Desupport perl, ruby bindings-- move them to /contrib

Summary:
Moved the Perl and Ruby bindings to an attic-type area
called "contrib" to mark them as not-officially supported parts
of the SDK distribution. The idea is that if someone (either a
DNAnexan or not) wants to revive it at some point, they would
have a useful starting point to consult, but otherwise this code
isn't presumed to have any guarantees and people shouldn't be
thinking about "will I break this" if they want to make other
changes.

* Stop building the corresponding Debian packages too

Test Plan:
* Ran make targets by hand
* Verified that no applets rely on the deb packages in their execDepends

Reviewers: gduggal

Reviewed By: gduggal

Differential Revision: https://dnanexus.phacility.com/D1224

.gitignore

@@ -12,15 +12,11 @@
 /src/.setup_doc_virtualenv
 /src/java/target/
 /src/java/src/main/java/com/dnanexus/DXToolkitVersion.java
-/src/perl/DNAnexus-*
 /src/python/dxpy/toolkit_version.py
 /src/python/coverage-reports/
-/src/ruby/lib/dxruby/version.rb
 /src/R/install_dxR_deps.Rout
 /src/R/dxR*.tar.gz
 /src/R/roxygen2_*
-/src/ruby/*.gem
-/src/ruby/.yardoc
 
 /src/openssl*.tar.gz
 /src/openssl

Readme.md

@@ -37,7 +37,6 @@ The Platform SDK contains API language bindings for the following platforms:
 
 * [Python](src/python/Readme.md) (requires Python 2.7)
 * C++
-* Perl
 * [Java](src/java/Readme.md) (requires Java 7 or higher)
 * [R](src/R/Readme.md)
 

build/Prebuilt-Readme.md

@@ -34,11 +34,11 @@ Supported languages
 * Python (requires Python 2.7)
 * C++
 
-If you wish to use bindings for the other supported languages (Java, Perl, R,
-Ruby), please see the [DNAnexus developer
-portal](https://wiki.dnanexus.com/Developer-Portal) for specific instructions
-for your language. In general you can either build from the source
-distribution, or install a prebuilt package specific to the language.
+If you wish to use bindings for the other supported languages (Java, R), please
+see the [DNAnexus developer portal](https://wiki.dnanexus.com/Developer-Portal)
+for specific instructions for your language. In general you can either build
+from the source distribution, or install a prebuilt package specific to the
+language.
 
 Runtime dependencies
 --------------------

build/package.sh

@@ -37,7 +37,7 @@ cd "${DNANEXUS_HOME}"
 make clean
 make
 rm Makefile
-rm -rf debian src/{java,javascript,perl,R,ruby,ua,python/build,{dx-verify-file,dx-contigset-to-fasta}/build} build/*_env share/dnanexus/lib/javascript
+rm -rf debian src/{java,javascript,R,ua,python/build,{dx-verify-file,dx-contigset-to-fasta}/build} build/*_env share/dnanexus/lib/javascript
 mv build/Prebuilt-Readme.md Readme.md
 
 "$(dirname $0)/fix_shebang_lines.sh" bin "/usr/bin/env python2.7"

contrib/Makefile

@@ -0,0 +1,5 @@
+api_wrappers:
+	$(MAKE) -C ./perl lib/DNAnexus/API.pm
+	$(MAKE) -C ./ruby lib/dxruby/api.rb
+
+.PHONY: api_wrappers

contrib/Readme.md

@@ -0,0 +1,11 @@
+Contributed components
+======================
+
+The components in this directory are **unsupported**, even though they
+are in the official source distribution.
+
+The intent of this space is to provide a centralized place where
+somewhat experimental or unsupported ideas can be maintained. You can
+use them as a starting point for your own work. If you can make a case
+for something in here to be fully supported, it can graduate and be
+moved out of this directory and into `/src`.

contrib/perl/.gitignore

@@ -0,0 +1 @@
+/DNAnexus-*

contrib/perl/Makefile

@@ -0,0 +1,7 @@
+SHELL=/bin/bash -e
+
+all: lib/DNAnexus/API.pm
+	(source ../../environment; dzil build; cd DNAnexus-0.0.1; perl Makefile.PL; make install DESTDIR="$(DNANEXUS_HOME)/lib/perl5" DESTINSTALLSITELIB="$(DNANEXUS_HOME)/lib/perl5")
+
+lib/DNAnexus/API.pm: ../../src/api_wrappers/wrapper_table.json generatePerlAPIWrappers.py
+	cat ../../src/api_wrappers/wrapper_table.json | ./generatePerlAPIWrappers.py > lib/DNAnexus/API.pm

contrib/perl/Readme.md

@@ -0,0 +1,22 @@
+DNAnexus Perl API
+=================
+
+Building
+--------
+
+    make all
+
+Using the package
+-----------------
+
+Before the Perl bindings can be initialized, you must set environment
+variables that supply DNAnexus configuration (including a token that
+authenticates you). You can do this with:
+
+    dx login
+    source <(dx env --bash)
+
+Tests / Sample Code
+-------------------
+
+    perl t/10-basics.t

src/perl/dist.ini → contrib/perl/dist.ini

@@ -3,7 +3,7 @@ author  = Andrey Kislyuk <[email protected]>
 license = Perl_5
 copyright_holder = DNAnexus
 copyright_year   = 2012
-version = 0.1
+version = 0.0.1
 
