } case CHARSXP: { field_desc = (GPB::FieldDescriptor*)desc->FindFieldByName(CHAR(name)); error_message = error_message + " '" + CHAR(name) + "'"; break; } case STRSXP: { field_desc = (GPB::FieldDescriptor*)desc->FindFieldByName(CHAR(STRING_ELT(name, 0))); error_message = error_message + " '" + CHAR(STRING_ELT(name, 0)) + "'"; break; } case REALSXP: case INTSXP: { field_desc = (GPB::FieldDescriptor*)desc->FindFieldByNumber(Rcpp::as(name)); break; } } if (!field_desc) { Rcpp::stop(error_message.c_str()); } return field_desc; VOID_END_RCPP return field_desc; } RPB_FUNCTION_VOID_1(check_libprotobuf_version, int minversion) { if (GOOGLE_PROTOBUF_VERSION < minversion) { throw std::range_error( "The protobuf library you are using is too old for this package, " "please upgrade"); } } RPB_FUNCTION_0(int, get_protobuf_library_version) { return GOOGLE_PROTOBUF_VERSION; } } // namespace rprotobuf RProtoBuf/src/RcppMacros.h0000644000175100001440000001642613037407202015172 0ustar hornikusers/* * Copyright 2013 Google Inc. All Rights Reserved. * Author: Murray Stokely * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License as * published by the Free Software Foundation; either version 2 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA * 02110-1301, USA. * */ /* * This file contains macros for taking C++ functions that expect * native C++ types, automatically generating new stub functions that * take SEXPs and call the appropriate Rcpp conversion functions * before calling the original function. It is based on slightly more * complex macros that were originally in Rcpp but have been * deprecated. * * In the future, Rcpp Modules would likely be a better more modern * way to implement RProtoBuf. */ #ifndef RPROTOBUF_RCPP_MACROS_H #define RPROTOBUF_RCPP_MACROS_H #include // RCPP_DECORATE, BEGIN_RCPP, END_RCPP #define RPB_FUNCTION_0(__OUT__,__NAME__) \ __OUT__ RCPP_DECORATE(__NAME__)(); \ extern "C" SEXP __NAME__(){ \ SEXP res = R_NilValue ; \ BEGIN_RCPP \ res = ::Rcpp::wrap( RCPP_DECORATE(__NAME__)() ) ; \ return res ; \ END_RCPP \ } \ __OUT__ RCPP_DECORATE(__NAME__)() #define RPB_FUNCTION_1(__OUT__,__NAME__, ___0) \ __OUT__ RCPP_DECORATE(__NAME__)(___0); \ extern "C" SEXP __NAME__(SEXP x0){ \ SEXP res = R_NilValue ; \ BEGIN_RCPP \ res = ::Rcpp::wrap( RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 )) ) ; \ return res ; \ END_RCPP \ } \ __OUT__ RCPP_DECORATE(__NAME__)(___0) #define RPB_FUNCTION_2(__OUT__,__NAME__, ___0, ___1) \ __OUT__ RCPP_DECORATE(__NAME__)(___0, ___1); \ extern "C" SEXP __NAME__(SEXP x0, SEXP x1){ \ SEXP res = R_NilValue ; \ BEGIN_RCPP \ res = ::Rcpp::wrap( RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 ), ::Rcpp::internal::converter( x1 )) ) ; \ return res ; \ END_RCPP \ } \ __OUT__ RCPP_DECORATE(__NAME__)(___0, ___1) #define RPB_FUNCTION_3(__OUT__,__NAME__, ___0, ___1, ___2) \ __OUT__ RCPP_DECORATE(__NAME__)(___0, ___1, ___2); \ extern "C" SEXP __NAME__(SEXP x0, SEXP x1, SEXP x2){ \ SEXP res = R_NilValue ; \ BEGIN_RCPP \ res = ::Rcpp::wrap( RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 ), ::Rcpp::internal::converter( x1 ), ::Rcpp::internal::converter( x2 )) ) ; \ return res ; \ END_RCPP \ } \ __OUT__ RCPP_DECORATE(__NAME__)(___0, ___1, ___2) #define RPB_FUNCTION_VOID_1(__NAME__, ___0) \ void RCPP_DECORATE(__NAME__)(___0); \ extern "C" SEXP __NAME__(SEXP x0){ \ BEGIN_RCPP \ RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 )); \ END_RCPP \ } \ void RCPP_DECORATE(__NAME__)(___0) #define RPB_FUNCTION_VOID_2(__NAME__, ___0, ___1) \ void RCPP_DECORATE(__NAME__)(___0, ___1); \ extern "C" SEXP __NAME__(SEXP x0, SEXP x1){ \ BEGIN_RCPP \ RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 ), ::Rcpp::internal::converter( x1 )); \ END_RCPP \ } \ void RCPP_DECORATE(__NAME__)(___0, ___1) #define RPB_FUNCTION_VOID_3(__NAME__, ___0, ___1, ___2) \ void RCPP_DECORATE(__NAME__)(___0, ___1, ___2); \ extern "C" SEXP __NAME__(SEXP x0, SEXP x1, SEXP x2){ \ BEGIN_RCPP \ RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 ), ::Rcpp::internal::converter( x1 ), ::Rcpp::internal::converter( x2 )); \ END_RCPP \ } \ void RCPP_DECORATE(__NAME__)(___0, ___1, ___2) #define RPB_FUNCTION_VOID_4(__NAME__, ___0, ___1, ___2, ___3) \ void RCPP_DECORATE(__NAME__)(___0, ___1, ___2, ___3); \ extern "C" SEXP __NAME__(SEXP x0, SEXP x1, SEXP x2, SEXP x3){ \ BEGIN_RCPP \ RCPP_DECORATE(__NAME__)(::Rcpp::internal::converter( x0 ), ::Rcpp::internal::converter( x1 ), ::Rcpp::internal::converter( x2 ), ::Rcpp::internal::converter( x3 )); \ END_RCPP \ } \ void RCPP_DECORATE(__NAME__)(___0, ___1, ___2, ___3) #define RPB_XP_METHOD_0(__NAME__,__CLASS__,__METHOD__ ) \ extern "C" SEXP __NAME__( SEXP xp ){ \ BEGIN_RCPP \ ::Rcpp::XPtr< __CLASS__ > ptr(xp) ; \ return ::Rcpp::wrap( ptr->__METHOD__( ) ) ; \ END_RCPP \ } #define RPB_XP_METHOD_VOID_0(__NAME__,__CLASS__,__METHOD__) \ extern "C" SEXP __NAME__( SEXP xp ){ \ BEGIN_RCPP \ ::Rcpp::XPtr< __CLASS__ > ptr(xp) ; \ ptr->__METHOD__( ) ; \ END_RCPP \ } #define RPB_XP_METHOD_CAST_0(__NAME__,__CLASS__,__METHOD__,__CAST__) \ extern "C" SEXP __NAME__( SEXP xp ){ \ BEGIN_RCPP \ ::Rcpp::XPtr< __CLASS__ > ptr(xp) ; \ return ::Rcpp::wrap( __CAST__( ptr->__METHOD__( ) ) ) ; \ END_RCPP \ } #define RPB_XP_METHOD_CAST_1(__NAME__,__CLASS__,__METHOD__,__CAST__) \ extern "C" SEXP __NAME__( SEXP xp , SEXP x0 ){ \ BEGIN_RCPP \ ::Rcpp::XPtr< __CLASS__ > ptr(xp) ; \ return ::Rcpp::wrap( __CAST__( ptr->__METHOD__( ::Rcpp::internal::converter( x0 ) ) ) ) ; \ END_RCPP \ } #endif RProtoBuf/src/ConnectionCopyingInputStream.h0000644000175100001440000000122213037407202020731 0ustar hornikusers#ifndef RPROTOBUF_ConnectionCopyingInputStream_H #define RPROTOBUF_ConnectionCopyingInputStream_H namespace rprotobuf { class ConnectionCopyingInputStream : public GPB::io::CopyingInputStream { public: ConnectionCopyingInputStream(SEXP con); int Read(void* buffer, int size); private: /* the actual connection object from R it is protected by the external pointer that wraps the ConnectionInputStream, which is the only thing that uses this class, so we don't need to take care of GC here */ SEXP con; Rcpp::Function readBin; }; } // namespace rprotobuf #endif RProtoBuf/src/wrapper_FileDescriptor.cpp0000644000175100001440000000532713037407202020130 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(FileDescriptor__, __NAME__) RPB_XP_METHOD_0(METHOD(as_character), GPB::FileDescriptor, DebugString) RPB_FUNCTION_1(S4_Message, METHOD(as_Message), Rcpp::XPtr d) { GPB::FileDescriptorProto* message = new GPB::FileDescriptorProto(); d->CopyTo(message); return S4_Message(message); } RPB_FUNCTION_1(Rcpp::CharacterVector, METHOD(getMemberNames), Rcpp::XPtr desc) { int ntypes = desc->message_type_count(); int nenums = desc->enum_type_count(); int nserv = desc->service_count(); int nexts = desc->extension_count(); Rcpp::CharacterVector res(ntypes + nenums + nserv + nexts); int i = 0; int j = 0; while (i < ntypes) { res[j] = desc->message_type(i)->name(); i++; j++; } i = 0; while (i < nenums) { res[j] = desc->enum_type(i)->name(); i++; j++; } i = 0; while (i < nserv) { res[j] = desc->service(i)->name(); i++; j++; } i = 0; while (i < nexts) { res[j] = desc->extension(i)->name(); i++; j++; } return res; } /** * @param xp (GPB::FileDescriptor*) external pointer * @return the descriptor as an R list */ RPB_FUNCTION_1(Rcpp::List, METHOD(as_list), Rcpp::XPtr desc) { int ntypes = desc->message_type_count(); int nenums = desc->enum_type_count(); int nserv = desc->service_count(); int nexts = desc->extension_count(); int n = ntypes + nenums + nserv + nexts; Rcpp::CharacterVector names(n); Rcpp::List res(n); int count = 0; for (int i = 0; i < ntypes; count++, i++) { res[count] = S4_Descriptor(desc->message_type(i)); names[count] = desc->message_type(i)->name(); } for (int i = 0; i < nenums; count++, i++) { res[count] = S4_EnumDescriptor(desc->enum_type(i)); names[count] = desc->enum_type(i)->name(); } for (int i = 0; i < nserv; count++, i++) { res[count] = S4_ServiceDescriptor(desc->service(i)); names[count] = desc->service(i)->name(); } for (int i = 0; i < nexts; count++, i++) { res[count] = S4_FieldDescriptor(desc->extension(i)); // always use full names for extensions names[count] = desc->extension(i)->full_name(); } res.names() = names; return res; } RPB_FUNCTION_1(std::string, METHOD(name), Rcpp::XPtr desc) { return desc->name(); } #undef METHOD } // namespace rprotobuf RProtoBuf/src/ConnectionOutputStream.h0000644000175100001440000000055513037407202017611 0ustar hornikusers#ifndef RPROTOBUF_ConnectionOutputStream_H #define RPROTOBUF_ConnectionOutputStream_H namespace rprotobuf { class ConnectionOutputStream : public GPB::io::CopyingOutputStreamAdaptor { public: ConnectionOutputStream(SEXP con, bool was_open); ~ConnectionOutputStream(); private: bool was_open; SEXP con; }; } // namespace rprotobuf #endif RProtoBuf/src/wrapper_ArrayOutputStream.cpp0000644000175100001440000000051313037407202020655 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { RPB_FUNCTION_2(S4_ArrayOutputStream, ArrayOutputStream__new, int size, int block_size) { return S4_ArrayOutputStream(size, block_size); } } RProtoBuf/src/ConnectionInputStream.h0000644000175100001440000000054713037407202017411 0ustar hornikusers#ifndef RPROTOBUF_ConnectionInputStream_H #define RPROTOBUF_ConnectionInputStream_H namespace rprotobuf { class ConnectionInputStream : public GPB::io::CopyingInputStreamAdaptor { public: ConnectionInputStream(SEXP con, bool was_open); ~ConnectionInputStream(); private: bool was_open; SEXP con; }; } // namespace rprotobuf #endif RProtoBuf/src/ZeroCopyInputStreamWrapper.cpp0000644000175100001440000000136113037407202020753 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" namespace rprotobuf { ZeroCopyInputStreamWrapper::ZeroCopyInputStreamWrapper(GPB::io::ZeroCopyInputStream* stream) : stream(stream) { coded_stream = new GPB::io::CodedInputStream(stream); } ZeroCopyInputStreamWrapper::~ZeroCopyInputStreamWrapper() { try { /* first clear the coded stream */ delete coded_stream; /* then the stream itself */ delete stream; } catch (...) { } } GPB::io::ZeroCopyInputStream* ZeroCopyInputStreamWrapper::get_stream() { return stream; } GPB::io::CodedInputStream* ZeroCopyInputStreamWrapper::get_coded_stream() { return coded_stream; } } // namespace rprotobuf RProtoBuf/src/Makevars.in0000644000175100001440000000033213037407202015036 0ustar hornikusers## -*- mode: makefile; -*- ## Configure tells us about locations for ## both Rcpp (ie libRcpp.so and Rcpp.h) and ## ProtoBuf headers and library via the variables PKG_CPPFLAGS= @PKG_CPPFLAGS@ PKG_LIBS= @PKG_LIBS@ RProtoBuf/src/ConnectionInputStream.cpp0000644000175100001440000000164413037407202017743 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "ConnectionInputStream.h" #include "ConnectionCopyingInputStream.h" namespace rprotobuf { ConnectionInputStream::ConnectionInputStream(SEXP con, bool was_open) : GPB::io::CopyingInputStreamAdaptor(new ConnectionCopyingInputStream(con)), was_open(was_open), con(con) { /* clean the wrapped stream on delete */ SetOwnsCopyingStream(true); } ConnectionInputStream::~ConnectionInputStream() { if (!was_open) { /* then we need to close it */ SEXP call = PROTECT(Rf_lang2(Rf_install("close"), con)); Rf_eval(call, R_GlobalEnv); UNPROTECT(1); /* call */ } /* con will be disposed by the R GC, it is protected as part of the protection of the external pointer that wraps this */ } } // namespace rprotobuf RProtoBuf/src/ConnectionOutputStream.cpp0000644000175100001440000000172113037407202020140 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "ConnectionOutputStream.h" #include "ConnectionCopyingOutputStream.h" namespace rprotobuf { ConnectionOutputStream::ConnectionOutputStream(SEXP con, bool was_open) : GPB::io::CopyingOutputStreamAdaptor(new ConnectionCopyingOutputStream(con)), was_open(was_open), con(con) { /* clean the wrapped stream on delete */ SetOwnsCopyingStream(true); } ConnectionOutputStream::~ConnectionOutputStream() { if (!was_open) { /* then we need to close it */ SEXP call = PROTECT(Rf_lang2(Rf_install("close"), con)); (void)Rf_eval(call, R_GlobalEnv); // Ignore SEXP return val of close(). UNPROTECT(1); /* call */ } /* con will be disposed by the R GC, it is protected as part of the protection of the external pointer that wraps this */ } } // namespace rprotobuf RProtoBuf/src/RWarningErrorCollector.h0000644000175100001440000000060413037407202017520 0ustar hornikusers#include /* For string */ #include "rprotobuf.h" namespace rprotobuf { class RWarningErrorCollector : public GPB::compiler::MultiFileErrorCollector { public: // implements ErrorCollector --------------------------------------- void AddError(const std::string& filename, int line, int column, const std::string& message); }; } // namespace rprotobuf RProtoBuf/src/wrapper_Message.cpp0000644000175100001440000011462213037407202016575 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "fieldtypes.h" #include "RcppMacros.h" #define SAME(x, y, tol) ((tol == 0.0 && x == y) || (((x - y) * (x - y) < tol* tol) ? 1 : 0)) namespace rprotobuf { /* helpers */ /* this is only to be called for repeated fields */ int MESSAGE_GET_REPEATED_INT(const GPB::Message* message, const GPB::FieldDescriptor* field_desc, int index) { const GPB::Reflection* ref = message->GetReflection(); switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: return (int)ref->GetRepeatedInt32(*message, field_desc, index); case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: return (int)ref->GetRepeatedInt64(*message, field_desc, index); case TYPE_UINT32: case TYPE_FIXED32: return (int)ref->GetRepeatedUInt32(*message, field_desc, index); case TYPE_UINT64: case TYPE_FIXED64: return (int)ref->GetRepeatedUInt64(*message, field_desc, index); case TYPE_ENUM: return ref->GetRepeatedEnum(*message, field_desc, index)->number(); default: Rcpp_error("cannot cast to int"); } return 0; // Unreachable for -Wall } /* this is only to be called for repeated fields */ double MESSAGE_GET_REPEATED_DOUBLE(const GPB::Message* message, const GPB::FieldDescriptor* field_desc, int index) { const GPB::Reflection* ref = message->GetReflection(); switch (field_desc->type()) { case TYPE_FLOAT: return (double)ref->GetRepeatedFloat(*message, field_desc, index); case TYPE_DOUBLE: return (double)ref->GetRepeatedDouble(*message, field_desc, index); default: Rcpp_error("cannot cast to double"); } return 0; // -Wall } #undef METHOD #define METHOD(__NAME__) RCPP_PP_CAT(Message__, __NAME__) /** * Clone a message * * @param xp external pointer to a message * @return a new message, clone of the input message */ RPB_FUNCTION_1(S4_Message, METHOD(clone), Rcpp::XPtr message) { /* cloning message as sheep */ GPB::Message* sheep = message->New(); sheep->CopyFrom(*message); return S4_Message(sheep); } /** * TRUE if the message has the specified field name. * FALSE otherwise. * * * @param xp external pointer to the Message * @param name name of the field */ RPB_FUNCTION_2(bool, METHOD(field_exists), Rcpp::XPtr message, std::string name) { const GPB::Descriptor* desc = message->GetDescriptor(); const GPB::FieldDescriptor* field_desc = desc->FindFieldByName(name); return (field_desc != NULL); } /** * TRUE if the message has the field name and it is populated. * FALSE otherwise. * * @param xp external pointer to the Message * @param name name of the field */ RPB_FUNCTION_2(bool, METHOD(has_field), Rcpp::XPtr message, std::string name) { const GPB::Descriptor* desc = message->GetDescriptor(); const GPB::FieldDescriptor* field_desc = desc->FindFieldByName(name); bool res = false; if (field_desc) { const GPB::Reflection* ref = message->GetReflection(); if (field_desc->is_repeated()) { res = ref->FieldSize(*message, field_desc) > 0; } else { res = ref->HasField(*message, field_desc); } } return res; } /** * Check if all required fields are set * * @param xp external pointer to the Message */ RPB_FUNCTION_1(bool, METHOD(is_initialized), Rcpp::XPtr message) { return message->IsInitialized(); } /** * Serialize a message to a file * * @param xp external pointer to a GPB::Message* * @param filename file name where to serialize */ RPB_FUNCTION_VOID_2(METHOD(serialize_to_file), Rcpp::XPtr message, const char* filename) { /* open the file in binary mode to write */ /* we make sure in the R side that filename is the full path of the file */ int file = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666); /* using partial to allow partially filled messages */ // TODO(mstokely): Check return value and throw Rcpp::stop if 0? message->SerializePartialToFileDescriptor(file); close(file); } /** * Create a raw vector that contains the content of the serialized message * * @param xp xternal pointer to the message */ RPB_FUNCTION_1(Rcpp::RawVector, METHOD(get_payload), Rcpp::XPtr message) { /* create a raw vector of the appropriate size */ int size = message->ByteSize(); Rcpp::RawVector payload(size); /* fill the array */ message->SerializePartialToArray(payload.begin(), size); return (payload); } RPB_XP_METHOD_VOID_0(METHOD(clear), GPB::Message, Clear) /** * Clear a field of a message * * @param xp (GPB::Message*) external pointer * @param field name or tag of the field */ RPB_FUNCTION_VOID_2(METHOD(clear_field), Rcpp::XPtr m, SEXP field) { const GPB::FieldDescriptor* field_desc = getFieldDescriptor(m, field); const GPB::Reflection* ref = m->GetReflection(); ref->ClearField(m, field_desc); } /** * Return a named list representation of the fields set in a message. * * @param xp external pointer to a Message * @return the message as an R list */ RPB_FUNCTION_1(Rcpp::List, METHOD(as_list), Rcpp::XPtr message) { const GPB::Descriptor* desc = message->GetDescriptor(); int nf = desc->field_count(); Rcpp::CharacterVector fieldNames(nf); Rcpp::List val(nf); /* TODO: not use getMessageField */ for (int i = 0; i < nf; i++) { const GPB::FieldDescriptor* fd = desc->field(i); val[i] = getMessageField(message, Rcpp::CharacterVector::create(fd->name())); fieldNames[i] = fd->name(); } val.names() = fieldNames; return val; } /** * The number of fields the message has. A field counts in these two situations: * - it is repeated and the array size is greater than 0 * - it is not repeated and the message has it * * @param xp external pointer to the Message */ RPB_FUNCTION_1(int, METHOD(length), Rcpp::XPtr message) { const GPB::Descriptor* desc = message->GetDescriptor(); const GPB::Reflection* ref = message->GetReflection(); int nfields = desc->field_count(); int res = 0; for (int i = 0; i < nfields; i++) { const GPB::FieldDescriptor* field_desc = desc->field(i); if (field_desc->is_repeated()) { if (ref->FieldSize(*message, field_desc) > 0) { res++; } } else { if (ref->HasField(*message, field_desc)) { res++; } } } return res; } /** * The number of extensions the message has. * * @param xp external pointer to the Message */ RPB_FUNCTION_1(int, METHOD(num_extensions), Rcpp::XPtr message) { const GPB::Reflection* ref = message->GetReflection(); int nexts = 0; vector fields; ref->ListFields(*message, &fields); for (unsigned int i = 0; i < fields.size(); i++) { if (fields[i]->is_extension()) { nexts++; } } return nexts; } /** * Get the message descriptor of a Message. * * @param xp (GPB::Message*) external pointer * @return the descriptor, as a Descriptor R S4 object */ RPB_FUNCTION_1(S4_Descriptor, METHOD(descriptor), Rcpp::XPtr message) { return (message->GetDescriptor()); } RPB_XP_METHOD_0(METHOD(as_character), GPB::Message, DebugString) RPB_XP_METHOD_0(METHOD(bytesize), GPB::Message, ByteSize) RPB_FUNCTION_2(int, METHOD(field_size), Rcpp::XPtr message, SEXP field) { const GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, field); int res = 0; if (field_desc->is_repeated()) { res = message->GetReflection()->FieldSize(*message, field_desc); } else { res = message->GetReflection()->HasField(*message, field_desc) ? 1 : 0; } return res; } RPB_FUNCTION_1(S4_FileDescriptor, METHOD(fileDescriptor), Rcpp::XPtr message) { return S4_FileDescriptor(message->GetDescriptor()->file()); } RPB_FUNCTION_VOID_3(METHOD(set_field_size), Rcpp::XPtr message, SEXP field, int target) { const GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, field); const GPB::Reflection* ref = message->GetReflection(); if (field_desc->is_repeated()) { int current = ref->FieldSize(*message, field_desc); if (target == 0) { ref->ClearField(message, field_desc); } else if (current > target) { while (current != target) { ref->RemoveLast(message, field_desc); current--; } } else if (current == target) { /* nothing to do */ } else {/* current < target */ while (current != target) { switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { ref->AddInt32(message, field_desc, (int32)0); break; } case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { ref->AddInt64(message, field_desc, (int64)0); break; } case TYPE_UINT32: case TYPE_FIXED32: { ref->AddUInt32(message, field_desc, (uint32)0); break; } case TYPE_UINT64: case TYPE_FIXED64: { ref->AddUInt32(message, field_desc, (uint64)0); break; } case TYPE_DOUBLE: { ref->AddDouble(message, field_desc, (double)0.0); break; } case TYPE_FLOAT: { ref->AddFloat(message, field_desc, (float)0.0); break; } case TYPE_BOOL: { ref->AddBool(message, field_desc, (bool)0); break; } case TYPE_STRING: case TYPE_BYTES: { ref->AddString(message, field_desc, ""); break; } case TYPE_MESSAGE: case TYPE_GROUP: { /* fill with the prototype for that message type */ Rcpp_error("growing repeated messages not implemented, patches welcome"); break; } case TYPE_ENUM: { /* fill with the prototype for that message type */ Rcpp_error("growing repeated enums not implemented yet, patches welcome"); break; } } /* switch */ current++; } /* while */ } } else { if (target == 0) { if (ref->HasField(*message, field_desc)) { ref->ClearField(message, field_desc); } } else { if (!ref->HasField(*message, field_desc)) { switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { ref->SetInt32(message, field_desc, (int32)0); break; } case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { ref->SetInt64(message, field_desc, (int64)0); break; } case TYPE_UINT32: case TYPE_FIXED32: { ref->SetUInt32(message, field_desc, (uint32)0); break; } case TYPE_UINT64: case TYPE_FIXED64: { ref->SetUInt32(message, field_desc, (uint64)0); break; } case TYPE_DOUBLE: { ref->SetDouble(message, field_desc, (double)0.0); break; } case TYPE_FLOAT: { ref->SetFloat(message, field_desc, (float)0.0); break; } case TYPE_BOOL: { ref->SetBool(message, field_desc, (bool)0); break; } case TYPE_STRING: case TYPE_BYTES: { ref->SetString(message, field_desc, ""); break; } case TYPE_MESSAGE: case TYPE_GROUP: { /* fill with the prototype for that message type */ Rcpp_error("not implemented yet, patches welcome"); break; } case TYPE_ENUM: { /* fill with the prototype for that message type */ Rcpp_error("not implemented yet, patches welcome"); break; } } } } } } /** * Returns the field names of the message. * * @param xp external pointer to a Message * * @return field names, as an R character vector (STRSXP) */ RPB_FUNCTION_1(Rcpp::CharacterVector, METHOD(fieldNames), Rcpp::XPtr message) { const GPB::Descriptor* desc = message->GetDescriptor(); int nfields = desc->field_count(); Rcpp::CharacterVector res(nfields); for (int i = 0; i < nfields; i++) { res[i] = desc->field(i)->name(); } return (res); } bool identical_messages_(const GPB::Message* m1, const GPB::Message* m2, double tol) { const GPB::Descriptor* d1 = m1->GetDescriptor(); const GPB::Descriptor* d2 = m2->GetDescriptor(); /* first of all, check if this is the same message type */ if (d1 != d2) { return false; } const GPB::Reflection* ref = m2->GetReflection(); /* iterate field descriptors */ int nf = d1->field_count(); for (int i = 0; i < nf; i++) { const GPB::FieldDescriptor* field_desc = d1->field(i); if (field_desc->is_repeated()) { /* test if the size differs */ int fs = ref->FieldSize(*m1, field_desc); if (fs != ref->FieldSize(*m2, field_desc)) return false; /* test all items */ switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedInt32(*m1, field_desc, j) != ref->GetRepeatedInt32(*m2, field_desc, j)) return false; } break; } case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedInt64(*m1, field_desc, j) != ref->GetRepeatedInt64(*m2, field_desc, j)) return false; } break; } case TYPE_UINT32: case TYPE_FIXED32: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedUInt32(*m1, field_desc, j) != ref->GetRepeatedUInt32(*m2, field_desc, j)) return false; } break; } case TYPE_UINT64: case TYPE_FIXED64: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedUInt64(*m1, field_desc, j) != ref->GetRepeatedUInt64(*m2, field_desc, j)) return false; } break; } case TYPE_DOUBLE: { for (int j = 0; j < fs; j++) { if (!SAME(ref->GetRepeatedDouble(*m1, field_desc, j), ref->GetRepeatedDouble(*m2, field_desc, j), tol)) return false; } break; } case TYPE_FLOAT: { for (int j = 0; j < fs; j++) { if (!SAME(ref->GetRepeatedFloat(*m1, field_desc, j), ref->GetRepeatedFloat(*m2, field_desc, j), tol)) return false; } break; } case TYPE_BOOL: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedBool(*m1, field_desc, j) != ref->GetRepeatedBool(*m2, field_desc, j)) return false; } break; } case TYPE_STRING: case TYPE_BYTES: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedString(*m1, field_desc, j) != ref->GetRepeatedString(*m2, field_desc, j)) return false; } break; } case TYPE_ENUM: { for (int j = 0; j < fs; j++) { if (ref->GetRepeatedEnum(*m1, field_desc, j) != ref->GetRepeatedEnum(*m2, field_desc, j)) return false; } break; } case TYPE_MESSAGE: case TYPE_GROUP: { for (int j = 0; j < fs; j++) { const GPB::Message* mm1 = &ref->GetRepeatedMessage(*m1, field_desc, j); const GPB::Message* mm2 = &ref->GetRepeatedMessage(*m2, field_desc, j); if (!identical_messages_(mm1, mm2, tol)) { return false; } } break; } default: Rcpp_error("unknown type"); } } else { switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { if (ref->GetInt32(*m1, field_desc) != ref->GetInt32(*m2, field_desc)) return false; break; } case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { if (ref->GetInt64(*m1, field_desc) != ref->GetInt64(*m2, field_desc)) return false; break; } case TYPE_UINT32: case TYPE_FIXED32: { if (ref->GetUInt32(*m1, field_desc) != ref->GetUInt32(*m2, field_desc)) return false; break; } case TYPE_UINT64: case TYPE_FIXED64: { if (ref->GetUInt64(*m1, field_desc) != ref->GetUInt64(*m2, field_desc)) return false; break; } case TYPE_DOUBLE: { if (ref->GetDouble(*m1, field_desc) != ref->GetDouble(*m2, field_desc)) return false; break; } case TYPE_FLOAT: { if (ref->GetFloat(*m1, field_desc) != ref->GetFloat(*m2, field_desc)) return false; break; } case TYPE_BOOL: { if (ref->GetBool(*m1, field_desc) != ref->GetBool(*m2, field_desc)) return false; break; } case TYPE_STRING: case TYPE_BYTES: { if (ref->GetString(*m1, field_desc) != ref->GetString(*m2, field_desc)) return false; break; } case TYPE_ENUM: { if (ref->GetEnum(*m1, field_desc) != ref->GetEnum(*m2, field_desc)) return false; break; } case TYPE_MESSAGE: case TYPE_GROUP: { const GPB::Message* mm1 = &ref->GetMessage(*m1, field_desc); const GPB::Message* mm2 = &ref->GetMessage(*m2, field_desc); if (!identical_messages_(mm1, mm2, tol)) { return false; } break; } default: Rcpp_error("unknown type"); } } } /* finally */ return true; } RPB_FUNCTION_2(bool, identical_messages, Rcpp::XPtr m1, Rcpp::XPtr m2) { return identical_messages_(m1, m2, 0.0); } RPB_FUNCTION_3(bool, all_equal_messages, Rcpp::XPtr m1, Rcpp::XPtr m2, double tol) { return identical_messages_(m1, m2, tol); } RPB_FUNCTION_VOID_4(METHOD(swap), Rcpp::XPtr message, SEXP field, Rcpp::IntegerVector left, Rcpp::IntegerVector right) { GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, field); const GPB::Reflection* ref = message->GetReflection(); if (!field_desc->is_repeated()) { throw std::range_error("swap can only be used with repeated fields"); } int n = LENGTH(left); /* we know that length(left) == length(right) */ for (int i = 0; i < n; i++) { ref->SwapElements(message, field_desc, left[i], right[i]); } } /** * Creates a new message by merging two messages of the same type. * * @param xp1 external pointer to a GPB::Message* * @param xp2 external pointer to a GPB::Message* * * @return a new message, as an R object of "Message" S4 class */ RPB_FUNCTION_2(S4_Message, METHOD(merge), Rcpp::XPtr m1, Rcpp::XPtr m2) { GPB::Message* merged = m1->New(); merged->MergeFrom(*m1); merged->MergeFrom(*m2); return S4_Message(merged); } /** * Add values to a repeated field. * * @param xp (GPB::Message*) external pointer * @param field field tag number or name * @param values values to append */ RPB_FUNCTION_VOID_3(METHOD(add_values), Rcpp::XPtr message, SEXP field, SEXP values) { const Reflection* ref = message->GetReflection(); const GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, field); if (values == R_NilValue || LENGTH(values) == 0) { return; } if (field_desc->is_repeated()) { /* first check */ switch (field_desc->type()) { case TYPE_ENUM: { CHECK_values_for_enum(field_desc, values); break; } case TYPE_MESSAGE: case TYPE_GROUP: { CHECK_messages(field_desc, values); break; } default: { // nothing } } int value_size = LENGTH(values); /* then add the values */ switch (field_desc->type()) { // {{{ int32 case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { ref->AddInt32(message, field_desc, GET_int32(values, i)); } break; } default: Rcpp::stop("Cannot convert to int32"); } break; } // }}} // {{{ int64 case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: for (int i = 0; i < value_size; i++) { ref->AddInt64(message, field_desc, GET_int64(values, i)); } break; default: Rcpp::stop("Cannot convert to int64"); } break; } // }}} // {{{ uint32 case TYPE_UINT32: case TYPE_FIXED32: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { ref->AddUInt32(message, field_desc, GET_uint32(values, i)); } break; } default: Rcpp::stop("Cannot convert to uint32"); } break; } // }}} // {{{ uint64 case TYPE_UINT64: case TYPE_FIXED64: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { ref->AddUInt64(message, field_desc, GET_uint64(values, i)); } break; } default: Rcpp::stop("Cannot convert to int64"); } break; } // }}} // {{{ double case TYPE_DOUBLE: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { ref->AddDouble(message, field_desc, GET_double(values, i)); } break; } default: Rcpp::stop("Cannot convert to double"); } break; } // }}} // {{{ float case TYPE_FLOAT: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { ref->AddFloat(message, field_desc, GET_float(values, i)); } break; } default: Rcpp::stop("Cannot convert to float"); } break; } // }}} // {{{ bool case TYPE_BOOL: { switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { ref->AddBool(message, field_desc, GET_bool(values, i)); } break; } default: Rcpp::stop("Cannot convert to bool"); } break; } // }}} // {{{ string case TYPE_STRING: { if (TYPEOF(values) == STRSXP) { for (int i = 0; i < value_size; i++) { ref->AddString(message, field_desc, COPYSTRING(CHAR(STRING_ELT(values, i)))); } } else { Rcpp::stop("Cannot convert to string"); } break; } // }}} // {{{ bytes case TYPE_BYTES: { if (TYPEOF(values) == RAWSXP) { ref->AddString(message, field_desc, GET_bytes(values, 0)); } else if (TYPEOF(values) == VECSXP) { for (int i = 0; i < value_size; i++) { ref->AddString(message, field_desc, GET_bytes(values, i)); } } else { Rcpp::stop("Cannot convert to bytes"); } break; } // }}} // {{{ message case TYPE_MESSAGE: case TYPE_GROUP: { if (TYPEOF(values) == VECSXP) { for (int i = 0; i < value_size; i++) { GPB::Message* mess = GET_MESSAGE_POINTER_FROM_S4(VECTOR_ELT(values, i)); /* we already know it is of the correct type because of premptive check above */ ref->AddMessage(message, field_desc)->CopyFrom(*mess); } } else { Rcpp::stop("type mismatch, expecting a list of 'Message' objects"); } break; } // }}} // {{{ enum case TYPE_ENUM: { const GPB::EnumDescriptor* enum_desc = field_desc->enum_type(); switch (TYPEOF(values)) { // {{{ numbers case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < value_size; i++) { int val = GET_int(values, i); ref->AddEnum(message, field_desc, enum_desc->FindValueByNumber(val)); } break; } // }}} // {{{ STRSXP case STRSXP: { for (int i = 0; i < value_size; i++) { std::string val = CHAR(STRING_ELT(values, i)); const GPB::EnumValueDescriptor* evd = enum_desc->FindValueByName(val); ref->AddEnum(message, field_desc, evd); } break; } // }}} default: Rcpp::stop("cannot set enum value"); } break; } // }}} default: { // nothing } } } else { Rcpp::stop("add can only be used on repeated fields"); } } /** * Fetch a subset of the values of a field. * * @param (GPB::Message*) external pointer * @param field name or tag number of the field * @param index */ RPB_FUNCTION_3(SEXP, METHOD(get_field_values), Rcpp::XPtr message, SEXP field, Rcpp::IntegerVector index) { GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, field); if (!field_desc->is_repeated()) { Rcpp_error("fetch can only be used on repeated fields"); } int n = index.size(); switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: case TYPE_UINT32: case TYPE_FIXED32: case TYPE_UINT64: case TYPE_FIXED64: case TYPE_ENUM: { Rcpp::IntegerVector res(n); for (int i = 0; i < n; i++) { res[i] = MESSAGE_GET_REPEATED_INT(message, field_desc, index[i]); } return res; } case TYPE_DOUBLE: case TYPE_FLOAT: { Rcpp::NumericVector res(n); for (int i = 0; i < n; i++) { res[i] = MESSAGE_GET_REPEATED_DOUBLE(message, field_desc, index[i]); } return res; } case TYPE_BOOL: { Rcpp::LogicalVector res(n); for (int i = 0; i < n; i++) { res[i] = MESSAGE_GET_REPEATED_DOUBLE(message, field_desc, index[i]); } return res; } case TYPE_STRING: { const GPB::Reflection* ref = message->GetReflection(); Rcpp::CharacterVector res(n); for (int i = 0; i < n; i++) { res[i] = ref->GetRepeatedString(*message, field_desc, index[i]); } return res; } case TYPE_BYTES: { const GPB::Reflection* ref = message->GetReflection(); Rcpp::List res(n); for (int i = 0; i < n; i++) { std::string s = ref->GetRepeatedString(*message, field_desc, index[i]); res[i] = std::vector(s.begin(), s.end()); } return res; } case TYPE_MESSAGE: case TYPE_GROUP: { const GPB::Reflection* ref = message->GetReflection(); Rcpp::List res(n); for (int i = 0; i < n; i++) { res[i] = S4_Message(CLONE(&ref->GetRepeatedMessage(*message, field_desc, i))); } return res; } default: throw std::range_error("unknown type"); } return R_NilValue; // Unreachable. For -Wall } /** * set the values of a repeated field * * @param xp (GPB::Message*) external pointer * @param field field tag number or name * @param index positions (0-based) * @param values new values */ RPB_FUNCTION_VOID_4(METHOD(set_field_values), Rcpp::XPtr message, SEXP field, Rcpp::IntegerVector index, SEXP values) { const GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, field); if (!field_desc->is_repeated()) { throw std::range_error("set can only be used on repeated fields"); } const GPB::Reflection* ref = message->GetReflection(); /* we know here that LENGTH(index) == LENGTH(values) */ int n = index.size(); switch (field_desc->type()) { case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { for (int i = 0; i < n; i++) { ref->SetRepeatedInt32(message, field_desc, index[i], GET_int32(values, i)); } break; } case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { for (int i = 0; i < n; i++) { ref->SetRepeatedInt64(message, field_desc, index[i], GET_int64(values, i)); } break; } case TYPE_UINT32: case TYPE_FIXED32: { for (int i = 0; i < n; i++) { ref->SetRepeatedUInt32(message, field_desc, GET_int(index, i), GET_uint32(values, i)); } break; } case TYPE_UINT64: case TYPE_FIXED64: { for (int i = 0; i < n; i++) { ref->SetRepeatedUInt64(message, field_desc, index[i], GET_uint64(values, i)); } break; } case TYPE_DOUBLE: { for (int i = 0; i < n; i++) { ref->SetRepeatedDouble(message, field_desc, index[i], GET_double(values, i)); } break; } case TYPE_FLOAT: { for (int i = 0; i < n; i++) { ref->SetRepeatedFloat(message, field_desc, index[i], GET_float(values, i)); } break; } case TYPE_BOOL: { for (int i = 0; i < n; i++) { ref->SetRepeatedBool(message, field_desc, index[i], GET_bool(values, i)); } break; } case TYPE_STRING: { for (int i = 0; i < n; i++) { ref->SetRepeatedString(message, field_desc, index[i], GET_stdstring(values, i)); } break; } case TYPE_BYTES: { for (int i = 0; i < n; i++) { ref->SetRepeatedString(message, field_desc, index[i], GET_bytes(values, i)); } break; } case TYPE_ENUM: { CHECK_values_for_enum(field_desc, values); const GPB::EnumDescriptor* enum_desc = field_desc->enum_type(); switch (TYPEOF(values)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { for (int i = 0; i < n; i++) { int val = GET_int(values, i); ref->SetRepeatedEnum(message, field_desc, i, enum_desc->FindValueByNumber(val)); } break; } case STRSXP: { Rcpp::CharacterVector vals(values); std::string val; for (int i = 0; i < n; i++) { val = vals[i]; const GPB::EnumValueDescriptor* evd = enum_desc->FindValueByName(val); ref->SetRepeatedEnum(message, field_desc, i, evd); } break; } default: throw std::range_error("impossible to convert to a enum"); } break; } case TYPE_MESSAGE: case TYPE_GROUP: { CHECK_messages(field_desc, values); Rcpp::List vals(values); for (int i = 0; i < n; i++) { GPB::Message* mess = GET_MESSAGE_POINTER_FROM_S4(vals[i]); ref->MutableRepeatedMessage(message, field_desc, i)->CopyFrom(*mess); } break; } default: throw std::range_error("unknown type"); } } #undef METHOD } RProtoBuf/src/wrapper_ArrayInputStream.cpp0000644000175100001440000000055113037407202020456 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RcppMacros.h" namespace rprotobuf { RPB_FUNCTION_2(S4_ArrayInputStream, ArrayInputStream__new, Rcpp::RawVector payload, int block_size) { return S4_ArrayInputStream(payload, block_size); } } RProtoBuf/src/Makevars.win0000644000175100001440000000056213037407202015232 0ustar hornikusers# Links against libprotobuf build from Rtools gcc toolchain. COMPILED_BY ?= gcc-4.6.3 PKG_CPPFLAGS= -I../windows/protobuf-3.0.0/include PKG_LIBS= -L../windows/protobuf-3.0.0/lib${subst gcc,,${COMPILED_BY}}${R_ARCH} -lprotobuf CXX_STD=CXX11 all: clean winlibs clean: rm -f $(OBJECTS) $(SHLIB) winlibs: "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" "../tools/winlibs.R" RProtoBuf/src/extensions.cpp0000644000175100001440000000356313037407202015651 0ustar hornikusers/* -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- * Copyright 2012 Google Inc. All Rights Reserved. * Author: Murray Stokely * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License as * published by the Free Software Foundation; either version 2 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA * 02110-1301, USA. * */ #include "rprotobuf.h" #include "Rcppsupport.h" namespace rprotobuf { RcppExport SEXP getExtension(SEXP pointer, SEXP sfielddesc) { /* grab the Message pointer */ Rcpp::XPtr message(pointer); const GPB::Reflection* ref = message->GetReflection(); const GPB::FieldDescriptor* field_desc = GET_FIELD_DESCRIPTOR_POINTER_FROM_S4(sfielddesc); // extractFieldAsSEXP returns a default (e.g. 0) even when // field doesn't exist, but returning NULL probably makes more // sense. // // TODO(mstokely): move this logic into extractField so that // all fields get this updated behavior, not just extensions. if (field_desc->is_repeated()) { if (ref->FieldSize(*message, field_desc) < 1) { return R_NilValue; } } else { if (!ref->HasField(*message, field_desc)) { return R_NilValue; } } return (extractFieldAsSEXP(message, field_desc)); } } // namespace rprotobuf RProtoBuf/src/ConnectionCopyingOutputStream.h0000644000175100001440000000124013037407202021132 0ustar hornikusers#ifndef RPROTOBUF_ConnectionCopyingOutputStream_H #define RPROTOBUF_ConnectionCopyingOutputStream_H namespace rprotobuf { class ConnectionCopyingOutputStream : public GPB::io::CopyingOutputStream { public: ConnectionCopyingOutputStream(SEXP con); bool Write(const void* buffer, int size); private: /* the actual connection object from R it is protected by the external pointer that wraps the ConnectionInputStream, which is the only thing that uses this class, so we don't need to take care of GC here */ SEXP con; Rcpp::Function writeBin; }; } // namespace rprotobuf #endif RProtoBuf/src/mutators.cpp0000644000175100001440000012527413037407202015334 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- // Copyright (C) 2010 - 2011 Dirk Eddelbuettel and Romain Francois // // This file is part of RProtoBuf. // // RProtoBuf is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 2 of the License, or // (at your option) any later version. // // RProtoBuf is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with RProtoBuf. If not, see . #include "rprotobuf.h" #include "fieldtypes.h" #include "RcppMacros.h" namespace rprotobuf { // {{{ GETDOUBLE /** * get the index'th value of x, as an double * * @param x some R data * @param index the index * @return x[index], as an double * @throws Rcpp::exception if x[index] cannot be converted to double */ /* FIXME: should we convert the NA's */ double GET_double(SEXP x, int index) { switch (TYPEOF(x)) { case INTSXP: return ((double)INTEGER(x)[index]); case REALSXP: return (REAL(x)[index]); case LGLSXP: return ((double)LOGICAL(x)[index]); case RAWSXP: return ((double)RAW(x)[index]); default: Rcpp::stop("cannot cast SEXP to double"); } return 0.0; // -Wall } // }}} float GET_float(SEXP x, int index) { switch (TYPEOF(x)) { case INTSXP: return ((float)INTEGER(x)[index]); case REALSXP: return ((float)REAL(x)[index]); case LGLSXP: return ((float)LOGICAL(x)[index]); case RAWSXP: return ((float)RAW(x)[index]); default: Rcpp::stop("cannot cast SEXP to double"); } return (float)0.0; // -Wall } int GET_int(SEXP x, int index) { switch (TYPEOF(x)) { case INTSXP: return (INTEGER(x)[index]); case REALSXP: return ((int)REAL(x)[index]); case LGLSXP: return ((int)LOGICAL(x)[index]); case RAWSXP: return ((int)RAW(x)[index]); default: Rcpp::stop("cannot cast SEXP to int"); } return 0; // -Wall, should not happen since we only call this when we know it works } template ValueType Int64FromString(const std::string& value) { std::stringstream ss(value); ValueType ret; if ((ss >> ret).fail() || !(ss >> std::ws).eof()) { std::string message = "Provided character value '" + value + "' cannot be cast to 64-bit integer."; Rcpp::stop(message.c_str()); } return ret; } template ValueType Int32FromString(const std::string& value) { std::stringstream ss(value); ValueType ret; if ((ss >> ret).fail() || !(ss >> std::ws).eof()) { std::string message = "Provided character value '" + value + "' cannot be cast to 32-bit integer."; Rcpp::stop(message.c_str()); } return ret; } int32 GET_int32(SEXP x, R_xlen_t vec_index) { switch (TYPEOF(x)) { case INTSXP: return ((int32)INTEGER(x)[vec_index]); case REALSXP: return ((int32)REAL(x)[vec_index]); case LGLSXP: return ((int32)LOGICAL(x)[vec_index]); case RAWSXP: return ((int32)RAW(x)[vec_index]); case STRSXP: return Int32FromString(CHAR(STRING_ELT(x, vec_index))); default: Rcpp::stop("cannot cast SEXP to int32"); } return (int32)0; // -Wall, should not happen since we only call this when we know it works } int64 GET_int64(SEXP x, R_xlen_t vec_index) { switch (TYPEOF(x)) { case INTSXP: return ((int64)INTEGER(x)[vec_index]); case REALSXP: return ((int64)REAL(x)[vec_index]); case LGLSXP: return ((int64)LOGICAL(x)[vec_index]); case RAWSXP: return ((int64)RAW(x)[vec_index]); case STRSXP: return Int64FromString(CHAR(STRING_ELT(x, vec_index))); default: Rcpp::stop("cannot cast SEXP to int64"); } return (int64)0; // -Wall, should not happen since we only call this when we know it works } uint32 GET_uint32(SEXP x, R_xlen_t vec_index) { switch (TYPEOF(x)) { case INTSXP: return ((uint32)INTEGER(x)[vec_index]); case REALSXP: return ((uint32)REAL(x)[vec_index]); case LGLSXP: return ((uint32)LOGICAL(x)[vec_index]); case RAWSXP: return ((uint32)RAW(x)[vec_index]); case STRSXP: return Int32FromString(CHAR(STRING_ELT(x, vec_index))); default: Rcpp::stop("cannot cast SEXP to uint32"); } return (uint32)0; // -Wall, should not happen since we only call this when we know it works } uint64 GET_uint64(SEXP x, R_xlen_t vec_index) { switch (TYPEOF(x)) { case INTSXP: return ((uint64)INTEGER(x)[vec_index]); case REALSXP: return ((uint64)REAL(x)[vec_index]); case LGLSXP: return ((uint64)LOGICAL(x)[vec_index]); case RAWSXP: return ((uint64)RAW(x)[vec_index]); case STRSXP: return Int64FromString(CHAR(STRING_ELT(x, vec_index))); default: Rcpp::stop("cannot cast SEXP to uint64"); } return (uint64)0; // -Wall, should not happen since we only call this when we know it works } bool GET_bool(SEXP x, R_xlen_t vec_index) { switch (TYPEOF(x)) { case INTSXP: if (INTEGER(x)[vec_index] == R_NaInt) { Rcpp::stop("NA boolean values can not be stored in bool protocol buffer fields"); } return ((bool)INTEGER(x)[vec_index]); case REALSXP: if (REAL(x)[vec_index] == R_NaReal) { Rcpp::stop("NA boolean values can not be stored in bool protocol buffer fields"); } return ((bool)REAL(x)[vec_index]); case LGLSXP: if (LOGICAL(x)[vec_index] == NA_LOGICAL) { Rcpp::stop("NA boolean values can not be stored in bool protocol buffer fields"); } return ((bool)LOGICAL(x)[vec_index]); case RAWSXP: return ((bool)RAW(x)[vec_index]); default: Rcpp::stop("cannot cast SEXP to bool"); } return (bool)0; // Unreachable. -Wall } std::string GET_stdstring(SEXP x, R_xlen_t vec_index) { if (TYPEOF(x) == STRSXP) { return (CHAR(STRING_ELT(x, vec_index))); } return ""; // Unreachable. -Wall } std::string GET_bytes(SEXP x, R_xlen_t vec_index) { switch (TYPEOF(x)) { case RAWSXP: if (vec_index == 0) { return (std::string((const char*)RAW(x), (size_t)LENGTH(x))); } else { Rcpp::stop("cannot cast SEXP to bytes"); } case VECSXP: if (TYPEOF(VECTOR_ELT(x, vec_index)) == RAWSXP) { return (std::string((const char*)RAW(VECTOR_ELT(x, vec_index)), (size_t)LENGTH(VECTOR_ELT(x, vec_index)))); } else { Rcpp::stop("cannot cast SEXP to bytes"); } default: Rcpp::stop("cannot cast SEXP to bytes"); } return ""; // Unreachable. -Wall } /** * indicates if this is a list of messages * * @param x a list (VECSXP), not a long vec * @return TRUE if all objects are instances of Message class */ Rboolean allAreMessages(SEXP x) { if (TYPEOF(x) != VECSXP) return _FALSE_; R_xlen_t n = LENGTH(x); // Caller verifies its not a long vec SEXP current; for (R_xlen_t i = 0; i < n; i++) { current = VECTOR_ELT(x, i); /* not an S4 object */ if (TYPEOF(current) != S4SXP) return _FALSE_; /* not a Message object */ if (!Rf_inherits(current, "Message")) return _FALSE_; } return _TRUE_; } /** * indicates if this is a list of raws * * @param x a list (VECSXP) * @return TRUE if all objects are instances of RAWSXP */ Rboolean allAreRaws(SEXP x) { if (TYPEOF(x) != VECSXP) return _FALSE_; R_xlen_t n = LENGTH(x); SEXP current; for (R_xlen_t i = 0; i < n; i++) { current = VECTOR_ELT(x, i); /* not a RAWSXP */ if (TYPEOF(current) != RAWSXP) return _FALSE_; } return _TRUE_; } /** * check that all the values contained in value are suitable for the * enum type * * @param field_desc field descriptor of an enum type * @param value value to potentially fill the enum * */ void CHECK_values_for_enum(const GPB::FieldDescriptor* field_desc, SEXP value) { BEGIN_RCPP const GPB::EnumDescriptor* enum_desc = field_desc->enum_type(); // N.B. n undefined if TYPEOF(value) not a vector, but we catch that below. R_xlen_t n = XLENGTH(value); switch (TYPEOF(value)) { // {{{ numbers case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { int nenums = enum_desc->value_count(); // Guaranteed to be > 0. std::vector possibles(nenums); for (int i = 0; i < nenums; i++) { possibles[i] = enum_desc->value(i)->number(); } /* loop around the numbers to see if they are in the possibles */ for (int i = 0; i < n; i++) { int val = GET_int(value, i); int ok = 0; for (int j = 0; j < nenums; j++) { if (val == possibles[j]) { ok = 1; break; } } if (!ok) { Rcpp::stop("wrong value for enum"); } } break; } // }}} // {{{ STRSXP case STRSXP: { int nenums = enum_desc->value_count(); std::vector possibles(nenums); for (int i = 0; i < nenums; i++) { possibles[i] = enum_desc->value(i)->name(); } /* loop around the numbers to see if they are in the possibles */ for (int i = 0; i < n; i++) { const char* val = CHAR(STRING_ELT(value, i)); int ok = 0; /* FIXME: there is probably something more efficient */ for (int j = 0; j < nenums; j++) { if (!possibles[j].compare(val)) { ok = 1; break; } } if (!ok) { Rcpp::stop("wrong value for enum"); } } break; } // }}} default: Rcpp::stop("impossible to convert to a enum"); } VOID_END_RCPP } /** * check that the values are suitable for the field descriptor * * @throws Rcpp::exception on error (uncaught) */ void CHECK_messages(const GPB::FieldDescriptor* field_desc, SEXP values) { if (TYPEOF(values) != VECSXP) { Rcpp::stop("expecting a list of messages"); } const char* target = field_desc->message_type()->full_name().c_str(); int n = LENGTH(values); for (int i = 0; i < n; i++) { if (!isMessage(VECTOR_ELT(values, i), target)) { // TODO(mstokely): When we have C++11 CXX11, use // std::to_string(i) // {{{ std::string s; std::stringstream out; out << i; s = out.str(); // }}} string message = "List element " + s + " is not a message " + "of the appropriate type ('" + target + "')"; Rcpp::stop(message.c_str()); } } } /** * check that all repeated values are ok before doing anything, * otherwise this could lead to modifying a few values then failing in * an inconsistent state. */ void CHECK_repeated_vals(const GPB::FieldDescriptor* field_desc, SEXP value, int value_size) { switch (field_desc->type()) { case TYPE_MESSAGE: case TYPE_GROUP: { switch (TYPEOF(value)) { case VECSXP: { /* check that it is a list of Messages of the appropriate type */ CHECK_messages(field_desc, value); break; } case S4SXP: { /* check that this is a message of the appropriate type */ if (!isMessage(value, field_desc->message_type()->full_name().c_str())) { string message = "Not a message of type '" + field_desc->message_type()->full_name() + "'"; Rcpp::stop(message.c_str()); } break; } default: Rcpp::stop("impossible to convert to a message"); } break; } case TYPE_ENUM: { const GPB::EnumDescriptor* enum_desc = field_desc->enum_type(); /* check first, it means we have to loop twice, but otherwise this could have some side effects before the exception is thrown */ /* FIXME: the checking should go before the resizing */ switch (TYPEOF(value)) { // {{{ numbers case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { int nenums = enum_desc->value_count(); std::vector possibles(nenums); for (int i = 0; i < nenums; i++) { possibles[i] = enum_desc->value(i)->number(); } /* loop around the numbers to see if they are in the possibles */ for (int i = 0; i < value_size; i++) { int val = GET_int(value, i); int ok = 0; for (int j = 0; j < nenums; j++) { if (val == possibles[j]) { ok = 1; break; } } if (!ok) { Rcpp::stop("wrong value for enum"); } } break; } // }}} // {{{ STRSXP case STRSXP: { int nenums = enum_desc->value_count(); std::vector possibles(nenums); for (int i = 0; i < nenums; i++) { possibles[i] = enum_desc->value(i)->name(); } /* loop around the numbers to see if they are in the possibles */ for (int i = 0; i < value_size; i++) { const char* val = CHAR(STRING_ELT(value, i)); int ok = 0; /* FIXME: there is probably something more efficient */ for (int j = 0; j < nenums; j++) { if (!possibles[j].compare(val)) { ok = 1; break; } } if (!ok) { Rcpp::stop("wrong value for enum"); } } break; } // }}} default: Rcpp::stop("impossible to convert to a enum"); } break; } case TYPE_DOUBLE: case TYPE_FLOAT: case TYPE_INT64: case TYPE_UINT64: case TYPE_INT32: case TYPE_FIXED64: case TYPE_FIXED32: case TYPE_BOOL: case TYPE_STRING: case TYPE_BYTES: case TYPE_UINT32: case TYPE_SFIXED32: case TYPE_SFIXED64: case TYPE_SINT32: case TYPE_SINT64: { ; // nothing, just to satisfy -Wall } } } /** * set a non-repeated message field to a new value * * @param message pointer to a message * @param ref pointer to reflection object for message * @param field_desc pointer to field descriptor to update * @param value new value for the field * @param value_size size of the new value for the field * @throws Rcpp::exception on error (uncaught) * @return void, the message is modified by reference */ void setNonRepeatedMessageField(GPB::Message* message, const Reflection* ref, const GPB::FieldDescriptor* field_desc, SEXP value, int value_size) { if (value_size > 1) { Rcpp::stop("cannot set non-repeated field to vector of length > 1"); } switch (GPB::FieldDescriptor::TypeToCppType(field_desc->type())) { // {{{ simple cases using macro expansion #undef HANDLE_SINGLE_FIELD #define HANDLE_SINGLE_FIELD(CPPTYPE, CAMEL, TYPE) \ case CPPTYPE: { \ ref->Set##CAMEL(message, field_desc, Rcpp::as(value)); \ break; \ } HANDLE_SINGLE_FIELD(CPPTYPE_DOUBLE, Double, double) HANDLE_SINGLE_FIELD(CPPTYPE_FLOAT, Float, float) case CPPTYPE_BOOL: { // TODO(mstokely): Rcpp should handle this! if ((TYPEOF(value) == LGLSXP) && (LOGICAL(value)[0] == NA_LOGICAL)) { Rcpp::stop("NA boolean values can not be stored in bool protocol buffer fields"); } else if ((TYPEOF(value) == INTSXP) && (INTEGER(value)[0] == R_NaInt)) { Rcpp::stop("NA boolean values can not be stored in bool protocol buffer fields"); } else if ((TYPEOF(value) == REALSXP) && (REAL(value)[0] == R_NaReal)) { Rcpp::stop("NA boolean values can not be stored in bool protocol buffer fields"); } ref->SetBool(message, field_desc, Rcpp::as(value)); break; } case CPPTYPE_INT32: { if (TYPEOF(value) == STRSXP) { const string int32str = COPYSTRING(CHAR(STRING_ELT(value, 0))); ref->SetInt32(message, field_desc, Int32FromString(int32str)); break; } else { ref->SetInt32(message, field_desc, Rcpp::as(value)); break; } } case CPPTYPE_UINT32: { if (TYPEOF(value) == STRSXP) { const string uint32str = COPYSTRING(CHAR(STRING_ELT(value, 0))); ref->SetUInt32(message, field_desc, Int32FromString(uint32str)); break; } else { // Rcpp::as is broken for uint32 types, so we just get Rcpp // to give us a valid double, ref->SetUInt32(message, field_desc, Rcpp::as(value)); break; } } #ifdef RCPP_HAS_LONG_LONG_TYPES case CPPTYPE_INT64: { // TODO(mstokely) Rcpp::as of a STRSEXP should just // work for strings representing int64s. if (TYPEOF(value) == STRSXP) { const string int64str = COPYSTRING(CHAR(STRING_ELT(value, 0))); ref->SetInt64(message, field_desc, Int64FromString(int64str)); break; } else { ref->SetInt64(message, field_desc, Rcpp::as(value)); break; } } case CPPTYPE_UINT64: { // TODO(mstokely) Rcpp::as of a STRSEXP should just // work for strings representing int64s. if (TYPEOF(value) == STRSXP) { const string int64str = COPYSTRING(CHAR(STRING_ELT(value, 0))); ref->SetUInt64(message, field_desc, Int64FromString(int64str)); break; } else { ref->SetUInt64(message, field_desc, Rcpp::as(value)); break; } } #endif #undef HANDLE_SINGLE_FIELD default: Rcpp::stop("Unsupported type"); // }}} // {{{ string case CPPTYPE_STRING: { switch (TYPEOF(value)) { case STRSXP: { ref->SetString(message, field_desc, COPYSTRING(CHAR(STRING_ELT(value, 0)))); break; } case RAWSXP: { ref->SetString(message, field_desc, GET_bytes(value, 0)); break; } case S4SXP: { /* check if value is a message */ if (!Rf_inherits(value, "Message")) { Rcpp::stop("Can only convert S4 objects of class 'Message'"); } GPB::Message* __mess = GET_MESSAGE_POINTER_FROM_S4(value); ref->SetString(message, field_desc, __mess->SerializeAsString()); break; } default: Rcpp::stop("Cannot convert to string"); } break; } // }}} // {{{ message case CPPTYPE_MESSAGE: { if (TYPEOF(value) == S4SXP && Rf_inherits(value, "Message")) { GPB::Message* mess = (GPB::Message*)EXTPTR_PTR(GET_SLOT(value, Rf_install("pointer"))); const char* type = mess->GetDescriptor()->full_name().c_str(); const char* target = field_desc->message_type()->full_name().c_str(); if (strcmp(type, target)) { Rcpp::stop("wrong message type"); } GPB::Message* m = ref->MutableMessage(message, field_desc); m->CopyFrom(*mess); } else { Rcpp::stop("type mismatch, expecting a 'Message' object"); } break; } // }}} // {{{ enum case CPPTYPE_ENUM: { const GPB::EnumDescriptor* enum_desc = field_desc->enum_type(); switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { int val = Rcpp::as(value); const GPB::EnumValueDescriptor* evd = enum_desc->FindValueByNumber(val); if (!evd) { Rcpp::stop("wrong value for enum"); } else { ref->SetEnum(message, field_desc, evd); } break; } case STRSXP: { std::string val = Rcpp::as(value); const GPB::EnumValueDescriptor* evd = enum_desc->FindValueByName(val); if (!evd) { Rcpp::stop("wrong value for enum"); } else { ref->SetEnum(message, field_desc, evd); } break; } default: Rcpp::stop("cannot set enum value"); } break; } // }}} } } /** * set a repeated message field to a new value * * @param message pointer to a message * @param ref pointer to reflection object for message * @param field_desc pointer to field descriptor to update * @param value new value for the field * @param value_size size of the new value for the field * @throws Rcpp::exception on error (uncaught) * @return void, the message is modified by reference */ void setRepeatedMessageField(GPB::Message* message, const Reflection* ref, const GPB::FieldDescriptor* field_desc, SEXP value, R_xlen_t value_size) { // The number of elements already in the repeated field. int field_size = ref->FieldSize(*message, field_desc); /* in case of messages or enum, we have to check that all values are ok before doing anything, othewise this could leed to modify a few values and then fail which is not good */ CHECK_repeated_vals(field_desc, value, value_size); /* Remove some items if there are too many. */ if (field_size > value_size) { /* we need to remove some */ while (field_size > value_size) { ref->RemoveLast(message, field_desc); field_size--; } } switch (field_desc->type()) { // {{{ int32 case TYPE_INT32: case TYPE_SINT32: case TYPE_SFIXED32: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: case STRSXP: // For int32, we support