Merge pull request #3144 from antgonza/pgsql-13.4

postgres 9.5->13.4

Author: wasade

.github/workflows/qiita-ci.yml

@@ -19,7 +19,7 @@ jobs:
     services:
       postgres:
         # Docker Hub image
-        image: postgres:9.5
+        image: postgres:13.4
         env:
           POSTGRES_DB: postgres
           POSTGRES_USER: postgres

qiita_db/artifact.py

@@ -520,7 +520,7 @@ def delete(cls, artifact_id):
                 raise qdb.exceptions.QiitaDBArtifactDeletionError(
                     artifact_id, "it is public")
 
-            all_artifacts = list(instance.descendants.nodes())
+            all_artifacts = list(set(instance.descendants.nodes()))
             all_artifacts.reverse()
             all_ids = tuple([a.id for a in all_artifacts])
 

qiita_db/base.py

@@ -184,7 +184,14 @@ def __init__(self, id_):
 
         with qdb.sql_connection.TRN:
             self._check_subclass()
-            if not self._check_id(id_):
+            try:
+                _id = self._check_id(id_)
+            except ValueError as error:
+                if 'INVALID_TEXT_REPRESENTATION' not in str(error):
+                    raise error
+                _id = False
+
+            if not _id:
                 raise qdb.exceptions.QiitaDBUnknownIDError(id_, self._table)
 
             if not self._check_portal(id_):

qiita_db/metadata_template/base_metadata_template.py

@@ -837,7 +837,7 @@ def _common_extend_steps(self, md_template):
 
             # check that we are within the limit of number of samples
             ms = self.max_samples()
-            nsamples = len(existing_samples) + len(new_samples) + len(self)
+            nsamples = len(curr_samples) + len(new_samples)
             if ms is not None and nsamples > ms:
                 raise ValueError(f'{nsamples} exceeds the max allowed number '
                                  f'of samples: {ms}')

qiita_db/study.py

@@ -1152,7 +1152,8 @@ def prep_templates(self, data_type=None):
             sql = """SELECT prep_template_id
                      FROM qiita.study_prep_template
                         JOIN qiita.prep_template USING (prep_template_id)
-                     WHERE study_id = %s{0}""".format(spec_data)
+                     WHERE study_id = %s{0}
+                     ORDER BY prep_template_id""".format(spec_data)
             qdb.sql_connection.TRN.add(sql, args)
             return [qdb.metadata_template.prep_template.PrepTemplate(ptid)
                     for ptid in qdb.sql_connection.TRN.execute_fetchflatten()]

qiita_db/test/test_study.py

@@ -796,7 +796,7 @@ def test_retrieve_artifacts_none(self):
         qdb.study.Study.delete(new.id)
 
     def test_retrieve_prep_templates(self):
-        self.assertEqual(
+        self.assertCountEqual(
             self.study.prep_templates(),
             [qdb.metadata_template.prep_template.PrepTemplate(1),
              qdb.metadata_template.prep_template.PrepTemplate(2)])

qiita_pet/handlers/admin_processing_job.py

@@ -60,6 +60,8 @@ def get(self):
                     continue
 
                 for job in cmd.processing_jobs:
+                    if job.hidden:
+                        continue
                     msg = '' if job.status != 'error' else job.log.msg
                     msg = msg.replace('\n', '</br>')
                     outputs = []

qiita_pet/test/rest/test_sample_detail.py

@@ -42,7 +42,7 @@ def test_samples_detail(self):
         obs = _sample_details(qiita_db.study.Study(1),
                               ['1.SKD7.640191', 'doesnotexist'])
         self.assertEqual(len(obs), len(exp))
-        self.assertEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
 
 class SampleDetailHandlerTests(RESTHandlerTestCase):
@@ -81,7 +81,7 @@ def test_get_valid_sample(self):
                             headers=self.headers)
         self.assertEqual(response.code, 200)
         obs = json_decode(response.body)
-        self.assertEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
     def test_post_samples_status_bad_request(self):
         body = {'malformed': 'with garbage'}
@@ -134,7 +134,7 @@ def test_post_samples_status(self):
                              data=body, asjson=True)
         self.assertEqual(response.code, 200)
         obs = json_decode(response.body)
-        self.assertEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
 
 if __name__ == '__main__':

qiita_ware/private_plugin.py

@@ -291,7 +291,7 @@ def delete_sample_or_column(job):
 
 
 def _delete_analysis_artifacts(analysis):
-    aids = [a.id for a in analysis.artifacts]
+    aids = [a.id for a in analysis.artifacts if not a.parents]
     aids.sort(reverse=True)
     for aid in aids:
         qdb.artifact.Artifact.delete(aid)
@@ -316,11 +316,10 @@ def delete_study(job):
             _delete_analysis_artifacts(analysis)
 
         for pt in study.prep_templates():
-            if pt.artifact:
-                to_delete = list(pt.artifact.descendants.nodes())
-                to_delete.reverse()
-                for td in to_delete:
-                    qdb.artifact.Artifact.delete(td.id)
+            if pt.artifact is not None:
+                # Artifact.delete will delete descendants so just delete
+                # the root
+                qdb.artifact.Artifact.delete(pt.artifact.id)
             MT.prep_template.PrepTemplate.delete(pt.id)
 
         if MT.sample_template.SampleTemplate.exists(study_id):

qiita_ware/test/test_private_plugin.py

@@ -443,31 +443,10 @@ def test_delete_study(self):
         job = self._create_job('delete_study', {'study': 1})
         private_task(job.id)
         self.assertEqual(job.status, 'error')
-        self.assertIn("Cannot delete artifact 2: Artifact 2 has been "
-                      "submitted to EBI", job.log.msg)
+        self.assertIn("Artifact 2 has been submitted to EBI", job.log.msg)
         # making sure the analysis, first thing to delete, still exists
         self.assertTrue(Analysis.exists(1))
 
-        # delete everything from the EBI submissions and the processing job so
-        # we can try again: test success (with tags)
-        with TRN:
-            sql = """DELETE FROM qiita.ebi_run_accession"""
-            TRN.add(sql)
-            sql = """DELETE FROM qiita.artifact_processing_job"""
-            TRN.add(sql)
-            TRN.execute()
-
-            # adding tags
-            Study(1).update_tags(self.user, ['my new tag!'])
-
-            job = self._create_job('delete_study', {'study': 1})
-            private_task(job.id)
-
-            self.assertEqual(job.status, 'success')
-            with self.assertRaises(QiitaDBUnknownIDError):
-                Study(1)
-
-    def test_delete_study_empty_study(self):
         info = {
             "timeseries_type_id": '1',
             "metadata_complete": 'true',
@@ -481,6 +460,10 @@ def test_delete_study_empty_study(self):
             "lab_person_id": StudyPerson(1)}
         new_study = Study.create(User('test@foo.bar'),
                                  "Fried Chicken Microbiome %s" % time(), info)
+
+        # adding tags
+        new_study.update_tags(User('test@foo.bar'), ['my new tag!'])
+
         # creating a sample information file
         metadata = pd.DataFrame.from_dict({
             'Sample1': {'physical_specimen_location': 'location1',