supersede #3092 (#3093)

Author: antgonza

qiita_db/software.py

@@ -425,10 +425,14 @@ def create(cls, software, name, description, parameters, outputs=None,
                              qdb.util.convert_to_id(at[0], 'artifact_type'),
                              at[1]])
                     else:
-                        sql_args.append(
-                            [pname, c_id,
-                             qdb.util.convert_to_id(at, 'artifact_type'),
-                             False])
+                        try:
+                            at_id = qdb.util.convert_to_id(at, 'artifact_type')
+                        except qdb.exceptions.QiitaDBLookupError:
+                            msg = (f'Error creating {software.name}, {name}, '
+                                   f'{description} - Unknown artifact_type: '
+                                   f'{at}')
+                            raise ValueError(msg)
+                        sql_args.append([pname, c_id, at_id, False])
 
                 sql = """INSERT INTO qiita.command_output
                             (name, command_id, artifact_type_id,

qiita_db/test/test_software.py

@@ -329,6 +329,16 @@ def test_create_error(self):
                 "This is a command for testing", self.parameters,
                 self.outputs)
 
+        # the output type doesn't exist
+        with self.assertRaisesRegex(ValueError, "Error creating QIIME, Split "
+                                    "libraries - wrong output, This is a "
+                                    "command for testing - Unknown "
+                                    "artifact_type: BLA!"):
+            qdb.software.Command.create(
+                self.software, "Split libraries - wrong output",
+                "This is a command for testing", self.parameters,
+                {'out': 'BLA!'})
+
     def test_create(self):
         # let's deactivate all current plugins and commands; this is not
         # important to test the creation but it is important to test if a

scripts/qiita-recover-jobs

@@ -65,13 +65,14 @@ def _retrieve_queue_jobs():
     return set(qiita_jids)
 
 
-def _count_jobs_in_arrays():
-    # a direct way to calculate how many jobs are in the queue is to count
-    # how many samples are in the preparation information file of the input
-    # artifact
-    jobs = [ProcessingJob(jid) for jid in _retrieve_queue_jobs()
-            if ProcessingJob(jid).command.name in ARRAY_COMMANDS]
-    return sum([len(job.input_artifacts[0].prep_templates[0]) for job in jobs])
+def _count_jobs_in_scheduler():
+    # first let's count all regular jobs
+    j1 = len(check_output(['qstat']).decode('ascii').split("\n"))
+    # now, let's count the jobs in job arrays
+    lines = check_output(['qstat', '-f']).decode('ascii').split("\n")
+    j2 = sum([int(x.split(',')[-1].split('-')[-1])
+              for x in lines if 'job_array_request' in x])
+    return j1 + j2
 
 
 def _get_jids_to_recover(recover_type):

setup.py

@@ -14,7 +14,7 @@
 
 
 classes = """
-    Development Status :: 3 - Alpha
+    Development Status :: 5 - Production/Stable
     License :: OSI Approved :: BSD License
     Topic :: Scientific/Engineering :: Bio-Informatics
     Topic :: Software Development :: Libraries :: Application Frameworks