add study plugin view tests (#1999, #2021)

CHANGELOG.rst

@@ -26,6 +26,7 @@ Added
     - Assay app unit tests (#1980)
     - Missing assay plugin ``__init__.py`` files (#2014)
     - Study plugin override via ISA-Tab comments (#1885)
+    - Token auth support in study plugin IGV XML serving views (#1999, #2021)
 
 Changed
 -------

irodsbackend/views.py

@@ -233,7 +233,8 @@ def get(self, request, *args, **kwargs):
 @fallback_to_auth_basic
 class BasicAuthView(View):
     """
-    View for verifying login credentials for local users in iRODS.
+    View for verifying login credentials for local users in iRODS. Allows using
+    Knox token in place of password.
 
     Should only be used in local development and testing situations or when an
     external LDAP/AD login is not available.

samplesheets/studyapps/cancer/tests/test_permissions.py

@@ -0,0 +1,57 @@
+"""Permission tests for the cancer study app"""
+
+# NOTE: Basic auth tested in test_views
+
+import os
+
+from django.urls import reverse
+
+from samplesheets.models import GenericMaterial
+from samplesheets.tests.test_io import SHEET_DIR
+from samplesheets.tests.test_permissions import SamplesheetsPermissionTestBase
+
+
+# Local constants
+SHEET_PATH = os.path.join(SHEET_DIR, 'bih_cancer.zip')
+SOURCE_ID = 'normal1'
+
+
+class TestIGVSessionFileRenderView(SamplesheetsPermissionTestBase):
+    """Tests for IGVSessionFileRenderView permissions"""
+
+    def setUp(self):
+        super().setUp()
+        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        self.source = GenericMaterial.objects.get(
+            study=self.study, name=SOURCE_ID
+        )
+        self.url = reverse(
+            'samplesheets.studyapps.cancer:igv',
+            kwargs={'genericmaterial': self.source.sodar_uuid},
+        )
+
+    def test_get(self):
+        """Test IGVSessionFileRenderView GET"""
+        good_users = [
+            self.superuser,
+            self.user_owner_cat,  # Inherited
+            self.user_delegate_cat,  # Inherited
+            self.user_contributor_cat,  # Inherited
+            self.user_guest_cat,  # Inherited
+            self.user_owner,
+            self.user_delegate,
+            self.user_contributor,
+            self.user_guest,
+        ]
+        bad_users = [self.user_finder_cat, self.user_no_roles]
+        self.assert_response(self.url, good_users, 200)
+        self.assert_response(self.url, bad_users, 302)
+        self.assert_response(self.url, self.anonymous, 401)
+        # Test public project
+        self.project.set_public()
+        self.assert_response(
+            self.url, [self.user_finder_cat, self.user_no_roles], 200
+        )
+        self.assert_response(self.url, self.anonymous, 401)

samplesheets/studyapps/cancer/tests/test_views.py

@@ -0,0 +1,103 @@
+"""View tests for the cancer study app"""
+
+# NOTE: We don't need to add files in iRODS to test this view
+
+import base64
+import os
+
+from django.urls import reverse
+
+# Projectroles dependency
+from projectroles.tests.test_views_api import (
+    SODARAPIViewTestMixin,
+    EMPTY_KNOX_TOKEN,
+)
+
+from samplesheets.models import GenericMaterial
+from samplesheets.tests.test_io import SHEET_DIR
+from samplesheets.tests.test_models import SampleSheetModelMixin
+from samplesheets.tests.test_views import SamplesheetsViewTestBase
+
+
+# Local constants
+SHEET_PATH = os.path.join(SHEET_DIR, 'bih_cancer.zip')
+SOURCE_ID = 'normal1'
+
+
+class TestIGVSessionFileRenderView(
+    SODARAPIViewTestMixin,
+    SampleSheetModelMixin,
+    SamplesheetsViewTestBase,
+):
+    """Tests for cancer plugin IGVSessionFileRenderView"""
+
+    @staticmethod
+    def _get_auth_header(username, password):
+        """Return basic auth header"""
+        credentials = base64.b64encode(
+            '{}:{}'.format(username, password).encode('utf-8')
+        ).strip()
+        return {
+            'HTTP_AUTHORIZATION': 'Basic {}'.format(credentials.decode('utf-8'))
+        }
+
+    def setUp(self):
+        super().setUp()
+        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        self.source = GenericMaterial.objects.get(
+            study=self.study, name=SOURCE_ID
+        )
+        self.url = reverse(
+            'samplesheets.studyapps.cancer:igv',
+            kwargs={'genericmaterial': self.source.sodar_uuid},
+        )
+
+    def test_get(self):
+        """Test IGVSessionFileRenderView GET"""
+        with self.login(self.user_contributor):
+            response = self.client.get(self.url)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(
+            response.get('Content-Disposition'),
+            'attachment; filename="{}.case.igv.xml"'.format(SOURCE_ID),
+        )
+        # NOTE: XML forming tested in TestGetIGVXML
+
+    def test_get_basic_auth(self):
+        """Test GET with basic auth"""
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(self.user_contributor.username, 'password')
+        )
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_token(self):
+        """Test GET with Knox token"""
+        knox_token = self.get_token(self.user_contributor)
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(self.user_contributor.username, knox_token)
+        )
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_token_invalid(self):
+        """Test GET with invalid Knox token"""
+        self.get_token(self.user_contributor)
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(
+                self.user_contributor.username, EMPTY_KNOX_TOKEN
+            )
+        )
+        self.assertEqual(response.status_code, 401)
+
+    def test_get_token_wrong_user(self):
+        """Test GET with Knox token and wrong user"""
+        knox_token = self.get_token(self.user_contributor)
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(self.user_delegate.username, knox_token)
+        )
+        self.assertEqual(response.status_code, 401)

