ensembl 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -2,3 +2,6 @@ source 'https://rubygems.org'
 
 # Specify your gem's dependencies in ensembl.gemspec
 gemspec
+
+gem 'pry', group: :pry
+gem 'pry-doc', group: :pry

data/README.md

@@ -2,7 +2,7 @@
 
 Gem to access ensembl.org database. Currently only supports Variation database tables and latest version.
 
-Some of the work is inspired of [ruby-ensembl-api] project
+Some of the work is inspired of [ruby-ensembl-api] project.
 
 ## Installation
 
@@ -30,14 +30,16 @@ Or install it yourself as:
 
 ### Custom database
     
-    # Set following values before using
+    # Set following values before using - Only Human databases is somewhat tested.
     
     Ensembl.host = 'myhost.example.com'
     Ensembl.port = 3306                                 # default
     Ensembl.username = 'anonymous'                      # default
     Ensembl.password = ''                               # default
-    Ensembl.database = 'homo_sapiens_variation_75_37'   # default
-
+    Ensembl.species = 'homo_sapiens'                    # default
+    Ensembl.version = 75                                # default
+    Ensembl.hg_version = 37                             # default
+    
 
 ## Contributing
 

data/Rakefile

@@ -1,6 +1,6 @@
 require "bundler/gem_tasks"
 
 task :console do
-  exec "irb -r ensembl -I ./lib"
+  exec "pry -r ensembl -I ./lib"
 end
 

data/ensembl.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |spec|
   spec.authors       = ["Kristjan Metsalu"]
   spec.email         = ["kristjan.metsalu@ut.ee"]
   spec.summary       = %q{ Gem to access Ensembl.org databases through API }
-  spec.description   = %q{ ensembl provides an ruby API to connect to ensembl databases. }
+  spec.description   = %q{ ensembl provides an ruby API to connect to Ensembl.org databases.  }
   spec.homepage      = "https://github.com/kmetsalu/ensembl"
   spec.license       = "MIT"
 
@@ -25,4 +25,5 @@ Gem::Specification.new do |spec|
 
   spec.add_development_dependency "bundler", "~> 1.6"
   spec.add_development_dependency "rake", '~> 10.3'
+  spec.add_development_dependency "pry", '~> 0.10'
 end

