Merge pull request #234 from lifeomic/PHC-5229

feat: PHC-5229 Add VCF ingest command

Author: cluebbehusen

lib/cmds/genomics_cmds/ingestions_cmds/create-vcf.js

@@ -0,0 +1,40 @@
+'use strict';
+
+const { post } = require('../../../api');
+const print = require('../../../print');
+
+exports.command = 'create-vcf <projectId> <vcfFileId> <manifestFileId>';
+exports.desc = 'Create VCF ingestion for <vcfFileId> and <manifestFileId> in <projectId>';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The project ID.',
+    type: 'string'
+  }).positional('vcfFileId', {
+    describe: 'The ID of the VCF file.',
+    type: 'string'
+  }).positional('manifestFileId', {
+    describe: 'The ID of the manifest file.',
+    type: 'string'
+  }).option('succeededEmail', {
+    describe: 'An email address to notify if the ingestion succeeds',
+    type: 'string'
+  }).option('failedEmail', {
+    describe: 'An email address to notify if the ingestion fails',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await post(argv, `/v1/genomic-ingestion/projects/${argv.projectId}/ingestions`, {
+    ingestionType: 'Vcf',
+    inputFiles: {
+      vcf: argv.vcfFileId,
+      manifest: argv.manifestFileId
+    },
+    notificationConfig: {
+      succeededEmail: argv.succeededEmail,
+      failedEmail: argv.failedEmail
+    }
+  });
+  print(response.data, argv);
+};

test/unit/commands/genomics-ingestions.test.js

@@ -29,6 +29,7 @@ const createFoundationBam = proxyquire('../../../lib/cmds/genomics_cmds/ingestio
 const createCarisBam = proxyquire('../../../lib/cmds/genomics_cmds/ingestions_cmds/create-caris-bam', mocks);
 const createNextGen = proxyquire('../../../lib/cmds/genomics_cmds/ingestions_cmds/create-nextgen', mocks);
 const getByGermlineCaseId = proxyquire('../../../lib/cmds/genomics_cmds/ingestions_cmds/get-by-germline-case-id', mocks);
+const createVcf = proxyquire('../../../lib/cmds/genomics_cmds/ingestions_cmds/create-vcf', mocks);
 
 test.always.afterEach(t => {
   getStub.resetHistory();
@@ -200,3 +201,28 @@ test.serial.cb('The "create-nextgen" command should create a NextGen ingestion',
 
   yargs.command(createNextGen).parse('create-nextgen projectId tarFileId');
 });
+
+test.serial.cb('The "create-vcf" command should create a VCF ingestion', t => {
+  const res = { data: { id: 'ingestionId' } };
+  postStub.onFirstCall().returns(res);
+  callback = () => {
+    t.is(postStub.callCount, 1);
+    t.is(postStub.getCall(0).args[1], '/v1/genomic-ingestion/projects/projectId/ingestions');
+    t.deepEqual(postStub.getCall(0).args[2], {
+      ingestionType: 'Vcf',
+      inputFiles: {
+        vcf: 'vcfFileId',
+        manifest: 'manifestFileId'
+      },
+      notificationConfig: {
+        succeededEmail: 'test@testing.com',
+        failedEmail: 'test@testing.com'
+      }
+    });
+    t.is(printSpy.callCount, 1);
+    t.true(printSpy.calledWith({ id: 'ingestionId' }));
+    t.end();
+  };
+
+  yargs.command(createVcf).parse('create-vcf projectId vcfFileId manifestFileId --succeededEmail test@testing.com --failedEmail test@testing.com');
+});