adding files to tests/bin

Author: antgonza

.github/workflows/qiita-plugin-ci.yml

@@ -88,9 +88,6 @@ jobs:
           conda activate klp
 
           # creating bcl-convert/sbatch/squeue executable
-          echo 'echo "$@"' > `pwd`/tests/bin/sbatch
-          echo 'echo -e "JOBID,STATE\n1234,COMPLETED"' > `pwd`/tests/bin/squeue
-          chmod +x `pwd`/tests/bin/sbatch `pwd`/tests/bin/squeue `pwd`/tests/bin/bcl-convert
           echo `pwd`/tests/bin/ >> "$GITHUB_PATH"
 
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt

src/sequence_processing_pipeline/ConvertJob.py

@@ -170,7 +170,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         self. mark_job_completed()
 

src/sequence_processing_pipeline/FastQCJob.py

@@ -206,7 +206,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         logging.debug(job_info)
 

src/sequence_processing_pipeline/MultiQCJob.py

@@ -217,7 +217,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         logging.debug(job_info)
 

src/sequence_processing_pipeline/NuQCJob.py

@@ -265,7 +265,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         job_id = job_info['job_id']
 

src/sequence_processing_pipeline/SeqCountsJob.py

@@ -80,7 +80,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         self.mark_job_completed()
 

src/sequence_processing_pipeline/TRIntegrateJob.py

@@ -105,7 +105,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         self.mark_job_completed()
 

src/sequence_processing_pipeline/TellReadJob.py

@@ -92,8 +92,7 @@ def run(self, callback=None):
             info = self.parse_logs()
             # prepend just the message component of the Error.
             info.insert(0, str(e))
-            info = str(e)
-            raise JobFailedError(info)
+            raise JobFailedError('\n'.join(info))
 
         self.mark_job_completed()
 

tests/bin/sbatch

@@ -0,0 +1 @@
+echo "$@"

tests/bin/squeue

@@ -0,0 +1 @@
+echo -e "JOBID,STATE\n1234,COMPLETED"

tests/test_Job.py

@@ -50,7 +50,8 @@ 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\n']
+        exp = ['bcl-convert\nbcl2fastq\nfake_squeue.py\nfastqc\n'
+               'sbatch\nsqueue\n']
 
         self.assertIn(obs['stdout'], exp)
         self.assertEqual(obs['stderr'], '')