cleanup (#1706)

samplesheets/forms.py

@@ -476,7 +476,7 @@ def clean(self):
 
 
 class IrodsDataRequestAcceptForm(forms.Form):
-    """Form for accepting an iRODS data requests"""
+    """Form for accepting an iRODS data request"""
 
     confirm = forms.BooleanField(required=True)
 

samplesheets/tests/test_models_taskflow.py

@@ -54,32 +54,32 @@ def setUp(self):
         # Create iRODS collections
         self.make_irods_colls(self.investigation)
         self.assay_path = self.irods_backend.get_path(self.assay)
-        self.path_obj = os.path.join(self.assay_path, TEST_FILE_NAME)
-        self.path_coll = os.path.join(self.assay_path, TEST_COLL_NAME)
+        self.obj_path = os.path.join(self.assay_path, TEST_FILE_NAME)
+        self.coll_path = os.path.join(self.assay_path, TEST_COLL_NAME)
         # Create objects
-        self.file_obj = self.irods.data_objects.create(self.path_obj)
-        self.coll = self.irods.collections.create(self.path_coll)
+        self.file_obj = self.irods.data_objects.create(self.obj_path)
+        self.coll = self.irods.collections.create(self.coll_path)
 
         # Create request
         self.request = self.make_irods_request(
             project=self.project,
             action=IRODS_REQUEST_ACTION_DELETE,
             status=IRODS_REQUEST_STATUS_ACTIVE,
-            path=self.path_obj,
+            path=self.obj_path,
             description=IRODS_REQUEST_DESC,
             user=self.user_owner_cat,
         )
 
     def test_is_data_object(self):
         """Test is_data_object()"""
         self.assertTrue(self.request.is_data_object())
-        self.request.path = self.path_coll
+        self.request.path = self.coll_path
         self.request.save()
         self.assertFalse(self.request.is_data_object())
 
     def test_is_collection(self):
         """Test is_collection()"""
         self.assertFalse(self.request.is_collection())
-        self.request.path = self.path_coll
+        self.request.path = self.coll_path
         self.request.save()
         self.assertTrue(self.request.is_collection())

samplesheets/tests/test_permissions_ajax.py

@@ -30,7 +30,7 @@
 IRODS_FILE_PATH = '/sodarZone/path/test1.txt'
 
 
-class TestSampleSheetsAjaxPermissionBase(
+class SampleSheetsAjaxPermissionTestBase(
     SampleSheetIOMixin, TestProjectPermissionBase
 ):
     """Base test class for samplesheets Ajax view permissions"""
@@ -42,7 +42,7 @@ def setUp(self):
         self.assay = self.study.assays.first()
 
 
-class TestSheetContextAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetContextAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetContextAjaxView"""
 
     def setUp(self):
@@ -106,7 +106,7 @@ def test_get_archive(self):
         self.assert_response(self.url, self.anonymous, 403)
 
 
-class TestStudyTablesAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestStudyTablesAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for StudyTablesAjaxView"""
 
     def setUp(self):
@@ -276,7 +276,7 @@ def test_get_not_allowed_archive(self):
         self.assert_response(self.url, users, 403, data=self.edit_data)
 
 
-class TestStudyLinksAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestStudyLinksAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for StudyLinksAjaxView"""
 
     def setUp(self):
@@ -322,7 +322,7 @@ def test_get_archive(self):
         self.assert_response(self.url, bad_users, 403)
 
 
-class TestSheetWarningsAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetWarningsAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetWarningsAjaxView"""
 
     def setUp(self):
@@ -384,7 +384,7 @@ def test_get_archive(self):
         self.assert_response(self.url, self.anonymous, 403)
 
 
-class TestSheetCellEditAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetCellEditAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetCellEditAjaxView"""
 
     def setUp(self):
@@ -446,7 +446,7 @@ def test_post_archive(self):
         self.assert_response(self.url, bad_users, 403, method='POST')
 
 
-class TestSheetRowInsertAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetRowInsertAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetRowInsertAjaxView"""
 
     def setUp(self):
@@ -508,7 +508,7 @@ def test_post_archive(self):
         self.assert_response(self.url, bad_users, 403, method='POST')
 
 
-class TestSheetRowDeleteAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetRowDeleteAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetRowDeleteAjaxView"""
 
     def setUp(self):
@@ -570,7 +570,7 @@ def test_post_archive(self):
         self.assert_response(self.url, bad_users, 403, method='POST')
 
 
-class TestSheetVersionSaveAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetVersionSaveAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetVersionSaveAjaxView"""
 
     def setUp(self):
@@ -632,7 +632,7 @@ def test_post_archive(self):
         self.assert_response(self.url, bad_users, 403, method='POST')
 
 
-class TestSheetEditFinishAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetEditFinishAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetEditFinishAjaxView"""
 
     def setUp(self):
@@ -694,7 +694,7 @@ def test_post_archive(self):
         self.assert_response(self.url, bad_users, 403, method='POST')
 
 
-class TestSheetEditConfigAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetEditConfigAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetEditConfigAjaxView"""
 
     def setUp(self):
@@ -758,7 +758,7 @@ def test_post_archive(self):
         self.assert_response(self.url, bad_users, 403, method='POST')
 
 
-class TestStudyDisplayConfigAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestStudyDisplayConfigAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for StudyDisplayConfigAjaxView"""
 
     def setUp(self):
@@ -819,7 +819,7 @@ def test_post_archive(self):
         self.assert_response(self.url, self.anonymous, 403, method='POST')
 
 
-class TestSheetVersionCompareAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestSheetVersionCompareAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for SheetVersionCompareAjaxView"""
 
     def setUp(self):
@@ -884,7 +884,7 @@ def test_get_archive(self):
         self.assert_response(self.url, [self.anonymous], 403)
 
 
-class TestIrodsDataRequestCreateAjaxView(TestSampleSheetsAjaxPermissionBase):
+class TestIrodsDataRequestCreateAjaxView(SampleSheetsAjaxPermissionTestBase):
     """Permission tests for IrodsDataRequestCreateAjaxView"""
 
     @classmethod
@@ -992,7 +992,7 @@ def test_post_archive(self):
 
 
 class TestIrodsDataRequestDeleteAjaxView(
-    IrodsDataRequestMixin, TestSampleSheetsAjaxPermissionBase
+    IrodsDataRequestMixin, SampleSheetsAjaxPermissionTestBase
 ):
     """Permission tests for IrodsDataRequestDeleteAjaxView"""
 

samplesheets/tests/test_views.py

@@ -131,7 +131,7 @@
 # TODO: Add testing for study table cache updates
 
 
-class TestViewsBase(
+class ViewTestBase(
     ProjectMixin, RoleMixin, RoleAssignmentMixin, SampleSheetIOMixin, TestCase
 ):
     """Base view for samplesheets views tests"""
@@ -170,7 +170,7 @@ def setUp(self):
         )
 
 
-class TestProjectSheetsView(TestViewsBase):
+class TestProjectSheetsView(ViewTestBase):
     """Tests for the project sheets view"""
 
     def setUp(self):
@@ -198,7 +198,7 @@ def test_render_no_sheets(self):
         self.assertNotIn('tables', response.context)
 
 
-class TestSheetImportView(SheetImportMixin, LandingZoneMixin, TestViewsBase):
+class TestSheetImportView(SheetImportMixin, LandingZoneMixin, ViewTestBase):
     """Tests for the investigation import view"""
 
     def setUp(self):
@@ -665,7 +665,7 @@ def test_import_no_plugin_assay(self):
         )
 
 
-class TestSheetTemplateSelectView(TestViewsBase):
+class TestSheetTemplateSelectView(ViewTestBase):
     """Tests for SheetTemplateSelectView"""
 
     def test_render(self):
@@ -702,7 +702,7 @@ def test_render_with_sheets(self):
             )
 
 
-class TestSheetTemplateCreateFormView(TestViewsBase):
+class TestSheetTemplateCreateFormView(ViewTestBase):
     """Tests for SheetTemplateCreateFormView"""
 
     def _get_post_data(self, tpl_name):
@@ -819,7 +819,7 @@ def test_post_multiple(self):
             self.assertEqual(self.project.investigations.count(), 1)
 