samplesheets/studyapps/germline/tests/test_permissions.py

@@ -0,0 +1,57 @@
+"""Permission tests for the germline study app"""
+
+# NOTE: Basic auth tested in test_views
+
+import os
+
+from django.urls import reverse
+
+from samplesheets.models import GenericMaterial
+from samplesheets.tests.test_io import SHEET_DIR
+from samplesheets.tests.test_permissions import SamplesheetsPermissionTestBase
+
+
+# Local constants
+SHEET_PATH = os.path.join(SHEET_DIR, 'bih_germline.zip')
+SOURCE_ID = 'p1'
+
+
+class TestIGVSessionFileRenderView(SamplesheetsPermissionTestBase):
+    """Tests for IGVSessionFileRenderView permissions"""
+
+    def setUp(self):
+        super().setUp()
+        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        self.source = GenericMaterial.objects.get(
+            study=self.study, name=SOURCE_ID
+        )
+        self.url = reverse(
+            'samplesheets.studyapps.germline:igv',
+            kwargs={'genericmaterial': self.source.sodar_uuid},
+        )
+
+    def test_get(self):
+        """Test IGVSessionFileRenderView GET"""
+        good_users = [
+            self.superuser,
+            self.user_owner_cat,  # Inherited
+            self.user_delegate_cat,  # Inherited
+            self.user_contributor_cat,  # Inherited
+            self.user_guest_cat,  # Inherited
+            self.user_owner,
+            self.user_delegate,
+            self.user_contributor,
+            self.user_guest,
+        ]
+        bad_users = [self.user_finder_cat, self.user_no_roles]
+        self.assert_response(self.url, good_users, 200)
+        self.assert_response(self.url, bad_users, 302)
+        self.assert_response(self.url, self.anonymous, 401)
+        # Test public project
+        self.project.set_public()
+        self.assert_response(
+            self.url, [self.user_finder_cat, self.user_no_roles], 200
+        )
+        self.assert_response(self.url, self.anonymous, 401)

samplesheets/studyapps/germline/tests/test_views.py

@@ -0,0 +1,104 @@
+"""View tests for the germline study app"""
+
+# NOTE: We don't need to add files in iRODS to test this view
+
+import base64
+import os
+
+from django.urls import reverse
+
+# Projectroles dependency
+from projectroles.tests.test_views_api import (
+    SODARAPIViewTestMixin,
+    EMPTY_KNOX_TOKEN,
+)
+
+from samplesheets.models import GenericMaterial
+from samplesheets.tests.test_io import SHEET_DIR
+from samplesheets.tests.test_models import SampleSheetModelMixin
+from samplesheets.tests.test_views import SamplesheetsViewTestBase
+
+
+# Local constants
+SHEET_PATH = os.path.join(SHEET_DIR, 'bih_germline.zip')
+SOURCE_ID = 'p1'
+FAMILY_ID = 'FAM_p1'
+
+
+class TestIGVSessionFileRenderView(
+    SODARAPIViewTestMixin,
+    SampleSheetModelMixin,
+    SamplesheetsViewTestBase,
+):
+    """Tests for germline plugin IGVSessionFileRenderView"""
+
+    @staticmethod
+    def _get_auth_header(username, password):
+        """Return basic auth header"""
+        credentials = base64.b64encode(
+            '{}:{}'.format(username, password).encode('utf-8')
+        ).strip()
+        return {
+            'HTTP_AUTHORIZATION': 'Basic {}'.format(credentials.decode('utf-8'))
+        }
+
+    def setUp(self):
+        super().setUp()
+        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        self.source = GenericMaterial.objects.get(
+            study=self.study, name=SOURCE_ID
+        )
+        self.url = reverse(
+            'samplesheets.studyapps.germline:igv',
+            kwargs={'genericmaterial': self.source.sodar_uuid},
+        )
+
+    def test_get(self):
+        """Test IGVSessionFileRenderView GET"""
+        with self.login(self.user_contributor):
+            response = self.client.get(self.url)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(
+            response.get('Content-Disposition'),
+            'attachment; filename="{}.pedigree.igv.xml"'.format(FAMILY_ID),
+        )
+        # NOTE: XML forming tested in TestGetIGVXML
+
+    def test_get_basic_auth(self):
+        """Test GET with basic auth"""
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(self.user_contributor.username, 'password')
+        )
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_token(self):
+        """Test GET with Knox token"""
+        knox_token = self.get_token(self.user_contributor)
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(self.user_contributor.username, knox_token)
+        )
+        self.assertEqual(response.status_code, 200)
+
+    def test_get_token_invalid(self):
+        """Test GET with invalid Knox token"""
+        self.get_token(self.user_contributor)
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(
+                self.user_contributor.username, EMPTY_KNOX_TOKEN
+            )
+        )
+        self.assertEqual(response.status_code, 401)
+
+    def test_get_token_wrong_user(self):
+        """Test GET with Knox token and wrong user"""
+        knox_token = self.get_token(self.user_contributor)
+        response = self.client.get(
+            self.url,
+            **self._get_auth_header(self.user_delegate.username, knox_token)
+        )
+        self.assertEqual(response.status_code, 401)