feat: CQDG-680 add FERLOAD_URL

atoulous · atoulous · commit f5f4da81e3e0 · 2024-06-19T14:28:40.000-04:00
diff --git a/.env.example b/.env.example
@@ -10,6 +10,9 @@ KEYCLOAK_URL=
 KEYCLOAK_REALM=
 KEYCLOAK_CLIENT=
 
+# Ferload
+FERLOAD_URL=
+
 # Suggestion configuration
 MAX_NUMBER_OF_GF_SUGGESTIONS=
 GENES_SUGGESTIONS_INDEX_NAME=
@@ -36,6 +39,4 @@ FILE_ID_KEY=
 STUDY_ID_KEY=
 PARTICIPANT_ID_KEY=
 BIOSPECIMEN_ID_KEY=
-FAMILY_ID_KEY=
-
-ADD_CAG_COUNT=
+FAMILY_ID_KEY=
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "cqdg-wrapper-next",
-  "version": "2.0.10",
+  "version": "2.0.11",
   "description": ":factory: a data-model aware GraphQL API that sits above an Elasticsearch cluster",
   "main": "src/index.js",
   "type": "module",
diff --git a/src/config/env.ts b/src/config/env.ts
@@ -11,6 +11,8 @@ export const keycloakURL = process.env.KEYCLOAK_URL || 'https://auth.qa.juno.cqd
 export const keycloakRealm = process.env.KEYCLOAK_REALM || 'CQDG';
 export const keycloakClient = process.env.KEYCLOAK_CLIENT || 'cqdg-client';
 
+export const ferloadURL = process.env.FERLOAD_URL || 'https://ferload.qa.juno.cqdg.ferlab.bio';
+
 export const esHost = process.env.ES_HOST || 'http://localhost:9200';
 export const esUser = process.env.ES_USER;
 export const esPass = process.env.ES_PASS;
diff --git a/src/graphql/biospecimen/model.ts b/src/graphql/biospecimen/model.ts
@@ -4,7 +4,7 @@ import { getBody } from '#src/services/elasticsearch/utils';
 import { BiospecimenType } from './types/biospecimen';
 
 const get = async (file_id, context) => {
-  const { body } = await context.es.get({ index: esBiospecimenIndex, file_id });
+  const { body } = await context.esClient.get({ index: esBiospecimenIndex, file_id });
   return body._source;
 };
 
@@ -14,7 +14,7 @@ const getBy = async ({ field, value, path, args, context }) => {
     : false;
   const body = getBody({ field, value, path, nested: isNested });
 
-  const res = await context.es.search({
+  const res = await context.esClient.search({
     index: esBiospecimenIndex,
     size: args.first,
     sort: args.sort,
diff --git a/src/graphql/file/model.ts b/src/graphql/file/model.ts
@@ -4,7 +4,7 @@ import { getBody } from '#src/services/elasticsearch/utils';
 import { FileType } from './types/file';
 
 const get = async (file_id, context) => {
-  const { body } = await context.es.get({ index: esFileIndex, file_id });
+  const { body } = await context.esClient.get({ index: esFileIndex, file_id });
   return body._source;
 };
 
@@ -14,7 +14,7 @@ const getBy = async ({ field, value, path, args, context }) => {
     : false;
   const body = getBody({ field, value, path, nested: isNested });
 
-  const res = await context.es.search({
+  const res = await context.esClient.search({
     index: esFileIndex,
     size: args.first,
     sort: args.sort,
diff --git a/src/graphql/file/resolver.ts b/src/graphql/file/resolver.ts
@@ -0,0 +1,63 @@
+import { hitsResolver } from '@ferlab/next/lib/common/resolvers';
+import fetch from 'node-fetch';
+
+import { ferloadURL } from '#src/config/env';
+
+import ParticipantModel from '../participant/model';
+
+export const hitsResolverNested = async (parent, args, type, esClient) => {
+  try {
+    const participant_ids = parent.participants.map((participant) => participant.participant_id);
+
+    const results = await ParticipantModel.getBy({
+      field: 'participant_id',
+      value: participant_ids,
+      path: '',
+      args,
+      esClient,
+    });
+
+    return results;
+  } catch (error) {
+    console.error('hitsResolverNested error', error);
+    return null;
+  }
+};
+
+const filesResolver = async (parent, args, type, context) => {
+  try {
+    const { esClient, auth } = context;
+    const filesHits = await hitsResolver(parent, args, type, esClient);
+    const file_ids: string[] = filesHits?.edges.map((file) => file.file_id);
+
+    const res = await fetch(`${ferloadURL}/permissions/by-list`, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+        Authorization: `Bearer ${auth?.token}`,
+      },
+      body: JSON.stringify({ file_ids }),
+    });
+
+    if (res.status !== 200) {
+      return filesHits;
+    }
+
+    const filesAuthorized: string[] = res?.json && (await res.json());
+
+    const filesWithUserAccess = filesHits?.edges.map((file) => {
+      let user_authorized = false;
+      if (filesAuthorized.includes(file.file_id)) {
+        user_authorized = true;
+      }
+      return { ...file, user_authorized };
+    });
+
+    return { ...filesHits, edges: filesWithUserAccess };
+  } catch (error) {
+    console.error('filesResolver error', error);
+    return null;
+  }
+};
+
+export default filesResolver;
diff --git a/src/graphql/file/types/file.ts b/src/graphql/file/types/file.ts
@@ -7,14 +7,15 @@ import {
   MatchBoxStateType,
 } from '@ferlab/next/lib/common/types';
 import GraphQLJSON from '@ferlab/next/lib/common/types/jsonType';
-import { GraphQLFloat, GraphQLInt, GraphQLList, GraphQLObjectType, GraphQLString } from 'graphql';
+import { GraphQLBoolean, GraphQLFloat, GraphQLInt, GraphQLList, GraphQLObjectType, GraphQLString } from 'graphql';
 
 import { esFileIndex } from '#src/config/env';
 
 import { BiospecimensType } from '../../biospecimen/types/biospecimen';
-import { ParticipantsType } from '../../participant/types/participant';
+import { ParticipantsType, ParticipantType } from '../../participant/types/participant';
 import { StudyType } from '../../study/types/study';
 import extendedMapping from '../extendedMapping';
+import filesResolver, { hitsResolverNested } from '../resolver';
 import FileAgg from './fileAgg';
 import SequencingExperimentType from './sequencingExperiment';
 
@@ -38,7 +39,12 @@ export const FileType = new GraphQLObjectType({
     study_code: { type: GraphQLString },
     study_id: { type: GraphQLString },
     study: { type: StudyType },
-    //todo: create resolve: get participants and samples from participant_index
+    data_access: { type: GraphQLString },
+    user_authorized: { type: GraphQLBoolean },
+    participants_by_index: {
+      type: ParticipantsType,
+      resolve: (parent, args, context) => hitsResolverNested(parent, args, ParticipantType, context.esClient),
+    },
     participants: { type: ParticipantsType },
     biospecimens: { type: BiospecimensType },
     sequencing_experiment: { type: SequencingExperimentType },
@@ -74,7 +80,7 @@ export const FilesType = new GraphQLObjectType({
     hits: {
       type: FileHitsType,
       args: hitsArgsType,
-      resolve: (parent, args, context) => hitsResolver(parent, args, FileType, context.esClient),
+      resolve: (parent, args, context) => filesResolver(parent, args, FileType, context),
     },
     mapping: { type: GraphQLJSON },
     extended: {
diff --git a/src/graphql/gene/model.ts b/src/graphql/gene/model.ts
@@ -3,7 +3,7 @@ import { getBody } from '../../services/elasticsearch/utils';
 import { GeneType } from './types/gene';
 
 const get = async (file_id, context) => {
-  const { body } = await context.es.get({ index: esGeneIndex, file_id });
+  const { body } = await context.esClient.get({ index: esGeneIndex, file_id });
   return body._source;
 };
 
@@ -13,7 +13,7 @@ const getBy = async ({ field, value, path, args, context }) => {
     : false;
   const body = getBody({ field, value, path, nested: isNested });
 
-  const res = await context.es.search({
+  const res = await context.esClient.search({
     index: esGeneIndex,
     size: args.first,
     sort: args.sort,
diff --git a/src/graphql/participant/model.ts b/src/graphql/participant/model.ts
@@ -1,23 +1,32 @@
+import { Client } from '@opensearch-project/opensearch';
+
 import { esParticipantIndex } from '#src/config/env';
 import { getBody } from '#src/services/elasticsearch/utils';
 
 import { ParticipantType } from './types/participant';
 
-const get = async (file_id, context) => {
-  const { body } = await context.es.get({ index: esParticipantIndex, file_id });
+const get = async (participant_id, esClient) => {
+  const { body } = await esClient.get({ index: esParticipantIndex, participant_id });
   return body._source;
 };
 
-const getBy = async ({ field, value, path, args, context }) => {
-  const body = getBody({ field, value, path, nested: ParticipantType?.extensions?.nestedFields?.includes(path) });
+interface IgetBy {
+  field: string;
+  value: string | string[];
+  path?: string;
+  args: any;
+  esClient: Client;
+}
 
-  const res = await context.es.search({
+const getBy = async ({ field, value, path, args, esClient }: IgetBy) => {
+  const nested = ParticipantType?.extensions?.nestedFields?.includes(path);
+  const body = getBody({ field, value, path, nested });
+  const res = await esClient.search({
     index: esParticipantIndex,
     size: args.first,
     sort: args.sort,
     body,
   });
-
   const hits = res?.body?.hits?.hits || [];
   return hits.map((hit) => hit._source) || [];
 };
diff --git a/src/graphql/study/model.ts b/src/graphql/study/model.ts
@@ -3,7 +3,7 @@ import { getBody } from '../../services/elasticsearch/utils';
 import { StudyType } from './types/study';
 
 const get = async (file_id, context) => {
-  const { body } = await context.es.get({ index: esStudyIndex, file_id });
+  const { body } = await context.esClient.get({ index: esStudyIndex, file_id });
   return body._source;
 };
 
@@ -13,7 +13,7 @@ const getBy = async ({ field, value, path, args, context }) => {
     : false;
   const body = getBody({ field, value, path, nested: isNested });
 
-  const res = await context.es.search({
+  const res = await context.esClient.search({
     index: esStudyIndex,
     size: args.first,
     sort: args.sort,
diff --git a/src/graphql/variant/model.ts b/src/graphql/variant/model.ts
@@ -3,7 +3,7 @@ import { getBody } from '../../services/elasticsearch/utils';
 import { VariantType } from './types/variant';
 
 const get = async (file_id, context) => {
-  const { body } = await context.es.get({ index: esVariantIndex, file_id });
+  const { body } = await context.esClient.get({ index: esVariantIndex, file_id });
   return body._source;
 };
 
@@ -13,7 +13,7 @@ const getBy = async ({ field, value, path, args, context }) => {
     : false;
   const body = getBody({ field, value, path, nested: isNested });
 
-  const res = await context.es.search({
+  const res = await context.esClient.search({
     index: esVariantIndex,
     size: args.first,
     sort: args.sort,
diff --git a/src/index.ts b/src/index.ts
@@ -46,7 +46,7 @@ const startApp = async () => {
       '/graphql',
       cors(),
       express.json({ limit: '50mb' }),
-      expressMiddleware(server, { context: resolveContext })
+      expressMiddleware(server, { context: ({ req }) => resolveContext(req) })
     );
     app.use('/download', downloadRouter(resolveContext));
     httpServer.listen({ port });
diff --git a/src/services/elasticsearch/utils.ts b/src/services/elasticsearch/utils.ts
@@ -1,4 +1,16 @@
 export const getBody = ({ field, value, path, nested = false }) => {
+  let must: any = [{ match: { [field]: value } }];
+
+  if (Array.isArray(value)) {
+    must = [
+      {
+        terms: {
+          [field]: value,
+        },
+      },
+    ];
+  }
+
   if (nested) {
     return {
       query: {
@@ -7,23 +19,16 @@ export const getBody = ({ field, value, path, nested = false }) => {
             {
               nested: {
                 path,
-                query: { bool: { must: [{ match: { [field]: value } }] } },
+                query: { bool: { must } },
               },
             },
           ],
         },
       },
     };
   }
+
   return {
-    query: {
-      bool: {
-        must: [
-          {
-            match: { [field]: value },
-          },
-        ],
-      },
-    },
+    query: { bool: { must } },
   };
 };

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "cqdg-wrapper-next",`
`3`		`- "version": "2.0.10",`
	`3`	`+ "version": "2.0.11",`
`4`	`4`	`"description": ":factory: a data-model aware GraphQL API that sits above an Elasticsearch cluster",`
`5`	`5`	`"main": "src/index.js",`
`6`	`6`	`"type": "module",`