Merge pull request #274 from bcgsc/feat/DEVSU-2049-kbmatches-to-poten…

…tial

[DEVSU-2049] kbmatches to potential

app/api/graphkb.js

@@ -93,7 +93,48 @@ const graphkbEvidenceLevels = async (graphkbToken) => {
   });
 };
 
+/* Get Statement info from GraphKB
+ *
+ * @param {string} graphkbToken the Authorization token for the connection to GraphKB
+ * @param {string} statementId the statement RID to query GraphKB with
+ *
+ * @returns {object} response body from graphkb
+ */
+const graphkbStatement = async (graphkbToken, statementId) => {
+  const {uri} = CONFIG.get('graphkb');
+
+  const query = {
+    filters: [
+      {'@rid': `${statementId}`},
+    ],
+    limit: 1,
+    target: 'Statement',
+    returnProperties: [
+      'conditions.@rid',
+      'conditions.@class',
+      'conditions.displayName',
+      'conditions.reference1.displayName',
+      'conditions.type.displayName',
+      'conditions.reference2.displayName',
+      'relevance.@rid',
+      'relevance.displayName',
+    ],
+  };
+
+  return request({
+    url: `${uri}/query`,
+    method: 'POST',
+    body: JSON.stringify(query),
+    json: true,
+    headers: {
+      Authorization: graphkbToken,
+      'Content-Type': 'application/json',
+    },
+  });
+};
+
 module.exports = {
   graphkbAutocomplete,
   graphkbEvidenceLevels,
+  graphkbStatement,
 };

app/routes/graphkb/index.js

@@ -1,9 +1,9 @@
-const HTTP_STATUS = require('http-status-codes');
+const {StatusCodes} = require('http-status-codes');
 const express = require('express');
 
 const logger = require('../../log');
 const loginMiddleware = require('../../middleware/graphkb');
-const {graphkbAutocomplete, graphkbEvidenceLevels} = require('../../api/graphkb');
+const {graphkbAutocomplete, graphkbEvidenceLevels, graphkbStatement} = require('../../api/graphkb');
 
 const router = express.Router({mergeParams: true});
 
@@ -15,11 +15,15 @@ router.use(loginMiddleware);
  */
 router.get('/:targetType(variant|therapy|evidenceLevel|context)', async (req, res) => {
   try {
-    const data = await graphkbAutocomplete(req.params.targetType, req.graphkbToken, req.query?.search);
-    return res.status(HTTP_STATUS.OK).json(data);
+    const data = await graphkbAutocomplete(
+      req.params.targetType,
+      req.graphkbToken,
+      req.query?.search,
+    );
+    return res.status(StatusCodes.OK).json(data);
   } catch (error) {
     logger.error(error);
-    return res.status(HTTP_STATUS.SERVICE_UNAVAILABLE).json(`GraphKB lookup error: ${error}`);
+    return res.status(StatusCodes.SERVICE_UNAVAILABLE).json(`GraphKB lookup error: ${error}`);
   }
 });
 
@@ -31,10 +35,25 @@ router.get('/evidence-levels', async (req, res) => {
   const {graphkbToken} = req;
   try {
     const data = await graphkbEvidenceLevels(graphkbToken);
-    return res.status(HTTP_STATUS.OK).json(data);
+    return res.status(StatusCodes.OK).json(data);
   } catch (error) {
     logger.error(error);
-    return res.status(HTTP_STATUS.SERVICE_UNAVAILABLE).json(`GraphKB lookup error: ${error}`);
+    return res.status(StatusCodes.SERVICE_UNAVAILABLE).json(`GraphKB lookup error: ${error}`);
+  }
+});
+
+/**
+ * Endpoint for retrieving Statement related info from GraphKB. This endpoint is used by the client
+ * for getting @rids from graphKB to be used to add kbmatches to potential therapeutic targets
+ */
+router.get('/statements/:statementId', async (req, res) => {
+  const {graphkbToken} = req;
+  try {
+    const data = await graphkbStatement(graphkbToken, req.params.statementId);
+    return res.status(StatusCodes.OK).json(data);
+  } catch (error) {
+    logger.error(error);
+    return res.status(StatusCodes.SERVICE_UNAVAILABLE).json(`GraphKB lookup error: ${error}`);
   }
 });
 