data/lib/ensembl/core/activerecord.rb

@@ -0,0 +1,462 @@
+module Ensembl
+  module Core
+    module StableIdHistory
+      def previous_stable_ids
+        StableIdEvent.where(new_stable_id: stable_id)
+      end
+    end
+
+    class Connection < ActiveRecord::Base
+      self.extend TableNameOverrides
+
+      self.abstract_class = true
+
+      self.establish_connection :adapter  => "mysql2",
+                                :host     => Ensembl.host,
+                                :username => Ensembl.username,
+                                :password => Ensembl.password,
+                                :database => Ensembl.species+'_core_'+Ensembl.version+'_'+Ensembl.hg_version,
+                                :reconnect => true
+
+    end
+
+    class ModelBase < Connection
+      self.extend PrimaryKeyOverrides
+
+      self.abstract_class = true
+    end
+
+    class AltAllele < ModelBase
+      belongs_to :gene
+      belongs_to :alt_allele_group
+    end
+
+    class AltAlleleAttrib < ModelBase
+      belongs_to :alt_allele
+    end
+
+    class AltAlleleGroup < ModelBase
+      has_many :alt_alleles
+    end
+
+    # TODO: Verify that is working
+    class Analysis < ModelBase
+      has_one :analysis_description
+    end
+
+    class AnalysisDescription < Connection
+      has_one :analysis
+    end
+
+    class AssociatedGroup < ModelBase
+      has_many :associated_xrefs
+    end
+
+    class AssociatedXref < ModelBase
+      belongs_to :object_xref
+      belongs_to :xref
+      belongs_to :source_xref, foreign_key: 'source_xref_id', class_name: 'Xref'
+      belongs_to :associated_group
+    end
+
+    class AttribType < ModelBase
+      has_many :seq_region_attrib
+    end
+
+    class Assembly < Connection
+      self.primary_key = 'asm_seq_region_id'
+
+      belongs_to :seq_region
+    end
+
+    class AssemblyException < ModelBase
+      belongs_to :seq_region
+      belongs_to :exc_seq_region, foreign_key: 'ex_seq_region_id', class_name: 'SeqRegion'
+    end
+
+    class CoordSystem < ModelBase
+      has_many :data_files
+    end
+
+    class DataFile < ModelBase
+      belongs_to :coord_system
+    end
+
+    class DensityFeature < ModelBase
+      belongs_to :seq_region
+      belongs_to :density_type
+    end
+
+    class DensityType < ModelBase
+      has_many :density_features
+    end
+
+    class Ditag < ModelBase
+      has_many :ditag_features
+    end
+
+    class DitagFeature < ModelBase
+      belongs_to :ditag
+      belongs_to :seq_region
+      belongs_to :analysis
+    end
+
+    class Dna < Connection
+      has_one :seq_region
+    end
+
+    class DnaAlignFeature < ModelBase
+      belongs_to :seq_region
+      belongs_to :analysis
+      belongs_to :external_db
+    end
+
+    class DependentXref < ModelBase
+      belongs_to :object_xref
+      belongs_to :master, foreign_key: 'master_xref_id', class_name: 'Xref'
+      belongs_to :dependent, foreign_key: 'dependent_xref_id', class_name: 'Xref'
+    end
+
+    class Exon < ModelBase
+      belongs_to :seq_region
+
+      has_many :exon_transcripts
+      has_many :transcripts, through: :exon_transcript
+
+    end
+
+    class ExonTranscript < Connection
+      belongs_to :exon
+      belongs_to :transcript
+    end
+
+    class ExternalDb < ModelBase
+      # FIXME: Hack because using type column in the database
+      self.inheritance_column = ':_no_inheritance_column'
+
+      has_many :seq_region_synonyms
+
+      scope :with_seq_region_synonyms, -> { where.not(seq_regions_synonyms.nil?)}
+    end
+
+    class ExternalSynonym < Connection
+      self.primary_key = 'xref_id'
+    end
+
+    class Gene < ModelBase
+      include StableIdHistory
+
+      belongs_to :analysis
+      belongs_to :seq_region
+      belongs_to :display_xref, foreign_key: 'display_xref_id', class_name: 'Xref'
+      belongs_to :transcript, foreign_key: 'canonical_transcript_id', class_name: 'Transcript'
+
+      has_many :gene_attribs
+      has_many :attrib_types, through: :gene_attribs
+
+      has_many :operon_transcript_genes
+      has_many :operon_transcripts, through: :operon_transcript_genes
+
+    end
+
+    # FIXME: Set up relations with stable IDs
+    class GeneArchive < Connection
+      belongs_to :peptide_archive
+      belongs_to :mapping_session
+    end
+
+    class GeneAttrib < ModelBase
+      belongs_to :gene
+      belongs_to :attrib_type
+    end
+
+    # TODO: Inspect relation with ObjectXref
+    class IdentityXref < Connection
+      self.primary_key = 'object_xref_id'
+    end
+
+    class Interpro < Connection
+
+    end
+
+    class IntronSupportingEvidence < ModelBase
+      belongs_to :analysis
+      belongs_to :seq_region
+
+    end
+
+    class GenomeStatistics < ModelBase
+
+    end
+
+    class Karyotype < ModelBase
+      belongs_to :seq_region
+
+    end
+
+    class Map < ModelBase
+
+    end
+
+    class MappingSession < ModelBase
+      has_many :stable_id_events
+    end
+
+    class MappingSet < ModelBase
+      has_many :seq_region_mappings
+    end
+
+    class Marker < ModelBase
+      has_many :marker_features
+      has_many :marker_synonyms
+      has_many :marker_map_locations
+    end
+
+    class MarkerFeature < ModelBase
+      belongs_to :marker
+      belongs_to :seq_region
+      belongs_to :analysis
+    end
+
+    class MarkerMapLocation < Connection
+      belongs_to :marker
+      belongs_to :map
+      belongs_to :marker_synonym
+    end
+
+    class MarkerSynonym < ModelBase
+      belongs_to :marker
+    end
+
+    class Meta < ModelBase
+
+    end
+
+    class MetaCoord < Connection
+      belongs_to :coord_system
