cleanup other tests (#1617)

irodsadmin/tests/test_commands.py

@@ -48,15 +48,13 @@ class TestIrodsOrphans(
     """Tests for the irodsorphans management command"""
 
     def setUp(self):
-        super().setUp()
+        # Init roles
+        self.init_roles()
         # Init super user
         self.user = self.make_user('user')
         self.user.is_superuser = True
         self.user.is_staff = True
         self.user.save()
-        # Init roles
-        self.init_roles()
-        # Init category with owner
         # Init project with owner
         self.project = self.make_project(
             'TestProject',

irodsinfo/tests/test_permissions.py

@@ -13,7 +13,6 @@ def setUp(self):
         # Create users
         self.superuser = self.make_user('superuser')
         self.superuser.is_superuser = True
-        self.superuser.is_staff = True
         self.superuser.save()
         self.regular_user = self.make_user('regular_user')
         # No user

irodsinfo/tests/test_views.py

@@ -27,10 +27,8 @@ def setUp(self):
         # Create users
         self.superuser = self.make_user('superuser')
         self.superuser.is_superuser = True
-        self.superuser.is_staff = True
         self.superuser.save()
         self.regular_user = self.make_user('regular_user')
-
         # No user
         self.anonymous = None
 

ontologyaccess/tests/test_api.py

@@ -38,16 +38,11 @@ def setUp(self):
         # Create users
         self.superuser = self.make_user('superuser')
         self.superuser.is_superuser = True
-        self.superuser.is_staff = True
         self.superuser.save()
-
         self.regular_user = self.make_user('regular_user')
-
-        # No user
         self.anonymous = None
-
         # Create Ontology and term
-        self.ontology = self._make_obo_ontology(
+        self.ontology = self.make_obo_ontology(
             name=OBO_NAME,
             file=OBO_FILE,
             ontology_id=OBO_ONTOLOGY_ID,
@@ -58,7 +53,7 @@ def setUp(self):
             default_namespace=OBO_DEFAULT_NAMESPACE,
             term_url=DEFAULT_TERM_URL,
         )
-        self.term = self._make_obo_term(
+        self.term = self.make_obo_term(
             ontology=self.ontology,
             term_id=OBO_TERM_ID,
             name=OBO_TERM_NAME,
@@ -68,7 +63,6 @@ def setUp(self):
             namespace=OBO_TERM_NAMESPACE,
             comment=OBO_TERM_COMMENT,
         )
-
         # Get API
         self.ontology_api = get_backend_api('ontologyaccess_backend')
 

ontologyaccess/tests/test_io.py

@@ -2,6 +2,7 @@
 
 import fastobo
 import os
+
 from urllib.request import urlopen
 
 from test_plus.test import TestCase
@@ -29,10 +30,10 @@
     # 'http://purl.obolibrary.org/obo/cl.obo',  # TODO: Fix (see #1064)
     # TODO: Also see issue #944
 ]
-
 OWL_BATCH_URLS = [
     'http://purl.obolibrary.org/obo/duo.owl',
-    'http://data.bioontology.org/ontologies/ROLEO/submissions/3/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb',
+    'http://data.bioontology.org/ontologies/ROLEO/submissions/3/download?'
+    'apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb',
 ]
 
 
@@ -44,8 +45,6 @@ def setUp(self):
 
     def test_import(self):
         """Test importing an example ontology"""
-
-        # Assert preconditions
         self.assertEqual(OBOFormatOntology.objects.count(), 0)
         self.assertEqual(OBOFormatOntologyTerm.objects.count(), 0)
 
@@ -54,7 +53,6 @@ def test_import(self):
             obo_doc=obo_doc, name=OBO_NAME, file=OBO_PATH
         )
 
-        # Assert postconditions
         self.assertEqual(OBOFormatOntology.objects.count(), 1)
         self.assertEqual(OBOFormatOntologyTerm.objects.count(), 7)
 
@@ -63,29 +61,22 @@ def test_import(self):
         self.assertEqual(
             term.synonyms[0], 'First synonym for example term 0000002'
         )
-
         term = ontology.get_term_by_id(EX_OBO_TERM_IDS['alt_ids'])
         self.assertEqual(len(term.alt_ids), 2)
         self.assertEqual(term.alt_ids[0], 'EX:8888883')
-
         term = ontology.get_term_by_id(EX_OBO_TERM_IDS['comment'])
         self.assertIsNotNone(term.comment)
-
         term = ontology.get_term_by_id(EX_OBO_TERM_IDS['namespace'])
         self.assertIsNotNone(term.namespace)
-
         term = ontology.get_term_by_id(EX_OBO_TERM_IDS['is_obsolete'])
         self.assertTrue(term.is_obsolete)
         self.assertEqual(term.replaced_by, 'EX:0000005')
-
         term = ontology.get_term_by_id(EX_OBO_TERM_IDS['no_def'])
         self.assertIsNone(term.definition)
 
     def test_import_batch(self):
         """Test importing ontologies in a batch (this may take a while)"""
-
         for url in OBO_BATCH_URLS:
-            # Assert preconditions
             self.assertEqual(OBOFormatOntology.objects.count(), 0)
             self.assertEqual(OBOFormatOntologyTerm.objects.count(), 0)
 
@@ -95,7 +86,6 @@ def test_import_batch(self):
                 obo_doc=obo_doc, name=file_name.split('.')[0].upper(), file=url
             )
 
-            # Assert postconditions
             self.assertIsNotNone(ontology, msg=file_name)
             self.assertEqual(
                 OBOFormatOntology.objects.count(), 1, msg=file_name
@@ -106,10 +96,8 @@ def test_import_batch(self):
             ontology.delete()
 
     def test_import_batch_owl(self):
-        """Test converting and importing OWL ontologies in a batch (this may take a while)"""
-
+        """Test importing OWL ontologies in batch (this may take a while)"""
         for url in OWL_BATCH_URLS:
-            # Assert preconditions
             self.assertEqual(OBOFormatOntology.objects.count(), 0)
             self.assertEqual(OBOFormatOntologyTerm.objects.count(), 0)
 
@@ -120,7 +108,6 @@ def test_import_batch_owl(self):
                 obo_doc=obo_doc, name=file_name.split('.')[0].upper(), file=url
             )
 
-            # Assert postconditions
             self.assertIsNotNone(ontology, msg=file_name)
             self.assertEqual(
                 OBOFormatOntology.objects.count(), 1, msg=file_name

ontologyaccess/tests/test_models.py

@@ -43,7 +43,7 @@ class OBOFormatOntologyModelMixin:
     """Helpers for OBOFormatOntology models creation"""
 
     @classmethod
-    def _make_obo_ontology(
+    def make_obo_ontology(
         cls,
         name,
         file,
@@ -72,7 +72,7 @@ def _make_obo_ontology(
         return OBOFormatOntology.objects.create(**values)
 
     @classmethod
-    def _make_obo_term(
+    def make_obo_term(
         cls,
         ontology,
         term_id,
@@ -105,7 +105,7 @@ class TestOBOFormatOntologyBase(OBOFormatOntologyModelMixin, TestCase):
     """Base class for OBOFormatOntology model tests"""
 
     def setUp(self):
-        self.ontology = self._make_obo_ontology(
+        self.ontology = self.make_obo_ontology(
             ontology_id=OBO_ONTOLOGY_ID,
             name=OBO_NAME,
             file=OBO_FILE,
@@ -116,7 +116,7 @@ def setUp(self):
             default_namespace=OBO_DEFAULT_NAMESPACE,
             term_url=DEFAULT_TERM_URL,
         )
-        self.term = self._make_obo_term(
+        self.term = self.make_obo_term(
             ontology=self.ontology,
             term_id=OBO_TERM_ID,
             name=OBO_TERM_NAME,

ontologyaccess/tests/test_permissions.py

@@ -43,7 +43,7 @@ def setUp(self):
         # No user
         self.anonymous = None
         # Create Ontology and term
-        self.ontology = self._make_obo_ontology(
+        self.ontology = self.make_obo_ontology(
             name=OBO_NAME,
             file=OBO_FILE,
             ontology_id=OBO_ONTOLOGY_ID,
@@ -54,7 +54,7 @@ def setUp(self):
             default_namespace=OBO_DEFAULT_NAMESPACE,
             term_url=DEFAULT_TERM_URL,
         )
-        self.term = self._make_obo_term(
+        self.term = self.make_obo_term(
             ontology=self.ontology,
             term_id=OBO_TERM_ID,
             name=OBO_TERM_NAME,

ontologyaccess/tests/test_views.py

@@ -44,14 +44,10 @@ def setUp(self):
         self.superuser.is_superuser = True
         self.superuser.is_staff = True
         self.superuser.save()
-
         self.regular_user = self.make_user('regular_user')
-
-        # No user
         self.anonymous = None
-
         # Create Ontology and term
-        self.ontology = self._make_obo_ontology(
+        self.ontology = self.make_obo_ontology(
             name=OBO_NAME,
             file=OBO_FILE,
             ontology_id=OBO_ONTOLOGY_ID,
@@ -62,7 +58,7 @@ def setUp(self):
             default_namespace=OBO_DEFAULT_NAMESPACE,
             term_url=DEFAULT_TERM_URL,
         )
-        self.term = self._make_obo_term(
+        self.term = self.make_obo_term(
             ontology=self.ontology,
             term_id=OBO_TERM_ID,
             name=OBO_TERM_NAME,
@@ -128,9 +124,7 @@ def test_render(self):
 
     def test_import(self):
         """Test importing an ontology"""
-        # Assert precondition
         self.assertEqual(OBOFormatOntology.objects.count(), 1)
-
         with open(OBO_PATH) as file:
             post_data = {
                 'file_upload': file,
@@ -142,11 +136,8 @@ def test_import(self):
                 response = self.client.post(
                     reverse('ontologyaccess:obo_import'), post_data
                 )
-
         self.assertEqual(response.status_code, 302)
         self.assertEqual(response.url, reverse('ontologyaccess:list'))
-
-        # Assert postconditions
         self.assertEqual(OBOFormatOntology.objects.count(), 2)
 
