Analysis refactor gui part6

qiita_core/tests/test_configuration_manager.py

@@ -201,6 +201,7 @@ def test_get_portal(self):
         obs._get_portal(self.conf)
         self.assertEqual(obs.portal_dir, "/gold_portal")
 
+
 CONF = """
 # ------------------------------ Main settings --------------------------------
 [main]

qiita_core/tests/test_util.py

@@ -64,5 +64,6 @@ def test_get_qiita_version(self):
         # testing just the version
         self.assertEqual(exp_version, qdb.__version__)
 
+
 if __name__ == '__main__':
     main()

qiita_db/exceptions.py

@@ -111,4 +111,5 @@ class QiitaDBWarning(UserWarning):
     """Warning specific for the QiitaDB domain"""
     pass
 
+
 warnings.simplefilter('always', QiitaDBWarning)

qiita_db/handlers/tests/test_artifact.py

@@ -239,5 +239,6 @@ def test_post(self):
                         data=data)
         self.assertEqual(obs.code, 200)
 
+
 if __name__ == '__main__':
     main()

qiita_db/handlers/tests/test_core.py

@@ -20,5 +20,6 @@ def test_post(self):
         self.assertEqual(obs.code, 200)
         self.assertFalse(qdb.user.User.exists('new_user@test.foo'))
 
+
 if __name__ == '__main__':
     main()

qiita_db/handlers/tests/test_oauth2.py

@@ -294,5 +294,6 @@ def test_authenticate_password_missing_info(self):
                'error_description': 'Oauth2 error: missing user information'}
         self.assertEqual(obs_body, exp)
 
+
 if __name__ == "__main__":
     main()

qiita_db/handlers/tests/test_plugin.py

@@ -197,5 +197,6 @@ def test_post(self):
                         data={})
         self.assertEqual(obs.code, 200)
 
+
 if __name__ == '__main__':
     main()

qiita_db/handlers/tests/test_prep_template.py

@@ -46,14 +46,18 @@ def test_get(self):
         path_builder = partial(join, db_test_template_dir)
 
         obs = loads(obs.body)
-        exp = {'data_type': '18S',
-               'artifact': 1,
-               'investigation_type': 'Metagenomics',
-               'study': 1,
-               'status': 'private',
-               'qiime-map': path_builder('1_prep_1_qiime_19700101-000000.txt'),
-               'prep-file': path_builder('1_prep_1_19700101-000000.txt')}
-        self.assertEqual(obs, exp)
+
+        # have to check per key because since patch 51 we are updating the
+        # test info files
+        self.assertEqual(obs['data_type'], '18S')
+        self.assertEqual(obs['artifact'], 1)
+        self.assertEqual(obs['investigation_type'], 'Metagenomics')
+        self.assertEqual(obs['study'], 1)
+        self.assertEqual(obs['status'], 'private')
+        self.assertTrue(obs['qiime-map'].startswith(
+            path_builder('1_prep_1_qiime_')))
+        self.assertTrue(obs['prep-file'].startswith(
+            path_builder('1_prep_1_')))
 
 
 class PrepTemplateDataHandlerTests(OauthTestingBase):

qiita_db/handlers/tests/test_processing_job.py

@@ -274,5 +274,6 @@ def test_post_processing_job_status(self):
         self.assertEqual(qdb.processing_job.ProcessingJob(job_id).status,
                          'running')
 
+
 if __name__ == '__main__':
     main()

qiita_db/handlers/tests/test_reference.py

@@ -51,5 +51,6 @@ def test_get(self):
         exp = {'name': 'Greengenes', 'version': '13_8', 'files': fps}
         self.assertEqual(loads(obs.body), exp)
 
+
 if __name__ == '__main__':
     main()

qiita_db/meta_util.py

@@ -154,9 +154,9 @@ def update_redis_stats():
         artifact filepaths that are not present in the file system
     """
     STUDY = qdb.study.Study
-    studies = {'public': STUDY.get_by_status('private'),
-               'private': STUDY.get_by_status('public'),
-               'sanbox': STUDY.get_by_status('sandbox')}
+    studies = {'public': STUDY.get_by_status('public'),
+               'private': STUDY.get_by_status('private'),
+               'sandbox': STUDY.get_by_status('sandbox')}
     number_studies = {k: len(v) for k, v in viewitems(studies)}
 
     number_of_samples = {}
@@ -186,7 +186,8 @@ def update_redis_stats():
 
     lat_longs = get_lat_longs()
 
-    num_studies_ebi = len(ebi_samples_prep)
+    num_studies_ebi = len([k for k, v in viewitems(ebi_samples_prep)
+                           if v >= 1])
     number_samples_ebi_prep = sum([v for _, v in viewitems(ebi_samples_prep)])
 
     # generating file size stats

qiita_db/metadata_template/base_metadata_template.py

@@ -1430,7 +1430,11 @@ def validate(self, restriction_dict):
             else:
                 valid_null = qdb.metadata_template.constants.EBI_NULL_VALUES
                 for column, datatype in viewitems(restriction.columns):
-                    for sample, val in viewitems(self.get_category(column)):
+                    # sorting by key (sample id) so we always check in the
+                    # same order, helpful for testing
+                    cats_by_column = self.get_category(column)
+                    for sample in sorted(cats_by_column):
+                        val = cats_by_column[sample]
                         # ignore if valid null value
                         if val in valid_null:
                             continue
@@ -1439,11 +1443,8 @@ def validate(self, restriction_dict):
                             val = str(val)
                             formats = [
                                 # 4 digits year
-                                '%m/%d/%Y %H:%M:%S', '%m/%d/%Y %H:%M',
-                                '%m/%d/%Y %H', '%m/%d/%Y', '%m/%Y', '%Y',
-                                # 2 digits year
-                                '%m/%d/%y %H:%M:%S', '%m/%d/%y %H:%M',
-                                '%m/%d/%y %H', '%m/%d/%y', '%m/%y', '%y'
+                                '%Y-%m-%d %H:%M:%S', '%Y-%m-%d %H:%M',
+                                '%Y-%m-%d %H', '%Y-%m-%d', '%Y-%m', '%Y'
                                 ]
                             date = None
                             for fmt in formats:

qiita_db/metadata_template/constants.py

@@ -89,4 +89,5 @@ def _col_iterator():
             for cols in viewkeys(restriction.columns):
                 yield cols
 
+
 CONTROLLED_COLS = set(col for col in _col_iterator())

qiita_db/metadata_template/test/test_prep_template.py

@@ -915,6 +915,8 @@ def test_create_qiime_mapping_file(self):
         exp = pd.read_csv(
             exp_fp, sep='\t', infer_datetime_format=False,
             parse_dates=False, index_col=False, comment='\t')
+        obs = obs.reindex_axis(sorted(obs.columns), axis=1)
+        exp = exp.reindex_axis(sorted(exp.columns), axis=1)
 
         assert_frame_equal(obs, exp)