chars. { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedInt32(message, field_desc, i, GET_int32(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddInt32(message, field_desc, GET_int32(value, i)); } } break; } default: Rcpp::stop("Cannot convert to int32"); } break; } // }}} // {{{ int64 case TYPE_INT64: case TYPE_SINT64: case TYPE_SFIXED64: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: case STRSXP: // For int64, we support chars. { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedInt64(message, field_desc, i, GET_int64(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddInt64(message, field_desc, GET_int64(value, i)); } } break; } default: Rcpp::stop("Cannot convert to int64"); } break; } // }}} // {{{ uint32 case TYPE_UINT32: case TYPE_FIXED32: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: case STRSXP: // For int32, we support chars. { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedUInt32(message, field_desc, i, GET_uint32(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddUInt32(message, field_desc, GET_uint32(value, i)); } } break; } default: Rcpp::stop("Cannot convert to uint32"); } break; } // }}} // {{{ uint64 case TYPE_UINT64: case TYPE_FIXED64: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: case STRSXP: // For int64, we support chars. { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedUInt64(message, field_desc, i, GET_uint64(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddUInt64(message, field_desc, GET_uint64(value, i)); } } break; } default: Rcpp::stop("Cannot convert to int64"); } break; } // }}} // {{{ double case TYPE_DOUBLE: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedDouble(message, field_desc, i, GET_double(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddDouble(message, field_desc, GET_double(value, i)); } } break; } default: Rcpp::stop("Cannot convert to double"); } break; } // }}} // {{{ float case TYPE_FLOAT: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedFloat(message, field_desc, i, GET_float(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddFloat(message, field_desc, GET_float(value, i)); } } break; } default: Rcpp::stop("Cannot convert to float"); } break; } // }}} // {{{ bool case TYPE_BOOL: { switch (TYPEOF(value)) { case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { R_xlen_t i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { ref->SetRepeatedBool(message, field_desc, i, GET_bool(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddBool(message, field_desc, GET_bool(value, i)); } } break; } default: Rcpp::stop("Cannot convert to bool"); } break; } // }}} // {{{ string case TYPE_STRING: case TYPE_BYTES: { switch (TYPEOF(value)) { case STRSXP: { /* in any case, fill the values up to field_size */ R_xlen_t i = 0; for (; i < field_size; i++) { ref->SetRepeatedString(message, field_desc, i, COPYSTRING(CHAR(STRING_ELT(value, i)))); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddString(message, field_desc, COPYSTRING(CHAR(STRING_ELT(value, i)))); } } break; } case RAWSXP: { /* in any case, fill the values up to field_size */ R_xlen_t i = 0; for (; i < field_size; i++) { ref->SetRepeatedString(message, field_desc, i, GET_bytes(value, 0)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddString(message, field_desc, GET_bytes(value, 0)); } } break; } case S4SXP: { /* check if value is a message */ if (!Rf_inherits(value, "Message")) { Rcpp::stop("Can only convert S4 objects of class 'Message'"); } GPB::Message* __mess = GET_MESSAGE_POINTER_FROM_S4(value); ref->SetRepeatedString(message, field_desc, 0, __mess->SerializeAsString()); break; } case VECSXP: { // we know it is a list of messages or raws because it // has been tested above if (LENGTH(value) > 0 && TYPEOF(VECTOR_ELT(value, 0)) == RAWSXP) { /* in any case, fill the values up to field_size */ R_xlen_t i = 0; for (; i < field_size; i++) { ref->SetRepeatedString(message, field_desc, i, GET_bytes(value, i)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { ref->AddString(message, field_desc, GET_bytes(value, i)); } } } else { // FIXME: we should probably use SerializeToString // as indicated in the protobuf api documentation // http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.message_lite.html#MessageLite.SerializeAsString.details GPB::Message* __mess; /* in any case, fill the values up to field_size */ R_xlen_t i = 0; for (; i < field_size; i++) { __mess = GET_MESSAGE_POINTER_FROM_S4(VECTOR_ELT(value, i)); ref->SetRepeatedString(message, field_desc, i, __mess->SerializeAsString()); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { __mess = GET_MESSAGE_POINTER_FROM_S4(VECTOR_ELT(value, i)); ref->AddString(message, field_desc, __mess->SerializeAsString()); } } } break; } default: Rcpp::stop("Cannot convert to string"); } break; } // }}} // {{{ message case TYPE_MESSAGE: case TYPE_GROUP: { if (TYPEOF(value) == S4SXP) { /* we know it is a message of the correct type (tested above) */ GPB::Message* mess = GET_MESSAGE_POINTER_FROM_S4(value); if (field_size == 1) { /* FIXME: we should not __copy__ the message */ ref->MutableRepeatedMessage(message, field_desc, 0)->CopyFrom(*mess); } else { /* FIXME */ ref->ClearField(message, field_desc); /* FIXME: we should not __copy__ the message */ ref->AddMessage(message, field_desc)->CopyFrom(*mess); } } else if (TYPEOF(value) == VECSXP) { /* in any case, fill the values up to field_size */ int i = 0; for (; i < field_size; i++) { GPB::Message* mess = GET_MESSAGE_POINTER_FROM_S4(VECTOR_ELT(value, i)); /* we already know it is of the correct type because of the premptive check above */ ref->MutableRepeatedMessage(message, field_desc, i)->CopyFrom(*mess); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { GPB::Message* mess = GET_MESSAGE_POINTER_FROM_S4(VECTOR_ELT(value, i)); /* we already know it is of the correct type because of the premptive check above */ ref->AddMessage(message, field_desc)->CopyFrom(*mess); } } } else { Rcpp::stop("type mismatch, expecting a 'Message' object or a list of them"); } break; } // }}} // {{{ enum case TYPE_ENUM: { const GPB::EnumDescriptor* enum_desc = field_desc->enum_type(); switch (TYPEOF(value)) { // {{{ numbers case INTSXP: case REALSXP: case LGLSXP: case RAWSXP: { int i = 0; /* in any case, fill the values up to field_size */ for (; i < field_size; i++) { int val = GET_int(value, i); ref->SetRepeatedEnum(message, field_desc, i, enum_desc->FindValueByNumber(val)); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { int val = GET_int(value, i); ref->AddEnum(message, field_desc, enum_desc->FindValueByNumber(val)); } } break; } // }}} // {{{ STRSXP case STRSXP: { /* in any case, fill the values up to field_size */ int i = 0; for (; i < field_size; i++) { std::string val = CHAR(STRING_ELT(value, i)); const GPB::EnumValueDescriptor* evd = enum_desc->FindValueByName(val); ref->SetRepeatedEnum(message, field_desc, i, evd); } /* then add some if needed */ if (value_size > field_size) { for (; i < value_size; i++) { std::string val = CHAR(STRING_ELT(value, i)); const GPB::EnumValueDescriptor* evd = enum_desc->FindValueByName(val); ref->AddEnum(message, field_desc, evd); } } break; } // }}} default: Rcpp::stop("cannot set enum value"); } } // }}} } } /** * set a message field to a new value * * @param pointer external pointer to a message * @param name name of the field, or an S4 FieldDescriptor object. * @param value new value for the field * * @return allways NULL, the message is modified by reference */ SEXP setMessageField(SEXP pointer, SEXP name, SEXP value) { BEGIN_RCPP RPB_DEBUG_BEGIN("setMessageField") PRINT_DEBUG_INFO("pointer", pointer); PRINT_DEBUG_INFO("name", name); PRINT_DEBUG_INFO("value", value); /* grab the Message pointer */ GPB::Message* message = GET_MESSAGE_POINTER_FROM_XP(pointer); /* check that we can get a file descriptor from name */ const GPB::FieldDescriptor* field_desc = getFieldDescriptor(message, name); const Reflection* ref = message->GetReflection(); if (value == R_NilValue || (Rf_isVector(value) && LENGTH(value) == 0)) { ref->ClearField(message, field_desc); return R_NilValue; } // {{{ preliminary checks R_xlen_t value_size = 1; if (Rf_isVector(value)) { if (IS_LONG_VEC(value)) { // field_size is an int, so presumably it would generate // a CHECK failure in protobuf code on 2^32 element anyway. Rcpp_error("Long vectors not supported for repeated fields."); } else { value_size = LENGTH(value); } } // if the R type is RAWSXP and the cpp type is string or bytes, // then value_size is actually one because the raw vector // is converted to a string GPB::FieldDescriptor::Type field_type = field_desc->type(); if (field_type == TYPE_STRING || field_type == TYPE_BYTES) { if (TYPEOF(value) == RAWSXP) { value_size = 1; } else if (TYPEOF(value) == STRSXP) { value_size = LENGTH(value); } else if (TYPEOF(value) == S4SXP && Rf_inherits(value, "Message")) { value_size = 1; /* we will store the message payload */ } else if (TYPEOF(value) == VECSXP && allAreMessages(value)) { value_size = LENGTH(value); } else if (TYPEOF(value) == VECSXP && allAreRaws(value)) { value_size = LENGTH(value); } else { Rcpp::stop("cannot convert to string"); } } // }}} if (field_desc->is_repeated()) { setRepeatedMessageField(message, ref, field_desc, value, value_size); } else { setNonRepeatedMessageField(message, ref, field_desc, value, value_size); } RPB_DEBUG_END("setMessageField") END_RCPP } RPB_FUNCTION_VOID_2(update_message, Rcpp::XPtr message, Rcpp::List list) { Rcpp::CharacterVector names = list.attr("names"); int n = list.size(); for (int i = 0; i < n; i++) { (void)setMessageField(message, names[i], list[i]); } } } // namespace rprotobuf RProtoBuf/src/RSourceTree.cpp0000644000175100001440000000315513037407202015651 0ustar hornikusers// -*- indent-tabs-mode: nil; tab-width: 4; show-trailing-whitespace: t; c-indent-level: 4; c-basic-offset: 4; -*- #include "rprotobuf.h" #include "RSourceTree.h" namespace rprotobuf { RSourceTree::RSourceTree() : directories() {} GPB::io::ZeroCopyInputStream* RSourceTree::Open(const std::string& filename) { /* first, try to open the file as it is */ int file_descriptor = open(filename.c_str(), O_RDONLY); if (file_descriptor < 0) { /* then try the directories */ std::set::iterator it; it = directories.begin(); std::string file; while (it != directories.end()) { file = *it; file += "/"; file += filename; file_descriptor = open(file.c_str(), O_RDONLY); if (file_descriptor > 0) break; ++it; } } if (file_descriptor < 0) { return NULL; } GPB::io::FileInputStream* result = new GPB::io::FileInputStream(file_descriptor); result->SetCloseOnDelete(true); return result; } void RSourceTree::addDirectory(const std::string& directory) { directories.insert(directory); } void RSourceTree::addDirectories(SEXP dirs) { int n = LENGTH(dirs); for (int i = 0; i < n; i++) { directories.insert(std::string(CHAR(STRING_ELT(dirs, i)))); } } void RSourceTree::removeDirectory(const std::string& directory) { directories.erase(directory); } void RSourceTree::removeDirectories(SEXP dirs) { int n = LENGTH(dirs); for (int i = 0; i < n; i++) { directories.erase(std::string(CHAR(STRING_ELT(dirs, i)))); } } } // namespace rprotobuf RProtoBuf/NAMESPACE0000644000175100001440000000573312566371245013414 0ustar hornikusers ## Package has dynamic library useDynLib(RProtoBuf) importFrom(methods, new, show, as, is) importFrom(utils, str, packageDescription) importFrom(stats, update) importFrom(tools, file_path_as_absolute) importFrom(RCurl, basicTextGatherer, curlPerform) importFrom(Rcpp, evalCpp) exportClasses( # descriptors "Descriptor", "FieldDescriptor", "EnumDescriptor", "ServiceDescriptor", "MethodDescriptor", "FileDescriptor", "EnumValueDescriptor", # message "Message", # rpc "RpcHTTP", # virtual streams "ZeroCopyInputStream", "ZeroCopyOutputStream", # concrete implementations "ArrayInputStream", "ArrayOutputStream", "FileInputStream", "FileOutputStream", "ConnectionInputStream", "ConnectionOutputStream" ) exportMethods( "new", "[[", "[[<-", "$", "$<-", "show", "serialize", "as.character", "update", "has", "clone", "merge", "read", "readASCII", "bytesize", "length", "str", "isInitialized", "clear", "size", "size<-", "swap", "descriptor", "set", "fetch", "toString", "identical", "==", "!=", "all.equal", "add", "fileDescriptor", "name", "names", "flush", "close", "setExtension", "getExtension", "containing_type", "field_count", "nested_type_count", "enum_type_count", "field", "nested_type", "enum_type", # FieldDescriptor "is_extension", "number", "label", "is_required", "is_repeated", "is_optional", "has_default_value", "default_value", "message_type", "enum_type", "type", "cpp_type", # EnumDescriptor "value_count", "value", # ServiceDescriptor "method_count", "method", # MethodDescriptor "input_type", "output_type", # rpc "invoke", # streams "Next", "ByteCount", "BackUp", "Skip", "ArrayInputStream", "ArrayOutputStream", "FileInputStream", "FileOutputStream", "GetErrno", "SetCloseOnDelete", "ConnectionInputStream", "ConnectionOutputStream", "ReadRaw", "ReadString", "ReadVarint32", "ReadLittleEndian32", "ReadLittleEndian64", "ReadVarint64", "WriteRaw", "WriteString", "WriteLittleEndian32", "WriteLittleEndian64", "WriteVarint32", "WriteVarint64" ) export( "P", "readProtoFiles", "asMessage" ) if( exists( ".DollarNames", asNamespace("utils") ) ) importFrom( utils, .DollarNames ) S3method(.DollarNames, Message ) S3method(.DollarNames, Descriptor ) S3method(.DollarNames, EnumDescriptor ) S3method(.DollarNames, EnumValueDescriptor ) S3method(.DollarNames, FileDescriptor ) S3method(.DollarNames, FieldDescriptor ) S3method(.DollarNames, ServiceDescriptor ) S3method(.DollarNames, MethodDescriptor ) S3method(.DollarNames, ZeroCopyInputStream ) S3method(.DollarNames, ZeroCopyOutputStream ) S3method( with, Message ) S3method( within, Message) S3method( as.list, Message ) S3method( as.list, Descriptor ) S3method( as.list, EnumDescriptor ) S3method( as.list, FileDescriptor ) S3method( as.list, ServiceDescriptor ) # constants exportPattern( "^TYPE_" ) exportPattern( "^CPPTYPE_" ) exportPattern( "^LABEL_" ) # copied from RProtoBufUtils export( "serialize_pb", "unserialize_pb", "can_serialize_pb" ) # export( run_unit_tests ) RProtoBuf/demo/0000755000175100001440000000000012440004312013064 5ustar hornikusersRProtoBuf/demo/io.R0000644000175100001440000000164412440004312013623 0ustar hornikusersrequire( RProtoBuf ) ### read messages from files and binary connections # read a message from a file name f <- system.file( "examples", "addressbook.pb", package = "RProtoBuf" ) m1 <- read( tutorial.AddressBook, f ) writeLines( as.character( m1 ) ) # read the same message from a (binary) file connection con <- file( f, open = "rb" ) m2 <- read( tutorial.AddressBook, con ) # this also works: # m2 <- tutorial.AddressBook$read( con ) writeLines( as.character( m2 ) ) close( con ) # TODO: we need another example from a more fancy connection (pipe, ...) stopifnot( identical( as.character(m1), as.character(m2) ) ) ### write messages to files and binary connections tf1 <- tempfile() serialize( m1, tf1 ) tf2 <- tempfile() con <- file( tf2, open = "wb" ) serialize( m2, con ) close( con ) # test that the two binary files are identical stopifnot( identical( readBin( tf1, raw(0), 1000), readBin( tf2, raw(0), 1000) ) ) RProtoBuf/demo/addressbook.R0000644000175100001440000000325012440004312015507 0ustar hornikusers# load the package require( RProtoBuf ) # read all the proto files in the proto directory # of the package "RProtoBuf" # (this is also done in the startup of the package, so this call is # actually redundant) readProtoFiles( package = "RProtoBuf" ) # creating three Person messages # create a prototype with a simple call to new on the # descriptor for the Person message type, and then update the message # with fields romain <- update( new( tutorial.Person ), email = "romain@r-enthusiasts.com", id = 1, name = "Romain Francois", phone = new( tutorial.Person.PhoneNumber , number = "+33(0)...", type = "MOBILE" ) ) # directly supply parameters to the constructor dirk <- new( tutorial.Person, email = "edd@debian.org", id = 2, name = "Dirk Eddelbuettel" ) # update the phone repeated field with a list of PhoneNumber messages dirk$phone <- list( new( tutorial.Person.PhoneNumber , number = "+01...", type = "MOBILE" ), new( tutorial.Person.PhoneNumber , number = "+01...", type = "HOME" ) ) # build the address book book <- new( tutorial.AddressBook, person = list( romain, dirk ) ) # debug string. This is not what is transferred in the wire writeLines( as.character( book ) ) # the serialized message # see also the io demo to see how to serialize messages to connections # and files serialize( book, NULL ) # number of bytes taken by the message on the wire bytesize( book ) length( serialize( book, NULL ) ) # swap two persons in the address book # (1-based indexing) book$swap( "person", 1L , 2L ) writeLines( as.character( book ) ) # number of "person" in the book book$size( "person" ) # clear the message book$clear( ) writeLines( as.character( book ) ) RProtoBuf/demo/00Index0000644000175100001440000000015312440004312014215 0ustar hornikusersaddressbook Demonstration of RProtoBuf functionality io Input/Output handling of protocol buffer messages RProtoBuf/R/0000755000175100001440000000000012762053206012356 5ustar hornikusersRProtoBuf/R/clear.R0000644000175100001440000000202212440004312013546 0ustar hornikuserssetGeneric( "clear", function(object, field, ...){ standardGeneric( "clear" ) } ) setMethod( "clear", signature( "Message", "missing" ), function(object, field, ...){ .Call( "Message__clear", object@pointer, PACKAGE = "RProtoBuf" ) invisible( object ) } ) setMethod( "clear", signature( "Message", "character" ), function(object, field, ...){ .Call( "Message__clear_field", object@pointer, field, PACKAGE = "RProtoBuf" ) invisible( object ) } ) setMethod( "clear", signature( "Message", "integer" ), function(object, field, ...){ .Call( "Message__clear_field", object@pointer, field, PACKAGE = "RProtoBuf" ) invisible( object ) } ) setMethod( "clear", signature( "Message", "numeric" ), function(object, field, ...){ .Call( "Message__clear_field", object@pointer, as.integer(field), PACKAGE = "RProtoBuf" ) invisible( object ) } ) setMethod( "clear", signature( "Message", "raw" ), function(object, field, ...){ .Call( "Message__clear_field", object@pointer, as.integer(field), PACKAGE = "RProtoBuf" ) invisible( object ) } ) RProtoBuf/R/swap.R0000644000175100001440000000067012440004312013441 0ustar hornikuserssetGeneric("swap", function( object, field, left, right) { standardGeneric( "swap" ) } ) setMethod( "swap", "Message", function( object, field, left, right ){ left <- as.integer( left ) - 1L right <- as.integer( right ) - 1L if( length(left) != length(right) ){ stop( "left and right should have the same length" ) } .Call( "Message__swap", object@pointer, field, left, right, PACKAGE = "RProtoBuf" ) invisible( object ) } ) RProtoBuf/R/has.R0000644000175100001440000000105712440004312013242 0ustar hornikusers setGeneric( "has", function( object, name, ... ){ standardGeneric( "has" ) } ) ._has_message <- function( object, name, ...){ if (!.Call( "Message__field_exists", object@pointer, name, PACKAGE = "RProtoBuf" )) { return(NULL) } else { return(.Call( "Message__has_field", object@pointer, name, PACKAGE = "RProtoBuf" )) } } ._has_enum_name <- function( object, name, ...){ return(.Call( "has_enum_name", object@pointer, name, package = "RProtoBuf")) } setMethod( "has", "Message", ._has_message ) setMethod( "has", "EnumDescriptor", ._has_enum_name) RProtoBuf/R/extensions.R0000644000175100001440000000377012440004312014672 0ustar hornikusers# Copyright 2012 Google Inc. All Rights Reserved. # Author: mstokely@google.com (Murray Stokely) # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA # 02110-1301, USA. setGeneric( "setExtension", function(object, field, values){ standardGeneric( "setExtension" ) } ) setMethod( "setExtension", "Message", function( object, field, values ){ if (!inherits(field, "FieldDescriptor")) { stop("setExtension requires a FieldDescriptor") } if (!is_extension(field)) { stop(paste(name(field), "is not an extension FieldDescriptor.")) } .Call( "setMessageField", object@pointer, field, values, PACKAGE = "RProtoBuf" ) invisible( object ) } ) setGeneric( "getExtension", function(object, field){ standardGeneric( "getExtension" ) } ) setMethod( "getExtension", "Message", function( object, field){ if (!inherits(field, "FieldDescriptor")) { stop("getExtension requires a FieldDescriptor") } if (!is_extension(field)) { stop(paste(name(field), "is not an extension FieldDescriptor.")) } # This check causes a CHECK failure in the C++ code, so give # a more user-friendly error here. if (containing_type(field)@type != object@type) { stop(paste("Field", name(field), "does not match message type (", containing_type(field)@type, "!=", object@type, ")")) } .Call( "getExtension", object@pointer, field, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/http.handler.R0000644000175100001440000000103112440004312015052 0ustar hornikusers RProtoBuf.http.handler <- function(path, query, body) { if( !all( c("service", "method" ) %in% names(query) ) ){ stop( "need service and method " ) } service <- query[["service"]] method <- query[["method"]] m <- get( sprintf( "%s.%s", service, method ), as.environment( "RProtoBuf:DescriptorPool" ) ) if( is.null( m ) ){ stop( "unknown method" ) } input <- if( length( body ) ){ m$input_type()$read( body ) } else{ new( m$input_type() ) } res <- invoke( m, input ) list( serialize( res, NULL ) ) } RProtoBuf/R/size.R0000644000175100001440000000203312440004312013434 0ustar hornikusers setGeneric( "bytesize", function(object, ...){ standardGeneric( "bytesize" ) } ) setMethod( "bytesize", "Message", function(object, ...){ .Call( "Message__bytesize", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "size", function( object, field, ... ){ standardGeneric( "size" ) } ) setMethod( "size", "Message", function(object, field, ...){ if( is.character( field ) || is.numeric( field ) ){ .Call( "Message__field_size", object@pointer, field, PACKAGE = "RProtoBuf" ) } else{ stop( "field should be a character or a number" ) } } ) setGeneric( "size<-", function( object, field, ..., value ){ standardGeneric( "size<-" ) } ) setMethod( "size<-", "Message", function(object, field, ..., value){ if( !is.numeric( value ) ){ stop("value should be a number") } value <- as.integer( value )[1] if( is.character( field ) || is.numeric( field ) ){ .Call( "Message__set_field_size", object@pointer, field, value, PACKAGE = "RProtoBuf" ) } else{ stop( "field should be a character or a number" ) } object } ) RProtoBuf/R/clone.R0000644000175100001440000000040612440004312013564 0ustar hornikusers setGeneric( "clone", function( object, ... ){ standardGeneric( "clone" ) } ) ._clone.message <- function( object, ... ){ message <- .Call( "Message__clone", object@pointer ) update( message, ... ) message } setMethod( "clone", "Message", ._clone.message ) RProtoBuf/R/descriptor.R0000644000175100001440000000233312440004312014643 0ustar hornikusers setGeneric( "descriptor", function(object, ...){ standardGeneric( "descriptor" ) } ) setMethod( "descriptor", "Message", function(object, ...){ .Call( "Message__descriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "fileDescriptor", function(object, ...){ standardGeneric( "fileDescriptor" ) } ) setMethod( "fileDescriptor", "Message", function(object, ...){ .Call( "Message__fileDescriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "fileDescriptor", "Descriptor", function(object, ...){ .Call( "Descriptor__fileDescriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "fileDescriptor", "EnumDescriptor", function(object, ...){ .Call( "EnumDescriptor__fileDescriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "fileDescriptor", "FieldDescriptor", function(object, ...){ .Call( "FieldDescriptor__fileDescriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "fileDescriptor", "ServiceDescriptor", function(object, ...){ .Call( "ServiceDescriptor__fileDescriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "fileDescriptor", "MethodDescriptor", function(object, ...){ .Call( "MethodDescriptor__fileDescriptor", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/internals.R0000644000175100001440000000366612440004312014476 0ustar hornikusers# set of functions not supposed to be called by the end user # these are thin wrappers around C functions, to help with # the error trapping on R side #' thin wrapper around the C function of the same name #' #' @param files list of proto files to import #' @param dir directory in which to look for proto files (ignored if files is given) #' @param package if specified, proto files are imported from the "proto" directory #' of the package #' @return invisible(NULL) readProtoFiles <- function(files, dir, package = "RProtoBuf", pattern = "\\.proto$", lib.loc = NULL ){ if( missing( files ) ){ if( missing( dir ) ){ if( missing(package) ){ dir <- getwd() } else { dir <- system.file( "proto", package = package, lib.loc = lib.loc ) if( !file.exists( dir ) ){ stop( sprintf("package '%s' does not have a 'proto' directory", package) ) } } } files <- list.files( dir, pattern = pattern, full.names = TRUE ) } else { if( !is.character( files ) ){ stop( "'file' should be a character vector" ) } ex <- sapply( files, file.exists ) if( ! any( ex ) ){ stop( "none of the files exist" ) } # TODO: we need to pass the full path of the file # or create a mapping from the current working directory # in the DiskSourceTree files <- sapply(files[ex], function(x) file_path_as_absolute(x) ) } directories <- unique( c( getwd(), dirname(files) ) ) .Call( "readProtoFiles", files, directories, PACKAGE = "RProtoBuf" ) invisible(NULL) } getProtobufLibVersion <- function( format = FALSE ){ version <- .Call( "get_protobuf_library_version", PACKAGE = "RProtoBuf" ) if( format ){ major <- version %/% 10^6 minor <- ( tmp <- (version - major * 10^6) ) %/% 10^3 revision <- (tmp - minor * 10^3 ) sprintf( "%d.%d.%d", major, minor, revision ) } else { version } } RProtoBuf/R/00classes.R0000644000175100001440000004675212440004312014277 0ustar hornikusers# :tabSize=4:indentSize=4:noTabs=false:folding=explicit:collapseFolds=1: # this has to be IMPLEMENTATIONS <- new.env( parent = emptyenv() ) # invisible version of .Call .icall <- function(...) invisible(.Call(...)) # {{{ class definitions # we need to formalize connection so that the S4 methods # ConnectionInputStream and ConnectionOutputStream can # dispatch connections setOldClass( "connection" ) # FIXME: there is probably another way # TODO: include other subclasses of connections setOldClass( c("file", "connection" ) ) setOldClass( c("url", "connection" ) ) setClass( "Descriptor", representation( pointer = "externalptr", # pointer to a google::protobuf::Descriptor c++ object type = "character" # message type ), prototype = list( pointer = NULL, type = character(0) ) ) setClass( "FieldDescriptor", representation( pointer = "externalptr" , # pointer to a google::protobuf::FieldDescriptor c++ object name = "character", full_name = "character", type = "character" ), prototype = list( pointer = NULL, name = character(0), full_name = character(0), type = character(0) ) ) setClass( "EnumDescriptor", representation( pointer = "externalptr" , # pointer to a google::protobuf::EnumDescriptor c++ object name = "character", full_name = "character", type = "character" # TODO(mstokely): enums don't really have another type, remove? ), prototype = list( pointer = NULL, name = character(0), full_name = character(0), type = character(0) ) ) setClass( "ServiceDescriptor", representation( pointer = "externalptr", # pointer to a google::protobuf::ServiceDescriptor c++ object name = "character" # full name of the service ), prototype = list( pointer = NULL, name = character(0) ) ) setClass( "MethodDescriptor", representation( pointer = "externalptr", # pointer to a google::protobuf::ServiceDescriptor c++ object name = "character" , # full name of the service service = "character" # full name of the service that defines this method ), prototype = list( pointer = NULL, name = character(0), service = character(0) ) ) setClass( "FileDescriptor", representation( pointer = "externalptr", # pointer to a google::protobuf::FileDescriptor c++ object filename = "character", # filename package = "character" # the package ), prototype = list( pointer = NULL, filename = character(0), package = character(0) ) ) setClass( "EnumValueDescriptor", representation( pointer = "externalptr", # pointer to a google::protobuf::EnumValueDescriptor c++ object name = "character", full_name = "character" ), prototype = list( pointer = NULL, name = character(0), full_name = character(0) ) ) # actual objects setClass( "Message", representation( pointer = "externalptr", # pointer to sa google::protobuf::Message object type = "character" # message type (fully qualified, with package path) ), prototype = list( pointer = NULL, type = character(0) ) ) # rpc setClass( "RpcHTTP", representation( host = "character", port = "integer", root = "character" ), prototype = list( host = "127.0.0.1", port = 4444L, root = "" ) ) # streams setClass( "ZeroCopyInputStream", representation( pointer = "externalptr" ), prototype = list( pointer = NULL ), contains = "VIRTUAL" ) setClass( "ArrayInputStream", contains = "ZeroCopyInputStream" ) setClass( "FileInputStream", contains = "ZeroCopyInputStream" ) setClass( "ConnectionInputStream", contains = "ZeroCopyInputStream" ) setClass( "ZeroCopyOutputStream", representation( pointer = "externalptr" ), prototype = list( pointer = NULL ), contains = "VIRTUAL" ) setClass( "ArrayOutputStream", contains = "ZeroCopyInputStream" ) setClass( "FileOutputStream", contains = "ZeroCopyInputStream" ) setClass( "ConnectionOutputStream", contains = "ZeroCopyOutputStream" ) # }}} # {{{ new newProto <- function( descriptor, ... ){ message <- .Call( "newProtoMessage", descriptor, PACKAGE = "RProtoBuf" ) update( message, ... ) message } setGeneric("new") setMethod("new", signature(Class="Descriptor"), function(Class, ...) newProto(Class, ...)) # }}} # {{{ P P <- function( type, file ){ if( !missing(file) ){ readProtoFiles( file ) } if( missing( type ) ){ stop( "'type' is required" ) } if( !is.character(type) ){ stop( "'type' is not a character vector" ) } if( length(type) != 1L){ stop( "'type' should have exactly one element" ) } desc <- .Call( "getProtobufDescriptor", type, PACKAGE = "RProtoBuf" ) if( is.null( desc ) ){ # See if it is an extension desc <- .Call("getExtensionDescriptor", type, PACKAGE="RProtoBuf") if (is.null(desc)) { # See if it is an enum desc <- .Call("getEnumDescriptor", type, PACKAGE="RProtoBuf") if (is.null(desc)) { stop( sprintf( "could not find descriptor for message type '%s' ", type ) ) } } } desc } # }}} # {{{ show setMethod( "show", c( "Message" ), function(object){ tmp <- sprintf( "message of type '%s' with %d field%s set", object@type, length(object), if (length(object) == 1) "" else "s" ) nexts <- .Call("Message__num_extensions", object@pointer, PACKAGE="RProtoBuf") if (nexts > 0) { tmp <- paste(tmp, sprintf("and %d extension%s", nexts, if (nexts == 1) "" else "s")) } cat(tmp, fill=TRUE) } ) setMethod( "show", c( "Descriptor" ), function(object){ cat( sprintf( "descriptor for type '%s' ", object@type ) , fill=TRUE) } ) setMethod( "show", c( "FieldDescriptor" ), function(object){ cat( sprintf( "descriptor for field '%s' of type '%s' ", object@name, object@type ), fill=TRUE) } ) setMethod( "show", c( "EnumDescriptor" ), function(object){ cat( sprintf( "descriptor for enum '%s' with %d values", object@name, value_count(object) ) , fill=TRUE) } ) setMethod( "show", c( "ServiceDescriptor" ), function(object){ cat( sprintf( "service descriptor <%s>", object@name ) , fill=TRUE) } ) setMethod( "show", c( "FileDescriptor" ), function(object){ cat( sprintf( "file descriptor for package %s (%s)", object@package, object@filename) , fill=TRUE) } ) setMethod( "show", c( "EnumValueDescriptor" ), function(object){ cat( sprintf( "enum value descriptor %s", object@full_name), fill=TRUE) } ) # }}} # {{{ dollar extractors setMethod("$", "Message", function(x, name) { switch( name, "has" = function( ... ) has(x, ...), "clone" = function( ... ) .Call( "Message__clone" , x@pointer, ..., PACKAGE = "RProtoBuf"), "isInitialized" = function() .Call( "Message__is_initialized", x@pointer, PACKAGE = "RProtoBuf"), "descriptor" = function() .Call( "Message__descriptor" , x@pointer, PACKAGE = "RProtoBuf" ), "size" = function(field, ...) size(x, field, ... ), "bytesize" = function() bytesize(x), "swap" = function(...) swap(x,...), "update" = function(...) update(x, ...), "str" = function() str(x), "as.character" = function() as.character(x), "as.list" = function() as.list(x), "asMessage" = function() asMessage(x), "setExtension" = function(field, values, ...) setExtension(x, field, values, ...), "getExtension" = function(field, ...) getExtension(x, field, ...), "set" = function(...) set( x, ... ), "fetch" = function(...) fetch(x, ... ), "toString" = function(...) toString( x, ... ), "add" = function(...) add( x, ...), "serialize" = function(...) serialize( x, ... ), "clear" = function(...) clear( x, ... ), "fileDescriptor" = function() fileDescriptor(x ), # default .Call( "getMessageField", x@pointer, name, PACKAGE = "RProtoBuf" ) ) } ) setMethod("$<-", "Message", function(x, name, value) { .Call( "setMessageField", x@pointer, name, value, PACKAGE = "RProtoBuf" ) x } ) setMethod("$", "Descriptor", function(x, name) { switch( name, "new" = function( ... ) newProto( x, ... ) , "read" = function( input ) read( x, input ) , "readASCII" = function(input, ...) readASCII(x, input, ...), "toString" = function(...) toString(x, ...) , "as.character" = function(...) as.character(x, ...) , "as.list" = function(...) as.list(x, ...) , "asMessage" = function() asMessage(x), "fileDescriptor" = function() fileDescriptor(x ), "name" = function(...) name(x, ... ), "containing_type" = function() containing_type(x), "field_count" = function() field_count(x), "nested_type_count" = function() nested_type_count(x), "enum_type_count" = function() enum_type_count(x), "field" = function(...) field( x, ... ), "nested_type" = function(...) nested_type( x, ...), "enum_type" = function(...) enum_type( x, ...), # default .Call( "do_dollar_Descriptor", x@pointer, name ) ) } ) setMethod( "$", "EnumDescriptor", function(x, name ){ switch( name, "as.character" = function() as.character(x), "as.list"= function() as.list(x) , "asMessage" = function() asMessage(x), "toString" = function(...) toString(x, ...) , "name" = function(...) name(x, ...), "fileDescriptor" = function() fileDescriptor(x ), "containing_type" = function() containing_type(x), "length" = function() length(x), "value_count" = function() value_count(x), "value" = function(...) value(x, ...), "has" = function(name, ...) has(x, name, ...), # default .Call( "get_value_of_enum", x@pointer, name, PACKAGE = "RProtoBuf" ) ) } ) setMethod( "$", "FieldDescriptor", function(x, name ){ switch( name, "as.character" = function() as.character(x), "asMessage" = function() asMessage(x), "toString" = function(...) toString(x, ...) , "name" = function(...) name(x, ...), "fileDescriptor" = function() fileDescriptor(x ), "containing_type" = function() containing_type(x), "is_extension" = function() is_extension(x), "number" = function() number(x), "type" = function(...) type(x, ...), "cpp_type" = function(...) cpp_type(x, ...), "label" = function(...) label(x, ...), "is_repeated" = function() is_repeated(x), "is_required" = function() is_required(x), "is_optional" = function() is_optional(x), "has_default_value" = function() has_default_value(x), "default_value" = function() default_value(x), "enum_type" = function() enum_type(x), "message_type" = function() message_type(x), invisible(NULL) ) } ) setMethod( "$", "ServiceDescriptor", function(x, name ){ switch( name, "as.character" = function() as.character(x), "asMessage" = function() asMessage(x), "toString" = function(...) toString(x, ...) , "name" = function(...) name(x, ...), "fileDescriptor" = function() fileDescriptor(x ), "method_count" = function() method_count(x), "method" = function(...) method(x, ... ), .Call( "ServiceDescriptor__method", x@pointer, name, PACKAGE = "RProtoBuf" ) ) } ) setMethod( "$", "FileDescriptor", function(x, name ){ switch( name, "as.character" = function() as.character(x), "toString" = function(...) toString(x, ...) , "asMessage" = function() asMessage(x), "as.list" = function() as.list(x), "name" = function(...) name(x, ... ), "package" = function() x@package, as.list(x)[[name]] ) }) setMethod( "$", "EnumValueDescriptor", function(x, name ){ switch( name, "as.character" = function() as.character(x), "toString" = function(...) toString(x, ...) , "asMessage" = function() asMessage(x), "name" = function(...) name(x, ... ), "number" = function() number(x), "enum_type" = function(...) enum_type( x, ...), invisible(NULL) ) }) setMethod( "$", "MethodDescriptor", function(x, name ){ switch( name, "invoke" = function(...) invoke(x, ...), "implementation" = if( x@name %in% names(IMPLEMENTATIONS) ){ get( x@name, IMPLEMENTATIONS ) }, "name" = function(...) name(x, ...), "toString" = function() toString(x) , "as.character" = function() as.character(x), "fileDescriptor" = function() fileDescriptor(x ), "input_type" = function() input_type(x), "output_type" = function() output_type(x), invisible( NULL) ) } ) setMethod( "$<-", "MethodDescriptor", function(x, name, value ){ if( identical( name, "implementation" ) ){ check_valid_implementation( x, value ) assign( x@name, value, envir = IMPLEMENTATIONS ) } x } ) setMethod( "$", "ZeroCopyInputStream", function(x, name ){ switch( name, # ZeroCopyInputStream C++ methods "Next" = function(...) Next(x, ...), "ByteCount" = function(...) ByteCount(x, ...), "Skip" = function(...) Skip(x, ...), "BackUp" = function(...) BackUp(x, ...), # CodedInputStream related "ReadRaw" = function(...) ReadRaw(x, ...), "ReadString" = function(...) ReadString(x, ...), "ReadVarint32"= function() ReadVarint32(x), "ReadVarint64" = function() ReadVarint64(x), "ReadLittleEndian32" = function() ReadLittleEndian32(x), "ReadLittleEndian64" = function() ReadLittleEndian64(x), # default invisible(NULL) ) } ) setMethod( "$", "ZeroCopyOutputStream", function(x, name ){ switch( name, # ZeroCopyInputStream C++ methods "Next" = function(...) Next(x, ...), "ByteCount" = function(...) ByteCount(x, ...), "BackUp" = function(...) BackUp(x, ...), # CodedOutputStream related "WriteRaw" = function(...) WriteRaw(x, ...), "WriteString" = function(...) WriteString(x, ...), "WriteLittleEndian32" = function(...) WriteLittleEndian32(x,...), "WriteLittleEndian64" = function(...) WriteLittleEndian64(x,...), "WriteVarint32" = function(...) WriteVarint32(x, ...), "WriteVarint64" = function(...) WriteVarint64(x, ...), # default invisible(NULL) ) } ) # }}} # {{{ [[ setMethod( "[[", "Message", function(x, i, j, ..., exact = TRUE){ if( missing( i ) ){ stop( "`i` is required" ) } if( !missing(j) ){ warning( "`j` is ignored" ) } ## This works correctly by number or name. e.g. p[[1]] or p[["name"]] if( is.character( i ) || is.numeric( i ) ){ .Call( "getMessageField", x@pointer, i, PACKAGE = "RProtoBuf" ) } else { stop( "wrong type, `i` should be a character or a number" ) } } ) setMethod( "[[", "Descriptor", function(x, i, j, ..., exact = TRUE){ if( missing( i ) ){ stop( "`i` is required" ) } if( !missing(j) ){ warning( "`j` is ignored" ) } if( is.character( i ) ) { # gets a named field, nested type, or enum. .Call("Descriptor_getField", x@pointer, i, package="RProtoBuf") } else if (is.numeric( i ) ) { return(as.list(x)[[i]]) } else { stop( "wrong type, `i` should be a character or a number" ) } } ) setMethod( "[[", "EnumDescriptor", function(x, i, j, ..., exact = TRUE){ if( missing( i ) ){ stop( "`i` is required" ) } if( !missing(j) ){ warning( "`j` is ignored" ) } if (is.character(i) || is.numeric(i)) { return(as.list(x)[[i]]) } else { stop( "wrong type, `i` should be a character or a number" ) } } ) setMethod("[[", "ServiceDescriptor", function(x, i, j, ..., exact = TRUE){ if( missing( i ) ){ stop( "`i` is required" ) } if( !missing(j) ){ warning( "`j` is ignored" ) } if( is.character( i ) || is.numeric( i ) ){ .Call( "ServiceDescriptor__method", x@pointer, name, PACKAGE = "RProtoBuf" ) } else{ stop( "wrong type, `i` should be a character or a number" ) } } ) # }}} # {{{ [[<- setReplaceMethod( "[[", "Message", function(x, i, j, ..., exact = TRUE, value ){ # TODO: we might want to relax this later, i.e # allow to mutate repeated fields like this: # x[[ "field", 1:2 ]] <- 1:2 if( missing( i ) ){ stop( "`i` is required" ) } if( !missing(j) ){ warning( "`j` is ignored" ) } if( is.character( i ) || is.numeric( i ) ){ .Call( "setMessageField", x@pointer, i, value, PACKAGE = "RProtoBuf" ) } else { stop( "wrong type, `i` should be a character or a number" ) } x } ) # }}} # {{{ update setGeneric( "update" ) setMethod( "update", "Message", function( object, ... ){ dots <- list( ... ) if( !length( dots ) ){ return( object ) } names <- names( dots ) named <- dots[ names != "" ] if( !length( named ) ){ return( object ) } .Call( "update_message", object@pointer, named ) object } ) # }}} # {{{ length setGeneric( "length" ) setMethod( "length", "Message", function( x ){ .Call( "Message__length", x@pointer, PACKAGE = "RProtoBuf" ) } ) # Returns number of fields, enums, types in message descriptor. # May be more than field_count which is only fields. # e.g. length(tutorial.Person) > field_count(tutorial.Person) setMethod( "length", "Descriptor", function( x ){ length(as.list(x)) } ) setMethod( "length", "EnumDescriptor", function( x ){ .Call( "EnumDescriptor__length", x@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "length", "ServiceDescriptor", function( x ){ .Call( "ServiceDescriptor_method_count", x@pointer, PACKAGE = "RProtoBuf" ) } ) # }}} # {{{ str # we need to do this otherwise it gets messed up by the length method setGeneric( "str" ) setMethod( "str", "Message", function( object, ...){ txt <- sprintf( ' Formal class \'Message\' [package "RProtoBuf"] with 2 slots ..@ pointer: ..@ type : chr "%s" ', object@type ) writeLines( txt ) } ) # }}} # {{{ name setGeneric( "name", function(object, full = FALSE){ standardGeneric( "name" ) }) setMethod( "name", c( object = "Descriptor" ) , function(object, full = FALSE){ .Call( "Descriptor__name", object@pointer, full, PACKAGE = "RProtoBuf" ) }) setMethod( "name", c( object = "FieldDescriptor" ) , function(object, full = FALSE){ .Call( "FieldDescriptor__name", object@pointer, full, PACKAGE = "RProtoBuf" ) }) setMethod( "name", c( object = "EnumDescriptor" ) , function(object, full = FALSE){ .Call( "EnumDescriptor__name", object@pointer, full, PACKAGE = "RProtoBuf" ) }) setMethod( "name", c( object = "EnumValueDescriptor" ) , function(object, full = FALSE){ .Call( "EnumDescriptor__name", object@pointer, full, PACKAGE = "RProtoBuf" ) }) setMethod( "name", c( object = "ServiceDescriptor" ) , function(object, full = FALSE){ .Call( "ServiceDescriptor__name", object@pointer, full, PACKAGE = "RProtoBuf" ) }) setMethod( "name", c( object = "MethodDescriptor" ) , function(object, full = FALSE){ .Call( "MethodDescriptor__name", object@pointer, full, PACKAGE = "RProtoBuf" ) }) setMethod( "name", c( object = "FileDescriptor" ) , function(object, full = FALSE){ filename <- .Call( "FileDescriptor__name", object@pointer, PACKAGE = "RProtoBuf" ) if( full ) filename else basename( filename ) }) # }}} # {{{ names # as.list() and names() don't make as much sense for FieldDescriptors, # EnumValueDescriptors, etc. setMethod( "names", c( x = "Message" ) , function(x){ names(as.list(x)) }) setMethod( "names", c( x = "Descriptor" ) , function(x){ names(as.list(x)) }) setMethod( "names", c( x = "EnumDescriptor" ) , function(x){ names(as.list(x)) }) # }}} # {{{ as setAs("Descriptor", "Message", function(from){ .Call( "Descriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) setAs("FieldDescriptor", "Message", function(from){ .Call( "FieldDescriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) setAs("EnumDescriptor", "Message", function(from){ .Call( "EnumDescriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) setAs("ServiceDescriptor", "Message", function(from){ .Call( "ServiceDescriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) setAs("MethodDescriptor", "Message", function(from){ .Call( "MethodDescriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) setAs("FileDescriptor", "Message", function(from){ .Call( "FileDescriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) setAs("EnumValueDescriptor", "Message", function(from){ .Call( "EnumValueDescriptor__as_Message", from@pointer, PACKAGE = "RProtoBuf" ) }) asMessage <- function( x, ... ){ as( x, "Message", ... ) } # }}} # {{{ enum_type setGeneric( "enum_type", function( object, index, name ){ standardGeneric( "enum_type" ) }) # }}} RProtoBuf/R/completion.R0000644000175100001440000000763312440004312014646 0ustar hornikusers# :tabSize=4:indentSize=4:noTabs=false:folding=explicit:collapseFolds=1: # implementation of completion for proto messages # through the .DollarNames method (R>= 2.10.0) # S4 dispatch does not work for .DollarNames, so we'll use S3 # {{{ bring .DollarNames from the future if necessary if( !exists( ".DollarNames", envir = asNamespace("utils") ) ){ .DollarNames <- function(x, pattern) UseMethod(".DollarNames") } # }}} # {{{ Message .DollarNames.Message <- function(x, pattern = "" ){ names <- c( .Call( "Message__fieldNames", x@pointer, PACKAGE = "RProtoBuf" ) , "has(", "clone()", "clone(", "isInitialized()", "serialize(", "clear()", "clear(", "size(", "bytesize()", "fetch(", "swap(", "str()", "as.character()", "update(", "as.list()", "setExtension(", "getExtension(", "descriptor()", "set(", "toString(", "add(", "fileDescriptor()" ) grep( pattern, names, value = TRUE ) } # }}} # {{{ Descriptor .DollarNames.Descriptor <- function(x, pattern = "" ){ names <- c( .Call( "Descriptor__getMemberNames", x@pointer, PACKAGE = "RProtoBuf" ), "new(", "read(", "readASCII(", "fileDescriptor()", "name(", "toString()", "as.character()", "asMessage()", "containing_type()", "field_count()", "nested_type_count()", "enum_type_count", "field(", "nested_type(", "enum_type(" ) grep( pattern, names, value = TRUE ) } # }}} # {{{ EnumDescriptor .DollarNames.EnumDescriptor <- function(x, pattern = "" ){ names <- c( .Call( "EnumDescriptor__getConstantNames", x@pointer, PACKAGE = "RProtoBuf" ), "name(", "fileDescriptor()", "as.character()", "toString()", "containing_type()", "length()", "value_count()", "value(", "has(", "asMessage()") grep( pattern, names, value = TRUE ) } # }}} # {{{ EnumValueDescriptor .DollarNames.EnumValueDescriptor <- function(x, pattern = "" ){ names <- c("number()", "name()", "enum_type()", "as.character()", "toString()", "asMessage()") grep( pattern, names, value = TRUE ) } # }}} # {{{ FieldDescriptor .DollarNames.FieldDescriptor <- function(x, pattern = "" ){ names <- c("as.character()", "toString()", "name(", "fileDescriptor()", "containing_type()", "is_extension()", "number()", "type(", "cpp_type(", "label(", "is_repeated()", "is_required()", "is_optional()", "message_type()", "enum_type()", "asMessage()", "has_default_value()", "default_value(" ) grep( pattern, names, value = TRUE ) } # }}} # {{{ ServiceDescriptor .DollarNames.ServiceDescriptor <- function(x, pattern = "" ){ names <- c( .Call( "ServiceDescriptor__getMethodNames", x@pointer, PACKAGE = "RProtoBuf" ), "as.character()", "toString()", "name(", "fileDescriptor()", "method_count()", "method(name=", "method(index=" ) grep( pattern, names, value = TRUE ) } # }}} # {{{ MethodDescriptor .DollarNames.MethodDescriptor <- function(x, pattern = "" ){ names <- c("as.character()", "toString()", "name(", "fileDescriptor()", "input_type()", "output_type()" ) grep( pattern, names, value = TRUE ) } # }}} # {{{ FileDescriptor .DollarNames.FileDescriptor <- function(x, pattern = "" ){ names <- c( .Call( "FileDescriptor__getMemberNames", x@pointer, PACKAGE = "RProtoBuf" ), "as.character()", "toString()", "name(", "as.list()", "asMessage()", "package()") grep( pattern, names, value = TRUE ) } # }}} # {{{ ZeroCopyInputStream .DollarNames.ZeroCopyInputStream <- function(x, pattern = "" ){ names <- c("Next()", "ByteCount()", "Skip(", "BackUp(", "ReadRaw(", "ReadString()", "ReadVarint32()", "ReadVarint64()", "ReadLittleEndian32()", "ReadLittleEndian64()" ) grep( pattern, names, value = TRUE ) } # }}} # {{{ ZeroCopyOutputStream .DollarNames.ZeroCopyOutputStream <- function(x, pattern = "" ){ names <- c("Next(", "ByteCount()", "BackUp(", "WriteRaw(", "WriteString(", "WriteLittleEndian32(", "WriteLittleEndian64(", "WriteVarint32(", "WriteVarint64(" ) grep( pattern, names, value = TRUE ) } # }}} RProtoBuf/R/unit_tests.R0000644000175100001440000000020212440004312014657 0ustar hornikusers run_unit_tests <- function(){ script <- system.file( "unitTests", "runTests.R", package = "RProtoBuf" ) source( script ) } RProtoBuf/R/wrapper_CodedOutputStream.R0000644000175100001440000000702412440004312017642 0ustar hornikuserssetGeneric( "WriteRaw", function(object, payload){ standardGeneric("WriteRaw") } ) setMethod( "WriteRaw", c(object="ZeroCopyOutputStream", payload = "raw" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteRaw", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setGeneric( "WriteString", function(object, payload){ standardGeneric("WriteString") } ) setMethod( "WriteString", c(object="ZeroCopyOutputStream", payload = "character" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteString", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setGeneric( "WriteLittleEndian32", function(object, payload){ standardGeneric("WriteLittleEndian32") } ) setMethod( "WriteLittleEndian32", c(object="ZeroCopyOutputStream", payload = "integer" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteLittleEndian32", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteLittleEndian32", c(object="ZeroCopyOutputStream", payload = "numeric" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteLittleEndian32", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteLittleEndian32", c(object="ZeroCopyOutputStream", payload = "raw" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteLittleEndian32", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setGeneric( "WriteLittleEndian64", function(object, payload){ standardGeneric("WriteLittleEndian64") } ) setMethod( "WriteLittleEndian64", c(object="ZeroCopyOutputStream", payload = "integer" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteLittleEndian64", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteLittleEndian64", c(object="ZeroCopyOutputStream", payload = "numeric" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteLittleEndian64", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteLittleEndian64", c(object="ZeroCopyOutputStream", payload = "raw" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteLittleEndian64", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setGeneric( "WriteVarint32", function(object, payload){ standardGeneric("WriteVarint32") } ) setMethod( "WriteVarint32", c(object="ZeroCopyOutputStream", payload = "integer" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteVarint32", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteVarint32", c(object="ZeroCopyOutputStream", payload = "numeric" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteVarint32", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteVarint32", c(object="ZeroCopyOutputStream", payload = "raw" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteVarint32", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setGeneric( "WriteVarint64", function(object, payload){ standardGeneric("WriteVarint64") } ) setMethod( "WriteVarint64", c(object="ZeroCopyOutputStream", payload = "integer" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteVarint64", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteVarint64", c(object="ZeroCopyOutputStream", payload = "numeric" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteVarint64", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "WriteVarint64", c(object="ZeroCopyOutputStream", payload = "raw" ), function(object, payload){ .Call( "ZeroCopyOutputStream_WriteVarint64", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/rexp_obj.R0000644000175100001440000000766012762053206014322 0ustar hornikusers# Functions to convert an arbitrary R object into a protocol buffer # using the universal rexp.proto descriptor. # # Written by Jeroen Ooms # Modified 2014 by Murray Stokely to support language and environment types rexp_obj <- function(obj){ if(isS4(obj)) { # Some S4 objects do not return "S4" from typeof. e.g. lubridate interval # These must be natively encoded or we will lose the S4 flag. return(rexp_native(obj)) } sm <- typeof(obj); msg <- switch(sm, "character" = rexp_string(obj), "raw" = rexp_raw(obj), "double" = rexp_double(obj), "complex" = rexp_complex(obj), "integer" = rexp_integer(obj), "list" = rexp_list(obj), "logical" = rexp_logical(obj), "NULL" = rexp_null(), return(rexp_native(obj)) ); attrib <- attributes(obj) msg$attrName <- names(attrib) msg$attrValue <- lapply(attrib, rexp_obj) msg } rexp_string <- function(obj){ xvalue <- lapply(as.list(obj), function(x){ new(pb(rexp.STRING), strval=x, isNA=is.na(x)) }) new(pb(rexp.REXP), rclass = 0, stringValue=xvalue) } # For objects that only make sense in R, we just fall back # to R's default serialization. rexp_native <- function(obj){ new(pb(rexp.REXP), rclass= 8, nativeValue = base::serialize(obj, NULL)) } rexp_raw <- function(obj){ new(pb(rexp.REXP), rclass= 1, rawValue = obj) } rexp_double <- function(obj){ new(pb(rexp.REXP), rclass=2, realValue = obj) } rexp_complex <- function(obj){ xvalue <- lapply(as.list(obj), function(x){ new(pb(rexp.CMPLX), real=Re(x), imag=Im(x)) }) new(pb(rexp.REXP), rclass=3, complexValue = xvalue) } rexp_integer <- function(obj){ new(pb(rexp.REXP), rclass=4, intValue = obj) } rexp_list <- function(obj){ xobj <- lapply(obj, rexp_obj) new(pb(rexp.REXP), rclass=5, rexpValue = xobj) } rexp_logical <- function(obj){ xobj <- as.integer(obj) xobj[is.na(obj)] <- 2 new(pb(rexp.REXP), rclass=6, booleanValue = xobj) } rexp_null <- function(){ new(pb(rexp.REXP), rclass=7) } unrexp <- function(msg){ stopifnot(is(msg, "Message")) stopifnot(msg@type == "rexp.REXP") myrexp <- as.list(msg) xobj <- switch(as.character(myrexp$rclass), "0" = unrexp_string(myrexp), "1" = unrexp_raw(myrexp), "2" = unrexp_double(myrexp), "3" = unrexp_complex(myrexp), "4" = unrexp_integer(myrexp), "5" = unrexp_list(myrexp), "6" = unrexp_logical(myrexp), "7" = unrexp_null(), "8" = unrexp_native(myrexp), stop("Unsupported rclass:", myrexp$rclass) ) if(length(myrexp$attrValue)){ attrib <- lapply(myrexp$attrValue, unrexp) names(attrib) <- myrexp$attrName attributes(xobj) <- attrib } xobj } unrexp_string <- function(myrexp){ mystring <- unlist(lapply(myrexp$stringValue, "[[", "strval")) isNA <- unlist(lapply(myrexp$stringValue, "[[", "isNA")) mystring[isNA] <- NA as.character(mystring) } unrexp_raw <- function(myrexp){ myrexp$rawValue } unrexp_double <- function(myrexp){ myrexp$realValue } unrexp_complex <- function(myrexp){ xvalue <- lapply(myrexp$complexValue, function(x){ complex(real=x$real, imaginary=x$imag) }) as.complex(unlist(xvalue)) } unrexp_integer <- function(myrexp){ myrexp$intValue } unrexp_list <- function(myrexp){ lapply(myrexp$rexpValue, unrexp) } unrexp_logical <- function(myrexp){ xvalue <- myrexp$booleanValue xvalue[xvalue==2] <- NA as.logical(xvalue) } unrexp_null <- function(){ NULL } unrexp_native <- function(myrexp){ buf <- myrexp$nativeValue if(!length(buf)) return(NULL) unserialize(buf) } #Helper function to lookup a PB descriptor pb <- function(name){ descriptor <- deparse(substitute(name)) if(!exists(descriptor, "RProtoBuf:DescriptorPool")){ stop("No ProtoBuf Descriptor for: ", descriptor) } get(descriptor, "RProtoBuf:DescriptorPool") } #Checks if object can be serialized can_serialize_pb <- rexp_valid <- function(obj) { # We can now serialize everything. just call back to R serialization return(TRUE) } RProtoBuf/R/wrapper_ZeroCopyInputStream.R0000644000175100001440000001634512440004312020203 0ustar hornikusers# :tabSize=4:indentSize=4:noTabs=false:folding=explicit:collapseFolds=1: # {{{ generics setGeneric( "flush" ) setGeneric( "close" ) setGeneric( "GetErrno", function(object){ standardGeneric( "GetErrno" ) } ) setGeneric( "SetCloseOnDelete", function(object, close=FALSE){ standardGeneric( "SetCloseOnDelete" ) } ) # }}} # {{{ methods setGeneric( "Next", function(object, payload){ standardGeneric( "Next" ) } ) setGeneric( "BackUp", function(object, count){ standardGeneric( "BackUp" ) } ) setGeneric( "ByteCount", function(object){ standardGeneric( "ByteCount" ) } ) setGeneric( "Skip", function(object, count){ standardGeneric( "Skip" ) } ) # }}} # {{{ zero input stream setMethod( "Next", c( object = "ZeroCopyInputStream", payload = "missing"), function(object, payload){ .Call( "ZeroCopyInputStream_Next", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "BackUp", "ZeroCopyInputStream", function(object, count){ invisible(.Call( "ZeroCopyInputStream_BackUp", object@pointer, count, PACKAGE = "RProtoBuf" )) } ) setMethod( "ByteCount", "ZeroCopyInputStream", function(object){ .Call( "ZeroCopyInputStream_ByteCount", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "Skip", "ZeroCopyInputStream", function(object, count){ invisible( .Call( "ZeroCopyInputStream_Skip", object@pointer, count, PACKAGE = "RProtoBuf" ) ) } ) # }}} # {{{ zero copy output stream setMethod( "Next", c( object = "ZeroCopyOutputStream", payload = "raw" ), function(object, payload){ .Call( "ZeroCopyOutputStream_Next", object@pointer, payload, PACKAGE = "RProtoBuf" ) } ) setMethod( "BackUp", "ZeroCopyOutputStream", function(object, count){ invisible( .Call( "ZeroCopyOutputStream_BackUp", object@pointer, count, PACKAGE = "RProtoBuf" ) ) } ) setMethod( "ByteCount", "ZeroCopyOutputStream", function(object){ .Call( "ZeroCopyOutputStream_ByteCount", object@pointer, PACKAGE = "RProtoBuf" ) } ) # }}} # {{{ ArrayInputStream setGeneric( "ArrayInputStream", function(payload, block_size){ standardGeneric( "ArrayInputStream" ) } ) setMethod( "ArrayInputStream", c( payload = "raw", block_size = "missing" ) , function(payload, block_size){ .Call( "ArrayInputStream__new", payload, -1L, PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayInputStream", c( payload = "raw", block_size = "integer" ) , function(payload, block_size){ .Call( "ArrayInputStream__new", payload, block_size, PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayInputStream", c( payload = "raw", block_size = "numeric" ) , function(payload, block_size){ .Call( "ArrayInputStream__new", payload, as.integer(block_size), PACKAGE = "RProtoBuf" ) } ) # }}} # {{{ ArrayOutputStream constructor function setGeneric( "ArrayOutputStream", function(size, block_size){ standardGeneric( "ArrayOutputStream" ) } ) setMethod( "ArrayOutputStream", signature( size = "integer", block_size = "missing" ), function(size, block_size){ .Call( "ArrayOutputStream__new", size, -1L, PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayOutputStream", signature( size = "integer", block_size = "integer" ), function(size, block_size){ .Call( "ArrayOutputStream__new", size, block_size, PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayOutputStream", signature( size = "integer", block_size = "numeric" ), function(size, block_size){ .Call( "ArrayOutputStream__new", size, as.integer(block_size) , PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayOutputStream", signature( size = "numeric", block_size = "missing" ), function(size, block_size){ .Call( "ArrayOutputStream__new", as.integer(size), -1L, PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayOutputStream", signature( size = "numeric", block_size = "integer" ),function(size, block_size){ .Call( "ArrayOutputStream__new", as.integer(size), block_size, PACKAGE = "RProtoBuf" ) } ) setMethod( "ArrayOutputStream", signature( size = "numeric", block_size = "numeric" ), function(size, block_size){ .Call( "ArrayOutputStream__new", as.integer(size), as.integer(block_size) , PACKAGE = "RProtoBuf" ) } ) # }}} # {{{ FileInputStream setGeneric( "FileInputStream", function(filename, block_size = -1L, close.on.delete = FALSE ){ standardGeneric( "FileInputStream" ) } ) setMethod( "FileInputStream", signature( filename = "character", block_size = "integer", close.on.delete = "logical" ), function(filename, block_size = -1L, close.on.delete = FALSE){ full_filename <- file_path_as_absolute(filename) .Call( "FileInputStream_new", filename, block_size, close.on.delete, PACKAGE = "RProtoBuf" ) } ) setMethod( "close", "FileInputStream", function(con, ...){ .Call( "FileInputStream_Close", con@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "GetErrno", "FileInputStream", function(object){ .Call( "FileInputStream_GetErrno", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "SetCloseOnDelete", "FileInputStream", function(object, close=FALSE){ invisible( .Call( "FileInputStream_SetCloseOnDelete", object@pointer, isTRUE(close), PACKAGE = "RProtoBuf" ) ) } ) # }}} # {{{ FileOutputStream setGeneric( "FileOutputStream", function(filename, block_size = -1L, close.on.delete = FALSE ){ standardGeneric( "FileOutputStream" ) } ) setMethod( "FileOutputStream", signature( filename = "character", block_size = "integer", close.on.delete = "logical" ), function(filename, block_size = -1L, close.on.delete = FALSE){ if( !file.exists( filename ) ){ if( !file.exists( dirname(filename) ) ){ stop( "directory does not exist" ) } filename <- normalizePath(filename, mustWork=FALSE) } else{ filename <- file_path_as_absolute(filename) } .Call( "FileOutputStream_new", filename, block_size, close.on.delete, PACKAGE = "RProtoBuf" ) } ) setMethod( "flush", "FileOutputStream", function(con){ .Call( "FileOutputStream_Flush", con@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "close", "FileOutputStream", function(con, ...){ .Call( "FileOutputStream_Close", con@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "GetErrno", "FileOutputStream", function(object){ .Call( "FileOutputStream_GetErrno", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "SetCloseOnDelete", "FileOutputStream", function(object, close=FALSE){ invisible( .Call( "FileOutputStream_SetCloseOnDelete", object@pointer, isTRUE(close), PACKAGE = "RProtoBuf" ) ) } ) # }}} # {{{ ConnectionInputStream setGeneric( "ConnectionInputStream", function(object, ...){ standardGeneric( "ConnectionInputStream" ) } ) setMethod( "ConnectionInputStream", "connection", function(object, ...){ sc <- summary( object ) if( ! identical( sc[["can read"]], "yes") ){ stop( "cannot read from connection" ) } if( ! identical( sc[["text"]], "binary" ) ){ stop( "not a binary connection" ) } was_open <- isOpen( object ) if( ! was_open ){ open( object ) } .Call( "ConnectionInputStream_new", object, was_open, PACKAGE = "RProtoBuf" ) } ) # }}} # {{{ ConnectionOutputStream setGeneric( "ConnectionOutputStream", function(object, ...){ standardGeneric( "ConnectionOutputStream" ) } ) setMethod( "ConnectionOutputStream", "connection", function(object, ...){ sc <- summary( object ) if( ! identical( sc[["can write"]], "yes") ){ stop( "cannot write to connection" ) } if( ! identical( sc[["text"]], "binary" ) ){ stop( "not a binary connection" ) } was_open <- isOpen( object ) if( ! was_open ){ open( object ) } .Call( "ConnectionOutputStream_new", object, was_open, PACKAGE = "RProtoBuf" ) } ) # }}} RProtoBuf/R/identical.R0000644000175100001440000000146412440004312014425 0ustar hornikusers setGeneric( "identical" ) setMethod( "identical", c(x="Message", y = "Message" ), function( x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.set = TRUE){ .Call( "identical_messages", x@pointer, y@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "==", c( e1 = "Message", e2 = "Message" ), function(e1, e2 ){ .Call( "identical_messages", e1@pointer, e2@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "!=", c( e1 = "Message", e2 = "Message" ), function(e1, e2 ){ ! .Call( "identical_messages", e1@pointer, e2@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "all.equal" ) setMethod( "all.equal", c( target = "Message", current = "Message" ), function(target, current, tolerance = .Machine$double.eps^0.5, ...){ .Call( "all_equal_messages", target@pointer, current@pointer, tolerance, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/initialized.R0000644000175100001440000000035612440004312014775 0ustar hornikusers setGeneric( "isInitialized", function( object, ... ){ standardGeneric( "isInitialized" ) } ) setMethod( "isInitialized", "Message", function(object, ... ){ .Call( "Message__is_initialized", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/wrapper_EnumDescriptor.R0000644000175100001440000000221112440004312017163 0ustar hornikusers setGeneric( "value_count", function(object ){ standardGeneric( "value_count" ) } ) setMethod( "value_count", "EnumDescriptor", function(object){ .Call( "EnumDescriptor__value_count", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "value", function(object, index, name, number ){ standardGeneric( "value" ) } ) setMethod( "value", "EnumDescriptor", function(object, index, name, number){ has_index <- !missing(index) has_number <- !missing(number) has_name <- !missing(name) if( as.integer(has_index) + as.integer(has_number) + as.integer(has_name) != 1L ){ stop( "need exactly one of `index`, `number` or `name`" ) } if( has_index ){ stopifnot(is.numeric(index)) return( .Call( "EnumDescriptor__getValueByIndex", object@pointer, as.integer(index)-1L, PACKAGE = "RProtoBuf" ) ) } if( has_number ){ stopifnot(is.numeric(number)) return( .Call( "EnumDescriptor__getValueByNumber", object@pointer, as.integer(number), PACKAGE = "RProtoBuf" ) ) } if( has_name ){ stopifnot(is.character(name)) return( .Call( "EnumDescriptor__getValueByName", object@pointer, as.character(name), PACKAGE = "RProtoBuf" ) ) } } ) RProtoBuf/R/lookup.R0000644000175100001440000000077012440004312014001 0ustar hornikusers # attaches the descriptor pool to the search path at the given # position OTABLE <- NULL NAMESPACE <- environment() attachDescriptorPool <- function(pos = 2) { if (is.null(OTABLE)) { ##unlockBinding( "OTABLE", NAMESPACE ) otable <- .Call("newProtocolBufferLookup", pos, PACKAGE = "RProtoBuf") #attach(otable, pos=pos, name="RProtoBuf:DescriptorPool") assign("OTABLE", otable, envir = NAMESPACE, inherits = FALSE) lockBinding("OTABLE", NAMESPACE ) } } RProtoBuf/R/debug_string.R0000644000175100001440000000417212440004312015144 0ustar hornikusers ._toString_Message <- function(x, ...){ .Call( "Message__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_Descriptor <- function(x, ...){ .Call( "Descriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_EnumDescriptor <- function(x, ...){ .Call( "EnumDescriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_FieldDescriptor <- function(x, ...){ .Call( "FieldDescriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_ServiceDescriptor <- function(x, ...){ .Call( "ServiceDescriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_MethodDescriptor <- function(x, ...){ .Call( "MethodDescriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_FileDescriptor <- function(x, ...){ .Call( "FileDescriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } ._toString_EnumValueDescriptor <- function(x, ...){ .Call( "EnumValueDescriptor__as_character", x@pointer, PACKAGE = "RProtoBuf" ) } setMethod( "as.character", "Message", ._toString_Message ) setMethod( "as.character", "Descriptor", ._toString_Descriptor ) setMethod( "as.character", "EnumDescriptor", ._toString_EnumDescriptor ) setMethod( "as.character", "FieldDescriptor", ._toString_FieldDescriptor ) setMethod( "as.character", "ServiceDescriptor", ._toString_ServiceDescriptor ) setMethod( "as.character", "MethodDescriptor", ._toString_MethodDescriptor ) setMethod( "as.character", "FileDescriptor", ._toString_FileDescriptor ) setMethod( "as.character", "EnumValueDescriptor", ._toString_EnumValueDescriptor ) setGeneric( "toString" ) setMethod( "toString", "Message", ._toString_Message ) setMethod( "toString", "Descriptor", ._toString_Descriptor ) setMethod( "toString", "EnumDescriptor", ._toString_EnumDescriptor ) setMethod( "toString", "FieldDescriptor", ._toString_FieldDescriptor ) setMethod( "toString", "ServiceDescriptor", ._toString_ServiceDescriptor ) setMethod( "toString", "MethodDescriptor", ._toString_MethodDescriptor ) setMethod( "toString", "FileDescriptor", ._toString_FileDescriptor ) setMethod( "toString", "EnumValueDescriptor", ._toString_EnumValueDescriptor ) RProtoBuf/R/serialize_pb.R0000644000175100001440000000315112710022354015142 0ustar hornikusers#' Serialize R object to Protocol Buffer Message. #' #' Serializes R objects to a general purpose protobuf message using the same #' \code{rexp.proto} descriptor and mapping between R objects and protobuf #' mesages as RHIPE. #' #' Clients need both the message and the \code{rexp.proto} descriptor to parse #' serialized R objects. The latter is included in the the package installation #' \code{proto} directory: \code{system.file(package="RProtoBuf", "proto/rexp.proto")} #' #' The following storage types are natively supported by the descriptor: #' \code{character}, \code{raw}, \code{double}, \code{complex}, \code{integer}, #' \code{list}, and \code{NULL}. Objects with other storage types, such as #' functions, environments, S4 classes, etc, are serialized using base R #' \code{\link{serialize}} and stored in the proto \code{native} type. #' Missing values, attributes and numeric precision will be preserved. #' #' @param object R object to serialize #' @param connection passed on to \code{\link{serialize}} #' @param ... additional arguments passed on to \code{\link{serialize}} #' @aliases unserialize_pb can_serialize_pb #' @export unserialize_pb #' @export can_serialize_pb #' @export #' @examples msg <- tempfile(); #' serialize_pb(iris, msg); #' obj <- unserialize_pb(msg); #' identical(iris, obj); #' serialize_pb <- function(object, connection, ...){ #convert object to protobuf message msg <- rexp_obj(object); #serialize the message serialize(msg, connection = connection, ...); } unserialize_pb <- function(connection){ #convert object to protobuf message unrexp(read(pb(rexp.REXP), connection)); } RProtoBuf/R/serialize.R0000644000175100001440000000264212440004312014457 0ustar hornikusers # serialization of protobuf messages # at the moment, we grab the payload as a raw vector and send this # to the connection, but in the future, we will directly stream out # the payload to the connection setGeneric( "serialize" ) setMethod( "serialize", c( object = "Message" ) , function( object, connection, ascii = FALSE, refhook = NULL){ stopifnot(object$isInitialized()) iscon <- inherits(connection, "connection") isnull <- is.null( connection ) if( is.character( connection ) ){ # pretend it is a file name if( !file.exists(connection) ){ if( !file.exists( dirname(connection) ) ){ stop( "directory does not exist" ) } file <- normalizePath(connection, mustWork=FALSE) } else{ file <- file_path_as_absolute(connection) } .Call( "Message__serialize_to_file", object@pointer, file, PACKAGE = "RProtoBuf" ) invisible( NULL) } else if( iscon || isnull ) { # first grab the payload as a raw vector, payload <- .Call( "Message__get_payload", object@pointer, PACKAGE = "RProtoBuf" ) if( isnull ){ # just return it if the connection is NULL payload } else{ # otherwise write the payload to the connection # FIXME: we might want to be more clever about this so that # we don't have to store the full payload in memory # but for now it will do just fine writeBin( payload, connection ) invisible( NULL ) } } } ) RProtoBuf/R/with.R0000644000175100001440000000145712440004312013446 0ustar hornikusers# S3 dispatch does not work for some reason generateActiveBindings <- function(data){ env <- new.env( parent = environment() ) xp <- data@pointer names <- .Call( "Message__fieldNames", xp, PACKAGE = "RProtoBuf" ) if( !is.null(names) && length(names) ){ lapply( names, function(x ){ makeActiveBinding( x, function(v){ if( missing(v) ){ # get .Call( "getMessageField", xp, x ) } else { # set .Call( "setMessageField", xp, x, v ) } }, env ) } ) } env } with.Message <- function( data, expr, ...){ envir <- generateActiveBindings(data) eval( substitute( expr ), envir = envir ) } within.Message <- function(data, expr, ... ){ envir <- generateActiveBindings(data) eval( substitute( expr ), envir = envir ) data } RProtoBuf/R/aslist.R0000644000175100001440000000124612440004312013766 0ustar hornikusersas.list.Message <- function( x, ...){ .Call( "Message__as_list", x@pointer, PACKAGE = "RProtoBuf" ) } as.list.Descriptor <- function(x, ...){ # Fields, then nested types, then enum types defined in the message # are returned in a list. .Call( "Descriptor__as_list", x@pointer, PACKAGE = "RProtoBuf" ) } as.list.EnumDescriptor <- function( x, ...){ .Call( "EnumDescriptor__as_list", x@pointer, PACKAGE = "RProtoBuf" ) } as.list.FileDescriptor <- function( x, ...){ .Call( "FileDescriptor__as_list", x@pointer, PACKAGE = "RProtoBuf" ) } as.list.ServiceDescriptor <- function( x, ...){ .Call( "ServiceDescriptor__as_list", x@pointer, PACKAGE = "RProtoBuf" ) } RProtoBuf/R/set.R0000644000175100001440000000274112440004312013263 0ustar hornikusers## TODO(mstokely): Set and fetch are undocumented in Message-class.Rd ## And untested. Are they usful? setGeneric( "set", function(object, field, index, values ){ standardGeneric( "set" ) } ) setMethod( "set", "Message", function(object, field, index, values ){ if( !is.numeric( index ) ){ stop( "index should be numbers" ) } if( inherits( values, "Message" ) ){ values <- list( values ) } # TODO: we need to handle R type = RAWSXP and cpp type == string or bytes if( !identical( length( values ), length(index) ) ){ # TODO: we might want to be more flexible about that later # recycling, ... stop( "`index` should have the same length as `values`" ) } fsize <- size( object, field ) if( any( index > fsize ) || any( index < 1) ){ stop( sprintf( "index should only contain values between 1 and %d", fsize ) ) } .Call( "Message__set_field_values", object@pointer, field, index - 1L , values, PACKAGE = "RProtoBuf" ) # we work by reference invisible( NULL ) } ) setGeneric( "fetch", function(object, field, index ){ standardGeneric( "fetch" ) } ) setMethod( "fetch", "Message", function(object, field, index ){ if( !is.numeric( index ) ){ stop( "index should be numbers" ) } fsize <- size( object, field ) if( any( index > fsize ) || any( index < 1) ){ stop( sprintf( "index should only contain values between 1 and %d", fsize ) ) } .Call( "Message__get_field_values", object@pointer, field, index - 1L , PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/merge.R0000644000175100001440000000052212440004312013562 0ustar hornikuserssetGeneric( "merge" ) setMethod( "merge", c( x = "Message", y = "Message" ), function( x, y , ... ){ if( !identical( x@type, y@type ) ){ stop(sprintf("incompatible message types, cannot merge '%s' and '%s'", x@type, y@type)) } message <- .Call( "Message__merge", x@pointer, y@pointer ) message } ) RProtoBuf/R/read.R0000644000175100001440000000372712440004312013410 0ustar hornikusers setGeneric( "read", function( descriptor, input ){ standardGeneric( "read" ) } ) setMethod( "read", c( descriptor = "Descriptor" , input = "character" ), function(descriptor, input ){ file <- file_path_as_absolute( input ) .Call( "Descriptor__readMessageFromFile", descriptor@pointer, file, PACKAGE = "RProtoBuf" ) } ) setMethod( "read", c( descriptor = "Descriptor", input = "raw" ), function(descriptor, input ){ .Call( "Descriptor__readMessageFromRawVector", descriptor@pointer, input, PACKAGE="RProtoBuf" ) } ) setMethod( "read", c( descriptor = "Descriptor" ), function( descriptor, input ){ if( !inherits( input, "connection" ) ){ stop( "can only read from connections" ) } wasopen <- identical( summary(input)[["opened"]], "opened" ) if( !wasopen ) open( input, "rb") stopifnot(summary(input)[["text"]] == "binary") message <- .Call( "Descriptor__readMessageFromConnection", descriptor@pointer, input, PACKAGE = "RProtoBuf" ) if( !wasopen ) close( input ) message } ) setGeneric( "readASCII", function( descriptor, input, partial=FALSE ){ standardGeneric( "readASCII" ) } ) setMethod( "readASCII", c( descriptor = "Descriptor" , input = "character" ), function(descriptor, input, partial=FALSE){ stopifnot(is.logical(partial), length(partial) == 1) .Call( "Descriptor__readASCIIFromString", descriptor@pointer, input, partial, PACKAGE = "RProtoBuf" ) } ) setMethod( "readASCII", c( descriptor = "Descriptor" ), function( descriptor, input, partial=FALSE){ stopifnot(is.logical(partial), length(partial) == 1) if( !inherits( input, "connection" ) ){ stop( "can only read from connections" ) } wasopen <- identical( summary(input)[["opened"]], "opened" ) if( !wasopen ) open( input, "rb" ) stopifnot(summary(input)[["text"]] == "binary") message <- .Call( "Descriptor__readASCIIFromConnection", descriptor@pointer, input, partial, PACKAGE = "RProtoBuf" ) if( !wasopen ) close( input ) message } ) RProtoBuf/R/add.R0000644000175100001440000000050512440004312013214 0ustar hornikusers setGeneric( "add", function(object, field, values){ standardGeneric( "add" ) } ) setMethod( "add", "Message", function( object, field, values ){ if( is( values, "Message" ) ){ values <- list( values ) } .Call( "Message__add_values", object@pointer, field, values, PACKAGE = "RProtoBuf" ) invisible( object ) } ) RProtoBuf/R/wrapper_FieldDescriptor.R0000644000175100001440000000754412440004312017320 0ustar hornikusers setGeneric( "is_extension", function(object){ standardGeneric("is_extension") } ) setMethod( "is_extension", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__is_extension", object@pointer, PACKAGE = "RProtoBuf" ) }) setMethod( "number", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__number", object@pointer, PACKAGE = "RProtoBuf" ) } ) TYPE_DOUBLE <- 1L TYPE_FLOAT <- 2L TYPE_INT64 <- 3L TYPE_UINT64 <- 4L TYPE_INT32 <- 5L TYPE_FIXED64 <- 6L TYPE_FIXED32 <- 7L TYPE_BOOL <- 8L TYPE_STRING <- 9L TYPE_GROUP <- 10L TYPE_MESSAGE <- 11L TYPE_BYTES <- 12L TYPE_UINT32 <- 13L TYPE_ENUM <- 14L TYPE_SFIXED32 <- 15L TYPE_SFIXED64 <- 16L TYPE_SINT32 <- 17L TYPE_SINT64 <- 18L .TYPES <- sapply(ls( pattern="^TYPE_" ), function(x) get(x)) setGeneric( "type", function(object, as.string = FALSE){ standardGeneric( "type" ) } ) setMethod( "type", "FieldDescriptor", function(object, as.string = FALSE){ type <- .Call( "FieldDescriptor__type", object@pointer, PACKAGE = "RProtoBuf" ) if( as.string ) { names(which(.TYPES == type)) } else { type } } ) CPPTYPE_INT32 <- 1L CPPTYPE_INT64 <- 2L CPPTYPE_UINT32 <- 3L CPPTYPE_UINT64 <- 4L CPPTYPE_DOUBLE <- 5L CPPTYPE_FLOAT <- 6L CPPTYPE_BOOL <- 7L CPPTYPE_ENUM <- 8L CPPTYPE_STRING <- 9L CPPTYPE_MESSAGE <- 10L .CPPTYPES <- sapply(ls( pattern="^CPPTYPE_" ), function(x) get(x)) setGeneric( "cpp_type", function(object, as.string = FALSE ){ standardGeneric( "cpp_type" ) } ) setMethod( "cpp_type", "FieldDescriptor", function(object, as.string = FALSE){ cpptype <- .Call( "FieldDescriptor__cpp_type", object@pointer, PACKAGE = "RProtoBuf" ) if( as.string ) { names(which(.CPPTYPES == cpptype)) } else { cpptype } } ) LABEL_OPTIONAL <- 1L LABEL_REQUIRED <- 2L LABEL_REPEATED <- 3L .LABELS <- sapply(ls( pattern="^LABEL_" ), function(x) get(x)) setGeneric( "label", function(object, as.string = FALSE ){ standardGeneric( "label" ) } ) setMethod( "label", "FieldDescriptor", function(object, as.string = FALSE){ lab <- .Call( "FieldDescriptor__label", object@pointer, PACKAGE = "RProtoBuf" ) if( as.string ) { names(which(.LABELS == lab)) } else { lab } } ) setGeneric( "is_repeated", function(object ){ standardGeneric( "is_repeated" ) } ) setMethod( "is_repeated", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__is_repeated", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "is_optional", function(object){ standardGeneric( "is_optional" ) } ) setMethod( "is_optional", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__is_optional", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "is_required", function(object ){ standardGeneric( "is_required" ) } ) setMethod( "is_required", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__is_required", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "has_default_value", function(object ){ standardGeneric( "has_default_value" ) } ) setMethod( "has_default_value", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__has_default_value", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "default_value", function(object ){ standardGeneric( "default_value" ) } ) setMethod( "default_value", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__default_value", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "message_type", function(object ){ standardGeneric( "message_type" ) } ) setMethod( "message_type", "FieldDescriptor", function(object){ .Call( "FieldDescriptor__message_type", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "enum_type", c( object = "FieldDescriptor", index = "missing", name = "missing"), function(object){ .Call( "FieldDescriptor__enum_type", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/wrapper_EnumValueDescriptor.R0000644000175100001440000000066212440004312020170 0ustar hornikusers setMethod( "enum_type", c( object = "EnumValueDescriptor", index = "missing", name = "missing"), function(object, index, name){ .Call( "EnumValueDescriptor__enum_type", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "number", function(object){ standardGeneric( "number" ) } ) setMethod( "number", "EnumValueDescriptor", function(object){ .Call( "EnumValueDescriptor__number", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/field_count.R0000644000175100001440000000515012440004312014760 0ustar hornikuserssetGeneric( "field_count", function(object){ standardGeneric( "field_count" ) } ) setMethod( "field_count", "Descriptor", function(object){ .Call( "Descriptor__field_count", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "nested_type_count", function(object){ standardGeneric( "nested_type_count" ) } ) setMethod( "nested_type_count", "Descriptor", function(object){ .Call( "Descriptor__nested_type_count", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "enum_type_count", function(object){ standardGeneric( "enum_type_count" ) } ) setMethod( "enum_type_count", "Descriptor", function(object){ .Call( "Descriptor__enum_type_count", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "field", function(object, index, number, name){ standardGeneric( "field" ) } ) setMethod( "field", "Descriptor", function( object, index, number, name){ has_index <- !missing(index) has_number <- !missing(number) has_name <- !missing(name) if( as.integer(has_index) + as.integer(has_number) + as.integer(has_name) != 1L ){ stop( "need exactly one of `index`, `number` or `name`" ) } if( has_index ){ return( .Call( "Descriptor__field", object@pointer, as.integer(index)-1L, PACKAGE = "RProtoBuf" ) ) } if( has_number ){ return( .Call( "Descriptor__FindFieldByNumber", object@pointer, as.integer(number), PACKAGE = "RProtoBuf" ) ) } if( has_name ){ return( .Call( "Descriptor__FindFieldByName", object@pointer, as.character(name), PACKAGE = "RProtoBuf" ) ) } } ) setGeneric( "nested_type", function(object, index, name){ standardGeneric( "nested_type" ) } ) setMethod( "nested_type", "Descriptor", function(object, index, name ){ has_index <- !missing(index) has_name <- !missing(name) if( !identical( as.integer(has_index) + as.integer(has_name), 1L ) ){ stop( "need exactly one of `index` or `name`" ) } if( has_index ){ return( .Call( "Descriptor__nested_type", object@pointer, as.integer(index)-1L, PACKAGE = "RProtoBuf" ) ) } if( has_name ){ return( .Call( "Descriptor__FindNestedTypeByName", object@pointer, as.character(name), PACKAGE = "RProtoBuf" ) ) } } ) setMethod( "enum_type", "Descriptor", function(object, index, name){ has_index <- !missing(index) has_name <- !missing(name) if( !identical( as.integer(has_index) + as.integer(has_name), 1L ) ){ stop( "need exactly one of `index` or `name`" ) } if( has_index ){ return( .Call( "Descriptor__enum_type", object@pointer, as.integer(index)-1L, PACKAGE = "RProtoBuf" ) ) } if( has_name ){ return( .Call( "Descriptor__FindEnumTypeByName", object@pointer, as.character(name), PACKAGE = "RProtoBuf" ) ) } }) RProtoBuf/R/rpc.R0000644000175100001440000000454712440004312013262 0ustar hornikusers setGeneric( "invoke", function( method, message, protocol){ standardGeneric( "invoke" ) } ) check_valid_implementation <- function( method, implementation ){ if( !is.function( implementation ) ){ stop( "should be a function" ) } if( !identical( length(formals(implementation)), 1L ) ){ stop( "should have exactly one argument" ) } invisible(NULL) } check_valid_input_message <- function( method, message){ # check that message is of correct type valid <- .Call( "valid_input_message", method@pointer, message@pointer, PACKAGE = "RProtoBuf" ) if( !valid ){ expected <- .Call( "get_method_input_type", method@pointer, PACKAGE = "RProtoBuf" )@type stop( sprintf( "invalid input message, expecting a message of type : %s", expected ) ) } } setMethod( "invoke", c(method = "MethodDescriptor", message = "Message", protocol = "missing" ), function( method, message, protocol){ # check that the message is valid check_valid_input_message( method, message ) # grab the implementation if( exists( method@name, envir = IMPLEMENTATIONS ) ){ impl <- get( method@name, envir = IMPLEMENTATIONS ) check_valid_implementation( method, impl ) result <- impl( message ) valid <- .Call( "valid_output_message", method@pointer, result@pointer, PACKAGE = "RProtoBuf" ) if( !valid ){ stop( "invalid method output" ) } result } else{ warning( "unimplemented method, returning output message prototype" ) .Call( "get_method_output_prototype", method@pointer, PACKAGE = "RProtoBuf" ) } # return the message } ) setMethod( "invoke" , c( method = "MethodDescriptor", message = "Message", protocol = "RpcHTTP"), function(method, message, protocol ){ # check that the message is valid check_valid_input_message( method, message ) root <- protocol@root[1] if( ! grepl( "^/", root ) ) root <- paste( "/", root, sep = "" ) if( ! grepl( "/$", root ) ) root <- paste( root, "/", sep = "" ) url <- sprintf( "http://%s:%d%s?service=%s&method=%s", protocol@host, protocol@port, root, method@service, method$name() ) reader <- basicTextGatherer() header <- c( "Content-Type" = "application/x-protobuf", "Accept" = "application/x-protobuf" ) curlPerform( url = url, httpheader = header, postfields = serialize(message, NULL) , writefunction = reader$update ) response <- charToRaw( reader$value() ) read( method$output_type(), response ) } ) RProtoBuf/R/zzz.R0000644000175100001440000000113412440004312013320 0ustar hornikusers .onLoad <- function(libname, pkgname ){ ##minversion <- packageDescription(pkgname, lib.loc=libname)$MinimumLibProtoVersion ##minversion <- as.integer( gsub( "[[:space:]]+", "", minversion ) ) ##.Call( "check_libprotobuf_version", minversion, PACKAGE = "RProtoBuf" ) readProtoFiles( package=pkgname, lib.loc=libname ) attachDescriptorPool( pos = length(search()) ) options("RProtoBuf.int64AsString" = FALSE) #if( exists( ".httpd.handlers.env", asNamespace( "tools" ) ) ){ # e <- tools:::.httpd.handlers.env # e[["RProtoBuf"]] <- RProtoBuf.http.handler #} } RProtoBuf/R/wrapper_MethodDescriptor.R0000644000175100001440000000071612440004312017507 0ustar hornikusers setGeneric( "input_type", function(object){ standardGeneric( "input_type" ) } ) setGeneric( "output_type", function(object){ standardGeneric( "output_type" ) } ) setMethod( "input_type", "MethodDescriptor", function(object){ .Call("MethodDescriptor__input_type", object@pointer, PACKAGE = "RProtoBuf" ) } ) setMethod( "output_type", "MethodDescriptor", function(object){ .Call("MethodDescriptor__output_type", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/containing_type.R0000644000175100001440000000174612440004312015666 0ustar hornikusers setGeneric( "containing_type", function(object){ standardGeneric( "containing_type" ) } ) setMethod( "containing_type", "Descriptor", function(object){ retval <- .Call( "Descriptor__containing_type", object@pointer, PACKAGE = "RProtoBuf" ) if (length(retval@type) == 0) { # Descriptors do not always have containing types. # In such cases NULL is better return value than malformed Descriptor. return(NULL) } else { return(retval) } } ) setMethod( "containing_type", "EnumDescriptor", function(object){ retval <- .Call( "EnumDescriptor__containing_type", object@pointer, PACKAGE = "RProtoBuf" ) if (length(name(retval)) == 0) { # If this enum type is nested in a message type, this # is that message type. Otherwise, NULL. return(NULL) } else { return(retval) } } ) setMethod( "containing_type", "FieldDescriptor", function(object){ # Never NULL .Call( "FieldDescriptor__containing_type", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/wrapper_CodedInputStream.R0000644000175100001440000000443512440004312017444 0ustar hornikusers setGeneric( "ReadRaw", function(object, size ){ standardGeneric( "ReadRaw" ) } ) setMethod( "ReadRaw", c( object="ZeroCopyInputStream", size = "integer" ), function(object, size){ .Call( "ZeroCopyInputStream_ReadRaw", object@pointer, size, PACKAGE = "RProtoBuf" ) } ) setMethod("ReadRaw", c( object="ZeroCopyInputStream", size = "numeric" ), function(object, size) { if (size %% 1 == 0) { .Call( "ZeroCopyInputStream_ReadRaw", object@pointer, as.integer(size), PACKAGE = "RProtoBuf" ) } else { stop("Size must be a whole number.") } } ) setGeneric( "ReadString", function(object, size ){ standardGeneric( "ReadString" ) } ) setMethod( "ReadString", c( object="ZeroCopyInputStream", size = "integer" ), function(object, size){ .Call( "ZeroCopyInputStream_ReadString", object@pointer, size, PACKAGE = "RProtoBuf" ) } ) setMethod("ReadString", c( object="ZeroCopyInputStream", size = "numeric" ), function(object, size) { if (size %% 1 == 0) { .Call("ZeroCopyInputStream_ReadString", object@pointer, as.integer(size), PACKAGE = "RProtoBuf" ) } else { stop("Size must be a whole number.") } } ) setGeneric( "ReadVarint32", function(object){ standardGeneric( "ReadVarint32" ) } ) setMethod( "ReadVarint32", c( object="ZeroCopyInputStream"), function(object){ .Call( "ZeroCopyInputStream_ReadVarint32", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "ReadLittleEndian32", function(object){ standardGeneric( "ReadLittleEndian32" ) } ) setMethod( "ReadLittleEndian32", c( object="ZeroCopyInputStream"), function(object){ .Call( "ZeroCopyInputStream_ReadLittleEndian32", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "ReadLittleEndian64", function(object){ standardGeneric( "ReadLittleEndian64" ) } ) setMethod( "ReadLittleEndian64", c( object="ZeroCopyInputStream"), function(object){ .Call( "ZeroCopyInputStream_ReadLittleEndian64", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "ReadVarint64", function(object){ standardGeneric( "ReadVarint64" ) } ) setMethod( "ReadVarint64", c( object="ZeroCopyInputStream"), function(object){ .Call( "ZeroCopyInputStream_ReadVarint64", object@pointer, PACKAGE = "RProtoBuf" ) } ) RProtoBuf/R/wrapper_ServiceDescriptor.R0000644000175100001440000000154112440004312017664 0ustar hornikuserssetGeneric( "method_count", function(object ){ standardGeneric( "method_count" ) } ) setMethod( "method_count", "ServiceDescriptor", function(object){ .Call( "ServiceDescriptor_method_count", object@pointer, PACKAGE = "RProtoBuf" ) } ) setGeneric( "method", function(object, index, name ){ standardGeneric( "method" ) } ) setMethod( "method", "ServiceDescriptor", function(object, index, name){ has_index <- !missing(index) has_name <- !missing(name) if( as.integer(has_index) + as.integer(has_name) != 1L ){ stop( "need exactly one of `index` or `name`" ) } if( has_index ){ return( .Call( "ServiceDescriptor_getMethodByIndex", object@pointer, as.integer(index)-1L, PACKAGE = "RProtoBuf" ) ) } if( has_name ){ return( .Call( "ServiceDescriptor_getMethodByName", object@pointer, as.character(name), PACKAGE = "RProtoBuf" ) ) } } ) RProtoBuf/vignettes/0000755000175100001440000000000013037407202014160 5ustar hornikusersRProtoBuf/vignettes/figures/0000755000175100001440000000000012740551644015636 5ustar hornikusersRProtoBuf/vignettes/figures/histogram-mapreduce-diag1.pdf0000644000175100001440000006024712263403512023253 0ustar hornikusers%PDF-1.3 % 4 0 obj << /Length 5 0 R /Filter /FlateDecode >> stream x՛I +8)">TQOI\^@xo:0TΣ2$;I,I^[w2U Xa~le1a1<Ő'[Լ3B=b^\ˢd^y (SԼ.,j^3{l춳} NN)%6Њ V}e)VSSAa_8S"$dETH1㈏^H ZlH=%-TE,IF٦bEI6e ٳ(?30>WaVԊ8O͈bEXQ~^KV%F+ jEZQV9 (YQ?y#Ŋa,V]‹]YB\i} RqlEnAiWbј$+1a ɊDf@يbE7=b)GdŊ"`\ۤo͌HB]*Q$F1*Fل`顄,>&\b-&e@Dt<Cl2ۮA7zapMtI׸5kkgn^onI楹߿3OO71skrIe7!(=e,vSw*]I]:qu7-b̖,:'ahf|}B2&Ү$By]!#C^o[/ r` r uO  9ls1 K\ Αh. 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Many formats commonly used to import and export data between different programs or systems, such as CSV or JSON, are verbose, inefficient, not type-safe, or tied to a specific programming language. Protocol Buffers are a popular method of serializing structured data between applications -- while remaining independent of programming languages or operating systems. They offer a unique combination of features, performance, and maturity that seems particularly well suited for data-driven applications and numerical computing. The \pkg{RProtoBuf} package provides a complete interface to Protocol Buffers from the \proglang{R} environment for statistical computing. This paper outlines the general class of data serialization requirements for statistical computing, describes the implementation of the \pkg{RProtoBuf} package, and illustrates its use with example applications in large-scale data collection pipelines and web services. } \Keywords{\proglang{R}, \pkg{Rcpp}, Protocol Buffers, serialization, cross-platform} \Plainkeywords{R, Rcpp, Protocol Buffers, serialization, cross-platform} \Volume{71} \Issue{2} \Month{July} \Year{2016} \Submitdate{2014-02-05} \Acceptdate{2015-04-13} %\DOI{10.18637/jss.v071.i02} %% The address of (at least) one author should be given %% in the following format: \Address{ Dirk Eddelbuettel \\ Debian Project \\ River Forest, IL, United States of America\\ E-mail: \email{edd@debian.org}\\ URL: \url{http://dirk.eddelbuettel.com/}\\ Murray Stokely\\ Google, Inc.\\ 1600 Amphitheatre Parkway\\ Mountain View, CA, United States of America\\ E-mail: \email{murray@stokely.org}\\ URL: \url{http://www.stokely.org/}\\ Jeroen Ooms\\ UCLA Department of Statistics\\ University of California, Los Angeles\\ Los Angeles, CA, United States of America\\ E-mail: \email{jeroen.ooms@stat.ucla.edu}\\ URL: \url{https://jeroenooms.github.io/} } %% It is also possible to add a telephone and fax number %% before the e-mail in the following format: %% Telephone: +43/512/507-7103 %% Fax: +43/512/507-2851 %% for those who use Sweave please include the following line (with % symbols): %% need no \usepackage{Sweave.sty} %% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% <>= library(RProtoBuf) rprotobuf.version <- packageDescription("RProtoBuf")$Version rprotobuf.date <- packageDescription("RProtoBuf")$Date now.date <- strftime(Sys.Date(), "%B %d, %Y") @ \begin{document} \SweaveOpts{concordance=FALSE,prefix.string=figures/fig} %% include your article here, just as usual %% Note that you should use the \pkg{}, \proglang{} and \code{} commands. % We don't want a left margin for Sinput or Soutput for our table 1. %\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=0em} %\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=0em} %\DefineVerbatimEnvironment{Scode}{Verbatim}{xleftmargin=2em} % Setting the topsep to 0 reduces spacing from input to output and % improves table 1. \fvset{listparameters={\setlength{\topsep}{0pt}}} \renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}} %% DE: I tend to have wider option(width=...) so this %% guarantees better line breaks <>= ## cf http://www.jstatsoft.org/style#q12 options(prompt = "R> ", continue = "+ ", width = 70, useFancyQuotes = FALSE, digits = 4) @ \maketitle \section{Introduction} Modern data collection and analysis pipelines increasingly involve collections of decoupled components in order to better manage software complexity through reusability, modularity, and fault isolation \citep{Wegiel:2010:CTT:1932682.1869479}. These pipelines are frequently built using different programming languages for the different phases of data analysis -- collection, cleaning, modeling, analysis, post-processing, and presentation -- in order to take advantage of the unique combination of performance, speed of development, and library support offered by different environments and languages. Each stage of such a data analysis pipeline may produce intermediate results that need to be stored in a file, or sent over the network for further processing. Given these requirements, how do we safely and efficiently share intermediate results between different applications, possibly written in different languages, and possibly running on different computer systems? In computer programming, \emph{serialization} is the process of translating data structures, variables, and session states into a format that can be stored or transmitted and then later reconstructed in the original form \citep{clinec++}. Programming languages such as \proglang{R} \citep{r}, \proglang{Julia} \citep{julia}, \proglang{Java}, and \proglang{Python} \citep{python} include built-in support for serialization, but the default formats are usually language-specific and thereby lock the user into a single environment. Data analysts and researchers often use character-separated text formats such as CSV \citep{shafranovich2005common} to export and import data. However, anyone who has ever used CSV files will have noticed that this method has many limitations: It is restricted to tabular data, lacks type-safety, and has limited precision for numeric values. Moreover, ambiguities in the format itself frequently cause problems. For example, conventions on which characters are used as separator or decimal point vary by country. \emph{Extensible markup language} (XML) is a well-established and widely-supported format with the ability to define just about any arbitrarily complex schema \citep{nolan2013xml}. However, it pays for this complexity with comparatively large and verbose messages, and added complexity at the parsing side (these problems are somewhat mitigated by the availability of mature libraries and parsers). Because XML is text-based and has no native notion of numeric types or arrays, it is usually not a very practical format to store numeric data sets as they appear in statistical applications. A more modern format is \emph{\proglang{JavaScript} object notation} (JSON), which is derived from the object literals of \proglang{JavaScript}, and already widely-used on the world wide web. Several \proglang{R} packages implement functions to parse and generate JSON data from \proglang{R} objects \citep{rjson,RJSONIO,jsonlite}. JSON natively supports arrays and four primitive types: numbers, strings, booleans, and null. However, as it also is a text-based format, numbers are stored in human-readable decimal notation which is inefficient and leads to loss of type (double versus integer) and precision. A number of binary formats based on JSON have been proposed that reduce the parsing cost and improve efficiency, but these formats are not widely supported. Furthermore, such formats lack a separate schema for the serialized data and thus still duplicate field names with each message sent over the network or stored in a file. Once the data serialization needs of an application become complex enough, developers typically benefit from the use of an \emph{interface description language}, or \emph{IDL}. IDLs like Protocol Buffers \citep{protobuf}, Apache Thrift \citep{Apache:Thrift}, and Apache Avro \citep{Apache:Avro} provide a compact well-documented schema for cross-language data structures and efficient binary interchange formats. Since the schema is provided separately from the data, the data can be efficiently encoded to minimize storage costs when compared with simple ``schema-less'' binary interchange formats. %Many sources compare data serialization formats %and show Protocol Buffers perform favorably to the alternatives; see %\citet{Sumaray:2012:CDS:2184751.2184810} for one such comparison. Protocol Buffers perform well in the comparison of such formats by \citet{Sumaray:2012:CDS:2184751.2184810}. This paper describes an \proglang{R} interface to Protocol Buffers, and is organized as follows. Section~\ref{sec:protobuf} provides a general high-level overview of Protocol Buffers as well as a basic motivation for their use. Section~\ref{sec:rprotobuf-basic} describes the interactive \proglang{R} interface provided by the \pkg{RProtoBuf} package, and introduces the two main abstractions: \emph{Messages} and \emph{Descriptors}. Section~\ref{sec:rprotobuf-classes} details the implementation of the main \proglang{S}4 classes and methods. Section~\ref{sec:types} describes the challenges of type coercion between \proglang{R} and other languages. Section~\ref{sec:evaluation} introduces a general \proglang{R} language schema for serializing arbitrary \proglang{R} objects and compares it to the serialization capabilities built directly into \proglang{R}. Sections~\ref{sec:mapreduce} and \ref{sec:opencpu} provide real-world use cases of \pkg{RProtoBuf} in MapReduce and web service environments, respectively, before Section~\ref{sec:summary} concludes. \makeatletter \if@nojss This vignette corresponds to the paper published in the \textsl{Journal of Statistical Software}. For citations, please see the output of \proglang{R} function \texttt{citation("RProtoBuf")}. This version corresponds to \pkg{RProtoBuf} version \Sexpr{rprotobuf.version} and was typeset on \Sexpr{now.date}. \fi \makeatother \section{Protocol Buffers} \label{sec:protobuf} Protocol Buffers are a modern, language-neutral, platform-neutral, extensible mechanism for sharing and storing structured data. Some of their features, particularly in the context of data analysis, are: % \begin{itemize} \item \emph{Portable}: Enable users to send and receive data between applications as well as different computers or operating systems. \item \emph{Efficient}: Data is serialized into a compact binary representation for transmission or storage. \item \emph{Extensible}: New fields can be added to Protocol Buffer schemas in a forward-compatible way that does not break older applications. \item \emph{Stable}: Protocol Buffers have been in wide use for over a decade. \end{itemize} % \begin{figure}[t!] \centering \includegraphics[width=0.9\textwidth]{protobuf-distributed-system-crop.pdf} \caption{Example usage of Protocol Buffers.} \label{fig:protobuf-distributed-usecase} \end{figure} % Figure~\ref{fig:protobuf-distributed-usecase} illustrates an example communication work flow with Protocol Buffers and an interactive \proglang{R} session. Common use cases include populating a request remote-procedure call (RPC) Protocol Buffer in \proglang{R} that is then serialized and sent over the network to a remote server. The server deserializes the message, acts on the request, and responds with a new Protocol Buffer over the network. The key difference to, say, a request to an \pkg{Rserve} \citep{Urbanek:2003:Rserve,CRAN:Rserve} instance is that the remote server may be implemented in any language. %, with no dependence on \proglang{R}. While traditional IDLs have at times been criticized for code bloat and complexity, Protocol Buffers are based on a simple list and records model that is flexible and easy to use. The schema for structured Protocol Buffer data is defined in \code{.proto} files, which may contain one or more message types. Each message type has one or more fields. A field is specified with a unique number (called a \emph{tag number}), a name, a value type, and a field rule specifying whether the field is optional, required, or repeated. The supported value types are numbers, enumerations, booleans, strings, raw bytes, or other nested message types. The \code{.proto} file syntax for defining the structure of Protocol Buffer data is described comprehensively on Google Code at \url{http://code.google.com/apis/protocolbuffers/docs/proto.html}. Table~\ref{tab:proto} shows an example \code{.proto} file that defines the \code{tutorial.Person} type\footnote{The compound name \code{tutorial.Person} in \proglang{R} is derived from the name of the message (\emph{Person}) and the name of the package defined at the top of the \code{.proto} file in which it is defined (\emph{tutorial}).}. The \proglang{R} code in the right column shows an example of creating a new message of this type and populating its fields. \noindent \begin{table}[t!] \begin{tabular}{p{0.45\textwidth}p{0.5\textwidth}} \toprule Schema : \code{addressbook.proto} & Example \proglang{R} session\\ \cmidrule{1-2} \begin{minipage}{.40\textwidth} \vspace{2mm} \begin{example} package tutorial; message Person { required string name = 1; required int32 id = 2; optional string email = 3; enum PhoneType { MOBILE = 0; HOME = 1; WORK = 2; } message PhoneNumber { required string number = 1; optional PhoneType type = 2; } repeated PhoneNumber phone = 4; } \end{example} \vspace{2mm} \end{minipage} & \begin{minipage}{.55\textwidth} <>= library("RProtoBuf") p <- new(tutorial.Person, id=1, name="Dirk") p$name p$name <- "Murray" cat(as.character(p)) serialize(p, NULL) class(p) @ \end{minipage} \\ \bottomrule \end{tabular} \caption{The schema representation from a \code{.proto} file for the \code{tutorial.Person} class (left) and simple \proglang{R} code for creating an object of this class and accessing its fields (right).} \label{tab:proto} \end{table} For added speed and efficiency, the \proglang{C++}, \proglang{Java}, and \proglang{Python} bindings to Protocol Buffers are used with a compiler that translates a Protocol Buffer schema description file (ending in \code{.proto}) into language-specific classes that can be used to create, read, write, and manipulate Protocol Buffer messages. The \proglang{R} interface, in contrast, uses a reflection-based API that makes some operations slightly slower but which is much more convenient for interactive data analysis. All messages in \proglang{R} have a single class structure, but different accessor methods are created at runtime based on the named fields of the specified message type, as described in the next section. \section{Basic usage: Messages and descriptors} \label{sec:rprotobuf-basic} This section describes how to use the \proglang{R} API to create and manipulate Protocol Buffer messages in \proglang{R}, and how to read and write the binary representation of the message (often called the \emph{payload}) to files and arbitrary binary \proglang{R} connections. The two fundamental building blocks of Protocol Buffers are \emph{Messages} and \emph{Descriptors}. Messages provide a common abstract encapsulation of structured data fields of the type specified in a Message Descriptor. Message Descriptors are defined in \code{.proto} files and define a schema for a particular named class of messages. \subsection[Importing Message Descriptors from .proto files]{Importing Message Descriptors from \code{.proto} files} To create or parse a Protocol Buffer message, one must first read in the Message Descriptor (\emph{message type}) from a \code{.proto} file. A small number of message types are imported when the package is first loaded, including the \code{tutorial.Person} type we saw in the last section. All other types must be imported from \code{.proto} files using the \code{readProtoFiles} function, which can either import a single file, all files in a directory, or every \code{.proto} file provided by a particular \proglang{R} package. After importing proto files, the corresponding Message Descriptors are available by name from the \code{RProtoBuf:DescriptorPool} environment in the \proglang{R} search path. This environment is implemented with the user-defined tables framework from the \pkg{RObjectTables} package available from the OmegaHat project \citep{RObjectTables}. Instead of being associated with a static hash table, this environment dynamically queries the in-memory database of loaded descriptors during normal variable lookup. This allows new descriptors to be parsed from \code{.proto} files and added to the global namespace.\footnote{Note that there is a significant performance overhead with this \pkg{RObjectTables} implementation. Because the table is on the search path and is not cacheable, lookups of symbols that are behind it in the search path cannot be added to the global object cache, and \proglang{R} must perform an expensive lookup through all of the attached environments and the Protocol Buffer definitions to find common symbols (most notably those in base) from the global environment. Fortunately, proper use of namespaces and package imports reduces the impact of this for code in packages.} \subsection*{Creating, accessing, and modifying messages.} New messages are created with the \code{new} function which accepts a Message Descriptor and optionally a list of ``name = value'' pairs to set in the message. %The objects contained in the special environment are %descriptors for their associated message types. Descriptors will be %discussed in detail in another part of this document, but for the %purpose of this section, descriptors are just used with the \code{new} %function to create messages. <<>>= p <- new(tutorial.Person, name = "Murray", id = 1) @ % \subsection*{Access and modify fields of a message} Once the message is created, its fields can be queried and modified using the dollar operator of \proglang{R}, making Protocol Buffer messages seem like lists. <<>>= p$name p$id p$email <- "murray@stokely.org" @ As opposed to \proglang{R} lists, no partial matching is performed and the name must be given entirely. The \verb|[[| operator can also be used to query and set fields of a message, supplying either their name or their tag number: <<>>= p[["name"]] <- "Murray Stokely" p[[ 2 ]] <- 3 p[["email"]] @ Protocol Buffers include a 64-bit integer type, but \proglang{R} lacks native 64-bit integer support. A workaround is available and described in Section~\ref{sec:int64} for working with large integer values. \subsection*{Printing, reading, and writing Messages} % \textbf{Printing, Reading, and Writing Messages} Protocol Buffer messages and descriptors implement \code{show} methods that provide basic information about the message: <<>>= p @ %For additional information, such as for debugging purposes, The \code{as.character} method provides a more complete ASCII representation of the contents of a message. <<>>= writeLines(as.character(p)) @ % \subsection{Serializing messages} A primary benefit of Protocol Buffers is an efficient binary wire-format representation. The \code{serialize} method is implemented for Protocol Buffer messages to serialize a message into a sequence of bytes (raw vector) that represents the message. The raw bytes can then be parsed back into the original message safely as long as the message type is known and its descriptor is available. <<>>= serialize(p, NULL) @ The same method can be used to serialize messages to files or arbitrary binary connections: <<>>= tf1 <- tempfile() serialize(p, tf1) readBin(tf1, raw(0), 500) @ %\subsection{Parsing messages} The \pkg{RProtoBuf} package defines the \code{read} and \code{readASCII} functions to read messages from files, raw vectors, or arbitrary connections. \code{read} expects to read the message payload from binary files or connections and \code{readASCII} parses the human-readable ASCII output that is created with \code{as.character}. The binary representation of the message does not contain information that can be used to dynamically infer the message type, so we have to provide this information to the \code{read} function in the form of a descriptor: <<>>= msg <- read(tutorial.Person, tf1) writeLines(as.character(msg)) @ The \code{input} argument of \code{read} can also be a binary readable \proglang{R} connection, such as a binary file connection, or a raw vector of serialized bytes. \section{Under the hood: S4 classes and methods} \label{sec:rprotobuf-classes} The \pkg{RProtoBuf} package uses the \proglang{S}4 system to store information about descriptors and messages. Each \proglang{R} object contains an external pointer to an object managed by the \pkg{protobuf} \proglang{C++} library, and the \proglang{R} objects make calls into more than 100 \proglang{C++} functions that provide the glue code between the \proglang{R} language classes and the underlying \proglang{C++} classes. \proglang{S}4 objects are immutable, and so the methods that modify field values of a message return a new copy of the object with \proglang{R}'s usual functional copy on modify semantics\footnote{\pkg{RProtoBuf} was designed and implemented before Reference Classes were introduced to offer a new class system with mutable objects. If \pkg{RProtoBuf} were implemented today Reference Classes would almost certainly be a better design choice than \proglang{S}4 classes.}. Using the \proglang{S}4 system allows the package to dispatch methods that are not generic in the \proglang{S}3 sense, such as \code{new} and \code{serialize}. The \pkg{Rcpp} package \citep{eddelbuettel2011rcpp,eddelbuettel2013seamless} is used to facilitate this integration of the \proglang{R} and \proglang{C++} code for these objects. Each method is wrapped individually which allows us to add user-friendly custom error handling, type coercion, and performance improvements at the cost of a more verbose implementation. The \pkg{RProtoBuf} package in many ways motivated the development of \pkg{Rcpp} Modules \citep{eddelbuettel2013exposing}, which provide a more concise way of wrapping \proglang{C++} functions and classes in a single entity. Since \pkg{RProtoBuf} users are most often switching between two or more different languages as part of a larger data analysis pipeline, both generic function and message passing OO style calling conventions are supported: \begin{itemize} \item The functional dispatch mechanism of the the form \verb|method(object, arguments)| (common to \proglang{R}). \item The message passing object-oriented notation of the form \verb|object$method(arguments)|. \end{itemize} Additionally, \pkg{RProtoBuf} supports tab completion for all classes. Completion possibilities include method names for all classes, plus \emph{dynamic dispatch} on names or types specific to a given object. This functionality is implemented with the \code{.DollarNames} S3 generic function defined in the \pkg{utils} package that is included with \proglang{R} \citep{r}. Table~\ref{class-summary-table} lists the six primary message and descriptor classes in \pkg{RProtoBuf}. The package documentation provides a complete description of the slots and methods for each class. % [bp] \begin{table}[t!] \centering \begin{tabular}{lccl} \hline Class & Slots & Methods & Dynamic dispatch\\ \hline `\code{Message}' & 2 & 20 & yes (field names)\\ `\code{Descriptor}' & 2 & 16 & yes (field names, enum types, nested types)\\ `\code{FieldDescriptor}' & 4 & 18 & no\\ `\code{EnumDescriptor}' & 4 & 11 & yes (enum constant names)\\ `\code{EnumValueDescriptor}' & 3 & \phantom{1}6 & no\\ `\code{FileDescriptor}' & 3 & \phantom{1}6 & yes (message/field definitions)\\ \hline \end{tabular} \caption{\label{class-summary-table}Overview of class, slot, method and dispatch relationships.} \end{table} \subsection{Messages} The `\code{Message}' \proglang{S}4 class represents Protocol Buffer messages and is the core abstraction of \pkg{RProtoBuf}. Each `\code{Message}' contains a pointer to a `\code{Descriptor}' which defines the schema of the data defined in the message, as well as a number of `\code{FieldDescriptor}'s for the individual fields of the message. <<>>= new(tutorial.Person) @ \subsection{Descriptors} Descriptors describe the type of a message. This includes what fields a message contains and what the types of those fields are. Message descriptors are represented in \proglang{R} by the `\code{Descriptor}' \proglang{S}4 class. The class contains the slots \code{pointer} and \code{type}. Similarly to messages, the \verb|$| operator can be used to retrieve descriptors that are contained in the descriptor, or invoke methods. When \pkg{RProtoBuf} is first loaded it calls \code{readProtoFiles} which reads in the example file \code{addressbook.proto} included with the package. The \code{tutorial.Person} descriptor and all other descriptors defined in the loaded \code{.proto} files are then available on the search path\footnote{This explains why the example in Table~\ref{tab:proto} lacked an explicit call to \code{readProtoFiles}.}. \subsubsection*{Field descriptors} \label{subsec-field-descriptor} <<>>= tutorial.Person$email tutorial.Person$email$is_required() tutorial.Person$email$type() tutorial.Person$email$as.character() class(tutorial.Person$email) @ \subsubsection*{Enum and EnumValue descriptors} \label{subsec-enum-descriptor} The \code{EnumDescriptor} type contains information about what values a type defines, while the \code{EnumValueDescriptor} describes an individual enum constant of a particular type. The \verb|$| operator can be used to retrieve the value of enum constants contained in the EnumDescriptor, or to invoke methods. <<>>= tutorial.Person$PhoneType tutorial.Person$PhoneType$WORK class(tutorial.Person$PhoneType) tutorial.Person$PhoneType$value(1) tutorial.Person$PhoneType$value(name="HOME") tutorial.Person$PhoneType$value(number=1) class(tutorial.Person$PhoneType$value(1)) @ \subsubsection*{File descriptors} \label{subsec-file-descriptor} The class `\code{FileDescriptor}' represents file descriptors in \proglang{R}. The \verb|$| operator can be used to retrieve named fields defined in the `\code{FileDescriptor}', or to invoke methods. % < < > > = % f <- tutorial.Person$fileDescriptor() % f % f$Person % @ \begin{Schunk} \begin{Sinput} R> f <- tutorial.Person$fileDescriptor() R> f \end{Sinput} \begin{Soutput} file descriptor for package tutorial \ (/usr/local/lib/R/site-library/RProtoBuf/proto/addressbook.proto) \end{Soutput} \begin{Sinput} R> f$Person \end{Sinput} \begin{Soutput} descriptor for type 'tutorial.Person' \end{Soutput} \end{Schunk} \section{Type coercion} \label{sec:types} One of the benefits of using an interface definition language (IDL) like Protocol Buffers is that it provides a highly portable basic type system. This permits different language and hardware implementations to map to the most appropriate type in different environments. Table~\ref{table-get-types} details the correspondence between the field type and the type of data that is retrieved by \verb|$| and \verb|[[| extractors. Three types in particular need further attention due to specific differences in the \proglang{R} language: booleans, unsigned integers, and 64-bit integers. \begin{table}[t!] \centering \begin{small} \begin{tabular}{lp{5cm}p{5.5cm}} \toprule Field type & \proglang{R} type (non repeated) & \proglang{R} type (repeated) \\ \cmidrule(r){2-3} double & \code{double} vector & \code{double} vector \\ float & \code{double} vector & \code{double} vector \\[3mm] uint32 & \code{double} vector & \code{double} vector \\ fixed32 & \code{double} vector & \code{double} vector \\[3mm] int32 & \code{integer} vector & \code{integer} vector \\ sint32 & \code{integer} vector & \code{integer} vector \\ sfixed32 & \code{integer} vector & \code{integer} vector \\[3mm] int64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ uint64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ sint64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ fixed64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\ sfixed64 & \code{integer} or \code{character} vector & \code{integer} or \code{character} vector \\[3mm] bool & \code{logical} vector & \code{logical} vector \\[3mm] string & \code{character} vector & \code{character} vector \\ bytes & \code{character} vector & \code{character} vector \\[3mm] enum & \code{integer} vector & \code{integer} vector \\[3mm] message & \code{S4} object of class \code{Message} & \code{list} of \code{S4} objects of class \code{Message} \\ \bottomrule \end{tabular} \end{small} \caption{\label{table-get-types}Correspondence between field type and \proglang{R} type retrieved by the extractors. \proglang{R} lacks native 64-bit integers, so the \code{RProtoBuf.int64AsString} option is available to return large integers as characters to avoid losing precision; see Section~\ref{sec:int64} below. All but the \code{Message} type can be represented in vectors of one or more elements; for the latter a list is used.} \end{table} \subsection{Booleans} \proglang{R} booleans can accept three values: \code{TRUE}, \code{FALSE}, and \code{NA}. However, most other languages, including the Protocol Buffer schema, only accept \code{TRUE} or \code{FALSE}. This means that we simply can not store \proglang{R} logical vectors that include all three possible values as booleans. The library will refuse to store \code{NA}s in Protocol Buffer boolean fields, and users must instead choose another type (such as enum or integer) capable of storing three distinct values. <>= if (!exists("JSSPaper.Example1", "RProtoBuf:DescriptorPool")) { readProtoFiles(file="proto/int64.proto") } @ % We want a cleaner error message here. \begin{CodeChunk} \begin{CodeInput} R> a <- new(JSSPaper.Example1) R> a$optional_bool <- TRUE R> a$optional_bool <- FALSE R> a$optional_bool <- NA \end{CodeInput} \begin{CodeOutput} Error: NA boolean values can not be stored in bool Protocol Buffer fields \end{CodeOutput} \end{CodeChunk} \subsection{Unsigned integers} \proglang{R} lacks a native unsigned integer type. Values between $2^{31}$ and $2^{32} - 1$ read from unsigned integer Protocol Buffer fields must be stored as doubles in \proglang{R}. <<>>= as.integer(2^31-1) as.integer(2^31 - 1) + as.integer(1) 2^31 class(2^31) @ \subsection{64-bit integers} \label{sec:int64} \proglang{R} also does not support the native 64-bit integer type. Numeric vectors with integer values greater or equal to $2^{31}$ can only be stored as floating-point double precision variables. This conversion incurs a loss of precision, and \proglang{R} loses the ability to distinguish between some distinct integer variables: <<>>= 2^53 == (2^53 + 1) @ Most modern languages do have support for 64-bit integer values, which becomes problematic when \pkg{RProtoBuf} is used to exchange data with a system that requires this integer type. To work around this, \pkg{RProtoBuf} allows users to get and set 64-bit integer values by specifying them as character strings. On 64-bit platforms, character strings representing large decimal numbers will be coerced to \code{int64} during assignment to 64-bit Protocol Buffer types to work around the lack of native 64-bit types in \proglang{R} itself. The values are stored as distinct \code{int64} values in memory. But when accessed from \proglang{R} language code, they will be coerced into numeric (floating-point) values. If the full 64-bit precision is required, the \code{RProtoBuf.int64AsString} option can be set to \code{TRUE} to return \code{int64} values from messages as character strings. Such character values are useful because they can accurately be used as unique identifiers, and can easily be passed to \proglang{R} packages such as \pkg{int64} \citep{int64} or \pkg{bit64} \citep{bit64} which represent 64-bit integers in \proglang{R}. \section[Converting R data structures into Protocol Buffers]{Converting \proglang{R} data structures into Protocol Buffers} \label{sec:evaluation} The previous sections discussed functionality in the \pkg{RProtoBuf} package for creating, manipulating, parsing, and serializing Protocol Buffer messages of a defined schema. This is useful when there are pre-existing systems with defined schemas or significant software components written in other languages that need to be accessed from within \proglang{R}. The package also provides methods for converting arbitrary \proglang{R} data structures into Protocol Buffers and vice versa with a universal \proglang{R} object schema. The \code{serialize\_pb} and \code{unserialize\_pb} functions serialize arbitrary \proglang{R} objects into a universal Protocol Buffer message: <<>>= msg <- serialize_pb(iris, NULL) identical(iris, unserialize_pb(msg)) @ In order to accomplish this, \pkg{RProtoBuf} uses the same catch-all \code{proto} schema used by \pkg{RHIPE} for exchanging \proglang{R} data with Hadoop \citep{rhipe}. This schema, which we will refer to as \code{rexp.proto}, is printed in %appendix \ref{rexp.proto}. the appendix. The Protocol Buffer messages generated by \pkg{RProtoBuf} and \pkg{RHIPE} are naturally compatible between the two systems because they use the same schema. This shows the power of using a schema-based cross-platform format such as Protocol Buffers: interoperability is achieved without effort or close coordination. The \code{rexp.proto} schema natively supports all main \proglang{R} storage types holding \emph{data}. These include \code{NULL}, \code{list} and vectors of type \code{logical}, \code{character}, \code{double}, \code{integer}, and \code{complex}. In addition, every type can contain a named set of attributes, as is the case in \proglang{R}. The storage types \code{function}, \code{language}, and \code{environment} are specific to \proglang{R} and have no equivalent native type in Protocol Buffers. These three types are supported by first serializing with \code{base::serialize} in \proglang{R} and then stored in a raw bytes field. \subsection[Evaluation: Serializing R data sets]{Evaluation: Serializing \proglang{R} data sets} \label{sec:compression} <>= datasets <- as.data.frame(data(package="datasets")$results) datasets$name <- sub("\\s+.*$", "", datasets$Item) n <- nrow(datasets) @ This section evaluates the effectiveness of serializing arbitrary \proglang{R} data structures into Protocol Buffers. We use the \Sexpr{n} standard data sets included in the \pkg{datasets} package included with \proglang{R} as our evaluation data. These data sets include data frames, matrices, time series, tables, lists, and some more exotic data classes. For each data set, we compare how many bytes are used to store the data set using four different methods: \begin{itemize} \item normal \proglang{R} serialization \citep{serialization}, \item \proglang{R} serialization followed by gzip, \item normal Protocol Buffer serialization, and \item Protocol Buffer serialization followed by gzip. \end{itemize} <>= datasets$object.size <- unname(sapply(datasets$name, function(x) object.size(eval(as.name(x))))) datasets$R.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize(eval(as.name(x)), NULL)))) datasets$R.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize(eval(as.name(x)), NULL)))) datasets$R.serialize.size.gz <- unname(sapply(datasets$name, function(x) length(memCompress(serialize(eval(as.name(x)), NULL), "gzip")))) datasets$RProtoBuf.serialize.size <- unname(sapply(datasets$name, function(x) length(serialize_pb(eval(as.name(x)), NULL)))) datasets$RProtoBuf.serialize.size.gz <- unname(sapply(datasets$name, function(x) length(memCompress(serialize_pb(eval(as.name(x)), NULL), "gzip")))) clean.df <- data.frame(dataset=datasets$name, object.size=datasets$object.size, "serialized"=datasets$R.serialize.size, "gzipped serialized"=datasets$R.serialize.size.gz, "RProtoBuf"=datasets$RProtoBuf.serialize.size, "gzipped RProtoBuf"=datasets$RProtoBuf.serialize.size.gz, "ratio.serialized" = datasets$R.serialize.size / datasets$object.size, "ratio.rprotobuf" = datasets$RProtoBuf.serialize.size / datasets$object.size, "ratio.serialized.gz" = datasets$R.serialize.size.gz / datasets$object.size, "ratio.rprotobuf.gz" = datasets$RProtoBuf.serialize.size.gz / datasets$object.size, "savings.serialized" = 1-(datasets$R.serialize.size / datasets$object.size), "savings.rprotobuf" = 1-(datasets$RProtoBuf.serialize.size / datasets$object.size), "savings.serialized.gz" = 1-(datasets$R.serialize.size.gz / datasets$object.size), "savings.rprotobuf.gz" = 1-(datasets$RProtoBuf.serialize.size.gz / datasets$object.size), check.names=FALSE) all.df<-data.frame(dataset="TOTAL", object.size=sum(datasets$object.size), "serialized"=sum(datasets$R.serialize.size), "gzipped serialized"=sum(datasets$R.serialize.size.gz), "RProtoBuf"=sum(datasets$RProtoBuf.serialize.size), "gzipped RProtoBuf"=sum(datasets$RProtoBuf.serialize.size.gz), "ratio.serialized" = sum(datasets$R.serialize.size) / sum(datasets$object.size), "ratio.rprotobuf" = sum(datasets$RProtoBuf.serialize.size) / sum(datasets$object.size), "ratio.serialized.gz" = sum(datasets$R.serialize.size.gz) / sum(datasets$object.size), "ratio.rprotobuf.gz" = sum(datasets$RProtoBuf.serialize.size.gz) / sum(datasets$object.size), "savings.serialized" = 1-(sum(datasets$R.serialize.size) / sum(datasets$object.size)), "savings.rprotobuf" = 1-(sum(datasets$RProtoBuf.serialize.size) / sum(datasets$object.size)), "savings.serialized.gz" = 1-(sum(datasets$R.serialize.size.gz) / sum(datasets$object.size)), "savings.rprotobuf.gz" = 1-(sum(datasets$RProtoBuf.serialize.size.gz) / sum(datasets$object.size)), check.names=FALSE) clean.df<-rbind(clean.df, all.df) @ Figure~\ref{fig:compression} shows the space savings $\left(1 - \frac{\textrm{Compressed Size}}{\textrm{Uncompressed Size}}\right)$ for each of the data sets using each of these four methods. The associated table shows the exact data sizes for some outliers and the aggregate of all 104 data sets. Note that Protocol Buffer serialization results in slightly smaller byte streams compared to native \proglang{R} serialization in most cases (red dots), but this difference disappears if the results are compressed with gzip (blue triangles). % Sizes are comparable but Protocol Buffers provide simple getters and % setters in multiple languages instead of requiring other programs to % parse the \proglang{R} serialization % format. % \citep{serialization}. The \code{crimtab} dataset of anthropometry measurements of British prisoners \citep{garson1900metric} and the \code{airquality} dataset of air quality measurements in New York show the greatest difference in the space savings when using Protocol Buffers compared to \proglang{R} native serialization. The \code{crimtab} dataset is a 42 $\times$ 22 table of integers, most equal to 0, and the \code{airquality} dataset is a data frame of 154 observations of 1 numeric and 5 integer variables. In both data sets, the large number of small integer values can be very efficiently encoded by the \emph{Varint} integer encoding scheme used by Protocol Buffers which use a variable number of bytes for each value. The other extreme is represented by the \code{faithful} dataset of waiting time and eruptions of the Old Faithful geyser in Yellowstone National Park, Wyoming, USA \citep{azzalini1990look}. This dataset is a data frame with 272 observations of 2 numeric variables. The \proglang{R} native serialization of repeated numeric values is more space-efficient, resulting in a slightly smaller object size compared to the serialized Protocol Buffer equivalent. This evaluation shows that the \code{rexp.proto} universal \proglang{R} object schema included in \pkg{RProtoBuf} does not in general provide any significant saving in file size compared to the normal serialization mechanism in \proglang{R}. % redundant: which is seen as equally compact. The benefits of \pkg{RProtoBuf} accrue more naturally in applications where multiple programming languages are involved, or when a more concise application-specific schema has been defined. The example in the next section satisfies both of these conditions. \begin{figure}[t!] \begin{center} <>= old.mar<-par("mar") new.mar<-old.mar new.mar[3]<-0 new.mar[4]<-0 my.cex<-1.3 par("mar"=new.mar) plot(clean.df$savings.serialized, clean.df$savings.rprotobuf, pch=1, col="red", las=1, xlab="Serialization Space Savings", ylab="Protocol Buffer Space Savings", xlim=c(0,1),ylim=c(0,1),cex.lab=my.cex, cex.axis=my.cex) points(clean.df$savings.serialized.gz, clean.df$savings.rprotobuf.gz,pch=2, col="blue") # grey dotted diagonal abline(a=0,b=1, col="grey",lty=2,lwd=3) # find point furthest off the X axis. clean.df$savings.diff <- clean.df$savings.serialized - clean.df$savings.rprotobuf clean.df$savings.diff.gz <- clean.df$savings.serialized.gz - clean.df$savings.rprotobuf.gz # The one to label. tmp.df <- clean.df[which(clean.df$savings.diff == min(clean.df$savings.diff)),] # This minimum means most to the left of our line, so pos=2 is label to the left text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=2, cex=my.cex) # Some gziped version # text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=2, cex=my.cex) # Second one is also an outlier tmp.df <- clean.df[which(clean.df$savings.diff == sort(clean.df$savings.diff)[2]),] # This minimum means most to the left of our line, so pos=2 is label to the left text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=2, cex=my.cex) #text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=my.cex) tmp.df <- clean.df[which(clean.df$savings.diff == max(clean.df$savings.diff)),] # This minimum means most to the right of the diagonal, so pos=4 is label to the right # Only show the gziped one. #text(tmp.df$savings.serialized, tmp.df$savings.rprotobuf, labels=tmp.df$dataset, pos=4, cex=my.cex) text(tmp.df$savings.serialized.gz, tmp.df$savings.rprotobuf.gz, labels=tmp.df$dataset, pos=4, cex=my.cex) #outlier.dfs <- clean.df[c(which(clean.df$savings.diff == min(clean.df$savings.diff)), legend("topleft", c("Raw", "Gzip Compressed"), pch=1:2, col=c("red", "blue"), cex=my.cex) #interesting.df <- clean.df[unique(c(which(clean.df$savings.diff == min(clean.df$savings.diff)), # which(clean.df$savings.diff == max(clean.df$savings.diff)), # which(clean.df$savings.diff.gz == max(clean.df$savings.diff.gz)), # which(clean.df$dataset == "TOTAL"))),c("dataset", "object.size", "serialized", "gzipped serialized", "RProtoBuf", "gzipped RProtoBuf", "savings.serialized", "savings.serialized.gz", "savings.rprotobuf", "savings.rprotobuf.gz")] interesting.df <- clean.df[as.character(clean.df[,1]) %in% c("crimtab", "airquality", "faithful", "TOTAL"), c("dataset", "object.size", "serialized", "gzipped serialized", "RProtoBuf", "gzipped RProtoBuf", "savings.serialized", "savings.serialized.gz", "savings.rprotobuf", "savings.rprotobuf.gz")] interesting.df <- interesting.df[c(2,1,3,4),] # Print without .00 in xtable interesting.df$object.size <- as.integer(interesting.df$object.size) par("mar"=old.mar) @ \includegraphics[width=0.45\textwidth]{figures/fig-SER} % latex table generated in R 3.0.2 by xtable 1.7-0 package % Wed Nov 26 15:31:30 2014 % updated to R 3.3.1 on Sun Jul 10 17:29:41 CDT 2016 %\begin{table}[ht] %\begin{center} \begin{tabular}{rlrrrrr} \hline Data set & \code{object.size} & \multicolumn{2}{c}{\proglang{R} serialization} & \multicolumn{2}{c}{\pkg{RProtoBuf} serialization} \\ & & default & gzipped & default & gzipped \\ \hline \code{crimtab} & 7,936 & 4,641 (41.5\%) & 714 (91.0\%) & 1,655 (79.1\%) & 576 (92.7\%)\\ \code{airquality} & 5,496 & 4,551 (17.2\%) & 1,242 (77.4\%) & 2,874 (47.7\%) & 1,294 (76.4\%)\\ \code{faithful} & 5,136 & 4,543 (11.5\%) & 1,339 (73.9\%) & 4,936 \phantom{0}(3.9\%) & 1,776 (65.4\%)\\ \hline All & 609,024 & 463,833 (24\%) & 139,814 (77\%) & 436,746 (28\%) & 142,783 (77\%)\\ \hline \end{tabular} \end{center} \caption{(Top) Relative space savings of Protocol Buffers and native \proglang{R} serialization over the raw object sizes of each of the 104 data sets in the \pkg{datasets} package. Points to the left of the dashed $y=x$ line represent datasets that are more efficiently encoded with Protocol Buffers. (Bottom) Absolute space savings of three outlier datasets and the aggregate performance of all datasets. R version 3.3.1 was used for both the figure and the table. } \label{fig:compression} \end{figure} \section{Application: Distributed data collection with MapReduce} \label{sec:mapreduce} Protocol Buffers are used extensively at Google for almost all RPC protocols, and to store structured information on a variety of persistent storage systems \citep{dean2009designs}. Since the initial release in 2010, hundreds of Google's statisticians and software engineers use the \pkg{RProtoBuf} package on a daily basis to interact with these systems from within \proglang{R}. The current section illustrates the power of Protocol Buffers to collect and manage large structured data in one language before analyzing it in \proglang{R}. Our example uses MapReduce \citep{dean2008mapreduce}, which has emerged in the last decade as a popular design pattern to facilitate parallel processing of big data using distributed computing clusters. Big data sets in fields such as particle physics and information processing are often stored in binned (histogram) form in order to reduce storage requirements \citep{scott2009multivariate}. Because analysis over such large data sets may involve very rare phenomenon or deal with highly skewed data sets or inflexible raw data storage systems, unbiased sampling is often not feasible. In these situations, MapReduce and binning may be combined as a pre-processing step for a wide range of statistical and scientific analyses \citep{blocker2013}. There are two common patterns for generating histograms of large data sets in a single pass with MapReduce. In the first method, each mapper task generates a histogram over a subset of the data that it has been assigned, serializes this histogram and sends it to one or more reducer tasks which merge the intermediate histograms from the mappers. In the second method, illustrated in Figure~\ref{fig:mr-histogram-pattern1}, each mapper rounds a data point to a bucket width and outputs that bucket as a key and '1' as a value. Reducers count how many times each key occurs and outputs a histogram to a data store. \begin{figure}[t!] \begin{center} \includegraphics[width=0.9\textwidth]{figures/histogram-mapreduce-diag1.pdf} \end{center} \caption{Diagram of MapReduce histogram generation pattern.} \label{fig:mr-histogram-pattern1} \end{figure} In both methods, the mapper tasks must choose identical bucket boundaries in advance if we are to construct the histogram in a single pass, even though they are analyzing disjoint parts of the input set that may cover different ranges. All distributed tasks involved in the pre-processing as well as any downstream data analysis tasks must share a schema of the histogram representation to coordinate effectively. The \pkg{HistogramTools} package \citep{histogramtools} enhances \pkg{RProtoBuf} by providing a concise schema for \proglang{R} histogram objects: \begin{example} package HistogramTools; message HistogramState { repeated double breaks = 1; repeated int32 counts = 2; optional string name = 3; } \end{example} This \code{HistogramState} message type is designed to be helpful if some of the Map or Reduce tasks are written in \proglang{R}, or if those components are written in other languages and only the resulting output histograms need to be manipulated in \proglang{R}. \subsection[A simple single-machine example for Python to R serialization]{A simple single-machine example for \proglang{Python} to \proglang{R} serialization} To create \code{HistogramState} messages in \proglang{Python} for later consumption by \proglang{R}, we first compile the \code{histogram.proto} descriptor into a python module using the \code{protoc} compiler: \begin{verbatim} protoc histogram.proto --python_out=. \end{verbatim} This generates a Python module called \code{histogram\_pb2.py}, containing both the descriptor information as well as methods to read and manipulate the histogram message data. The following simple Python script uses this generated module to create a histogram (to which breakpoints and binned data are added), and writes out the Protocol Buffer representation to a file: \begin{Code} from histogram_pb2 import HistogramState; hist = HistogramState() hist.counts.extend([2, 6, 2, 4, 6]) hist.breaks.extend(range(6)) hist.name="Example Histogram Created in Python" outfile = open("/tmp/hist.pb", "wb") outfile.write(hist.SerializeToString()) outfile.close() \end{Code} The Protocol Buffer created from this \proglang{Python} script can then be read into \proglang{R} and converted to a native \proglang{R} histogram object for plotting. The code below first attaches the \pkg{HistogramTools} package which imports \pkg{RProtoBuf}. Then reads all of the \code{.proto} descriptor definitions provided by \pkg{HistogramTools} and adds them to the environment as described in Section~\ref{sec:rprotobuf-basic}. Next the serialized Protocol Buffer is parsed using the \code{HistogramTools.HistogramState} schema. Finally the Protocol Buffer representation of the histogram is converted to a native \proglang{R} histogram object with \code{as.histogram} and passes the result to \code{plot} (see Figure~\ref{figure}). \lstdefinelanguage{jss} {sensitive=false, morecomment=[l]{R>}} \lstset{language=jss, basicstyle=\ttfamily, numbers=left, numberstyle=\tiny, stepnumber=2, numbersep=5pt, columns=fullflexible, keepspaces=true, showstringspaces=false, commentstyle=\textsl} %\begin{Code} \begin{lstlisting} R> library("HistogramTools") R> readProtoFiles(package="HistogramTools") R> hist <- HistogramTools.HistogramState$read("/tmp/hist.pb") R> hist [1] "message of type 'HistogramTools.HistogramState' with 3 fields set" R> plot(as.histogram(hist), main="") \end{lstlisting} %\end{Code} %% DEdd 2016-07-10 Taking a shortcut here an showing a prepared %% HistogramTools chart to not depend on HistogramTools %% on Travis CI etc \begin{center} <>= require(HistogramTools) readProtoFiles(package="HistogramTools") hist <- HistogramTools.HistogramState$read("proto/hist.pb") plot(as.histogram(hist), main="") @ \includegraphics[width=0.45\textwidth]{figures/HistogramTools} \end{center} This simple example uses a constant histogram generated in \proglang{Python} to illustrate the serialization concepts without requiring the reader to be familiar with the interface of any particular MapReduce implementation. In practice, using Protocol Buffers to pass histograms between another programming language and \proglang{R} would provide a much greater benefit in a distributed context. For example, a first-class data type to represent histograms would prevent individual histograms from being split up and would allow the use of combiners on Map workers to process large data sets more efficiently than simply passing around lists of counts and buckets. One of the authors has used this design pattern with \proglang{C++} MapReduces over very large data sets to write out histogram protocol buffers for several large-scale studies of distributed storage systems \citep{sciencecloud,janus}. \section{Application: Data interchange in web services} \label{sec:opencpu} The previous section described an application where data from a program written in another language was saved to persistent storage and then read into \proglang{R} for further analysis. This section describes another common use case where Protocol Buffers are used as the interchange format for client-server communication. Network protocols such as HTTP provide mechanisms for client-server communication, i.e., how to initiate requests, authenticate, send messages, etc. However, network protocols generally do not regulate the \emph{content} of messages: they allow transfer of any media type, such as web pages, static files or multimedia content. When designing systems where various components require exchange of specific data structures, we need something on top of the network protocol that prescribes how these structures are to be represented in messages (buffers) on the network. Protocol Buffers solve this problem by providing a cross-platform method for serializing arbitrary structures into well defined messages, which can then be exchanged using any protocol. \subsection[Interacting with R through HTTPS and Protocol Buffers]{Interacting with \proglang{R} through HTTPS and Protocol Buffers} One example of a system that supports Protocol Buffers to interact with \proglang{R} is OpenCPU \citep{opencpu}. OpenCPU is a framework for embedded statistical computation and reproducible research based on \proglang{R} and \LaTeX. It exposes a HTTP(S) API to access and manipulate \proglang{R} objects and execute remote \proglang{R} function calls. Clients do not need to understand or generate any \proglang{R} code: HTTP requests are automatically mapped to function calls, and arguments/return values can be posted/retrieved using several data interchange formats, such as Protocol Buffers. OpenCPU uses the \code{rexp.proto} descriptor and the \code{serialize\_pb} and \code{unserialize\_pb} functions described in Section~\ref{sec:evaluation} to convert between \proglang{R} objects and Protocol Buffer messages. \subsection[HTTP GET: Retrieving an R object]{HTTP GET: Retrieving an \proglang{R} object} The \code{HTTP GET} method is used to read a resource from OpenCPU. For example, to access the data set \code{Animals} from the package \code{MASS}, a client performs the following HTTP request: \begin{verbatim} GET https://demo.ocpu.io/MASS/data/Animals/pb \end{verbatim} The postfix \code{/pb} in the URL tells the server to send this object in the form of a Protocol Buffer message. % Alternative formats include \code{/json}, \code{/csv}, \code{/rds} and others. If the request is successful, OpenCPU returns the serialized object with HTTP status code 200 and HTTP response header \code{Content-Type: application/x-protobuf}. The latter is the conventional MIME type that formally notifies the client to interpret the response as a Protocol Buffer. Because both HTTP and Protocol Buffers have libraries available for many languages, clients can be implemented in just a few lines of code. Below is example code for both \proglang{R} and Python that retrieves an \proglang{R} data set encoded as a Protocol Buffer message from OpenCPU. In \proglang{R}, we use the HTTP client from the \code{httr} package \citep{httr}. In this example we download a data set which is part of the base \proglang{R} distribution, so we can verify that the object was transferred without loss of information. <>= library("RProtoBuf") library("httr") req <- GET('https://demo.ocpu.io/MASS/data/Animals/pb') output <- unserialize_pb(req$content) identical(output, MASS::Animals) @ Similarly, to retrieve the same data set in a \proglang{Python} client, we first compile the \code{rexp.proto} descriptor into a python module using the \code{protoc} compiler: \begin{verbatim} protoc rexp.proto --python_out=. \end{verbatim} This generates \proglang{Python} module called \code{rexp\_pb2.py}, containing both the descriptor information as well as methods to read and manipulate the \proglang{R} object message. We use the HTTP client from the \code{urllib2} module in our example to retrieve the encoded Protocol Buffer from the remote server then parse and print it from \proglang{Python}. \begin{verbatim} import urllib2 from rexp_pb2 import REXP req = urllib2.Request('https://demo.ocpu.io/MASS/data/Animals/pb') res = urllib2.urlopen(req) msg = REXP() msg.ParseFromString(res.read()) print(msg) \end{verbatim} The \code{msg} object contains all data from the \code{Animals} data set. From here we can easily extract the desired fields for further use in \proglang{Python}. \subsection[HTTP POST: Calling an R function]{HTTP POST: Calling an \proglang{R} function} The previous example used a simple \code{HTTP GET} method to retrieve an \proglang{R} object from a remote service (\pkg{OpenCPU}) encoded as a Protocol Buffer. In many cases simple \code{HTTP GET} methods are insufficient, and a more complete RPC system may need to create compact Protocol Buffers for each request to send to the remote server in addition to parsing the response Protocol Buffers. The \pkg{OpenCPU} framework allows us to do arbitrary \proglang{R} function calls from within any programming language by encoding the arguments in the request Protocol Buffer. The following example \proglang{R} client code performs the remote function call \code{stats::rnorm(n = 42, mean = 100)}. The function arguments (in this case \code{n} and \code{mean}) as well as the return value (a vector with 42 random numbers) are transferred using Protocol Buffer messages. RPC in \pkg{OpenCPU} works like the \code{do.call} function in \proglang{R}, hence all arguments are contained within a list. <>= library("httr") library("RProtoBuf") args <- list(n=42, mean=100) payload <- serialize_pb(args, NULL) req <- POST ( url = "https://demo.ocpu.io/stats/R/rnorm/pb", body = payload, add_headers ( "Content-Type" = "application/x-protobuf" ) ) output <- unserialize_pb(req$content) print(output) @ The \pkg{OpenCPU} server basically performs the following steps to process the above RPC request: <>= fnargs <- unserialize_pb(inputmsg) val <- do.call(stats::rnorm, fnargs) outputmsg <- serialize_pb(val) @ \section{Summary} \label{sec:summary} Over the past decade, many formats for interoperable data exchange have become available, each with its unique features, strengths and weaknesses. Text based formats such as CSV and JSON are easy to use, and will likely remain popular among statisticians for many years to come. However, in the context of increasingly complex analysis stacks and applications involving distributed computing as well as mixed language analysis pipelines, choosing a more sophisticated data interchange format may reap considerable benefits. %Protocol Buffers is itself not a protocol. %Forward-compatibility is one of the features. No need to re-iterate those The Protocol Buffers standard and library offer a unique combination of features, performance, and maturity, that seems particularly well suited for data-driven applications and numerical computing. The \pkg{RProtoBuf} package builds on the Protocol Buffers \proglang{C++} library, and extends the \proglang{R} system with the ability to create, read, write, parse, and manipulate Protocol Buffer messages. \pkg{RProtoBuf} has been used extensively inside Google for the past five years by statisticians, analysts, and software engineers. At the time of this writing there are over 300 active users of \pkg{RProtoBuf} using it to read data from and otherwise interact with distributed systems written in \proglang{C++}, \proglang{Java}, \proglang{Python}, and other languages. We hope that making Protocol Buffers available to the \proglang{R} community will contribute to better software integration and allow for building even more advanced applications and analysis pipelines with \proglang{R}. \section*{Acknowledgments} The first versions of \pkg{RProtoBuf} were written during 2009--2010. Very significant contributions, both in code and design, were made by Romain Fran\c{c}ois whose continued influence on design and code is greatly appreciated. Several features of the package reflect the design of the \pkg{rJava} package by Simon Urbanek \citep{rjava}. The user-defined table mechanism, implemented by Duncan Temple Lang for the purpose of the \pkg{RObjectTables} package, allows for the dynamic symbol lookup. Kenton Varda was generous with his time in reviewing code and explaining obscure Protocol Buffer semantics. Karl Millar and Tim Hesterberg were very helpful in reviewing code and offering suggestions. Saptarshi Guha's work on \pkg{RHIPE} and implementation of a universal message type for \proglang{R} language objects allowed us to add the \code{serialize_pb} and \code{unserialize_pb} methods for turning arbitrary \proglang{R} objects into Protocol Buffers without a specialized pre-defined schema. Feedback from two anonymous referees greatly improved both the presentation of this paper and the package contents. \bibliography{RProtoBuf-paper} \begin{appendix} \section[The rexp.proto schema descriptor]{The \code{rexp.proto} schema descriptor} \label{rexp.proto} Below a print of the \code{rexp.proto} schema (originally designed by \citealt{rhipe}) that is included with the \pkg{RProtoBuf} package and used by \code{serialize\_pb} and \code{unserialize\_pb}. \begin{verbatim} package rexp; message REXP { enum RClass { STRING = 0; RAW = 1; REAL = 2; COMPLEX = 3; INTEGER = 4; LIST = 5; LOGICAL = 6; NULLTYPE = 7; LANGUAGE = 8; ENVIRONMENT = 9; FUNCTION = 10; } enum RBOOLEAN { F=0; T=1; NA=2; } required RClass rclass = 1; repeated double realValue = 2 [packed=true]; repeated sint32 intValue = 3 [packed=true]; repeated RBOOLEAN booleanValue = 4; repeated STRING stringValue = 5; optional bytes rawValue = 6; repeated CMPLX complexValue = 7; repeated REXP rexpValue = 8; repeated string attrName = 11; repeated REXP attrValue = 12; optional bytes languageValue = 13; optional bytes environmentValue = 14; optional bytes functionValue = 15; } message STRING { optional string strval = 1; optional bool isNA = 2 [default=false]; } message CMPLX { optional double real = 1 [default=0]; required double imag = 2; } \end{verbatim} \end{appendix} \end{document} RProtoBuf/vignettes/RProtoBuf-intro.Rnw0000644000175100001440000021004012740533555017673 0ustar hornikusers\documentclass[11pt]{article} %\VignetteIndexEntry{RProtoBuf-intro} %\VignetteEngine{highlight::highlight} %\VignetteKeywords{RProtoBuf, Protocol Buffers, package} %\VignetteDepends{RProtoBuf} \usepackage{url} \usepackage{color} \usepackage[colorlinks]{hyperref} \definecolor{link}{rgb}{0,0,0.3} \hypersetup{ colorlinks,% citecolor=link,% filecolor=link,% linkcolor=link,% urlcolor=link } \setlength{\oddsidemargin}{0pt} \setlength{\textwidth}{17cm} % uh-oh, I use letter :) \setcounter{tocdepth}{2} \usepackage{microtype} %% cf http://www.khirevich.com/latex/microtype/ \usepackage[T1]{fontenc} %% cf http://www.khirevich.com/latex/font/ \usepackage[bitstream-charter]{mathdesign} %% cf http://www.khirevich.com/latex/font/ <>= library("RProtoBuf") options("width"=65) rpb.version <- packageDescription("RProtoBuf")$Version prettyDate <- format(Sys.Date(), "%B %e, %Y") @ % closing $ needed here \author{Romain Fran\c{c}ois \and Dirk Eddelbuettel \and Murray Stokely} \title{RProtoBuf: An R API for Protocol Buffers} \date{Version \Sexpr{rpb.version} as of \Sexpr{prettyDate}} \begin{document} \maketitle \abstract{ \noindent \textsl{Protocol Buffers} is a software project by Google that is used extensively internally and also released under an Open Source license. It provides a way of encoding structured data in an efficient yet extensible format. Google formally supports APIs for C++, Java and Python. This vignette describes version \Sexpr{rpb.version} of the \texttt{RProtoBuf} package which brings support for protocol buffer messages to R. } \tableofcontents \section{Protocol Buffers} Protocol buffers are a language-neutral, platform-neutral, extensible way of serializing structured data for use in communications protocols, data storage, and more. Protocol Buffers offer key features such as an efficient data interchange format that is both language- and operating system-agnostic yet uses a lightweight and highly performant encoding, object serialization and de-serialization as well data and configuration management. Protocol buffers are also forward compatible: updates to the \texttt{proto} files do not break programs built against the previous specification. While benchmarks are not available, Google states on the project page that in comparison to XML, protocol buffers are at the same time \textsl{simpler}, between three to ten times \textsl{smaller}, between twenty and one hundred times \textsl{faster}, as well as less ambiguous and easier to program. The protocol buffers code is released under an open-source (BSD) license. The protocol buffer project (\url{http://code.google.com/p/protobuf/}) contains a C++ library and a set of runtime libraries and compilers for C++, Java and Python. With these languages, the workflow follows standard practice of so-called Interface Description Languages (IDL) (c.f. \href{http://en.wikipedia.org/wiki/Interface_description_language}{Wikipedia on IDL}). This consists of compiling a protocol buffer description file (ending in \texttt{.proto}) into language specific classes that can be used to create, read, write and manipulate protocol buffer messages. In other words, given the 'proto' description file, code is automatically generated for the chosen target language(s). The project page contains a tutorial for each of these officially supported languages: \url{http://code.google.com/apis/protocolbuffers/docs/tutorials.html} Besides the officially supported C++, Java and Python implementations, several projects have been created to support protocol buffers for many languages. The list of known languages to support protocol buffers is compiled as part of the project page: \url{http://code.google.com/p/protobuf/wiki/ThirdPartyAddOns} The protocol buffer project page contains a comprehensive description of the language: \url{http://code.google.com/apis/protocolbuffers/docs/proto.html} \section{Basic use: Protocol Buffers and R} This section describes how to use the R API to create and manipulate protocol buffer messages in R, and how to read and write the binary \emph{payload} of the messages to files and arbitrary binary R connections. \subsection{Importing proto files dynamically} In contrast to the other languages (Java, C++, Python) that are officially supported by Google, the implementation used by the \texttt{RProtoBuf} package does not rely on the \texttt{protoc} compiler (with the exception of the two functions discussed in the previous section). This means that no initial step of statically compiling the proto file into C++ code that is then accessed by R code is necessary. Instead, \texttt{proto} files are parsed and processed \textsl{at runtime} by the protobuf C++ library---which is much more appropriate for a dynamic language. The \texttt{readProtoFiles} function allows importing \texttt{proto} files in several ways. <<>>= args( readProtoFiles ) @ Using the \texttt{file} argument, one can specify one or several file paths that ought to be proto files. <<>>= proto.dir <- system.file( "proto", package = "RProtoBuf" ) proto.file <- file.path( proto.dir, "addressbook.proto" ) <>= readProtoFiles( proto.file ) @ With the \texttt{dir} argument, which is ignored if the \texttt{file} is supplied, all files matching the \texttt{.proto} extension will be imported. <<>>= dir( proto.dir, pattern = "\\.proto$", full.names = TRUE ) <>= readProtoFiles( dir = proto.dir ) @ Finally, with the \texttt{package} argument (ignored if \texttt{file} or \texttt{dir} is supplied), the function will import all \texttt{.proto} files that are located in the \texttt{proto} sub-directory of the given package. A typical use for this argument is in the \texttt{.onLoad} function of a package. <>= readProtoFiles( package = "RProtoBuf" ) @ Once the proto files are imported, all message descriptors are are available in the R search path in the \texttt{RProtoBuf:DescriptorPool} special environment. The underlying mechanism used here is described in more detail in section~\ref{sec-lookup}. <<>>= ls( "RProtoBuf:DescriptorPool" ) @ \subsection{Creating a message} The objects contained in the special environment are descriptors for their associated message types. Descriptors will be discussed in detail in another part of this document, but for the purpose of this section, descriptors are just used with the \texttt{new} function to create messages. <<>>= p <- new( tutorial.Person, name = "Romain", id = 1 ) @ \subsection{Access and modify fields of a message} Once the message is created, its fields can be queried and modified using the dollar operator of R, making protocol buffer messages seem like lists. <<>>= p$name p$id p$email <- "francoisromain@free.fr" @ However, as opposed to R lists, no partial matching is performed and the name must be given entirely. The \verb|[[| operator can also be used to query and set fields of a mesages, supplying either their name or their tag number : <<>>= p[["name"]] <- "Romain Francois" p[[ 2 ]] <- 3 p[[ "email" ]] @ Protocol buffers include a 64-bit integer type, but R lacks native 64-bit integer support. A workaround is available and described in Section~\ref{sec:int64} for working with large integer values. % TODO(mstokely): Document extensions here. % There are none in addressbook.proto though. \subsection{Display messages} Protocol buffer messages and descriptors implement \texttt{show} methods that provide basic information about the message : <<>>= p @ For additional information, such as for debugging purposes, the \texttt{as.character} method provides a more complete ASCII representation of the contents of a message. <<>>= writeLines( as.character( p ) ) @ \subsection{Serializing messages} However, the main focus of protocol buffer messages is efficiency. Therefore, messages are transported as a sequence of bytes. The \texttt{serialize} method is implemented for protocol buffer messages to serialize a message into the sequence of bytes (raw vector in R speech) that represents the message. <<>>= serialize( p, NULL ) @ The same method can also be used to serialize messages to files : <<>>= tf1 <- tempfile() tf1 serialize( p, tf1 ) readBin( tf1, raw(0), 500 ) @ Or to arbitrary binary connections: <<>>= tf2 <- tempfile() con <- file( tf2, open = "wb" ) serialize( p, con ) close( con ) readBin( tf2, raw(0), 500 ) @ \texttt{serialize} can also be used in a more traditionnal object oriented fashion using the dollar operator : <<>>= # serialize to a file p$serialize( tf1 ) # serialize to a binary connection con <- file( tf2, open = "wb" ) p$serialize( con ) close( con ) @ \subsection{Parsing messages} The \texttt{RProtoBuf} package defines the \texttt{read} function to read messages from files, raw vector (the message payload) and arbitrary binary connections. <<>>= args( read ) @ The binary representation of the message (often called the payload) does not contain information that can be used to dynamically infer the message type, so we have to provide this information to the \texttt{read} function in the form of a descriptor : <<>>= message <- read( tutorial.Person, tf1 ) writeLines( as.character( message ) ) @ The \texttt{input} argument of \texttt{read} can also be a binary readable R connection, such as a binary file connection: <<>>= con <- file( tf2, open = "rb" ) message <- read( tutorial.Person, con ) close( con ) writeLines( as.character( message ) ) @ Finally, the payload of the message can be used : <<>>= # reading the raw vector payload of the message payload <- readBin( tf1, raw(0), 5000 ) message <- read( tutorial.Person, payload ) @ \texttt{read} can also be used as a pseudo method of the descriptor object : <<>>= # reading from a file message <- tutorial.Person$read( tf1 ) # reading from a binary connection con <- file( tf2, open = "rb" ) message <- tutorial.Person$read( con ) close( con ) # read from the payload message <- tutorial.Person$read( payload ) @ \section{Classes, Methods and Pseudo Methods} The \texttt{RProtoBuf} package uses the S4 system to store information about descriptors and messages, but the information stored in the R object is very minimal and mainly consists of an external pointer to a C++ variable that is managed by the \texttt{proto} C++ library. <<>>= str( p ) @ Using the S4 system allows the \texttt{RProtoBuf} package to dispatch methods that are not generic in the S3 sense, such as \texttt{new} and \texttt{serialize}. The \texttt{RProtoBuf} package combines the \emph{R typical} dispatch of the form \verb|method( object, arguments)| and the more traditional object oriented notation \verb|object$method(arguments)|. \subsection{messages} Messages are represented in R using the \texttt{Message} S4 class. The class contains the slots \texttt{pointer} and \texttt{type} as described on the Table~\ref{Message-class-table}. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & external pointer to the \texttt{Message} object of the C++ proto library. Documentation for the \texttt{Message} class is available from the protocol buffer project page: \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.message.html#Message} \\ \hline \texttt{type} & fully qualified path of the message. For example a \texttt{Person} message has its \texttt{type} slot set to \texttt{tutorial.Person} \\ \hline \end{tabular} \caption{\label{Message-class-table}Description of slots for the \texttt{Message} S4 class} \end{table} Although the \texttt{RProtoBuf} package uses the S4 system, the \verb|@| operator is very rarely used. Fields of the message are retrieved or modified using the \verb|$| or \verb|[[| operators as seen on the previous section, and pseudo-methods can also be called using the \verb|$| operator. Table~\ref{Message-methods-table} describes the methods defined for the \texttt{Message} class : \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{has} & \ref{Message-method-has} & Indicates if a message has a given field. \\ \texttt{clone} & \ref{Message-method-clone} & Creates a clone of the message \\ \texttt{isInitialized} & \ref{Message-method-isInitialized} & Indicates if a message has all its required fields set\\ \texttt{serialize} & \ref{Message-method-serialize} & serialize a message to a file or a binary connection or retrieve the message payload as a raw vector\\ \texttt{clear} & \ref{Message-method-clear} & Clear one or several fields of a message, or the entire message\\ \texttt{size} & \ref{Message-method-size} & The number of elements in a message field\\ \texttt{bytesize} & \ref{Message-method-bytesize} & The number of bytes the message would take once serialized\\ \hline \texttt{swap} & \ref{Message-method-swap} & swap elements of a repeated field of a message\\ \texttt{set} & \ref{Message-method-set} & set elements of a repeated field\\ \texttt{fetch} & \ref{Message-method-fetch} & fetch elements of a repeated field\\ \texttt{setExtension} & \ref{Message-method-setExtension} & set an extension of a message\\ \texttt{getExtension} & \ref{Message-method-getExtension} & get the value of an extension of a message\\ \texttt{add} & \ref{Message-method-add} & add elements to a repeated field \\ \hline \texttt{str} & \ref{Message-method-str} & the R structure of the message\\ \texttt{as.character} & \ref{Message-method-ascharacter} & character representation of a message\\ \texttt{toString} & \ref{Message-method-toString} & character representation of a message (same as \texttt{as.character}) \\ \texttt{as.list} & \ref{Message-method-aslist} & converts message to a named R list\\ \texttt{update} & \ref{Message-method-update} & updates several fields of a message at once\\ \texttt{descriptor} & \ref{Message-method-descriptor} & get the descriptor of the message type of this message\\ \texttt{fileDescriptor} & \ref{Message-method-fileDescriptor} & get the file descriptor of this message's descriptor\\ \hline \end{tabular} \end{small} \caption{\label{Message-methods-table}Description of methods for the \texttt{Message} S4 class} \end{table} \subsubsection{Retrieve fields} \label{Message-method-getfield} The \verb|$| and \verb|[[| operators allow extraction of a field data. <>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2, phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$name message$email message[[ "phone" ]] # using the tag number message[[ 2 ]] # id @ Neither \verb|$| nor \verb|[[| support partial matching of names. The \verb|$| is also used to call methods on the message, and the \verb|[[| operator can use the tag number of the field. Table~\ref{table-get-types} details correspondance between the field type and the type of data that is retrieved by \verb|$| and \verb|[[|. \begin{table}[h] \centering \begin{small} \begin{tabular}{|c|p{5cm}p{5cm}|} \hline field type & R type (non repeated) & R type (repeated) \\ \hline \hline double & \texttt{double} vector & \texttt{double} vector \\ float & \texttt{double} vector & \texttt{double} vector \\ \hline uint32 & \texttt{double} vector & \texttt{double} vector \\ fixed32 & \texttt{double} vector & \texttt{double} vector \\ \hline int32 & \texttt{integer} vector & \texttt{integer} vector \\ sint32 & \texttt{integer} vector & \texttt{integer} vector \\ sfixed32 & \texttt{integer} vector & \texttt{integer} vector \\ \hline int64 & \texttt{integer} or \texttt{character} vector \footnotemark & \texttt{integer} or \texttt{character} vector \\ uint64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ sint64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ fixed64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ sfixed64 & \texttt{integer} or \texttt{character} vector & \texttt{integer} or \texttt{character} vector \\ \hline bool & \texttt{logical} vector & \texttt{logical} vector \\ \hline string & \texttt{character} vector & \texttt{character} vector \\ bytes & \texttt{character} vector & \texttt{character} vector \\ \hline enum & \texttt{integer} vector & \texttt{integer} vector \\ \hline message & \texttt{S4} object of class \texttt{Message} & \texttt{list} of \texttt{S4} objects of class \texttt{Message} \\ \hline \end{tabular} \end{small} \caption{\label{table-get-types}Correspondance between field type and R type retrieved by the extractors. \footnotesize{1. R lacks native 64-bit integers, so the \texttt{RProtoBuf.int64AsString} option is available to return large integers as characters to avoid losing precision. This option is described in Section~\ref{sec:int64}}. R also lacks an unsigned integer type.} \end{table} \subsubsection{Modify fields} \label{Message-method-setfield} The \verb|$<-| and \verb|[[<-| operators are implemented for \texttt{Message} objects to set the value of a field. The R data is coerced to match the type of the message field. <<>>= message <- new( tutorial.Person, name = "foo", id = 2 ) message$email <- "foo@bar.com" message[[ "id" ]] <- 2 message[[ 1 ]] <- "foobar" writeLines( message$as.character() ) @ Table~\ref{table-message-field-setters} describes the R types that are allowed in the right hand side depending on the target type of the field. \begin{table}[h] \centering \begin{small} \begin{tabular}{|p{5cm}|p{7cm}|} \hline internal type & allowed R types \\ \hline \hline \texttt{double}, \texttt{float} & \texttt{integer}, \texttt{raw}, \texttt{double}, \texttt{logical} \\ \hline \texttt{int32}, \texttt{int64}, \texttt{uint32}, \texttt{uint64}, \texttt{sint32}, \texttt{sint64}, \texttt{fixed32}, \texttt{fixed64}, \texttt{sfixed32}, \texttt{sfixed64} & \texttt{integer}, \texttt{raw}, \texttt{double}, \texttt{logical}, \texttt{character} \\ \hline \texttt{bool} & \texttt{integer}, \texttt{raw}, \texttt{double}, \texttt{logical} \\ \hline \texttt{bytes}, \texttt{string} & \texttt{character} \\ \hline \texttt{enum} & \texttt{integer}, \texttt{double}, \texttt{raw}, \texttt{character} \\ \hline \texttt{message}, \texttt{group} & \texttt{S4}, of class \texttt{Message} of the appropriate message type, or a \texttt{list} of \texttt{S4} objects of class \texttt{Message} of the appropriate message type.\\ \hline \end{tabular} \end{small} \caption{\label{table-message-field-setters}Allowed R types depending on internal field types. } \end{table} \subsubsection{Message\$has method} \label{Message-method-has} The \texttt{has} method indicates if a field of a message is set. For repeated fields, the field is considered set if there is at least on object in the array. For non-repeated fields, the field is considered set if it has been initialized. The \texttt{has} method is a thin wrapper around the \texttt{HasField} and \texttt{FieldSize} methods of the \texttt{google::protobuf::Reflection} C++ class. <<>>= message <- new( tutorial.Person, name = "foo" ) message$has( "name" ) message$has( "id" ) message$has( "phone" ) @ \subsubsection{Message\$clone method} \label{Message-method-clone} The \texttt{clone} function creates a new message that is a clone of the message. This function is a wrapper around the methods \texttt{New} and \texttt{CopyFrom} of the \texttt{google::protobuf::Message} C++ class. <<>>= m1 <- new( tutorial.Person, name = "foo" ) m2 <- m1$clone( ) m2$email <- "foo@bar.com" writeLines( as.character( m1 ) ) writeLines( as.character( m2 ) ) @ \subsubsection{Message\$isInitialized method} \label{Message-method-isInitialized} The \texttt{isInitialized} method quickly checks if all required fields have values set. This is a thin wrapper around the \texttt{IsInitialized} method of the \texttt{google::protobuf::Message} C++ class. <<>>= message <- new( tutorial.Person, name = "foo" ) message$isInitialized() message$id <- 2 message$isInitialized() @ \subsubsection{Message\$serialize method} \label{Message-method-serialize} The \texttt{serialize} method can be used to serialize the message as a sequence of bytes into a file or a binary connection. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) tf1 <- tempfile( ) tf1 message$serialize( tf1 ) tf2 <- tempfile( ) tf2 con <- file( tf2, open = "wb" ) message$serialize( con ) close( con ) @ The files \Sexpr{basename(tf1)} and \Sexpr{basename(tf2)} both contain the message payload as a sequence of bytes. The \texttt{readBin} function can be used to read the files as a raw vector in R: <<>>= readBin( tf1, raw(0), 500 ) readBin( tf2, raw(0), 500 ) @ The \texttt{serialize} method can also be used to directly retrieve the payload of the message as a raw vector: <<>>= message$serialize(NULL) @ \subsubsection{Message\$clear method} \label{Message-method-clear} The \texttt{clear} method can be used to clear all fields of a message when used with no argument, or a given field. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( as.character( message ) ) message$clear() writeLines( as.character( message ) ) message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$clear( "id" ) writeLines( as.character( message ) ) @ The \texttt{clear} method is a thin wrapper around the \texttt{Clear} method of the \texttt{google::protobuf::Message} C++ class. \subsubsection{Message\$size method} \label{Message-method-size} The \texttt{size} method is used to query the number of objects in a repeated field of a message : <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$size( "phone" ) size( message, "phone" ) @ The \texttt{size} method is a thin wrapper around the \texttt{FieldSize} method of the \texttt{google::protobuf::Reflection} C++ class. \subsubsection{Message\$bytesize method} \label{Message-method-bytesize} The \texttt{bytesize} method retrieves the number of bytes the message would take once serialized. This is a thin wrapper around the \texttt{ByteSize} method of the \texttt{google::protobuf::Message} C++ class. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$bytesize() bytesize( message ) length( message$serialize( NULL ) ) @ \subsubsection{Message\$swap method} \label{Message-method-swap} The \texttt{swap} method can be used to swap elements of a repeated field. <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$swap( "phone", 1, 2 ) writeLines( as.character( message$phone[[1]] ) ) writeLines( as.character( message$phone[[2]] ) ) swap( message, "phone", 1, 2 ) writeLines( as.character( message$phone[[1]] ) ) writeLines( as.character( message$phone[[2]] ) ) @ \subsubsection{Message\$set method} \label{Message-method-set} The \texttt{set} method can be used to set values of a repeated field. <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) number <- new( tutorial.Person.PhoneNumber, number = "+33(0)---", type = "WORK" ) message$set( "phone", 1, number ) writeLines( as.character( message ) ) @ \subsubsection{Message\$fetch method} \label{Message-method-fetch} The \texttt{fetch} method can be used to get values of a repeated field. <>= message <- new( tutorial.Person, name = "foo", phone = list( new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ), new( tutorial.Person.PhoneNumber, number = "+33(0)###", type = "MOBILE" ) ) ) message$fetch( "phone", 1 ) @ \subsubsection{Message\$setExtension method} \label{Message-method-setExtension} The \texttt{setExtension} method can be used to set an extension field of the Message. <>= if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } ## Test setting a singular extensions. test <- new(protobuf_unittest.TestAllExtensions) test$setExtension(protobuf_unittest.optional_int32_extension, as.integer(1)) @ \subsubsection{Message\$getExtension method} \label{Message-method-getExtension} The \texttt{getExtension} method can be used to get values of an extension. <>= test$getExtension(protobuf_unittest.optional_int32_extension) @ \subsubsection{Message\$add method} \label{Message-method-add} The \texttt{add} method can be used to add values to a repeated field. <>= message <- new( tutorial.Person, name = "foo") phone <- new( tutorial.Person.PhoneNumber, number = "+33(0)...", type = "HOME" ) message$add( "phone", phone ) writeLines( message$toString() ) @ \subsubsection{Message\$str method} \label{Message-method-str} The \texttt{str} method gives the R structure of the message. This is rarely useful. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) message$str() str( message ) @ \subsubsection{Message\$as.character method} \label{Message-method-ascharacter} The \texttt{as.character} method gives the debug string of the message. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( message$as.character() ) writeLines( as.character( message ) ) @ \subsubsection{Message\$toString method} \label{Message-method-toString} \texttt{toString} currently is an alias to the \texttt{as.character} function. <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) writeLines( message$toString() ) writeLines( toString( message ) ) @ \subsubsection{Message\$as.list method} \label{Message-method-aslist} The \texttt{as.list} method converts the message to an named R list <<>>= message <- new( tutorial.Person, name = "foo", email = "foo@bar.com", id = 2 ) as.list( message ) @ The names of the list are the names of the declared fields of the message type, and the content is the same as can be extracted with the \verb|$| operator described in section~\ref{Message-method-getfield}. \subsubsection{Message\$update method} \label{Message-method-update} The \texttt{update} method can be used to update several fields of a message at once. <>= message <- new( tutorial.Person ) update( message, name = "foo", id = 2, email = "foo@bar.com" ) writeLines( message$as.character() ) @ \subsubsection{Message\$descriptor method} \label{Message-method-descriptor} The \texttt{descriptor} method retrieves the descriptor of a message. See section~\ref{subsec-descriptor} for more information about message type descriptors. <<>>= message <- new( tutorial.Person ) message$descriptor() descriptor( message ) @ \subsubsection{Message\$fileDescriptor method} \label{Message-method-fileDescriptor} The \texttt{fileDescriptor} method retrieves the file descriptor of the descriptor associated with a message. See section~\ref{subsec-fileDescriptor} for more information about file descriptors. <<>>= message <- new( tutorial.Person ) message$fileDescriptor() fileDescriptor( message ) @ \subsection{message descriptors} \label{subsec-descriptor} Message descriptors are represented in R with the \emph{Descriptor} S4 class. The class contains the slots \texttt{pointer} and \texttt{type} : \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & external pointer to the \texttt{Descriptor} object of the C++ proto library. Documentation for the \texttt{Descriptor} class is available from the protocol buffer project page: \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.descriptor.html#Descriptor} \\ \hline \texttt{type} & fully qualified path of the message type. \\ \hline \end{tabular} \caption{\label{Descriptor-class-table}Description of slots for the \texttt{Descriptor} S4 class} \end{table} Similarly to messages, the \verb|$| operator can be used to extract information from the descriptor, or invoke pseudo-methods. Table~\ref{Descriptor-methods-table} describes the methods defined for the \texttt{Descriptor} class : \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{Method} & \textbf{Section} & \textbf{Description} \\ \hline \hline \texttt{new} & \ref{Descriptor-method-new} & Creates a prototype of a message described by this descriptor.\\ \texttt{read} & \ref{Descriptor-method-read} & Reads a message from a file or binary connection.\\ \texttt{readASCII} & \ref{Descriptor-method-readASCII} & Read a message in ASCII format from a file or text connection.\\ \hline \texttt{name} & \ref{Descriptor-method-name} & Retrieve the name of the message type associated with this descriptor.\\ \texttt{as.character} & \ref{Descriptor-method-ascharacter} & character representation of a descriptor\\ \texttt{toString} & \ref{Descriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}) \\ \texttt{as.list} & \ref{Descriptor-method-aslist} & return a named list of the field, enum, and nested descriptors included in this descriptor.\\ \texttt{asMessage} & \ref{Descriptor-method-asmessage} & return DescriptorProto message. \\ \hline \texttt{fileDescriptor} & \ref{Descriptor-method-filedescriptor} & Retrieve the file descriptor of this descriptor.\\ \texttt{containing\_type} & \ref{Descriptor-method-containingtype} & Retrieve the descriptor describing the message type containing this descriptor.\\ \texttt{field\_count} & \ref{Descriptor-method-fieldcount} & Return the number of fields in this descriptor.\\ \texttt{field} & \ref{Descriptor-method-field} & Return the descriptor for the specified field in this descriptor.\\ \texttt{nested\_type\_count} & \ref{Descriptor-method-nestedtypecount} & The number of nested types in this descriptor.\\ \texttt{nested\_type} & \ref{Descriptor-method-nestedtype} & Return the descriptor for the specified nested type in this descriptor.\\ \texttt{enum\_type\_count} & \ref{Descriptor-method-enumtypecount} & The number of enum types in this descriptor.\\ \texttt{enum\_type} & \ref{Descriptor-method-enumtype} & Return the descriptor for the specified enum type in this descriptor.\\ \hline \end{tabular} \end{small} \caption{\label{Descriptor-methods-table}Description of methods for the \texttt{Descriptor} S4 class} \end{table} \subsubsection{Extracting descriptors} The \verb|$| operator, when used on a descriptor object retrieves descriptors that are contained in the descriptor. This can be a field descriptor (see section~\ref{subsec-field-descriptor} ), an enum descriptor (see section~\ref{subsec-enum-descriptor}) or a descriptor for a nested type <<>>= # field descriptor tutorial.Person$email # enum descriptor tutorial.Person$PhoneType # nested type descriptor tutorial.Person$PhoneNumber # same as tutorial.Person.PhoneNumber @ \subsubsection{The new method} \label{Descriptor-method-new} The \texttt{new} method creates a prototype of a message described by the descriptor. <<>>= tutorial.Person$new( ) new( tutorial.Person ) @ Passing additional arguments to the method allows to directlt set the fields of the message at construction time. <<>>= tutorial.Person$new( email = "foo@bar.com" ) # same as update( tutorial.Person$new( ), email = "foo@bar.com" ) @ \subsubsection{The read method} \label{Descriptor-method-read} The \texttt{read} method is used to read a message from a file or a binary connection. <<>>= # start by serializing a message message <- new( tutorial.Person.PhoneNumber, type = "HOME", number = "+33(0)...." ) tf <- tempfile() serialize( message, tf ) # now read back the message m <- tutorial.Person.PhoneNumber$read( tf ) writeLines( as.character( m ) ) m <- read( tutorial.Person.PhoneNumber, tf ) writeLines( as.character( m ) ) @ \subsubsection{The readASCII method} \label{Descriptor-method-readASCII} The \texttt{readASCII} method is used to read a message from a text file or a character vector. <<>>= # start by generating the ASCII representation of a message text <- as.character(new(tutorial.Person, id=1, name="Murray")) text # Then read the ascii representation in as a new message object. msg <- tutorial.Person$readASCII(text) @ \subsubsection{The toString method} \label{Descriptor-method-tostring} \texttt{toString} currently is an alias to the \texttt{as.character} function. \subsubsection{The as.character method} \label{Descriptor-method-ascharacter} \texttt{as.character} prints the text representation of the descriptor as it would be specified in the \texttt{.proto} file. <<>>= desc <- tutorial.Person writeLines( desc$toString() ) writeLines( toString( desc ) ) writeLines( as.character(tutorial.Person) ) @ \subsubsection{as.list} \label{Descriptor-method-aslist} The \texttt{as.list} method returns a named list of the field, enum, and nested descriptors included in this descriptor. <<>>= tutorial.Person$as.list() @ \subsubsection{asMessage} \label{Descriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.DescriptorProto} of the Descriptor. <<>>= tutorial.Person$asMessage() @ \subsubsection{The fileDescriptor method} \label{Descriptor-method-filedescriptor} The \texttt{fileDescriptor} method retrieves the file descriptor of the descriptor. See section~\ref{subsec-fileDescriptor} for more information about file descriptors. <<>>= desc <- tutorial.Person desc$fileDescriptor() fileDescriptor( desc ) @ \subsubsection{The name method} \label{Descriptor-method-name} The \texttt{name} method can be used to retrieve the name of the message type associated with the descriptor. <<>>= # simple name tutorial.Person$name() # name including scope tutorial.Person$name(full = TRUE) @ \subsubsection{The containing\_type method} \label{Descriptor-method-containingtype} The \texttt{containing\_type} method retrieves the descriptor describing the message type containing this descriptor. <<>>= tutorial.Person$containing_type() tutorial.Person$PhoneNumber$containing_type() @ \subsubsection{The field\_count method} \label{Descriptor-method-fieldcount} Tme \texttt{field\_count} method retrieves the number of fields in this descriptor. <<>>= tutorial.Person$field_count() @ \subsubsection{The field method} \label{Descriptor-method-field} The \texttt{field} method returns the descriptor for the specified field in this descriptor. <<>>= tutorial.Person$field(1) @ \subsubsection{The nested\_type\_count method} \label{Descriptor-method-nestedtypecount} The \texttt{nested\_type\_count} method returns the number of nested types in this descriptor. <<>>= tutorial.Person$nested_type_count() @ \subsubsection{The nested\_type method} \label{Descriptor-method-nestedtype} The \texttt{nested\_type} method return the descriptor for the specified nested type in this descriptor. <<>>= tutorial.Person$nested_type(1) @ \subsubsection{The enum\_type\_count method} \label{Descriptor-method-enumtypecount} The \texttt{enum\_type\_count} method returns the number of enum types in this descriptor. <<>>= tutorial.Person$enum_type_count() @ \subsubsection{The enum\_type method} \label{Descriptor-method-enumtype} The \texttt{enum\_type} method returns the descriptor for the specified enum type in this descriptor. <<>>= tutorial.Person$enum_type(1) @ \subsection{field descriptors} \label{subsec-field-descriptor} The class \emph{FieldDescriptor} represents field descriptor in R. This is a wrapper S4 class around the \texttt{google::protobuf::FieldDescriptor} C++ class. Table~\ref{fielddescriptor-methods-table} describes the methods defined for the \texttt{FieldDescriptor} class. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & External pointer to the \texttt{FieldDescriptor} C++ variable \\ \hline \texttt{name} & simple name of the field \\ \hline \texttt{full\_name} & fully qualified name of the field \\ \hline \texttt{type} & name of the message type where the field is declared \\ \hline \end{tabular} \caption{\label{FieldDescriptor-class-table}Description of slots for the \texttt{FieldDescriptor} S4 class} \end{table} \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{as.character} & \ref{fielddescriptor-method-ascharacter} & character representation of a descriptor\\ \texttt{toString} & \ref{fielddescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}) \\ \texttt{asMessage} & \ref{fielddescriptor-method-asmessage} & return FieldDescriptorProto message. \\ \texttt{name} & \ref{fielddescriptor-method-name} & Return the name of the field descriptor.\\ \texttt{fileDescriptor} & \ref{fielddescriptor-method-filedescriptor} & Return the fileDescriptor where this field is defined.\\ \texttt{containing\_type} & \ref{fielddescriptor-method-containingtype} & Return the containing descriptor of this field.\\ \texttt{is\_extension} & \ref{fielddescriptor-method-isextension} & Return TRUE if this field is an extension.\\ \texttt{number} & \ref{fielddescriptor-method-number} & Gets the declared tag number of the field.\\ \texttt{type} & \ref{fielddescriptor-method-type} & Gets the type of the field.\\ \texttt{cpp\_type} & \ref{fielddescriptor-method-cpptype} & Gets the C++ type of the field.\\ \texttt{label} & \ref{fielddescriptor-method-label} & Gets the label of a field (optional, required, or repeated).\\ \texttt{is\_repeated} & \ref{fielddescriptor-method-isrepeated} & Return TRUE if this field is repeated.\\ \texttt{is\_required} & \ref{fielddescriptor-method-isrequired} & Return TRUE if this field is required.\\ \texttt{is\_optional} & \ref{fielddescriptor-method-isoptional} & Return TRUE if this field is optional.\\ \texttt{has\_default\_value} & \ref{fielddescriptor-method-hasdefaultvalue} & Return TRUE if this field has a default value.\\ \texttt{default\_value} & \ref{fielddescriptor-method-defaultvalue} & Return the default value.\\ \texttt{message\_type} & \ref{fielddescriptor-method-messagetype} & Return the message type if this is a message type field.\\ \texttt{enum\_type} & \ref{fielddescriptor-method-enumtype} & Return the enum type if this is an enum type field.\\ \hline \end{tabular} \end{small} \caption{\label{fielddescriptor-methods-table}Description of methods for the \texttt{FieldDescriptor} S4 class} \end{table} \subsubsection{as.character} \label{fielddescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the field descriptor. <<>>= writeLines( as.character( tutorial.Person$PhoneNumber ) ) @ \subsubsection{toString} \label{fielddescriptor-method-tostring} \texttt{toString} is an alias of \texttt{as.character}. <<>>= writeLines( tutorial.Person.PhoneNumber$toString() ) @ \subsubsection{asMessage} \label{fielddescriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.FieldDescriptorProto} of the FieldDescriptor. <<>>= tutorial.Person$id$asMessage() writeLines(as.character(tutorial.Person$id$asMessage())) @ \subsubsection{name} \label{fielddescriptor-method-name} The \texttt{name} method can be used to retrieve the name of the field descriptor. <<>>= # simple name. name( tutorial.Person$id ) # name including scope. name( tutorial.Person$id, full=TRUE ) @ \subsubsection{fileDescriptor} \label{fielddescriptor-method-filedescriptor} The \texttt{fileDescriptor} method can be used to retrieve the file descriptor of the field descriptor. <<>>= fileDescriptor(tutorial.Person$id) tutorial.Person$id$fileDescriptor() @ \subsubsection{containing\_type} \label{fielddescriptor-method-containingtype} The \texttt{containing\_type} method can be used to retrieve the descriptor for the message type that contains this descriptor. <<>>= containing_type(tutorial.Person$id) tutorial.Person$id$containing_type() @ \subsubsection{is\_extension} \label{fielddescriptor-method-isextension} The \texttt{is\_extension} method returns TRUE if this field is an extension. % TODO(ms): cross reference to a to be written section on extensions. <<>>= is_extension( tutorial.Person$id ) tutorial.Person$id$is_extension() @ \subsubsection{number} \label{fielddescriptor-method-number} The \texttt{number} method returns the declared tag number of this field. <<>>= number( tutorial.Person$id ) tutorial.Person$id$number() @ \subsubsection{type} \label{fielddescriptor-method-type} The \texttt{type} method can be used to retrieve the type of the field descriptor. <<>>= type( tutorial.Person$id ) tutorial.Person$id$type() @ \subsubsection{cpp\_type} \label{fielddescriptor-method-cpptype} The \texttt{cpp\_type} method can be used to retrieve the C++ type of the field descriptor. <<>>= cpp_type( tutorial.Person$id ) tutorial.Person$id$cpp_type() @ \subsubsection{label} \label{fielddescriptor-method-label} Gets the label of a field (optional, required, or repeated). The \texttt{label} method returns the label of a field (optional, required, or repeated). By defualt it returns a number value, but the optional \texttt{as.string} argument can be provided to return a human readable string representation. <<>>= label( tutorial.Person$id ) label( tutorial.Person$id , TRUE) tutorial.Person$id$label(TRUE) @ \subsubsection{is\_repeated} \label{fielddescriptor-method-isrepeated} The \texttt{is\_repeated} method returns TRUE if this field is repeated. <<>>= is_repeated( tutorial.Person$id ) tutorial.Person$id$is_repeated() @ \subsubsection{is\_required} \label{fielddescriptor-method-isrequired} The \texttt{is\_required} method returns TRUE if this field is required. <<>>= is_required( tutorial.Person$id ) tutorial.Person$id$is_required() @ \subsubsection{is\_optional} \label{fielddescriptor-method-isoptional} The \texttt{is\_optional} method returns TRUE if this field is optional. <<>>= is_optional( tutorial.Person$id ) tutorial.Person$id$is_optional() @ \subsubsection{has\_default\_value} \label{fielddescriptor-method-hasdefaultvalue} The \texttt{has\_default\_value} method returns TRUE if this field has a default value. <<>>= has_default_value(tutorial.Person$PhoneNumber$type) has_default_value(tutorial.Person$PhoneNumber$number) @ \subsubsection{default\_value} \label{fielddescriptor-method-defaultvalue} The \texttt{default\_value} method returns the default value of a field. <<>>= default_value( tutorial.Person$PhoneNumber$type ) default_value( tutorial.Person$PhoneNumber$number ) @ \subsubsection{message\_type} \label{fielddescriptor-method-messagetype} The \texttt{message\_type} method returns the message type if this is a message type field. <<>>= message_type(tutorial.Person$phone) tutorial.Person$phone$message_type() @ \subsubsection{enum\_type} \label{fielddescriptor-method-enumtype} The \texttt{enum\_type} method returns the enum type if this is an enum type field. <<>>= enum_type(tutorial.Person$PhoneNumber$type) @ \subsection{enum descriptors} \label{subsec-enum-descriptor} The class \emph{EnumDescriptor} is an R wrapper class around the C++ class \texttt{google::protobuf::EnumDescriptor}. Table~\ref{enumdescriptor-methods-table} describes the methods defined for the \texttt{EnumDescriptor} class. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & External pointer to the \texttt{EnumDescriptor} C++ variable \\ \hline \texttt{name} & simple name of the enum \\ \hline \texttt{full\_name} & fully qualified name of the enum \\ \hline \texttt{type} & name of the message type where the enum is declared \\ \hline \end{tabular} \caption{\label{EnumDescriptor-class-table}Description of slots for the \texttt{EnumDescriptor} S4 class} \end{table} \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{as.list} & \ref{enumdescriptor-method-aslist} & return a named integer vector with the values of the enum and their names.\\ \texttt{as.character} & \ref{enumdescriptor-method-ascharacter} & character representation of a descriptor\\ \texttt{toString} & \ref{enumdescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}) \\ \texttt{asMessage} & \ref{enumdescriptor-method-asmessage} & return EnumDescriptorProto message. \\ \texttt{name} & \ref{enumdescriptor-method-name} & Return the name of the enum descriptor.\\ \texttt{fileDescriptor} & \ref{enumdescriptor-method-filedescriptor} & Return the fileDescriptor where this field is defined.\\ \texttt{containing\_type} & \ref{enumdescriptor-method-containingtype} & Return the containing descriptor of this field.\\ \texttt{length} & \ref{enumdescriptor-method-length} & Return the number of constants in this enum.\\ \texttt{has} & \ref{enumdescriptor-method-has} & Return TRUE if this enum contains the specified named constant string.\\ \texttt{value\_count} & \ref{enumdescriptor-method-valuecount} & Return the number of constants in this enum (same as \texttt{length}).\\ \texttt{value} & \ref{enumdescriptor-method-value} & Return the EnumValueDescriptor of an enum value of specified index, name, or number.\\ \hline \end{tabular} \end{small} \caption{\label{enumdescriptor-methods-table}Description of methods for the \texttt{EnumDescriptor} S4 class} \end{table} \subsubsection{Extracting descriptors} The \verb|$| operator, when used on a EnumDescriptor object retrieves EnumValueDescriptors that are contained in the descriptor. <<>>= tutorial.Person$PhoneType$WORK name(tutorial.Person$PhoneType$value(number=2)) @ \subsubsection{as.list} \label{enumdescriptor-method-aslist} The \texttt{as.list} method creates a named R integer vector that captures the values of the enum and their names. <<>>= as.list( tutorial.Person$PhoneType ) @ \subsubsection{as.character} \label{enumdescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the enum type. <<>>= writeLines( as.character( tutorial.Person$PhoneType ) ) @ \subsubsection{toString} \label{enumdescriptor-method-tostring} The \texttt{toString} method brings the debug string of the enum type. <<>>= writeLines( toString( tutorial.Person$PhoneType ) ) @ \subsubsection{asMessage} \label{enumdescriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.EnumDescriptorProto} of the EnumDescriptor. <<>>= tutorial.Person$PhoneType$asMessage() writeLines(as.character(tutorial.Person$PhoneType$asMessage())) @ \subsubsection{name} \label{enumdescriptor-method-name} The \texttt{name} method can be used to retrieve the name of the enum descriptor. <<>>= # simple name. name( tutorial.Person$PhoneType ) # name including scope. name( tutorial.Person$PhoneType, full=TRUE ) @ \subsubsection{fileDescriptor} \label{enumdescriptor-method-filedescriptor} The \texttt{fileDescriptor} method can be used to retrieve the file descriptor of the enum descriptor. <<>>= fileDescriptor(tutorial.Person$PhoneType) tutorial.Person$PhoneType$fileDescriptor() @ \subsubsection{containing\_type} \label{enumdescriptor-method-containingtype} The \texttt{containing\_type} method can be used to retrieve the descriptor for the message type that contains this enum descriptor. <<>>= tutorial.Person$PhoneType$containing_type() @ \subsubsection{length} \label{enumdescriptor-method-length} The \texttt{length} method returns the number of constants in this enum. <<>>= length(tutorial.Person$PhoneType) tutorial.Person$PhoneType$length() @ \subsubsection{has} \label{enumdescriptor-method-has} The \texttt{has} method returns TRUE if this enum contains the specified named constant string. <<>>= tutorial.Person$PhoneType$has("WORK") tutorial.Person$PhoneType$has("nonexistant") @ \subsubsection{value\_count} \label{enumdescriptor-method-valuecount} The \texttt{value\_count} method returnst he number of constants in this enum. %TODO(ms): Duplicate of length, just like tostring/as.character. <<>>= value_count(tutorial.Person$PhoneType) tutorial.Person$PhoneType$value_count() @ \subsubsection{value} \label{enumdescriptor-method-value} The \texttt{value} method extracts an EnumValueDescriptor. Exactly one argument of 'index', 'number', or 'name' must be specified to identify which constant is desired. <<>>= tutorial.Person$PhoneType$value(1) tutorial.Person$PhoneType$value(name="HOME") tutorial.Person$PhoneType$value(number=1) @ \subsection{enum value descriptors} \label{subsec-EnumValueDescriptor} The class \emph{EnumValueDescriptor} is an R wrapper class around the C++ class \texttt{google::protobuf::EnumValueDescriptor}. Table~\ref{enumvaluedescriptor-methods-table} describes the methods defined for the \texttt{EnumValueDescriptor} class. \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & External pointer to the \texttt{EnumValueDescriptor} C++ variable \\ \hline \texttt{name} & simple name of the enum value \\ \hline \texttt{full\_name} & fully qualified name of the enum value \\ \hline \end{tabular} \caption{\label{EnumValueDescriptor-class-table}Description of slots for the \texttt{EnumValueDescriptor} S4 class} \end{table} \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{number} & \ref{enumvaluedescriptor-method-number} & return the number of this EnumValueDescriptor. \\ \texttt{name} & \ref{enumvaluedescriptor-method-name} & Return the name of the enum value descriptor.\\ \texttt{enum\_type} & \ref{enumvaluedescriptor-method-enumtype} & return the EnumDescriptor type of this EnumValueDescriptor. \\ \texttt{as.character} & \ref{enumvaluedescriptor-method-ascharacter} & character representation of a descriptor. \\ \texttt{toString} & \ref{enumvaluedescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}). \\ \texttt{asMessage} & \ref{enumvaluedescriptor-method-asmessage} & return EnumValueDescriptorProto message. \\ \hline \end{tabular} \end{small} \caption{\label{enumvaluedescriptor-methods-table}Description of methods for the \texttt{EnumValueDescriptor} S4 class} \end{table} \subsubsection{number} \label{enumvaluedescriptor-method-number} The \texttt{number} method can be used to retrieve the number of the enum value descriptor. <<>>= number( tutorial.Person$PhoneType$value(number=2) ) @ \subsubsection{name} \label{enumvaluedescriptor-method-name} The \texttt{name} method can be used to retrieve the name of the enum value descriptor. <<>>= # simple name. name( tutorial.Person$PhoneType$value(number=2) ) # name including scope. name( tutorial.Person$PhoneType$value(number=2), full=TRUE ) @ \subsubsection{enum\_type} \label{enumvaluedescriptor-method-enumtype} The \texttt{enum\_type} method can be used to retrieve the EnumDescriptor of the enum value descriptor. <<>>= enum_type( tutorial.Person$PhoneType$value(number=2) ) @ \subsubsection{as.character} \label{enumvaluedescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the enum value type. <<>>= writeLines( as.character( tutorial.Person$PhoneType$value(number=2) ) ) @ \subsubsection{toString} \label{enumvaluedescriptor-method-tostring} The \texttt{toString} method brings the debug string of the enum value type. <<>>= writeLines( toString( tutorial.Person$PhoneType$value(number=2) ) ) @ \subsubsection{asMessage} \label{enumvaluedescriptor-method-asmessage} The \texttt{asMessage} method returns a message of type \texttt{google.protobuf.EnumValueDescriptorProto} of the EnumValueDescriptor. <<>>= tutorial.Person$PhoneType$value(number=2)$asMessage() writeLines(as.character(tutorial.Person$PhoneType$value(number=2)$asMessage())) @ \subsection{file descriptors} \label{subsec-fileDescriptor} File descriptors describe a whole \texttt{.proto} file and are represented in R with the \emph{FileDescriptor} S4 class. The class contains the slots \texttt{pointer}, \texttt{filename}, and \texttt{package} : \begin{table}[h] \centering \begin{tabular}{|cp{10cm}|} \hline \textbf{slot} & \textbf{description} \\ \hline \texttt{pointer} & external pointer to the \texttt{FileDescriptor} object of the C++ proto library. Documentation for the \texttt{FileDescriptor} class is available from the protocol buffer project page: \url{http://developers.google.com/protocol-buffers/docs/reference/cpp/google.protobuf.descriptor.html#FileDescriptor} \\ \hline \texttt{filename} & fully qualified pathname of the \texttt{.proto} file.\\ \hline \texttt{package} & package name defined in this \texttt{.proto} file.\\ \hline \end{tabular} \caption{\label{FileDescriptor-class-table}Description of slots for the \texttt{FileDescriptor} S4 class} \end{table} Similarly to messages, the \verb|$| operator can be used to extract fields from the file descriptor (in this case, types defined in the file), or invoke pseuso-methods. Table~\ref{filedescriptor-methods-table} describes the methods defined for the \texttt{FileDescriptor} class. <<>>= f <- tutorial.Person$fileDescriptor() f f$Person @ \begin{table}[h] \centering \begin{small} \begin{tabular}{|ccp{8cm}|} \hline \textbf{method} & \textbf{section} & \textbf{description} \\ \hline \hline \texttt{name} & \ref{filedescriptor-method-name} & Return the filename for this FileDescriptorProto.\\ \texttt{package} & \ref{filedescriptor-method-package} & Return the file-level package name specified in this FileDescriptorProto.\\ \texttt{as.character} & \ref{filedescriptor-method-ascharacter} & character representation of a descriptor. \\ \texttt{toString} & \ref{filedescriptor-method-tostring} & character representation of a descriptor (same as \texttt{as.character}). \\ \texttt{asMessage} & \ref{filedescriptor-method-asmessage} & return FileDescriptorProto message. \\ \texttt{as.list} & \ref{filedescriptor-method-aslist} & return named list of descriptors defined in this file descriptor.\\ \hline \end{tabular} \end{small} \caption{\label{filedescriptor-methods-table}Description of methods for the \texttt{FileDescriptor} S4 class} \end{table} \subsubsection{as.character} \label{filedescriptor-method-ascharacter} The \texttt{as.character} method brings the debug string of the file descriptor. <<>>= writeLines( as.character(fileDescriptor(tutorial.Person)) ) @ \subsubsection{toString} \label{filedescriptor-method-tostring} \texttt{toString} is an alias of \texttt{as.character}. <<>>= writeLines( fileDescriptor(tutorial.Person)$toString() ) @ \subsubsection{asMessage} \label{filedescriptor-method-asmessage} The \texttt{asMessage} method returns a protocol buffer message representation of the file descriptor. <<>>= asMessage(tutorial.Person$fileDescriptor()) writeLines( as.character(asMessage(tutorial.Person$fileDescriptor())) ) @ \subsubsection{as.list} \label{filedescriptor-method-aslist} The \texttt{as.list} method creates a named R list that contains the descriptors defined in this file descriptor. <<>>= as.list( tutorial.Person$fileDescriptor() ) @ \subsubsection{name} \label{filedescriptor-method-name} The \texttt{name} method can be used to retrieve the file name associated with the file descriptor. The optional boolean argument can be specified if full pathnames are desired. <<>>= name( tutorial.Person$fileDescriptor() ) tutorial.Person$fileDescriptor()$name(TRUE) @ \subsubsection{package} \label{filedescriptor-method-package} The \texttt{package} method can be used to retrieve the package scope associated with this file descriptor. <<>>= tutorial.Person$fileDescriptor()$package() @ \subsection{service descriptors} \label{subsec-ServiceDescriptor} Not fully implemented. Needs to be connected to a concrete RPC implementation. The Google Protocol Buffers C++ open-source library does not include an RPC implementation, but this can be connected easily to others. \subsection{method descriptors} \label{subsec-MethodDescriptor} Not fully implemented. Needs to be connected to a concrete RPC implementation. The Google Protocol Buffers C++ open-source library does not include an RPC implementation, but this can be connected easily to others. \section{Utilities} \subsection{coercing objects to messages} The \texttt{asMessage} function uses the standard coercion mechanism of the \texttt{as} method, and so can be used as a shorthand : <<>>= # coerce a message type descriptor to a message # asMessage( tutorial.Person ) # coerce a enum descriptor asMessage( tutorial.Person.PhoneType ) # coerce a field descriptor asMessage( tutorial.Person$email ) # coerce a file descriptor asMessage( fileDescriptor( tutorial.Person ) ) @ \subsection{completion} The \texttt{RProtoBuf} package implements the \texttt{.DollarNames} S3 generic function (defined in the \texttt{utils} package) for all classes. Completion possibilities include pseudo method names for all classes, plus : \begin{itemize} \item field names for messages \item field names, enum types, nested types for message type descriptors \item names for enum descriptors \item names for top-level extensions \item message names for file descriptors \end{itemize} In the unlikely event that there is a user-defined field of exactly the same name as one of the pseudo methods, the user-defined field shall take precedence for completion purposes by design, since the method name can always be invoked directly. \subsection{with and within} The S3 generic \texttt{with} function is implemented for class \texttt{Message}, allowing to evaluate an R expression in an environment that allows to retrieve and set fields of a message simply using their names. <<>>= message <- new( tutorial.Person, email = "foo@bar.com" ) with( message, { # set the id field id <- 2 # set the name field from the email field name <- gsub( "[@]", " ", email ) sprintf( "%d [%s] : %s", id, email, name ) } ) @ The difference between \texttt{with} and \texttt{within} is the value that is returned. For \texttt{with} returns the result of the R expression, for \texttt{within} the message is returned. In both cases, the message is modified because \texttt{RProtoBuf} works by reference. \subsection{identical} The \texttt{identical} method is implemented to compare two messages. <<>>= m1 <- new( tutorial.Person, email = "foo@bar.com", id = 2 ) m2 <- update( new( tutorial.Person) , email = "foo@bar.com", id = 2 ) identical( m1, m2 ) @ The \verb|==| operator can be used as an alias to \texttt{identical}. <<>>= m1 == m2 m1 != m2 @ Alternatively, the \texttt{all.equal} function can be used, allowing a tolerance when comparing \texttt{float} or \texttt{double} values. \subsection{merge} \texttt{merge} can be used to merge two messages of the same type. <<>>= m1 <- new( tutorial.Person, name = "foobar" ) m2 <- new( tutorial.Person, email = "foo@bar.com" ) m3 <- merge( m1, m2 ) writeLines( as.character( m3 ) ) @ \subsection{P} The \texttt{P} function is an alternative way to retrieve a message descriptor using its type name. It is not often used because of the lookup mechanism described in section~\ref{sec-lookup}. <<>>= P("tutorial.Person") new( P("tutorial.Person") ) # but we can do this instead tutorial.Person new( tutorial.Person ) @ \section{Advanced Features} \subsection{Extensions} \label{sec-extensions} Extensions allow you to declare a range of field numbers in a message that are available for extension types. This allows others to declare new fields for a given message type possibly in their own \texttt{.proto} files without having to edit the original file. See \url{https://developers.google.com/protocol-buffers/docs/proto#extensions}. Notice that the last line of the \texttt{Person} message schema in \texttt{addressbook.proto} is the following line : \begin{verbatim} extensions 100 to 199; \end{verbatim} This specifies that other users in other .proto files can use tag numbers between 100 and 199 for extention types of this message. For example, the following file \texttt{extend.proto}: <>= extend.proto <- tempfile() writeLines(c( paste0('import "', name(tutorial.Person$fileDescriptor(), TRUE), '";'), "package tutorial;", paste0("extend Person {\n optional string nationality = 100;\n}")), extend.proto) @ <>= writeLines(readLines(extend.proto)) @ After importing this new \texttt{.proto} file with an extension defined, we can get or set the value of this extension in Messages of type \texttt{Person}. <<>>= library(RProtoBuf) readProtoFiles(extend.proto) person <- new(tutorial.Person, id=1, name="Murray") person person$setExtension(P("tutorial.nationality"), "USA") cat(as.character(person)) person$getExtension(P("tutorial.nationality")) @ The character output of this message places the extension type in brackets to differentiate it from other fields in the message, and so we know we need to use the \texttt{getExtension} method rather than a '\$' field extractor to get the value. \subsection{Descriptor lookup} \label{sec-lookup} The \texttt{RProtoBuf} package uses the user defined tables framework that is defined as part of the \texttt{RObjectTables} package available from the OmegaHat project. The feature allows \texttt{RProtoBuf} to install the special environment \emph{RProtoBuf:DescriptorPool} in the R search path. The environment is special in that, instead of being associated with a static hash table, it is dynamically queried by R as part of R's usual variable lookup. In other words, it means that when the R interpreter looks for a binding to a symbol (foo) in its search path, it asks to our package if it knows the binding "foo", this is then implemented by the \texttt{RProtoBuf} package by calling an internal method of the \texttt{protobuf} C++ library. \subsection{64-bit integer issues} \label{sec:int64} R does not have native 64-bit integer support. Instead, R treats large integers as doubles which have limited precision. For example, it loses the ability to distinguish some distinct integers: <<>>= 2^53 == (2^53 + 1) @ Protocol Buffers are frequently used to pass data between different systems, however, and most other systems these days have support for 64-bit integers. To work around this, RProtoBuf allows users to get and set 64-bit integer types by treating them as characters when running on a platform with a 64-bit long long type available. <>= if (!exists("protobuf_unittest.TestAllTypes", "RProtoBuf:DescriptorPool")) { unittest.proto.file <- system.file("unitTests", "data", "unittest.proto", package="RProtoBuf") readProtoFiles(file=unittest.proto.file) } @ If we try to set an int64 field in R to double values, we lose precision: % We comment out the raw Sweave here because it doesn't work on 32-bit % platforms but it is important to illustrate what the user is missing % out on so we hard code the output from a platform with 64-bit long % long type. % % <<>>= % test <- new(protobuf_unittest.TestAllTypes) % test$repeated_int64 <- c(2^53, 2^53+1) % length(unique(test$repeated_int64)) % @ \begin{Schunk} \begin{Sinput} > test <- new(protobuf_unittest.TestAllTypes) > test$repeated_int64 <- c(2^53, 2^53+1) > length(unique(test$repeated_int64)) \end{Sinput} \begin{Soutput} [1] 1 \end{Soutput} \end{Schunk} However, we can specify the values as character strings so that the C++ library on which RProtoBuf is based can store a true 64-bit integer representation of the data. % <<>>= % test$repeated_int64 <- c("9007199254740992", "9007199254740993") % @ \begin{Schunk} \begin{Sinput} > test$repeated_int64 <- c("9007199254740992", "9007199254740993") \end{Sinput} \end{Schunk} When reading the value back into R, numeric types are returned by default, but when the full precision is required a character value will be returned if the \texttt{RProtoBuf.int64AsString} option is set to \texttt{TRUE}. % TODO: the if statement prevents us from seeing line by line % output inside the block (E.g. the output of test$repeated_int64). % This reduces the usefulness of this example when we are on a 64-bit % platform. E.g. only the final ``2'' is returned. % <>= % options("RProtoBuf.int64AsString" = FALSE) % test$repeated_int64 % length(unique(test$repeated_int64)) % options("RProtoBuf.int64AsString" = TRUE) % test$repeated_int64 % length(unique(test$repeated_int64)) %@ \begin{Schunk} \begin{Sinput} > options("RProtoBuf.int64AsString" = FALSE) \end{Sinput} \begin{Soutput} $RProtoBuf.int64AsString [1] FALSE \end{Soutput} \begin{Sinput} > test$repeated_int64 \end{Sinput} \begin{Soutput} [1] 9.007199e+15 9.007199e+15 \end{Soutput} \begin{Sinput} > length(unique(test$repeated_int64)) \end{Sinput} \begin{Soutput} [1] 1 \end{Soutput} \begin{Sinput} > options("RProtoBuf.int64AsString" = TRUE) \end{Sinput} \begin{Soutput} $RProtoBuf.int64AsString [1] FALSE \end{Soutput} \begin{Sinput} > test$repeated_int64 \end{Sinput} \begin{Soutput} [1] "9007199254740992" "9007199254740993" \end{Soutput} \begin{Sinput} > length(unique(test$repeated_int64)) \end{Sinput} \begin{Soutput} [1] 2 \end{Soutput} \end{Schunk} <>= options("RProtoBuf.int64AsString" = FALSE) @ \subsection{Deprecated Feature: Protocol Buffer Groups} \label{sec:groups} Groups are a deprecated feature that offered another way to nest information in message definitions. For example, the \texttt{TestAllTypes} message type in \texttt{unittest.proto} includes an OptionalGroup type: \begin{verbatim} optional group OptionalGroup = 16 { optional int32 a = 17; } \end{verbatim} And although the feature is deprecated, it can be used with RProtoBuf: <>= test <- new(protobuf_unittest.TestAllTypes) test$optionalgroup$a <- 3 test$optionalgroup$a cat(as.character(test)) @ Note that groups simply combine a nested message type and a field into a single declaration. The field type is OptionalGroup in this example, and the field name is converted to lower-case 'optionalgroup' so as not to conflict with the type name. \section{Other approaches} Saptarshi Guha wrote another package that deals with integration of protocol buffer messages with R, taking a different angle : serializing any R object as a message, based on a single catch-all \texttt{proto} file. Saptarshi's package is available at \url{http://ml.stat.purdue.edu/rhipe/doc/html/ProtoBuffers.html}. Jeroen Ooms took a similar approach influenced by Saptarshi in his \texttt{RProtoBufUtils} package. Unlike Saptarshi's package, RProtoBufUtils depends on RProtoBuf for underlying message operations. This package is available at \url{https://github.com/jeroenooms/RProtoBufUtils}. % Phillip Yelland wrote another implementation, currently proprietary, % that has significant speed advantages when querying fields from a % large number of protocol buffers, but is less user friendly for the % basic cases documented here. \section{Plans for future releases} Protocol buffers have a mechanism for remote procedure calls (rpc) that is not yet used by \texttt{RProtoBuf}, but we may one day take advantage of this by writing a protocol buffer message R server, and client code as well, probably based on the functionality of the \texttt{Rserve} package. Extensions have been implemented in RProtoBuf and have been extensively used and tested, but they are not currently described in this vignette. Additional examples and documentation are needed for extensions. % \section{Troubleshouting} \section{Acknowledgments} % protobuf ? % saptarshi ? Some of the design of the package is based on the design of the \texttt{rJava} package by Simon Urbanek (dispatch on new, S4 class structures using external pointers, etc ...). We'd like to thank Simon for his indirect involvment on \texttt{RProtoBuf}. The user defined table mechanism, implemented by Duncan Temple Lang for the purpose of the \texttt{RObjectTables} package allowed the dynamic symbol lookup (see section~\ref{sec-lookup}). Many thanks to Duncan for this amazing feature. \end{document} RProtoBuf/vignettes/RProtoBuf-paper.bib0000644000175100001440000002516413003435510017631 0ustar hornikusers@Misc{apache:avro, author = {{Apache Software Foundation}}, title = {Apache Avro}, url = {http://avro.apache.org/}, note = {Data Serialization System, Version 1.8.1}, year = 2016, } @Misc{apache:thrift, author = {{Apache Software Foundation}}, title = {Apache Thrift}, url = {http://thrift.apache.org/}, note = {Software Framework for Scalable Cross-Language Services, Version 0.9.3}, year = 2015, } @Manual{cran:rserve, title = {\pkg{Rserve}: Binary \proglang{R} Server}, author = {Simon Urbanek}, year = 2013, note = {\proglang{R} package version 1.7-3}, url = {https://CRAN.R-Project.org/package=Rserve}, } @Manual{rjsonio, title = {\pkg{RJSONIO}: Serialize \proglang{R} Objects to JSON, \proglang{JavaScript} Object Notation}, author = {Duncan {Temple Lang}}, year = 2014, note = {\proglang{R} package version 1.3-0}, url = {https://CRAN.R-project.org/package=RJSONIO}, } @Manual{robjecttables, title = {User-Defined Tables in the \proglang{R} Search Path}, author = {Duncan {Temple Lang}}, year = 2012, url = {http://www.omegahat.net/RObjectTables/RObjectTables.pdf}, } @InProceedings{sumaray:2012:cds:2184751.2184810, author = {Audie Sumaray and S. 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= 2009, publisher = {John Wiley \& Sons}, doi = {10.1002/9781118575574}, } @Misc{serialization, author = {Luke Tierney}, title = {A New Serialization Mechanism for \proglang{R}}, url = {http://www.cs.uiowa.edu/~luke/R/serialize/serialize.ps}, year = 2003, } @Misc{shafranovich2005common, title = {Common Format and Mime Type for Comma-Separated Values (CSV) Files}, author = {Yakov Shafranovich}, year = 2005, url = {http://tools.ietf.org/html/rfc4180}, } @Book{MASS, title = {Modern Applied Statistics with \proglang{S}}, author = {W. N. Venables and B. D. Ripley}, publisher = {Springer-Verlag}, edition = {4th}, address = {New York}, year = 2002, } @Unpublished{julia, title = {\proglang{Julia}: A Fast Dynamic Language for Technical Computing}, author = {Jeff Bezanson and Stefan Karpinski and Viral B. Shah and Alan Edelman}, year = 2012, url = {http://arxiv.org/abs/1209.5145}, note = {{arXiv}:1209.5145 [cs.PL]}, } @Manual{python, author = {Van Rossum, Guido and {others}}, title = {\proglang{Python} Programming Language}, url = {http://www.python.org}, year = {2011} } @Manual{rjava, title = {\pkg{rJava}: Low-Level \proglang{R} to \proglang{Java} Interface}, author = {Simon Urbanek}, year = {2016}, note = {\proglang{R} package version 0.9-8}, url = {https://CRAN.R-project.org/package=rJava}, } RProtoBuf/vignettes/RProtoBuf-unitTests.Rnw0000644000175100001440000000420412717313674020547 0ustar hornikusers\documentclass[10pt]{article} %\VignetteIndexEntry{RProtoBuf-unitTests} %\VignetteKeywords{RProtoBuf, Protocol Buffers, package} %\VignetteDepends{RProtoBuf} \usepackage{vmargin} \setmargrb{0.75in}{0.75in}{0.75in}{0.75in} <>= require(RProtoBuf) prettyVersion <- packageDescription("RProtoBuf")$Version prettyDate <- format(Sys.Date(), "%B %e, %Y") library(RUnit) @ \usepackage{microtype} %% cf http://www.khirevich.com/latex/microtype/ \usepackage[T1]{fontenc} %% cf http://www.khirevich.com/latex/font/ \usepackage[bitstream-charter]{mathdesign} %% cf http://www.khirevich.com/latex/font/ \usepackage[colorlinks]{hyperref} \author{Romain Fran\c{c}ois \and Dirk Eddelbuettel \and Murray Stokely} \title{RProtoBuf : Unit testing results} \date{RProtoBuf version \Sexpr{prettyVersion} as of \Sexpr{prettyDate}} \begin{document} \maketitle \section*{Test Execution} <>= pkg <- "RProtoBuf" if (file.exists("unitTests-results")) unlink("unitTests-results", recursive = TRUE) dir.create("unitTests-results") pathRcppTests <<- system.file("unitTests", package = pkg) path <- system.file("unitTests", package=pkg) testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path) tests <- runTestSuite(testSuite) err <- getErrors(tests) if (err$nFail > 0) cat(sprintf("unit test problems: %d failures", err$nFail)) if (err$nErr > 0) cat(sprintf("unit test problems: %d errors", err$nErr)) printHTMLProtocol(tests, fileName=sprintf("unitTests-results/%s-unitTests.html", pkg)) printTextProtocol(tests, fileName=sprintf("unitTests-results/%s-unitTests.txt" , pkg)) #if (file.exists("/tmp")) { # invisible(sapply(c("txt", "html"), function(ext) { # fname <- sprintf("unitTests-results/%s-unitTests.%s", pkg, ext) # file.copy(fname, "/tmp", overwrite=TRUE) # })) #} @ \section*{Test Results} \begin{verbatim} <>= results <- sprintf("unitTests-results/%s-unitTests.txt", pkg) if (file.exists(results)) { writeLines(readLines(results)) } else{ writeLines("Unit test results not available") } @ \end{verbatim} \end{document} RProtoBuf/vignettes/RProtoBuf-quickref.Rnw0000644000175100001440000000774612440004312020347 0ustar hornikusers\documentclass[10pt,twocolumn,a4paper]{article} %\VignetteIndexEntry{RProtoBuf-quickref} %\VignetteEngine{highlight::highlight} %\VignetteKeywords{RProtoBuf, Protocol Buffers, package} %\VignetteDepends{RProtoBuf} \setlength{\hoffset}{-0.8in} \setlength{\voffset}{-0.8in} \setlength{\marginparwidth}{0pt} \setlength{\marginparsep}{0pt} \setlength{\oddsidemargin}{0pt} \setlength{\headheight}{0pt} \setlength{\topmargin}{0pt} \setlength{\headsep}{0pt} \setlength{\footskip}{0pt} \setlength{\textheight}{27cm} \setlength{\textwidth}{20cm} \usepackage[colorlinks]{hyperref} \usepackage{microtype} %% cf http://www.khirevich.com/latex/microtype/ \usepackage[T1]{fontenc} %% cf http://www.khirevich.com/latex/font/ \usepackage[bitstream-charter]{mathdesign} %% cf http://www.khirevich.com/latex/font/ <>= options(width= 50) library("RProtoBuf") rpb.version <- packageDescription("RProtoBuf")$Version @ % closing $ needed here \author{Romain Fran\c{c}ois \and Dirk Eddelbuettel \and Murray Stokely} \title{RProtoBuf \Sexpr{rpb.version}: Quick Reference Guide} \begin{document} \maketitle \thispagestyle{empty} \paragraph{example proto file} <>= ab.proto <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) writeLines( readLines( ab.proto ) ) @ \paragraph{read proto description files} <>= readProtoFiles( "somefile.proto" ) readProtoFiles( dir = somedir ) readProtoFiles( package = AnRPackage ) @ \paragraph{create a message} <>= message <- new( tutorial.Person, id = 0, name = "Romain Francois", email = "francoisromain@free.fr" ) @ \paragraph{serialize a message to a file or binary connection} <>= # to a file tf1 <- tempfile() message$serialize( tf1 ) # to a binary connection tf2 <- tempfile(); con <- file( tf2, open = "wb" ) message$serialize( con ) close(con) # retrieve the payload message$serialize( NULL ) @ \paragraph{read a message from a file or binary connection} <>= # from a file tutorial.Person$read( tf1 ) # from a connection con <- file( tf2, open = "rb" ) tutorial.Person$read( con ) <>= close( con ) @ \paragraph{Get/Set fields} <>= email <- message$email message$id <- 2 message[[ "name" ]] <- "Romain" id <- message[[ 2 ]] # tag number for 'id' @ \paragraph{Message methods} \begin{center} \begin{small} \begin{tabular}{cp{7cm}} \hline \texttt{has} & Indicates if a message has a given field. \\ \texttt{clone} & Creates a clone of the message \\ \texttt{isInitialized} & Indicates if a message has all its required fields set\\ \texttt{serialize} & serialize a message to a file or a binary connection or retrieve the message payload as a raw vector\\ \texttt{clear} & Clear one or several fields of a message, or the entire message\\ \texttt{size} & The number of elements in a message field\\ \texttt{bytesize} & The number of bytes the message would take once serialized\\ \hline \texttt{swap} & swap elements of a repeated field of a message\\ \texttt{set} & set elements of a repeated field\\ \texttt{fetch} & fetch elements of a repeated field\\ \texttt{add} & add elements to a repeated field \\ \hline \texttt{str} & the R structure of the message\\ \texttt{as.character} & character representation of a message\\ \texttt{toString} & character representation of a message (same as \texttt{as.character}) \\ \texttt{update} & updates several fields of a message at once\\ \texttt{descriptor} & get the descriptor of the message type of this message\\ \hline \end{tabular} \end{small} \end{center} <<>>= writeLines( message$toString() ) @ \paragraph{More info} \begin{center} \begin{small} \begin{tabular}{cp{7cm}} full vignette & \verb|vignette( "RProtoBuf")| \\ protobuf & \url{http://code.google.com/p/protobuf/} \\ RProtoBuf & \url{http://r-forge.r-project.org/projects/rprotobuf/}\\ mailing list & \url{https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rprotobuf-yada} \\ \end{tabular} \end{small} \end{center} \end{document} RProtoBuf/vignettes/inactive/0000755000175100001440000000000012440004312015752 5ustar hornikusersRProtoBuf/vignettes/inactive/Makefile.in0000644000175100001440000000275112440004312020024 0ustar hornikusers ## this is a 'fake' all as R-devel gets a race condition on RProtoBuf-intro and deletes the .tex file all: RProtoBuf-unitTests.pdf RProtoBuf-quickref.pdf ## 'real all' pdfall: RProtoBuf-unitTests.pdf RProtoBuf-intro.pdf RProtoBuf-quickref.pdf pdfclean: rm -fr *.pdf clean: rm -f RProtoBuf-intro.aux RProtoBuf-intro.log RProtoBuf-intro.out rm -f RProtoBuf-quickref.aux RProtoBuf-quickref.log RProtoBuf-quickref.out rm -f RProtoBuf-unitTests.aux RProtoBuf-unitTests.log RProtoBuf-unitTests.out rm -rf auto/ setvars: R_HOME= @R_HOME@ RPROG= $(R_HOME)/bin/R RSCRIPT=$(R_HOME)/bin/Rscript RProtoBuf-unitTests.pdf: unitTests/RProtoBuf-unitTests.R $(RSCRIPT) --default-packages="RProtoBuf,Rcpp,brew,RUnit,tools,utils" unitTests/RProtoBuf-unitTests.R RProtoBuf-intro.pdf: RProtoBuf/RProtoBuf.Rnw cp -f RProtoBuf/RProtoBuf.Rnw RProtoBuf-intro.Rnw $(RSCRIPT) -e "require('highlight'); require('tools'); Sweave('RProtoBuf-intro.Rnw', driver=HighlightWeaveLatex()); texi2dvi('RProtoBuf-intro.tex', pdf=TRUE, clean=TRUE)" cp -f RProtoBuf/RProtoBuf-fake.Rnw RProtoBuf-intro.Rnw RProtoBuf-quickref.pdf: RProtoBuf-quickref/RProtoBuf-quickref.Rnw touch RProtoBuf-quickref.Rnw rm RProtoBuf-quickref.Rnw cp -f RProtoBuf-quickref/RProtoBuf-quickref.Rnw . $(RSCRIPT) -e "require( 'highlight'); require('tools'); Sweave('RProtoBuf-quickref.Rnw', driver=HighlightWeaveLatex()); texi2dvi('RProtoBuf-quickref.tex', pdf=TRUE, clean=TRUE)" cp -f RProtoBuf-quickref/RProtoBuf-quickref-fake.Rnw RProtoBuf-quickref.Rnw RProtoBuf/vignettes/inactive/static-use.Rnw0000644000175100001440000001270112440004312020524 0ustar hornikusers% % This has been removed from the vignette because the corresponding % functionality is no longer in the package % \section{Static use: Revisiting the tutorial} In this section, we illustrate use of Protocol Buffers in a \textsl{static} fashion: based on the \texttt{proto} file, code is generated by the compiler and used by language-specific bindings. \subsection{The address book example} Through this document, we will use the \texttt{addressbook} example that is used by the official tutorials for Java, Python and C++. It is based on the following \texttt{proto} file: <>= ab.proto <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) writeLines( readLines( ab.proto ) ) @ The \texttt{proto} file defines : \begin{itemize} \item three message types \begin{itemize} \item \texttt{tutorial.Person}, \item \texttt{tutorial.Person.PhoneNumber} and \item \texttt{tutorial.AddressBook} \end{itemize} \item an enum type \texttt{tutorial.Person.PhoneType} with three values \texttt{MOBILE}, \texttt{HOME} and \texttt{WORK} \end{itemize} We see that a message type can contain several different items: \begin{itemize} \item sets of fields---for example the \texttt{Person} message type contains the required field \texttt{name} of primitive type \texttt{string} associated with the tag number 1; \item fields can be either required (as \texttt{name} or \texttt{id}) or optional (as \texttt{email}); \item other message type descriptions---\texttt{Person} contains the nested message type \texttt{PhoneNumber}; hence the fully qualified type of \texttt{PhoneNumber} is \texttt{tutorial.Person.PhoneNumber} \item enum type descriptions. \end{itemize} Using the \texttt{protoc} compiler, we can generate functions that access these Protocol Buffer messages and their components for both reading and writing using any of the three officially supported languages C++, Java and Python. For example, for C++ the call \begin{quote} \texttt{protoc --cpp\_out=. addressbook.proto} \end{quote} generates almost eighteen hundreed lines of code: seven hundred in a header file \texttt{addressbook.pb.h} and almost elevenhundred in a file \texttt{addressbook.pb.cc}. These two files are used in the tutorial application programs \texttt{add\_person.cc} and \texttt{list\_people.cc}. The former adds a new record to an address book defined by the \texttt{proto} file shown above, and the latter prints the contents of all records in the address book. \subsection{Simple R accessors for the address book example} The Protocol Buffers tutorial contains two simple standalone programs to, respectively, add a record and list all records from an address book as defined by the \texttt{proto} file shown above. In order to ease the transition from C++ to R when working with Protocol Buffers, we implemented two simple wrapper functions in C++ that accomplish essentially the same task, but are callable directly from R. This use the \texttt{Rcpp} package for interfacing C++ from R. \subsubsection*{Adding a record: \texttt{addPerson()}} The R function \texttt{addPerson()} accepts five arguments: <<>>= args( addPerson ) @ The first argument denotes the (binary) file into which the new address book record will be written. The next four argument describe the record to be added. Both \texttt{id} and \texttt{name} have to be of length one, whereas \texttt{emails} and \texttt{phones} can be of length zero as they correspond to optional fields. The actual implementation in C++ is close to the tutorial example and can be used as gentle first step in programming with R and Protocol Buffers. \subsubsection*{Listing all records: \texttt{listPeopleAsList()} and \texttt{listPeopleAsDataFrame()}} Displaying the content of an address book defined by the \texttt{proto} file above is straigtforward in the command-line example as records are simply printed to the screen. For our use, these data need to be read from the file and transfered back to R. Given the definition of the \texttt{proto} file, we face an interesting problem: some fields are optional, and some fields can be repeated numerous types. That means our data structure can be textsl{ragged}: the number of entries per record cannot be expected to be constant. Of course, R can handle such dynamic data structures rather easily. One approach is to use lists of lists which is implemented in \texttt{listPeopleasList()} which returns a \texttt{list} object to R with one entry per address book record. Each of these entries is itself a list comprised of two character vectors of length one (name and id) as well as further lists for emails and phone numbers. Similarly, we can use the fact that the id field is key identifying a person and return two \texttt{data.frames} to R that that can then be merged on the id. This allows for both potentially missing entries (as for the optional email fields) as well as repeated fields (as for the phone number records). The R function \texttt{listPeopleAsDataFrame()} implements this approach, and its corresponding C++ function is very close to the tutorial file \texttt{list\_people.cc}. Both these functions show how R can use the C++ code generated by the Protocol Buffers compiler. Binding the generated functions to R is straightforward --- but arguably tedious as new interface code needs to be written manually. But R as is dynamically-typed language, we would like to use Protocol Buffers in a less rigid fashion. The next few sections show how this can be done. RProtoBuf/vignettes/proto/0000755000175100001440000000000012754736105015337 5ustar hornikusersRProtoBuf/vignettes/proto/int64.proto0000644000175100001440000000025112754736105017366 0ustar hornikusers// mark as Protocol Buffers v2 format syntax = "proto2"; package JSSPaper; message Example1 { optional bool optional_bool = 1; repeated int64 repeated_int64 = 2; }RProtoBuf/vignettes/proto/hist.pb0000644000175100001440000000014512265140367016625 0ustar hornikusers ? @ @ @ @#Example Histogram Created in PythonRProtoBuf/README.md0000644000175100001440000000427213005123764013437 0ustar hornikusers## RProtoBuf [![Build Status](https://travis-ci.org/eddelbuettel/rprotobuf.svg)](https://travis-ci.org/eddelbuettel/rprotobuf) [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) [![CRAN](http://www.r-pkg.org/badges/version/RProtoBuf)](https://cran.r-project.org/package=RProtoBuf) [![Downloads](http://cranlogs.r-pkg.org/badges/RProtoBuf?color=brightgreen)](http://www.r-pkg.org/pkg/RProtoBuf) R Interface to [Google Protocol Buffers](https://developers.google.com/protocol-buffers/) ### What are Protocol Buffers? A serialization format developed by [Google](https://www.google.com) and used widely within Google, and by numerous other projects. Quoting from the [official website](https://developers.google.com/protocol-buffers/): > Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data – think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages. [Protocol Buffers](https://developers.google.com/protocol-buffers/) natively support C++, C#, Go, Java and Python. Many other languages are supported via contributed extensions. This package adds support for [R](https://www.r-project.org). ### Installation You can either install from source via this repo, or install [the CRAN package](https://cran.r-project.org/package=RProtoBuf) the usual way from [R](https://www.r-project.org) via ```r install.packages("RProtoBuf") ``` but do make sure you have the system requirements covered when building from source. Under Debian/Ubuntu you may need ```bash sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev ``` with similar commands on other operating systems or distributions. ### Documentation The package contains two pdf vignettes; the second one corresponds to [our JSS paper](https://www.jstatsoft.org/article/view/v071i02). ### Authors Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms ### License GPL (>= 2) RProtoBuf/MD50000644000175100001440000003147613037462513012501 0ustar hornikusersc23e68b132f3d80d30d0fa88da498c21 *ChangeLog bb9be03f8f78c38d10213356a6288bd9 *DESCRIPTION 9b76f6d15e53a5bddf140ca9df8b7d0c *NAMESPACE 9d4fc4eca08934288aa92ace963c6ad1 *R/00classes.R ad31e4eeef1cfcb9e6052da2884bf818 *R/add.R 9d141fa9b6995218d84192f2f8f48313 *R/aslist.R c4ae245b40eee8819918c5763194ad99 *R/clear.R 07b292067dd11bde7609abd9db303281 *R/clone.R b28d2343dd36ba673299bce87e7f9506 *R/completion.R 38ae44c79783992074c60338c61d02c3 *R/containing_type.R 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Protocol Buffers is a serialization format with an interface description language developed by Google. The original Google implementation for C++, Java and Python is available under a free software, open source license. Various other language implementations are either available or in development. . The design goals for Protocol Buffers emphasized simplicity and performance. In particular, it was designed to be faster than XML (no reproducible comparisons are publicly available to confirm this, however). Protocol Buffers is very similar to Facebook’s Thrift protocol, except it does not include a concrete RPC stack to use for defined services. Since Protocol Buffers was open sourced, a number of RPC stacks have emerged to fill this gap. . Prior to the release as open source, Protocol Buffers had been widely used at Google for storing and interchanging all kinds of structured information. Protocol Buffers serve as a basis for a custom RPC system that is used for practically all inter-machine communication at Google.