added debug logs

src/api/route-services/gem2s.js

@@ -19,6 +19,7 @@ const logger = getLogger();
 
 const pipelineHook = new PipelineHook();
 
+// TODO here we are reusing the jwt so if gem2s was longer than 1 hour it will fail.
 pipelineHook.register('uploadToAWS', [saveProcessingConfigFromGem2s, runQCPipeline]);
 pipelineHook.registerAll([sendNotification]);
 

src/api/route-services/pipeline-response.js

@@ -118,23 +118,33 @@ class PipelineService {
   }
 
   static async qcResponse(io, message) {
+    console.log('starting qc response', message);
     AWSXRay.getSegment().addMetadata('message', message);
+    console.log('validating request');
     await validateRequest(message, 'PipelineResponse.v1.yaml');
 
+    console.log('running hooks');
     await pipelineHook.run(message);
 
     const { experimentId } = message;
     const { error = false } = message.response || {};
 
     let output = null;
     // if there aren't errors proceed with the updates
+    console.log('and the rest is silence');
     if (!error && 'output' in message) {
       const { input: { sampleUuid, taskName } } = message;
 
+      console.log('getS3Output');
       output = await this.getS3Output(message);
+      console.log('updatePlotData');
       await this.updatePlotData(taskName, experimentId, output);
+      console.log('updateProcessingConfig');
       await this.updateProcessingConfig(taskName, experimentId, output, sampleUuid);
     }
+
+    console.log('and the rest is not silence');
+
     // we want to send the update to the subscribed both in successful and error case
     await this.sendUpdateToSubscribed(experimentId, message, output, error, io);
   }

src/utils/authMiddlewares.js

@@ -125,6 +125,7 @@ const checkAuthExpiredMiddleware = (req, res, next) => {
     return next(new UnauthenticatedError('token has expired'));
   }
 
+  console.log(`lcs checking ignore [${req.url}] [${req.method.toLowerCase()}]`);
   // check if we should ignore expired jwt token for this path and request type
   const longTimeoutEndpoints = [{ urlMatcher: /^\/v1\/experiments\/.{32}\/cellSets$/, method: 'PATCH' }];
   const isEndpointIgnored = longTimeoutEndpoints.some(
@@ -133,6 +134,7 @@ const checkAuthExpiredMiddleware = (req, res, next) => {
     ),
   );
 
+  console.log('isEndpointIgnored: ', isEndpointIgnored);
   // if endpoint is not in ignore list, the JWT is too old, send an error accordingly
   if (!isEndpointIgnored) {
     return next(new UnauthenticatedError('token has expired'));