 [GatherDir]
 [MetaYAML]

src/perl/lib/DNAnexus.pm → contrib/perl/lib/DNAnexus.pm

@@ -60,7 +60,7 @@ sub DXHTTPRequest($;$%) {
     $request->authorization($$SECURITY_CONTEXT{auth_token_type}.' '.$$SECURITY_CONTEXT{auth_token});
 
     $request->content(encode_json($data));
-    
+
     my $ua = LWP::UserAgent->new;
     my $response = $ua->request($request);
 
@@ -81,7 +81,7 @@ sub set_api_server_info(;$$$) {
     $host ||= 'api.dnanexus.com';
     $port ||= 443;
     $protocol ||= 'https';
-    
+
     $APISERVER_HOST = $host;
     $APISERVER_PORT = $port;
     $APISERVER = $protocol . "://" . $host . ":" . $port;
@@ -114,7 +114,7 @@ sub _initialize() {
         set_security_context(decode_json($ENV{DX_SECURITY_CONTEXT}));
     }
 
-    print $APISERVER_HOST, $APISERVER_PORT, $APISERVER_PROTOCOL, $APISERVER, $SECURITY_CONTEXT, $PROJECT_CONTEXT_ID, $_DEBUG;
+    # print $APISERVER_HOST, $APISERVER_PORT, $APISERVER_PROTOCOL, $APISERVER, $SECURITY_CONTEXT, $PROJECT_CONTEXT_ID, $_DEBUG;
 }
 
 _initialize();

src/perl/t/10-basics.t → contrib/perl/t/10-basics.t

@@ -20,12 +20,11 @@ use Test::More;
 
 use DNAnexus::API;
 
-$f = DNAnexus::API::systemFindDataObjects();
-for $i (@{$$f{results}}) {
-    print "$_\t$$i{$_}\n" for keys %$i;
+$resp = DNAnexus::API::systemFindDataObjects();
+for $result (@{$$resp{results}}) {
+    print "$_\t$$result{$_}\n" for keys %$result;
 }
 
 ok( 1 == 1 );
 
 done_testing();
-

contrib/ruby/.gitignore

@@ -0,0 +1,3 @@
+/lib/dxruby/version.rb
+/*.gem
+/.yardoc/

contrib/ruby/Makefile

@@ -0,0 +1,24 @@
+SHELL=/bin/bash -e
+
+default: ruby
+
+ruby: lib/dxruby/api.rb lib/dxruby/version.rb
+	gem build dxruby.gemspec
+	export GEM_HOME="$(DNANEXUS_HOME)/lib/rubygems"; gem install dxruby*.gem
+
+contrib/ruby/lib/dxruby/version.rb:
+	(if [ ! -e lib/dxruby/version.rb ]; then \
+	    echo -e "module DX\n  VERSION = \"0.0.0\"\nend\n" > lib/dxruby/version.rb; \
+	fi)
+	(if [ -d "$(DNANEXUS_HOME)/.git" ]; then \
+	    perl -e '$$ENV{GIT_TOOLKIT_VERSION} =~ /^v(\d+.\d+.\d+)/ and print "module DX\n  VERSION = \"$$1\"\nend\n"' > lib/dxruby/version.rb; \
+	fi)
+
+lib/dxruby/api.rb: ../../src/api_wrappers/wrapper_table.json generateRubyAPIWrappers.py
+	cat ../../src/api_wrappers/wrapper_table.json | ./generateRubyAPIWrappers.py > lib/dxruby/api.rb
+
+doc:
+	rm -rf ../../doc/ruby
+	yard --output-dir ../../doc/ruby
+
+.PHONY: default ruby doc

src/ruby/Readme.md → contrib/ruby/Readme.md

@@ -1,7 +1,5 @@
-dxruby: DNAnexus Ruby API
-=========================
-
-[API Documentation](http://autodoc.dnanexus.com/bindings/ruby/current/)
+DNAnexus Ruby API
+=================
 
 Build dependencies
 ------------------
@@ -24,17 +22,25 @@ toolchain. Instead, use `brew install ruby` to install the
 Building
 --------
 
-    make ruby
+    make
+    # For API documentation...
+    make doc
 
 Using the package
 -----------------
 
-The `environment` file will prepend to your `GEM_PATH` (see
-[Installing the toolkit](#installing-the-toolkit)). To use `dxruby`, run:
+Set `GEM_PATH` appropriately:
+
+    export GEM_PATH="${DNANEXUS_HOME}/lib/rubygems:$GEM_PATH"
+
+Then, in your Ruby code:
 
