bio-kb-illumina 0.0.0 → 0.1.0

data/Gemfile

@@ -3,6 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 
+
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
@@ -11,5 +12,5 @@ group :development do
   gem "jeweler", "~> 1.5.1"
   gem "rcov", ">= 0"
   gem "bio", ">= 1.4.1"
-  gem "activerecord"
+  gem "activerecord", ">= 3.0.3"
 end

data/Gemfile.lock

@@ -29,7 +29,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  activerecord
+  activerecord (>= 3.0.3)
   bio (>= 1.4.1)
   bundler (~> 1.0.0)
   jeweler (~> 1.5.1)

data/README.rdoc

@@ -4,7 +4,7 @@ Provide access to the IlluminaHumanAnnotations. Database comes form Bioconductor
 
 == TODO
 
-* Add all Illumina's annotation, Human, Mouse, others?
+* Add all Illumina's annotation for Mouse and other species?
 
 == Contributing to bio-kb-illumina
  

data/Rakefile

@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
   # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
   #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
   #  gem.add_development_dependency 'rspec', '> 1.2.3'
-  gem.version = "0.0.0"
+  #gem.version = "0.0.0"
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.1.0

data/bio-kb-illumina.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-kb-illumina}
-  s.version = "0.0.0"
+  s.version = "0.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Raoul J.P. Bonnal"]
-  s.date = %q{2010-11-24}
+  s.date = %q{2011-01-11}
   s.description = %q{Provide access to the IlluminaHumanAnnotations. Database comes form Bioconductor's package
      lumiHumanIDMapping}
   s.email = %q{ilpuccio.febo@gmail.com}
@@ -26,8 +26,9 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bio-kb-illumina.gemspec",
-    "data/lumiHumanIDMapping.sqlite",
+    "db/lumiHumanIDMapping.sqlite",
     "lib/bio-kb-illumina.rb",
+    "lib/bio/annotation/illumina/gene_expression.rb",
     "test/helper.rb",
     "test/test_bio-kb-illumina.rb"
   ]
@@ -51,14 +52,14 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<jeweler>, ["~> 1.5.1"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_development_dependency(%q<activerecord>, [">= 0"])
+      s.add_development_dependency(%q<activerecord>, [">= 3.0.3"])
     else
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.5.1"])
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<activerecord>, [">= 0"])
+      s.add_dependency(%q<activerecord>, [">= 3.0.3"])
     end
   else
     s.add_dependency(%q<shoulda>, [">= 0"])
@@ -66,7 +67,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<jeweler>, ["~> 1.5.1"])
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<activerecord>, [">= 0"])
+    s.add_dependency(%q<activerecord>, [">= 3.0.3"])
   end
 end
 

data/lib/bio-kb-illumina.rb

@@ -1,33 +1,10 @@
+#
+# Copyright:: Copyright (c) 2010
+# Raoul J.P. Bonnal <r@bioruby.org>
+# License:: The Ruby License
+#
+
 require 'active_record'
 
-module Bio
-  # I like the idea to have a Knowledge base system 
-  # intended to look for a generic information supplied by the user
-  module KB 
-    module Annotation
-      module Illumina
-        class GeneExpression < ActiveRecord::Base
-          
-          establish_connection(:adapter =>'sqlite3',
-          :database =>"#{File.dirname(__FILE__)}/../data/lumiHumanIDMapping.sqlite"
-          )
-          self.table_name =''
-          #HumanHT12_V3_0_R1_11283641_A
-          
-          def self.list_annotations
-              self.connection.tables.select{|table_name| table_name=~/Human/}
-          end           
-          
-          # Set the table for further use
-          def self.annotation=(annotation_name)
-            if self.list_annotations.include? annotation_name
-              self.table_name=annotation_name
-            else
-              puts "Annotation named: #{annotation_name} doesn't exist. Please selec one from #{self.list_annotations}"
-            end
-          end
-        end #GeneExpression
-      end #Illumina
-    end #Annotation
-  end #KB
-end #Bio
+require 'bio/annotation/illumina/gene_expression'
+

data/lib/bio/annotation/illumina/gene_expression.rb

@@ -0,0 +1,37 @@
+#
+# Copyright:: Copyright (c) 2010
+# Raoul J.P. Bonnal <r@bioruby.org>
+# License:: The Ruby License
+#
+
+module Bio
+  # I like the idea to have a Knowledge base system 
+  # intended to look for a generic information supplied by the user
+  module KB 
+    module Annotation
+      module Illumina
+        class GeneExpression < ActiveRecord::Base          
+          establish_connection(:adapter =>'sqlite3',
+          :database =>"#{File.dirname(__FILE__)}/../../../../data/lumiHumanIDMapping.sqlite"
+          )
+          #self.table_name = nil?
+          #HumanHT12_V3_0_R1_11283641_A
+          
+          def self.list_annotations
+              self.connection.tables.select{|table_name| table_name=~/Human/}
+          end           
+          
+          # Set the table for further use
+          def self.annotation=(annotation_name)
+            if self.list_annotations.include? annotation_name
+              self.reset_column_information
+              self.table_name=annotation_name
+            else
+              puts "Annotation named: #{annotation_name} doesn't exist. Please select one from #{self.list_annotations}"
+            end
+          end
+        end #GeneExpression
+      end #Illumina
+    end #Annotation
+  end #KB
+end #Bio

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
+  - 1
   - 0
-  - 0
-  version: 0.0.0
+  version: 0.1.0
 platform: ruby
 authors: 
 - Raoul J.P. Bonnal
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-11-24 00:00:00 +01:00
+date: 2011-01-11 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -96,8 +96,10 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version 
         segments: 
+        - 3
         - 0
-        version: "0"
+        - 3
+        version: 3.0.3
   type: :development
   prerelease: false
   version_requirements: *id006
@@ -121,8 +123,9 @@ files:
 - Rakefile
 - VERSION
 - bio-kb-illumina.gemspec
-- data/lumiHumanIDMapping.sqlite
+- db/lumiHumanIDMapping.sqlite
 - lib/bio-kb-illumina.rb
+- lib/bio/annotation/illumina/gene_expression.rb
 - test/helper.rb
 - test/test_bio-kb-illumina.rb
 has_rdoc: true
@@ -139,7 +142,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 717046961654346220
+      hash: -4243769106221584944
       segments: 
       - 0
       version: "0"