Save gem2s pipeline handle (#120)

* created gem2s endpoint * added skeleton parameter to state-machine-definition tests * passing all required params * fixed qc-pipeline skeleton * fixed gem2s pipeline skeleton name * renamed ARN to avoid clashes * converted gem2s pipeline steps into normal ones instead of maps * added last steps for gem2s * removed testing clutter * fixed some tests * Save gem2s pipeline handle Co-authored-by: Pol Alvarez <[email protected]> Co-authored-by: Martin Fosco <[email protected]>
hms-dbmi-cellenics · May 25, 2021 · b6804f0 · b6804f0
1 parent ba97ffc
commit b6804f0
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Showing 4 changed files with 37 additions and 6 deletions.
diff --git a/src/api/route-services/experiment.js b/src/api/route-services/experiment.js
@@ -246,7 +246,7 @@ class ExperimentService {
     return prettyData;
   }
 
-  async savePipelineHandle(experimentId, handle) {
+  async saveHandle(experimentId, handle, service) {
     const dynamodb = createDynamoDbInstance();
     let key = { experimentId };
 
@@ -257,7 +257,7 @@ class ExperimentService {
     const params = {
       TableName: this.experimentsTableName,
       Key: key,
-      UpdateExpression: 'set meta.pipeline = :x',
+      UpdateExpression: `set meta.${service} = :x`,
       ExpressionAttributeValues: data,
     };
 
@@ -266,6 +266,14 @@ class ExperimentService {
     const prettyData = convertToJsObject(result.Attributes);
     return prettyData;
   }
+
+  async saveQCHandle(experimentId, handle) {
+    return this.saveHandle(experimentId, handle, 'pipeline');
+  }
+
+  async saveGem2sHandle(experimentId, handle) {
+    return this.saveHandle(experimentId, handle, 'gem2s');
+  }
 }
 
 module.exports = ExperimentService;
diff --git a/src/api/routes/gem2s.js b/src/api/routes/gem2s.js
@@ -5,6 +5,7 @@ const getBackendStatus = require('../general-services/backend-status');
 const pipelineResponse = require('../route-services/pipeline-response');
 const parseSNSMessage = require('../../utils/parse-sns-message');
 const logger = require('../../utils/logging');
+
 const { expressAuthorizationMiddleware } = require('../../utils/authMiddlewares');
 
 module.exports = {
@@ -23,7 +24,7 @@ module.exports = {
       createGem2SPipeline(req.params.experimentId)
         .then((data) => {
           const experimentService = new ExperimentService();
-          experimentService.savePipelineHandle(req.params.experimentId, data)
+          experimentService.saveGem2sHandle(req.params.experimentId, data)
             .then(() => res.json(data));
         })
         .catch(next);

diff --git a/src/api/routes/pipelines.js b/src/api/routes/pipelines.js
@@ -17,14 +17,13 @@ module.exports = {
     },
   ],
   'pipelines#create': [
-    expressAuthorizationMiddleware,
     (req, res, next) => {
       const { processingConfig } = req.body;
 
       createQCPipeline(req.params.experimentId, processingConfig || [])
         .then((data) => {
           const experimentService = new ExperimentService();
-          experimentService.savePipelineHandle(req.params.experimentId, data)
+          experimentService.saveQCHandle(req.params.experimentId, data)
             .then(() => res.json(data));
         })
         .catch(next);

diff --git a/tests/api/route-services/experiment.test.js b/tests/api/route-services/experiment.test.js
@@ -236,7 +236,7 @@ describe('tests for the experiment service', () => {
     const updateItemSpy = mockDynamoUpdateItem();
     const dynamoTestData = AWS.DynamoDB.Converter.marshall({ ':x': jsTestData });
 
-    (new ExperimentService()).savePipelineHandle('12345', jsTestData)
+    (new ExperimentService()).saveQCHandle('12345', jsTestData)
       .then(() => {
         expect(updateItemSpy).toHaveBeenCalledWith(
           {
@@ -249,4 +249,27 @@ describe('tests for the experiment service', () => {
       })
       .then(() => done());
   });
+
+  it('Set gem2s Handle works', async (done) => {
+    const jsTestData = {
+      stateMachineArn: 'STATE-MACHINE-ID',
+      executionArn: 'EXECUTION-ID',
+    };
+
+    const updateItemSpy = mockDynamoUpdateItem();
+    const dynamoTestData = AWS.DynamoDB.Converter.marshall({ ':x': jsTestData });
+
+    (new ExperimentService()).saveGem2sHandle('12345', jsTestData)
+      .then(() => {
+        expect(updateItemSpy).toHaveBeenCalledWith(
+          {
+            TableName: 'experiments-test',
+            Key: { experimentId: { S: '12345' } },
+            UpdateExpression: 'set meta.gem2s = :x',
+            ExpressionAttributeValues: dynamoTestData,
+          },
+        );
+      })
+      .then(() => done());
+  });
 });