+
+    end
+
+    class MiscAttrib < Connection
+      belongs_to :misc_feature
+      belongs_to :attrib_type
+    end
+
+    class MiscFeature < ModelBase
+      belongs_to :seq_region
+
+      has_many :misc_attrib
+      has_many :misc_feature_misc_sets
+      has_many :misc_sets, through: :misc_feature_misc_sets
+    end
+
+    class MiscFeatureMiscSet < Connection
+      belongs_to :misc_feature
+      belongs_to :misc_set
+    end
+
+    class MiscSet < ModelBase
+      has_many :misc_feature_misc_sets
+      has_many :misc_sets, through: :misc_feature_misc_sets
+    end
+
+    class ObjectXref < ModelBase
+      belongs_to :xref
+      belongs_to :analysis
+    end
+
+    class OntologyXref < ModelBase
+      belongs_to :object_xref
+      belongs_to :source, foreign_key: 'source_xref_id', class_name: 'Xref'
+    end
+
+    class Operon < ModelBase
+      belongs_to :analysis
+      belongs_to :seq_region
+    end
+
+    class OperonTranscript < ModelBase
+      belongs_to :analysis
+      belongs_to :seq_region
+      belongs_to :operon
+
+      has_many :operon_transcript_genes
+      has_many :genes, through: :operon_transcript_genes
+    end
+
+    class PeptideArchive < ModelBase
+
+    end
+
+    class PredictionExon < ModelBase
+      belongs_to :seq_region
+      belongs_to :prediction_transcript
+    end
+
+    class PredictionTranscript < ModelBase
+      belongs_to :seq_region
+      belongs_to :analysis
+
+      has_many :prediction_exons
+    end
+
+    class ProteinAlignFeature < ModelBase
+      belongs_to :seq_region
+      belongs_to :analysis
+      belongs_to :external_db
+    end
+
+    class ProteinFeature < ModelBase
+      belongs_to :translation
+      belongs_to :analysis
+    end
+
+    class RepeatConsensus < ModelBase
+      has_many :repeat_features
+    end
+
+    class RepeatFeature < ModelBase
+      belongs_to :seq_region
+      belongs_to :repeat_consensus
+      belongs_to :analysis
+    end
+
+    class SeqRegion < ModelBase
+      has_one :dna
+      belongs_to :coord_system
+
+      has_many :genes
+      has_many :density_features
+      has_many :prediction_exons
+      has_many :prediction_transcripts
+      has_many :repeat_features
+      has_many :protein_align_features
+      has_many :seq_region_attribs
+      has_many :seq_region_synonyms
+      has_many :simple_features
+      has_many :splicing_events
+      has_many :transcripts
+
+    end
+
+    class SeqRegionAttrib < Connection
+      belongs_to :seq_region
+      belongs_to :attrib_type
+    end
+
+    class SeqRegionMapping < Connection
+      belongs_to :current, foreign_key: 'external_seq_region_id', class_name: 'SeqRegion'
+      belongs_to :previous, foreign_key: 'internal_seq_region_id', class_name: 'SeqRegion'
+      belongs_to :mapping_set
+    end
+
+    class SeqRegionSynonym < ModelBase
+      belongs_to :seq_region
+      belongs_to :external_db
+    end
+
+    class SimpleFeature < ModelBase
+      belongs_to :seq_region
+      belongs_to :analysis
+    end
+
+    class SplicingEvent < ModelBase
+      belongs_to :seq_region
+      belongs_to :attrib_type
+      belongs_to :gene
+
+      has_many :splicing_event_features
+    end
+
+    class SplicingEventFeature < ModelBase
+      belongs_to :splicing_event
+      belongs_to :exon
+      belongs_to :transcript
+    end
+
+    class SplicingTranscriptPair < ModelBase
+      belongs_to :splicing_event
+      belongs_to :transcript1, foreign_key: 'transcript_id_1', class_name: 'Transcript'
+      belongs_to :transcript2, foreign_key: 'transcript_id_2', class_name: 'Transcript'
+    end
+
+    # TODO: Fix inheritance
+    class SupportingFeature < Connection
+      belongs_to :exon
+
+    end
+
+    # FIXME: Setup stable ids
+    class StableIdEvent < Connection
+      # FIXME: Hack because using type column in the database
+      self.inheritance_column = ':_no_inheritance_column'
+
+      belongs_to :mapping_session
+    end
+
+    class Transcript < ModelBase
+      include StableIdHistory
+
+      belongs_to :gene
+      belongs_to :analysis
+      belongs_to :seq_region
+      belongs_to :display_xref, foreign_key: 'display_xref_id', class_name: 'Xref'
+      belongs_to :canonical_translation, foreign_key: 'canonical_translation_id', class_name: 'Translation'
+
+
+      has_many :transcript_attribs
+      has_many :translations
+
+    end
+
+    class TranscriptAttrib < Connection
+      belongs_to :transcript
+      belongs_to :attrib_type
+    end
+
+    # TODO: Fix inheritance
+    class TranscriptSupportingFeature < Connection
+      belongs_to :transcript
+    end
+
+    class TranscriptIntronSupportingEvidence < ModelBase
+      belongs_to :transcript
+      belongs_to :previous_exon
+      belongs_to :next_exon
+    end
+
+    class Translation < ModelBase
+      include StableIdHistory
+
+      belongs_to :transcript
+      belongs_to :start_exon, foreign_key: 'start_exon_id', class_name: 'Exon'
+      belongs_to :end_exon, foreign_key: 'end_exon_id', class_name: 'Exon'
+
+      has_many :protein_features
+      has_many :translation_attribs
+    end
+
+    class TranslationAttrib < Connection
+      belongs_to :translation
+      belongs_to :attrib_type
+    end
+
+    # TODO: inspect ensembl_object_type and ensembl_id
+    class UnmappedObject < ModelBase
+      belongs_to :analysis
+      belongs_to :external_db
+      belongs_to :unmapped_reason
+    end
+
+    class UnmappedReason < ModelBase
+      has_many :unmapped_objects
+    end
+
+    class Xref < ModelBase
+      belongs_to :external_db
+
+      has_many :object_xrefs
+
+    end
+  end
+end

data/lib/ensembl/variation/activerecord.rb

@@ -2,7 +2,27 @@ require 'active_record'
 
 module Ensembl
   module Variation
-    class Allele < Ensembl::ModelBase
+    class Connection < ActiveRecord::Base
+      self.extend TableNameOverrides
+
+      self.abstract_class = true
+
+      self.establish_connection :adapter  => "mysql2",
+                                :host     => Ensembl.host,
+                                :username => Ensembl.username,
+                                :password => Ensembl.password,
+                                :database => Ensembl.species+'_variation_'+Ensembl.version+'_'+Ensembl.hg_version,
+                                :reconnect => true
+
+    end
+
+    class ModelBase < Connection
+      self.extend PrimaryKeyOverrides
+
+      self.abstract_class = true
+    end
+
+    class Allele < ModelBase
       belongs_to :variation
       belongs_to :population
       belongs_to :subsnp_handle
@@ -10,78 +30,77 @@ module Ensembl
 
     end
 
-    class AlleleCode < Ensembl::ModelBase
+    class AlleleCode < ModelBase
       has_many :genotype_codes
 
     end
 
-    class AssociateStudy < Ensembl::Connection
+    class AssociateStudy < Connection
       belongs_to :study, foreign_key: 'study1_id', class_name: 'Study'
       belongs_to :associated_study, foreign_key: 'study2_id', class_name: 'Study'
 
     end
 
-    class Attrib < Ensembl::ModelBase
+    class Attrib < ModelBase
       belongs_to :attrib_type
-
     end
 
-    class AttribSet < Ensembl::ModelBase
+    class AttribSet < ModelBase
       belongs_to :attrib
 
     end
 
-    class AttribType < Ensembl::ModelBase
+    class AttribType < ModelBase
       has_many :attribs, class_name: 'Attrib'
       has_many :pheotype_feature_attrib
       has_many :phenotype_features, through: :phenotype_feature_attrib
 
     end
 
-    class CompressedGenotypeRegion < Ensembl::Connection
+    class CompressedGenotypeRegion < Connection
       belongs_to :individual
-
+      belongs_to :seq_region, class_name: 'Ensembl::Core::SeqRegion'
     end
 
-    class CompressedGenotypeVar < Ensembl::Connection
+    class CompressedGenotypeVar < Connection
       belongs_to :variation
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
 
     end
 
-    class CoordSystem < Ensembl::ModelBase
+    class CoordSystem < ModelBase
     end
 
