add include project for download (#46)

* add include project for download

* incorporate review comments

Author: adipaul1981

package-lock.json

@@ -1,7 +1,7 @@
 {
   "name": "kf-api-portal-reports",
   "version": "1.2.3",
-  "description": "The Kids First Download Clinical Data API offers an endpoint to generate a report of clinical data based on a query built using the Kids First Portal.",
+  "description": "The Download Clinical Data API offers an endpoint to generate a report of clinical data based on a query built using the:",
   "main": "index.js",
   "scripts": {
     "start": "node ./dist/index.js",
@@ -44,7 +44,7 @@
   },
   "dependencies": {
     "@elastic/elasticsearch": "^7.4.0",
-    "@kfarranger/middleware": "1.5.2",
+    "@arranger/middleware": "2.16.1",
     "cors": "^2.8.5",
     "dotenv": "^8.1.0",
     "excel4node": "^1.7.2",

package.json

@@ -10,6 +10,9 @@ export const ES_HOST = process.env.ES_HOST || 'kf-arranger-es-prd.kids-first.io:
 // ElasticSearch queries parameters
 export const ES_PAGESIZE: number = Number(process.env.ES_PAGESIZE) || 1000;
 
+// Project
+export const PROJECT: string = process.env.PROJECT || 'kids-first';
+
 // Keycloak configs
 export const KEYCLOAK_URL = process.env.KEYCLOAK_URL || 'https://kf-keycloak-qa.kf-strides.org/auth';
 export const KEYCLOAK_REALM = process.env.KEYCLOAK_REALM || 'kidsfirstdrc';

src/env.ts

@@ -0,0 +1,45 @@
+import { QueryConfig, ReportConfig, SheetConfig } from '../types';
+
+const biospecimens: SheetConfig = {
+    sheetName: 'Biospecimens',
+    root: 'biospecimens',
+    columns: [
+        { field: 'fhir_id' },
+        { field: 'external_id' },
+        { field: 'files.biospecimens.biospecimen_id', header: 'Biospecimens Biospecimens Id' },
+        {
+            field: 'files.biospecimens.age_at_biospecimen_collection',
+            header: 'Biospecimens Age At Biospecimen Collection',
+        },
+        { field: 'files.biospecimens.bio_repository', header: 'Biospecimens Bio Repository' },
+        { field: 'files.biospecimens.biospecimen_type', header: 'Biospecimens Biospecimen Type' },
+        { field: 'files.biospecimens.derived_sample_id', header: 'Biospecimens Derived Sample Id' },
+        { field: 'files.biospecimens.derived_sample_type', header: 'Biospecimens Derived Sample Type' },
+        { field: 'files.biospecimens.ncit_id_tissue_type', header: 'Biospecimens NCIT Id Tissue Type' },
+        { field: 'files.biospecimens.sample_id', header: 'Biospecimens Sample Id' },
+        { field: 'files.biospecimens.sample_type', header: 'Biospecimens Sample Type' },
+    ],
+    sort: [
+        {
+            'files.biospecimens.biospecimen_id': {
+                order: 'asc',
+            },
+        },
+        {
+            fhir_id: {
+                order: 'asc',
+            },
+        },
+    ],
+};
+
+const queryConfigs: QueryConfig = {
+    indexName: 'participant',
+    alias: 'participant_centric',
+};
+
+const sheetConfigs: SheetConfig[] = [biospecimens];
+
+const reportConfig: ReportConfig = { queryConfigs, sheetConfigs };
+
+export default reportConfig;

src/reports/biospecimen-data/configInclude.ts

@@ -1,10 +1,13 @@
 import { Request, Response } from 'express';
 import { Client } from '@elastic/elasticsearch';
 import generateReport from '../generateReport';
-import reportConfig from './config';
+import configKf from './configKf';
+import configInclude from './configInclude';
+import { PROJECT } from '../../env';
 import { normalizeConfigs } from '../../utils/configUtils';
 import ExtendedReportConfigs from '../../utils/extendedReportConfigs';
 import { reportGenerationErrorHandler } from '../../errors';
+import { ProjectType } from '../types';
 
 const clinicalDataReport = (esHost: string) => async (req: Request, res: Response) => {
     console.time('biospecimen-data');
@@ -13,6 +16,8 @@ const clinicalDataReport = (esHost: string) => async (req: Request, res: Respons
     const userId = req['kauth']?.grant?.access_token?.content?.sub;
     const accessToken = req.headers.authorization;
 
+    const reportConfig = PROJECT.toLowerCase().trim() === ProjectType.kidsFirst ? configKf : configInclude;
+
     let es = null;
     try {
         // prepare the ES client