refactor api views (wip) (#1706, #1734)

CHANGELOG.rst

@@ -31,7 +31,7 @@ Added
     - Enable ``tumor_normal_dna`` ISA-Tab template (#1697)
     - General iRODS access ticket management for assay collections (#804, #1717)
     - Disabled row delete button tooltips (#1731)
-    - ``IrodsDataRequest`` REST API views (#1588, #1706)
+    - ``IrodsDataRequest`` REST API views (#1588, #1706, #1734)
     - Davrods links in iRODS delete request list (#1339)
     - Batch accepting and rejecting for iRODS delete requests (#1340)
 - **Taskflowbackend**

samplesheets/tests/test_permissions_api_taskflow.py

@@ -19,7 +19,7 @@
 )
 from samplesheets.tests.test_views_taskflow import (
     SampleSheetTaskflowMixin,
-    TEST_FILE_NAME,
+    IRODS_FILE_NAME,
 )
 
 
@@ -111,8 +111,8 @@ def setUp(self):
         # Set up iRODS data
         self.make_irods_colls(self.investigation)
         self.assay_path = self.irods_backend.get_path(self.assay)
-        self.path = os.path.join(self.assay_path, TEST_FILE_NAME)
-        self.path_md5 = os.path.join(self.assay_path, f'{TEST_FILE_NAME}.md5')
+        self.path = os.path.join(self.assay_path, IRODS_FILE_NAME)
+        self.path_md5 = os.path.join(self.assay_path, f'{IRODS_FILE_NAME}.md5')
         # Create objects
         self.file_obj = self.irods.data_objects.create(self.path)
         self.md5_obj = self.irods.data_objects.create(self.path_md5)

samplesheets/tests/test_views_ajax_taskflow.py

@@ -18,7 +18,7 @@
 from samplesheets.tests.test_views_taskflow import (
     TestIrodsDataRequestViewsBase,
     SampleSheetTaskflowMixin,
-    TEST_FILE_NAME2,
+    IRODS_FILE_NAME2,
 )
 from samplesheets.views import IRODS_REQ_CREATE_ALERT as CREATE_ALERT
 from samplesheets.views_ajax import ALERT_LIB_FILES_EXIST
@@ -330,8 +330,8 @@ def test_create_exists_as_contributor_by_contributor2(self):
 
     def test_create_multiple(self):
         """Test creating multiple delete requests"""
-        path2 = os.path.join(self.assay_path, TEST_FILE_NAME2)
-        path2_md5 = os.path.join(self.assay_path, TEST_FILE_NAME2 + '.md5')
+        path2 = os.path.join(self.assay_path, IRODS_FILE_NAME2)
+        path2_md5 = os.path.join(self.assay_path, IRODS_FILE_NAME2 + '.md5')
         self.irods.data_objects.create(path2)
         self.irods.data_objects.create(path2_md5)
 
@@ -473,8 +473,8 @@ def test_delete_no_request(self):
 
     def test_delete_one_of_multiple(self):
         """Test deleting one of multiple requests"""
-        path2 = os.path.join(self.assay_path, TEST_FILE_NAME2)
-        path2_md5 = os.path.join(self.assay_path, TEST_FILE_NAME2 + '.md5')
+        path2 = os.path.join(self.assay_path, IRODS_FILE_NAME2)
+        path2_md5 = os.path.join(self.assay_path, IRODS_FILE_NAME2 + '.md5')
         self.irods.data_objects.create(path2)
         self.irods.data_objects.create(path2_md5)
 

samplesheets/tests/test_views_api.py

@@ -1,6 +1,7 @@
 """Tests for REST API views in the samplesheets app"""
 
 import json
+import os
 
 from django.test import override_settings
 from django.urls import reverse
@@ -15,12 +16,23 @@
 # Sodarcache dependency
 from sodarcache.models import JSONCacheItem
 
+# Timeline dependency
+from timeline.models import ProjectEvent
+
 # Landingzones dependency
 from landingzones.models import LandingZone
 from landingzones.tests.test_models import LandingZoneMixin
 
 from samplesheets.io import SampleSheetIO
-from samplesheets.models import Investigation, Assay, GenericMaterial, ISATab
+from samplesheets.models import (
+    Investigation,
+    Assay,
+    GenericMaterial,
+    ISATab,
+    IrodsDataRequest,
+    IRODS_REQUEST_ACTION_DELETE,
+    IRODS_REQUEST_STATUS_ACTIVE,
+)
 from samplesheets.rendering import (
     SampleSheetTableBuilder,
     STUDY_TABLE_CACHE_ITEM,
@@ -31,6 +43,7 @@
     SHEET_DIR,
     SHEET_DIR_SPECIAL,
 )
+from samplesheets.tests.test_models import IrodsDataRequestMixin
 from samplesheets.tests.test_sheet_config import SheetConfigMixin
 from samplesheets.tests.test_views import (
     TestViewsBase,
@@ -58,6 +71,7 @@
 SHEET_NAME_ALT = 'i_small.zip'
 SHEET_PATH_ALT = SHEET_DIR + 'i_small2_alt.zip'
 SHEET_PATH_NO_PLUGIN_ASSAY = SHEET_DIR_SPECIAL + 'i_small_assay_no_plugin.zip'
+IRODS_FILE_NAME = 'test1.txt'
 IRODS_FILE_MD5 = '0b26e313ed4a7ca6904b0e9369e5b957'
 
 
@@ -609,6 +623,54 @@ def test_get_json(self):
         self.assertEqual(response.data, expected)
 
 
+class TestIrodsDataRequestDestroyAPIView(
+    IrodsDataRequestMixin, TestSampleSheetAPIBase
+):
+    """Tests for IrodsDataRequestDestroyAPIView"""
+
+    def _assert_tl_count(self, count):
+        """Assert timeline ProjectEvent count"""
+        self.assertEqual(
+            ProjectEvent.objects.filter(
+                event_name='irods_request_delete'
+            ).count(),
+            count,
+        )
+
+    def setUp(self):
+        super().setUp()
+        # Import investigation
+        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        # Set up iRODS backend and paths
+        self.irods_backend = get_backend_api('omics_irods')
+        self.assay_path = self.irods_backend.get_path(self.assay)
+        self.obj_path = os.path.join(self.assay_path, IRODS_FILE_NAME)
+
+    def test_delete(self):
+        """Test deleting a request"""
+        self._assert_tl_count(0)
+        obj = self.make_irods_request(
+            project=self.project,
+            action=IRODS_REQUEST_ACTION_DELETE,
+            path=self.obj_path,
+            status=IRODS_REQUEST_STATUS_ACTIVE,
+            user=self.user,
+        )
+        self.assertEqual(IrodsDataRequest.objects.count(), 1)
+        with self.login(self.user):
+            response = self.client.delete(
+                reverse(
+                    'samplesheets:api_irods_request_delete',
+                    kwargs={'irodsdatarequest': obj.sodar_uuid},
+                )
+            )
+        self.assertEqual(response.status_code, 204)
+        self.assertEqual(IrodsDataRequest.objects.count(), 0)
+        self._assert_tl_count(1)
+
+
 class TestSampleDataFileExistsAPIView(TestSampleSheetAPIBase):
     """Tests for SampleDataFileExistsAPIView"""