Analysis refactor gui part6 (#2116)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Solving merge conflicts

Author: josenavas

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()