added linkouts queries/resolvers for GeneFamily and PanGeneSet (#126)

* added linkouts queries/resolvers for GeneFamily and PanGeneSet; depends on legumeinfo/microservices#613 * removed console.log debug
legumeinfo · Jan 10, 2024 · e6a6338 · e6a6338
1 parent 0f586d6
commit e6a6338
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Showing 7 changed files with 64 additions and 6 deletions.
diff --git a/src/data-sources/microservices/microservices.api.ts b/src/data-sources/microservices/microservices.api.ts
@@ -46,4 +46,26 @@ export class MicroservicesAPI extends RESTDataSource {
         return await this.post('genomic_region_linkouts', options);
     }
 
+    async getLinkoutsForGeneFamily(identifier: string): Promise<GraphQLLinkout[]> {
+        const options = {
+            headers: {
+              'Content-Type': 'application/json',
+              'Accept': 'application/json',
+            },
+            body: JSON.stringify({gene_families: [identifier]}),
+        };
+        return await this.post('gene_family_linkouts', options);
+    }
+
+    async getLinkoutsForPanGeneSet(identifier: string): Promise<GraphQLLinkout[]> {
+        const options = {
+            headers: {
+              'Content-Type': 'application/json',
+              'Accept': 'application/json',
+            },
+            body: JSON.stringify({pan_gene_sets: [identifier]}),
+        };
+        return await this.post('pan_gene_set_linkouts', options);
+    }
+
 }
diff --git a/src/resolvers/intermine/gene-family.ts b/src/resolvers/intermine/gene-family.ts
@@ -1,11 +1,14 @@
-import { DataSources, IntermineAPI } from '../../data-sources/index.js';
+import { DataSources, IntermineAPI, MicroservicesAPI } from '../../data-sources/index.js';
 import { inputError, KeyOfType } from '../../utils/index.js';
 import { ResolverMap } from '../resolver.js';
 import { annotatableFactory } from './annotatable.js';
 
 
-export const geneFamilyFactory = (sourceName: KeyOfType<DataSources, IntermineAPI>):
-ResolverMap => ({
+export const geneFamilyFactory = 
+    (
+        sourceName: KeyOfType<DataSources, IntermineAPI>,
+        microservicesSource: KeyOfType<DataSources, MicroservicesAPI>,
+    ): ResolverMap => ({
     Query: {
         geneFamily: async (_, { identifier }, { dataSources }) => {
             const {data: family} = await dataSources[sourceName].getGeneFamily(identifier);
@@ -48,5 +51,9 @@ ResolverMap => ({
                 // @ts-ignore: implicit type any error
                 .then(({data: results}) => results);
         },
+        linkouts: async (geneFamily, _, { dataSources }) => {
+            const {identifier} = geneFamily;
+            return dataSources[microservicesSource].getLinkoutsForGeneFamily(identifier);
+        },
     },
 });
diff --git a/src/resolvers/intermine/pan-gene-set.ts b/src/resolvers/intermine/pan-gene-set.ts
@@ -1,11 +1,14 @@
-import { DataSources, IntermineAPI } from '../../data-sources/index.js';
+import { DataSources, IntermineAPI, MicroservicesAPI } from '../../data-sources/index.js';
 import { inputError, KeyOfType } from '../../utils/index.js';
 import { ResolverMap } from '../resolver.js';
 import { annotatableFactory } from './annotatable.js';
 
 
-export const panGeneSetFactory = (sourceName: KeyOfType<DataSources, IntermineAPI>):
-ResolverMap => ({
+export const panGeneSetFactory = 
+    (
+        sourceName: KeyOfType<DataSources, IntermineAPI>,
+        microservicesSource: KeyOfType<DataSources, MicroservicesAPI>,
+    ): ResolverMap => ({
     Query: {
         panGeneSet: async (_, { identifier }, { dataSources }) => {
             const {data: panGeneSet} = await dataSources[sourceName].getPanGeneSet(identifier);
@@ -36,5 +39,9 @@ ResolverMap => ({
                 // @ts-ignore: implicit type any error
                 .then(({data: results}) => results);
         },
+        linkouts: async (panGeneSet, _, { dataSources }) => {
+            const {identifier} = panGeneSet;
+            return dataSources[microservicesSource].getLinkoutsForPanGeneSet(identifier);
+        },
     },
 });
diff --git a/src/resolvers/microservices/linkouts.ts b/src/resolvers/microservices/linkouts.ts
@@ -14,5 +14,13 @@ ResolverMap => ({
             return dataSources[sourceName].getLinkoutsForLocation(identifier, start, end)
               .then((results) => ({results}));
         },
+        geneFamilyLinkouts: async (_, { identifier }, { dataSources }) => {
+            return dataSources[sourceName].getLinkoutsForGeneFamily(identifier)
+              .then((results) => ({results}));
+        },
+        panGeneSetLinkouts: async (_, { identifier }, { dataSources }) => {
+            return dataSources[sourceName].getLinkoutsForPanGeneSet(identifier)
+              .then((results) => ({results}));
+        },
     },
 });
diff --git a/src/types/GeneFamily.graphql b/src/types/GeneFamily.graphql
@@ -23,4 +23,6 @@ type GeneFamily implements Annotatable {
   genes: [Gene!]!
   proteinDomains: [ProteinDomain!]!
   tallies: [GeneFamilyTally!]!
+  ## microservices
+  linkouts: [Linkout!]!
 }
diff --git a/src/types/PanGeneSet.graphql b/src/types/PanGeneSet.graphql
@@ -13,5 +13,7 @@ type PanGeneSet implements Annotatable {
   dataSets: [DataSet!]!
   genes: [Gene!]!
   proteins: [Protein!]!
+  ## microservices
+  linkouts: [Linkout!]!
 }
 
diff --git a/src/types/Query.graphql b/src/types/Query.graphql
@@ -256,6 +256,14 @@ type LocationLinkoutsResults {
   results: [Linkout!]!
 }
 
+type GeneFamilyLinkoutsResults {
+  results: [Linkout!]!
+}
+
+type PanGeneSetLinkoutsResults {
+  results: [Linkout!]!
+}
+
 
 # Top-level queries
 
@@ -328,5 +336,7 @@ type Query {
   ### microservices queries
   geneLinkouts(identifier: ID!): GeneLinkoutsResults
   locationLinkouts(identifier: ID!, start: Int!, end: Int!): LocationLinkoutsResults
+  geneFamilyLinkouts(identifier: ID!): GeneFamilyLinkoutsResults
+  panGeneSetLinkouts(identifier: ID!): PanGeneSetLinkoutsResults
 
 }