fix #2574

qiita_db/study.py

@@ -823,6 +823,34 @@ def ebi_study_accession(self, value):
             qdb.sql_connection.TRN.add(sql, [value, self.id])
             qdb.sql_connection.TRN.execute()
 
+    def _ebi_submission_jobs(self):
+        """Helper code to avoid duplication"""
+        plugin = qdb.software.Software.from_name_and_version(
+            'Qiita', 'alpha')
+        cmd = plugin.get_command('submit_to_EBI')
+
+        sql = """SELECT processing_job_id,
+                    pj.command_parameters->>'artifact' as aid,
+                    processing_job_status, can_be_submitted_to_ebi,
+                    array_agg(ebi_run_accession)
+                 FROM qiita.processing_job pj
+                 LEFT JOIN qiita.processing_job_status
+                    USING (processing_job_status_id)
+                 LEFT JOIN qiita.artifact ON (
+                    artifact_id = (
+                        pj.command_parameters->>'artifact')::INT)
+                 LEFT JOIN qiita.ebi_run_accession era USING (artifact_id)
+                 LEFT JOIN qiita.artifact_type USING (artifact_type_id)
+                 WHERE pj.command_parameters->>'artifact' IN (
+                    SELECT artifact_id::text
+                    FROM qiita.study_artifact WHERE study_id = {0})
+                    AND pj.command_id = {1}
+                 GROUP BY processing_job_id, aid, processing_job_status,
+                    can_be_submitted_to_ebi""".format(self._id, cmd.id)
+        qdb.sql_connection.TRN.add(sql)
+
+        return qdb.sql_connection.TRN.execute_fetchindex()
+
     @property
     def ebi_submission_status(self):
         """The EBI submission status of this study
@@ -846,24 +874,11 @@ def ebi_submission_status(self):
             if self.ebi_study_accession:
                 status = 'submitted'
 
-            plugin = qdb.software.Software.from_name_and_version(
-                'Qiita', 'alpha')
-            cmd = plugin.get_command('submit_to_EBI')
-
-            sql = """SELECT processing_job_id, command_parameters->>'artifact',
-                        processing_job_status
-                     FROM qiita.processing_job
-                     LEFT JOIN qiita.processing_job_status
-                        USING (processing_job_status_id)
-                     WHERE command_parameters->>'artifact' IN (
-                        SELECT artifact_id::text
-                        FROM qiita.study_artifact
-                        WHERE study_id = {0}) AND command_id = {1}""".format(
-                            self._id, cmd.id)
-            qdb.sql_connection.TRN.add(sql)
             jobs = defaultdict(dict)
-            for info in qdb.sql_connection.TRN.execute_fetchindex():
-                jid, aid, js = info
+            for info in self._ebi_submission_jobs():
+                jid, aid, js, cbste, era = info
+                if not cbste or era != [None]:
+                    continue
                 jobs[js][aid] = jid
 
             if 'queued' in jobs or 'running' in jobs:

qiita_db/test/test_study.py

@@ -593,6 +593,27 @@ def test_ebi_study_accession_setter(self):
 
     def test_ebi_submission_status(self):
         self.assertEqual(self.study.ebi_submission_status, 'submitted')
+
+        # let's test that even with a failed job nothing changes
+        # add a failed job for an artifact (2) that can be submitted
+        user = qdb.user.User('test@foo.bar')
+        qp = qdb.software.Software.from_name_and_version('Qiita', 'alpha')
+        cmd = qp.get_command('submit_to_EBI')
+        params = qdb.software.Parameters.load(cmd, values_dict={
+            'artifact': 2, 'submission_type': 'ADD'})
+        job = qdb.processing_job.ProcessingJob.create(user, params, True)
+        job._set_error('Killed by Admin')
+        # and just to be careful add a failed job for an artifact (1) that
+        # cannot be submitted
+        qp = qdb.software.Software.from_name_and_version('Qiita', 'alpha')
+        cmd = qp.get_command('submit_to_EBI')
+        params = qdb.software.Parameters.load(cmd, values_dict={
+            'artifact': 1, 'submission_type': 'ADD'})
+        job = qdb.processing_job.ProcessingJob.create(user, params, True)
+        job._set_error('Killed by Admin')
+        # should still return submited
+        self.assertEqual(self.study.ebi_submission_status, 'submitted')
+
         new = qdb.study.Study.create(
             qdb.user.User('test@foo.bar'),
             'NOT Identification of the Microbiomes for Cannabis Soils 5',

qiita_ware/ebi.py

@@ -147,13 +147,6 @@ def __init__(self, artifact_id, action):
             LogEntry.create('Runtime', error_msg)
             raise EBISubmissionError(error_msg)
 
-        status = self.study.ebi_submission_status
-        if status in self.valid_ebi_submission_states:
-            error_msg = ("Cannot perform parallel EBI submission for the same "
-                         "study. Current status of the study: %s" % status)
-            LogEntry.create('Runtime', error_msg)
-            raise EBISubmissionError(error_msg)
-
         self.artifact_id = artifact_id
         self.study_title = self.study.title
         self.study_abstract = self.study.info['study_abstract']

qiita_ware/private_plugin.py

@@ -18,6 +18,7 @@
 from qiita_ware.commands import submit_VAMPS, submit_EBI
 from qiita_ware.metadata_pipeline import (
     create_templates_from_qiime_mapping_file)
+from qiita_ware.exceptions import EBISubmissionError
 
 
 def build_analysis_files(job):
@@ -98,6 +99,14 @@ def submit_to_EBI(job):
         param_vals = job.parameters.values
         artifact_id = int(param_vals['artifact'])
         submission_type = param_vals['submission_type']
+        artifact = qdb.artifact.Artifact(artifact_id)
+
+        for info in artifact.study._ebi_submission_jobs():
+            jid, aid, js, cbste, era = info
+            if js in ('running', 'queued') and jid != job.id:
+                error_msg = ("Cannot perform parallel EBI submission for "
+                             "the same study. Current job running: %s" % js)
+                raise EBISubmissionError(error_msg)
         submit_EBI(artifact_id, submission_type, True)
         job._set_status('success')
 

qiita_ware/test/test_private_plugin.py

@@ -8,7 +8,8 @@
 
 from unittest import TestCase, main
 from os.path import join, dirname, abspath, exists, isdir
-from os import close, remove
+from os import close, remove, environ
+
 from shutil import rmtree
 from tempfile import mkstemp
 from json import loads, dumps
@@ -418,11 +419,15 @@ def test_submit_to_EBI(self):
                                  artifact.study.ebi_submission_status)
                 checked_submitting = False
         # once it fails wait for a few to check status again
-        sleep(10)
+        sleep(5)
         exp = 'Some artifact submissions failed: %d' % artifact.id
         obs = artifact.study.ebi_submission_status
         self.assertEqual(obs, exp)
-
+        # make sure that the error is correct, we have 2 options
+        if environ.get('ASPERA_SCP_PASS', '') != '':
+            self.assertIn('1.SKM2.640199', job.log.msg)
+        else:
+            self.assertIn('ASCP Error:', job.log.msg)
         # wait for everything to finish to avoid DB deadlocks
         sleep(5)