feat: CQDG-000 version 2 0 14

Ferlab-Ste-Justine · Jul 9, 2024 · c4a3448 · c4a3448
1 parent 2b6e9d4
commit c4a3448
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Showing 7 changed files with 293 additions and 192 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cqdg-wrapper-next",
-  "version": "2.0.13",
+  "version": "2.0.14",
   "description": ":factory: a data-model aware GraphQL API that sits above an Elasticsearch cluster",
   "main": "src/index.js",
   "type": "module",

diff --git a/src/graphql/biospecimen/types/biospecimen.ts b/src/graphql/biospecimen/types/biospecimen.ts
@@ -10,10 +10,10 @@ import GraphQLJSON from '@ferlab/next/lib/common/types/jsonType';
 import { GraphQLInt, GraphQLList, GraphQLObjectType, GraphQLString } from 'graphql';
 
 import { esBiospecimenIndex } from '#src/config/env';
+import { FilesType } from '#src/graphql/file/types/file';
+import { ParticipantType } from '#src/graphql/participant/types/participant';
+import { StudyType } from '#src/graphql/study/types/study';
 
-import { FilesType } from '../../file/types/file';
-import { ParticipantType } from '../../participant/types/participant';
-import { StudyType } from '../../study/types/study';
 import extendedMapping from '../extendedMapping';
 import BiospecimenAgg from './biospecimenAgg';
 

diff --git a/src/graphql/file/types/file.ts b/src/graphql/file/types/file.ts
@@ -10,8 +10,8 @@ import GraphQLJSON from '@ferlab/next/lib/common/types/jsonType';
 import { GraphQLBoolean, GraphQLFloat, GraphQLInt, GraphQLList, GraphQLObjectType, GraphQLString } from 'graphql';
 
 import { esFileIndex } from '#src/config/env';
-import { BiospecimensType, BiospecimenType } from '#src/graphql/biospecimen/types/biospecimen';
-import { ParticipantsType, ParticipantType } from '#src/graphql/participant/types/participant';
+import { BiospecimensType } from '#src/graphql/biospecimen/types/biospecimen';
+import { ParticipantsType } from '#src/graphql/participant/types/participant';
 import { StudyType } from '#src/graphql/study/types/study';
 
 import extendedMapping from '../extendedMapping';
@@ -50,7 +50,26 @@ export const FileType = new GraphQLObjectType({
     sequencing_experiment: { type: SequencingExperimentType },
   }),
   extensions: {
-    nestedFields: ['participants', ...ParticipantType.extensions.nestedFields, 'biospecimens', 'biospecimens.files'],
+    nestedFields: [
+      'biospecimens',
+      'biospecimens.participant.diagnoses',
+      'biospecimens.participant.family_relationships',
+      'biospecimens.participant.icd_tagged',
+      'biospecimens.participant.mondo',
+      'biospecimens.participant.mondo_tagged',
+      'biospecimens.participant.observed_phenotype_tagged',
+      'biospecimens.participant.observed_phenotypes',
+      'participants',
+      'participants.biospecimens',
+      'participants.diagnoses',
+      'participants.familyRelationships',
+      'participants.icd_tagged',
+      'participants.mondo',
+      'participants.mondo_tagged',
+      'participants.observed_phenotype_tagged',
+      'participants.observed_phenotypes',
+      'participants.phenotypes_tagged',
+    ],
     esIndex: esFileIndex,
   },
 });

diff --git a/src/graphql/participant/types/participant.ts b/src/graphql/participant/types/participant.ts
@@ -10,10 +10,10 @@ import GraphQLJSON from '@ferlab/next/lib/common/types/jsonType';
 import { GraphQLBoolean, GraphQLEnumType, GraphQLInt, GraphQLList, GraphQLObjectType, GraphQLString } from 'graphql';
 
 import { esParticipantIndex } from '#src/config/env';
+import { BiospecimensType } from '#src/graphql/biospecimen/types/biospecimen';
+import { FilesType } from '#src/graphql/file/types/file';
+import { StudyType } from '#src/graphql/study/types/study';
 
-import { BiospecimensType } from '../../biospecimen/types/biospecimen';
-import { FilesType } from '../../file/types/file';
-import { StudyType } from '../../study/types/study';
 import extendedMapping from '../extendedMapping';
 import DiagnosesType from './diagnoses';
 import FamilyRelationshipsType from './familyRelationships';

diff --git a/src/graphql/study/types/study.ts b/src/graphql/study/types/study.ts
@@ -10,8 +10,8 @@ import GraphQLJSON from '@ferlab/next/lib/common/types/jsonType';
 import { GraphQLBoolean, GraphQLFloat, GraphQLInt, GraphQLList, GraphQLObjectType, GraphQLString } from 'graphql';
 
 import { esStudyIndex } from '#src/config/env';
+import DataSetsType from '#src/graphql/file/types/dataSets';
 
-import DataSetsType from '../../file/types/dataSets';
 import extendedMapping from '../extendedMapping';
 import DataCategoriesType from './dataCategories';
 import DataTypesType from './dataTypes';

diff --git a/src/index.ts b/src/index.ts
@@ -16,8 +16,6 @@ import keycloakConfig from './config/keycloak';
 import schema from './graphql/schema';
 import esClient from './services/elasticsearch/client';
 
-console.log(devMode);
-
 const startApp = async () => {
   try {
     const keycloak = new Keycloak({}, keycloakConfig);