bel-rdf-jena 0.4.0.beta1-java → 0.4.0.beta2-java

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Files changed (6) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +3 -2
  3. data/CHANGELOG.md +5 -2
  4. data/README.md +38 -2
  5. data/bin/bel-rdf-jena +33 -0
  6. metadata +30 -15
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data/.gemspec CHANGED
@@ -1,6 +1,6 @@
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  Gem::Specification.new do |spec|
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  spec.name = 'bel-rdf-jena'
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- spec.version = '0.4.0.beta1'
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+ spec.version = '0.4.0.beta2'
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  spec.summary = """
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  Rdf Repository plugin for bel.rb using Apache Jena.
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  """.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
@@ -38,7 +38,8 @@ Gem::Specification.new do |spec|
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  ]
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  spec.platform = 'java'
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- spec.add_runtime_dependency 'rdf-jena'
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+ spec.add_runtime_dependency 'bel', '~> 0.4.0.beta'
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+ spec.add_runtime_dependency 'rdf-jena', '~> 0.3.3'
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  spec.post_install_message = %Q{
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  ******************************
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  * bel-rdf-jena plugin *
data/CHANGELOG.md CHANGED
@@ -3,7 +3,10 @@ All notable changes to bel-rdf-jena will be documented in this file. The curated
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  This project adheres to [Semantic Versioning](http://semver.org/).
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+ ## [0.4.0.beta2][0.4.0.beta2] - 2015-12-11
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+ ### Added
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+ - Added bel-rdf-jena executable that allows creation of Apache Jena TDB databases from RDF files.
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+
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  ## [0.4.0.beta1][0.4.0.beta1] - 2015-12-01
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- ### Fixed
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- ### Changed
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  ### Added
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+ - Added RDF Repository plugin for bel.rb using rdf-jena gem.
data/README.md CHANGED
@@ -5,13 +5,49 @@ This implements an RdfRepository plugin for [bel.rb](https://github.com/OpenBEL/
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  ## Features
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  - Plugs in rdf-jena as an Rdf Repository plugin.
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+ - `rdf-jena` executable that allows creation of Apache Jena TDB database.
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  ## Requirements
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  - JRuby 1.7 or 9k series (due to rdf-jena).
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- How can I use this?
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- ------------------
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+ ## Install
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+
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+ First install the gem using:
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+
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+ ```bash
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+ gem install bel-rdf-jena
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+ ```
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+
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+ Now the plugin is installed and can be used by bel.rb.
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+
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+ ## Getting started
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+
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+ ### bel-rdf-jena executable
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+
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+ This gem includes an executable that can create an RDF database (Apache Jena TDB) from one or more RDF files.
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+
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+ You will have the `bel-rdf-jena` executable available to you (i.e. on your `PATH`) once you install this gem. Keep in mind that you may have to add `$GEM_HOME/bin` to your `PATH` to pick up installed executables.
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+
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+ Now to create an Apache Jena TDB database provide a directory and one or more.
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+
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+ Example:
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+
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+ ```bash
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+ bel-rdf-jena --dir /opt/data/resources_rdf --file biological-concepts-rdf.ttl
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+ ```
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+
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+ Note: It may take a while to load your RDF data. Apache Jena does a good job of balancing performance and memory allocation. You can increase memory allocation for the process by specifying the `-J-Xmx4g` (i.e. max heap size of 4 Gb) option in `JRUBY_OPTS`.
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+
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+ Example:
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+
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+ ```bash
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+ JRUBY_OPTS="-J-Xmx4g" bel-rdf-jena --dir /opt/data/resources_rdf --file biological-concepts-rdf.ttl
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+ ```
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+
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+ Tip: For the `biological-concepts-rdf.ttl` file found on the [OpenBEL build server](http://build.openbel.org/browse/OR) try setting this to `-J-Xmx4g` or `-J-Xmx8g` if possible.
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+
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+ ### Plugin to bel.rb for accessing Annotations and Namespaces
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  bel.rb provides an [approach to plugins](https://github.com/OpenBEL/bel.rb/wiki/Plugins-in-bel.rb) that is meant to be uncomplicated. The following steps will get you started:
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data/bin/bel-rdf-jena ADDED
@@ -0,0 +1,33 @@
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+ #!/usr/bin/env jruby
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+ require 'optparse'
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+ require 'rdf/jena'
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+ require 'rdf/turtle'
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+
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+ # options; any default go here
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+ options = {}
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+
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+ # parse options from cli
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+ OptionParser.new do |opts|
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+ opts.banner = %Q{
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+ Builds an Apache Jena TDB database from RDF files.
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+
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+ Usage: bel-rdf-jena -d [DIR] -f [FILE] -f [FILE] ...
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+ }.gsub(/^ +/, '')
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+
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+ opts.on('-d', '--dir DIR', 'The directory where the TDB database will live.') do |dir|
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+ options[:dir] = dir
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+ end
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+
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+ opts.on('-f', '--file FILE', 'An RDF file to load.', 'Can be used multiple times.') do |file|
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+ (options[:files] ||= []) << file
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+ end
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+ end.parse!
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+
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+ tdb_repository = RDF::Jena::Repository.new(options[:dir])
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+
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+ options[:files].each do |file|
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+ $stdout.puts %Q{Loading RDF from "#{file}".}
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+ tdb_repository.insert_file(file)
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+ end
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+
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+ $stdout.puts %Q{Created TDB database at "#{options[:dir]}".}
metadata CHANGED
@@ -1,34 +1,49 @@
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  --- !ruby/object:Gem::Specification
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  name: bel-rdf-jena
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  version: !ruby/object:Gem::Version
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- version: 0.4.0.beta1
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+ version: 0.4.0.beta2
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  platform: java
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  authors:
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  - Anthony Bargnesi
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- autorequire:
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+ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2015-12-01 00:00:00.000000000 Z
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+ date: 2015-12-12 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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- name: rdf-jena
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 0.4.0.beta
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+ name: bel
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+ prerelease: false
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  type: :runtime
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 0.4.0.beta
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+ - !ruby/object:Gem::Dependency
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 0.3.3
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+ name: rdf-jena
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  prerelease: false
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+ type: :runtime
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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- description: " An rdf repository plugin for bel.rb that uses Apache Jena's TDB data
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- storage to support default and named graphs. "
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+ version: 0.3.3
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+ description: " An rdf repository plugin for bel.rb that uses Apache Jena's TDB data\
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+ \ storage to support default and named graphs. "
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  email:
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  - abargnesi@selventa.com
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- executables: []
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+ executables:
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+ - bel-rdf-jena
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  extensions: []
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  extra_rdoc_files: []
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  files:
@@ -38,6 +53,7 @@ files:
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  - INSTALL_RUBY.md
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  - LICENSE
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  - README.md
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+ - bin/bel-rdf-jena
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  - lib/bel/rdf_repository/plugins/jena.rb
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  homepage: https://github.com/OpenBEL/bel.rb-rdf-jena
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  licenses:
@@ -89,10 +105,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: 1.3.1
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  requirements: []
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- rubyforge_project:
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- rubygems_version: 2.4.5.1
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- signing_key:
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+ rubyforge_project:
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+ rubygems_version: 2.4.8
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+ signing_key:
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  specification_version: 4
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  summary: Rdf Repository plugin for bel.rb using Apache Jena.
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  test_files: []
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- has_rdoc: