goactive 0.1.0

data/MIT-LICENSE

@@ -0,0 +1,21 @@
+Copyright (c) 2006-2007, Regents of the University of Colorado.
+Developer:: Simon Chiang, Biomolecular Structure Program
+Support:: UCHSC School of Medicine Deans Academic Enrichment Fund
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this
+software and associated documentation files (the "Software"), to deal in the Software
+without restriction, including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or
+substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/README

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+= GOActive
+
+Gene Ontology ActiveRecord models.
+
+== Description
+
+GOActive is a gem/rails plugin containing ActiveRecord models for the Gene Ontology (GO) database
+and migrations to assist in setting up a local version of GO.  GOActive is a part of the 
+BioActive[http://rubyforge.org/projects/bioactive] project.
+
+== Features/Problems
+
+Currently the GOActive models have only been used in one tiny application.  As such, very little
+work has gone into developing the models beyond defining obvious associations in the 
+database.  Nonetheless, the basic associations are numerous so GOActive is a good starting point
+for new ruby/rails projects that need them.  
+
+If you find your work improves these models, please do get in contact with me and pass your 
+development back into the community.  Additionally, if you have models for another biological 
+database, see the BioActive[http://rubyforge.org/projects/bioactive] project on 
+RubyForge[http://rubyforge.org] for a nice place to share them.
+
+== Installation
+
+GOActive can be installed as a gem or as a rails plugin. 
+
+=== For the gem:
+
+  % gem install goactive
+
+If you don't have the activerecord gem, you'll be prompted to install dependencies.  Then in 
+your scripts:
+  
+  # load the gem
+  require 'goactive'
+  
+  # create a connection to your GO database
+  ActiveRecord....
+  
+  # now use the models as you please
+  dbxref = Dbxref.find :first, :conditions => ["xref_key = ? and xref_dbname = ?", "", "Uniprot"]
+  dbxref.gene_product.associated_terms.first.name # => 
+
+=== For the plugin:
+
+The plugin is most easily utilized by first installing the {Rails Engines}[http://rails-engines.org/] plugin.  
+Last I checked all you need to do is this (from your rails project of course):
+
+  % script/plugin install http://svn.rails-engines.org/plugins/engines
+
+Check their website for details if this doesn't work.  Installing GOActive is similar:
+
+  % script/plugin install svn://rubyforge.org/var/svn/bioactive/goactive
+
+Note: The goactive install command requires you have svn installed.  Without it you'll get no response 
+or something like 'Plugin not found'.  On Windows, even if you have a Subversion client like 
+TortoiseSVN[http://tortoisesvn.tigris.org/], svn is often not available.  Use whatever client you have to 
+manually checkout the files from 'svn://rubyforge...' into your plugins directory.
+
+Now you have the plugin which will be, like all plugins, automatically discovered by your application.
+Unless you do some fancy connection-magic, you'll need to install and run migrations to setup the 
+GO database on your computer.
+
+  % script/generate plugin_migration
+  % rake db:migrate
+  
+== License
+
+Copyright (c) 2006-2007, Regents of the University of Colorado.
+Developer:: Simon Chiang, Biomolecular Structure Program
+Support:: UCHSC School of Medicine Deans Academic Enrichment Fund
+Licence:: MIT-Style
+

data/app/models/assoc_rel.rb

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+class AssocRel < ActiveRecord::Base
+	set_table_name "assoc_rel"
+	belongs_to :from, :class_name => "Association", :foreign_key => "from_id"
+	belongs_to :to, :class_name => "Association", :foreign_key => "to_id"
+	belongs_to :relationship_type, :class_name => "Term", :foreign_key => "term_id"
+end

data/app/models/association.rb

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+class Association < ActiveRecord::Base
+	set_table_name "association"
+	belongs_to :term
+	belongs_to :gene_product
+	belongs_to :db, :foreign_key => "source_db_id"
+	has_many :association_qualifiers
+	has_many :qualifiers, :through => :association_qualifiers
+	has_many :evidences
+	
+	has_and_belongs_to_many :associations,
+		:class_name => "Association",
+		:join_table => "assoc_rel",
+		:foreign_key => "from_id",
+		:association_foreign_key => "to_id"
+	has_and_belongs_to_many :reverse_associations,
+		:class_name => "Association",
+		:join_table => "assoc_rel",
+		:foreign_key => "to_id",
+		:association_foreign_key => "from_id"
+end

