bio-rdf 0.0.1.pre1 → 0.0.1

metadata

@@ -1,8 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: bio-rdf
 version: !ruby/object:Gem::Version
-  version: 0.0.1.pre1
-  prerelease: 6
+  version: 0.0.1
+  prerelease: 
 platform: ruby
 authors:
 - Pjotr Prins
@@ -10,11 +10,22 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-07 00:00:00.000000000Z
+date: 2012-05-01 00:00:00.000000000Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: &15565000 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *15565000
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &16197900 !ruby/object:Gem::Requirement
+  requirement: &15564160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +33,32 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16197900
+  version_requirements: *15564160
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &15562720 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *15562720
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: &15560480 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *15560480
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &16196760 !ruby/object:Gem::Requirement
+  requirement: &15559440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,21 +66,21 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *16196760
+  version_requirements: *15559440
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &16195560 !ruby/object:Gem::Requirement
+  requirement: &15558220 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *16195560
+  version_requirements: *15558220
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &16194300 !ruby/object:Gem::Requirement
+  requirement: &15557260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +88,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *16194300
+  version_requirements: *15557260
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &16193260 !ruby/object:Gem::Requirement
+  requirement: &15515240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +99,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *16193260
+  version_requirements: *15515240
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &16192040 !ruby/object:Gem::Requirement
+  requirement: &15514680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,7 +110,7 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *16192040
+  version_requirements: *15514680
 description: Store relationships in a triple-store, such as gene enrichment and QTL,
   and use this information for inference and causality
 email: pjotr.public01@thebird.nl
@@ -87,19 +120,27 @@ extensions: []
 extra_rdoc_files:
 - LICENSE.txt
 - README.md
-- README.rdoc
 files:
 - .document
 - .travis.yml
 - Gemfile
 - LICENSE.txt
 - README.md
-- README.rdoc
 - Rakefile
 - VERSION
 - bin/bio-rdf
+- doc/design.md
+- features/parse_broad_gsea_cls.feature
+- features/parse_broad_gsea_cls.rb
+- features/parse_broad_gsea_results.feature
+- features/parse_broad_gsea_results.rb
+- features/support/env.rb
 - lib/bio-rdf.rb
+- lib/bio-rdf/parsers/gsea/broadgsea.rb
 - lib/bio-rdf/rdf.rb
+- spec/spec_helper.rb
+- test/data/parsers/gsea/Run1_C2.SUMMARY.RESULTS.REPORT.0.txt
+- test/data/parsers/gsea/Run1_C2.SUMMARY.RESULTS.REPORT.1.txt
 - test/helper.rb
 - test/test_bio-rdf.rb
 homepage: http://github.com/pjotrp/bioruby-rdf
@@ -117,13 +158,13 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -868237054466869818
+      hash: 4447990018592781869
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
-  - - ! '>'
+  - - ! '>='
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.10

data/README.rdoc

@@ -1,46 +0,0 @@
-= bio-rdf
-
-{<img
-src="https://secure.travis-ci.org/pjotrp/bioruby-rdf.png"
-/>}[http://travis-ci.org/#!/pjotrp/bioruby-rdf]
-
-Full description goes here
-
-Note: this software is under active development!
-
-== Installation
-
-        gem install bio-rdf
-
-== Usage
-
-== Developers
-
-To use the library 
-
-        require 'bio-rdf
-
-The API doc is online. For more code examples see also the test files in
-the source tree.
-        
-== Project home page
-
-Information on the source tree, documentation, issues and how to contribute, see
-
-  http://github.com/pjotrp/bioruby-rdf
-
-== Cite
-
-  If you use this software, please cite one of
- 
-* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
-* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
-
-== Biogems.info
-
-This Biogem is published at http://biogems.info/index.html#bio-rdf
-
-== Copyright
-
-Copyright (c) 2012 Pjotr Prins. See LICENSE.txt for further details.
-