jandot-ruby-ensembl-api 0.9.2

data/lib/ensembl/db_connection.rb

@@ -0,0 +1,148 @@
+require 'rubygems'
+require 'activerecord'
+
+module Ensembl
+  DB_ADAPTER = 'mysql'
+  DB_HOST = 'ensembldb.ensembl.org'
+  DB_USERNAME = 'anonymous'
+  DB_PASSWORD = ''
+
+  class OldDummyDBConnection < ActiveRecord::Base
+    self.abstract_class = true
+    
+    establish_connection(
+                        :adapter => Ensembl::DB_ADAPTER,
+                        :host => Ensembl::DB_HOST,
+                        :database => '',
+                        :username => Ensembl::DB_USERNAME,
+                        :password => Ensembl::DB_PASSWORD
+                        )
+  end
+
+  class NewDummyDBConnection < ActiveRecord::Base
+    self.abstract_class = true
+    
+    establish_connection(
+                        :adapter => Ensembl::DB_ADAPTER,
+                        :host => Ensembl::DB_HOST,
+                        :database => '',
+                        :username => Ensembl::DB_USERNAME,
+                        :password => Ensembl::DB_PASSWORD,
+                        :port => 5306
+                        )
+  end
+
+  
+  module Core
+    # = DESCRIPTION
+    # The Ensembl::Core::DBConnection is the actual connection established
+    # with the Ensembl server.
+    class DBConnection < ActiveRecord::Base
+      self.abstract_class = true
+      self.pluralize_table_names = false
+
+      # = DESCRIPTION
+      # The Ensembl::Core::DBConnection#connect method makes the connection
+      # to the Ensembl core database for a given species. By default, it connects
+      # to release 50 for that species. You _could_ use a lower number, but
+      # some parts of the API might not work, or worse: give the wrong results.
+      #
+      # = USAGE
+      #  # Connect to release 50 of human
+      #  Ensembl::Core::DBConnection.connect('homo_sapiens')
+      #
+      #  # Connect to release 42 of chicken
+      #  Ensembl::Core::DBConnection.connect('gallus_gallus')
+      #
+      # ---
+      # *Arguments*:
+      # * species:: species to connect to. Arguments should be in snake_case
+      # * ensembl_release:: the release of the database to connect to
+      #  (default = 50)
+      def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
+        dummy_dbconnection = ( release > 47 ) ? Ensembl::NewDummyDBConnection.connection : Ensembl::OldDummyDBConnection.connection
+        db_name = nil
+        
+        if args[:database]
+          db_name = args[:database]
+        else  
+          db_name = dummy_dbconnection.select_values('show databases').select{|v| v =~ /#{species}_core_#{release.to_s}/}[0]
+        end
+
+        if db_name.nil?
+          warn "WARNING: No connection to database established. Check that the species is in snake_case (was: #{species})."
+        else
+          port = ( release > 47 ) ? 5306 : nil
+          establish_connection(
+                              :adapter => args[:adapter] || Ensembl::DB_ADAPTER,
+                              :host => args[:host] || Ensembl::DB_HOST,
+                              :database => args[:database] || db_name,
+                              :username => args[:username] || Ensembl::DB_USERNAME,
+                              :password => args[:password] || Ensembl::DB_PASSWORD,
+                              :port => args[:port] || port
+                            ) 
+          self.retrieve_connection                                                       
+        end
+        
+      end
+
+    end
+
+  end
+
+  module Variation
+    # = DESCRIPTION
+    # The Ensembl::Variation::DBConnection is the actual connection established
+    # with the Ensembl server.
+    class DBConnection < ActiveRecord::Base
+      self.abstract_class = true
+      self.pluralize_table_names = false
+
+      # = DESCRIPTION
+      # The Ensembl::Variation::DBConnection#connect method makes the connection
+      # to the Ensembl variation database for a given species. By default, it connects
+      # to release 50 for that species. You _could_ use a lower number, but
+      # some parts of the API might not work, or worse: give the wrong results.
+      #
+      # = USAGE
+      #  # Connect to release 50 of human
+      #  Ensembl::Variation::DBConnection.connect('homo_sapiens')
+      #
+      #  # Connect to release 42 of chicken
+      #  Ensembl::Variation::DBConnection.connect('gallus_gallus')
+      #
+      # ---
+      # *Arguments*:
+      # * species:: species to connect to. Arguments should be in snake_case
+      # * ensembl_release:: the release of the database to connect to
+      #  (default = 50)
+      def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
+        dummy_dbconnection = ( release > 47 ) ? Ensembl::NewDummyDBConnection.connection : Ensembl::OldDummyDBConnection.connection
+        db_name = nil
+        if args[:database]
+          db_name = args[:database]
+        else  
+          db_name = dummy_dbconnection.select_values('show databases').select{|v| v =~ /#{species}_variation_#{release.to_s}/}[0]
+        end
+        
+        if db_name.nil?
+          warn "WARNING: No connection to database established. Check that the species is in snake_case (was: #{species})."
+        else
+          port = ( release > 47 ) ? 5306 : nil
+          establish_connection(
+                              :adapter => Ensembl::DB_ADAPTER,
+                              :host => args[:host] || Ensembl::DB_HOST,
+                              :database => db_name,
+                              :username => args[:username] || Ensembl::DB_USERNAME,
+                              :password => args[:password] || Ensembl::DB_PASSWORD,
+                              :port => args[:port] || port
+                            )
+          self.retrieve_connection                                                                                                                             
+        end
+        
+      end
+
+    end
+
+  end
+end

data/lib/ensembl/variation/activerecord.rb

@@ -0,0 +1,308 @@
+#
+# = ensembl/variation/activerecord.rb - ActiveRecord mappings to Ensembl variation
+#
+# Copyright::   Copyright (C) 2008 Jan Aerts <http://jandot.myopenid.com>
+# License::     The Ruby License
+#
+
+nil
+module Ensembl
+  # = DESCRIPTION
+  # The Ensembl::Variation module covers the variation databases from
+  # ensembldb.ensembl.org.
+  module Variation
+    # = DESCRIPTION
+    # The Allele class describes a single allele of a variation. In addition to
+    # the nucleotide(s) (or absence of) that representing the allele frequency
+    # and population information may be present.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # = USAGE
+    #  allele = Allele.find(1)
+    #  puts allele.to_yaml
+    class Allele < DBConnection
+      set_primary_key 'allele_id'
+      belongs_to :sample
+      belongs_to :variation
+      belongs_to :population
+    end
+
+    # = DESCRIPTION
+    # The AlleleGroup class represents a grouping of alleles that have tight 
+    # linkage and are usually present together. This is commonly known as a 
+    # Haplotype or Haplotype Block. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # = USAGE
+    #  allele_group = AlleleGroup.find(1)
+    #  puts allele_group.to_yaml
+    class AlleleGroup < DBConnection
+      set_primary_key 'allele_group_id'
+      belongs_to :variation_group
+      belongs_to :source
+      belongs_to :sample
+      belongs_to :allele_group_allele
+    end
+    
+    # = DESCRIPTION
+    # The AlleleGroupAllele class represents a connection class between Allele and AlleleGroup. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class AlleleGroupAllele < DBConnection
+      belongs_to :variation
+      belongs_to :allele_group
+    end
+    
+    # = DESCRIPTION
+    # The Sample class gives information about the biological samples stored in the database. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Sample < DBConnection
+      set_primary_key "sample_id"
+      has_one :individual
+      has_one :sample_synonym
+      has_many :individual_genotype_multiple_bp
+      has_many :compressed_genotype_single_bp
+      has_many :read_coverage
+      has_one :population
+      has_many :tagged_variation_features
+    end
+
+    # = DESCRIPTION
+    # The IndividualPopulation class is used to connect Individual and Population classes. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class IndividualPopulation < DBConnection
+      belongs_to :individual
+      belongs_to :population
+    end
+    
+    # = DESCRIPTION
+    # The Individual class gives information on the single individuals used 
+    # to retrieve one or more biological samples.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Individual < DBConnection
+      belongs_to :sample
+      # CAN'T FIGURE OUT SOME TABLE FIELDS
+    end
+    
+    class IndividualGenotypeMultipleBp < DBConnection
+      belongs_to :sample
+      belongs_to :variation
+    end
+    
+    class CompressedGenotypeSingleBp < DBConnection
+      belongs_to :sample
+    end  
+    
+    class ReadCoverage < DBConnection
+      belongs_to :sample
+    end
+    
+    class Population < DBConnection
+      belongs_to :sample
+    end
+    
+    class PopulationStructure < DBConnection
