Merge pull request #1130 from griffithlab/civicpy_features

Updates needed for CIViCpy to support fusions and factors

client/src/app/generated/civic.apollo-helpers.ts

@@ -1825,7 +1825,7 @@ export type PhenotypePopoverFieldPolicy = {
 	name?: FieldPolicy<any> | FieldReadFunction<any>,
 	url?: FieldPolicy<any> | FieldReadFunction<any>
 };
-export type QueryKeySpecifier = ('acmgCode' | 'acmgCodesTypeahead' | 'activities' | 'activity' | 'assertion' | 'assertions' | 'browseDiseases' | 'browseFeatures' | 'browseMolecularProfiles' | 'browseSources' | 'browseVariantGroups' | 'browseVariants' | 'clingenCode' | 'clingenCodesTypeahead' | 'clinicalTrial' | 'clinicalTrials' | 'comment' | 'comments' | 'contributors' | 'countries' | 'dataReleases' | 'disease' | 'diseasePopover' | 'diseaseTypeahead' | 'entityTypeahead' | 'events' | 'evidenceItem' | 'evidenceItems' | 'factors' | 'feature' | 'featureTypeahead' | 'flag' | 'flags' | 'fusions' | 'gene' | 'genes' | 'molecularProfile' | 'molecularProfiles' | 'nccnGuideline' | 'nccnGuidelinesTypeahead' | 'notifications' | 'organization' | 'organizationLeaderboards' | 'organizations' | 'phenotype' | 'phenotypePopover' | 'phenotypeTypeahead' | 'phenotypes' | 'previewCommentText' | 'previewMolecularProfileName' | 'remoteCitation' | 'revision' | 'revisions' | 'search' | 'searchByPermalink' | 'searchGenes' | 'source' | 'sourcePopover' | 'sourceSuggestionValues' | 'sourceSuggestions' | 'sourceTypeahead' | 'subscriptionForEntity' | 'therapies' | 'therapy' | 'therapyPopover' | 'therapyTypeahead' | 'timepointStats' | 'user' | 'userLeaderboards' | 'userTypeahead' | 'users' | 'validateRevisionsForAcceptance' | 'variant' | 'variantGroup' | 'variantGroups' | 'variantType' | 'variantTypePopover' | 'variantTypeTypeahead' | 'variantTypes' | 'variants' | 'variantsTypeahead' | 'viewer' | QueryKeySpecifier)[];
+export type QueryKeySpecifier = ('acmgCode' | 'acmgCodesTypeahead' | 'activities' | 'activity' | 'assertion' | 'assertions' | 'browseDiseases' | 'browseFeatures' | 'browseMolecularProfiles' | 'browseSources' | 'browseVariantGroups' | 'browseVariants' | 'clingenCode' | 'clingenCodesTypeahead' | 'clinicalTrial' | 'clinicalTrials' | 'comment' | 'comments' | 'contributors' | 'countries' | 'dataReleases' | 'disease' | 'diseasePopover' | 'diseaseTypeahead' | 'entityTypeahead' | 'events' | 'evidenceItem' | 'evidenceItems' | 'factor' | 'factors' | 'feature' | 'featureTypeahead' | 'flag' | 'flags' | 'fusion' | 'fusions' | 'gene' | 'genes' | 'molecularProfile' | 'molecularProfiles' | 'nccnGuideline' | 'nccnGuidelinesTypeahead' | 'notifications' | 'organization' | 'organizationLeaderboards' | 'organizations' | 'phenotype' | 'phenotypePopover' | 'phenotypeTypeahead' | 'phenotypes' | 'previewCommentText' | 'previewMolecularProfileName' | 'remoteCitation' | 'revision' | 'revisions' | 'search' | 'searchByPermalink' | 'searchGenes' | 'source' | 'sourcePopover' | 'sourceSuggestionValues' | 'sourceSuggestions' | 'sourceTypeahead' | 'subscriptionForEntity' | 'therapies' | 'therapy' | 'therapyPopover' | 'therapyTypeahead' | 'timepointStats' | 'user' | 'userLeaderboards' | 'userTypeahead' | 'users' | 'validateRevisionsForAcceptance' | 'variant' | 'variantGroup' | 'variantGroups' | 'variantType' | 'variantTypePopover' | 'variantTypeTypeahead' | 'variantTypes' | 'variants' | 'variantsTypeahead' | 'viewer' | QueryKeySpecifier)[];
 export type QueryFieldPolicy = {
 	acmgCode?: FieldPolicy<any> | FieldReadFunction<any>,
 	acmgCodesTypeahead?: FieldPolicy<any> | FieldReadFunction<any>,
@@ -1855,11 +1855,13 @@ export type QueryFieldPolicy = {
 	events?: FieldPolicy<any> | FieldReadFunction<any>,
 	evidenceItem?: FieldPolicy<any> | FieldReadFunction<any>,
 	evidenceItems?: FieldPolicy<any> | FieldReadFunction<any>,
+	factor?: FieldPolicy<any> | FieldReadFunction<any>,
 	factors?: FieldPolicy<any> | FieldReadFunction<any>,
 	feature?: FieldPolicy<any> | FieldReadFunction<any>,
 	featureTypeahead?: FieldPolicy<any> | FieldReadFunction<any>,
 	flag?: FieldPolicy<any> | FieldReadFunction<any>,
 	flags?: FieldPolicy<any> | FieldReadFunction<any>,
+	fusion?: FieldPolicy<any> | FieldReadFunction<any>,
 	fusions?: FieldPolicy<any> | FieldReadFunction<any>,
 	gene?: FieldPolicy<any> | FieldReadFunction<any>,
 	genes?: FieldPolicy<any> | FieldReadFunction<any>,

client/src/app/generated/civic.apollo.ts

@@ -4794,6 +4794,8 @@ export type Query = {
   evidenceItem?: Maybe<EvidenceItem>;
   /** List and filter evidence items. */
   evidenceItems: EvidenceItemConnection;
+  /** Find a single gene by CIViC ID or NCIt ID */
+  factor?: Maybe<Factor>;
   /** List and filter factors. */
   factors: FactorConnection;
   /** Find a single feature by CIViC ID */
@@ -4804,6 +4806,8 @@ export type Query = {
   flag?: Maybe<Flag>;
   /** List and filter flags. */
   flags: FlagConnection;
+  /** Find a single gene by CIViC ID */
+  fusion?: Maybe<Fusion>;
   /** List and filter fusions. */
   fusions: FusionConnection;
   /** Find a single gene by CIViC ID or Entrez symbol */
@@ -5174,6 +5178,12 @@ export type QueryEvidenceItemsArgs = {
 };
 
 
+export type QueryFactorArgs = {
+  id?: InputMaybe<Scalars['Int']['input']>;
+  ncitId?: InputMaybe<Scalars['String']['input']>;
+};
+
+
 export type QueryFactorsArgs = {
   after?: InputMaybe<Scalars['String']['input']>;
   before?: InputMaybe<Scalars['String']['input']>;
@@ -5213,6 +5223,11 @@ export type QueryFlagsArgs = {
 };
 
 
+export type QueryFusionArgs = {
+  id?: InputMaybe<Scalars['Int']['input']>;
+};
+
+
 export type QueryFusionsArgs = {
   after?: InputMaybe<Scalars['String']['input']>;
   before?: InputMaybe<Scalars['String']['input']>;

client/src/app/generated/server.model.graphql

@@ -8722,6 +8722,11 @@ type Query {
     variantOrigin: VariantOrigin
   ): EvidenceItemConnection!
 
+  """
+  Find a single gene by CIViC ID or NCIt ID
+  """
+  factor(id: Int, ncitId: String): Factor
+
   """
   List and filter factors.
   """
@@ -8818,6 +8823,11 @@ type Query {
     state: FlagState
   ): FlagConnection!
 
+  """
+  Find a single gene by CIViC ID
+  """
+  fusion(id: Int): Fusion
+
   """
   List and filter fusions.
   """

server/app/graphql/types/entities/feature_type.rb

@@ -24,6 +24,14 @@ class FeatureType < Types::BaseObject
     field :deprecation_reason, Types::FeatureDeprecationReasonType, null: true
     field :creation_activity, Types::Activities::CreateFeatureActivityType, null: true
 
+    def id
+      if object.class.name == 'Feature'
+        object.id
+      else
+        object.feature.id
+      end
+    end
+
     def feature_aliases
       if object.class.name == 'Feature'
         to_load = object

server/app/graphql/types/query_type.rb

@@ -60,6 +60,17 @@ def authorized?(object, args, context)
       argument :entrez_symbol, String, required: false
     end
 
+    field :factor, Types::Entities::FactorType, null: true do
+      description "Find a single gene by CIViC ID or NCIt ID"
+      argument :id, Int, required: false
+      argument :ncit_id, String, required: false
+    end
+
+    field :fusion, Types::Entities::FusionType, null: true do
+      description "Find a single gene by CIViC ID"
+      argument :id, Int, required: false
+    end
+
     field :feature, Types::Entities::FeatureType, null: true do
       description "Find a single feature by CIViC ID"
       argument :id, Int, required: false
@@ -211,13 +222,28 @@ def gene(id: :unspecified, entrez_symbol: :unspecified)
       if (id == :unspecified && entrez_symbol == :unspecified) || (id != :unspecified && entrez_symbol != :unspecified)
         raise GraphQL::ExecutionError.new('Must specify exactly one of id or entrezSymbol')
       end
-      if (id != :unspecified) 
-        Features::Gene.find_by(id: id)
+      if (id != :unspecified)
+        Feature.find_by(feature_instance_type: 'Features::Gene', id: id)&.feature_instance
       else
         Features::Gene.find_by(name: entrez_symbol)
       end
     end
 
+    def factor(id: :unspecified, ncit_id: :unspecified)
+      if (id == :unspecified && ncit_id == :unspecified) || (id != :unspecified && ncit_id != :unspecified)
+        raise GraphQL::ExecutionError.new('Must specify exactly one of id or ncitId')
+      end
+      if (id != :unspecified)
+        Feature.find_by(feature_instance_type: 'Features::Factor', id: id)&.feature_instance
+      else
+        Features::Factor.find_by(ncit_id: ncit_id)
+      end
+    end
+
+    def fusion(id: )
+      Feature.find_by(feature_instance_type: 'Features::Fusion', id: id)&.feature_instance
+    end
+
     def feature(id: )
       Feature.find_by(id: id)
     end