-    class FailedAllele < Ensembl::ModelBase
+    class FailedAllele < ModelBase
       belongs_to :failed_description
       belongs_to :allele
 
     end
 
-    class FailedDescription < Ensembl::ModelBase
+    class FailedDescription < ModelBase
       belongs_to :failed_variation
 
     end
 
-    class FailedStructuralVariation < Ensembl::ModelBase
+    class FailedStructuralVariation < ModelBase
       belongs_to :structural_variation
       belongs_to :failed_description
 
     end
 
-    class FailedVariation < Ensembl::ModelBase
+    class FailedVariation < ModelBase
       belongs_to :variation
       has_one :failed_description
 
     end
 
-    class GenotypeCode < Ensembl::ModelBase
+    class GenotypeCode < ModelBase
       belongs_to :allele_code
       belongs_to :genotype_code
 
     end
 
-    class Individual < Ensembl::ModelBase
+    class Individual < ModelBase
       belongs_to :individual_type
       belongs_to :father, foreign_key: 'father_individual_id', class_name: 'Individual'
       belongs_to :mother, foreign_key: 'mother_individual_id', class_name: 'Individual'
@@ -92,57 +111,59 @@ module Ensembl
       has_many :individual_synonyms, foreign_key: :synonym_id
       has_many :synonyms, through: :individual_synonyms
 
+      has_many :individual_genotype_multiple_bps
+
       scope :with_fathers, -> { where.not(father:nil) }
       scope :with_mothers, -> { where.not(mother:nil) }
 
     end
 
-    class IndividualGenotypeMultipleBp < Ensembl::Connection
+    class IndividualGenotypeMultipleBp < Connection
       belongs_to :variation
       belongs_to :individual
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
 
     end
 
-    class IndividualPopulation < Ensembl::Connection
+    class IndividualPopulation < Connection
       belongs_to :individual
       belongs_to :population
-
     end
 
-    class IndividualSynonym < Ensembl::Connection
+    class IndividualSynonym < Connection
       belongs_to :individual
       belongs_to :source
       belongs_to :synonym, class_name: 'Individual'
 
     end
 
-    class IndividualType < Ensembl::ModelBase
+    class IndividualType < ModelBase
       has_many :individuals
     end
 
-    class Meta < Ensembl::ModelBase
+    class Meta < ModelBase
       # TODO: Link with others
     end
 
-    class MetaCoord < Ensembl::Connection
+    class MetaCoord < Connection
     end
 
-    class MotifFreatureVariation < Ensembl::ModelBase
+    class MotifFreatureVariation < ModelBase
       belongs_to :variation_feature
     end
 
-    class Phenotype < Ensembl::ModelBase
+    class Phenotype < ModelBase
       has_many :phenotype_features
     end
 
-    class PhenotypeFeature < Ensembl::ModelBase
-      # Hack because using type column in the database
+    class PhenotypeFeature < ModelBase
+      # FIXME: Hack because using type column in the database
       self.inheritance_column = ':_no_inheritance_column'
 
       belongs_to :phenotype
       belongs_to :source
       belongs_to :study
+      belongs_to :seq_region, class_name: 'Ensembl::Core::SeqRegion'
 
       has_many :phenotype_feature_attrib
       has_many :attrib_types, through: :phenotype_feature_attrib
@@ -153,15 +174,17 @@ module Ensembl
 
     end
 
-    class PhenotypeFeatureAttrib < Ensembl::Connection
+    class PhenotypeFeatureAttrib < Connection
       belongs_to :attrib_type
       belongs_to :phenotype_feature
 
     end
 
-    class Population < Ensembl::ModelBase
+    class Population < ModelBase
+      self.extend Ensembl::SearchByName
+
       has_many :population_synonyms
-      has_many :synonyms, through: :population_synonyms, source: :synonym
+      #has_many :synonyms, through: :population_synonyms, source: :synonym
       has_many :alleles
 
       has_many :individual_populations
@@ -169,61 +192,82 @@ module Ensembl
 
       has_many :population_structures, foreign_key: 'super_population_id'
       has_many :sub_populations, through: :population_structures, source: :sub_population
+      has_many :parents, through: :population_structures, source: :super_populaton#, foreign_key: 'sub_population_id'
 
       has_many :population_genotypes
 
+      def parent
+        ps=PopulationStructure.find_by(sub_population: id)
+        ps.super_population unless ps.nil?
+      end
+
       def all_individual_populations
-        IndividualPopulation.where(population_id: sub_populations.pluck(:population_id))
+        IndividualPopulation.where(population_id: sub_population_ids(self)<<id)
       end
 
       def all_individuals
         Individual.where individual_id: all_individual_populations.pluck(:individual_id)
       end
 
+      def all_population_genotypes
+        PopulationGenotype.where(population_id: sub_population_ids(self)<<id)
+      end
+
+      private
+        def sub_population_ids(population,array=[])
+          subs=population.sub_populations
+          subs.each do |p|
+            array<<p.id
+            sub_population_ids(p,array)
+          end
+        end
     end
 
