Merge pull request #2082 from antgonza/sanbox-to-sandbox

sanbox to sandbox

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

@@ -213,5 +213,6 @@ 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_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

@@ -162,7 +162,7 @@ def update_redis_stats():
     STUDY = qdb.study.Study
     studies = {'public': STUDY.get_by_status('public'),
                'private': STUDY.get_by_status('private'),
-               'sanbox': STUDY.get_by_status('sandbox')}
+               'sandbox': STUDY.get_by_status('sandbox')}
     number_studies = {k: len(v) for k, v in viewitems(studies)}
 
     number_of_samples = {}
@@ -192,7 +192,8 @@ 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/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/sql_connection.py

@@ -934,5 +934,6 @@ def add_post_rollback_func(self, func, *args, **kwargs):
         """
         self._post_rollback_funcs.append((func, args, kwargs))
 
+
 # Singleton pattern, create the transaction for the entire system
 TRN = Transaction()

qiita_db/support_files/patches/python_patches/51.py

@@ -45,17 +45,20 @@ def transform_date(value):
     }
 
     # loop over the old formats to see which one is it
-    date = None
-    for i, fmt in enumerate(formats):
-        try:
-            date = datetime.strptime(value, fmt)
-            break
-        except ValueError:
-            pass
-    if date is not None:
-        value = date.strftime(formats[fmt])
+    if value is not None:
+        date = None
+        for i, fmt in enumerate(formats):
+            try:
+                date = datetime.strptime(value, fmt)
+                break
+            except ValueError:
+                pass
+        if date is not None:
+            value = date.strftime(formats[fmt])
+
     return value
 
+
 if cols_sample:
     with TRN:
         # a few notes: just getting the preps with duplicated values; ignoring

qiita_db/test/test_base.py

@@ -138,5 +138,6 @@ def test_check_status_unknown_status_list(self):
         with self.assertRaises(ValueError):
             self.tester.check_status(["foo", "bar"], exclude=True)
 
+
 if __name__ == '__main__':
     main()

qiita_db/test/test_commands.py

@@ -582,5 +582,6 @@ def test_complete_error(self):
 max_barcode_errors\t1.5
 """
 
+
 if __name__ == "__main__":
     main()

qiita_db/test/test_logger.py

@@ -67,5 +67,6 @@ def test_clear_info(self):
         log_entry.clear_info()
         self.assertEqual(log_entry.info, [])
 
+
 if __name__ == '__main__':
     main()

qiita_db/test/test_meta_util.py

@@ -184,9 +184,9 @@ def test_update_redis_stats(self):
 
         portal = qiita_config.portal
         vals = [
-            ('number_studies', {'sanbox': '0', 'public': '0',
+            ('number_studies', {'sandbox': '0', 'public': '0',
                                 'private': '1'}, r_client.hgetall),
-            ('number_of_samples', {'sanbox': '0', 'public': '0',
+            ('number_of_samples', {'sandbox': '0', 'public': '0',
                                    'private': '27'}, r_client.hgetall),
             ('num_users', '4', r_client.get),
             ('lat_longs', EXP_LAT_LONG, r_client.get),
@@ -217,5 +217,6 @@ def test_update_redis_stats(self):
     ' [0.291867635913, 68.5945325743], [85.4121476399, 15.6526750776],'
     ' [68.0991287718, 34.8360987059]]')
 
+
 if __name__ == '__main__':
     main()

qiita_db/test/test_reference.py

@@ -88,5 +88,6 @@ def test_tree_fp_empty(self):
         ref = qdb.reference.Reference(2)
         self.assertEqual(ref.tree_fp, '')
 
+
 if __name__ == '__main__':
     main()

qiita_db/test/test_software.py

@@ -924,5 +924,6 @@ def test_graph(self):
 CLIENT_SECRET = %s
 """
 
+
 if __name__ == '__main__':
     main()

qiita_db/test/test_sql_connection.py

@@ -660,5 +660,6 @@ def test_index(self):
 
         self.assertEqual(qdb.sql_connection.TRN.index, 0)
 
+
 if __name__ == "__main__":
     main()

qiita_db/test/test_user.py

@@ -473,5 +473,6 @@ def test_jobs_defaults(self):
         # no jobs
         self.assertEqual(qdb.user.User('admin@foo.bar').jobs(), [])
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -510,5 +510,6 @@ def test_artifact_status_put_req_unknown_status(self):
                'message': 'Unknown visiblity value: BADSTAT'}
         self.assertEqual(obs, exp)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/api_proxy/tests/test_ontology.py

@@ -35,5 +35,6 @@ def test_ontology_patch_handler_errors(self):
                'message': 'Ontology "ONTOLOGY" does not exist'}
         self.assertEqual(obs, exp)
 
+
 if __name__ == '__main__':
     main()

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -544,5 +544,6 @@ def test_prep_template_delete_req_no_prep(self):
                'message': 'Prep template 3100 does not exist'}
         self.assertEqual(obs, exp)
 
+
 if __name__ == '__main__':
     main()

qiita_pet/handlers/api_proxy/tests/test_processing.py

@@ -174,5 +174,6 @@ def test_workflow_handler_patch_req_error(self):
                'message': 'Incorrect path parameter'}
         self.assertEqual(obs, exp)
 
+
 if __name__ == '__main__':
     main()

qiita_pet/handlers/study_handlers/tests/test_artifact.py

@@ -168,5 +168,6 @@ def test_post_admin(self):
 
         self.assertEqual(Artifact(3).visibility, 'sandbox')
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_base.py

