add cytof tests (#1980), add missing init files (#2014)

CHANGELOG.rst

@@ -20,6 +20,8 @@ Added
 - **Samplesheets**
     - REST API list view pagination (#1994)
     - ``notify_email_irods_request`` user app setting (#1939)
+    - Assay app unit tests (#1980)
+    - Missing assay plugin ``__init__.py`` files (#2014)
 
 Changed
 -------

samplesheets/assayapps/cytof/tests/test_plugins.py

@@ -0,0 +1,145 @@
+"""Plugin tests for the the cytof assay plugin"""
+
+import os
+
+from copy import deepcopy
+
+from django.conf import settings
+
+from samplesheets.models import Investigation
+from samplesheets.rendering import SampleSheetTableBuilder, SIMPLE_LINK_TEMPLATE
+from samplesheets.plugins import SampleSheetAssayPluginPoint, get_backend_api
+from samplesheets.tests.test_views import (
+    SheetTemplateCreateMixin,
+    SamplesheetsViewTestBase,
+)
+from samplesheets.views import CUBI_TPL_DICT, MISC_FILES_COLL
+
+
+table_builder = SampleSheetTableBuilder()
+
+
+# Local constants
+PLUGIN_NAME = 'samplesheets_assay_cytof'
+ASSAY_NAME = 'testassayname'
+PANEL_NAME = 'testpanel'
+REPORT_NAME = 'report.txt'
+FILE_NAME = 'file1.txt'
+FILE_NAME2 = 'file2.txt'
+FILE_NAME3 = 'file3.txt'
+
+
+class TestCytofPlugin(SheetTemplateCreateMixin, SamplesheetsViewTestBase):
+    """Tests for cytof assay plugin"""
+
+    def setUp(self):
+        super().setUp()
+        self.make_sheets_from_cubi_tpl(CUBI_TPL_DICT['mass_cytometry'])
+        self.investigation = Investigation.objects.get(project=self.project)
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        self.study_tables = table_builder.build_study_tables(self.study)
+        self.assay_table = self.study_tables['assays'][
+            str(self.assay.sodar_uuid)
+        ]
+        self.irods_backend = get_backend_api('omics_irods')
+        self.assay_path = self.irods_backend.get_path(self.assay)
+        self.base_url = settings.IRODS_WEBDAV_URL + self.assay_path
+        self.plugin = SampleSheetAssayPluginPoint.get_plugin(PLUGIN_NAME)
+
+    def test_get_row_path_filled(self):
+        """Test get_row_path() with filled out assay name"""
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        row_path = self.plugin.get_row_path(
+            self.assay_table['table_data'][0],
+            self.assay_table,
+            self.assay,
+            self.assay_path,
+        )
+        expected = os.path.join(self.assay_path, ASSAY_NAME)
+        self.assertEqual(row_path, expected)
+
+    def test_get_row_path_default(self):
+        """Test get_row_path() with default template values"""
+        # NOTE: Assay name is not filled by default, so we return None
+        row_path = self.plugin.get_row_path(
+            self.assay_table['table_data'][0],
+            self.assay_table,
+            self.assay,
+            self.assay_path,
+        )
+        self.assertEqual(row_path, None)
+
+    def test_update_row_filled_panel(self):
+        """Test update_row() with filled panel name"""
+        # Update unset values
+        self.assay_table['table_data'][0][15]['value'] = PANEL_NAME
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        self.assay_table['table_data'][0][26]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][31]['value'] = FILE_NAME2
+        self.assay_table['table_data'][0][36]['value'] = FILE_NAME3
+        # Set expected data
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[15]['value'] = SIMPLE_LINK_TEMPLATE.format(
+            label=PANEL_NAME,
+            url=os.path.join(self.base_url, MISC_FILES_COLL, PANEL_NAME),
+        )
+        row_ex[26]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME)
+        row_ex[31]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME2)
+        row_ex[36]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME3)
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)
+
+    def test_update_row_filled_report(self):
+        """Test update_row() with filled report file"""
+        self.assay_table['table_data'][0][16]['value'] = REPORT_NAME
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        self.assay_table['table_data'][0][26]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][31]['value'] = FILE_NAME2
+        self.assay_table['table_data'][0][36]['value'] = FILE_NAME3
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[16]['value'] = SIMPLE_LINK_TEMPLATE.format(
+            label=REPORT_NAME,
+            url=os.path.join(self.base_url, ASSAY_NAME, REPORT_NAME),
+        )
+        row_ex[26]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME)
+        row_ex[31]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME2)
+        row_ex[36]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME3)
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)
+
+    def test_update_row_filled_barcode(self):
+        """Test update_row() with filled barcode key"""
+        # Rename header
+        self.assay_table['field_header'][15]['value'] = 'Barcode Key'
+        self.assay_table['table_data'][0][15]['value'] = PANEL_NAME
+        self.assay_table['table_data'][0][20]['value'] = ASSAY_NAME
+        self.assay_table['table_data'][0][26]['value'] = FILE_NAME
+        self.assay_table['table_data'][0][31]['value'] = FILE_NAME2
+        self.assay_table['table_data'][0][36]['value'] = FILE_NAME3
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row_ex[15]['value'] = SIMPLE_LINK_TEMPLATE.format(
+            label=PANEL_NAME,
+            url=os.path.join(self.base_url, MISC_FILES_COLL, PANEL_NAME),
+        )
+        row_ex[26]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME)
+        row_ex[31]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME2)
+        row_ex[36]['link'] = os.path.join(self.base_url, ASSAY_NAME, FILE_NAME3)
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)
+
+    # TODO: Test with empty file names after fixing #2017
+
+    def test_update_row_default(self):
+        """Test update_row() with default template values"""
+        row_ex = deepcopy(self.assay_table['table_data'][0])
+        row = self.plugin.update_row(
+            self.assay_table['table_data'][0], self.assay_table, self.assay, 0
+        )
+        self.assertEqual(row, row_ex)

samplesheets/tests/test_views.py

@@ -145,6 +145,54 @@
 # TODO: Add testing for study table cache updates
 
 
+# Base Classes and Mixins ------------------------------------------------------
+
+
+class SheetTemplateCreateMixin:
+    """Sheet template creation helpers"""
+
+    def get_tpl_post_data(self, sheet_tpl):
+        """
+        Return POST data for creating sheet from template.
+
+        :param sheet_tpl: IsaTabTemplate object
+        :return: Dict
+        """
+        ret = {TPL_DIR_FIELD: clean_sheet_dir_name(self.project.title)}
+        if not isinstance(sheet_tpl, IsaTabTemplate):  # Custom template
+            tpl_config = json.loads(sheet_tpl.configuration)
+        else:  # CUBI template
+            tpl_config = sheet_tpl.configuration
+        for k, v in tpl_config.items():
+            if isinstance(v, str):
+                if '{{' in v or '{%' in v:
+                    continue
+                ret[k] = v
+            elif isinstance(v, list):
+                ret[k] = v[0]
+            elif isinstance(v, dict):
+                ret[k] = json.dumps(v)
+        return ret
+
+    def make_sheets_from_cubi_tpl(self, sheet_tpl):
+        """
+        Create investigation from CUBI templates by posting to the template
+        create view.
+
+        :param sheet_tpl: IsaTabTemplate object
+        """
+        url = reverse(
+            'samplesheets:template_create',
+            kwargs={'project': self.project.sodar_uuid},
+        )
+        with self.login(self.user):
+            response = self.client.post(
+                url + '?sheet_tpl=' + sheet_tpl.name,
+                data=self.get_tpl_post_data(sheet_tpl),
+            )
+        self.assertEqual(response.status_code, 302, msg=sheet_tpl.name)
+
+
 class SamplesheetsViewTestBase(
     ProjectMixin, RoleMixin, RoleAssignmentMixin, SampleSheetIOMixin, TestCase
 ):
@@ -184,6 +232,9 @@ def setUp(self):
         )
 
 
+# Test Cases -------------------------------------------------------------------
+
+
 class TestProjectSheetsView(SamplesheetsViewTestBase):
     """Tests for the project sheets view"""
 
@@ -806,35 +857,13 @@ def test_get_custom_backend_disabled(self):
 
 
 class TestSheetTemplateCreateView(
+    SheetTemplateCreateMixin,
     CookiecutterISATemplateMixin,
     CookiecutterISAFileMixin,
     SamplesheetsViewTestBase,
 ):
     """Tests for SheetTemplateCreateView"""
 
-    def _get_post_data(self, sheet_tpl):
-        """
-        Return POST data for creation from template
-
-        :param sheet_tpl: IsaTabTemplate object
-        :return: Dict
-        """
-        ret = {TPL_DIR_FIELD: clean_sheet_dir_name(self.project.title)}
-        if not isinstance(sheet_tpl, IsaTabTemplate):  # Custom template
-            tpl_config = json.loads(sheet_tpl.configuration)
-        else:  # CUBI template
-            tpl_config = sheet_tpl.configuration
-        for k, v in tpl_config.items():
-            if isinstance(v, str):
-                if '{{' in v or '{%' in v:
-                    continue
-                ret[k] = v
-            elif isinstance(v, list):
-                ret[k] = v[0]
-            elif isinstance(v, dict):
-                ret[k] = json.dumps(v)
-        return ret
-
     def _make_custom_template(self):
         """Make custom template with data"""
         with open(TEMPLATE_JSON_PATH, 'rb') as f:
@@ -930,15 +959,9 @@ def test_post_batch_cubi(self):
         """Test POST with supported templates and default values"""
         for t in ISA_TEMPLATES:
             self.assertIsNone(self.project.investigations.first())
-            post_data = self._get_post_data(t)
-            with self.login(self.user):
-                response = self.client.post(
-                    self.url + '?sheet_tpl=' + t.name,
-                    data=post_data,
-                )
+            self.make_sheets_from_cubi_tpl(t)
             isa_tab = ISATab.objects.first()
             self.assertEqual(isa_tab.tags, ['CREATE'])
-            self.assertEqual(response.status_code, 302, msg=t.name)
             self.assertIsNotNone(
                 self.project.investigations.first(), msg=t.name
             )
@@ -948,7 +971,7 @@ def test_post_batch_file_name_slash(self):
         """Test POST with slashes in values used for file names"""
         for t in ISA_TEMPLATES:
             self.assertIsNone(self.project.investigations.first())
-            post_data = self._get_post_data(t)
+            post_data = self.get_tpl_post_data(t)
             for k in TPL_FILE_NAME_FIELDS:
                 if k in post_data:
                     post_data[k] += '/test'
@@ -967,7 +990,7 @@ def test_post_multiple(self):
         """Test POST with multiple requests (should fail)"""
         tpl = ISA_TEMPLATES[0]
         url = self.url + '?sheet_tpl=' + tpl.name
-        post_data = self._get_post_data(tpl)
+        post_data = self.get_tpl_post_data(tpl)
         with self.login(self.user):
             response = self.client.post(url, data=post_data)
             self.assertEqual(response.status_code, 302)
@@ -980,7 +1003,7 @@ def test_post_custom(self):
         """Test POST with custom template"""
         self._make_custom_template()
         self.assertIsNone(self.project.investigations.first())
-        post_data = self._get_post_data(self.template)
+        post_data = self.get_tpl_post_data(self.template)
         with self.login(self.user):
             response = self.client.post(
                 self.url + '?sheet_tpl=' + self.template.name,