debug CI: Exception not being caught

sequence_processing_pipeline/Job.py

@@ -219,7 +219,7 @@ def submit_job(self, script_path, job_parameters=None,
         logging.debug("job scheduler call: %s" % cmd)
 
         if self.force_job_fail:
-            raise JobFailedError("This job died.")
+            raise JobFailedError("I AM MESSAGE ONE")
 
         # if system_call does not raise a PipelineError(), then the scheduler
         # successfully submitted the job. In this case, it should return

sequence_processing_pipeline/NuQCJob.py

@@ -249,18 +249,22 @@ def run(self, callback=None):
         # job_script_path formerly known as:
         #  process.multiprep.pangenome.adapter-filter.pe.sbatch
 
+        print("SUBMITTING JOB...")
         try:
             job_info = self.submit_job(job_script_path,
                                        job_parameters=' '.join(job_params),
                                        exec_from=self.log_path,
                                        callback=callback)
         except JobFailedError as e:
+            print("I AM HERE")
             # When a job has failed, parse the logs generated by this specific
             # job to return a more descriptive message to the user.
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError('\n'.join(info))
+            # raise JobFailedError('\n'.join(info))
+            raise JobFailedError("I AM MESSAGE TWO")
+        print("IF YOU CAN SEE THIS MESSAGE THEN JobFailedError WAS NOT CAUGHT AS EXPECTED")
 
         job_id = job_info['job_id']
         logging.debug(f'NuQCJob {job_id} completed')
@@ -450,14 +454,14 @@ def _generate_job_script(self):
         return job_script_path
 
     def parse_logs(self):
+        print("PARSE_LOGS() CALLED")
         log_path = join(self.output_path, 'Logs')
         # sorted lists give predictable results
         files = sorted(glob.glob(join(log_path, '*.out')))
 
         msgs = []
 
         for some_file in files:
-            print("PARSE_LOGS.SOME_FILE: %s" % some_file)
             with open(some_file, 'r') as f:
                 msgs += [line for line in f.readlines()
                          if 'error' in line.lower()]

sequence_processing_pipeline/tests/test_NuQCJob.py

@@ -567,11 +567,8 @@ def setUp(self):
                                      "[ERROR] Another Standin Error (ASE)."]
         }
 
-        self.foobar = []
-
         for log_file in log_files:
             fp = join(self.qc_log_path, log_file)
-            self.foobar.append(fp)
 
             with open(fp, 'w') as f:
                 lines = log_files[log_file]
@@ -654,19 +651,13 @@ def test_error_msg_from_logs(self):
         exp = ("This job died.\n[ERROR] Another Standin Error (ASE).\n[ERROR]"
                " Generic Standin Error (GSE).")
 
-        for foo in self.foobar:
-            print("checking %s..." % foo)
-            self.assertTrue(exists(foo))
-            with open(foo, 'r') as f:
-                lines = f.readlines()
-                print("\tLINES: %s" % lines)
-
         try:
             job.run()
         except JobFailedError as e:
-            print(">>>%s<<<" % str(e))
-            print(">>>%s<<<" % exp)
-            self.assertEqual(str(e), exp)
+            print("JobFailedError CAUGHT: %s" % str(e))
+            #print(">>>%s<<<" % str(e))
+            #print(">>>%s<<<" % exp)
+            #self.assertEqual(str(e), exp)
 
         self.assertTrue(False)