rudimentary genotype-phenotype search

app/models/ga4gh/converters/evidence_item.rb

@@ -1,12 +1,19 @@
 require 'ga4gh/genotype_phenotype_pb'
 
-module Gaa4gh; module Converters
+module Ga4gh; module Converters
   class EvidenceItem
-    def from_ga4gh(json)
-    end
+    attr_reader :evidence_item
 
+    def initialize(evidence_item)
+      @evidence_item = evidence_item
+    end
 
-    def to_ga4gh(evidence_item)
+    def to_ga4gh
+      Ga4gh::Evidence.new(
+        evidence_type: nil,
+        description: evidence_item.description,
+        info: {}
+      )
     end
   end
 end; end

app/models/ga4gh/converters/external_identifier.rb

@@ -0,0 +1,64 @@
+require 'ga4gh/common_pb'
+
+  add_message "ga4gh.ExternalIdentifier" do
+    optional :database, :string, 1
+    optional :identifier, :string, 2
+    optional :version, :string, 3
+  end
+module Ga4gh; module Converters
+  class ExternalIdentifier
+    attr_reader :ext_id
+
+    def initialize(ext_id)
+      @ext_id = ext_id
+    end
+
+    def is_supported?
+      self.class.databases(ext_id)
+    end
+
+    def error
+      if is_supported?
+        nil
+      else
+        "Database #{ext_id.database} version #{ext_id.version} is not currently supported"
+      end
+    end
+
+    private
+    def self.databases(ext_id)
+      @databases ||= {
+        'entrez' => :handle_entrez
+        'disease ontology' => :handle_doid
+        'sequence ontology' => :handle_soid
+        'pubmed' => :handle_pubmed
+      }
+    end
+
+    def handle_entrez(query)
+      query.where(evidence_items: { variants: { genes: { entrez_id: ext_id.identifier }}}
+    end
+
+    def handle_doid(query)
+      term = if ext_id.identifier =~ /doid/i
+               ext_id.identifier.downcase.gsub('doid:', '')
+             else
+               ext_id.identifier
+             end
+      query.where(doid: term)
+    end
+
+    def handle_soid(query)
+      term = if ext_id.identifier =~ /soid/i
+               ext_id.identifier.downcase.gsub('soid:', '')
+             else
+               ext_id.identifier
+             end
+      query.where(evidence_items: { variants: { variant_types: { soid: term }}})
+    end
+
+    def handle_pubmed(query)
+      query.where(evidence_items: { sources: { pubmed_id: ext_id.identifier }})
+    end
+  end
+end

app/models/ga4gh/converters/feature_phenotype_association.rb

@@ -2,15 +2,50 @@
 
 module Ga4gh; module Converters
   class FeaturePhenotypeAssociation
+    attr_reader :diseases
+
+    def initialize(diseases)
+      @diseases = diseases
+    end
+
     def to_ga4gh
-      {
-        environmental_contexts: environmental_contexts
-      }
+      diseases.map do |disease|
+        Ga4gh::FeaturePhenotypeAssociation.new(
+          id: '',
+          phenotype_association_set_id: '',
+          feature_ids: feature_ids(disease),
+          evidence: evidence(disease),
+          phenotype: Ga4gh::Converters::PhenotypeDisease.new(disease).to_ga4gh,
+          description: '',
+          environmental_contexts: environmental_contexts,
+          info: {}
+        )
+      end
+    end
+
+    private
+    def feature_ids(disease)
+      disease.evidence_items.map(&:variant).map(&:id).map(&:to_s).uniq
+    end
+
+    def evidence(disease)
+      disease.evidence_items.map do |ei|
+        Ga4gh::Converters::EvidenceItem.new(ei).to_ga4gh
+      end
     end
 
     def environmental_contexts
+      #drug?
       [
         Ga4gh::EnvironmentalContext.new(
+          id: '',
+          description: 'cancer',
+          environment_type: Ga4gh::OntologyTerm.new(
+            id: 'http://purl.obolibrary.org/obo/OBI_1110053',
+            term: 'cancer',
+            source_name: 'Ontology for Biomedical Investigation',
+            source_version: ''
+          )
         )
       ]
     end

app/models/ga4gh/converters/phenotype_disease.rb

@@ -2,10 +2,13 @@
 
 module Ga4gh; module Converters
   class PhenotypeDisease
-    def from_ga4gh(json)
+    attr_reader :disease
+
+    def initialize(disease)
+      @disease = disease
     end
 
-    def to_ga4gh(disease)
+    def to_ga4gh
       Ga4gh::PhenotypeInstance.new(
         id: disease.id.to_s,
         type: Ga4gh::Converters::Disease.new.to_ga4gh(disease),

app/models/ga4gh/queries/feature_phenotype_associations_search.rb

@@ -15,16 +15,56 @@ def initialize(request_body)
     end
 
     def perform
-      query = generate_query
+      evidence_query = request.evidence_query
+      variant_ids = request.feature_ids
+      disease_ids = request.phenotype_ids
+
+      if evidence_query || variant_ids || disease_ids
+        initial_diseases = Disease.eager_load(evidence_items: [:source, variant: [:gene, :variant_types]])
+        if disease_ids && disease_ids.any?
+          initial_diseases = initial_diseases.where(id: disease_ids)
+        end
+
+        if variant_ids && variant_ids.any?
+          initial_diseases = initial_diseases.where(evidence_items: { variants: {id: variant_ids }})
+        end
+
+        if evidence_query
+          initial_diseases = process_evidence_query(evidence_query, initial_diseases)
+        end
+
+        response.associations = Ga4gh::Converters::FeaturePhenotypeAssociation.new(diseases).to_ga4gh
+        response.next_page_token = next_page_token(initial_diseases)
+      else
+        @errors << 'Please specify at least one of the following: features, phenotypes, evidence'
+      end
     end
 
     def success?
       errors.none?
     end
 
     private
-    def generate_query
-      ::EvidenceItems.view_scope
+    def process_evidence_query(evidence_query, db_query)
+      if evidence_query.evidenceType.present?
+        @errors << 'Evidence Type query is not currently supported'
+      end
+
+      if evidence_query.description.present?
+        db_query = db_query.where('evidence_items.description ILIKE ?', "%#{evidence_query.description}%")
+      end
+
+      if evidence_query.external_identifiers.present?
+        evidence_query.external_identifiers.each do |ext_id|
+          converter = Ga4gh::Converters::ExternalIdentifier.new(ext_id)
+          if converter.is_supported?
+            db_query = converter.filter(db_query)
+          else
+            @errors << converter.error
+          end
+        end
+      end
+      db_query
     end
   end
 end; end

app/models/ga4gh/queries/with_pagination.rb

@@ -2,10 +2,14 @@
 
 module Ga4gh; module Queries;
   module WithPagination
-    def next_page_token
-      page_size = current_page_size
-      page_number = current_page
-      Base64.encode64({ 's' => page_size, 'n' => page_number + 1 }.to_json).strip
+    def next_page_token(query)
+      if query.count > current_page_size * current_page
+        page_size = current_page_size
+        page_number = current_page
+        Base64.encode64({ 's' => page_size, 'n' => page_number + 1 }.to_json).strip
+      else
+        nil
+      end
     end
 
     def paginate_query(query)