+      # CAN'T FIGURE OUT SOME TABLE FIELDS
+    end
+    
+    # = DESCRIPTION
+    # The PopulationGenotype class gives information about alleles and allele 
+    # frequencies for a SNP observed within a population or a group of samples. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class PopulationGenotype < DBConnection
+      set_primary_key "population_genotype_id"
+      belongs_to :variation
+      belongs_to :population
+    end
+    
+    # = DESCRIPTION
+    # The SampleSynonym class represents information about alternative names 
+    # for sample entries. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class SampleSynonym < DBConnection
+      set_primary_key "sample_synonym_id"
+      belongs_to :source
+      belongs_to :sample
+      belongs_to :population
+    end
+    
+    # = DESCRIPTION
+    # The Source class gives information on the different databases and SNP 
+    # panels used to retrieve the data
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Source < DBConnection
+      set_primary_key "source_id"
+      has_many :sample_synonyms
+      has_many :allele_groups
+      has_many :variations
+      has_many :variation_groups
+      has_many :httags
+      has_many :variation_synonyms
+    end
+    
+    # = DESCRIPTION
+    # The VariationSynonym class gives information on alterative names used 
+    # for Variation entries. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationSynonym < DBConnection
+      set_primary_key "variation_synonym_id"
+      belongs_to :variation
+      belongs_to :source
+    end
+    
+    # = DESCRIPTION
+    # The Variation class represents single nucleotide polymorhisms (SNP) or variations 
+    # and provides information like the names (IDs), the validation status and 
+    # the allele information.
+    #
+    # *BUG*: fields like validation_status and consequence_type are created 
+    # using SET option directly in MySQL. These fields are bad interpreted by
+    # ActiveRecord, returning always 0.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Variation < DBConnection
+      set_primary_key "variation_id"
+      belongs_to :source
+      has_one :variation_synonym
+      has_one :flanking_sequence
+      has_many :allele_group_alleles
+      has_many :allele_groups, :through => :allele_group_alleles
+      has_many :population_genotypes
+      has_many :alleles
+      has_one :variation_feature
+      has_many :variation_group_variations
+      has_many :variation_groups, :through => :variation_group_variations
+      has_many :individual_genotype_multiple_bps
+    end
+    
+    # = DESCRIPTION
+    # The VariationGroup class represents a group of variations (SNPs) that are 
+    # linked and present toghether. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationGroup < DBConnection
+      set_primary_key "variation_group_id"
+      belongs_to :source
+      has_one :variation_group_variation
+      has_one :httag
+      has_one :variation_group_feature
+      has_one :allele_group
+    end
+    
+    # = DESCRIPTION
+    # The VariationGroupVariation class is a connection class. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationGroupVariation < DBConnection
+      belongs_to :variation
+      belongs_to :variation_group
+    end
+    
+    # = DESCRIPTION
+    # The VariationFeature class gives information about the genomic position of 
+    # each Variation, including also validation status and consequence type. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationFeature < DBConnection
+      set_primary_key "variation_feature_id"
+      belongs_to :variation
+      has_many :tagged_variation_features
+      has_many :samples, :through => :tagged_variation_features
+      has_many :transcript_variations
+    end
+    
+    # = DESCRIPTION
+    # The VariationGroupFeature class gives information on the genomic position 
+    # of each VariationGroup.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class VariationGroupFeature < DBConnection
+      set_primary_key "variation_group_feature_id"
+      belongs_to :variation_group
+    end
+    
+    # = DESCRIPTION
+    # The TranscriptVariation class gives information about the position of 
+    # a VariationFeature, mapped on an annotated transcript.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class TranscriptVariation < DBConnection
+      set_primary_key "transcript_variation_id"
+      belongs_to :variation_feature
+    end
+    
+    # = DESCRIPTION
+    # The FlankingSequence class gives information about the genomic coordinates 
+    # of the flanking sequences, for a single VariationFeature. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class FlankingSequence < DBConnection
+      belongs_to :variation
+    end
+    
+    # = DESCRIPTION
+    # The TaggedVariationFeature class is a connection class. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class TaggedVariationFeature < DBConnection
+      belongs_to :variation_feature
+      belongs_to :sample
+    end
+    
+    class Httag < DBConnection
+      set_primary_key "httag_id"
+      belongs_to :variation_group
+      belongs_to :source
+    end
+    
+  end
+end