-    class PopulationSynonym < Ensembl::Connection
-      belongs_to :synonym, foreign_key: 'synonym_id', class_name: 'Population'
+    class PopulationSynonym < Connection
+      #belongs_to :synonym, foreign_key: 'synonym_id', class_name: 'Population'
       belongs_to :population
       belongs_to :source
     end
 
-    class PopulationGenotype < Ensembl::ModelBase
+    class PopulationGenotype < ModelBase
       belongs_to :variation
       belongs_to :population
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
-      belongs_to :genotype_code
 
+      belongs_to :genotype_code
+      has_one :allele_code, through: :genotype_code
     end
 
-    class PopulationStructure < Ensembl::Connection
-      belongs_to :population, foreign_key: 'super_population_id', class_name: 'Population'
+    class PopulationStructure < Connection
+      belongs_to :super_population, foreign_key: 'super_population_id', class_name: 'Population'
       belongs_to :sub_population, foreign_key: 'sub_population_id', class_name: 'Population'
-
     end
 
-    class ProteinFunctionPredictions < Ensembl::Connection
-    end
+    class ProteinFunctionPredictions < Connection
 
-    class Publication < Ensembl::ModelBase
     end
 
-    class RegulatoryFeatureVariation < Ensembl::ModelBase
-      belongs_to :variation_feature
+    class Publication < ModelBase
 
     end
 
-    class SeqRegion < Ensembl::ModelBase
-      belongs_to :coord_system
-
+    class RegulatoryFeatureVariation < ModelBase
+      belongs_to :variation_feature
     end
 
-    class StrainGtypePoly < Ensembl::Connection
+    # class SeqRegion < Ensembl::Core::SeqRegion
+    #   belongs_to :coord_system
+    #   has_many :compressed_genotype_regions
+    #   has_many :phenotype_features
+    #   has_many :structureal_variation_features
+    # end
+
+    class StrainGtypePoly < Connection
       belongs_to :variation
 
     end
 
-    class StructuralVariation < Ensembl::ModelBase
+    class StructuralVariation < ModelBase
       belongs_to :source
       belongs_to :study
 
@@ -245,13 +289,13 @@ module Ensembl
 
     end
 
-    class StructuralVariationAssociation < Ensembl::Connection
+    class StructuralVariationAssociation < Connection
       belongs_to :structural_variation
       belongs_to :supporting_structural_variation, foreign_key: 'supporting_structural_variation_id', class_name: 'StructuralVariation'
     end
 
-    class StructuralVariationFeature < Ensembl::ModelBase
-      belongs_to :seq_region
+    class StructuralVariationFeature < ModelBase
+      belongs_to :seq_region, class_name: 'Ensembl::Core::SeqRegion'
       belongs_to :structural_variation
       belongs_to :source
       belongs_to :study
@@ -262,67 +306,66 @@ module Ensembl
 
     end
 
-    class StructuralVariationSample < Ensembl::ModelBase
+    class StructuralVariationSample < ModelBase
       belongs_to :structural_variation
       belongs_to :individual
     end
 
-    class Study < Ensembl::ModelBase
-      has_many :study_variations
-      has_many :variations, through: :study_variations
+    class Source < ModelBase
 
     end
 
-    class Source < Ensembl::ModelBase
-
-    end
-
-    class Study < Ensembl::ModelBase
+    class Study < ModelBase
       has_many :associate_studies, foreign_key: 'study1_id'
       has_many :associated_studies, through: :associate_studies, source: :associated_study
 
       # FIXME: No data in database
+      has_many :study_variations
       has_many :variations, through: :study_variations
     end
 
     # FIXME: No data in database
-    class StudyVariation < Ensembl::Connection
+    class StudyVariation < Connection
       belongs_to :study
       belongs_to :variation
     end
 
-    class SubmitterHandle < Ensembl::Connection
+    class SubmitterHandle < Connection
       self.primary_key = 'handle_id'
     end
 
-    class SubsnpHandle < Ensembl::Connection
+    class SubsnpHandle < Connection
       self.primary_key = 'subsnp_id'
 
       has_many :subsnp_maps
     end
 
-    class SubsnpMap < Ensembl::Connection
+    class SubsnpMap < Connection
       belongs_to :variation
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
     end
 
-    class TaggedVariationFeature < Ensembl::ModelBase
+    class TaggedVariationFeature < ModelBase
       belongs_to :variation_feature
       belongs_to :population
     end
 
