fix #2574

qiita_db/study.py

@@ -850,20 +850,30 @@ def ebi_submission_status(self):
                 'Qiita', 'alpha')
             cmd = plugin.get_command('submit_to_EBI')
 
-            sql = """SELECT processing_job_id, command_parameters->>'artifact',
-                        processing_job_status
-                     FROM qiita.processing_job
+            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)
-                     WHERE command_parameters->>'artifact' IN (
+                     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 command_id = {1}""".format(
-                            self._id, cmd.id)
+                        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)
             jobs = defaultdict(dict)
             for info in qdb.sql_connection.TRN.execute_fetchindex():
-                jid, aid, js = info
+                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',