 
-class TestSheetExcelExportView(TestViewsBase):
+class TestSheetExcelExportView(ViewTestBase):
     """Tests for the sample sheet Excel export view"""
 
     def setUp(self):
@@ -863,7 +863,7 @@ def test_render_assay(self):
         self.assertEqual(tl_event.event_name, 'sheet_export_excel')
 
 
-class TestSheetISAExportView(TestViewsBase):
+class TestSheetISAExportView(ViewTestBase):
     """Tests for the investigation ISA-Tab export view"""
 
     def setUp(self):
@@ -930,7 +930,7 @@ def test_get_version(self):
         )
 
 
-class TestSheetDeleteView(TestViewsBase):
+class TestSheetDeleteView(ViewTestBase):
     """Tests for the investigation delete view"""
 
     def setUp(self):
@@ -1056,7 +1056,7 @@ def test_delete_study_cache(self):
         self.assertEqual(JSONCacheItem.objects.count(), 0)
 
 
-class TestSheetVersionListView(TestViewsBase):
+class TestSheetVersionListView(ViewTestBase):
     """Tests for the sample sheet version list view"""
 
     def test_render(self):
@@ -1098,7 +1098,7 @@ def test_render_no_sheets(self):
         self.assertIsNone(response.context['current_version'])
 
 
-class TestSheetVersionRestoreView(TestViewsBase):
+class TestSheetVersionRestoreView(ViewTestBase):
     """Tests for the sample sheet version restore view"""
 
     def setUp(self):
@@ -1184,7 +1184,7 @@ def test_restore_study_cache(self):
         self.assertEqual(JSONCacheItem.objects.count(), 1)
 
 
-class TestSheetVersionUpdateView(TestViewsBase):
+class TestSheetVersionUpdateView(ViewTestBase):
     """Tests for the sample sheet version update view"""
 
     def setUp(self):
@@ -1229,7 +1229,7 @@ def test_update(self):
         self.assertEqual(self.isatab.date_created, date_created)
 
 
-class TestSheetVersionDeleteView(TestViewsBase):
+class TestSheetVersionDeleteView(ViewTestBase):
     """Tests for the sample sheet version delete view"""
 
     def setUp(self):
@@ -1267,7 +1267,7 @@ def test_post(self):
         self.assertEqual(ISATab.objects.count(), 0)
 
 
-class TestSheetVersionDeleteBatchView(SampleSheetModelMixin, TestViewsBase):
+class TestSheetVersionDeleteBatchView(SampleSheetModelMixin, ViewTestBase):
     """Tests for the sample sheet version batch delete view"""
 
     def setUp(self):
@@ -1334,7 +1334,7 @@ def test_delete(self):
         self.assertEqual(ISATab.objects.count(), 0)
 
 
-class TestProjectSearchResultsView(TestViewsBase):
+class TestProjectSearchResultsView(ViewTestBase):
     """Tests for ProjectSearchResultsView view with sample sheet input"""
 
     def _get_items(self, response):
@@ -1442,7 +1442,7 @@ def test_search_multi(self):
         self.assertEqual(len(items), 2)
 
 
-class TestSheetVersionCompareView(TestViewsBase):
+class TestSheetVersionCompareView(ViewTestBase):
     """Tests for the SheetVersionCompareView"""
 
     def setUp(self):
@@ -1501,7 +1501,7 @@ def test_render_no_permission(self):
         self.assertRedirects(response, reverse('home'))
 
 
-class TestSheetVersionCompareFileView(TestViewsBase):
+class TestSheetVersionCompareFileView(ViewTestBase):
     """Tests for the SheetVersionCompareFileView"""
 
     def setUp(self):
@@ -1566,7 +1566,7 @@ def test_render_no_permission(self):
         self.assertRedirects(response, reverse('home'))
 
 
-class TestIrodsDataRequestListView(IrodsDataRequestMixin, TestViewsBase):
+class TestIrodsDataRequestListView(IrodsDataRequestMixin, ViewTestBase):
     """Tests for IrodsDataRequestListView"""
 
     def test_list(self):