[1] . Data structures and services are defined in the Proto Definition file (.proto) which is then compiled with protoc. This compilation generates code that matches the services. For example, example.proto will produce example.pb.cc and example.pb.h which will define C++ classes for each Message and Service example.proto defines. . Protocol Buffers allow serialization into any number of formats. In the officially supported implementations there is a full Reflection interface available, making it easy to serialize protos as XML and JSON. . Though the primary purpose of Protocol Buffers is to facilitate network communication, its simplicity and speed make Protocol Buffers a great replacement of data-centric C++ classes and structs. RProtoBuf/build/0000755000175100001440000000000013037407201013246 5ustar hornikusersRProtoBuf/build/vignette.rds0000644000175100001440000000046113037407201015606 0ustar hornikusersՓN0 dzltb0>}4ev5jS$!MUq6]*pAU?[MsP0PሗMa-`D^n7JhTfk%- [ɒCDI$UQəB-J_H/'~%o]4˞z]hp36^? ׀6G Ek'"_FUa3Iy?? qJgf9;;oVksO;[QIyjuΟ{%CH*b[]ן%9)lE9O&q oє#RProtoBuf/DESCRIPTION0000644000175100001440000000253213037462513013666 0ustar hornikusersPackage: RProtoBuf Version: 0.4.8 Date: 2017-01-17 Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms Maintainer: Dirk Eddelbuettel Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3) Description: Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our paper in the Journal of Statistical Software (2016, v71i02). Either version 2 or 3 of the 'Protocol Buffers' 'API' is supported. Depends: R (>= 3.0.0), methods Imports: utils, stats, tools, Rcpp, RCurl LinkingTo: Rcpp Suggests: RUnit, highlight VignetteBuilder: highlight SystemRequirements: ProtoBuf libraries and compiler version 2.2.0 or later; version 3.0.0 or later is supported as well. On Debian/Ubuntu these can be installed as libprotoc-dev and libprotobuf-dev, while on Fedora/CentOS protobuf-devel and protobuf-compiler are needed. BugReports: https://github.com/eddelbuettel/rprotobuf/issues URL: https://github.com/eddelbuettel/rprotobuf License: GPL (>= 2) NeedsCompilation: yes Packaged: 2017-01-17 12:30:58.196848 UTC; edd Repository: CRAN Date/Publication: 2017-01-17 19:41:15 RProtoBuf/configure0000755000175100001440000046312012743454477014110 0ustar hornikusers#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.69 for RProtoBuf 0.4. # # # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. # # # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. 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RProtoBuf/ChangeLog0000644000175100001440000025617213037201575013744 0ustar hornikusers2017-01-16 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Roll minor version and date * tools/winlibs.R: Use proto3 library from rwinlib repo * src/Makevars.win: Update to proto 3.0.0 paths * inst/unitTests/runit.proto3.R: New test file * inst/unitTests/data/proto3.proto: Support for new test file 2016-10-29 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.4.7 2016-10-24 Dirk Eddelbuettel * DESCRIPTION (Version): Roll minor version and date * src/lookup.cpp: Replace omegahat.org with omagehat.net * vignettes/RProtoBuf-paper.bib: Ditto 2016-09-09 Dirk Eddelbuettel * DESCRIPTION (Version, Date): New release 0.4.6 * README.md: Expanded, added three short sections 2016-09-08 Dirk Eddelbuettel * inst/NEWS.Rd: Ditto, also replace \cpkg{} with \CRANpkg{} * README.md: Use https for CRAN URL 2016-09-06 Dirk Eddelbuettel * vignettes/RProtoBuf-paper.Rnw: Comment-out the use of the \DOI macro from (updated) jss.cls: cannot ship jss.cls (or R will warn) and cannot use \DOI as (as R-release and older do not know \DOI) 2016-09-01 Dirk Eddelbuettel [ Entry for anonymous PR #18 by 'oliverbock' ] * R/rexp_obj.R (unrexp_string): Ensure zero-length strings can be serialized; special case of native encoding for S4 objects * inst/unitTests/runit.serialize_pb.R: New tests 2016-08-29 Dirk Eddelbuettel * DESCRIPTION (Version, Date): New release 0.4.5 2016-08-16 Dirk Eddelbuettel * DESCRIPTION (SystemRequirements): Add explicit note that Protocol Buffers 3.0.0 are supported as well 2016-08-15 Dirk Eddelbuettel * DESCRIPTION (Version): Rolling minor version * inst/proto/addressbook.proto: Added 'syntax = "proto2";' * inst/proto/helloworld.proto: Idem * inst/proto/rexp.proto: Idem * inst/unitTests/data/bytes.proto: Idem * inst/unitTests/data/encoding.proto: Idem * inst/unitTests/data/nested.proto: Idem * inst/unitTests/data/unittest.proto: Idem * inst/unitTests/data/unittest_import.proto: Idem * vignettes/proto/int64.proto: Idem * inst/unitTests/runit.addressbook.R (test.ascii): Comment-out one sub-test concerned with access under bad file modes 2016-08-13 Dirk Eddelbuettel * .travis.yml: Switch to using run.sh for Travis CI, also switch to using a build matrix across ProtoBuf versions 2 and 3 2016-07-19 Craig Radcliffe * configure.in: Make sure that CXXFLAGS is from the environment when writing to src/Makevars 2016-07-10 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.4.4 * vignettes/RProtoBuf-paper.Rnw: Added, based on pending JSS publication * vignettes/RProtoBuf-paper.bib: Ditto * vignettes/figures/*: Ditto * vignettes/proto/*: Ditto * vignettes/jss.cls: Ditto * vignettes/jss.bst: Ditto * inst/CITATION: Update to version provided by JSS * README.md: Updated to use of canonical URLs for CRAN 2016-05-19 Dirk Eddelbuettel * vignettes/RProtoBuf-unitTests.Rnw: Do not write unit test results to /tmp per request from CRAN to not write outside test directories 2016-04-26 Dirk Eddelbuettel * CONTRIBUTING.md: New workflow document 2016-04-25 Jeroen Ooms * R/rexp_obj.R: Fix zero-length edge case * R/serialize_pb.R: Improved documentation * man/serialize_pb.Rd: Ditto 2016-04-21 Jeroen Ooms * src/Makevars.win: Accomodate new Windows toolchain 2016-04-21 Jonathon Love * inst/unitTests/runit.addressbook.R: Set to mode 0644 * inst/unitTests/runit.bytes.R: Ditto 2016-02-11 Dirk Eddelbuettel * DESCRIPTION (License): Set to GPL (>= 2) which is what the code files with actual copyright and license headers had all along * README.md: Idem 2015-08-25 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.4.3 2015-08-24 Dirk Eddelbuettel * README.md: Additional badges * inst/unitTests/runit.FieldDescriptor.R: Added msg field 2015-08-23 Dirk Eddelbuettel * tools/winlibs.R: Actually tests against R 3.3.0 2015-08-23 Jeroen Ooms * tools/winlibs.R: Test for R 3.3.0 on Windows 2015-08-23 Dirk Eddelbuettel * NAMESPACE: Added imports for as and is from methods * DESCRIPTION: Removed several of the (largely redundant) URLs, and minor edits in Description: to update to current standard * man/RProtoBuf-package.Rd: Updated, removed old URLs. * .travis.yml: Accelerate by installing dependencies via apt-get 2015-08-05 Balasubramanian Narasimhan * NAMESPACE: Added import for show from methods package 2015-07-08 Jeroen Ooms * tools/winlibs.R: Update URL to windows build of the required ProtoBuf library 2015-01-16 Dirk Eddelbuettel * DESCRIPTION: Minor edits 2015-01-16 Jeroen Ooms * DESCRIPTION: Make SystemRequirements: more explicit 2014-12-11 Jeroen Ooms * DESCRIPTION: Update URLs 2014-12-10 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.4.2 2014-12-10 Jeroen Ooms * src/Makevars.win: Use new ProtoBuf 2.6.1 builds on Windows * tools/winlibs.R: Helper function used for Windows build * inst/unitTests/runit.int64.R: Fixed a windows bug 2014-12-08 Jeroen Ooms * inst/proto/rexp.proto: Add a new type 'native' * R/rexp_obj.R: Modify (un)serialize_pb to serialize() non-data types as 'native' types 2014-12-04 Dirk Eddelbuettel * .travis.yml: Added after move to GitHub * README.md: Added minimal first version with Travis badge 2014-12-04 Murray Stokely * inst/unitTests/runit.int64.R: restore options on exit from this function to make the test indempotent. 2014-12-01 Dirk Eddelbuettel * man/Message-class.Rd: Completed documentation * man/Descriptor-class.Rd: Ditto * man/EnumDescriptor-class.Rd: Ditto 2014-12-01 Murray Stokely * R/wrapper_ZeroCopyInputStream.R: Avoid file.create for getting absolute path of a temporary file name (JSS reviewer feedback) * R/serialize.R: Idem. 2014-11-26 Murray Stokely Address feedback from anonymous reviewer for JSS to make this package more complete: * inst/unitTests/runit.serialize_pb.R: Add a test to verify that we can serialize all 100+ built-in datasets with R and get an identical object to the original once unserialized. * R/rexp_obj.R: Serialize function, language, and environment objects by just falling back to R's native serialization and using raw bytes to store them. This at least lets us round-trip encode all native R types, even though these three only make sense in the context of R. Greatly simplify the can_serialize_pb function. * inst/proto/rexp.proto: Add support for function, language, and environment objects. 2014-11-25 Dirk Eddelbuettel * vignettes/RProtoBuf-intro.Rnw: Applied a few corrections spotted by Tim Hesterberg and communicated in email. 2014-11-24 Murray Stokely * inst/unitTests/runit.golden.message.R: remove trailing whitespace. * man/P.Rd: Improve output of example. 2014-09-15 Murray Stokely Address feedback from anonymous reviewers for our Journal of Statistical Software submission: * src/wrapper_EnumDescriptor.cpp (rprotobuf): Correct the definition of as.list for EnumDescriptors to return a proper list instead of a named vector. * man/aslist.Rd: clarify order of returned list for descriptor objects. * NAMESPACE: add names as exported method. * R/00classes.R (show): Update the default print methods to use cat() with fill=TRUE instead of show() to eliminate the confusing [1] since the classes in RProtoBuf are not vectorized. * Make Descriptor and EnumDescriptor objects subsettable with "[[". * Add length() method for Descriptor objects. * Add names() method for Message, Descriptor, and EnumDescriptor objects. * inst/unitTests/runit.enums.R (test.enums): Add test of subsetting an EnumDescriptor object. * inst/unitTests/runit.descriptors.R (test.descriptor): Add test for subsetting of descriptor objects. * DESCRIPTION (Version): Increment. 2014-04-02 Murray Stokely Two patches from Karl Millar : * src/S4_classes.h (rprotobuf): Change handling of S4_EnumDescriptor when passed a NULL pointer to just create empty object with empty name and full_name rather than setting to R_NilValue. * src/wrapper_EnumDescriptor.cpp (rprotobuf): Change return value of getValue* functions on EnumDescriptor and return an EnumValueDescriptor or R_NilValue on failure. 2014-04-01 Murray Stokely * tests/runUnitTests.R: Add improved checks to ensure R CMD CHECK fails if there are any errors in the tests, not just failures. 2014-03-25 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.4.1 2014-03-24 Murray Stokely * inst/unitTests/runit.int64.R (test.int64): Check Rcpp:::capabilities() to ensure we have long long support in Rcpp before trying to run the 64-bit integer tests. * inst/unitTests/data/unittest.proto: Comment out TestEnumWithDupValue. This causes problems with the newest libprotobuf-2.5 which now wants an option to be specified to enable enum aliasing like this. * configure.in: if we can't find the libproto headers with the default CPPFLAGS/CXXFLAGS, manually add /usr/local/include and try again. 2014-03-10 Murray Stokely * src/DescriptorPoolLookup.cpp (rprotobuf): Import all top-level enums defined in an imported .proto file. * src/rprotobuf.cpp (rprotobuf): Add a function to get the enum descriptor associated with a named enum. * inst/unitTests/runit.enums.R (test.enums): Test that we import top-level enums from .proto files correctly. * R/00classes.R (P): Correct a bug in the show() method for EnumDescriptor that prevented useful output in some contexts. 2014-02-21 Murray Stokely * inst/unitTests/runit.messages.R (test.message): Add a test for the deprecated group feature which works fine with RProtoBuf. The type is converted to lower case, which users often forget. * vignettes/RProtoBuf-intro.Rnw (subsection{Deprecated Feature: Protocol Buffer Groups}): document groups. * inst/CITATION: Add a manual CITATION file pointing to the preprint on arxiv.org in addition to the normal auto-generated citation(). 2014-01-19 Dirk Eddelbuettel * DESCRIPTION: Finalize release 0.4.0 with initial Windows support * src/S4_classes.h: Adapt to S4 access function renaming in Rcpp 0.10.7 and later, with special thanks to Kevin Ushey 2014-01-13 Murray Stokely * inst/unitTests/runit.int64.R (test.int64): Skip this test with a warning if running on a machine with sizeof(long long) < 8. * vignettes/RProtoBuf-intro.Rnw (subsection{64-bit integer issues}): Hide 64-bit field accesses with if conditional to avoid running code that won't work on platforms without 64-bit long longs. * DESCRIPTION (Version): Increment to 0.4.0 2014-01-09 Murray Stokely * R/read.R: Add a logical argument 'partial' to readASCII that accepts uninitialized message fragments. * src/wrapper_Descriptor.cpp (rprotobuf): Idem * inst/unitTests/runit.addressbook.R (test.ascii): Add tests for above. 2014-01-04 Murray Stokely * R/wrapper_CodedInputStream.R: Accept numeric size arguments for ReadRaw and ReadString to make this more user friendly for interactive use by calling as.integer() as needed. * R/00classes.R (P): Add missing object prameters in ZeroCopyInputStream calls to ReadRaw and ReadString. * inst/unitTests/data/encoding.proto: Add example messages used in the encoding documentation. * inst/unitTests/runit.serialize.R (test.encoding): Add tests verifying the exact byte serialization as described in the encoding documentation. (test.arrayinputstream): Add new test of ArrayInputStreams. * src/wrapper_ZeroCopyInputStream.cpp (rprotobuf): Add BEGIN/END_RCPP macros to gracefully catch exceptions and return them as R language errors. * src/streams.cpp (rprotobuf): Idem. * man/ArrayInputStream-class.Rd: Add some examples of using ArrayInputStream. 2014-01-04 Dirk Eddelbuettel * src: Deprecate files SocketCopyingInputStream.{cpp,h}, sisocks.h as the current RProtoBuf design does not provide networking capabilities 2013-12-31 Murray Stokely * src/wrapper_Message.cpp: Fix type coercion bug in add() method for uint32s and add a missing break statement that erroneously raised an error when setting some int64 fields. Make more function arguments const and remove a superfluous BEGIN_RCPP/END_RCPP. Also add comment about long-vector support. All of these fixes were highlighted by Flexelint. * inst/unitTests/runit.int64.R (test.int64): Add tests for above. * inst/unitTests/runit.extremevalues.R (test.uint32): Idem. * src/wrapper_FieldDescriptor.cpp (RPB_HANDLE_CASE): Remove unreachable statement in a macro. * src/wrapper_Descriptor.cpp (rprotobuf): Remove unused variable, rename another variable for clarity, and add some TODOs. * src/wrapper_FileDescriptor.cpp (rprotobuf): Idem. * src/DescriptorPoolLookup.cpp (rprotobuf): Remove unreachable statement. * src/extensions.cpp: Remove unused header. * src/mutators.cpp (rprotobuf): Update code to check for Long vectors and use the safer R_xlen_t type everywhere. Protocol Buffers repeated fields seem to be limited to int size indices as with normal R vectors. * src/rprotobuf.h: Idem 2013-12-30 Murray Stokely * inst/unitTests/runit.extremevalues.R (test.uint32): Add test verifying that we can store 2^32 - 1 properly in repeated or optional protobuf fields. * src/extractors.cpp (rprotobuf): Correct handling of uint32 for repeated fields. * src/wrapper_Message.cpp (rprotobuf): Remove Rf_error in favor of Rcpp_error so that we throw an exception and unwind the stack to deallocate objects before jumping to R's error. * src/DescriptorPoolLookup.cpp (rprotobuf): Idem. * R/size.R: Correct an incorrect method name that prevented size<- from working. * man/size.Rd: Document the behavior of size<- * (C++): Ran all the C++ files and most of the headers through clang-format as described in the STYLE file on R-Forge. Basically, we now use 4-char indents and 100-char limit for line wrap. 2013-12-28 Murray Stokely * src/extractors.cpp (rprotobuf): Correct handling of uint32 for single values greater than 2^31 by returning as R numeric types to avoid losing precision since R doesn't have unsigned int types but C++ does. Works around an Rcpp bug https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1360&group_id=155&atid=637 2013-12-27 Murray Stokely * src/mutators.cpp: Refactor setMessageField into four separate functions, correct a few minor typos, and wrap everything in a try/catch block so we catch any exceptions generated by Rcpp::as or other functions and forward it along to an R-language stop() error instead of terminating our R instance. * src/mutators.cpp (rprotobuf): Add more helpful error message specifying which element of a list is of the wrong type, and what the expected type is, when setting a list of messages. * inst/unitTests/runit.messages.R (test.message): Add unit tests for our handling of setting repeated message fields. * src/wrapper_Message.cpp: Add const qualifier to field_desc throughout file. * src/exceptions.cpp: Remove ancient exceptions handling code, migrate codebase to use standard exception classes and helper functions from Rcpp. * R/exceptions.R (throw): idem. 2013-12-26 Murray Stokely * src/mutators.cpp: Support setting int32 values with character vectors of a decimal number, as we do by necessity for int64s. Also, refuse to set non-repeated bools to NA, just as we do for repeated bool fields by raising a stop() error since protocol buffer bools are 2-valued and NA is the third-value of R bools. * inst/unitTests/runit.int32.R (test.int32): Add tests for above. * NAMESPACE: Add missing export for .DollarNames EnumValueDescriptor to allow completion on that class. * R/00classes.R: Update FileDescriptor '$' dispatch to work properly for the names of fields defined in the FileDescriptor, instead of just returning NULL even for types returned by $ completion. * vignettes/RProtoBuf-intro.Rnw (subsubsection{Retrieve fields}): Update the type mapping tables to note that characters can be extracted from 64-bit integer types with the RProtoBuf.int64AsString type and note that int32 and int64 types can be set to character values representing decimal numbers. * TODO: Update todo list. * inst/unitTests/runit.bool.R (test.bool): Add more tests about boolean values, NA handling, etc. 2013-12-23 Murray Stokely * DESCRIPTION (Version): increment. * inst/proto/addressbook.proto: Reserved extension fields in tutorial.Person. * vignettes/RProtoBuf-intro.Rnw (subsection{Extensions}): Added a new section documenting protocol buffer extensions. 2013-12-20 Murray Stokely * R/00classes.R: Correct a bug that incorrectly dispatched as.character() when as.list() was called on Descriptor objects. 2013-12-18 Murray Stokely * R/completion.R (.DollarNames.EnumValueDescriptor): Add $-completion for EnumValueDescriptor and FileDescriptor classes as with other S4 RProtoBuf classes here. * R/00classes.R (P): Ensure that the FileDescriptor $name() method accepts a boolean for full paths just like the generic name() method. * R/wrapper_EnumDescriptor.R: Add better error checking. Expect exceptions if wrong types are provided for arguments rather than just returning NULL. 2013-12-18 Dirk Eddelbuettel * vignettes/RProtoBuf-intro.Rnw: Use with vignette builder * vignettes/RProtoBuf-quickref.Rnw: Idem * vignettes/RProtoBuf-unitTests.Rnw: Rewritten / simplified * DESCRIPTION: Increased dependency to R (>= 3.0.0) * configure.in: No longer create vignettes/Makefile 2013-12-17 Murray Stokely * R/completion.R (.DollarNames.Message): Add missing methods to dollar completion list for Message and Descriptor objects * vignettes/RProtoBuf/RProtoBuf.Rnw (subsection{messages}): Add missing methods to Table 2 (Messages) and add a table and new sections of methods for Descriptor objects. 2013-12-16 Dirk Eddelbuettel * src/rprotobuf.h (RCPP_ENUM_TRAITS): Don't use extern "C" on internal functions returning atomistic or C++ types 2013-12-15 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.3.2 * tests/runUnitTests.R: Minor rewrite and cleanup from doRUnit.R with a tip of the hat to Murray's version in his HistogramTools package 2013-12-14 Dirk Eddelbuettel * src/lookup.cpp (rprotobuf): Descrictor pools attached directly * R/lookup.R (attachDescriptorPool): No longer attach them here * src/rprotobuf.h: Updated function declaration 2013-12-14 Murray Stokely * src/mutators.cpp (rprotobuf): Fix a bug which incorrectly prevented users from setting raw non-repeated fields under some circumstances. * inst/unitTests/runit.bytes.R (test.all): Verify raw(10) can be set to required bytes fields to verify correct behavior for use case mentioned on rprotobuf-yada list. 2013-11-13 Murray Stokely * R/extensions.R: Give a user friendly error message if someone tries to set an extension to a message of the wrong type instead of causing a C++ check failure that terminates your R session. * inst/unitTests/runit.extensions.R (test.extension): Add test. 2013-10-23 Murray Stokely * src/lookup.cpp (rprotobuf): Remove stop() error in object table assignment as this was causing errors with the '<<-' operator in any code using RProtoBuf. * inst/unitTests/runit.import.R (test.assign.in.global): Add a test for the above. 2013-09-16 Murray Stokely * DESCRIPTION (Version): Increment to 0.3.1.1. * R/00classes.R: Improve show method for EnumValueDescriptor and add enum_type to '$' dispatch. * man/EnumValueDescriptor-class.Rd: Add examples and document missing methods. * src/wrapper_EnumValueDescriptor.cpp (rprotobuf): Add missing enum_type method. * inst/unitTests/runit.enums.R (test.enums): Add more tests. 2013-09-13 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.3.1 2013-09-13 Murray Stokely * vignettes/Makefile.in: Update configure to output R_HOME to the vignette makefile so we can avoid the use of a non-portable GNU makefile extension here. 2013-09-12 Murray Stokely * src/RcppMacros.h: Add Rcpp compatibility macros which are simplified versions of the now deprecated ones from Rcpp. 2013-09-11 Murray Stokely * configure.in: If pkg-config is not available add -lprotobuf to PKG_LIBS. This makes it easier to install on MacOS X 10.8, for example. 2013-09-06 Murray Stokely * src/rprotobuf.cpp (rprotobuf): Include the name of the field that could not be found in exceptions in getFieldDescriptor (errors from update / new, etc.). 2013-09-03 Murray Stokely * inst/NEWS.Rd: Summarize changes since the last release. * vignettes/RProtoBuf/RProtoBuf.Rnw: Add a new section on 64-bit issues, document the RProtoBuf.int64AsString option, break out the 'other approaches' section from the 'future work', and fix a few typos. 2013-08-30 Dirk Eddelbuettel * NAMESPACE: Import 'file_path_as_absolute' from package tools, and the two functions needed from the RCurl package * R/*R: Updated several files which no longer need 'tools:::' prefix * DESCRIPTION: Updated Depends: and Imports accordingly 2013-08-29 Murray Stokely * R/zzz.R (.onLoad): Rename option controlling int64 handling with package name prefix. * inst/unitTests/runit.int64.R (test.int64): Idem * src/extractors.cpp (rprotobuf): Add templated function to reduce code duplication in last changelist. * src/mutators.cpp (rprotobuf): Idem 2013-08-27 Murray Stokely * src/extractors.cpp (rprotobuf): Add support for a new option("int64AsString") that controls whether extractors for 64-bit integer fields return character strings or use Rcpp's default wrap type which coerces to numeric, possibly losing precision. * R/zzz.R (.onLoad): Initialize options("int64AsString" = FALSE). * src/Rcppsupport.h (rprotobuf): Add RepeatedFieldImporter classes for int64 and uint64 that return strings instead of int64s. * src/mutators.cpp (rprotobuf): Add support for setting int64 fields as R character vectors that are converted to int64 or uint64 C++ types with std::stringstream. This allows the user to get around the lack of 64-bit integer support in R when working interactively with RProtoBufs where a large precision number or identifier needs to be stored. * inst/unitTests/runit.int64.R: Add tests for the above. 2013-08-21 Murray Stokely * inst/unitTests/runit.addressbook.R (test.ascii): Add more tests. * src/wrapper_Descriptor.cpp (rprotobuf): Add better error handling for readASCII of text strings rather than returning an empty proto. * R/extensions.R: Add checks to ensure that a valid extension FieldDescriptor is passed to getExtension and setExtension. * inst/unitTests/runit.int64.R (test.int64): Add a test illustrating how RProtoBuf is broken in handling 64-bit integers (commented out for now). * man/P.Rd: Document behavior for extensions. * inst/unitTests/runit.extensions.R (test.extension): Add more tests. * src/wrapper_Message.cpp (rprotobuf): Add function for returning the number of extensions set in this message, to improve show() output. * src/rprotobuf.cpp (rprotobuf): Add support for looking up extensions by name and returning FieldDescriptors. * R/00classes.R (P): Add support for returning extension descriptors. 2013-07-14 Dirk Eddelbuettel * inst/unitTests/runit.extensions.R (test.extension): Comment-out test for setExtension against enum, at least for now * vignettes/RProtoBuf/RProtoBuf.Rnw: Added Murray to Authors, at last * vignettes/RProtoBuf-unitTests.Rnw: Idem * vignettes/RProtoBuf-quickref/RProtoBuf-quickref.Rnw: Idem 2013-07-13 Murray Stokely * inst/NEWS.Rd: Summarize new features since the last CRAN release last year. * DESCRIPTION: Increment version to 0.3. 2013-07-13 Dirk Eddelbuettel * man/Message-class.Rd: Added \alias entries for getExtension and setExtension * DESCRIPTION: Incremented Version to separate current test builds from previous release * DESCRIPTION: Removed 'MinimumLibProtoVersion: 2002000' which we no longer need as that version of Protocol Buffers was released a rather long time ago * R/zzz.R: Check for minimal version is now commented-out 2013-07-12 Murray Stokely * src/extensions.cpp: Replace custom extractor and mutator with call to existing functions in mutators.cpp and extractors.cpp that can be used for extensions and any other field type. * src/extensions.R: Idem * vignettes/RProtoBuf/RProtoBuf.Rnw: Document getExtension, setExtension methods. * man/Message-class.Rd: Idem * src/rprotobuf.h: Remove unused desc argument to extractFieldAsSEXP. * src/extractors.cpp: Idem * inst/unitTests/runit.extensions.R: Add additional tests for nested enum and message type extensions. 2013-07-11 Murray Stokely * R/extensions.R: Implement getExtension, setExtension methods. * src/extensions.cpp: Implement getExtension, setExtension. * R/set.R: Add a TODO noting these functions are undocumented. * R/00classes.R: Add setExtension, getExtension extractors for message objects. * R/completion.R: Add setExtension, getExtension. * NAMESPACE: Add setExtension, getExtension. * src/DescriptorPoolLookup.cpp: Add top-level extensions to descriptor pool. * src/rprotobuf.h: Add helper function for getting field descriptor objects. * src/wrapper_FileDescriptor.cpp: Add support for extensions to getMemberNames and as_list * src/lookup.cpp: Add support for looking up extensions. * inst/unitTests/runit.extensions.R: Add basic test for the above. 2013-07-10 Murray Stokely * man/aslist.Rd: Document behavior for enum and file descriptors and be more sparing with \dontrun in examples. * man/EnumDescriptor-class.Rd: Be more sparing with \dontrun in examples so we run more test code. * man/add.Rd: Idem * man/clone.Rd: Idem * man/Descriptor-class.Rd: Idem * man/FieldDescriptor-class.Rd: Idem * man/FileDescriptor-class.Rd: Idem * man/is_extension.Rd: Idem * man/label.Rd: Idem * man/Message-class.Rd: Idem * man/number.Rd: Idem * man/P.Rd: Idem * man/readProtoFiles.Rd: Idem * man/type.Rd: Idem * man/with.Rd: Idem * man/RProtoBuf-package.Rd: Idem 2013-07-08 Murray Stokely * R/has.R: add a has method for EnumDescriptor objects to return a logical indicating if the named constant exists or not. * R/00classes.R: fix a typo that prevented the length method from working properly for EnumDescriptor objects. Use this functionality to add the number of constants in the show method for EnumDescriptors. * R/wrapper_EnumValueDescriptor.R: add a number method to return the numeric value of this enum constant. * man/has.Rd: Add example of the above. * man/number.Rd: Add example of the above. * man/EnumDescriptor-class.Rd: Add example of the above. * man/EnumValueDescriptor-class.Rd: Add example of the above. 2013-02-21 Murray Stokely * R/00classes.R: add filename and package slots to FileDescriptor S4 class and provide more user-friendly show() methods for Messages and FileDescriptors that provide more context about the contained data. * src/S4_classes.h: populate package and filename slots when a FileDescriptor is created based on fields from the underlying C++ object. * inst/unitTests/runit.addressbook.R: add a basic test for FileDescriptors. * man/FileDescriptor-class.Rd: document the new slots in FileDescriptor and add examples. 2012-10-03 Murray Stokely * src/mutators.cpp (rprotobuf): Fix bug where LENGTH() is used on non-vectors when setting a repeated message field to a single Message object. This caused non-deterministic behavior after memory was read from a random location. * inst/unitTests/runit.golden.message.R (test.repeatedFields): Add tests for this case. 2012-09-25 Dirk Eddelbuettel * man/is_extension.Rd: Use \dontrun on examples as we cannot reload the same proto file twice * man/label.Rd: Idem * man/number.Rd: Idem * man/type.Rd: Idem 2012-09-24 Murray Stokely * R/has.R: Distinguish between non-existant and not-set fields in a message by returning NULL in the former case. * R/00classes.R: Idem * src/wrapper_Message.cpp (rprotobuf): Idem * inst/unitTests/runit.golden.message.R (test.has): Add test. * man/has.Rd: Add example of the above. 2012-09-21 Murray Stokely * Fix a bug causing segfaults in containing_type(). * R/containing_type.R: Return NULL instead of invalid descriptors when there is no containing type for an object. * src/S4_classes.h: Check for NULL pointers in the contructors for S4_Descriptor and S4_EnumDescriptor as these methods are called on the return value of e.g. containing_type() in the protobuf API without checking the return alue. * man/containing_type-methods.Rd: Add examples section showing cases where there is and is not a containing_type. * inst/unitTests/runit.FieldDescriptor.R (test.FieldDescriptor.class): Add tests for the above. 2012-08-21 Murray Stokely * src/mutators.cpp: Add better input checking when setting an optional field to avoid an uncaught exception that would kill the R session, and add a test. * inst/unitTests/runit.golden.message.R (test.invalidAssignments): Add test for this. 2012-08-18 Dirk Eddelbuettel * Applied two more patches by Murray and Karl: - Make readASCII() more robust to error conditions; adds tests to catch them. - Correct type(), cpp_type(), and label() methods when as.string=TRUE; add unit tests for these methods, add examples to the Rd files for these methods, and adds type and cpp_type to the NAMESPACE file where they were previously absent. 2012-08-09 Dirk Eddelbuettel * Applied two more patches by Murray: - R/wrapper_FieldDescriptor.R: correct more '_' and '__' mismatches - man/*: update manual pages for style, add examples - src/mutators.cpp: fix bug in handling of NA in boolean vectors - inst/unitTests/runit.golden.message.R: add unit test 2012-08-08 Dirk Eddelbuettel * DESCRIPTION: Release 0.2.5 * src/mutators.cpp: Applied patch by Murray to correctly deal with nested protocol buffer definitions * inst/unitTests/runit.nested.R: Added test from Murray * inst/unitTests/data/nested.proto: Nested protbuf def from Murray * R/serialize.R: Added patch by Murray to not serialize uninitalized protocol buffers (with missing required fields) * inst/unitTests/runit.serialize.R: Added tests for this * /man/add.Rd: Add patch by Murray for stylistic improvement and added examples * inst/NEWS.Rd: Converted NEWS file to .Rd format * DESCRIPTION: Changed Maintainer: to single person per CRAN Policy * vignettes/: Moved from inst/doc/ per CRAN Policy 2012-05-15 Dirk Eddelbuettel * DESCRIPTION: Release 0.2.4 * R/zzz.R (.onLoad): pass lib.loc=libname to readProtoFiles * R/internals.R (readProtoFiles): use lib.loc argument * man/readProtoFiles.Rd: Document new lib.loc argument 2012-05-14 Dirk Eddelbuettel * R/lookup.R: comment-out unlockBinding() which R CMD check does not like as it turns out that we do not need it here anyway * inst/unitTests/runit.addressbook.R (test.ascii): Small correction by converting to character before comparing * DESCRIPTION: Remove Depends: on int64 which is no longer used, lower Depends: on Rcpp to 0.9.6 which should be sufficient 2012-05-13 Dirk Eddelbuettel * src/rprotobuf.h: Added '#include ' to make g++-4.7 happy * src/*: Reversed out SVN revisions 426 to 434 related to int64 2012-04-07 Dirk Eddelbuettel * R/zzz.R: Add 'lib.loc=libname' to packageDescription() call as requested by Brian Ripley 2012-03-20 Dirk Eddelbuettel * Applied another patch by Murray: - src/mutators.cpp: Deal with case of repeated strings - inst/unitTests/runit.golden.message.R: test for this case 2011-07-17 Dirk Eddelbuettel * Applied another patch by Murray: - src/wrapper_Descriptor.cpp: Add missing readASCIIFromConnection C++ function that was called in read.R but not defined. - R/read.R: Remove an _ in the readASCII C++ functions to match the naming convention of the other nearby functions. - man/readASCII.Rd: Add examples of ascii export/import of messages. - inst/unitTests/runit.addressbook.R: Add tests of ascii export/import of messages. 2011-07-07 Dirk Eddelbuettel * src/wrapper_FileDescriptor.cpp (rprotobuf): Applied patch by Murray to correct a cut & paste error in variable name 2011-04-12 Dirk Eddelbuettel * DESCRIPTION: Release 0.2.3 2011-04-10 Dirk Eddelbuettel * src/extractors.cpp: Protect UINT64 and INT64 inside of #ifdef test for RCPP_HAS_LONG_LONG_TYPES which we now need for g++ 4.5 or later * src/mutators.cpp: Idem * wrapper_FieldDescriptor.cpp: Idem 2011-04-05 Dirk Eddelbuettel * inst/doc/Makefile: Call R and Rscript relative to R_HOME/bin 2011-04-04 Dirk Eddelbuettel * inst/doc/Makefile: Do not call clean in all target 2011-01-12 Dirk Eddelbuettel * R/with.R: Use envir= argument to eval() 2011-01-11 Dirk Eddelbuettel * DESCRIPTION: Release 0.2.2 * inst/THANKS: Added new file to say Thanks! 2011-01-10 Dirk Eddelbuettel * Applied another patch by Murray Stokely providing: - R/internals.R: generalise readProtoFiles() adding 'pattern' arg - man/readProtoFiles.Rd: documenting new 'pattern' argument - src/DescriptorPoolLookup.cpp: enhanced error message - inst/unitTests/runit.golden.message.R: new unit test for repeated fields fixed (which was issue addressed earlier) - inst/runit.import.R: new unit test for non-existing file 2011-01-07 Dirk Eddelbuettel * Applied patch by Murray Stokely providing all the following: - src/S4_classes.h: new 'name' and 'full_name' slots - R/00classes.R: idem - R/wrapper_EnumDescriptor.R: fix typo now permitting function call - src/wrapper_EnumDescriptor.cpp: add a bounds check - src/wrapper_EnumValueDescriptor.cpp: add a new name method - inst/unitTests/runit.enums.R: add new unit test * man/EnumValueDescriptor-class.Rd: Add documentation for name and full_name 2010-10-20 Dirk Eddelbuettel * inst/doc/Makefile: do not remove the pdf in 'clean' * inst/unitTests/runit.addressbook.R: stick 'book' into global env. 2010-10-18 Dirk Eddelbuettel * DESCRIPTION: Release 0.2.1 * ChangeLog: moved from inst/ * inst/NEWS: moved from top-level to that it gets installed with package 2010-10-13 Dirk Eddelbuettel * src/*: applied patch by Koert Kuipers to support raw bytes * inst/unitTests/runit.bytes.R: also added unit test by Koert 2010-09-11 Dirk Eddelbuettel * DESCRIPTION: Release 0.2.0 2010-09-10 Romain Francois * man/readASCII.Rd: Rd documentation for readASCII 2010-08-20 Romain Francois * R/read/.R: New readASCII method 2010-08-12 Romain Francois * src/*: restore R CMD check 2010-08-04 Dirk Eddelbuettel * inst/unitTests/runit.addressbook.R: start of new unit tests 2010-07-30 Romain Francois * src/*: correct many small errors so that the vignette builds again 2010-02-02 Dirk Eddelbuettel * configure.in: More rigorous checks for ProtoBuf headers, library, mininal version as well as availability of pkg-config. 2010-02-01 Dirk Eddelbuettel * inst/ChangeLog: added 2010-02-01 Romain Francois * Release 0.1-0 * [r274] /pkg/man/RProtoBuf-package.Rd: tidying up * [r273] /pkg/inst/doc/unitTests-results: * [r272] /pkg/inst/doc/unitTests/RProtoBuf-unitTests.R: minor cleanups for the unit test vignette (same as in Rcpp) * [r271] /pkg/DESCRIPTION, /pkg/inst/doc/unitTests/RProtoBuf-unitTests.R: OS_type: unix (for now) * [r270] /pkg/DESCRIPTION: version bump to 0.1-0 * [r269] /pkg/inst/doc/Makefile, /pkg/inst/doc/RProtoBuf-unitTests.R[DEL], /pkg/inst/doc/RProtoBuf-unitTests.Rnw, /pkg/inst/doc/unitTests, /pkg/inst/doc/unitTests/RProtoBuf-unitTests.R: minor cleanups for the unit test vignette (same as in Rcpp) 2010-01-23 Romain Francois * [r268] /pkg/inst/doc/Makefile, /pkg/inst/doc/RProtoBuf-unitTests.R, /pkg/inst/doc/RProtoBuf-unitTests.Rnw, /pkg/inst/doc/RProtoBuf-unitTests.Rnw.brew[DEL]: borrow simpler unit test vignette from Rcpp 2010-01-11 Romain Francois * [r267] /pkg/DESCRIPTION, /pkg/src/DescriptorPoolLookup.cpp, /pkg/src/rprotobuf.h: adapt to Rcpp::wrap 2009-12-29 Romain Francois * [r266] /pkg/DESCRIPTION, /pkg/inst/unitTests/runit.golden.message.R, /pkg/src/DescriptorPoolLookup.cpp: adapt to recent changes in Rcpp 2009-12-27 Romain Francois * [r265] /pkg/inst/unitTests/data/unittest.proto, /pkg/inst/unitTests/runit.golden.message.R, /pkg/src/constructors.cpp, /pkg/src/lookup.cpp: enum might not have containing types, which used to bomb new_RS4_EnumDescriptor. fixed and unit tested * [r264] /pkg/inst/doc, /pkg/inst/doc/Makefile, /pkg/inst/doc/RProtoBuf-unitTests.Rnw.brew: a bug in .tearDown prevented the unit tests from working properly 2009-12-26 Romain Francois * [r263] /pkg/inst/doc/Makefile, /pkg/inst/doc/RProtoBuf-unitTests.Rnw.brew, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/inst/unitTests/runit.golden.message.R[CPY], /pkg/inst/unitTests/runit.golden_message.R[DEL]: force cleaning pdfs before vignette creation * [r262] /pkg/src/lookup.cpp: not sorting manually anymore since std::set does it for free * [r261] /pkg/inst/unitTests/runit.draft.R[DEL], /pkg/inst/unitTests/runit.error.R[DEL], /pkg/inst/unitTests/runit.golden_message.R: started adding some proper tests * [r260] /pkg/DESCRIPTION, /pkg/src/DescriptorPoolLookup.cpp: using Rcpp >= 0.7.0.2 * [r259] /pkg/R/internals.R, /pkg/inst/unitTests/data/unittest.proto, /pkg/src/DescriptorPoolLookup.cpp, /pkg/src/DescriptorPoolLookup.h, /pkg/src/RSourceTree.cpp, /pkg/src/RSourceTree.h, /pkg/src/RWarningErrorCollector.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: fixed importing and use set in DescriptorPoolLookup * [r258] /pkg/inst/doc/Makefile, /pkg/inst/unitTests/data, /pkg/inst/unitTests/data/unittest.proto, /pkg/inst/unitTests/data/unittest_import.proto: added utils as default package in vignette makefile 2009-12-26 Dirk Eddelbuettel * [r257] /pkg/tests/doRUnit.R: wd var no longer needed either 2009-12-26 Romain Francois * [r256] /pkg/DESCRIPTION, /pkg/NAMESPACE, /pkg/cleanup, /pkg/inst/doc/Makefile, /pkg/inst/doc/RProtoBuf-unitTests.Rnw[DEL], /pkg/inst/doc/RProtoBuf-unitTests.Rnw.brew, /pkg/inst/unitTests/runTests.R, /pkg/inst/unitTests/runit.draft.R, /pkg/inst/unitTests/runit.error.R, /pkg/tests/doRUnit.R: revised display of information in unit test vignette * [r255] /pkg/NAMESPACE, /pkg/R/unit_tests.R, /pkg/inst/doc/RProtoBuf-unitTests.Rnw, /pkg/inst/unitTests, /pkg/inst/unitTests/runTests.R, /pkg/inst/unitTests/runit.draft.R, /pkg/tests, /pkg/tests/doRUnit.R: prepare for unit testing * [r254] /pkg/DESCRIPTION, /pkg/src/as.cpp, /pkg/src/rprotobuf.h: remove the external_pointer experiment (now in package CPP) 2009-12-24 Dirk Eddelbuettel * [r253] /pkg/src/ConnectionCopyingOutputStream.cpp, /pkg/src/ConnectionInputStream.cpp, /pkg/src/ConnectionOutputStream.cpp, /pkg/src/as.cpp, /pkg/src/rprotobuf.cpp: as.cpp: comment out unused rcpp namespace to fix odd "does not build on amd64" issue found by Saptarshi other files: minimal tweaks to shut 'g++ -Wall' up 2009-12-22 Romain Francois * [r252] /pkg/src/rprotobuf.h: .3 2009-12-20 Romain Francois * [r251] /pkg/DESCRIPTION, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/src/DescriptorPoolLookup.cpp, /pkg/src/as.cpp, /pkg/src/rprotobuf.h: start to use Rcpp 0.7.0 features 2009-12-19 Romain Francois * [r250] /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/src/rprotobuf.h: more completion for streams, and removed debugging messages which resulted in vignette crashing 2009-12-18 Romain Francois * [r249] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/wrapper_CodedOutputStream.R, /pkg/man/ZeroCopyOutputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: added methods for ZeroCopyOutputStream (actually using CodedOutputStream) 2009-12-17 Romain Francois * [r248] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/wrapper_CodedInputStream.R, /pkg/R/wrapper_CodedOutputStream.R, /pkg/man/ZeroCopyOutputStream-class.Rd, /pkg/man/completion.Rd, /pkg/src/streams.cpp: +WriteRaw.ZeroCopyOutoutStream and added completion for ZeroCopy{In,Out}outStream * [r247] /pkg/NAMESPACE, /pkg/R/wrapper_CodedInputStream.R, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ReadVarint64 2009-12-16 Romain Francois * [r246] /pkg/NAMESPACE, /pkg/R/wrapper_CodedInputStream.R, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ReadLittleEndian{32,64} * [r245] /pkg/NAMESPACE, /pkg/R/wrapper_CodedInputStream.R, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ReadVarint32 * [r244] /pkg/NAMESPACE, /pkg/R/wrapper_CodedInputStream.R, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ReadString * [r243] /pkg/src/rprotobuf.h: passing R CMD check again. solved problem related to finalization of Message* * [r242] /pkg/inst/doc/RProtoBuf-unitTests.Rnw[DEL]: * [r241] /pkg/inst/doc/RProtoBuf-unitTests.Rnw: * [r240] /pkg/R/wrapper_CodedInputStream.R, /pkg/man/ArrayInputStream-class.Rd, /pkg/src/extractors.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h, /pkg/src/set.cpp, /pkg/src/streams.cpp: passing R CMD check again. solved problem related to finalization of Message* * [r239] /pkg/src/constructors.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: finalizer for messages * [r238] /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: also use ZeroCopyOutputStreamWrapper * [r237] /pkg/R/wrapper_CodedInputStream.R, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: using ZeroCopyInputStreamWrapper * [r236] /pkg/src/ZeroCopyOutputStreamWrapper.cpp, /pkg/src/ZeroCopyOutputStreamWrapper.h: + ZeroCopyOutputStreamWrapper C++ class * [r235] /pkg/src/ZeroCopyInputStreamWrapper.cpp, /pkg/src/ZeroCopyInputStreamWrapper.h, /pkg/src/streams.cpp: added ZeroCopyInputStreamWrapper that wraps together a zcis and a cis, so that there is no need to create a cis each time 2009-12-15 Romain Francois * [r234] /pkg/NAMESPACE, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: added ReadRaw.ZeroCopyInputSytream * [r233] /pkg/src/ConnectionCopyingInputStream.cpp, /pkg/src/ConnectionCopyingInputStream.h, /pkg/src/ConnectionCopyingOutputStream.cpp, /pkg/src/ConnectionCopyingOutputStream.h, /pkg/src/ConnectionInputStream.cpp, /pkg/src/ConnectionInputStream.h, /pkg/src/ConnectionOutputStream.cpp, /pkg/src/ConnectionOutputStream.h, /pkg/src/read.cpp, /pkg/src/streams.cpp: rework Connection{In,Out}putStream * [r232] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/ConnectionInputStream-class.Rd, /pkg/man/ConnectionInputStream-methods.Rd, /pkg/man/ConnectionOutputStream-class.Rd, /pkg/man/ConnectionOutputStream-methods.Rd, /pkg/src/ConnectionInputStream.cpp, /pkg/src/ConnectionInputStream.h, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: added (R side of and not yet functional, but hey) Connection{In,Out}putStream classes and methods 2009-12-14 Romain Francois * [r231] /pkg/man/Descriptor-class.Rd[CPY], /pkg/man/EnumDescriptor-class.Rd[CPY], /pkg/man/EnumValueDescriptor-class.Rd[CPY], /pkg/man/FieldDescriptor-class.Rd[CPY], /pkg/man/FileDescriptor-class.Rd[CPY], /pkg/man/Message-class.Rd[CPY], /pkg/man/MethodDescriptor-class.Rd[CPY], /pkg/man/ServiceDescriptor-class.Rd[CPY], /pkg/man/protobufDescriptor-class.Rd[DEL], /pkg/man/protobufEnumDescriptor-class.Rd[DEL], /pkg/man/protobufEnumValueDescriptor-class.Rd[DEL], /pkg/man/protobufFieldDescriptor-class.Rd[DEL], /pkg/man/protobufFileDescriptor-class.Rd[DEL], /pkg/man/protobufMessage-class.Rd[DEL], /pkg/man/protobufMethodDescriptor-class.Rd[DEL], /pkg/man/protobufServiceDescriptor-class.Rd[DEL]: remove the 'protobuf' prefix of Rd file names * [r230] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/FileInputStream-class.Rd, /pkg/man/FileInputStream-methods.Rd, /pkg/man/FileOutputStream-class.Rd, /pkg/man/FileOutputStream-methods.Rd, /pkg/man/GetErrno-methods.Rd, /pkg/man/SetCloseOnDelete-methods.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +File{In,Out}putStream classes and methods * [r229] /pkg/NAMESPACE, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/ArrayOutputStream-class.Rd, /pkg/man/ArrayOutputStream-methods.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ArrayOutputStream class and constructor method 2009-12-12 Romain Francois * [r228] /pkg/R/wrapper_ZeroCopyInputStream.R: added some invisible's * [r227] /pkg/R/00classes.R, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/ArrayInputStream-class.Rd, /pkg/man/ArrayInputStream-methods.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: allow block size for ArrayInputStream * [r226] /java/src/org/rproject/rprotobuf/ProtobufHttpServer.java, /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/ArrayInputStream-class.Rd, /pkg/man/ArrayInputStream-methods.Rd, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/man/ZeroCopyOutputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ArrayInputStream class 2009-12-11 Romain Francois * [r225] /pkg/R/00classes.R, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/man/ZeroCopyOutputStream-class.Rd, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ZeroCopyOutputStream S4 class * [r224] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/wrapper_ZeroCopyInputStream.R, /pkg/man/BackUp-methods.Rd, /pkg/man/ByteCount-methods.Rd, /pkg/man/Next-methods.Rd, /pkg/man/Skip-methods.Rd, /pkg/man/ZeroCopyInputStream-class.Rd, /pkg/src/mutators.cpp, /pkg/src/rpc_over_http.cpp, /pkg/src/rprotobuf.h, /pkg/src/streams.cpp: +ZeroCopyInputStream S4 class * [r223] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/man/CodedInputStream-class.Rd[DEL], /pkg/src/CodedInputStream_wrapper.cpp[DEL], /pkg/src/constructors.cpp, /pkg/src/rprotobuf.h: changed my mind, don't want to expose CodedInputStream (yet) * [r222] /pkg/src/CodedInputStream_wrapper.cpp, /pkg/src/constructors.cpp, /pkg/src/rprotobuf.h: added constructor and finalizer for CodedInputStream * [r221] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/rpc.R, /pkg/man/CodedInputStream-class.Rd, /pkg/man/RpcHTTP-class.Rd, /pkg/src/SocketCopyingInputStream.cpp, /pkg/src/rpc_over_http.cpp, /pkg/src/rprotobuf.h: added RpcHTTP@root slot, and CodedInputStream class 2009-12-10 Romain Francois * [r220] /pkg/inst/proto/helloworld.proto, /pkg/src/DescriptorPoolLookup.cpp, /pkg/src/DescriptorPoolLookup.h, /pkg/src/lookup.cpp, /pkg/src/methods.cpp, /pkg/src/read.cpp, /pkg/src/rpc_over_http.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: now using runtime descriptors correctly * [r219] /java/build.xml, /java/proto/helloworld.proto, /java/src/org/rproject/rprotobuf/HelloWorldInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufHandler.java, /java/src/org/rproject/rprotobuf/ProtobufMethodInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufMethodPool.java: added hello world example * [r218] /java/src/org/rproject/rprotobuf/EchoInvoker.java, /java/src/org/rproject/rprotobuf/MethodImplementation.java, /java/src/org/rproject/rprotobuf/ProtobufMethodPool.java: added annotation (not used yet) * [r217] /java/build.xml, /java/proto, /java/proto/addressbook.proto, /java/src/org/rproject/rprotobuf/EchoInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufMethodInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufMethodPool.java: more generic java code 2009-12-09 Romain Francois * [r216] /java/start.sh: added convenience start script for the java server * [r215] /java/src/org/rproject/rprotobuf/ProtobufMethodPool.java: more flexible java server code * [r214] /java/README, /java/build.xml, /java/lib, /java/lib/protobuf-java-2.2.0.jar, /java/src/org/rproject/rprotobuf/EchoInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufHandler.java, /java/src/org/rproject/rprotobuf/ProtobufMethodInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufMethodPool.java, /pkg/inst/proto/addressbook.proto: more flexible java server code * [r213] /java/README, /java/src/org/rproject/rprotobuf/ProtobufHandler.java, /java/src/org/rproject/rprotobuf/ProtobufHttpServer.java, /java/src/org/rproject/rprotobuf/ProtobufMethodInvoker.java, /java/src/org/rproject/rprotobuf/ProtobufMethodPool.java, /pkg/src/rpc_over_http.cpp: functional rpc over http R client and java server 2009-12-08 Romain Francois * [r212] /pkg/src/channel.cpp[DEL], /pkg/src/rpc_over_http.cpp, /pkg/src/rprotobuf.h: started to work on rpc over http * [r211] /java, /java/build.properties, /java/build.xml, /java/src, /java/src/org, /java/src/org/rproject, /java/src/org/rproject/rprotobuf, /java/src/org/rproject/rprotobuf/ProtobufHttpServer.java: added dummy java rpc over http server * [r210] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/rpc.R, /pkg/man/RpcHTTP-class.Rd, /pkg/man/invokeLocally.Rd: added invoke, removed invokeLocally, added RpcHTTP class to represent the rpc over http protocol 2009-12-08 Dirk Eddelbuettel * [r209] /pkg/R/listPeople.R, /pkg/src/clear_person_R.cpp, /pkg/src/list_people_R.cpp: minor robustification against empty addressbook file 2009-12-06 Dirk Eddelbuettel * [r208] /pkg/NAMESPACE, /pkg/R/addPerson.R, /pkg/man/addPerson.Rd, /pkg/src/clear_person_R.cpp: added clearPerson() support with kudos to Romain as usual :) 2009-12-06 Romain Francois * [r207] /pkg/inst/proto/protobufrpc.proto[DEL]: not using protobuf-rpc anymore * [r206] /pkg/src/DescriptorPoolLookup.cpp, /pkg/src/EnumDescriptor_wrapper.cpp, /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/Makevars.in, /pkg/src/RSourceTree.cpp, /pkg/src/RSourceTree.h, /pkg/src/RWarningErrorCollector.cpp, /pkg/src/RWarningErrorCollector.h, /pkg/src/RconnectionCopyingInputStream.h, /pkg/src/ServiceDescriptor_wrapper.cpp, /pkg/src/SocketCopyingInputStream.h, /pkg/src/add.cpp, /pkg/src/as.cpp, /pkg/src/ascharacter.cpp, /pkg/src/aslist.cpp, /pkg/src/channel.cpp, /pkg/src/clear.cpp, /pkg/src/clone.cpp, /pkg/src/completion.cpp, /pkg/src/constructors.cpp, /pkg/src/containing_type.cpp, /pkg/src/extractors.cpp, /pkg/src/field_count.cpp, /pkg/src/fileDescriptor.cpp, /pkg/src/has.cpp, /pkg/src/identical.cpp, /pkg/src/initialized.cpp, /pkg/src/length.cpp, /pkg/src/lookup.cpp, /pkg/src/merge.cpp, /pkg/src/methods.cpp, /pkg/src/mutators.cpp, /pkg/src/name.cpp, /pkg/src/read.