add some prints

Author: antgonza

src/sequence_processing_pipeline/Job.py

@@ -261,9 +261,11 @@ def _query_slurm(self, job_ids):
         # query_slurm encapsulates the handling of squeue.
         count = 0
         while True:
+            print ('------> _query_slurm')
             result = self._system_call("squeue -t all -j "
                                        f"{','.join(job_ids)} "
                                        "-o '%i,%T'")
+            print (result)
 
             if result['return_code'] == 0:
                 # there was no issue w/squeue, break this loop and
@@ -362,6 +364,7 @@ def submit_job(self, script_path, job_parameters=None,
             cmd = f'cd {exec_from};' + cmd
 
         logging.debug("job scheduler call: %s" % cmd)
+        print ('===>', cmd)
 
         if self.force_job_fail:
             raise JobFailedError("This job died.")

tests/bin/sbatch

@@ -50,7 +50,7 @@ def my_callback(jid=None, status=None):
         obs = job._system_call('ls ' + join(package_root, 'tests', 'bin'),
                                callback=my_callback)
 
-        exp = ['bcl-convert\nbcl2fastq\nfake_squeue.py\nfastqc\nsbatch\n']
+        exp = ['bcl-convert\nbcl2fastq\nfake_squeue.py\nfastqc\n']
 
         self.assertIn(obs['stdout'], exp)
         self.assertEqual(obs['stderr'], '')