-    class TranscriptVariation < Ensembl::ModelBase
+    class TranscriptVariation < ModelBase
       belongs_to :variation_feature
 
     end
 
-    class TranslationMd5 < Ensembl::ModelBase
+    class TranslationMd5 < ModelBase
 
     end
 
-    class Variation < Ensembl::ModelBase
+    class Variation < ModelBase
+      self.extend Ensembl::SearchByName
+
       belongs_to :source
+
       has_many :variation_synonyms
+
       has_many :failed_variations
       has_many :alleles
       has_many :population_genotypes
@@ -334,71 +377,108 @@ module Ensembl
       has_many :variation_genenames
       has_many :variation_hgvs, class_name: 'VariationHgvs'
       has_many :variation_sets
+      has_many :variation_features
+
+      has_many :individual_genotype_multiple_bps
+      has_many :compressed_genotype_vars
 
       def phenotype_features
         PhenotypeFeature.where(object_id: name, type: 'Variation')
       end
 
+      def synonyms
+        variation_synonyms.map{ |vs| vs.name }
+      end
+
+
+      # Find Variation by also using VariationSynonyms
+      # @name: name of the variation
+      # @return: [Variation]
+      def self.find_by_name(name)
+        v  = self.find_by(name: name)
+        vs = VariationSynonym.eager_load(:variation).find_by(name: name) if v.nil?
+        vs.variation unless vs.nil?
+      end
+
       def all_phenotype_features
         object_ids = variation_synonyms.pluck :name
         object_ids<<name
         PhenotypeFeature.where(object_id: object_ids, type: 'Variation')
       end
+
+      # def population_genotypes
+      #   PopulationGenotype.where(variation_id: id)
+      # end
     end
 
-    class VariationCitation < Ensembl::Connection
+    class VariationCitation < Connection
       self.table_name = 'variation_citation'
       belongs_to :variation
       belongs_to :publication
     end
 
-    class VariationFeature < Ensembl::ModelBase
+    class VariationFeature < ModelBase
       belongs_to :variation
       belongs_to :source
+      belongs_to :seq_region, class_name: 'Ensembl::Core::SeqRegion'
+
       has_many :transcript_variations
       has_many :motif_freature_variations
       has_many :tagged_variation_features
 
+      def variation_sets
+        VariationSets.where[variation_set_id: [variation_set_id.split(',').map{|id| id.to_i }]] unless variation_set_id.nil?
+      end
+
+      def class_type
+        Attrib.find(class_attrib_id) unless class_attrib_id.nil?
+      end
     end
 
-    class VariationGenename < Ensembl::Connection
+    class VariationGenename < Connection
       belongs_to :variation
     end
 
-    class VariationHgvs < Ensembl::Connection
+    class VariationHgvs < Connection
       belongs_to :variation
     end
 
-    class VariationSet < Ensembl::ModelBase
+    class VariationSet < ModelBase
+      self.extend Ensembl::SearchByName
+
       belongs_to :short_name, foreign_key: 'short_name_attrib_id', class_name: 'Attrib'
       has_many :structural_variations
 
-      has_many :variation_set_structures
-      has_many :sub_variation_sets, through: :variation_set_structures, source: :sub_variation_set
+      #has_many :variation_set_structures, foreign_key: 'variation_set_super'
+      has_many :sub_variation_set_structures, foreign_key: 'variation_set_super', class_name: 'VariationSetStructure'
+      has_many :sub_variation_sets, through: :sub_variation_set_structures , source: :sub_variation_set
+
+      has_many :super_variation_set_structures, foreign_key: 'variation_set_sub', class_name: 'VariationSetStructure'
+      has_many :super_variation_sets, through: :super_variation_set_structures , source: :super_variation_set
+
+      has_many :variation_set_variations
+      has_many :variations, through: :variation_set_variations
 
-      has_many :variations
     end
 
-    class VariationSetStructuralVariation < Ensembl::Connection
+    class VariationSetStructuralVariation < Connection
       belongs_to :structural_variation
       belongs_to :variation_set
     end
 
-    class VariationSetStructure < Ensembl::Connection
-      belongs_to :super_variation_set, foreign_key: 'super_variation_set_id', class_name: 'VariationSet'
-      belongs_to :sub_variation_set, foreign_key: 'sub_variation_set_id', class_name: 'VariationSet'
+    class VariationSetStructure < Connection
+      belongs_to :super_variation_set, foreign_key: 'variation_set_super', class_name: 'VariationSet'
+      belongs_to :sub_variation_set, foreign_key: 'variation_set_sub', class_name: 'VariationSet'
     end
 