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp, /pkg/src/set.cpp, /pkg/src/size.cpp, /pkg/src/swap.cpp: not using using * [r205] /pkg/src/RTcpChannel.cpp[DEL]: removing * [r204] /pkg/src/RTcpChannel.h[DEL]: removing * [r203] /pkg/src/RTcpChannel.cpp: ùù * [r202] /pkg/src/RTcpChannel.h: ùù * [r201] /pkg/DESCRIPTION, /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/EnumDescriptor_wrapper.R, /pkg/R/EnumValueDescriptor_wrapper.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/MethodDescriptor_wrapper.R, /pkg/R/ServiceDescriptor_wrapper.R, /pkg/R/add.R, /pkg/R/aslist.R, /pkg/R/clear.R, /pkg/R/clone.R, /pkg/R/completion.R, /pkg/R/containing_type.R, /pkg/R/debug_string.R, /pkg/R/descriptor.R, /pkg/R/exceptions.R, /pkg/R/field_count.R, /pkg/R/has.R, /pkg/R/identical.R, /pkg/R/initialized.R, /pkg/R/merge.R, /pkg/R/read.R, /pkg/R/rpc.R, /pkg/R/serialize.R, /pkg/R/set.R, /pkg/R/size.R, /pkg/R/swap.R, /pkg/R/with.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/P.Rd, /pkg/man/RProtoBuf-package.Rd, /pkg/man/add.Rd, /pkg/man/asMessage.Rd, /pkg/man/aslist.Rd, /pkg/man/bytesize.Rd, /pkg/man/clear.Rd, /pkg/man/clone.Rd, /pkg/man/completion.Rd, /pkg/man/containing_type-methods.Rd, /pkg/man/descriptor.Rd, /pkg/man/enum_type.Rd, /pkg/man/enum_type_count.Rd, /pkg/man/fetch.Rd, /pkg/man/field.Rd, /pkg/man/field_count.Rd, /pkg/man/fileDescriptor.Rd, /pkg/man/has.Rd, /pkg/man/invokeLocally.Rd, /pkg/man/isInitialized.Rd, /pkg/man/is_extension.Rd, /pkg/man/label.Rd, /pkg/man/merge.Rd, /pkg/man/name.Rd, /pkg/man/nested_type.Rd, /pkg/man/nested_type_count.Rd, /pkg/man/number.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/man/protobufEnumDescriptor-class.Rd, /pkg/man/protobufEnumValueDescriptor-class.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/man/protobufFileDescriptor-class.Rd, /pkg/man/protobufMessage-class.Rd, /pkg/man/protobufMethodDescriptor-class.Rd, /pkg/man/protobufServiceDescriptor-class.Rd, /pkg/man/read.Rd, /pkg/man/set.Rd, /pkg/man/size.Rd, /pkg/man/sizegets.Rd, /pkg/man/swap.Rd, /pkg/man/type.Rd, /pkg/man/with.Rd, /pkg/src/add.cpp, /pkg/src/constructors.cpp, /pkg/src/extractors.cpp, /pkg/src/lookup.cpp, /pkg/src/merge.cpp, /pkg/src/mutators.cpp, /pkg/src/read.cpp, /pkg/src/rprotobuf.cpp: removing the protobuf prefix of the S4 classes 2009-12-05 Romain Francois * [r200] /pkg/NAMESPACE, /pkg/R/MethodDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/R/rpc.R, /pkg/man/protobufMethodDescriptor-class.Rd: + {in,out}put_type.MethodDescriptor * [r199] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/ServiceDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/man/protobufServiceDescriptor-class.Rd: + method.ServiceDescriptor * [r198] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/EnumValueDescriptor_wrapper.R, /pkg/R/ServiceDescriptor_wrapper.R, /pkg/man/protobufServiceDescriptor-class.Rd, /pkg/src/ServiceDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: added some methods for ServiceDescriptor * [r197] /pkg/R/EnumDescriptor_wrapper.R, /pkg/man/protobufEnumValueDescriptor-class.Rd: added EnumValueDescriptor class * [r196] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/EnumDescriptor_wrapper.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/R/debug_string.R, /pkg/R/field_count.R, /pkg/man/protobufDescriptor-class.Rd, /pkg/man/protobufEnumDescriptor-class.Rd, /pkg/man/protobufEnumValueDescriptor-class.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/EnumDescriptor_wrapper.cpp, /pkg/src/as.cpp, /pkg/src/ascharacter.cpp, /pkg/src/constructors.cpp, /pkg/src/rprotobuf.h: added EnumValueDescriptor class 2009-12-05 Dirk Eddelbuettel * [r195] /pkg/inst/doc/RProtoBuf.Rnw: added some stuff near the beginning about 'static' use which motivates the dynamic use nicely some spit and polish for intro as well 2009-12-04 Romain Francois * [r194] /pkg/R/00classes.R, /pkg/man/protobufEnumDescriptor-class.Rd, /pkg/src/EnumDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: +length.protobufEnumDescriptor * [r193] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: +{message,enum}_type.FieldDescriptor * [r192] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: + {has_default_value,default_value}.FieldDescriptor~ * [r191] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/man/label.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: +{label,is_repeated,is_required,is_optional}.FieldDescriptor * [r190] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/man/type.Rd, /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: +{type.cpp_type}.FieldDescriptor * [r189] /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: +number.FieldDescriptor * [r188] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/completion.R, /pkg/man/number.Rd, /pkg/man/protobufFieldDescriptor-class.Rd: +number.FieldDescriptor * [r187] /pkg/TODO: updated TODO * [r186] /pkg/R/field_count.R: minor fix * [r185] /pkg/NAMESPACE, /pkg/R/FieldDescriptor_wrapper.R, /pkg/R/field_count.R, /pkg/man/is_extension.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/FieldDescriptor_wrapper.cpp, /pkg/src/rprotobuf.h: + is_extension.FieldDescriptor * [r184] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/field_count.R, /pkg/man/enum_type.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/src/field_count.cpp, /pkg/src/rprotobuf.h: + enum_type.Descriptor method 2009-12-03 Romain Francois * [r183] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/field_count.R, /pkg/man/nested_type.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/src/field_count.cpp, /pkg/src/rprotobuf.h: +nested_type.Descriptor method * [r182] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/field_count.R, /pkg/man/enum_type_count.Rd, /pkg/man/field.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/src/field_count.cpp, /pkg/src/rprotobuf.h: added field.Descriptor method * [r181] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/field_count.R, /pkg/man/nested_type_count.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/src/field_count.cpp, /pkg/src/rprotobuf.h: nested_type_count.protobufDescriptor * [r180] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/field_count.R, /pkg/man/field_count.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/src/field_count.cpp, /pkg/src/rprotobuf.h: + field_count.protobufDescriptor method * [r179] /pkg/DESCRIPTION: added BugReports description field * [r178] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/containing_type.R, /pkg/man/containing_type-methods.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/man/protobufEnumDescriptor-class.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/containing_type.cpp, /pkg/src/rprotobuf.h: added containing_type.protobuf{Descriptor,FieldDescriptor,EnumDescriptor} 2009-12-03 Dirk Eddelbuettel * [r177] /pkg/NAMESPACE, /pkg/R/addPerson.R, /pkg/man/addPerson.Rd, /pkg/man/listPeople.Rd, /pkg/src/add_person_R.cpp: added simple addPerson() R function, manual page and C++ implementation 2009-12-02 Romain Francois * [r176] /pkg/src/initialized.cpp: isInitialized gains the names of the fields that are not initialized * [r175] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/asMessage.Rd, /pkg/src/as.cpp, /pkg/src/rprotobuf.h: added asMessage function * [r174] /pkg/NAMESPACE, /pkg/man/throw.Rd[DEL], /pkg/src/exceptions.cpp: throw not exported anymore * [r173] /pkg/man/protobufFileDescriptor-class.Rd: added name.protobufFileDescriptor * [r172] /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/src/name.cpp, /pkg/src/rprotobuf.h: added more fileDescriptor methods * [r171] /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/descriptor.R, /pkg/R/rpc.R, /pkg/man/fileDescriptor.Rd, /pkg/src/fileDescriptor.cpp, /pkg/src/rprotobuf.h: added more fileDescriptor methods * [r170] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/aslist.R, /pkg/man/aslist.Rd, /pkg/man/protobufServiceDescriptor-class.Rd, /pkg/src/aslist.cpp, /pkg/src/completion.cpp, /pkg/src/rprotobuf.h: added as.list.protobufServiceDescriptor * [r169] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/rpc.R, /pkg/man/completion.Rd, /pkg/man/protobufServiceDescriptor-class.Rd, /pkg/src/extractors.cpp, /pkg/src/rprotobuf.h: misc * [r168] /pkg/R/00classes.R, /pkg/man/name.Rd, /pkg/src/name.cpp, /pkg/src/rprotobuf.h: more name methods * [r167] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/name.Rd, /pkg/man/protobufServiceDescriptor-class.Rd, /pkg/src/name.cpp, /pkg/src/rprotobuf.h: added name method and implementations for Decriptor and FieldDescriptor 2009-12-01 Romain Francois * [r166] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/aslist.R, /pkg/R/completion.R, /pkg/man/aslist.Rd, /pkg/man/completion.Rd, /pkg/man/protobufFileDescriptor-class.Rd, /pkg/src/aslist.cpp, /pkg/src/completion.cpp, /pkg/src/rprotobuf.h: added as.list.protobufFileDescriptor * [r165] /pkg/R/debug_string.R, /pkg/src/ascharacter.cpp, /pkg/src/rprotobuf.h: completion, toString, as.character for protobufFileDescriptor * [r164] /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/man/completion.Rd, /pkg/man/protobufFileDescriptor-class.Rd: completion, toString, as.character for protobufFileDescriptor * [r163] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/descriptor.R, /pkg/R/rpc.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/fileDescriptor.Rd, /pkg/man/protobufFileDescriptor-class.Rd, /pkg/src/constructors.cpp, /pkg/src/fileDescriptor.cpp, /pkg/src/rprotobuf.h: added protobufFileDescriptor S4 class + fileDescriptor method 2009-11-30 Romain Francois * [r162] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/rpc.R, /pkg/src/RTcpChannel.cpp, /pkg/src/RTcpChannel.h, /pkg/src/SocketCopyingInputStream.cpp, /pkg/src/SocketCopyingInputStream.h, /pkg/src/channel.cpp, /pkg/src/rprotobuf.h: playing with sockets 2009-11-23 Romain Francois * [r161] /www/index.php: update the page 2009-11-22 Romain Francois * [r160] /pkg/src/RTcpChannel.cpp, /pkg/src/RTcpChannel.h: * [r159] /pkg/src/sisocks.h: added sisocks.h header from Rserve * [r158] /pkg/src/Makevars.in, /pkg/src/RTcpChannel.cpp, /pkg/src/RTcpChannel.h: slowly putting things in place for rpc (inspired from the protobuf-rpc project) * [r157] /pkg/src/serialize.cpp: discovered the SerializeToArray method, simplify code * [r156] /pkg/src/mutators.cpp, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp: allow messages as input of string and bytes fields * [r155] /pkg/inst/proto/protobufrpc.proto, /pkg/src: added proto file from protobufrpc project * [r154] /pkg/R/set.R, /pkg/src/Makevars.in, /pkg/src/mutators.cpp: allow raw vector as input of string or bytes fields 2009-11-21 Romain Francois * [r153] /www/index.php: start to make the project page * [r152] /pkg/DESCRIPTION: suggesting svUnit (unit tests) * [r151] /pkg/inst/doc, /pkg/inst/doc/RProtoBuf-unitTests.Rnw: added (empty) unit test vignette * [r150] /pkg/inst/doc/RProtoBuf.Rnw: update the main vignette to show reading from payload * [r149] /pkg/R/read.R, /pkg/R/serialize.R, /pkg/man/read.Rd, /pkg/src/read.cpp, /pkg/src/rprotobuf.h: reading messages from raw vector (payload) * [r148] /pkg/NEWS, /pkg/R/read.R: open the connection at start on read 2009-11-18 Romain Francois * [r147] /pkg/inst/proto/addressbook.proto: for the quickref vignette in one page 2009-11-18 Dirk Eddelbuettel * [r146] /pkg/cleanup: also remove temp files for quickref vignette 2009-11-17 Romain Francois * [r145] /pkg/src/mutators.cpp, /pkg/src/size.cpp, /pkg/src/swap.cpp: removed the conditional compiling for protobuf 2.1 * [r144] /pkg/man/invokeLocally.Rd, /pkg/man/protobufMethodDescriptor-class.Rd, /pkg/man/protobufServiceDescriptor-class.Rd: pleasing R CMD check 2009-11-16 Dirk Eddelbuettel * [r143] /pkg/configure, /pkg/configure.in: further improvements to configure via pkg-config * [r142] /pkg/cleanup: let cleanup nuke a few LaTeX files 2009-11-16 Romain Francois * [r141] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/debug_string.R, /pkg/R/rpc.R, /pkg/TODO, /pkg/inst/proto/addressbook.proto, /pkg/man/protobufMethodDescriptor-class.Rd, /pkg/man/protobufServiceDescriptor-class.Rd, /pkg/src/ascharacter.cpp, /pkg/src/constructors.cpp, /pkg/src/lookup.cpp, /pkg/src/methods.cpp, /pkg/src/read.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: starting to play with (local) rpc services 2009-11-16 Dirk Eddelbuettel * [r140] /pkg/configure: updated configure * [r139] /pkg/DESCRIPTION, /pkg/configure.in: updated configure.in to use pkg-config updated DESCRIPTON 2009-11-16 Romain Francois * [r138] /pkg/inst/doc: * [r137] /pkg/inst/doc/RProtoBuf-quickref.Rnw: added quick ref vignette * [r136] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/add.R, /pkg/R/completion.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/add.Rd, /pkg/src/add.cpp, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.h: added add method to add values to a repeated field 2009-11-14 Romain Francois * [r135] /pkg/NAMESPACE, /pkg/R/identical.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/protobufMessage-class.Rd, /pkg/src/identical.cpp, /pkg/src/rprotobuf.h: added all.equal * [r134] /pkg/DESCRIPTION, /pkg/man/RProtoBuf-package.Rd: updated DESCRIPTION and package help page * [r133] /pkg/R/identical.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/protobufMessage-class.Rd: added == and != * [r132] /pkg/NAMESPACE, /pkg/R/identical.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/protobufMessage-class.Rd, /pkg/src/identical.cpp, /pkg/src/rprotobuf.h: added identical method to compare two messages * [r131] /pkg/inst/doc/RProtoBuf.Rnw: some more vignette content 2009-11-13 Romain Francois * [r130] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/debug_string.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/protobufDescriptor-class.Rd, /pkg/man/protobufEnumDescriptor-class.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/man/protobufMessage-class.Rd: added toString as an alias to as.character * [r129] /pkg/inst/doc/RProtoBuf.Rnw: some more vignette content * [r128] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/set.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/fetch.Rd, /pkg/src/extractors.cpp, /pkg/src/rprotobuf.h, /pkg/src/set.cpp: added fetch method * [r127] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/set.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/completion.Rd, /pkg/man/set.Rd, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.h: added set method 2009-11-13 Dirk Eddelbuettel * [r126] /pkg/inst/doc/RProtoBuf.Rnw: a few more updates * [r125] /pkg/inst/doc/RProtoBuf.Rnw: few small updates and tweaks * [r124] /pkg/DESCRIPTION: updated DESCRIPTION 2009-11-12 Romain Francois * [r123] /pkg/inst/doc/RProtoBuf.Rnw: some more vignette content * [r122] /pkg/R/00classes.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/src/rprotobuf.h: added $ for protobufFieldDescriptor (for completeness) * [r121] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/descriptor.R, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/man/descriptor.Rd, /pkg/src/extractors.cpp: added descriptor method * [r120] /pkg/R/internals.R, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: added (unexported) function getProtobufLibVersion * [r119] /pkg/src/mutators.cpp: use the correct version for the test #if GOOGLE_PROTOBUF_VERSION < 200200 * [r118] /pkg/src/mutators.cpp: use the correct version for the test #if GOOGLE_PROTOBUF_VERSION < 200200 * [r117] /pkg/inst/doc/RProtoBuf.Rnw: no hardcoding Sweave location * [r116] /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/inst/doc/RProtoBuf.Rnw: some more vignette content 2009-11-12 Dirk Eddelbuettel * [r115] /pkg/src/mutators.cpp: make -Wall happy by commenting out one var, and providing more switch targets 2009-11-12 Romain Francois * [r114] /pkg/inst/doc/RProtoBuf.Rnw: some more vignette content * [r113] /pkg/inst/doc/RProtoBuf.Rnw, /pkg/src/size.cpp, /pkg/src/swap.cpp: correct swaping messages with 2.1 libproto * [r112] /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/swap.R, /pkg/demo/addressbook.R, /pkg/inst/doc/RProtoBuf.Rnw: make swap use 1-based indexing * [r111] /pkg/R/00classes.R, /pkg/inst/doc/RProtoBuf.Rnw: some more content on the vignette * [r110] /pkg/src/rprotobuf.cpp: added some code to control which version of the libprotobuf we require (currently 2.1, but will be 2.2 soon) * [r109] /pkg/DESCRIPTION, /pkg/NAMESPACE, /pkg/R/zzz.R, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: added some code to control which version of the libprotobuf we require (currently 2.1, but will be 2.2 soon) * [r108] /pkg/inst/doc, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/src/mutators.cpp, /pkg/src/size.cpp, /pkg/src/swap.cpp: added some conditional compiling to make it work with libprotobuf < 2.2 2009-11-11 Romain Francois * [r107] /pkg/inst/doc/RProtoBuf.Rnw, /pkg/inst/proto/addressbook.proto: some more content for the vignette * [r106] /pkg/inst/doc/RProtoBuf.tex[DEL]: removed tex file * [r105] /pkg/inst/doc, /pkg/inst/doc/RProtoBuf.Rnw, /pkg/inst/doc/RProtoBuf.tex, /pkg/inst/proto/addressbook.proto: started vignette * [r104] /pkg/DESCRIPTION: Rcpp >= 0.6.8 2009-11-10 Romain Francois * [r103] /pkg/R/swap.R, /pkg/demo/addressbook.R: some more code in demo * [r102] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/swap.R, /pkg/man/swap.Rd, /pkg/src/clear.cpp, /pkg/src/rprotobuf.h, /pkg/src/swap.cpp: added swap * [r101] /pkg/R/00classes.R, /pkg/R/clear.R, /pkg/R/completion.R, /pkg/man/clear.Rd, /pkg/src/clear.cpp, /pkg/src/rprotobuf.h, /pkg/src/size.cpp: added field argument to clear * [r100] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/size.R, /pkg/man/size.Rd, /pkg/man/sizegets.Rd, /pkg/src/rprotobuf.h, /pkg/src/size.cpp: + size<- * [r99] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/size.R, /pkg/man/size.Rd, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h, /pkg/src/size.cpp: added size method * [r98] /pkg/src/mutators.cpp: minot tweaks * [r97] /pkg/src/mutators.cpp: fail mutation before resizing * [r96] /pkg/src/mutators.cpp, /pkg/src/rprotobuf.h: nicer and more efficient mutator code (discovered Reflection->RemoveLast method) * [r95] /pkg/R/00classes.R: using a switch in $ * [r94] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/clear.R, /pkg/man/clear.Rd, /pkg/src/aslist.cpp, /pkg/src/clear.cpp, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.h: added clear method * [r93] /pkg/src/RWarningErrorCollector.cpp, /pkg/src/RWarningErrorCollector.h, /pkg/src/rprotobuf.cpp: properly implement MultiFileErrorCollector to send an R warning instead of printing stuff to cout * [r92] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/man/protobufMessage-class.Rd, /pkg/src/extractors.cpp, /pkg/src/mutators.cpp: added [[ and [[<- methods for messages using the declared tag number 2009-11-09 Romain Francois * [r91] /pkg/src/DescriptorPoolLookup.cpp, /pkg/src/DescriptorPoolLookup.h, /pkg/src/lookup.cpp, /pkg/src/rprotobuf.cpp: maintain list of currently known types in attached DescriptorPool 2009-11-09 Dirk Eddelbuettel * [r90] /pkg/src/list_people_R.cpp: remove RcppList implementation which we now get from Rcpp (>= 0.6.7) 2009-11-09 Romain Francois * [r89] /pkg/src/rprotobuf.cpp: using RSourceTree instead of DiskSourceTree * [r88] /pkg/src/RSourceTree.cpp, /pkg/src/RSourceTree.h: adding a simple SourceTree implementation * [r87] /pkg/DESCRIPTION, /pkg/man/RProtoBuf-package.Rd: required Rcpp >= 0.6.7 * [r86] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/initialized.R, /pkg/man/isInitialized.Rd, /pkg/man/protobufMessage-class.Rd, /pkg/src/initialized.cpp, /pkg/src/rprotobuf.h: added isInitialized method * [r85] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/man/protobufMessage-class.Rd, /pkg/src/length.cpp, /pkg/src/rprotobuf.h: added length method for messages * [r84] /pkg/R/internals.R: minor * [r83] /pkg/NAMESPACE, /pkg/R/size.R, /pkg/demo/io.R, /pkg/man/RProtoBuf-package.Rd, /pkg/man/bytesize.Rd, /pkg/src/rprotobuf.h, /pkg/src/size.cpp: added bytesize method * [r82] /pkg/TODO, /pkg/demo/00Index, /pkg/demo/addressbook.R, /pkg/demo/io.R, /pkg/src/RconnectionCopyingInputStream.cpp: added io demo showing how to use binary connections to read and write messages 2009-11-08 Romain Francois * [r81] /pkg/src/RconnectionCopyingInputStream.cpp: minor doc tweaks * [r80] /pkg/src/RconnectionCopyingInputStream.cpp, /pkg/src/RconnectionCopyingInputStream.h: factoring out getReadBinCall * [r79] /pkg/src/RconnectionCopyingInputStream.cpp: minor doc tweaks * [r78] /pkg/R/read.R, /pkg/src/RconnectionCopyingInputStream.cpp, /pkg/src/RconnectionCopyingInputStream.h, /pkg/src/read.cpp, /pkg/src/rprotobuf.h: reading from binary connections * [r77] /pkg/R/read.R, /pkg/R/serialize.R, /pkg/man/read.Rd, /pkg/src/read.cpp, /pkg/src/serialize.cpp: silence R CMD check 2009-11-08 Dirk Eddelbuettel * [r76] /pkg/man/protobufMessage-class.Rd: small correction to tail of example * [r75] /pkg/src/rprotobuf.h: make it work with version 2.1 of ProtoBuf 2009-11-08 Romain Francois * [r74] /pkg/man/protobufMessage-class.Rd: minor doc tweaks * [r73] /pkg/R/serialize.R, /pkg/man/protobufMessage-class.Rd: minor doc tweaks * [r72] /pkg/R/serialize.R, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp: workaround for serializing to binary connections * [r71] /pkg/R/serialize.R, /pkg/src/connections.h, /pkg/src/read.cpp, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp: use partial on serialize and parse to allow message lacking required fields 2009-11-07 Dirk Eddelbuettel * [r70] /pkg/DESCRIPTION: finally set Date svn property on this to have the Date filled in automatically 2009-11-06 Romain Francois * [r69] /pkg/R/serialize.R, /pkg/man/protobufMessage-class.Rd, /pkg/src/read.cpp, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp: serialize message to a file * [r68] /pkg/man/read.Rd: mention the read pseudi method * [r67] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/completion.R, /pkg/R/read.R, /pkg/man/read.Rd, /pkg/src/read.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: reading messages from files 2009-11-05 Dirk Eddelbuettel * [r66] /pkg/src/Makevars.in: simplification in that we no longer need to list all .cpp files as dependants 2009-11-05 Romain Francois * [r65] /pkg/TODO: added services to the TODO list * [r64] /pkg/DESCRIPTION: added more urls and a MailingList field 2009-11-05 Dirk Eddelbuettel * [r63] /pkg/demo/00Index: make 'R CMD check' happy * [r62] /pkg/src/Makevars.in: adjusted Makevars.in for addressbook.proto in inst/proto/ * [r61] /pkg/inst/proto/addressbook.proto[CPY], /pkg/src/addressbook.proto[DEL]: moved addressbook.proto from src/ to inst/proto/ * [r60] /pkg/inst/examples/addressbook.proto[DEL], /pkg/inst/proto/addressbook.proto[DEL]: removed two extra addressbook.proto files 2009-11-05 Romain Francois * [r59] /pkg/NAMESPACE, /pkg/R/merge.R, /pkg/demo/00Index, /pkg/man/merge.Rd, /pkg/src/Makevars.in, /pkg/src/merge.cpp, /pkg/src/rprotobuf.h: + merge * [r58] /pkg/R/clone.R: added clone 2009-11-04 Romain Francois * [r57] /pkg/demo, /pkg/demo/addressbook.R: added demo file 2009-11-04 Dirk Eddelbuettel * [r56] /pkg/src/aslist.cpp, /pkg/src/mutators.cpp, /pkg/src/update.cpp: commented-out two unused variables and init'ed another, all to make 'g++ -Wall' 2009-11-04 Romain Francois * [r55] /pkg/TODO: added TODO * [r54] /pkg/DESCRIPTION, /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/aslist.R, /pkg/R/completion.R, /pkg/R/debug_string.R, /pkg/R/has.R, /pkg/R/with.R, /pkg/man/P.Rd, /pkg/man/RProtoBuf-package.Rd, /pkg/man/aslist.Rd, /pkg/man/clone.Rd, /pkg/man/completion.Rd, /pkg/man/has.Rd, /pkg/man/protobufDescriptor-class.Rd, /pkg/man/protobufEnumDescriptor-class.Rd, /pkg/man/protobufFieldDescriptor-class.Rd, /pkg/man/protobufMessage-class.Rd, /pkg/man/with.Rd, /pkg/src/Makevars.in, /pkg/src/ascharacter.cpp, /pkg/src/aslist.cpp, /pkg/src/clone.cpp, /pkg/src/completion.cpp, /pkg/src/connections.h, /pkg/src/constructors.cpp, /pkg/src/exceptions.cpp, /pkg/src/extractors.cpp, /pkg/src/has.cpp, /pkg/src/lookup.cpp, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp, /pkg/src/update.cpp: lots of updates. fully working mutators 2009-11-02 Dirk Eddelbuettel * [r53] /pkg/src/completion.cpp, /pkg/src/constructors.cpp, /pkg/src/exceptions.cpp, /pkg/src/extractors.cpp, /pkg/src/lookup.cpp, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp: switch from four namespace to just one * [r52] /pkg/src/extractors.cpp: add default initialisation for SEXP to keep g++ -Wall happy 2009-11-02 Romain Francois * [r51] /pkg/src/Makevars.in, /pkg/src/constructors.cpp, /pkg/src/mutators.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: minimal implementation of mutators (only non-repeated fields atm) * [r50] /pkg/R/zzz.R, /pkg/src/lookup.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: enable lookup mechanism (using full path for now) 2009-11-01 Romain Francois * [r49] /pkg/R/zzz.R: added readProtoFiles to simplify importing of proto definitions from package * [r48] /pkg/NAMESPACE, /pkg/R/internals.R, /pkg/R/zzz.R, /pkg/inst/proto, /pkg/inst/proto/addressbook.proto, /pkg/man/readProtoFiles.Rd: added readProtoFiles to simplify importing of proto definitions from packages 2009-10-31 Romain Francois * [r47] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/man/throw.Rd: +Rd.throw * [r46] /pkg/man/protobufFieldDescriptor-class.Rd: +Rd.protobufFieldDescriptor * [r45] /pkg/man/protobufEnumDescriptor-class.Rd: added Rd for protobufEnumDescriptor * [r44] /pkg/R/00classes.R, /pkg/man/protobufDescriptor-class.Rd: added protobufDescriptor type * [r43] /pkg/man/protobufMessage-class.Rd: added Rd for protobufMessage class * [r42] /pkg/NAMESPACE, /pkg/R/debug_string.R, /pkg/man/P.Rd, /pkg/man/listPeople.Rd, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: added Rd for P, implement as.character for protobufMessage and protobufDescriptor * [r41] /pkg/src/constructors.cpp, /pkg/src/rprotobuf.cpp: minor fixes * [r40] /pkg/NAMESPACE, /pkg/R/serialize.R, /pkg/src/Makevars.in, /pkg/src/rprotobuf.h, /pkg/src/serialize.cpp: hooks for serialize method for protobufMessage * [r39] /pkg/NAMESPACE, /pkg/R/exceptions.R, /pkg/src/Makevars.in, /pkg/src/exceptions.cpp, /pkg/src/extractors.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: start playing with Exception handling, we need to call throwException instead of Rf_error in the c code 2009-10-30 Romain Francois * [r38] /pkg/R/exceptions.R, /pkg/src/extractors.cpp: extracting repeated fields, for now repeated messages are just returned as list of 'protobufMessage' objects * [r37] /pkg/NAMESPACE, /pkg/R/completion.R, /pkg/src/Makevars.in, /pkg/src/completion.cpp, /pkg/src/constructors.cpp, /pkg/src/extractors.cpp, /pkg/src/rprotobuf.h: implemented completions for Messages (giving field names) and Descriptors (fields, enums and nested types) * [r36] /pkg/src/constructors.cpp, /pkg/src/extractors.cpp, /pkg/src/fieldtypes.h, /pkg/src/rprotobuf.h: implement extraction of (almost) all types from messages with $ (missing ENUM type) * [r35] /pkg/R/00classes.R, /pkg/src/Makevars.in, /pkg/src/extractors.cpp, /pkg/src/fieldtypes.h, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: prepare the field extraction * [r34] /pkg/R/00classes.R, /pkg/src/constructors.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: implement new.protobufMessage that generates a new mutable Message using the generated Message factory * [r33] /pkg/src/constructors.cpp: some more doc in constructors.cpp * [r32] /pkg/R/internals.R, /pkg/src/constructors.cpp, /pkg/src/lookup.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: use R_NO_REMAP and Rf_ prefixes to avoid name clashes (install, error, ...) 2009-10-29 Romain Francois * [r31] /pkg/R/00classes.R, /pkg/R/internals.R, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: removed hard coded path * [r30] /pkg/R/00classes.R, /pkg/src/constructors.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: added enum types to $.Descriptor * [r29] /pkg/R/00classes.R: added $ extraction of nested types or fields by name * [r28] /pkg/R/00classes.R, /pkg/src/constructors.cpp: added $ extraction of nested types or fields by name * [r27] /pkg/src/Makevars.in, /pkg/src/constructors.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: added $ extraction of nested types or fields by name * [r26] /pkg/R/00classes.R, /pkg/src/rprotobuf.cpp: grab the descriptor from the pool in getProtobufDescriptor 2009-10-29 Dirk Eddelbuettel * [r25] /pkg/src/lookup.cpp: add two simple return() statements to make 'g++ -Wall' happy 2009-10-29 Romain Francois * [r24] /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/R/internals.R, /pkg/src/rprotobuf.cpp: grab the descriptor from the pool in getProtobufDescriptor * [r23] /pkg/R/00classes.R, /pkg/R/internals.R, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: collect information about a proto file * [r22] /pkg/src/lookup.cpp, /pkg/src/rprotobuf.h: objects returns character(0) instead of NULL, more consistent with attach( new.env() ) * [r21] /pkg/R/lookup.R, /pkg/src/Makevars.in, /pkg/src/lookup.cpp, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: added skeleton for lookup mechanism * [r20] /pkg/DESCRIPTION, /pkg/NAMESPACE, /pkg/R/00classes.R, /pkg/src/Makevars.in, /pkg/src/rprotobuf.cpp, /pkg/src/rprotobuf.h: skeleton for R S4 classes representing proto messages as external pointers 2009-10-27 Dirk Eddelbuettel * [r19] /pkg/src/Makevars.in: add CXXPICFLAGS which is needed on amd64 * [r18] /pkg/src/list_people_R.cpp: corrected listPeopleAsList() for special case of person 3 with no phones * [r17] /pkg/src/Makevars.in: support configure and automated build of all pieces incl conversion from proto file to header and source and then object * [r16] /pkg/src/list_people_R.cpp: suppress one more set of g++ warning, align function names * [r15] /pkg/cleanup: add more cleanup targets * [r14] /pkg/R/listPeople.R: align function names with C++ source * [r13] /pkg/configure, /pkg/configure.in: added configure support * [r12] /pkg/src/Makevars[DEL], /pkg/src/Makevars.in[CPY]: moved to Makevars.in and configure, also re-create header and source from proto * [r11] /pkg/src/addressbook.pb.cc[DEL], /pkg/src/addressbook.pb.h[DEL]: removed as they are now recreated * [r10] /pkg/configure.in: beginnings of a configure script, not yet ready * [r9] /pkg/NAMESPACE: added (nested) list support * [r8] /pkg/man/listPeople.Rd: documented (nested) list support * [r7] /pkg/R/listPeople.R: added (nested) list support * [r6] /pkg/src/list_people_R.cpp: add support for R lists, possibly nested this was a good test for Rcpp and should get folded into Rcpp * [r5] /pkg/src/addressbook.pb.cc, /pkg/src/addressbook.pb.h: rebuild with Ubuntu protoc -- probably need to farm this out to a proper Makefile or Makevar target 2009-10-22 Dirk Eddelbuettel * [r4] /pkg/src/list_people_R.cpp: add support for case of no phone entry * [r3] /pkg/src/Makevars: add -lpthread to PKG_LIBS * [r2] /pkg/DESCRIPTION, /pkg/NAMESPACE, /pkg/R, /pkg/R/listPeople.R, /pkg/README, /pkg/cleanup, /pkg/inst, /pkg/inst/examples, /pkg/inst/examples/AddressBookFile, /pkg/inst/examples/addressbook.proto, /pkg/man, /pkg/man/listPeople.Rd, /pkg/src, /pkg/src/Makevars, /pkg/src/addressbook.pb.cc, /pkg/src/addressbook.pb.h, /pkg/src/addressbook.proto, /pkg/src/list_people_R.cpp: A very basic first proof of concept package reading a binary protobuf file 2009-05-28 Stefan Theussl * [r1] /README, /pkg, /www, /www/index.php: R-Forge: updated repository structure RProtoBuf/man/0000755000175100001440000000000012710022354012721 5ustar hornikusersRProtoBuf/man/sizegets.Rd0000644000175100001440000000047612440004312015046 0ustar hornikusers\name{sizegets} \docType{methods} \alias{size<-} \alias{size<--methods} \alias{size<-,Message-method} \title{Set the size of a field} \description{ Sets the size of a repeated field. } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{ sets the size of a message field } }} \keyword{methods} RProtoBuf/man/ServiceDescriptor-class.Rd0000644000175100001440000000337512707407313017772 0ustar hornikusers\name{ServiceDescriptor-class} \Rdversion{1.1} \docType{class} \alias{ServiceDescriptor-class} \alias{as.character,ServiceDescriptor-method} \alias{toString,ServiceDescriptor-method} \alias{show,ServiceDescriptor-method} \alias{$,ServiceDescriptor-method} \alias{[[,ServiceDescriptor-method} \alias{length,ServiceDescriptor-method} \alias{method_count} \alias{method_count-methods} \alias{method_count,ServiceDescriptor-method} \alias{method} \alias{method-methods} \alias{method,ServiceDescriptor-method} \title{Class "ServiceDescriptor"} \description{R representation of Service Descriptors} \section{Objects from the Class}{ TODO } \section{Slots}{ \describe{ \item{\code{pointer}:}{External pointer to a \code{google::protobuf::ServiceDescriptor} C++ object } \item{\code{name}:}{fully qualified name of the service } } } \section{Methods}{ \describe{ \item{as.character}{\code{signature(x = "ServiceDescriptor")}: debug string of the service } \item{toString}{\code{signature(x = "ServiceDescriptor")}: debug string of the service} \item{show}{\code{signature(x = "ServiceDescriptor")}: ... } \item{$}{\code{signature(x = "ServiceDescriptor")}: invoke pseudo methods or retrieve method descriptors contained in this service descriptor. } \item{[[}{\code{signature(x = "ServiceDescriptor")}: extracts methods descriptors contained in this service descriptor} \item{length}{\code{signature(x = "ServiceDescriptor")}: number of \linkS4class{MethodDescriptor} } \item{method_count}{\code{signature(x = "ServiceDescriptor")}: number of \linkS4class{MethodDescriptor} } \item{method}{\code{signature(x = "ServiceDescriptor")}: retrieves a \linkS4class{MethodDescriptor} } } } \author{ Romain Francois } \keyword{classes} RProtoBuf/man/type.Rd0000644000175100001440000000246512440004312014172 0ustar hornikusers\name{type-methods} \alias{type} \alias{type-methods} \alias{cpp_type} \alias{cpp_type-methods} \alias{TYPE_DOUBLE} \alias{TYPE_FLOAT} \alias{TYPE_INT64} \alias{TYPE_UINT64} \alias{TYPE_INT32} \alias{TYPE_FIXED64} \alias{TYPE_FIXED32} \alias{TYPE_BOOL} \alias{TYPE_STRING} \alias{TYPE_GROUP} \alias{TYPE_MESSAGE} \alias{TYPE_BYTES} \alias{TYPE_UINT32} \alias{TYPE_ENUM} \alias{TYPE_SFIXED32} \alias{TYPE_SFIXED64} \alias{TYPE_SINT32} \alias{TYPE_SINT64} \alias{CPPTYPE_INT32} \alias{CPPTYPE_INT64} \alias{CPPTYPE_UINT32} \alias{CPPTYPE_UINT64} \alias{CPPTYPE_DOUBLE} \alias{CPPTYPE_FLOAT} \alias{CPPTYPE_BOOL} \alias{CPPTYPE_ENUM} \alias{CPPTYPE_STRING} \alias{CPPTYPE_MESSAGE} \title{Gets the type or the C++ type of a field} \description{ Gets the type or the C++ type of a field } \arguments{ \item{object}{A \linkS4class{FieldDescriptor} object.} \item{as.string}{If true, print a string representation of the type.} } \seealso{ The method is implemented for the \linkS4class{FieldDescriptor} class } \keyword{methods} \examples{ \dontrun{ proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P( "tutorial.Person" )} type(Person$id) type(Person$id, as.string=TRUE) cpp_type(Person$email) cpp_type(Person$email, TRUE) }RProtoBuf/man/asMessage.Rd0000644000175100001440000000144312440004312015114 0ustar hornikusers\name{asMessage} \alias{asMessage} \title{ coerce an object to a protobuf message } \description{ coerce an object to the \linkS4class{Message} class. This is a short-hand to the \link{as} method with the \code{Class} argument set to "Message" } \usage{ asMessage(x, ...) } \arguments{ \item{x}{object to coerce to a protobuf message} \item{\dots}{Passed to \code{\link{as}} } } \value{ a \linkS4class{Message} object } \author{ Romain Francois } \examples{ # coerce a message type descriptor to a message asMessage( tutorial.Person ) # coerce a enum descriptor asMessage( tutorial.Person.PhoneType ) # coerce a field descriptor asMessage( tutorial.Person$email ) # coerce a file descriptor asMessage( fileDescriptor( tutorial.Person ) ) } \keyword{ programming } RProtoBuf/man/ByteCount-methods.Rd0000644000175100001440000000050312440004312016555 0ustar hornikusers\name{ByteCount-methods} \docType{methods} \alias{ByteCount} \alias{ByteCount-methods} \title{The number of bytes read/written since the object was created} \description{ The number of bytes read/written since the object was created } \seealso{ \linkS4class{ZeroCopyInputStream} implements ByteCount. } \keyword{methods} RProtoBuf/man/FileInputStream-class.Rd0000644000175100001440000000322612440004312017363 0ustar hornikusers\name{FileInputStream-class} \Rdversion{1.1} \docType{class} \alias{FileInputStream-class} \alias{close,FileInputStream-method} \alias{GetErrno,FileInputStream-method} \alias{SetCloseOnDelete,FileInputStream-method} \title{Class "FileInputStream" } \description{A \linkS4class{ZeroCopyInputStream} reading from a file} \section{Objects from the Class}{ Objects can be created by the \link{FileInputStream} function } \section{Slots}{ \describe{ \item{\code{pointer}:}{ External pointer to the \code{google::protobuf::io::FileInputStream} C++ object} } } \section{Extends}{ Class \code{"\linkS4class{ZeroCopyInputStream}"}, directly. } \section{Methods}{ \describe{ \item{close}{\code{signature(con="FileInputStream")}: Flushes any buffers and closes the underlying file. Returns false if an error occurs during the process; use \code{GetErrno} to examine the error } \item{GetErrno}{\code{signature(object="FileInputStream")}: If an I/O error has occurred on this file descriptor, this is the errno from that error. Otherwise, this is zero. Once an error occurs, the stream is broken and all subsequent operations will fail. } \item{SetCloseOnDelete}{\code{signature(object="FileInputStream")}: set the close on delete behavior. } } See \linkS4class{ZeroCopyInputStream} for inherited methods } \references{ The \code{FileInputStream} class from the protobuf C++ library. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.io.zero_copy_stream_impl_lite.html#FileInputStream} } \author{ Romain Francois } \seealso{ \linkS4class{ZeroCopyInputStream} for methods } \keyword{classes} RProtoBuf/man/set.Rd0000644000175100001440000000060112440004312013772 0ustar hornikusers\name{set-methods} \docType{methods} \alias{set} \alias{set-methods} \alias{set,Message-method} \title{set a subset of values of a repeated field of a message} \description{ set a subset of values of a repeated field of a message } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{set a subset of values of a repeated field of a message} }} \keyword{methods} RProtoBuf/man/FileOutputStream-methods.Rd0000644000175100001440000000076012440004312020122 0ustar hornikusers\name{FileOutputStream-methods} \docType{methods} \alias{FileOutputStream} \alias{FileOutputStream-methods} \alias{FileOutputStream,character,integer,logical-method} \title{Creates an FileOutputStream} \description{ Constructor for \linkS4class{FileOutputStream} objects } \section{Methods}{ \describe{ \item{\code{signature(filename = "character", block_size = "logical", close.on.delete = "logical" )}}{Creates a \linkS4class{FileOutputStream} writing to the given file.} }} \keyword{methods} RProtoBuf/man/descriptor.Rd0000644000175100001440000000065512440004312015366 0ustar hornikusers\name{descriptor-methods} \docType{methods} \alias{descriptor} \alias{descriptor-methods} \alias{descriptor,Message-method} \title{Get the descriptor of a message} \description{ Get the \linkS4class{Descriptor} associated with a \linkS4class{Message} } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{ Get the descriptor of the message, as a \linkS4class{Descriptor} instance } }} \keyword{methods} RProtoBuf/man/fileDescriptor.Rd0000644000175100001440000000233712440004312016165 0ustar hornikusers\name{fileDescriptor-methods} \docType{methods} \alias{fileDescriptor} \alias{fileDescriptor-methods} \alias{fileDescriptor,Descriptor-method} \alias{fileDescriptor,Message-method} \alias{fileDescriptor,EnumDescriptor-method} \alias{fileDescriptor,FieldDescriptor-method} \alias{fileDescriptor,ServiceDescriptor-method} \alias{fileDescriptor,MethodDescriptor-method} \title{gets the file descriptor of an object} \description{ Gets the file descriptor of an object } \section{Methods}{ \describe{ \item{\code{signature(object = "Descriptor")}}{ retrieves the file descriptor associated with this descriptor} \item{\code{signature(object = "Message")}}{ retrieves the file descriptor associated with the descriptor of this message } \item{\code{signature(object = "EnumDescriptor")}}{ retrieves the file descriptor associated with the enum descriptor } \item{\code{signature(object = "FieldDescriptor")}}{ retrieves the file descriptor associated with the field descriptor } \item{\code{signature(object = "ServiceDescriptor")}}{ retrieves the file descriptor associated with the service descriptor } \item{\code{signature(object = "MethodDescriptor")}}{ retrieves the file descriptor associated with the method descriptor } }} \keyword{methods} RProtoBuf/man/is_extension.Rd0000644000175100001440000000056312440004312015715 0ustar hornikusers\name{is_extension-methods} \alias{is_extension} \alias{is_extension-methods} \title{Indicates if a field descriptor is an extension} \description{ Indicates if a field descriptor is an extension } \seealso{ The method is implemented for the \linkS4class{FieldDescriptor} class } \keyword{methods} \examples{ Person <- P( "tutorial.Person" ) is_extension(Person$id) }RProtoBuf/man/has.Rd0000644000175100001440000000311712440004312013757 0ustar hornikusers\name{has-methods} \docType{methods} \alias{has} \alias{has-methods} \alias{has,Message-method} \title{Indicates if an object has the given field set} \description{ This generic method, currently implemented for \linkS4class{Message} and \linkS4class{EnumDescriptor} indicates if the message or enum descriptor has the given field set. For messages and non-repeated fields, a call to the \code{HasField} method of the corresponding \code{Message} is issued. For messages and repeated fields, a call to the \code{FieldSize} method is issued, and the message is declared to have the field if the size is greater than 0. \code{NULL} is returned if the descriptor for the message does not contain the given field at all. For EnumDescriptors, a boolean value indicates if the given name is present in the enum definition. } \section{Methods}{ \describe{ \item{has}{\code{signature(object = "Message")}: Indicates if the message has a given field.} \item{has}{\code{signature(object = "EnumDescriptor")}: Indicates if the EnumDescriptor has a given named element.} } } \examples{ unitest.proto.file <- system.file("unitTests", "data", "unittest.proto", package = "RProtoBuf" ) readProtoFiles(file = unitest.proto.file) test <- new(protobuf_unittest.TestAllTypes) test$has("optional_int32") # FALSE test$add("repeated_int32", 1:10) test$has("repeated_int32") # TRUE test$has("nonexistant") # NULL has(protobuf_unittest.TestAllTypes$NestedEnum, "FOO") has(protobuf_unittest.TestAllTypes$NestedEnum, "BAR") has(protobuf_unittest.TestAllTypes$NestedEnum, "XXX") } \keyword{methods} RProtoBuf/man/Skip-methods.Rd0000644000175100001440000000024312440004312015550 0ustar hornikusers\name{Skip-methods} \docType{methods} \alias{Skip} \alias{Skip-methods} \title{Skips a number of bytes} \description{ Skips a number of bytes } \keyword{methods} RProtoBuf/man/P.Rd0000644000175100001440000000157112440004312013405 0ustar hornikusers\name{P} \alias{P} \title{Protocol Buffer descriptor importer} \description{ The \code{P} function searches for a protocol message descriptor in the descriptor pool. } \usage{ P(type, file) } \arguments{ \item{type}{Fully qualified type name of the protocol buffer or extension} \item{file}{optional proto file. If given, the definition contained in the file is first registered with the pool of message descriptors} } \value{ An object of class \linkS4class{Descriptor} for message types or \linkS4class{FieldDescriptor} for extensions. An error is generated otherwise. } \author{ Romain Francois } \examples{ \dontrun{ proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{ Person <- P("tutorial.Person") } cat(as.character( Person )) } \keyword{ interface } RProtoBuf/man/add.Rd0000644000175100001440000000120112440004312013724 0ustar hornikusers\name{add-methods} \docType{methods} \alias{add} \alias{add-methods} \alias{add,Message-method} \title{add elements of a repeated field of a message} \description{ Add elements to a repeated field of a message. } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{add elements to a repeated field of a message} }} \examples{ unitest.proto.file <- system.file("unitTests", "data", "unittest.proto", package = "RProtoBuf" ) readProtoFiles(file = unitest.proto.file) test <- new(protobuf_unittest.TestAllTypes) test$add("repeated_int32", 1) test$add("repeated_int32", 2:10) test$repeated_int32 } \keyword{methods} RProtoBuf/man/FieldDescriptor-class.Rd0000644000175100001440000001257112440004312017375 0ustar hornikusers\name{FieldDescriptor-class} \Rdversion{1.1} \docType{class} \alias{FieldDescriptor-class} \alias{show,FieldDescriptor-method} \alias{$,FieldDescriptor-method} \alias{as.character,FieldDescriptor-method} \alias{toString,FieldDescriptor-method} \alias{containing_type,FieldDescriptor-method} \alias{is_extension,FieldDescriptor-method} \alias{number,FieldDescriptor-method} \alias{type,FieldDescriptor-method} \alias{cpp_type,FieldDescriptor-method} \alias{label,FieldDescriptor-method} \alias{is_required} \alias{is_optional} \alias{is_repeated} \alias{is_required-methods} \alias{is_optional-methods} \alias{is_repeated-methods} \alias{is_required,FieldDescriptor-method} \alias{is_optional,FieldDescriptor-method} \alias{is_repeated,FieldDescriptor-method} \alias{has_default_value} \alias{has_default_value-methods} \alias{has_default_value,FieldDescriptor-method} \alias{default_value} \alias{default_value-methods} \alias{default_value,FieldDescriptor-method} \alias{message_type} \alias{message_type-methods} \alias{message_type,FieldDescriptor-method} \alias{enum_type,FieldDescriptor,missing,missing-method} \title{Class "FieldDescriptor"} \description{R representation of message type field descriptor. This is a thin wrapper around the C++ class \code{FieldDescriptor} } \section{Objects from the Class}{ Objects typically are retrieved from \linkS4class{FieldDescriptor} } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to the \code{FieldDescriptor} c++ object } \item{\code{name}:}{ name of the field within the message type } \item{\code{full_name}:}{Fully qualified name of the field} \item{\code{type}:}{Fully qualified name of the type that contains this field } } } \section{Methods}{ \describe{ \item{show}{\code{signature(object = "FieldDescriptor")}: small description } \item{as.character}{\code{signature(x = "FieldDescriptor")}: returns the debug string of the field descriptor. This is retrieved by a call to the \code{DebugString} method of the FieldDescriptor object. } \item{toString}{\code{signature(x = "FieldDescriptor")}: same as \code{as.character} } \item{$}{\code{signature(x = "FieldDescriptor")}: used to invoke pseudo methods } \item{containing_type}{\code{signature(object = "FieldDescriptor")} : returns a \linkS4class{Descriptor} of the message type that contains this field descriptor.} \item{is_extension}{\code{signature(object = "FieldDescriptor")} : indicates if this is an extension.} \item{number}{\code{signature(object = "FieldDescriptor")} : gets the declared tag number of this field.} \item{type}{\code{signature(object = "FieldDescriptor")} : type of this field.} \item{cpp_type}{\code{signature(object = "FieldDescriptor")} : c++ type of this field.} \item{label}{\code{signature(object = "FieldDescriptor")} : label of this field.} \item{is_required}{\code{signature(object = "FieldDescriptor")} : is this field required.} \item{is_optional}{\code{signature(object = "FieldDescriptor")} : is this field optional.} \item{is_repeated}{\code{signature(object = "FieldDescriptor")} : is this field repeated.} \item{has_default_value}{\code{signature(object = "FieldDescriptor")} : indicates if this field has a default value.} \item{default_value}{\code{signature(object = "FieldDescriptor")} : the default value of this field.} \item{message_type}{\code{signature(object = "FieldDescriptor")} : the \linkS4class{Descriptor} for the associated message type. Generates an error if this field is not a message type field.} \item{enum_type}{\code{signature(object = "FieldDescriptor")} : the \linkS4class{EnumDescriptor} for the associated enum type.Generates an error if this field is not an enum type field } } } \references{ The \code{FieldDescriptor} C++ class } \author{ Romain Francois } \seealso{ \linkS4class{Descriptor} } \examples{ \dontrun{ # example proto file supplied with this package proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # reading a proto file and creating the descriptor Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P("tutorial.Person") } # field descriptor object Person$email # debug string as.character( Person$email ) # or as a pseudo method Person$email$as.character() Person$email$is_required() Person$email$is_optional() Person$email$is_repeated() Person$email$has_default_value() Person$email$default_value() Person$email$is_extension() # Get the default values has_default_value(Person$id) has_default_value(Person$email) has_default_value(Person$phone) default_value(Person$id) default_value(Person$email) default_value(Person$phone) # Get the types of field descriptors type(Person$id) type(Person$id, as.string=TRUE) cpp_type(Person$email) cpp_type(Person$email, TRUE) # Get the label of a field descriptor label(Person$id) label(Person$email) label(Person$phone) label(Person$id, TRUE) label(Person$email, TRUE) label(Person$phone, TRUE) LABEL_OPTIONAL LABEL_REQUIRED LABEL_REPEATED # Test if a field is optional is_optional(Person$id) is_optional(Person$email) is_optional(Person$phone) # Test if a field is repeated is_repeated(Person$id) is_repeated(Person$email) is_repeated(Person$phone) # Test if a field is required is_required(Person$id) is_required(Person$email) is_required(Person$phone) # Return the class of a message field message_type(Person$phone) } \keyword{classes} RProtoBuf/man/ConnectionInputStream-class.Rd0000644000175100001440000000145412440004312020604 0ustar hornikusers\name{ConnectionInputStream-class} \Rdversion{1.1} \docType{class} \alias{ConnectionInputStream-class} \title{Class "ConnectionInputStream" } \description{A \linkS4class{ZeroCopyInputStream} reading from a binary R connection} \section{Objects from the Class}{ Objects can be created by the \link{ConnectionInputStream} function } \section{Slots}{ \describe{ \item{\code{pointer}:}{ External pointer to the \code{rprotobuf::ConnectionInputStream} C++ object} } } \section{Extends}{ Class \code{"\linkS4class{ZeroCopyInputStream}"}, directly. } \section{Methods}{ See \linkS4class{ZeroCopyInputStream} } \references{ The internal C++ class \code{ConnectionInputStream} } \author{ Romain Francois } \seealso{ \linkS4class{ZeroCopyInputStream} for methods } \keyword{classes} RProtoBuf/man/nested_type.Rd0000644000175100001440000000051012440004312015521 0ustar hornikusers\name{nested_type-methods} \alias{nested_type} \alias{nested_type-methods} \title{Extract a message type descriptor for a nested type} \description{ Extract a \linkS4class{Descriptor} nested in another \linkS4class{Descriptor} } \seealso{ The method is implemented for the \linkS4class{Descriptor} class } \keyword{methods} RProtoBuf/man/swap.Rd0000644000175100001440000000107212440004312014154 0ustar hornikusers\name{swap-methods} \docType{methods} \alias{swap} \alias{swap-methods} \alias{swap,Message-method} \title{swap elements of a repeated field of a message} \description{ swap elements of a repeated field of a message. } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{swap elements of a repeated field of a message} }} \references{ See the \code{SwapElements} of the \code{Reflection} class, part of the protobuf library. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.message.html} } \keyword{methods} RProtoBuf/man/ArrayInputStream-class.Rd0000644000175100001440000000302512440004312017557 0ustar hornikusers\name{ArrayInputStream-class} \Rdversion{1.1} \docType{class} \alias{ArrayInputStream-class} \title{Class "ArrayInputStream" } \description{A \linkS4class{ZeroCopyInputStream} backed by an in-memory array of bytes} \section{Objects from the Class}{ Objects can be created by the \link{ArrayInputStream} function } \section{Slots}{ \describe{ \item{\code{pointer}:}{ External pointer to the \code{google::protobuf::io::ArrayInputStream} C++ object} } } \section{Extends}{ Class \code{"\linkS4class{ZeroCopyInputStream}"}, directly. } \section{Methods}{ See \linkS4class{ZeroCopyInputStream} } \references{ The \code{ArrayInputStream} class from the protobuf C++ library. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.io.zero_copy_stream_impl_lite.html#ArrayInputStream} } \author{ Romain Francois } \seealso{ \linkS4class{ZeroCopyInputStream} for methods } \examples{ stream <- ArrayInputStream(as.raw(0:10)) stream$ReadRaw(5) stringsstream <- ArrayInputStream(as.raw(c(0x74, 0x65, 0x73, 0x74, 0x69, 0x6e, 0x67))) stringsstream$ReadString(7) intstream <- ArrayInputStream(as.raw(c(0x9e, 0xa7, 0x05))) intstream$ReadVarint32() } % local({ % stream <- ArrayInputStream( as.raw(0:10) ) % stopifnot( identical( stream$Next(), as.raw(0:10) ) ) % stream$BackUp( 5 ) % stopifnot( identical( stream$Next(), as.raw(6:10) ) ) % % # limiting the block size % stream <- ArrayInputStream( as.raw(0:10), 5 ) % stopifnot( identical(length( stream$Next() ), 5L ) ) % }) \keyword{classes} RProtoBuf/man/MethodDescriptor-class.Rd0000644000175100001440000000276312707407313017612 0ustar hornikusers\name{MethodDescriptor-class} \Rdversion{1.1} \docType{class} \alias{MethodDescriptor-class} \alias{as.character,MethodDescriptor-method} \alias{toString,MethodDescriptor-method} \alias{$,MethodDescriptor-method} \alias{$<-,MethodDescriptor-method} \alias{input_type} \alias{input_type-methods} \alias{input_type,MethodDescriptor-method} \alias{output_type} \alias{output_type-methods} \alias{output_type,MethodDescriptor-method} \title{Class "MethodDescriptor"} \description{R representation of Service Descriptors} \section{Objects from the Class}{ TODO } \section{Slots}{ \describe{ \item{\code{pointer}:}{External pointer to a \code{google::protobuf::MethodDescriptor} C++ object } \item{\code{name}:}{fully qualified name of the method} \item{\code{service}:}{fully qualified name of the service that defines this method} } } \section{Methods}{ \describe{ \item{as.character}{\code{signature(x = "MethodDescriptor")}: debug string of the method } \item{toString}{\code{signature(x = "MethodDescriptor")}: debug string of the method} \item{$}{\code{signature(x = "MethodDescriptor")}: ... } \item{$<-}{\code{signature(x = "MethodDescriptor")}: ... } \item{input_type}{\code{signature(object = "MethodDescriptor")}: the \linkS4class{Descriptor} of the input type of the method} \item{output_type}{\code{signature(object = "MethodDescriptor")}: the \linkS4class{Descriptor} of the output type of the method } } } \author{ Romain Francois } \keyword{classes} RProtoBuf/man/ConnectionOutputStream-methods.Rd0000644000175100001440000000074312440004312021343 0ustar hornikusers\name{ConnectionOutputStream-methods} \docType{methods} \alias{ConnectionOutputStream} \alias{ConnectionOutputStream-methods} \alias{ConnectionOutputStream,connection-method} \title{Creates an ConnectionOutputStream} \description{ Constructor for \linkS4class{ConnectionOutputStream} objects } \section{Methods}{ \describe{ \item{\code{signature(object="connection")}}{ Creates a \linkS4class{ConnectionOutputStream} writing to the given R binary connection.} }} \keyword{methods} RProtoBuf/man/enum_type.Rd0000644000175100001440000000050112440004312015203 0ustar hornikusers\name{enum_type-methods} \alias{enum_type} \alias{enum_type-methods} \title{Extract an enum type descriptor for a nested type} \description{ Extract a \linkS4class{EnumDescriptor} contained in a \linkS4class{Descriptor} } \seealso{ The method is implemented for the \linkS4class{Descriptor} class } \keyword{methods} RProtoBuf/man/EnumDescriptor-class.Rd0000644000175100001440000000732612707407313017276 0ustar hornikusers\name{EnumDescriptor-class} \Rdversion{1.1} \docType{class} \alias{EnumDescriptor-class} \alias{show,EnumDescriptor-method} \alias{has,EnumDescriptor-method} \alias{as.character,EnumDescriptor-method} \alias{toString,EnumDescriptor-method} \alias{$,EnumDescriptor-method} \alias{containing_type,EnumDescriptor-method} \alias{length,EnumDescriptor-method} \alias{value_count} \alias{value_count-methods} \alias{value_count,EnumDescriptor-method} \alias{value} \alias{value-methods} \alias{value,EnumDescriptor-method} \alias{[[,EnumDescriptor-method} \alias{names,EnumDescriptor-method} \title{Class "EnumDescriptor" } \description{ R representation of an enum descriptor. This is a thin wrapper around the \code{EnumDescriptor} c++ class. } \section{Objects from the Class}{ Objects of this class are typically retrieved as members of \linkS4class{Descriptor} objects } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to the \code{EnumDescriptor} instance} \item{\code{name}:}{ simple name of the enum } \item{\code{full_name}:}{fully qualified name } \item{\code{type}:}{fully qualified name of the type that contains this enumeration} } } \section{Methods}{ \describe{ \item{show}{\code{signature(object = "EnumDescriptor")}: small information } \item{as.character}{\code{signature(x = "EnumDescriptor")}: returns the debug string of the enum descriptor. This is retrieved by a call to the \code{DebugString} method of the EnumDescriptor object. } \item{toString}{\code{signature(x = "EnumDescriptor")}: same as \code{as.character} } \item{$}{\code{signature(x = "EnumDescriptor")}: get the number associated with the name} \item{has}{\code{signature(object = "EnumDescriptor")}: indicate if the given name is a constant present in this enum.} \item{containing_type}{\code{signature(object = "EnumDescriptor")} : returns a \linkS4class{Descriptor} of the message type that contains this enum descriptor, or NULL if this is a top level enum descriptor.} \item{length}{\code{signature(x = "EnumDescriptor")} : number of constants in this enum.} \item{value_count}{\code{signature(object = "EnumDescriptor")} : number of constants in this enum.} \item{value}{\code{signature(object = "EnumDescriptor")} : extracts an \linkS4class{EnumValueDescriptor}. Exactly one argument of \code{index}, \code{number} or \code{name} has to be used. If \code{index} is used, the enum value descriptor is retrieved by position, using the \code{value} method of the C++ class. If \code{number} is used, the enum value descriptor is retrieved using the value of the constant, using the \code{FindValueByNumber} C++ method. If \code{name} is used, the enum value descriptor is retrieved using the name of the constant, using the \code{FindValueByName} C++ method. } \item{[[}{\code{signature(x = "EnumDescriptor")}: extracts field identified by its name or declared tag number} \item{names}{\code{signature(x = "EnumDescriptor")} : extracts names of this enum} } } \references{ The \code{EnumDescriptor} C++ class } \author{ Romain Francois } \seealso{The \linkS4class{Descriptor} class} \examples{ \dontrun{ # example proto file supplied with this package proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # reading a proto file and creating the descriptor Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P("tutorial.Person") } # enum type Person$PhoneType has(Person$PhoneType, "MOBILE") has(Person$PhoneType, "HOME") has(Person$PhoneType, "WORK") has(Person$PhoneType, "FOOBAR") length(Person$PhoneType) } \keyword{classes} RProtoBuf/man/FileInputStream-methods.Rd0000644000175100001440000000075312440004312017723 0ustar hornikusers\name{FileInputStream-methods} \docType{methods} \alias{FileInputStream} \alias{FileInputStream-methods} \alias{FileInputStream,character,integer,logical-method} \title{Creates an FileInputStream} \description{ Constructor for \linkS4class{FileInputStream} objects } \section{Methods}{ \describe{ \item{\code{signature(filename = "character", block_size = "logical", close.on.delete = "logical" )}}{Creates a \linkS4class{FileInputStream} reading from the given file.} }} \keyword{methods} RProtoBuf/man/RpcHTTP-class.Rd0000644000175100001440000000121012440004312015523 0ustar hornikusers\name{RpcHTTP-class} \Rdversion{1.1} \docType{class} \alias{RpcHTTP-class} \title{Class "RpcHTTP" } \description{Support for protobuf rpc over HTTP} \section{Objects from the Class}{ Objects can be created by calls of the form \code{new("RpcHTTP", host = "somehost", port = port.number, root = "" )} } \section{Slots}{ \describe{ \item{\code{host}:}{Host name} \item{\code{port}:}{port number} \item{\code{root}:}{root directory of the protobuf http server} } } \author{ Romain Francois } \seealso{ \link{invoke} uses objects of this class to perform a method invocation over http. } \keyword{classes} RProtoBuf/man/FileDescriptor-class.Rd0000644000175100001440000000330512440004312017224 0ustar hornikusers\name{FileDescriptor-class} \Rdversion{1.1} \docType{class} \alias{FileDescriptor-class} \alias{as.character,FileDescriptor-method} \alias{toString,FileDescriptor-method} \alias{$,FileDescriptor-method} \alias{show,FileDescriptor-method} \alias{name,FileDescriptor-method} \title{Class "FileDescriptor"} \description{Class "FileDescriptor"} \section{Objects from the Class}{ Objects are usually created using the \code{\link{fileDescriptor}} method } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to a \code{google::protobuf::FileDescriptor} C++ object } \item{\code{package}:}{the package name defined in the file, e.g. 'tutorial'.} \item{\code{filename}:}{the filename of this FileDescriptor} } } \section{Methods}{ \describe{ \item{$}{\code{signature(x = "FileDescriptor")}: used to invoke a pseudo method of the file descriptor or get a top level message, enum or service descriptor} \item{toString}{\code{signature(x = "FileDescriptor" )} : gets the debug string} \item{as.character}{\code{signature(x = "FileDescriptor" )} : gets the debug string} \item{show}{\code{signature(x = "FileDescriptor" )} : prints small text} \item{name}{\code{signature(object = "FileDescriptor" )} : name of the file} } } \references{ The \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.descriptor.html#FileDescriptor} } \author{ Romain Francois } \keyword{classes} \seealso{ \linkS4class{Descriptor} } \examples{ # example proto file supplied with this package desc <- P("tutorial.Person") person <- new(desc) person$fileDescriptor() name(person$fileDescriptor()) # [1] "addressbook.proto" as.character(person$fileDescriptor()) } RProtoBuf/man/ArrayOutputStream-methods.Rd0000644000175100001440000000254612440004312020325 0ustar hornikusers\name{ArrayOutputStream-methods} \docType{methods} \alias{ArrayOutputStream} \alias{ArrayOutputStream-methods} \alias{ArrayOutputStream,integer,missing-method} \alias{ArrayOutputStream,integer,integer-method} \alias{ArrayOutputStream,integer,numeric-method} \alias{ArrayOutputStream,numeric,missing-method} \alias{ArrayOutputStream,numeric,integer-method} \alias{ArrayOutputStream,numeric,numeric-method} \title{Creates an ArrayOutputStream} \description{ Constructor for \linkS4class{ArrayOutputStream} objects } \section{Methods}{ \describe{ \item{\code{signature(size = "integer", block_size = "missing" )}}{Creates a \linkS4class{ArrayOutputStream} using of the given size} \item{\code{signature(size = "integer", block_size = "integer" )}}{Creates a \linkS4class{ArrayOutputStream} ... same with block size. } \item{\code{signature(size = "integer", block_size = "numeric" )}}{Creates a \linkS4class{ArrayOutputStream} ... same with block size. } \item{\code{signature(size = "numeric", block_size = "missing" )}}{Creates a \linkS4class{ArrayOutputStream} using of the given size} \item{\code{signature(size = "numeric", block_size = "integer" )}}{Creates a \linkS4class{ArrayOutputStream} ... same with block size. } \item{\code{signature(size = "numeric", block_size = "numeric" )}}{Creates a \linkS4class{ArrayOutputStream} ... same with block size. } }} \keyword{methods} RProtoBuf/man/completion.Rd0000644000175100001440000000411712440004312015356 0ustar hornikusers\name{completion} \alias{.DollarNames.Message} \alias{.DollarNames.Descriptor} \alias{.DollarNames.EnumDescriptor} \alias{.DollarNames.FieldDescriptor} \alias{.DollarNames.FileDescriptor} \alias{.DollarNames.ServiceDescriptor} \alias{.DollarNames.MethodDescriptor} \alias{.DollarNames.ZeroCopyInputStream} \alias{.DollarNames.ZeroCopyOutputStream} \title{ Completion support for protocol buffer messages and descriptors } \description{ These functions support completion of protocol buffer messages and descriptors. } \usage{ \S3method{.DollarNames}{Message}(x, pattern = "") \S3method{.DollarNames}{Descriptor}(x, pattern = "") \S3method{.DollarNames}{EnumDescriptor}(x, pattern = "") \S3method{.DollarNames}{FieldDescriptor}(x, pattern = "") \S3method{.DollarNames}{FileDescriptor}(x, pattern = "") \S3method{.DollarNames}{ServiceDescriptor}(x, pattern = "") \S3method{.DollarNames}{MethodDescriptor}(x, pattern = "") \S3method{.DollarNames}{ZeroCopyInputStream}(x, pattern = "") \S3method{.DollarNames}{ZeroCopyOutputStream}(x, pattern = "") } \arguments{ \item{x}{message (\linkS4class{Message}) or descriptor (\linkS4class{Descriptor}) } \item{pattern}{filter} } \value{ Character vector containing potential completions. For \linkS4class{Message} objects, completions are the fields of the message and a set of pseudo methods ("has") For \linkS4class{EnumDescriptor} objects, completions are the names of the possible constants For \linkS4class{Descriptor} objects, completions are the names of the fields, enum types and nested message types defined in the associated message type. For \linkS4class{FileDescriptor} objects, completions are the names of the top-level descriptors (message, enum or service) contained in the associated file, or pseudo methods. } \author{ Romain Francois } \examples{ # creating a prototype message from the descriptor p <- new( tutorial.Person ) .DollarNames( p ) .DollarNames( tutorial.Person ) # but this is usually used with the expansion on the command line # means "press the TAB key" # p$ # Person$ } \keyword{ programming } RProtoBuf/man/BackUp-methods.Rd0000644000175100001440000000041512440004312016010 0ustar hornikusers\name{BackUp-methods} \docType{methods} \alias{BackUp} \alias{BackUp-methods} \title{Backs up a number of bytes from a stream} \description{ Backs up a number of bytes from a stream } \seealso{ \linkS4class{ZeroCopyInputStream} implements BackUp. } \keyword{methods} RProtoBuf/man/ZeroCopyOutputStream-class.Rd0000644000175100001440000000533012440004312020455 0ustar hornikusers\name{ZeroCopyOutputStream-class} \Rdversion{1.1} \docType{class} \alias{ZeroCopyOutputStream-class} \alias{ByteCount,ZeroCopyOutputStream-method} \alias{BackUp,ZeroCopyOutputStream-method} \alias{Next,ZeroCopyOutputStream,raw-method} \alias{$,ZeroCopyOutputStream-method} \alias{WriteRaw} \alias{WriteRaw-methods} \alias{WriteRaw,ZeroCopyOutputStream,raw-method} \alias{WriteString} \alias{WriteString-methods} \alias{WriteString,ZeroCopyOutputStream,character-method} \alias{WriteLittleEndian32} \alias{WriteLittleEndian32-methods} \alias{WriteLittleEndian32,ZeroCopyOutputStream,integer-method} \alias{WriteLittleEndian32,ZeroCopyOutputStream,numeric-method} \alias{WriteLittleEndian32,ZeroCopyOutputStream,raw-method} \alias{WriteLittleEndian64} \alias{WriteLittleEndian64-methods} \alias{WriteLittleEndian64,ZeroCopyOutputStream,integer-method} \alias{WriteLittleEndian64,ZeroCopyOutputStream,numeric-method} \alias{WriteLittleEndian64,ZeroCopyOutputStream,raw-method} \alias{WriteVarint32} \alias{WriteVarint32-methods} \alias{WriteVarint32,ZeroCopyOutputStream,integer-method} \alias{WriteVarint32,ZeroCopyOutputStream,numeric-method} \alias{WriteVarint32,ZeroCopyOutputStream,raw-method} \alias{WriteVarint64} \alias{WriteVarint64-methods} \alias{WriteVarint64,ZeroCopyOutputStream,integer-method} \alias{WriteVarint64,ZeroCopyOutputStream,numeric-method} \alias{WriteVarint64,ZeroCopyOutputStream,raw-method} \title{Virtual Class "ZeroCopyOutputStream" } \description{R wrapper for the ZeroCopyOutputStream c++ class} \section{Objects from the Class}{ This is a virtual class } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to the \code{google::protobuf::io::ZeroCopyOutputStream} object} } } \section{Methods}{ \describe{ \item{$}{\code{signature(x="ZeroCopyOutputStream")}: invokes a method} \item{Next}{\code{signature(object="ZeroCopyOutputStream", payload = "raw" )}: push the raw vector into the stream. Returns the number of bytes actually written.} \item{BackUp}{\code{signature(object="ZeroCopyOutputStream")}: Backs up a number of bytes, so that the end of the last buffer returned by \code{Next} is not actually written.} \item{ByteCount}{\code{signature(object="ZeroCopyOutputStream")}: Returns the total number of bytes written since this object was created. } \item{WriteRaw}{\code{signature(object="ZeroCopyOuputStream", payload = "raw"}: write the raw bytes to the stream} } } \author{ Romain Francois } \references{ The \code{google::protobuf::io::ZeroCopyOutputStream} C++ class. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.io.zero_copy_stream.html#ZeroCopyOutputStream} } \seealso{ TODO: add classes that extend } \keyword{classes} RProtoBuf/man/field_count.Rd0000644000175100001440000000035612440004312015501 0ustar hornikusers\name{field_count-methods} \alias{field_count} \alias{field_count-methods} \title{The number of fields} \description{ The number of fields } \seealso{ The method is implemented for the \linkS4class{Descriptor} class } \keyword{methods} RProtoBuf/man/number.Rd0000644000175100001440000000115212440004312014471 0ustar hornikusers\name{number-methods} \alias{number} \alias{number-methods} \title{Gets the declared tag number of a field} \description{ Gets the declared tag number of a field } \seealso{ The method is implemented for \linkS4class{FieldDescriptor} and \linkS4class{EnumValueDescriptor} classes. } \keyword{methods} \examples{ \dontrun{ proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{ Person <- P("tutorial.Person") } number(Person$id) number(Person$email) as.character(Person) number(value(tutorial.Person$PhoneType, name="HOME")) }RProtoBuf/man/merge.Rd0000644000175100001440000000125312440004312014302 0ustar hornikusers\name{merge-methods} \alias{merge,Message,Message-method} \title{Merge two messages of the same type} \description{ Merge two \linkS4class{Message} objects of the same type. } \section{Methods}{ \describe{ \item{\code{signature(x = "Message", y = "Message")}}{ merge two messages of the same type } }} \section{Errors}{ An error of class "IncompatibleType" is thrown if the two messages are not of the same message type. } \keyword{methods} \examples{ m1 <- new( tutorial.Person, email = "francoisromain@free.fr" ) m2 <- new( tutorial.Person, id = 5 ) m3 <- merge( m1, m2 ) writeLines( as.character( m1 ) ) writeLines( as.character( m2 ) ) writeLines( as.character( m3 ) ) } RProtoBuf/man/ConnectionInputStream-methods.Rd0000644000175100001440000000073412440004312021142 0ustar hornikusers\name{ConnectionInputStream-methods} \docType{methods} \alias{ConnectionInputStream} \alias{ConnectionInputStream-methods} \alias{ConnectionInputStream,connection-method} \title{Creates an ConnectionInputStream} \description{ Constructor for \linkS4class{ConnectionInputStream} objects } \section{Methods}{ \describe{ \item{\code{signature(object="connection")}}{Creates a \linkS4class{ConnectionInputStream} reading from the given R binary connection.} }} \keyword{methods} RProtoBuf/man/ArrayInputStream-methods.Rd0000644000175100001440000000147312440004312020122 0ustar hornikusers\name{ArrayInputStream-methods} \docType{methods} \alias{ArrayInputStream} \alias{ArrayInputStream-methods} \alias{ArrayInputStream,raw,missing-method} \alias{ArrayInputStream,raw,integer-method} \alias{ArrayInputStream,raw,numeric-method} \title{Creates an ArrayInputStream} \description{ Constructor for \linkS4class{ArrayInputStream} objects } \section{Methods}{ \describe{ \item{\code{signature(payload = "raw", block_size = "missing" )}}{Creates a \linkS4class{ArrayInputStream} using the raw vector as the payload of the stream} \item{\code{signature(payload = "raw", block_size = "integer" )}}{Creates a \linkS4class{ArrayInputStream} ... same with block size. } \item{\code{signature(payload = "raw", block_size = "numeric" )}}{Creates a \linkS4class{ArrayInputStream} ... same with block size. } }} \keyword{methods} RProtoBuf/man/FileOutputStream-class.Rd0000644000175100001440000000352612440004312017567 0ustar hornikusers\name{FileOutputStream-class} \Rdversion{1.1} \docType{class} \alias{FileOutputStream-class} \alias{close,FileOutputStream-method} \alias{flush,FileOutputStream-method} \alias{GetErrno,FileOutputStream-method} \alias{SetCloseOnDelete,FileOutputStream-method} \title{Class "FileOutputStream" } \description{A \linkS4class{ZeroCopyOutputStream} reading from a file} \section{Objects from the Class}{ Objects can be created by the \link{FileOutputStream} function } \section{Slots}{ \describe{ \item{\code{pointer}:}{ External pointer to the \code{google::protobuf::io::FileOutputStream} C++ object} } } \section{Extends}{ Class \code{"\linkS4class{ZeroCopyOutputStream}"}, directly. } \section{Methods}{ \describe{ \item{close}{\code{signature(con="FileOutputStream")}: Flushes any buffers and closes the underlying file. Returns false if an error occurs during the process; use \code{GetErrno} to examine the error } \item{flush}{\code{signature(con="FileOutputStream")}: Flushes FileOutputStream's buffers but does not close the underlying file } \item{GetErrno}{\code{signature(object="FileInputStream")}: If an I/O error has occurred on this file descriptor, this is the errno from that error. Otherwise, this is zero. Once an error occurs, the stream is broken and all subsequent operations will fail. } \item{SetCloseOnDelete}{\code{signature(object="FileOutputStream")}: set the close on delete behavior. } } See \linkS4class{ZeroCopyOutputStream} for inherited methods } \references{ The \code{FileOutputStream} class from the protobuf C++ library. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.io.zero_copy_stream_impl_lite.html#FileOutputStream} } \author{ Romain Francois } \seealso{ \linkS4class{ZeroCopyOutputStream} for methods } \keyword{classes} RProtoBuf/man/Next-methods.Rd0000644000175100001440000000040312440004312015556 0ustar hornikusers\name{Next-methods} \docType{methods} \alias{Next} \alias{Next-methods} \title{Obtains a chunk of data from the stream} \description{ Obtains a chunk of data from the stream } \seealso{ \linkS4class{ZeroCopyInputStream} implements Next. } \keyword{methods} RProtoBuf/man/serialize_pb.Rd0000644000175100001440000000262612710022354015666 0ustar hornikusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/serialize_pb.R \name{serialize_pb} \alias{can_serialize_pb} \alias{serialize_pb} \alias{unserialize_pb} \title{Serialize R object to Protocol Buffer Message.} \usage{ serialize_pb(object, connection, ...) } \arguments{ \item{object}{R object to serialize} \item{connection}{passed on to \code{\link{serialize}}} \item{...}{additional arguments passed on to \code{\link{serialize}}} } \description{ Serializes R objects to a general purpose protobuf message using the same \code{rexp.proto} descriptor and mapping between R objects and protobuf mesages as RHIPE. } \details{ Clients need both the message and the \code{rexp.proto} descriptor to parse serialized R objects. The latter is included in the the package installation \code{proto} directory: \code{system.file(package="RProtoBuf", "proto/rexp.proto")} The following storage types are natively supported by the descriptor: \code{character}, \code{raw}, \code{double}, \code{complex}, \code{integer}, \code{list}, and \code{NULL}. Objects with other storage types, such as functions, environments, S4 classes, etc, are serialized using base R \code{\link{serialize}} and stored in the proto \code{native} type. Missing values, attributes and numeric precision will be preserved. } \examples{ msg <- tempfile(); serialize_pb(iris, msg); obj <- unserialize_pb(msg); identical(iris, obj); } RProtoBuf/man/clone.Rd0000644000175100001440000000171012440004312014301 0ustar hornikusers\name{clone-methods} \docType{methods} \alias{clone} \alias{clone-methods} \alias{clone,Message-method} \title{Clone protocol buffer messages} \description{ Generic "clone" function and associated method for \linkS4class{Message} objects } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{ clone the message } }} \examples{ \dontrun{ # example proto file supplied with this package proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # reading a proto file and creating the descriptor Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P("tutorial.Person")} # creating a prototype message from the descriptor sheep <- new( Person, email = "francoisromain@free.fr", id = 2 ) # cloning the sheep newsheep <- clone( sheep ) # clone and update at once newsheep <- clone( sheep, id = 3 ) # this can also be used as a pseudo method sheep$clone() sheep$clone( id = 3 ) } \keyword{methods} RProtoBuf/man/bytesize.Rd0000644000175100001440000000112712440004312015041 0ustar hornikusers\name{bytesize-methods} \docType{methods} \alias{bytesize} \alias{bytesize-methods} \alias{bytesize,Message-method} \title{The number of bytes taken by a message } \description{ The number of bytes taken by a \linkS4class{Message} } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{ The number of bytes the message would take when serialized } }} \keyword{methods} \examples{ message <- new( tutorial.Person, name = "dddd", email = "eeeeeee", id = 1 ) bytesize( message ) \dontshow{ stopifnot( identical( bytesize(message), length(serialize(message, NULL ) ) ) ) } } RProtoBuf/man/name.Rd0000644000175100001440000000125312440004312014123 0ustar hornikusers\name{name} \docType{methods} \alias{name} \alias{name-methods} \alias{name,Descriptor-method} \alias{name,FieldDescriptor-method} \alias{name,EnumDescriptor-method} \alias{name,ServiceDescriptor-method} \alias{name,MethodDescriptor-method} \title{Name or full name of a descriptor} \description{ name or full name of a descriptor } \section{Methods}{ \describe{ \item{\code{signature(object = "Descriptor")}}{ ... } \item{\code{signature(object = "FieldDescriptor")}}{ ... } \item{\code{signature(object = "EnumDescriptor")}}{ ... } \item{\code{signature(object = "ServiceDescriptor")}}{ ... } \item{\code{signature(object = "MethodDescriptor")}}{ ... } }} \keyword{methods} RProtoBuf/man/SetCloseOnDelete-methods.Rd0000644000175100001440000000067212440004312020011 0ustar hornikusers\name{SetCloseOnDelete-methods} \docType{methods} \alias{SetCloseOnDelete} \alias{SetCloseOnDelete-methods} \title{set the close on delete behavior} \description{ By default, the file descriptor is not closed when a stream is destroyed, use \code{SetCloseOnDelete( stream, TRUE ) } to change that. } \section{Methods}{ See classes \linkS4class{FileInputStream} and \linkS4class{FileOutputStream} for implementations. } \keyword{methods} RProtoBuf/man/ArrayOutputStream-class.Rd0000644000175100001440000000170212440004312017760 0ustar hornikusers\name{ArrayOutputStream-class} \Rdversion{1.1} \docType{class} \alias{ArrayOutputStream-class} \title{Class "ArrayOutputStream" } \description{A \linkS4class{ZeroCopyOutputStream} backed by an in-memory array of bytes} \section{Objects from the Class}{ Objects can be created by the \link{ArrayOutputStream} function } \section{Slots}{ \describe{ \item{\code{pointer}:}{ External pointer to the \code{google::protobuf::io::ArrayOutputStream} C++ object} } } \section{Extends}{ Class \code{"\linkS4class{ZeroCopyOutputStream}"}, directly. } \section{Methods}{ See \linkS4class{ZeroCopyOutputStream} } \references{ The \code{ArrayOutputStream} class from the protobuf C++ library. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.io.zero_copy_stream_impl_lite.html#ArrayOutputStream} } \author{ Romain Francois } \seealso{ \linkS4class{ZeroCopyOutputStream} for methods } \keyword{classes} RProtoBuf/man/containing_type-methods.Rd0000644000175100001440000000116212440004312020035 0ustar hornikusers\name{containing_type-methods} \alias{containing_type} \alias{containing_type-methods} \title{Gets the message type descriptor that contains a descriptor} \description{ Gets a \linkS4class{Descriptor} describing the message type that contains the descriptor. } \seealso{ The method is implemented for these classes : \linkS4class{Descriptor}, \linkS4class{EnumDescriptor}, \linkS4class{FieldDescriptor} } \examples{ # Containing type of a field is the message descriptor tutorial.Person$id$containing_type() # No containing type for the top-level message descriptor. tutorial.Person$containing_type() } \keyword{methods} RProtoBuf/man/size.Rd0000644000175100001440000000237012440004312014156 0ustar hornikusers\name{size-methods} \docType{methods} \alias{size} \alias{size-methods} \alias{size,Message-method} \title{Size of a message field} \description{ The number of object currently in a given field of a protocol buffer message. For non repeated fields, the size is 1 if the message has the field, 0 otherwise. For repeated fields, the size is the number of objects in the array. For repeated fields, the size can also be assigned to in order to shrink or grow the vector. Numeric types are given a default value of 0 when the new size is greater than the existing size. Character types are given a default value of "". Growing a repeated field in this way is not supported for message, group, and enum types. } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{Number of objects in a message field} }} \examples{ unitest.proto.file <- system.file("unitTests", "data", "unittest.proto", package = "RProtoBuf" ) readProtoFiles(file = unitest.proto.file) test <- new(protobuf_unittest.TestAllTypes) test$size("optional_int32") test$add("repeated_int32", 1:10) test$size("repeated_int32") test$repeated_int32 size(test, "repeated_int32") <- 5 test$repeated_int32 size(test, "repeated_int32") <- 15 test$repeated_int32 } \keyword{methods} RProtoBuf/man/Message-class.Rd0000644000175100001440000001334612707407313015716 0ustar hornikusers\name{Message-class} \Rdversion{1.1} \docType{class} \alias{Message-class} \alias{as.character,Message-method} \alias{$<-,Message-method} \alias{$,Message-method} \alias{[[,Message-method} \alias{[[<-,Message-method} \alias{serialize,Message-method} \alias{show,Message-method} \alias{update,Message-method} \alias{length,Message-method} \alias{names,Message-method} \alias{str,Message-method} \alias{toString,Message-method} \alias{identical,Message,Message-method} \alias{==,Message,Message-method} \alias{!=,Message,Message-method} \alias{all.equal,Message,Message-method} \alias{getExtension,Message-method} \alias{setExtension,Message-method} \alias{getExtension} \alias{setExtension} \title{Class "Message" } \description{ R representation of protocol buffer messages. This is a thin wrapper around the \code{Message} c++ class that holds the actual message as an external pointer. } \section{Objects from the Class}{ Objects are typically created by the \code{new} function invoked on a \linkS4class{Descriptor} object. } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to the c++ \code{Message} object} \item{\code{type}:}{fully qualified name of the message type} } } \section{Methods}{ \describe{ \item{as.character}{\code{signature(x = "Message")}: returns the debug string of the message. This is built from a call to the \code{DebugString} message of the \code{Message} object} \item{toString}{\code{signature(x = "Message")}: same as \code{as.character} } \item{$<-}{\code{signature(x = "Message")}: set the value of a field of the message. } \item{$}{\code{signature(x = "Message")}: gets the value of a field. Primitive types are brought back to R as R objects of the closest matching R type. Messages are brought back as instances of the \code{Message} class.} \item{[[}{\code{signature(x = "Message")}: extracts a field identified by its name or declared tag number } \item{[[<-}{\code{signature(x = "Message")}: replace the value of a field identified by its name or declared tag number } \item{serialize}{\code{signature(object = "Message")}: serialize a message. If the "connection" argument is \code{NULL}, the payload of the message is returned as a raw vector, if the "connection" argument is a binary writable connection, the payload is written into the connection. If "connection" is a character vector, the message is sent to the file (in binary format). } \item{show}{\code{signature(object = "Message")}: displays a short text about the message } \item{update}{\code{signature(object = "Message")}: set several fields of the message at once } \item{length}{\code{signature(x = "Message")}: The number of fields actually contained in the message. A field counts in these two situations: the field is repeated and the field size is greater than 0, the field is not repeated and the message has the field.} \item{setExtension}{\code{signature(object = "Message")}: set an extension field of the Message.} \item{getExtension}{\code{signature(object = "Message")}: get the value of an extension field of the Message.} \item{str}{\code{signature(object = "Message")}: displays the structure of the message } \item{identical}{\code{signature(x = "Message", y = "Message")}: Test if two messages are exactly identical } \item{==}{\code{signature(e1 = "Message", e2 = "Message")}: Same as \code{identical} } \item{!=}{\code{signature(e1 = "Message", e2 = "Message")}: Negation of \code{identical} } \item{all.equal}{\code{signature(e1 = "Message", e2 = "Message")}: Test near equality } \item{names}{\code{signature(x = "Message")}: extracts the names of the message. } } } \references{ The \code{Message} class from the C++ proto library. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.message.html} } \author{ Romain Francois } \seealso{ \code{\link{P}} creates objects of class \linkS4class{Descriptor} that can be used to create messages. } \examples{ \dontrun{ # example proto file supplied with this package proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # reading a proto file and creating the descriptor Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{ Person <- P("tutorial.Person") } PhoneNumber <- P( "tutorial.Person.PhoneNumber" ) # creating a prototype message from the descriptor p <- new( Person ) p$email # not set, returns default value p$id # not set, returns default value as.character( p ) # empty has( p, "email" ) # is the "email" field set has( p, "phone" ) # is the "email" field set length( p ) # number of fields actually set # update several fields at once romain <- update( new( Person ), email = "francoisromain@free.fr", id = 1, name = "Romain Francois", phone = new( PhoneNumber , number = "+33(0)...", type = "MOBILE" ) ) # supply parameters to the constructor dirk <- new( Person, email = "edd@debian.org", id = 2, name = "Dirk Eddelbuettel" ) # update the phone repeated field with a list of PhoneNumber messages dirk$phone <- list( new( PhoneNumber , number = "+01...", type = "MOBILE" ), new( PhoneNumber , number = "+01...", type = "HOME" ) ) # with/within style saptarshi <- within( new(Person), { id <- 3 name <- "Saptarshi Guha" email <- "saptarshi.guha@gmail.com" } ) # make an addressbook book <- new( tutorial.AddressBook, person = list( romain, dirk, saptarshi ) ) # serialize the message to a file tf <- tempfile( ) serialize( book, tf ) # the payload of the message serialize( book, NULL ) # read the file into a new message m <- tutorial.AddressBook$read( tf ) writeLines( as.character( m ) ) sapply( m$person, function(p) p$name ) } \keyword{classes} RProtoBuf/man/field.Rd0000644000175100001440000000042712440004312014270 0ustar hornikusers\name{field-methods} \alias{field} \alias{field-methods} \title{Extract a field descriptor} \description{ Extract a \linkS4class{FieldDescriptor} from a \linkS4class{Descriptor} } \seealso{ The method is implemented for the \linkS4class{Descriptor} class } \keyword{methods} RProtoBuf/man/ConnectionOutputStream-class.Rd0000644000175100001440000000146412440004312021006 0ustar hornikusers\name{ConnectionOutputStream-class} \Rdversion{1.1} \docType{class} \alias{ConnectionOutputStream-class} \title{Class "ConnectionOutputStream" } \description{A \linkS4class{ZeroCopyOutputStream} writing to a binary R connection} \section{Objects from the Class}{ Objects can be created by the \link{ConnectionOutputStream} function } \section{Slots}{ \describe{ \item{\code{pointer}:}{ External pointer to the \code{rprotobuf::ConnectionOutputStream} C++ object} } } \section{Extends}{ Class \code{"\linkS4class{ZeroCopyOutputStream}"}, directly. } \section{Methods}{ See \linkS4class{ZeroCopyOutputStream} } \references{ The internal C++ class \code{ConnectionOutputStream} } \author{ Romain Francois } \seealso{ \linkS4class{ZeroCopyOutputStream} for methods } \keyword{classes} RProtoBuf/man/RProtoBuf-package.Rd0000644000175100001440000000206112566371245016501 0ustar hornikusers\name{RProtoBuf-package} \alias{RProtoBuf-package} \alias{RProtoBuf} \docType{package} \title{R Interface to the Protocol Buffers API} \description{ Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal RPC protocols and file formats. This package provides R API to create, manipulate, parse and serialize protocol buffer messages from R } \author{Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms.} \references{\url{https://github.com/eddelbuettel/rprotobuf}} \keyword{package} \seealso{\linkS4class{Message} for some examples} \examples{ \dontrun{ # an example proto file system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # create a message of type AddressBook, defined in the example proto file demo( "addressbook", package = "RProtoBuf" ) # using R binary connections and files to read and write messages demo( "io", package = "RProtoBuf" ) # more documentation in the vignette vignette( "RProtoBuf", package = "RProtoBuf" ) } } RProtoBuf/man/aslist.Rd0000644000175100001440000000272012440004312014502 0ustar hornikusers\name{as.list.Message} \alias{as.list.Message} \alias{as.list.Descriptor} \alias{as.list.EnumDescriptor} \alias{as.list.FileDescriptor} \alias{as.list.ServiceDescriptor} \title{ Grab the protocol buffer message as an R list } \description{ Utility to grab the protocol buffer message as an R list, with one item per field. } \usage{ \S3method{as.list}{Message}(x, ...) \S3method{as.list}{Descriptor}(x, ...) \S3method{as.list}{EnumDescriptor}(x, ...) \S3method{as.list}{FileDescriptor}(x, ...) \S3method{as.list}{ServiceDescriptor}(x, ...) } \arguments{ \item{x}{A protocol buffer message, instance of \linkS4class{Message}, or a protocol message descriptor, instance of \linkS4class{Descriptor} } \item{\dots}{ignored} } \value{ For messages, a list of the content of the fields is returned. For message type descriptors, a list containing nested type descriptors (\linkS4class{Descriptor} objects), enum type descriptors (\linkS4class{EnumDescriptor} objects), then field descriptors (\linkS4class{FieldDescriptor} objects) in that order. For enum descriptors, a named list of the enumerated values. For file descriptors, a named list of descriptors defined in the specified file descriptor. For service descriptors, ... } \author{ Romain Francois } \examples{ Person <- P( "tutorial.Person" ) romain <- new( Person, email = "francoisromain@free.fr", id = 1 ) as.list( romain ) as.list( Person ) as.list( Person$PhoneType) } \keyword{ programming } RProtoBuf/man/clear.Rd0000644000175100001440000000271112440004312014271 0ustar hornikusers\name{clear-methods} \docType{methods} \alias{clear} \alias{clear-methods} \alias{clear,Message,character-method} \alias{clear,Message,integer-method} \alias{clear,Message,missing-method} \alias{clear,Message,numeric-method} \alias{clear,Message,raw-method} \title{Clear a field or all fields of the message and set them to their default values} \description{ Clear one field or all fields of the message and set them to their default values } \section{Methods}{ \describe{ \item{\code{signature(object = "Message", field = "missing")}}{Clear all fields of the message and set them to their default values } \item{\code{signature(object = "Message", field = "character")}}{ Clear the field identified by its name } \item{\code{signature(object = "Message", field = "integer")}}{ Clear the field identified by its tag number } \item{\code{signature(object = "Message", field = "numeric")}}{ Clear the field identified by its tag number } \item{\code{signature(object = "Message", field = "raw")}}{ Clear the field identified by its tag number} }} \keyword{methods} \examples{ message <- new( tutorial.Person, name = "dddd", email = "eeeeeee", id = 1 ) writeLines( as.character( message ) ) clear( message ) # clear works also as a pseudo method : message$clear() writeLines( as.character( message ) ) # clear single fields message <- new( tutorial.Person, name = "dddd", email = "eeeeeee", id = 1 ) message$clear( "name" ) writeLines( as.character( message ) ) } RProtoBuf/man/GetErrno-methods.Rd0000644000175100001440000000057012440004312016372 0ustar hornikusers\name{GetErrno-methods} \docType{methods} \alias{GetErrno} \alias{GetErrno-methods} \title{Get the error number for an I/O error} \description{ If an I/O error has occurred on this file descriptor, this is the errno from that error } \section{Methods}{ See classes \linkS4class{FileInputStream} and \linkS4class{FileOutputStream} for implementations. } \keyword{methods} RProtoBuf/man/with.Rd0000644000175100001440000000233212440004312014155 0ustar hornikusers\name{with.Message} \alias{with.Message} \alias{within.Message} \title{ with and within methods for protocol buffer messages } \description{ Convenience wrapper that allow getting and setting fields of protocol buffer messages from within the object } \usage{ \S3method{with}{Message}(data, expr, ...) \S3method{within}{Message}(data, expr, ...) } \arguments{ \item{data}{A protocol buffer message, instance of \linkS4class{Message} } \item{expr}{R expression to evaluate} \item{\dots}{ignored} } \details{ The expression is evaluated in an environment that allows to set and get fields of the message The fields of the message are mapped to active bindings (see \link{makeActiveBinding}) so that they can be accessed and modified from within the environment. } \value{ \code{with} returns the value of the expression and \code{within} returns the \code{data} argument. } \author{ Romain Francois } \examples{ \dontrun{ proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P( "tutorial.Person") } romain <- within( new( Person ), { email <- "francoisromain@free.fr" id <- 10L } ) } \keyword{ classes } RProtoBuf/man/label.Rd0000644000175100001440000000153612440004312014266 0ustar hornikusers\name{label-methods} \alias{label} \alias{label-methods} \alias{LABEL_OPTIONAL} \alias{LABEL_REQUIRED} \alias{LABEL_REPEATED} \title{Gets the label of a field} \description{ Gets the label of a field (optional, required, or repeated). } \arguments{ \item{object}{A \linkS4class{FieldDescriptor} object.} \item{as.string}{If true, print a string representation of the type.} } \seealso{ The method is implemented for the \linkS4class{FieldDescriptor} class } \keyword{methods} \examples{ \dontrun{ proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{ Person <- P("tutorial.Person") } label(Person$id) label(Person$email) label(Person$phone) label(Person$id, TRUE) label(Person$email, TRUE) label(Person$phone, TRUE) LABEL_OPTIONAL LABEL_REQUIRED LABEL_REPEATED }RProtoBuf/man/read.Rd0000644000175100001440000000272412440004312014122 0ustar hornikusers\name{read-methods} \docType{methods} \alias{read} \alias{read-methods} \alias{read,Descriptor,character-method} \alias{read,Descriptor,raw-method} \alias{read,Descriptor,ANY-method} \title{Read a protocol buffer message from a connection} \description{ Read a \linkS4class{Message} from a connection using its associated \linkS4class{Descriptor} } \section{Methods}{ \describe{ \item{\code{signature(descriptor = "Descriptor", input = "character")}}{ Read the message from a file } \item{\code{signature(descriptor = "Descriptor")}}{ Read from a binary connection. } \item{\code{signature(descriptor = "Descriptor", input = "raw")}}{ Read the message from a raw vector } }} \keyword{methods} \examples{ # example file that contains a "tutorial.AddressBook" message book <- system.file( "examples", "addressbook.pb", package = "RProtoBuf" ) # read the message message <- read( tutorial.AddressBook, book ) # or using the pseudo method message <- tutorial.AddressBook$read( book ) # write its debug string writeLines( as.character( message ) ) # grab the name of each person sapply( message$person, function(p) p$name ) # read from a binary file connection f <- file( book, open = "rb" ) message2 <- read( tutorial.AddressBook, f ) close( f ) # read from a message payload (raw vector) payload <- readBin( book, raw(0), 5000 ) message3 <- tutorial.AddressBook$read( payload ) \dontshow{ stopifnot( identical( message, message2) ) stopifnot( identical( message, message3) ) } } RProtoBuf/man/isInitialized.Rd0000644000175100001440000000131612440004312016004 0ustar hornikusers\name{isInitialized-methods} \docType{methods} \alias{isInitialized} \alias{isInitialized-methods} \alias{isInitialized,Message-method} \title{Indicates if a protocol buffer message is initialized} \description{ Indicates if a \linkS4class{Message} is initialized. A message is initialized if all its required fields are set. } \section{Methods}{ \describe{ \item{\code{ signature(object = "Message")}}{ is the message initialized} }} \examples{ message <- new( tutorial.Person, name = "" ) isInitialized( message ) # FALSE (id is not set) message$isInitialized() # FALSE message <- new( tutorial.Person, name = "", id = 2 ) isInitialized( message ) # TRUE message$isInitialized() # TRUE } \keyword{methods} RProtoBuf/man/EnumValueDescriptor-class.Rd0000644000175100001440000000521612440004312020251 0ustar hornikusers\name{EnumValueDescriptor-class} \Rdversion{1.1} \docType{class} \alias{EnumValueDescriptor-class} \alias{show,EnumValueDescriptor-method} \alias{as.character,EnumValueDescriptor-method} \alias{toString,EnumValueDescriptor-method} \alias{$,EnumValueDescriptor-method} \alias{name,EnumValueDescriptor-method} \alias{number,EnumValueDescriptor-method} \alias{enum_type,EnumValueDescriptor,missing,missing-method} \title{Class "EnumValueDescriptor" } \description{ R representation of an enum value descriptor. This is a thin wrapper around the \code{EnumValueDescriptor} c++ class. } \section{Objects from the Class}{ Objects of this class are typically retrieved with the \code{value} method of the \linkS4class{EnumDescriptor} class } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to the \code{EnumValueDescriptor} instance} \item{\code{name}:}{ simple name of the enum } \item{\code{full_name}:}{fully qualified name } } } \section{Methods}{ \describe{ \item{show}{\code{signature(object = "EnumValueDescriptor")}: small information } \item{as.character}{\code{signature(x = "EnumValueDescriptor")}: returns the debug string of the enum descriptor. This is retrieved by a call to the \code{DebugString} method of the EnumDescriptor object. } \item{toString}{\code{signature(x = "EnumValueDescriptor")}: same as \code{as.character} } \item{$}{\code{signature(x = "EnumValueDescriptor")}: invoke pseudo methods } \item{name}{\code{signature(object = "EnumValueDescriptor", full = "logical")}: return the name of this enum constant.} \item{number}{\code{signature(object = "EnumValueDescriptor")}: return the numeric value of this enum constant.} \item{enum_type}{\code{signature(object = "EnumDescriptor")} : retrieves the \linkS4class{EnumDescriptor} related to this value descriptor.} } } \references{ The \code{EnumValueDescriptor} C++ class. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.descriptor.html#EnumValueDescriptor} } \author{ Romain Francois } \examples{ \dontrun{ # example proto file supplied with this package proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # reading a proto file and creating the descriptor Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P( "tutorial.Person" ) } # enum type Person$PhoneType # enum value type value(Person$PhoneType, 1) name(value(Person$PhoneType, 1)) name(value(Person$PhoneType, 1), TRUE) number(value(Person$PhoneType, number=1)) enum_type(value(Person$PhoneType, number=1)) } \keyword{classes} RProtoBuf/man/invokeLocally.Rd0000644000175100001440000000107412440004312016017 0ustar hornikusers\name{invoke-methods} \docType{methods} \alias{invoke} \alias{invoke-methods} \alias{invoke,MethodDescriptor,Message,missing-method} \alias{invoke,MethodDescriptor,Message,RpcHTTP-method} \title{invoke a protobuf rpc method} \description{ invoke a protobuf rpc method } \section{Methods}{ \describe{ \item{\code{signature(method = "MethodDescriptor", message = "Message")}}{invoke a protobuf rpc method locally.} \item{\code{signature(method = "MethodDescriptor", message = "Message", protocol = "RpcHTTP" )}}{invoke a protobuf rpc method over http.} }} \keyword{methods} RProtoBuf/man/Descriptor-class.Rd0000644000175100001440000001216412440004312016427 0ustar hornikusers\name{Descriptor-class} \Rdversion{1.1} \docType{class} \alias{Descriptor-class} \alias{as.character,Descriptor-method} \alias{$<-,Descriptor-method} \alias{$,Descriptor-method} \alias{new,Descriptor-method} \alias{show,Descriptor-method} \alias{toString,Descriptor-method} \alias{containing_type,Descriptor-method} \alias{field_count,Descriptor-method} \alias{nested_type_count,Descriptor-method} \alias{enum_type_count,Descriptor-method} \alias{field,Descriptor-method} \alias{nested_type,Descriptor-method} \alias{enum_type,Descriptor,ANY,ANY-method} \alias{[[,Descriptor-method} \alias{names,Descriptor-method} \alias{length,Descriptor-method} \title{Class "Descriptor" } \description{ full descriptive information about a protocol buffer message type. This is a thin wrapper around the C++ class \code{Descriptor}} \section{Objects from the Class}{ Objects are usually created by calls to the \code{\link{P}} function. } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer holding a \code{Descriptor} object } \item{\code{type}:}{full name of the corresponding message type} } } \section{Methods}{ \describe{ \item{as.character}{\code{signature(x = "Descriptor")}: returns the debug string of the descriptor. This is retrieved by a call to the \code{DebugString} method of the Descriptor object. } \item{toString}{\code{signature(x = "Descriptor")}: same as \code{as.character} } \item{$}{\code{signature(x = "Descriptor")}: retrieves a descriptor for a member of the message type. This can either be another "Descriptor" instance describing a nested type, or a \linkS4class{EnumDescriptor} object describing an enum type, or a \linkS4class{FieldDescriptor} object describing a field of the message} \item{new}{\code{signature(Class = "Descriptor")}: creates a prototype message (\linkS4class{Message}) of this descriptor} \item{show}{\code{signature(object = "Descriptor")}: simple information} \item{containing_type}{\code{signature(object = "Descriptor")} : returns a descriptor of the message type that contains this message descriptor, or \code{NULL} if this is a top-level message type.} \item{field_count}{\code{signature(object = "Descriptor")} : The number of fields of this message type. } \item{nested_type_count}{\code{signature(object = "Descriptor")} : The number of nested types of this message type. } \item{enum_type_count}{\code{signature(object = "Descriptor")} : The number of enum types of this message type. } \item{field}{\code{signature(object = "Descriptor")} : extract a field descriptor from a descriptor. Exactly one argument of \code{index}, \code{number} or \code{name} has to be used. If \code{index} is used, the field descriptor is retrieved by position, using the \code{field} method of the \code{google::protobuf::Descriptor} C++ class. If \code{number} is used, the field descriptor is retrieved using the tag number, with the \code{FindFieldByNumber} C++ method. If \code{name} is used, the field descriptor is retrieved by name using the \code{FindFieldByName} } \item{nested_type}{\code{signature(object = "Descriptor")} : extracts a message type descriptor that is nested in this descriptor. Exactly one argument of \code{index} of \code{name} has to be used. If \code{index} is used, the nested type will be retrieved using its position with the \code{nested_type} method of the \code{google::protobuf::Descriptor} C++ class. If \code{name} is used, the nested type will be retrieved using its name, with the \code{FindNestedTypeByName} C++ method } \item{enum_type}{\code{signature(object = "Descriptor")} : extracts an enum type descriptor that is contained in this descriptor. Exactly one argument of \code{index} of \code{name} has to be used. If \code{index} is used, the enum type will be retrieved using its position with the \code{enum_type} method of the \code{google::protobuf::Descriptor} C++ class. If \code{name} is used, the enum type will be retrieved using its name, with the \code{FindEnumTypeByName} C++ method } \item{[[}{\code{signature(x = "Descriptor")}: extracts a field identified by its name or declared tag number} \item{names}{\code{signature(x = "Descriptor")} : extracts names of this descriptor} \item{length}{\code{signature(x = "Descriptor")} : extracts length of this descriptor} } } \references{ The \code{Descriptor} c++ class. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.descriptor.html#Descriptor} } \author{ Romain Francois } \seealso{ the \code{\link{P}} function creates "Descriptor" messages. } \examples{ \dontrun{ # example proto file supplied with this package proto.file <- system.file( "proto", "addressbook.proto", package = "RProtoBuf" ) # reading a proto file and creating the descriptor Person <- P( "tutorial.Person", file = proto.file ) } \dontshow{Person <- P( "tutorial.Person" ) } # enum type Person$PhoneType # nested type Person$PhoneNumber # field Person$email # use this descriptor to create a message new( Person ) } \keyword{classes} RProtoBuf/man/readASCII.Rd0000644000175100001440000000231112440004312014663 0ustar hornikusers\name{readASCII-methods} \docType{methods} \alias{readASCII} \alias{readASCII-methods} \alias{readASCII,Descriptor,ANY-method} \alias{readASCII,Descriptor,character-method} \title{read a message in ASCII format} \description{ Method to read a Message in ASCII format } \section{Methods}{ \describe{ \item{\code{signature(descriptor = "Descriptor", input = "ANY")}}{ Read the message from a connection (file, etc ...) } \item{\code{signature(descriptor = "Descriptor", input = "character")}}{ Read the message directly from the character string } }} \keyword{methods} \examples{ # example file that contains a "tutorial.AddressBook" message book <- system.file( "examples", "addressbook.pb", package = "RProtoBuf" ) # read the message message <- read( tutorial.AddressBook, book ) # Output in text format to a temporary file out.file <- tempfile() writeLines( as.character(message), file(out.file)) # Verify that we can read back in the message from a text file. message2 <- readASCII( tutorial.AddressBook, file(out.file, "rb")) # Verify that we can read back in the message from an unopened file. message3 <- readASCII( tutorial.AddressBook, file(out.file)) \dontshow{ stopifnot( identical( message, message2) ) } } RProtoBuf/man/ZeroCopyInputStream-class.Rd0000644000175100001440000000666612440004312020271 0ustar hornikusers\name{ZeroCopyInputStream-class} \Rdversion{1.1} \docType{class} \alias{ZeroCopyInputStream-class} \alias{Skip,ZeroCopyInputStream-method} \alias{ByteCount,ZeroCopyInputStream-method} \alias{BackUp,ZeroCopyInputStream-method} \alias{Next,ZeroCopyInputStream,missing-method} \alias{$,ZeroCopyInputStream-method} \alias{ReadRaw} \alias{ReadRaw-methods} \alias{ReadRaw,ZeroCopyInputStream,integer-method} \alias{ReadRaw,ZeroCopyInputStream,numeric-method} \alias{ReadString} \alias{ReadString-methods} \alias{ReadString,ZeroCopyInputStream,integer-method} \alias{ReadString,ZeroCopyInputStream,numeric-method} \alias{ReadVarint32} \alias{ReadVarint32-methods} \alias{ReadVarint32,ZeroCopyInputStream-method} \alias{ReadLittleEndian32} \alias{ReadLittleEndian32-methods} \alias{ReadLittleEndian32,ZeroCopyInputStream-method} \alias{ReadLittleEndian64} \alias{ReadLittleEndian64-methods} \alias{ReadLittleEndian64,ZeroCopyInputStream-method} \alias{ReadVarint64} \alias{ReadVarint64-methods} \alias{ReadVarint64,ZeroCopyInputStream-method} \title{Virtual Class "ZeroCopyInputStream" } \description{R wrapper for the ZeroCopyInputStream c++ class} \section{Objects from the Class}{ This is a virtual class } \section{Slots}{ \describe{ \item{\code{pointer}:}{external pointer to the \code{google::protobuf::io::ZeroCopyInputStream} object} } } \section{Methods}{ \describe{ \item{$}{\code{signature(x="ZeroCopyInputStream")}: invokes a method} \item{Next}{\code{signature(object="ZeroCopyInputStream")}: Get a number of bytes from the stream as a raw vector. } \item{Skip}{\code{signature(object="ZeroCopyInputStream")}: skip a number of bytes} \item{BackUp}{\code{signature(object="ZeroCopyInputStream")}: Backs up a number of bytes, so that the next call to \code{Next} returns data again that was already returned by the last call to \code{Next}.} \item{ByteCount}{\code{signature(object="ZeroCopyInputStream")}: Returns the total number of bytes read since this object was created. } \item{ReadRaw}{\code{signature(object="ZeroCopyInputStream", size = "integer")}: read raw bytes from the stream} \item{ReadRaw}{\code{signature(object="ZeroCopyInputStream", size = "numeric")}: read raw bytes from the stream} \item{ReadString}{\code{signature(object="ZeroCopyInputStream", size = "integer")}: same as \code{ReadRaw} but formats the result as a string} \item{ReadString}{\code{signature(object="ZeroCopyInputStream", size = "numeric")}: same as \code{ReadRaw} but formats the result as a string} \item{ReadVarint32}{\code{signature(object="ZeroCopyInputStream")}: Read an unsigned integer with Varint encoding, truncating to 32 bits. } \item{ReadLittleEndian32}{\code{signature(object="ZeroCopyInputStream")}: Read a 32-bit little-endian integer. } \item{ReadLittleEndian64}{\code{signature(object="ZeroCopyInputStream")}: Read a 64-bit little-endian integer. In R the value is stored as a \code{double} which looses some precision (no other way) } \item{ReadVarint64}{\code{signature(object="ZeroCopyInputStream")}: Read a 64-bit integer with varint encoding. In R the value is stored as a \code{double} which looses some precision (no other way) } } } \author{ Romain Francois } \references{ The \code{google::protobuf::io::ZeroCopyInputStream} C++ class. \url{http://code.google.com/apis/protocolbuffers/docs/reference/cpp/google.protobuf.io.zero_copy_stream.html#ZeroCopyInputStream} } \seealso{ TODO: add classes that extend } \keyword{classes} RProtoBuf/man/fetch.Rd0000644000175100001440000000053412440004312014275 0ustar hornikusers\name{fetch-methods} \docType{methods} \alias{fetch} \alias{fetch-methods} \alias{fetch,Message-method} \title{Fetch content of a repeated field} \description{ Fetch content of a repeated field of a message } \section{Methods}{ \describe{ \item{\code{signature(object = "Message")}}{Fetch content of a message repeated field} }} \keyword{methods} RProtoBuf/man/enum_type_count.Rd0000644000175100001440000000040112440004312016412 0ustar hornikusers\name{enum_type_count-methods} \alias{enum_type_count} \alias{enum_type_count-methods} \title{The number of enum types} \description{ The number of enum types } \seealso{ The method is implemented for the \linkS4class{Descriptor} class } \keyword{methods} RProtoBuf/man/readProtoFiles.Rd0000644000175100001440000000225112440004312016124 0ustar hornikusers\name{readProtoFiles} \alias{readProtoFiles} \title{ protocol buffer descriptor importer } \description{ Imports proto files into the descriptor pool that is then used by the \code{P} function to resolve message type names. } \usage{ readProtoFiles(files, dir, package="RProtoBuf", pattern="\\\\.proto$", lib.loc=NULL) } \arguments{ \item{files}{Proto files} \item{dir}{Directory. If \code{files} is not specified, files with the "proto" extension in the \code{dir} directory are imported} \item{package}{R package name. If \code{files} and \code{dir} are missing, "proto" files in the "proto" directory of the package tree are imported.} \item{pattern}{A filename pattern to match proto files.} \item{lib.loc}{Library location.} } \value{ \code{NULL}, invisibly. } \author{ Romain Francois } \seealso{ \code{\link{P}} } \examples{ \dontrun{ # from a package readProtoFiles( package = "RProtoBuf" ) # from a directory proto.dir <- system.file( "proto", package = "RProtoBuf" ) readProtoFiles( dir = proto.dir ) # set of files proto.files <- list.files( proto.dir, full.names = TRUE ) readProtoFiles( proto.files ) } } \keyword{ programming } RProtoBuf/man/nested_type_count.Rd0000644000175100001440000000040012440004312016727 0ustar hornikusers\name{nested_type_count-methods} \alias{nested_type_count} \alias{nested_type_count-methods} \title{The number of fields} \description{ The number of fields } \seealso{ The method is implemented for the \linkS4class{Descriptor} class } \keyword{methods} RProtoBuf/configure.win0000644000175100001440000000000012440004312014626 0ustar hornikusersRProtoBuf/cleanup0000755000175100001440000000065612440004312013524 0ustar hornikusers#!/bin/sh rm -f config.* src/Makedeps src/Makevars \ src/addressbook.pb.cc src/addressbook.pb.h \ src/protobufrpc.pb.cc src/protobufrpc.pb.h \ src/*.o src/*.d src/*.a src/*.dll src/*.so src/*.rc */*~ *~ \ src/symbols.rds \ vignettes/RProtoBuf*.aux vignettes/RProtoBuf*.log \ vignettes/RProtoBuf*.out vignettes/RProtoBuf*.toc \ vignettes/RProtoBuf*.tex vignettes/RProtoBuf*.pdf rm -rf inst/doc/auto RProtoBuf/tools/0000755000175100001440000000000013037201575013315 5ustar hornikusersRProtoBuf/tools/winlibs.R0000644000175100001440000000070013037201575015104 0ustar hornikusers# Build against protobuf libs compiled with Rtools # by Jeroen Ooms. Last updated: August 2016 if (!file.exists("../windows/protobuf-3.0.0/include/google/protobuf/descriptor.h")) { if (getRversion() < "3.3.0") setInternet2() download.file("https://github.com/rwinlib/protobuf/archive/v3.0.0.zip", "lib.zip", quiet = TRUE) dir.create("../windows", showWarnings = FALSE) unzip("lib.zip", exdir = "../windows") unlink("lib.zip") } RProtoBuf/.Rinstignore0000644000175100001440000000002212440004312014436 0ustar hornikusersinst/doc/Makefile