test/graphkb.mock.js

@@ -54,5 +54,58 @@ jest.mock('../app/api/graphkb', () => {
         }],
       };
     },
+
+    graphkbStatement: async (graphkbToken, statementId) => {
+      if (!graphkbToken) {
+        throw new Error('Invalid token');
+      }
+      if (!statementId) {
+        throw new Error('No statementId given');
+      }
+
+      return {
+        metadata: {
+          records: 1,
+        },
+        result: [
+          {
+            conditions: [
+              {
+                '@class': 'PositionalVariant',
+                '@rid': '#159:5455',
+                displayName: 'BRAF:p.V600E',
+                reference1: {
+                  displayName: 'BRAF',
+                },
+                reference2: null,
+                type: {
+                  displayName: 'missense mutation',
+                },
+              },
+              {
+                '@class': 'Therapy',
+                '@rid': '#123:40604',
+                displayName: 'panitumumab [DB01269]',
+                reference1: null,
+                reference2: null,
+                type: null,
+              },
+              {
+                '@class': 'Disease',
+                '@rid': '#135:19439',
+                displayName: 'colorectal adenocarcinoma [COADREAD]',
+                reference1: null,
+                reference2: null,
+                type: null,
+              },
+            ],
+            relevance: {
+              '@rid': '#146:46',
+              displayName: 'resistance',
+            },
+          },
+        ],
+      };
+    },
   };
 });

test/routes/graphkb.test.js

@@ -1,4 +1,4 @@
-const HTTP_STATUS = require('http-status-codes');
+const {StatusCodes} = require('http-status-codes');
 const supertest = require('supertest');
 const getPort = require('get-port');
 // get test user info
@@ -16,7 +16,7 @@ const testAutocompleteWithKeyword = async (request, type, keyword) => {
     .get(`${BASE_URL}/${type}?search=${keyword}`)
     .auth(username, password)
     .type('json')
-    .expect(HTTP_STATUS.OK);
+    .expect(StatusCodes.OK);
 
   expect(body).toEqual(
     expect.objectContaining({
@@ -38,7 +38,7 @@ const testAutocompleteWithoutKeyword = async (request, type) => {
     .get(`${BASE_URL}/${type}`)
     .auth(username, password)
     .type('json')
-    .expect(HTTP_STATUS.OK);
+    .expect(StatusCodes.OK);
 
   expect(body).toEqual(
     expect.objectContaining({
@@ -129,9 +129,45 @@ describe('GET /graphkb/evidence-levels', () => {
       .get(`${BASE_URL}/evidence-levels`)
       .auth(username, password)
       .type('json')
-      .expect(HTTP_STATUS.OK);
+      .expect(StatusCodes.OK);
 
     expect(body.result.length).toBeGreaterThan(0);
     expect(body.result[0]).toHaveProperty('description');
   });
 });
+
+describe('GET /graphkb/statements/:statementId', () => {
+  let server;
+  let request;
+
+  beforeAll(async () => {
+    const port = await getPort({port: CONFIG.get('web:port')});
+    server = await listen(port);
+    request = supertest(server);
+  });
+
+  afterAll(async () => {
+    await server.close();
+  });
+
+  test('returns one statement with the correct params', async () => {
+    const {body} = await request
+      .get(`${BASE_URL}/statements/156:13495`)
+      .auth(username, password)
+      .type('json')
+      .expect(StatusCodes.OK);
+
+    expect(body.result.length).toEqual(1);
+    expect(body.metadata.records).toEqual(1);
+    expect(body.result[0]).toHaveProperty('conditions');
+    expect(body.result[0].conditions[0]).toHaveProperty('@rid');
+    expect(body.result[0].conditions[0]).toHaveProperty('@class');
+    expect(body.result[0].conditions[0]).toHaveProperty('displayName');
+    expect(body.result[0].conditions[0]).toHaveProperty('reference1');
+    expect(body.result[0].conditions[0]).toHaveProperty('reference2');
+    expect(body.result[0].conditions[0]).toHaveProperty('type');
+    expect(body.result[0]).toHaveProperty('relevance');
+    expect(body.result[0].relevance).toHaveProperty('@rid');
+    expect(body.result[0].relevance).toHaveProperty('displayName');
+  });
+});