-```
-require 'rubygems'
-require 'dxruby'
-```
+    require 'rubygems'
+    require 'dxruby'
 
 In Ruby 1.9, `require 'rubygems'` is not necessary.
+
+Tests / Sample Code
+-------------------
+
+    ruby test/test_dxruby.rb

debian/.gitignore

@@ -2,10 +2,6 @@
 /dx-toolkit.*
 /dx-java-bindings/
 /dx-java-bindings.*
-/dx-perl-bindings/
-/dx-perl-bindings.*
 /dx-r-bindings/
 /dx-r-bindings.*
-/dx-ruby-bindings/
-/dx-ruby-bindings.*
 /files

debian/control

@@ -3,7 +3,7 @@ Maintainer: Phil Sung <[email protected]>
 Section: science
 Priority: optional
 Standards-Version: 3.9.3
-Build-Depends: debhelper (>= 8), python-virtualenv, libboost1.55-all-dev | libboost1.48-all-dev, r-base-core, libdist-zilla-perl, openjdk-7-jdk, maven2
+Build-Depends: debhelper (>= 8), python-virtualenv, libboost1.55-all-dev | libboost1.48-all-dev, r-base-core, openjdk-7-jdk, maven2
 
 Package: dx-toolkit
 Architecture: any
@@ -18,15 +18,3 @@ Architecture: any
 Depends: ${misc:Depends}, openjdk-7-jre-headless | openjdk-8-jre-headless, dx-toolkit
 Description: Java bindings to DNAnexus Platform
  Bindings for interacting with the DNAnexus platform from Java.
-
-Package: dx-perl-bindings
-Architecture: any
-Depends: ${misc:Depends}, ${perl:Depends}, perl, dx-toolkit
-Description: Perl bindings to DNAnexus Platform
- Bindings for interacting with the DNAnexus platform from Perl.
-
-Package: dx-ruby-bindings
-Architecture: any
-Depends: ${misc:Depends}, ruby1.9.1, dx-toolkit, ruby-json
-Description: Ruby bindings to DNAnexus Platform
- Bindings for interacting with the DNAnexus platform from Ruby.

debian/rules

@@ -7,7 +7,5 @@ override_dh_auto_build:
 override_dh_auto_install:
 	DESTDIR="$(CURDIR)/debian/dx-toolkit" PREFIX="/usr" $(MAKE) -C src debian_install
 	DESTDIR="$(CURDIR)/debian/dx-java-bindings" PREFIX="/usr" $(MAKE) -C src debian_java_install
-	DESTDIR="$(CURDIR)/debian/dx-perl-bindings" PREFIX="/usr" $(MAKE) -C src debian_perl_install
-	DESTDIR="$(CURDIR)/debian/dx-ruby-bindings" PREFIX="/usr" $(MAKE) -C src debian_ruby_install
 
 override_dh_auto_test:

environment

@@ -38,15 +38,12 @@ if [ "$DNANEXUS_HOME" == "/etc/profile.d" ]; then
   # Private Python packages. We really ought not pollute PYTHONPATH with these though.
   export PYTHONPATH="/usr/share/dnanexus/lib/python2.7/site-packages:$PYTHONPATH"
   export CLASSPATH="/usr/share/java/dnanexus-api-0.1.0.jar:${CLASSPATH}"
-  export GEM_PATH="/usr/share/dnanexus/lib/rubygems:$GEM_PATH"
 
 else
 
   export PATH="${DNANEXUS_HOME}/bin:$PATH"
   export PYTHONPATH="${DNANEXUS_HOME}/share/dnanexus/lib/python2.7/site-packages:${DNANEXUS_HOME}/lib/python:$PYTHONPATH"
-  export PERL5LIB="${DNANEXUS_HOME}/lib/perl5:$PERL5LIB"
   export CLASSPATH="${DNANEXUS_HOME}/lib/java/*:${CLASSPATH}"
-  export GEM_PATH="${DNANEXUS_HOME}/lib/rubygems:$GEM_PATH"
 
 fi
 

environment.csh

@@ -32,22 +32,10 @@ else
     setenv PYTHONPATH "$DNANEXUS_HOME/share/dnanexus/lib/python2.7/site-packages:$DNANEXUS_HOME/lib/python"
 endif
 
-if $?PERL5LIB then
-    setenv PERL5LIB "$DNANEXUS_HOME/lib/perl5:$PERL5LIB"
-else
-    setenv PERL5LIB "$DNANEXUS_HOME/lib/perl5"
-endif
-
 if $?CLASSPATH then
     setenv CLASSPATH "$DNANEXUS_HOME/lib/java/*:$CLASSPATH"
 else
     setenv CLASSPATH "$DNANEXUS_HOME/lib/java/*"
 endif
 
-if $?GEM_PATH then
-    setenv GEM_PATH "$DNANEXUS_HOME/lib/rubygems:$GEM_PATH"
-else
-    setenv GEM_PATH "$DNANEXUS_HOME/lib/rubygems"
-endif
-
 setenv PYTHONIOENCODING UTF-8