Merge pull request #3217 from antgonza/general-fixes

fix #3216 + other smaller fixes

Author: charles-cowart

qiita_core/util.py

@@ -96,6 +96,7 @@ def get_qiita_version():
     try:
         repo = Repo(git_repo_path)
         sha = repo.active_branch.commit.hexsha
+        repo.__del__()
     except (InvalidGitRepositoryError, TypeError):
         sha = ''
 

qiita_db/analysis.py

@@ -69,6 +69,22 @@ class Analysis(qdb.base.QiitaObject):
     _portal_table = "analysis_portal"
     _analysis_id_column = 'analysis_id'
 
+    @classmethod
+    def iter(cls):
+        """Iter over the analyses"""
+        with qdb.sql_connection.TRN:
+            sql = """SELECT DISTINCT analysis_id
+                     FROM qiita.analysis
+                     JOIN qiita.analysis_portal USING (analysis_id)
+                     JOIN qiita.portal_type USING (portal_type_id)
+                     WHERE portal = %s
+                     ORDER BY analysis_id"""
+            qdb.sql_connection.TRN.add(sql, [qiita_config.portal])
+            aids = qdb.sql_connection.TRN.execute_fetchflatten()
+
+        for aid in aids:
+            yield cls(aid)
+
     @classmethod
     def get_by_status(cls, status):
         """Returns all Analyses with given status

qiita_db/metadata_template/base_metadata_template.py

@@ -63,8 +63,10 @@ def _helper_get_categories(table):
                  WHERE sample_id = '{1}'""".format(table, QIITA_COLUMN_NAME)
         qdb.sql_connection.TRN.add(sql)
         results = qdb.sql_connection.TRN.execute_fetchflatten()
-        if results:
+        if results and results != [None]:
             results = sorted(loads(results[0]))
+        else:
+            results = []
         return results
 
 

qiita_db/sql_connection.py

@@ -198,7 +198,10 @@ def _raise_execution_error(self, sql, sql_args, error):
             ec_lu = errorcodes.lookup(error.pgcode)
             raise ValueError(
                 "Error running SQL: %s. MSG: %s\n" % (ec_lu, str(error)))
-        except (KeyError, AttributeError, TypeError):
+        # the order of except statements is important, do not change
+        except (KeyError, AttributeError, TypeError) as error:
+            raise ValueError("Error running SQL query: %s" % str(error))
+        except ValueError as error:
             raise ValueError("Error running SQL query: %s" % str(error))
 
     @_checker

qiita_db/test/test_analysis.py

@@ -22,6 +22,16 @@
 # -----------------------------------------------------------------------------
 
 
+class TestAnalysisIter(TestCase):
+    def test_iter(self):
+        obs = list(qdb.analysis.Analysis.iter())
+        exp = [
+            qdb.analysis.Analysis(1), qdb.analysis.Analysis(2),
+            qdb.analysis.Analysis(3), qdb.analysis.Analysis(4),
+            qdb.analysis.Analysis(5), qdb.analysis.Analysis(6)]
+        self.assertCountEqual(obs, exp)
+
+
 @qiita_test_checker()
 class TestAnalysis(TestCase):
     def setUp(self):

qiita_pet/handlers/admin_processing_job.py

@@ -19,7 +19,8 @@
 
 class AdminProcessingJobBaseClass(BaseHandler):
     def _check_access(self):
-        if self.current_user.level not in {'admin', 'wet-lab admin'}:
+        if self.current_user is None or self.current_user.level not in {
+                'admin', 'wet-lab admin'}:
             raise HTTPError(403, reason="User %s doesn't have sufficient "
                             "privileges to view error page" %
                             self.current_user.email)

scripts/qiita-recover-jobs

@@ -50,6 +50,7 @@ def _retrieve_queue_jobs():
 
     # ignore the merge-jobs and get unique values
     qiita_jids = jobs.NAME.str.replace('merge-', '').unique()
+    qiita_jids = [x.replace('.txt', '') for x in qiita_jids]
 
     return set(qiita_jids)