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

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |spec|
   spec.name                     = 'bel-rdf-jena'
-  spec.version                  = '0.4.0.beta1'
+  spec.version                  = '0.4.0.beta2'
   spec.summary                  = """
                                     Rdf Repository plugin for bel.rb using Apache Jena.
                                   """.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
@@ -38,7 +38,8 @@ Gem::Specification.new do |spec|
                                   ]
 
   spec.platform                 = 'java'
-  spec.add_runtime_dependency     'rdf-jena'
+  spec.add_runtime_dependency     'bel',      '~> 0.4.0.beta'
+  spec.add_runtime_dependency     'rdf-jena', '~> 0.3.3'
   spec.post_install_message     = %Q{
 ******************************
 *  bel-rdf-jena plugin       *

data/CHANGELOG.md

@@ -3,7 +3,10 @@ All notable changes to bel-rdf-jena will be documented in this file. The curated
 
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.4.0.beta2][0.4.0.beta2] - 2015-12-11
+### Added
+- Added bel-rdf-jena executable that allows creation of Apache Jena TDB databases from RDF files.
+
 ## [0.4.0.beta1][0.4.0.beta1] - 2015-12-01
-### Fixed
-### Changed
 ### Added
+- Added RDF Repository plugin for bel.rb using rdf-jena gem.

data/README.md

@@ -5,13 +5,49 @@ This implements an RdfRepository plugin for [bel.rb](https://github.com/OpenBEL/
 ## Features
 
 - Plugs in rdf-jena as an Rdf Repository plugin.
+- `rdf-jena` executable that allows creation of Apache Jena TDB database.
 
 ## Requirements
 
 - JRuby 1.7 or 9k series (due to rdf-jena).
 
-How can I use this?
-------------------
+## Install
+
+First install the gem using:
+
+```bash
+gem install bel-rdf-jena
+```
+
+Now the plugin is installed and can be used by bel.rb.
+
+## Getting started
+
+### bel-rdf-jena executable
+
+This gem includes an executable that can create an RDF database (Apache Jena TDB) from one or more RDF files.
+
+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.
+
+Now to create an Apache Jena TDB database provide a directory and one or more.
+
+Example:
+
+```bash
+bel-rdf-jena --dir /opt/data/resources_rdf --file biological-concepts-rdf.ttl
+```
+
+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`.
+
+Example:
+
+```bash
+JRUBY_OPTS="-J-Xmx4g" bel-rdf-jena --dir /opt/data/resources_rdf --file biological-concepts-rdf.ttl
+```
+
+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.
+
+### Plugin to bel.rb for accessing Annotations and Namespaces
 
 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:
 

data/bin/bel-rdf-jena

@@ -0,0 +1,33 @@
+#!/usr/bin/env jruby
+require 'optparse'
+require 'rdf/jena'
+require 'rdf/turtle'
+
+# options; any default go here
+options = {}
+
+# parse options from cli
+OptionParser.new do |opts|
+  opts.banner = %Q{
+    Builds an Apache Jena TDB database from RDF files.
+
+    Usage: bel-rdf-jena -d [DIR] -f [FILE] -f [FILE] ...
+  }.gsub(/^ +/, '')
+
+  opts.on('-d', '--dir DIR', 'The directory where the TDB database will live.') do |dir|
+    options[:dir] = dir
+  end
+
+  opts.on('-f', '--file FILE', 'An RDF file to load.', 'Can be used multiple times.') do |file|
+		(options[:files] ||= []) << file
+	end 
+end.parse!
+
+tdb_repository = RDF::Jena::Repository.new(options[:dir])
+
+options[:files].each do |file|
+  $stdout.puts %Q{Loading RDF from "#{file}".}
+  tdb_repository.insert_file(file)
+end
+
+$stdout.puts %Q{Created TDB database at "#{options[:dir]}".}

metadata

@@ -1,34 +1,49 @@
 --- !ruby/object:Gem::Specification
 name: bel-rdf-jena
 version: !ruby/object:Gem::Version
-  version: 0.4.0.beta1
+  version: 0.4.0.beta2
 platform: java
 authors:
 - Anthony Bargnesi
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2015-12-01 00:00:00.000000000 Z
+date: 2015-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: rdf-jena
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.4.0.beta
+  name: bel
+  prerelease: false
   type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.0.beta
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.3
+  name: rdf-jena
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
-description: " An rdf repository plugin for bel.rb that uses Apache Jena's TDB data
-  storage to support default and named graphs. "
+        version: 0.3.3
+description: " An rdf repository plugin for bel.rb that uses Apache Jena's TDB data\
+  \ storage to support default and named graphs. "
 email:
 - abargnesi@selventa.com
-executables: []
+executables:
+- bel-rdf-jena
 extensions: []
 extra_rdoc_files: []
 files:
@@ -38,6 +53,7 @@ files:
 - INSTALL_RUBY.md
 - LICENSE
 - README.md
+- bin/bel-rdf-jena
 - lib/bel/rdf_repository/plugins/jena.rb
 homepage: https://github.com/OpenBEL/bel.rb-rdf-jena
 licenses:
@@ -89,10 +105,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.4.5.1
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.4.8
+signing_key:
 specification_version: 4
 summary: Rdf Repository plugin for bel.rb using Apache Jena.
 test_files: []
-has_rdoc: