Merge pull request #53 from molgenis/feat/genes

Retrieve embedded genes data

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-api",
-  "version": "2.1.0",
+  "version": "2.2.0",
   "description": "Report API for Variant Call Format (VCF) Report Templates",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

src/ApiClient.ts

@@ -34,6 +34,7 @@ interface Data {
 interface BinaryData extends BinaryDataNode {
   vcfGz: Buffer;
   fastaGz: BinaryDataNode;
+  genesGz: Buffer;
 }
 
 interface BinaryDataNode {
@@ -82,6 +83,10 @@ export class ApiClient implements Api {
     return Promise.resolve(buffer);
   }
 
+  getGenesGz(): Promise<Buffer> {
+    return Promise.resolve(this.reportData.binary.genesGz);
+  }
+
   private get<T extends Resource>(resource: string, params: Params = {}): Promise<PagedItems<T>> {
     return new Promise((resolve, reject) => {
       if (!this.reportData.data[resource]) {

src/ApiData.ts

@@ -34,6 +34,7 @@ export interface Items<T extends Resource> {
 export interface EncodedData extends EncodedDataContainer {
   vcfGz: string;
   fastaGz: EncodedDataContainer;
+  genesGz: string;
 }
 
 export interface Resource {

src/__tests__/ApiClient.test.ts

@@ -58,7 +58,8 @@ beforeEach(() => {
         '2:47637200-47637300': new Base85().encode(
           Buffer.from(gzipSync(fs.readFileSync(__dirname + '/interval1.fasta')))
         )
-      }
+      },
+      genesGz: new Base85().encode(Buffer.from(gzipSync(fs.readFileSync(__dirname + '/example.gff'))))
     }
   };
   api = new ApiClient(reportData);
@@ -661,3 +662,9 @@ test('getFastaGz - existing interval in other contig', async () => {
   const fastaGz = await api.getFastaGz('1', 47637250);
   expect(fastaGz).toBe(null);
 });
+
+test('getGenesGz', async () => {
+  const genesGz = await api.getGenesGz();
+  // null check, because size check differs between local machine and Travis
+  expect(genesGz).not.toBe(null);
+});

src/__tests__/example.gff

@@ -0,0 +1,2 @@
+##gff-version 3
+1	BestRefSeq	exon	10002981	10003083	.	+	.	ID=exon-NM_001297778.1-1;gene=NMNAT1