data/app/models/association_qualifier.rb

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+class AssociationQualifier < ActiveRecord::Base
+	set_table_name "association_qualifier"
+	belongs_to :association
+	belongs_to :qualifier, :class_name => 'Term', :foreign_key => 'term_id'
+end

data/app/models/db.rb

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+class Db < ActiveRecord::Base
+	set_table_name "db"
+	has_many :associations, :foreign_key => "source_db_id"
+end

data/app/models/dbxref.rb

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+class Dbxref < ActiveRecord::Base
+	set_table_name "dbxref"
+	has_many :evidence
+	
+	# confusing name... 
+	has_many :evidence_dbxrefs
+	has_many :evidences, :through => :evidence_dbxrefs
+	
+  # apparently a has_one relationship, as per the 'unique' flag on the field in the database schema
+	has_one :gene_product 
+	has_many :seq_dbxrefs
+	has_many :seqs, :through => :seq_dbxrefs
+	has_many :term_dbxrefs
+	has_many :terms, :through => :term_dbxrefs
+	has_many :term_definitions
+  
+  def associated_terms=(input)
+    @associated_terms = input
+  end
+  
+  def associated_terms
+    unless @associated_terms
+      @associated_terms = if gene_product.nil?
+        []
+      else
+        term_ids = gene_product.associations.collect {|a| a.term_id}.uniq
+        
+        # selecting the graph paths in this way is MUCH quicker than using 
+        # GraphPath.find because it doesn't instantiate GraphPath objects
+        associated_ids =  GraphPath.connection.select_all(%Q{select term1_id from #{GraphPath.table_name} where term2_id in (#{term_ids.join(',')})}) 
+        associated_ids =  associated_ids.collect {|gp| gp["term1_id"] }.uniq
+        
+        Term.find(:all, :conditions => ["id in (?)", associated_ids])
+      end
+    end
+    @associated_terms
+  end
+end

data/app/models/evidence.rb

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+class Evidence < ActiveRecord::Base
+	set_table_name "evidence"
+	belongs_to :association
+	belongs_to :dbxref
+	has_many :evidence_dbxrefs
+	has_many :dbxrefs, :through => :evidence_dbxrefs
+end

data/app/models/evidence_dbxref.rb

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+class EvidenceDbxref < ActiveRecord::Base
+	set_table_name "evidence_dbxref"
+	belongs_to :evidence
+	belongs_to :dbxref
+end

data/app/models/gene_product.rb

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+class GeneProduct < ActiveRecord::Base
+	set_table_name "gene_product"
+	has_many :associations
+	belongs_to :dbxref
+	belongs_to :species
+	belongs_to :secondary_species, :class_name => "Species", :foreign_key => "secondary_species_id"
+	belongs_to :type, :class_name => "Term", :foreign_key => "type_id"
+	has_many :properties, :class_name => "GeneProductProperty"
+	has_many :gene_product_seqs
+	has_many :sequences, :through => :gene_product_seqs
+	has_many :synonyms, :class_name => "GeneProductSynonym"
+end

data/app/models/gene_product_count.rb

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+class GeneProductCount < ActiveRecord::Base
+	set_table_name "gene_product_count"
+	belongs_to :term
+end

data/app/models/gene_product_property.rb

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+class GeneProductProperty < ActiveRecord::Base
+	set_table_name "gene_product_property"
+	belongs_to :gene_product
+end

data/app/models/gene_product_seq.rb

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+class GeneProductSeq < ActiveRecord::Base
+	set_table_name "gene_product_seq"
+	belongs_to :gene, :class_name => 'GeneProduct', :foreign_key => 'gene_product_id'
+	belongs_to :seq
+end

data/app/models/gene_product_synonym.rb

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+class GeneProductSynonym < ActiveRecord::Base
+	set_table_name "gene_product_synonym"
+	belongs_to :gene_product
+end

data/app/models/graph_path.rb

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+class GraphPath < ActiveRecord::Base
+	set_table_name "graph_path"
+	belongs_to :term1, :class_name => 'Term', :foreign_key => :term1_id
+	belongs_to :term2, :class_name => 'Term', :foreign_key => :term2_id
+	has_many :graph_path2terms
+end

data/app/models/graph_path2term.rb

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+class GraphPath2term < ActiveRecord::Base
+	set_table_name "graph_path2term"
+	belongs_to :graph_path
+	belongs_to :term
+end

data/app/models/instance_data.rb

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+class InstanceData < ActiveRecord::Base
+	set_table_name "instance_data"
+end

data/app/models/seq.rb

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+class Seq < ActiveRecord::Base
+	set_table_name "seq"
+	has_many :gene_product_seqs
+	has_many :genes, :through => :gene_product_seqs
+	#belongs_to :display what does display id refer to??
+	has_many :seq_dbxrefs
+	has_many :dbxrefs, :through => :seq_dbxrefs
+	has_many :properties, :class_name => 'SeqProperty'
+end

data/app/models/seq_dbxref.rb

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+class SeqDbxref < ActiveRecord::Base
+	set_table_name "seq_dbxref"
+	belongs_to :seq
+	belongs_to :dbxref
+end

data/app/models/seq_property.rb

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+class SeqProperty < ActiveRecord::Base
+	set_table_name "seq_property"
+	belongs_to :seq
+end

data/app/models/source_audit.rb

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+class SourceAudit < ActiveRecord::Base
+	set_table_name "source_audit"
+end

data/app/models/species.rb

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+class Species < ActiveRecord::Base
+	set_table_name "species"
+	has_many :gene_products
+	
+	# kind of misleading as a name?
+	has_many :secondary_gene_products, :class_name => "GeneProduct", :foreign_key => "secondary_species_id"
+	
+	# Still not sure what ncbi_taxa_id refers to...
+	#belongs_to :ncbi_taxa
+end

data/app/models/term.rb

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+class Term < ActiveRecord::Base
+	set_table_name "term"
+	has_many :associations
+	#has_many :association_relationships
+	has_many :association_qualifiers
+	#has_many :associations, :through => :association_qualifiers
+	has_many :gene_products, :foreign_key => 'type_id'
+	has_many :gene_product_counts
+	
+	# graph path terms
+	has_and_belongs_to_many :graph_path_children,
+		:class_name => "Term",
+		:join_table => "graph_path",
+		:foreign_key => "term1_id",
+		:association_foreign_key => "term2_id"
+	has_and_belongs_to_many :graph_path_parents,
+		:class_name => "Term",
+		:join_table => "graph_path",
+		:foreign_key => "term2_id",
+		:association_foreign_key => "term1_id"
+		
+	has_many :graph_path2terms
+	
+	# term2term relationships:
+	#has_many :term2term_relationships
+	has_and_belongs_to_many :children,
+		:class_name => "Term",
+		:join_table => "term2term",
+		:foreign_key => "term1_id",
+		:association_foreign_key => "term2_id"
+	has_and_belongs_to_many :parents,
+		:class_name => "Term",
+		:join_table => "term2term",
+		:foreign_key => "term2_id",
+		:association_foreign_key => "term1_id"
+		
+	has_many :audits, :class_name => 'TermAudit'
+	has_many :term_dbxrefs
+	has_many :dbxrefs, :through => :term_dbxrefs
+	has_many :definitions, :class_name => 'TermDefinition'
+	has_many :properties, :class_name => 'TermProperty'
+	has_many :subsets, :class_name => 'TermSubset'
+	# has_many :subset_members, :class_name => 'TermSubset', :foreign_key => 'subset_id'
+	has_many :synonyms, :class_name => 'TermSynonym'
+	#has_many :synonym_types
+end

data/app/models/term2term.rb

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+class Term2term < ActiveRecord::Base
+	set_table_name "term2term"
+	belongs_to :relationship, :class_name => 'Term', :foreign_key => 'relationship_type_id'
+	belongs_to :parent, :class_name => 'Term', :foreign_key => 'term1_id'
+	belongs_to :child, :class_name => 'Term', :foreign_key => 'term2_id'
+end

data/app/models/term_audit.rb

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+class TermAudit < ActiveRecord::Base
+	set_table_name "term_audit"
+	belongs_to :term
+end

data/app/models/term_dbxref.rb

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+class TermDbxref < ActiveRecord::Base
+	set_table_name "term_dbxref"
+	belongs_to :term
+	belongs_to :dbxref
+end

data/app/models/term_definition.rb

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+class TermDefinition < ActiveRecord::Base
+	set_table_name "term_definition"
+	belongs_to :term
+	belongs_to :dbxref
+end

data/app/models/term_property.rb

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+class TermProperty < ActiveRecord::Base
+	set_table_name "term_property"
+	belongs_to :term
+end

data/app/models/term_subset.rb

@@ -0,0 +1,5 @@
+class TermSubset < ActiveRecord::Base
+	set_table_name "term_subset"
+	belongs_to :term
+	belongs_to :subset, :class_name => 'Term'
+end

data/app/models/term_synonym.rb

@@ -0,0 +1,5 @@
+class TermSynonym < ActiveRecord::Base
+	set_table_name "term_synonym"
+	belongs_to :term
+	belongs_to :synonym_type, :class_name => 'Term', :foreign_key => 'synonym_type_id'
+end

data/lib/goactive.rb

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+# GOActive
+require 'active_record'
+
+Dir.glob(File.dirname(__FILE__) + "/../app/models/*.rb") do |file|
+  require file
+end

data/test/goactive_test.rb

@@ -0,0 +1,8 @@
+require 'test/unit'
+
+class GoactiveTest < Test::Unit::TestCase
+  # Replace this with your real tests.
+  def test_this_plugin
+    flunk
+  end
+end

data/test/goactive_test_helper.rb

@@ -0,0 +1,5 @@
+require 'test/unit'
+require 'gemdev'
+require 'joinfix'
+
+Test::Unit::TestCase.fixture_path = File.dirname(__FILE__) + "/fixtures"

data/test/goactive_test_suite.rb

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+$:.unshift File.join(File.dirname(__FILE__), '../lib')
+
+ENV["ALL"] = 'true'
+Dir.glob("./**/*_test.rb").each {|test| require test}

data/test/units/assoc_rel_test.rb

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+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class AssocRelTest < Test::Unit::TestCase
+  fixtures :assoc_rel
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/association_qualifier_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class AssociationQualifierTest < Test::Unit::TestCase
+  fixtures :association_qualifier
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/association_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class AssociationTest < Test::Unit::TestCase
+  fixtures :association
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/db_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class DbTest < Test::Unit::TestCase
+  fixtures :db
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/dbxref_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class DbxrefTest < Test::Unit::TestCase
+  fixtures :dbxref
+  
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/evidence_dbxref_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class EvidenceDbxrefTest < Test::Unit::TestCase
+  fixtures :evidence_dbxref
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/evidence_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class EvidenceTest < Test::Unit::TestCase
+  fixtures :evidence
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/gene_product_count_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GeneProductCountTest < Test::Unit::TestCase
+  fixtures :gene_product_count
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/gene_product_property_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GeneProductPropertyTest < Test::Unit::TestCase
+  fixtures :gene_product_property
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/gene_product_seq_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GeneProductSeqTest < Test::Unit::TestCase
+  fixtures :gene_product_seq
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/gene_product_synonym_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GeneProductSynonymTest < Test::Unit::TestCase
+  fixtures :gene_product_synonym
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/gene_product_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GeneProductTest < Test::Unit::TestCase
+  fixtures :gene_product
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/graph_path2term_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GraphPath2termTest < Test::Unit::TestCase
+  fixtures :graph_path2term
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/graph_path_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class GraphPathTest < Test::Unit::TestCase
+  fixtures :graph_path
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/instance_data_test.rb

@@ -0,0 +1,11 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class InstanceDataTest < Test::Unit::TestCase
+  fixtures :instance_data
+  set_fixture_class :instance_data => "InstanceData"
+  
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/seq_dbxref_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class SeqDbxrefTest < Test::Unit::TestCase
+  fixtures :seq_dbxref
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/seq_property_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class SeqPropertyTest < Test::Unit::TestCase
+  fixtures :seq_property
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/seq_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class SeqTest < Test::Unit::TestCase
+  fixtures :seq
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/source_audit_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class SourceAuditTest < Test::Unit::TestCase
+  fixtures :source_audit
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/species_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class SpeciesTest < Test::Unit::TestCase
+  fixtures :species
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term2term_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class Term2termTest < Test::Unit::TestCase
+  fixtures :term2term
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_audit_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermAuditTest < Test::Unit::TestCase
+  fixtures :term_audit
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_dbxref_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermDbxrefTest < Test::Unit::TestCase
+  fixtures :term_dbxref
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_definition_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermDefinitionTest < Test::Unit::TestCase
+  fixtures :term_definition
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_property_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermPropertyTest < Test::Unit::TestCase
+  fixtures :term_property
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_subset_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermSubsetTest < Test::Unit::TestCase
+  fixtures :term_subset
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_synonym_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermSynonymTest < Test::Unit::TestCase
+  fixtures :term_synonym
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

data/test/units/term_test.rb

@@ -0,0 +1,10 @@
+require File.dirname(__FILE__) + '/../goactive_test_helper'
+
+class TermTest < Test::Unit::TestCase
+  fixtures :term
+
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

metadata

@@ -0,0 +1,146 @@
+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.9.2
+specification_version: 1
+name: goactive
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+date: 2007-05-31 00:00:00 -06:00
+summary: ActiveRecord models for GO.
+require_paths: 
+- lib
+email: simon.chiang@uchsc.edu
+homepage: http://rubyforge.org/projects/bioactive/
+rubyforge_project: 
+description: 
+autorequire: goactive
+default_executable: 
+bindir: bin
+has_rdoc: true
+required_ruby_version: !ruby/object:Gem::Version::Requirement 
+  requirements: 
+  - - ">"
+    - !ruby/object:Gem::Version 
+      version: 0.0.0
+  version: 
+platform: ruby
+signing_key: 
+cert_chain: 
+post_install_message: 
+authors: 
+- Simon Chiang
+files: 
+- test/fixtures
+- test/fixtures/association.yml
+- test/fixtures/association_qualifier.yml
+- test/fixtures/db.yml
+- test/fixtures/dbxref.yml
+- test/fixtures/evidence.yml
+- test/fixtures/evidence_dbxref.yml
+- test/fixtures/gene_product.yml
+- test/fixtures/gene_product_count.yml
+- test/fixtures/gene_product_property.yml
+- test/fixtures/gene_product_seq.yml
+- test/fixtures/gene_product_synonym.yml
+- test/fixtures/graph_path.yml
+- test/fixtures/graph_path2term.yml
+- test/fixtures/instance_data.yml
+- test/fixtures/seq.yml
+- test/fixtures/seq_dbxref.yml
+- test/fixtures/seq_property.yml
+- test/fixtures/source_audit.yml
+- test/fixtures/species.yml
+- test/fixtures/term.yml
+- test/fixtures/term2term.yml
+- test/fixtures/term_audit.yml
+- test/fixtures/term_dbxref.yml
+- test/fixtures/term_definition.yml
+- test/fixtures/term_property.yml
+- test/fixtures/term_subset.yml
+- test/fixtures/term_synonym.yml
+- test/goactive_test.rb
+- test/goactive_test_helper.rb
+- test/goactive_test_suite.rb
+- test/units
+- test/units/association_qualifier_test.rb
+- test/units/association_test.rb
+- test/units/assoc_rel_test.rb
+- test/units/dbxref_test.rb
+- test/units/db_test.rb
+- test/units/evidence_dbxref_test.rb
+- test/units/evidence_test.rb
+- test/units/gene_product_count_test.rb
+- test/units/gene_product_property_test.rb
+- test/units/gene_product_seq_test.rb
+- test/units/gene_product_synonym_test.rb
+- test/units/gene_product_test.rb
+- test/units/graph_path2term_test.rb
+- test/units/graph_path_test.rb
+- test/units/instance_data_test.rb
+- test/units/seq_dbxref_test.rb
+- test/units/seq_property_test.rb
+- test/units/seq_test.rb
+- test/units/source_audit_test.rb
+- test/units/species_test.rb
+- test/units/term2term_test.rb
+- test/units/term_audit_test.rb
+- test/units/term_dbxref_test.rb
+- test/units/term_definition_test.rb
+- test/units/term_property_test.rb
+- test/units/term_subset_test.rb
+- test/units/term_synonym_test.rb
+- test/units/term_test.rb
+- lib/goactive.rb
+- app/models
+- app/models/association.rb
+- app/models/association_qualifier.rb
+- app/models/assoc_rel.rb
+- app/models/db.rb
+- app/models/dbxref.rb
+- app/models/evidence.rb
+- app/models/evidence_dbxref.rb
+- app/models/gene_product.rb
+- app/models/gene_product_count.rb
+- app/models/gene_product_property.rb
+- app/models/gene_product_seq.rb
+- app/models/gene_product_synonym.rb
+- app/models/graph_path.rb
+- app/models/graph_path2term.rb
+- app/models/instance_data.rb
+- app/models/seq.rb
+- app/models/seq_dbxref.rb
+- app/models/seq_property.rb
+- app/models/source_audit.rb
+- app/models/species.rb
+- app/models/term.rb
+- app/models/term2term.rb
+- app/models/term_audit.rb
+- app/models/term_dbxref.rb
+- app/models/term_definition.rb
+- app/models/term_property.rb
+- app/models/term_subset.rb
+- app/models/term_synonym.rb
+- README
+- MIT-LICENSE
+test_files: 
+- test/goactive_test_suite.rb
+rdoc_options: []
+
+extra_rdoc_files: 
+- README
+- MIT-LICENSE
+executables: []
+
+extensions: []
+
+requirements: []
+
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: activerecord
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Version::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.15.3
+    version: