add sheet version create tag (#1296), add templatetag tests (#1723)

docs_manual/source/app_samplesheets_version.rst

@@ -29,6 +29,8 @@ Most Recent
     The most recently updated version.
 Import
     Version imported into SODAR from existing ISA-Tab files.
+Create
+    Version created from Template.
 Edit
     Version edited within the Sample Sheets app of SODAR.
 Restore

samplesheets/forms.py

@@ -351,6 +351,7 @@ def save(self):
                 project=self.project,
                 archive_name=None,
                 user=self.current_user,
+                from_template=True,
             )
 
 

samplesheets/io.py

@@ -518,6 +518,7 @@ def import_isa(
         replace=False,
         replace_uuid=None,
         save_isa=True,
+        from_template=False,
     ):
         """
         Import ISA investigation and its studies/assays from a dictionary of
@@ -530,6 +531,7 @@ def import_isa(
         :param replace: Whether replacing an existing sheet (bool)
         :param replace_uuid: Investigation UUID if replacing (UUID or string)
         :param save_isa: Save ISA-Tab as backup after importing (bool)
+        :param from_template: Whether importing from a template (bool)
         :return: Investigation
         :raise: SampleSheetExportException if critical warnings are raised
         """
@@ -820,7 +822,7 @@ def import_isa(
         # Save original ISA-Tab data
         # TODO: TBD: Prevent saving if previous data matches current one?
         if save_isa:
-            tags = ['IMPORT']
+            tags = ['CREATE'] if from_template else ['IMPORT']
             if replace:
                 tags.append('REPLACE')
             self.save_isa(

samplesheets/templatetags/samplesheets_tags.py

@@ -17,6 +17,7 @@
 
 # Local constants
 TAG_COLORS = {
+    'CREATE': 'info',
     'IMPORT': 'info',
     'EDIT': 'warning',
     'REPLACE': 'danger',

samplesheets/tests/test_templatetags.py

@@ -0,0 +1,218 @@
+"""Tests for template tags in the samplesheets app"""
+
+from django.conf import settings
+from django.urls import reverse
+
+from test_plus.test import TestCase
+
+from projectroles.models import SODAR_CONSTANTS
+from projectroles.plugins import get_backend_api
+from projectroles.tests.test_models import (
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
+)
+
+from samplesheets.models import GENERIC_MATERIAL_TYPES
+from samplesheets.templatetags import samplesheets_tags as s_tags
+from samplesheets.tests.test_models import (
+    SampleSheetModelMixin,
+    INV_IDENTIFIER,
+    INV_FILE_NAME,
+    INV_TITLE,
+    DEFAULT_DESCRIPTION,
+    DEFAULT_COMMENTS,
+    INV_ARCHIVE_NAME,
+    STUDY_IDENTIFIER,
+    STUDY_FILE_NAME,
+    STUDY_TITLE,
+    ASSAY_FILE_NAME,
+    ASSAY_TECH_PLATFORM,
+    ASSAY_TECH_TYPE,
+    ASSAY_MEASURE_TYPE,
+)
+
+# Local constants
+IRODS_SAMPLE_COLL = settings.IRODS_SAMPLE_COLL
+DEFAULT_TAG_COLOR = s_tags.DEFAULT_TAG_COLOR
+TAG_COLORS = s_tags.TAG_COLORS
+REQUEST_STATUS_CLASSES = s_tags.REQUEST_STATUS_CLASSES
+
+
+class TestSamplesheetsTemplateTags(
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
+    SampleSheetModelMixin,
+    TestCase,
+):
+    """Tests for template tags in the samplesheets app"""
+
+    def setUp(self):
+        # Init roles
+        self.init_roles()
+        # Make owner user
+        self.user_owner = self.make_user('owner')
+        # Init project and assignment
+        self.project = self.make_project(
+            'TestProject', SODAR_CONSTANTS['PROJECT_TYPE_PROJECT'], None
+        )
+        self.owner_as = self.make_assignment(
+            self.project, self.user_owner, self.role_owner
+        )
+        # Set up Investigation
+        self.investigation = self.make_investigation(
+            identifier=INV_IDENTIFIER,
+            file_name=INV_FILE_NAME,
+            project=self.project,
+            title=INV_TITLE,
+            description=DEFAULT_DESCRIPTION,
+            comments=DEFAULT_COMMENTS,
+            archive_name=INV_ARCHIVE_NAME,
+        )
+        # Set up Study
+        self.study = self.make_study(
+            identifier=STUDY_IDENTIFIER,
+            file_name=STUDY_FILE_NAME,
+            investigation=self.investigation,
+            title=STUDY_TITLE,
+            description=DEFAULT_DESCRIPTION,
+            comments=DEFAULT_COMMENTS,
+        )
+        # Set up Assay
+        self.assay = self.make_assay(
+            file_name=ASSAY_FILE_NAME,
+            study=self.study,
+            tech_platform=ASSAY_TECH_PLATFORM,
+            tech_type=ASSAY_TECH_TYPE,
+            measurement_type=ASSAY_MEASURE_TYPE,
+            arcs=[],
+            comments=DEFAULT_COMMENTS,
+        )
+        # Setup iRODS backend for the test
+        self.irods_backend = get_backend_api('omics_irods')
+
+    def test_get_investigation(self):
+        """Test get_investigation()"""
+        self.assertEqual(
+            s_tags.get_investigation(self.project), self.investigation
+        )
+
+    def test_get_investigation_no_investigation(self):
+        """Test get_investigation() without investigation"""
+        self.investigation.delete()
+        self.assertEqual(s_tags.get_investigation(self.project), None)
+
+    def test_get_search_item_type_with_material_types(self):
+        """Test get_search_item_type() with material types"""
+        for material_type in GENERIC_MATERIAL_TYPES:
+            item = {'type': material_type}
+            expected = GENERIC_MATERIAL_TYPES[material_type]
+            self.assertEqual(s_tags.get_search_item_type(item), expected)
+
+    def test_get_search_item_type_with_file(self):
+        """Test get_search_item_type() with special case 'file'"""
+        item = {'type': 'file'}
+        self.assertEqual(s_tags.get_search_item_type(item), 'Data File')
+
+    def test_get_irods_tree(self):
+        """Test get_irods_tree()"""
+        ret = s_tags.get_irods_tree(self.investigation)
+        # Assert that IRODS_SAMPLE_COLL exists in the returned string
+        self.assertIn(IRODS_SAMPLE_COLL, ret)
+        # Assert that study path exists in the returned string
+        self.assertIn(self.irods_backend.get_sub_path(self.study), ret)
+        # Assert that assay path exists in the returned string
+        study_path, assay_path = self.irods_backend.get_sub_path(
+            self.assay
+        ).split('/')
+        self.assertIn(study_path, ret)
+        self.assertIn(assay_path, ret)
+
+    def test_get_material_search_url(self):
+        """Test get_material_search_url()"""
+        item = {'study': self.study, 'name': 'Sample1'}
+        url = s_tags.get_material_search_url(item)
+        expected = reverse(
+            'samplesheets:project_sheets',
+            kwargs={'project': self.project.sodar_uuid},
+        )
+        expected += '#/study/{}/filter/Sample1'.format(self.study.sodar_uuid)
+        self.assertEqual(url, expected)
+
+    def test_get_irods_path_with_project(self):
+        """Test get_irods_path() with project"""
+        expected = self.irods_backend.get_path(self.project)
+        self.assertEqual(s_tags.get_irods_path(self.project), expected)
+
+    def test_get_irods_path_with_assay(self):
+        """Test get_irods_path() with assay"""
+        expected = self.irods_backend.get_path(self.assay)
+        self.assertEqual(s_tags.get_irods_path(self.assay), expected)
+
+    def test_get_irods_path_with_project_and_sub_path(self):
+        """Test get_irods_path() with project and sub_path"""
+        project_path = self.irods_backend.get_path(self.project)
+        sub_path = 'subfolder1/subfolder2'
+        expected = project_path + '/' + sub_path
+        self.assertEqual(
+            s_tags.get_irods_path(self.project, sub_path), expected
+        )
+
+    def test_get_irods_path_with_assay_and_sub_path(self):
+        """Test get_irods_path() with assay and sub_path"""
+        assay_path = self.irods_backend.get_path(self.assay)
+        sub_path = 'subfolder1/subfolder2'
+        expected = assay_path + '/' + sub_path
+        self.assertEqual(s_tags.get_irods_path(self.assay, sub_path), expected)
+
+    def test_get_icon_study(self):
+        """Test get_icon() with Study"""
+        icon_html = s_tags.get_icon(self.study)
+        self.assertIn('text-info', icon_html)
+        self.assertIn('mdi:folder-table', icon_html)
+
+    def test_get_icon_assay(self):
+        """Test get_icon() with Assay"""
+        icon_html = s_tags.get_icon(self.assay)
+        self.assertIn('text-danger', icon_html)
+        self.assertIn('mdi:table-large', icon_html)
+
+    def test_get_isatab_tag_html_with_tags_in_tag_colors(self):
+        """Test get_isatab_tag_html() with tags in TAG_COLORS"""
+        isatab = type('MockISATab', (object,), {'tags': TAG_COLORS.keys()})
+        tag_html = s_tags.get_isatab_tag_html(isatab)
+        for tag, color in TAG_COLORS.items():
+            self.assertIn(color, tag_html)
+
+    def test_get_isatab_tag_html_with_unknown_tag(self):
+        """Test get_isatab_tag_html() with an unknown tag"""
+        isatab = type('MockISATab', (object,), {'tags': ['UNKNOWN_TAG']})
+        tag_html = s_tags.get_isatab_tag_html(isatab)
+        self.assertIn(DEFAULT_TAG_COLOR, tag_html)
+
+    def test_get_request_status_class_with_valid_status(self):
+        """
+        Test get_request_status_class() with values in REQUEST_STATUS_CLASSES
+        """
+        for status, css_class in REQUEST_STATUS_CLASSES.items():
+            irods_request = type(
+                'MockIrodsRequest', (object,), {'status': status}
+            )
+            self.assertEqual(
+                s_tags.get_request_status_class(irods_request), css_class
+            )
+
+    def test_get_request_status_class_with_unknown_status(self):
+        """Test get_request_status_class() with an unknown status"""
+        irods_request = type(
+            'MockIrodsRequest', (object,), {'status': 'UNKNOWN'}
+        )
+        self.assertEqual(s_tags.get_request_status_class(irods_request), '')
+
+    def test_trim_base_path(self):
+        """Test trim_base_path() with a realistic iRODS path"""
+        prefix = '/base_path'
+        path = prefix + '/project/subfolder1/subfolder2'
+        expected = '/project/subfolder1/subfolder2'
+        self.assertEqual(s_tags.trim_base_path(path, prefix), expected)

samplesheets/tests/test_ui.py

@@ -205,7 +205,7 @@ def test_render_alert(self):
     # NOTE: For further vue app tests, see samplesheets/vueapp/tests
 
 
-class TestSheetTemplateCreateFormView(TestProjectSheetsUIBase):
+class TestSheetTemplateCreateView(TestProjectSheetsUIBase):
     """Tests for the sheet template creation view UI"""
 
     def test_render_field_visibility(self):
@@ -278,6 +278,11 @@ def test_list(self):
         self.assert_element_exists(
             [self.user_contributor], self.url, 'sodar-ss-version-alert', False
         )
+        # Ensure badge is shown for current version
+        self.login_and_redirect(self.user_contributor, self.url)
+        self.assertIsNotNone(
+            self.selenium.find_element(By.CLASS_NAME, 'badge-info')
+        )
 
     def test_list_no_versions(self):
         """Test UI rendering for list items with no versions"""

samplesheets/tests/test_views.py

@@ -703,8 +703,8 @@ def test_render_with_sheets(self):
             )
 
 
-class TestSheetTemplateCreateFormView(ViewTestBase):
-    """Tests for SheetTemplateCreateFormView"""
+class TestSheetTemplateCreateView(ViewTestBase):
+    """Tests for SheetTemplateCreateView"""
 
     def _get_post_data(self, tpl_name):
         """
@@ -798,6 +798,8 @@ def test_post_batch(self):
                     + t,
                     data=post_data,
                 )
+            isa_tab = ISATab.objects.first()
+            self.assertEqual(isa_tab.tags, ['CREATE'])
             self.assertEqual(response.status_code, 302, msg=t)
             self.assertIsNotNone(self.project.investigations.first(), msg=t)
             self.project.investigations.first().delete()