     # TODO: Add test for OWL import
@@ -168,15 +159,12 @@ def test_render(self):
 
     def test_update(self):
         """Test updating an ontology"""
-        # Assert precondition
         self.assertEqual(OBOFormatOntology.objects.count(), 1)
-
         post_data = {
             'name': OBO_NAME,
             'title': OBO_TITLE_UPDATED,
             'term_url': OBO_TERM_URL_ALT,
         }
-
         with self.login(self.superuser):
             response = self.client.post(
                 reverse(
@@ -185,11 +173,8 @@ def test_update(self):
                 ),
                 post_data,
             )
-
         self.assertEqual(response.status_code, 302)
         self.assertEqual(response.url, reverse('ontologyaccess:list'))
-
-        # Assert postconditions
         self.assertEqual(OBOFormatOntology.objects.count(), 1)
         self.ontology.refresh_from_db()
         self.assertEqual(self.ontology.title, OBO_TITLE_UPDATED)
@@ -212,19 +197,15 @@ def test_render(self):
 
     def test_delete(self):
         """Test deleting an ontology"""
-        # Assert precondition
         self.assertEqual(OBOFormatOntology.objects.count(), 1)
-
         with self.login(self.superuser):
             response = self.client.post(
                 reverse(
                     'ontologyaccess:obo_delete',
                     kwargs={'oboformatontology': self.ontology.sodar_uuid},
                 )
             )
-
         self.assertEqual(response.status_code, 302)
         self.assertEqual(response.url, reverse('ontologyaccess:list'))
-        # Assert postconditions
         self.assertEqual(OBOFormatOntology.objects.count(), 0)
         self.assertEqual(OBOFormatOntologyTerm.objects.count(), 0)

ontologyaccess/tests/test_views_ajax.py

@@ -10,6 +10,7 @@
 )
 
 
+# Local constants
 OBO_ONTOLOGY_ID_ALT = 'alt.obo'
 OBO_ONTOLOGY_NAME_ALT = 'ALT'
 OBO_ONTOLOGY_FILE_ALT = 'alt.obo'
@@ -25,7 +26,6 @@ def test_list(self):
         """Test listing ontologies"""
         with self.login(self.superuser):
             response = self.client.get(reverse('ontologyaccess:ajax_obo_list'))
-
         self.assertEqual(response.status_code, 200)
         response_data = json.loads(response.content)
         expected = {
@@ -49,15 +49,14 @@ class TestOBOTermQueryAjaxView(TestOntologyAccessViewBase):
 
     def setUp(self):
         super().setUp()
-
         # Create second ontology and term
-        self.ontology2 = self._make_obo_ontology(
+        self.ontology2 = self.make_obo_ontology(
             name=OBO_ONTOLOGY_NAME_ALT,
             file=OBO_ONTOLOGY_FILE_ALT,
             ontology_id=OBO_ONTOLOGY_ID_ALT,
             title=OBO_ONTOLOGY_TITLE_ALT,
         )
-        self.term2 = self._make_obo_term(
+        self.term2 = self.make_obo_term(
             ontology=self.ontology2,
             term_id=OBO_TERM_ID_ALT,
             name=OBO_TERM_NAME_ALT,
@@ -103,7 +102,6 @@ def test_query_limit(self):
                 reverse('ontologyaccess:ajax_obo_term_query'),
                 data=query_data,
             )
-
         self.assertEqual(response.status_code, 200)
         response_data = json.loads(response.content)
         self.assertEqual(len(response_data['terms']), 1)
@@ -196,15 +194,14 @@ class TestOBOTermListAjaxView(TestOntologyAccessViewBase):
 
     def setUp(self):
         super().setUp()
-
         # Create second ontology and term
-        self.ontology2 = self._make_obo_ontology(
+        self.ontology2 = self.make_obo_ontology(
             name=OBO_ONTOLOGY_NAME_ALT,
             file=OBO_ONTOLOGY_FILE_ALT,
             ontology_id=OBO_ONTOLOGY_ID_ALT,
             title=OBO_ONTOLOGY_TITLE_ALT,
         )
-        self.term2 = self._make_obo_term(
+        self.term2 = self.make_obo_term(
             ontology=self.ontology2,
             term_id=OBO_TERM_ID_ALT,
             name=OBO_TERM_NAME_ALT,