Merge af223ed into 7c798a1

qiita_db/handlers/processing_job.py

@@ -110,13 +110,12 @@ def post(self, job_id):
         """
         with qdb.sql_connection.TRN:
             job = _get_job(job_id)
-            job_status = job.status
-            if job_status != 'running':
-                raise HTTPError(403, 'Job in a non-running state')
-            else:
-                payload = loads(self.request.body)
-                step = payload['step']
+            payload = loads(self.request.body)
+            step = payload['step']
+            try:
                 job.step = step
+            except qdb.exceptions.QiitaDBOperationNotPermittedError as e:
+                raise HTTPError(403, str(e))
 
         self.finish()
 

qiita_db/handlers/tests/test_processing_job.py

@@ -119,7 +119,8 @@ def test_post_non_running_job(self):
             '/qiita_db/jobs/063e553b-327c-4818-ab4a-adfe58e49860/step/',
             payload, headers=self.header)
         self.assertEqual(obs.code, 403)
-        self.assertEqual(obs.body, 'Job in a non-running state')
+        self.assertEqual(obs.body, "Cannot change the step of a job whose "
+                                   "status is not 'running'")
 
     def test_post(self):
         payload = dumps({'step': 'Step 1 of 4: demultiplexing'})

qiita_plugins/biom_type/biom_type_plugin/plugin.py

@@ -12,7 +12,7 @@
 import traceback
 import sys
 
-from qiita_client import QiitaClient, format_payload
+from qiita_client import QiitaClient
 
 from biom_type_plugin.validate import validate
 from biom_type_plugin.summary import generate_html_summary
@@ -53,25 +53,26 @@ def execute_job(server_url, job_id, output_dir):
                           config.get('main', 'CLIENT_SECRET'),
                           server_cert=config.get('main', 'SERVER_CERT'))
 
-    # Request job information
+    # Request job information. If there is a problem retrieving the job
+    # information, the QiitaClient already raises an error
     job_info = qclient.get_job_info(job_id)
-    # Check if we have received the job information so we can start it
-    if job_info and job_info['success']:
-        # Starting the heartbeat
-        qclient.start_heartbeat(job_id)
-        # Execute the given task
-        task_name = job_info['command']
-        task = TASK_DICT[task_name]
+    # Starting the heartbeat
+    qclient.start_heartbeat(job_id)
+    # Execute the given task
+    task_name = job_info['command']
+    task = TASK_DICT[task_name]
 
-        if not exists(output_dir):
-            makedirs(output_dir)
-        try:
-            payload = task(qclient, job_id, job_info['parameters'], output_dir)
-        except Exception:
-            exc_str = repr(traceback.format_exception(*sys.exc_info()))
-            error_msg = ("Error executing %s: \n%s" % (task_name, exc_str))
-            payload = format_payload(False, error_msg=error_msg)
-        # The job completed
-        qclient.complete_job(job_id, payload)
-    else:
-        raise RuntimeError("Can't get job (%s) information" % job_id)
+    if not exists(output_dir):
+        makedirs(output_dir)
+    try:
+        success, artifacts_info, error_msg = task(
+            qclient, job_id, job_info['parameters'], output_dir)
+    except Exception:
+        exc_str = repr(traceback.format_exception(*sys.exc_info()))
+        error_msg = ("Error executing %s: \n%s" % (task_name, exc_str))
+        success = False
+        artifacts_info = None
+
+    # The job completed
+    qclient.complete_job(job_id, success, error_msg=error_msg,
+                         artifacts_info=artifacts_info)

qiita_plugins/biom_type/biom_type_plugin/summary.py

@@ -15,11 +15,9 @@
 from StringIO import StringIO
 
 import seaborn as sns
-from qiita_client import format_payload
 
 
-def generate_html_summary(qclient, job_id, parameters, out_dir,
-                          return_html=False):
+def generate_html_summary(qclient, job_id, parameters, out_dir):
     """Generates the HTML summary of a BIOM artifact
 
     Parameters
@@ -32,30 +30,18 @@ def generate_html_summary(qclient, job_id, parameters, out_dir,
         The parameter values to validate and create the artifact
     out_dir : str
         The path to the job's output directory
-    return_html : bool, optional
-        True will return the html str, useful for testing
 
     Returns
     -------
-    dict(, [str])
-        The results of the job and if return_html is True an array of str
-
-    Raises
-    ------
-    ValueError
-        If there is any error gathering the information from the server
+    bool, None, str
+        Whether the job is successful
+        Ignored
+        The error message, if not successful
     """
     # Step 1: gather file information from qiita using REST api
     artifact_id = parameters['input_data']
     qclient_url = "/qiita_db/artifacts/%s/filepaths/" % artifact_id
     fps_info = qclient.get(qclient_url)
-    if not fps_info or not fps_info['success']:
-        error_msg = "Could not get artifact filepath information: %s"
-        if fps_info:
-            error_msg = error_msg % fps_info['error']
-        else:
-            error_msg = error_msg % "could not connect with the server"
-        raise ValueError(error_msg)
 
     # if we get to this point of the code we are sure that this is a biom file
     # and that it only has one element
@@ -107,9 +93,12 @@ def generate_html_summary(qclient, job_id, parameters, out_dir,
         of.write('\n'.join(artifact_information))
 
     # Step 3: add the new file to the artifact using REST api
-    reply = qclient.patch(qclient_url, 'add', '/html_summary/', value=of_fp)
-
-    payload = format_payload(
-        success=reply['success'], error_msg=reply['error'], artifacts_info=[])
-
-    return payload if not return_html else (payload, artifact_information)
+    success = True
+    error_msg = ""
+    try:
+        qclient.patch(qclient_url, 'add', '/html_summary/', value=of_fp)
+    except Exception as e:
+        success = False
+        error_msg = str(e)
+
+    return success, None, error_msg