feat(agora): migrating mongoose api and openapi yaml files (AG-1552)

apps/agora/api/src/api.ts

@@ -1,7 +1,18 @@
 import express from 'express';
 import mongoose from 'mongoose';
-import { dataVersionRoute } from './components/dataversion';
-import { teamMemberImageRoute, teamsRoute } from './components/teams';
+import {
+  allBiodomainsRoute,
+  biodomainsRoute,
+  comparisonGenesRoute,
+  dataVersionRoute,
+  distributionRoute,
+  geneRoute,
+  genesRoute,
+  nominatedGenesRoute,
+  searchGeneRoute,
+  teamMemberImageRoute,
+  teamsRoute,
+} from './components';
 
 const mongoUri = process.env.MONGODB_URI;
 
@@ -19,7 +30,15 @@ mongoose.connection.on('error', console.error.bind(console, 'MongoDB connection
 
 const router = express.Router();
 mongoose.connection.once('open', async () => {
+  router.get('/biodomains', allBiodomainsRoute);
+  router.get('/biodomains/:id', biodomainsRoute);
   router.get('/dataversion', dataVersionRoute);
+  router.get('/distribution', distributionRoute);
+  router.get('/genes/search', searchGeneRoute);
+  router.get('/genes/comparison', comparisonGenesRoute);
+  router.get('/genes/nominated', nominatedGenesRoute);
+  router.get('/genes/:id', geneRoute);
+  router.get('/genes', genesRoute);
   router.get('/teams', teamsRoute);
   router.get('/teamMembers/:name/image', teamMemberImageRoute);
 });

apps/agora/api/src/components/biodomains.ts

@@ -0,0 +1,84 @@
+// -------------------------------------------------------------------------- //
+// Internal
+// -------------------------------------------------------------------------- //
+import { Request, Response, NextFunction } from 'express';
+import { cache, setHeaders } from '../helpers';
+import { AllBioDomainsCollection, BioDomains, BioDomainsCollection } from '../models';
+import { BioDomainInfo } from '../../app/models';
+
+// -------------------------------------------------------------------------- //
+// Functions
+// -------------------------------------------------------------------------- //
+export async function getAllBioDomains() {
+  const cacheKey = 'all-biodomains';
+  let result: BioDomainInfo[] | null | undefined = cache.get(cacheKey);
+
+  if (result) {
+    return result;
+  }
+
+  result = await AllBioDomainsCollection.find().lean().sort().exec();
+
+  cache.set(cacheKey, result);
+  return result || undefined;
+}
+
+export async function getAllGeneBioDomains() {
+  const cacheKey = 'all-genebiodomains';
+  let result: BioDomains[] | null | undefined = cache.get(cacheKey);
+
+  if (result) {
+    return result;
+  }
+
+  result = await BioDomainsCollection.find().lean().sort().exec();
+
+  cache.set(cacheKey, result);
+  return result || undefined;
+}
+
+export async function getBioDomains(ensg: string) {
+  const cacheKey = ensg + '-biodomains';
+  let result: BioDomains | null | undefined = cache.get(cacheKey);
+
+  if (result) {
+    return result;
+  }
+
+  result = await BioDomainsCollection.findOne({
+    ensembl_gene_id: ensg,
+  })
+    .lean()
+    .exec();
+
+  cache.set(cacheKey, result);
+  return result || undefined;
+}
+
+// -------------------------------------------------------------------------- //
+// Routes
+// -------------------------------------------------------------------------- //
+export async function allBiodomainsRoute(req: Request, res: Response, next: NextFunction) {
+  try {
+    const result = await getAllBioDomains();
+    setHeaders(res);
+    res.json(result);
+  } catch (err) {
+    next(err);
+  }
+}
+
+export async function biodomainsRoute(req: Request, res: Response, next: NextFunction) {
+  if (!req.params || !req.params.id) {
+    res.status(404).send('Not found');
+    return;
+  }
+
+  try {
+    const result = await getBioDomains(<string>req.params.id);
+    setHeaders(res);
+    res.json(result?.gene_biodomains);
+  } catch (err) {
+    next(err);
+  }
+}