Fix summary (#2037)

* Removing travis debugging

* Fixing error and adding a specific test

* Adding qiita-private script to avoid connecting to the ipython cluster

* Adding exec bit

Author: josenavas

qiita_db/processing_job.py

@@ -600,7 +600,7 @@ def complete(self, success, artifacts_data=None, error=None):
             else:
                 if self.command.software.type == 'artifact definition':
                     job_params = self.parameters.values
-                    if job_params['provenance'] is not None:
+                    if job_params.get('provenance') is not None:
                         # This artifact definition job is a result of a command
                         # run, if it fails, set up the status of the "parent"
                         # job also as failed, and assign the sem error message

qiita_db/test/test_processing_job.py

@@ -404,6 +404,15 @@ def test_complete_no_artifact_data(self):
         job.complete(True)
         self.assertEqual(job.status, 'success')
 
+        job = qdb.processing_job.ProcessingJob.create(
+            qdb.user.User('test@foo.bar'),
+            qdb.software.Parameters.load(
+                qdb.software.Command(5),
+                values_dict={"input_data": 1}))
+        job._set_status('running')
+        job.complete(False, error='Some Error')
+        self.assertEqual(job.status, 'error')
+
     def test_complete_type(self):
         fd, fp = mkstemp(suffix="_table.biom")
         self._clean_up_files.append(fp)

scripts/qiita

@@ -491,15 +491,5 @@ def update():
     _activate_or_update_plugins(update=True)
 
 
-# #############################################################################
-# PRIVATE COMMANDS
-# #############################################################################
-@private.command()
-@click.argument('job_id', required=True, type=click.STRING)
-@click.argument('payload', required=True, type=click.STRING)
-def complete_job(job_id, payload):
-    qdb.commands.complete_job_cmd(job_id, payload)
-
-
 if __name__ == '__main__':
     qiita()

scripts/qiita-private

@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+import click
+import qiita_db as qdb
+
+
+@click.group()
+def qiita_private():
+    pass
+
+
+@qiita_private.command()
+@click.argument('job_id', required=True, type=click.STRING)
+@click.argument('payload', required=True, type=click.STRING)
+def complete_job(job_id, payload):
+    qdb.commands.complete_job_cmd(job_id, payload)
+
+if __name__ == '__main__':
+    qiita_private()

scripts/qiita-private-launcher

@@ -31,14 +31,12 @@ source ~/.bash_profile
 @click.argument('arguments', required=True, nargs=-1)
 def start(qiita_env, command, arguments):
     """Starts the plugin environment"""
-    cmd = ['qiita private', command]
+    cmd = ['qiita-private', command]
     cmd.extend(["'%s'" % arg for arg in arguments])
     fd, fp = mkstemp(suffix=".sh")
     close(fd)
     with open(fp, 'w') as f:
         f.write(SCRIPT % (qiita_env, ' '.join(cmd)))
-    with open("/home/travis/trying_to_debug.txt", "w") as f:
-        f.write(SCRIPT % (qiita_env, ' '.join(cmd)))
     cmd = "bash %s" % fp
     proc = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE)
     stdout, stderr = proc.communicate()