@@ -58,5 +58,6 @@ def test_get(self):
         self.assertEqual(response.code, 200)
         self.assertNotEqual(response.body, "")
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_ebi_handlers.py

@@ -53,5 +53,6 @@ def test_get_no_exist(self):
         response = self.get('/ebi_submission/100')
         self.assertEqual(response.code, 404)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_edit_handlers.py

@@ -154,5 +154,6 @@ def test_get(self):
         # make sure responds properly
         self.assertEqual(response.body, 'False')
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_listing_handlers.py

@@ -355,5 +355,6 @@ def test_get_emp_portal(self):
         self.assertEqual(response.code, 200)
         self.assertEqual(loads(response.body), self.empty)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_prep_template.py

@@ -72,5 +72,6 @@ def test_get_files_not_allowed(self):
             {'type': 'BIOM', 'prep_file': 'uploaded_file.txt', 'study_id': 1})
         self.assertEqual(response.code, 405)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_processing.py

@@ -24,5 +24,6 @@ class ListOptionsHandler(TestHandlerBase):
     # TODO: Missing tests
     pass
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_sample_template.py

@@ -121,5 +121,6 @@ def test_post_error(self):
                "message": "Category NOEXIST does not exist in sample template"}
         self.assertEqual(loads(res.body), exp)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_vamps_handlers.py

@@ -14,5 +14,6 @@ class VAMPSHandlerTests(TestHandlerBase):
     # TODO: Missing tests
     pass
 
+
 if __name__ == "__main__":
     main()

qiita_pet/portal.py

@@ -84,4 +84,5 @@ def _get_study_list(self, config):
         """Get the configuration of the study_list section"""
         self.example_search = config.get('study_list', 'EXAMPLE_SEARCH')
 
+
 portal_styling = PortalStyleManager()

qiita_pet/test/test_base_handlers.py

@@ -13,5 +13,6 @@ def test_get(self):
         response = self.get('/THISPAGENOEXIST')
         self.assertEqual(response.code, 404)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/test/test_logger.py

@@ -14,5 +14,6 @@ def test_post(self):
         response = self.post('/admin/error/', {'numrecords': 20})
         self.assertEqual(response.code, 405)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/test/test_ontology.py

@@ -19,5 +19,6 @@ def test_patch(self):
         exp = {'status': 'success', 'message': ''}
         self.assertEqual(loads(response.body), exp)
 
+
 if __name__ == '__main__':
     main()

qiita_pet/test/test_prep_template.py

@@ -74,5 +74,6 @@ def test_delete(self):
                        "with it"}
         self.assertEqual(loads(response.body), exp)
 
+
 if __name__ == '__main__':
     main()

qiita_pet/test/test_upload.py

@@ -17,5 +17,6 @@ def test_get(self):
         response = self.get('/upload/')
         self.assertEqual(response.code, 400)
 
+
 if __name__ == "__main__":
     main()

qiita_pet/test/test_user_handlers.py

@@ -59,5 +59,6 @@ def test_get(self):
         response = self.get('/user/jobs/')
         self.assertEqual(response.code, 200)
 
+
 if __name__ == "__main__":
     main()

qiita_ware/context.py

@@ -269,6 +269,7 @@ def _submit(ctx, channel, f, *args, **kwargs):
     ctx.submit_async(_redis_wrap, f, redis_deets, *args, **kwargs)
     return uuid
 
+
 # likely want this in qiita_ware.__init__
 context = Dispatch()
 submit = partial(_submit, context)

qiita_ware/executor.py

@@ -97,4 +97,5 @@ def _submit(ctx, user, parameters):
     ctx.submit_async(_redis_wrap, execute, redis_deets, job.id)
     return job.id
 
+
 plugin_submit = partial(_submit, context)

qiita_ware/test/test_dispatchable.py

@@ -181,5 +181,6 @@ def test_delete_sample_or_column(self):
                           '"samples" and "columns"'}
         self.assertEqual(obs, exp)
 
+
 if __name__ == '__main__':
     main()

qiita_ware/test/test_ebi.py

@@ -1584,5 +1584,6 @@ def test_parse_EBI_reply(self):
 </RECEIPT>
 """
 
+
 if __name__ == "__main__":
     main()

qiita_ware/test/test_util.py

@@ -182,6 +182,7 @@ def test_hdf5IO_open(self):
 
         os.remove(name)
 
+
 # comment indicates the expected random value
 sequences = [
     ('a_1', 'AATTGGCC-a1'),  # 2, 3624216819017203053

scripts/qiita-env

@@ -175,5 +175,6 @@ def rem_portal(portal):
     except qdb.exceptions.QiitaDBLookupError:
         raise click.BadParameter("Portal name does not exist!")
 
+
 if __name__ == '__main__':
     env()

scripts/qiita-private

@@ -23,5 +23,6 @@ def qiita_private():
 def complete_job(job_id, payload):
     qdb.commands.complete_job_cmd(job_id, payload)
 
+
 if __name__ == '__main__':
     qiita_private()

scripts/qiita-test-install

@@ -271,6 +271,7 @@ class QiitaConfig(TestCase):
             ('.'.join(map(str, version)), str_acceptable_min_version,
              str_acceptable_max_version))
 
+
 system_info_header = """
 System information
 ==================