-    class VariationSetVariation < Ensembl::Connection
+    class VariationSetVariation < Connection
       belongs_to :variation
       belongs_to :variation_set
     end
 
-    class VariationSynonym < Ensembl::ModelBase
+    class VariationSynonym < ModelBase
       belongs_to :variation
       belongs_to :source
     end
-
-
   end
 end

data/lib/ensembl/version.rb

@@ -1,3 +1,3 @@
 module Ensembl
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

data/lib/ensembl.rb

@@ -24,8 +24,16 @@ module Ensembl
       @password||=''
     end
 
-    def database
-      @database||='homo_sapiens_variation_75_37'
+    def hg_version
+      @hg_version||='37'
+    end
+
+    def version
+      @version||='75'
+    end
+
+    def species
+      @species||='homo_sapiens'
     end
 
   end
@@ -42,24 +50,63 @@ module Ensembl
     end
   end
 
-  class Connection < ActiveRecord::Base
-    self.extend TableNameOverrides
-
-    self.abstract_class = true
-
-    self.establish_connection :adapter  => "mysql2",
-                              :host     => Ensembl.host,
-                              :username => Ensembl.username,
-                              :password => Ensembl.password,
-                              :database => Ensembl.database
-
+  module SearchByName
+    def search(name)
+      table=self.arel_table
+      self.where(table[:name].matches("%#{name}%"))
+    end
   end
 
-  class ModelBase < Connection
-    self.extend PrimaryKeyOverrides
+  # class BaseConnection < ActiveRecord::Base
+  #   self.extend TableNameOverrides
+  #   self.abstract_class = true
+  # end
+
+  # module Core
+  #   class Connection < ActiveRecord::Base
+  #     self.extend TableNameOverrides
+  #
+  #     self.abstract_class = true
+  #
+  #     self.establish_connection :adapter  => "mysql2",
+  #     :host     => Ensembl.host,
+  #     :username => Ensembl.username,
+  #     :password => Ensembl.password,
+  #     :database => Ensembl.species+'_core_'+Ensembl.version+'_'+Ensembl.hg_version,
+  #     :reconnect => true
+  #
+  #   end
+  #
+  #   class ModelBase < Connection
+  #     self.extend PrimaryKeyOverrides
+  #
+  #     self.abstract_class = true
+  #   end
+  # end
+  #
+  # module Variation
+  #   class Connection < ActiveRecord::Base
+  #     self.extend TableNameOverrides
+  #
+  #     self.abstract_class = true
+  #
+  #     self.establish_connection :adapter  => "mysql2",
+  #                               :host     => Ensembl.host,
+  #                               :username => Ensembl.username,
+  #                               :password => Ensembl.password,
+  #                               :database => Ensembl.species+'_variation_'+Ensembl.version+'_'+Ensembl.hg_version,
+  #                               :reconnect => true
+  #
+  #   end
+  #
+  #   class ModelBase < Connection
+  #     self.extend PrimaryKeyOverrides
+  #
+  #     self.abstract_class = true
+  #   end
+  # end
 
-    self.abstract_class = true
-  end
 end
 
-require File.dirname(__FILE__) + '/ensembl/variation/activerecord.rb'
+require File.dirname(__FILE__) + '/ensembl/core/activerecord.rb'
+require File.dirname(__FILE__) + '/ensembl/variation/activerecord.rb'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ensembl
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - Kristjan Metsalu
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-27 00:00:00.000000000 Z
+date: 2014-07-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mysql2
@@ -66,7 +66,21 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
-description: " ensembl provides an ruby API to connect to ensembl databases. "
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+description: " ensembl provides an ruby API to connect to Ensembl.org databases.  "
 email:
 - kristjan.metsalu@ut.ee
 executables: []
@@ -80,6 +94,7 @@ files:
 - Rakefile
 - ensembl.gemspec
 - lib/ensembl.rb
+- lib/ensembl/core/activerecord.rb
 - lib/ensembl/variation/activerecord.rb
 - lib/ensembl/version.rb
 homepage: https://github.com/kmetsalu/ensembl
@@ -107,3 +122,4 @@ signing_key:
 specification_version: 4
 summary: Gem to access Ensembl.org databases through API
 test_files: []
+has_rdoc: