add dna_sequencing tests, refactor (#1980)

samplesheets/assayapps/cytof/tests/test_plugins.py

@@ -4,23 +4,12 @@
 
 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()
+from samplesheets.assayapps.tests.base import AssayPluginTestBase
+from samplesheets.rendering import SIMPLE_LINK_TEMPLATE
+from samplesheets.views import MISC_FILES_COLL
 
 
 # Local constants
-PLUGIN_NAME = 'samplesheets_assay_cytof'
 ASSAY_NAME = 'testassayname'
 PANEL_NAME = 'testpanel'
 REPORT_NAME = 'report.txt'
@@ -29,23 +18,11 @@
 FILE_NAME3 = 'file3.txt'
 
 
-class TestCytofPlugin(SheetTemplateCreateMixin, SamplesheetsViewTestBase):
+class TestCytofAssayPlugin(AssayPluginTestBase):
     """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)
+    plugin_name = 'samplesheets_assay_cytof'
+    template_name = 'mass_cytometry'
 
     def test_get_row_path_filled(self):
         """Test get_row_path() with filled out assay name"""

samplesheets/assayapps/dna_sequencing/tests/test_plugins.py

@@ -0,0 +1,50 @@
+"""Plugin tests for the the dna_sequencing assay plugin"""
+
+import os
+
+from copy import deepcopy
+
+from samplesheets.assayapps.tests.base import AssayPluginTestBase
+
+
+# Local constants
+MATERIAL_NAME = 'alpha'
+MATERIAL_NAME_UPDATE = 'alpha-material-update'
+
+
+class TestDNASequencingAssayPlugin(AssayPluginTestBase):
+    """Tests for dna_sequencing assay plugin"""
+
+    plugin_name = 'samplesheets_assay_dna_sequencing'
+    template_name = 'generic'
+
+    def test_get_row_path(self):
+        """Test get_row_path()"""
+        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, MATERIAL_NAME)
+        self.assertEqual(row_path, expected)
+
+    def test_get_row_path_rename(self):
+        """Test get_row_path() with renamed material name"""
+        self.assay_table['table_data'][0][-1]['value'] = MATERIAL_NAME_UPDATE
+        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, MATERIAL_NAME_UPDATE)
+        self.assertEqual(row_path, expected)
+
+    def test_update_row(self):
+        """Test update_row()"""
+        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/assayapps/tests/base.py

@@ -0,0 +1,38 @@
+"""Base classes and helpers for assay plugin tests"""
+
+from django.conf import settings
+
+from samplesheets.models import Investigation
+from samplesheets.rendering import SampleSheetTableBuilder
+from samplesheets.plugins import SampleSheetAssayPluginPoint, get_backend_api
+from samplesheets.tests.test_views import (
+    SheetTemplateCreateMixin,
+    SamplesheetsViewTestBase,
+)
+from samplesheets.views import CUBI_TPL_DICT
+
+
+table_builder = SampleSheetTableBuilder()
+
+
+class AssayPluginTestBase(SheetTemplateCreateMixin, SamplesheetsViewTestBase):
+    """Base test class for assay plugins"""
+
+    plugin_name = None
+    template_name = None
+
+    def setUp(self):
+        super().setUp()
+        self.make_sheets_from_cubi_tpl(CUBI_TPL_DICT[self.template_name])
+        self.investigation = Investigation.objects.get(project=self.project)
+        # NOTE: This assumes one study and assay, extend setup() to add more
+        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(self.plugin_name)