add suffix check in flow, update tests (#2064)

Author: mikkonie

landingzones/tests/test_views_taskflow.py

@@ -12,6 +12,7 @@
 from django.urls import reverse
 
 # Projectroles dependency
+from projectroles.app_settings import AppSettingAPI
 from projectroles.models import SODAR_CONSTANTS
 from projectroles.plugins import get_backend_api
 
@@ -43,6 +44,7 @@
 from landingzones.views import ZONE_MOVE_INVALID_STATUS
 
 
+app_settings = AppSettingAPI()
 User = auth.get_user_model()
 
 
@@ -55,6 +57,7 @@
 PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
 
 # Local constants
+APP_NAME = 'landingzones'
 SHEET_PATH = SHEET_DIR + 'i_small.zip'
 ZONE_TITLE = '20190703_172456'
 ZONE_SUFFIX = 'Test Zone'
@@ -675,6 +678,41 @@ def test_validate_md5_file_only(self):
         self.assertEqual(len(self.zone_coll.data_objects), 1)
         self.assertEqual(len(self.assay_coll.data_objects), 0)
 
+    def test_validate_prohibit(self):
+        """Test validating zone with prohibited file name suffix"""
+        app_settings.set(
+            APP_NAME, 'file_name_prohibit', 'txt', project=self.project
+        )
+        irods_obj = self.make_irods_object(self.zone_coll, TEST_OBJ_NAME)
+        self.make_irods_md5_object(irods_obj)
+        zone = LandingZone.objects.first()
+        self.assertEqual(zone.status, ZONE_STATUS_ACTIVE)
+        self.assertEqual(len(self.zone_coll.data_objects), 2)
+        self.assertEqual(len(self.assay_coll.data_objects), 0)
+        self.assertEqual(len(mail.outbox), 1)
+        self.assertEqual(
+            AppAlert.objects.filter(alert_name='zone_validate').count(), 0
+        )
+
+        with self.login(self.user):
+            response = self.client.post(self.url_validate)
+            self.assertRedirects(response, self.url_redirect)
+
+        self.assert_zone_status(zone, ZONE_STATUS_FAILED)
+        self.assertEqual(len(self.zone_coll.data_objects), 2)
+        self.assertEqual(len(self.assay_coll.data_objects), 0)
+        self.assertEqual(len(mail.outbox), 1)
+        tl_event = TimelineEvent.objects.filter(
+            event_name='zone_validate'
+        ).first()
+        self.assertIsInstance(tl_event, TimelineEvent)
+        self.assertEqual(
+            tl_event.get_status().status_type, self.timeline.TL_STATUS_FAILED
+        )
+        self.assertEqual(
+            AppAlert.objects.filter(alert_name='zone_move').count(), 0
+        )
+
     def test_move_invalid_status(self):
         """Test validating and moving with invalid zone status (should fail)"""
         irods_obj = self.make_irods_object(self.zone_coll, TEST_OBJ_NAME)

landingzones/views.py

@@ -12,6 +12,7 @@
 from django.views.generic import TemplateView, CreateView, UpdateView
 
 # Projectroles dependency
+from projectroles.app_settings import AppSettingAPI
 from projectroles.plugins import get_backend_api
 from projectroles.views import (
     LoggedInPermissionMixin,
@@ -38,6 +39,7 @@
 from landingzones.models import LandingZone
 
 
+app_settings = AppSettingAPI()
 logger = logging.getLogger(__name__)
 User = auth.get_user_model()
 
@@ -386,9 +388,14 @@ def _submit_validate_move(self, zone, validate_only, request=None):
             tl_event.set_status(timeline.TL_STATUS_SUBMIT)
 
         flow_data = self.get_flow_data(
-            zone,
-            'landing_zone_move',
-            {'zone_uuid': str(zone.sodar_uuid)},
+            zone=zone,
+            flow_name='landing_zone_move',
+            data={
+                'zone_uuid': str(zone.sodar_uuid),
+                'file_name_prohibit': app_settings.get(
+                    APP_NAME, 'file_name_prohibit', project=project
+                ),
+            },
         )
         if validate_only:
             flow_data['validate_only'] = True

taskflowbackend/flows/landing_zone_move.py

@@ -16,7 +16,8 @@
 
 
 SAMPLE_COLL = settings.IRODS_SAMPLE_COLL
-ZONE_INFO_CALC = 'Calculating missing checksums in iRODS'
+ZONE_INFO_CHECK = 'Checking availability and file types of {count} file{plural}'
+ZONE_INFO_CALC = 'Computing missing checksums in iRODS'
 ZONE_INFO_VALIDATE = 'Validating {count} file{plural}'
 ZONE_INFO_READ_ONLY = ', write access disabled'
 
@@ -39,6 +40,9 @@ def build(self, force_fail=False):
         sample_path = self.irods_backend.get_path(zone.assay)
         zone_path = self.irods_backend.get_path(zone)
         admin_name = self.irods.username
+        file_name_prohibit = None
+        if self.flow_data.get('file_name_prohibit'):
+            file_name_prohibit = self.flow_data['file_name_prohibit'].split(',')
 
         # HACK: Set zone status in the Django site
         zone.set_status(
@@ -151,6 +155,46 @@ def build(self, force_fail=False):
                     )
                 )
 
+        self.add_task(
+            lz_tasks.SetLandingZoneStatusTask(
+                name='Set landing zone status to VALIDATING (check)',
+                project=self.project,
+                inject={
+                    'landing_zone': zone,
+                    'status': ZONE_STATUS_VALIDATING,
+                    'status_info': ZONE_INFO_CHECK.format(
+                        count=file_count, plural=file_count_msg_plural
+                    )
+                    + (ZONE_INFO_READ_ONLY if not validate_only else ''),
+                    'flow_name': self.flow_name,
+                },
+            )
+        )
+        if file_name_prohibit:
+            self.add_task(
+                irods_tasks.BatchCheckFileSuffixTask(
+                    name='Batch check file types for zone data objects',
+                    irods=self.irods,
+                    inject={
+                        'file_paths': zone_objects_nomd5,
+                        'suffixes': file_name_prohibit,
+                        'zone_path': zone_path,
+                    },
+                )
+            )
+        self.add_task(
+            irods_tasks.BatchCheckFileExistTask(
+                name='Batch check file and MD5 checksum file existence for '
+                'zone data objects',
+                irods=self.irods,
+                inject={
+                    'file_paths': zone_objects_nomd5,
+                    'md5_paths': zone_objects_md5,
+                    'zone_path': zone_path,
+                },
+            )
+        )
+
         self.add_task(
             lz_tasks.SetLandingZoneStatusTask(
                 name='Set landing zone status to VALIDATING (calculate)',
@@ -190,19 +234,6 @@ def build(self, force_fail=False):
                 },
             )
         )
-
-        self.add_task(
-            irods_tasks.BatchCheckFileExistTask(
-                name='Batch check file and MD5 checksum file existence for '
-                'zone data objects',
-                irods=self.irods,
-                inject={
-                    'file_paths': zone_objects_nomd5,
-                    'md5_paths': zone_objects_md5,
-                    'zone_path': zone_path,
-                },
-            )
-        )
         self.add_task(
             irods_tasks.BatchValidateChecksumsTask(
                 name='Batch validate MD5 checksums of {} data objects'.format(

taskflowbackend/tests/test_flows.py

@@ -80,7 +80,7 @@
 COLL_NAME = 'test_coll'
 SUB_COLL_NAME = 'sub'
 OBJ_COLL_NAME = 'obj'
-OBJ_NAME = 'test_file'
+OBJ_NAME = 'test_file.txt'
 SHEET_PATH = SHEET_DIR + 'i_small.zip'
 UPDATED_TITLE = 'NewTitle'
 UPDATED_DESC = 'updated description'
@@ -1085,6 +1085,33 @@ def test_validate_no_checksum(self):
         self.assertIsNotNone(obj.replicas[0].checksum)
         self.assertEqual(obj.replicas[0].checksum, self.get_md5_checksum(obj))
 
+    def test_validate_prohibit(self):
+        """Test landing_zone_move validation with prohibited file name"""
+        coll_path = os.path.join(self.zone_path, COLL_NAME)
+        zone_coll = self.irods.collections.create(coll_path)
+        obj = self.make_irods_object(zone_coll, OBJ_NAME)
+        obj_path = obj.path
+        self.make_irods_md5_object(obj)
+        self.assertEqual(self.irods.data_objects.exists(obj_path), True)
+        self.assertEqual(
+            self.irods.data_objects.exists(obj_path + '.md5'), True
+        )
+        flow_data = {
+            'zone_uuid': str(self.zone.sodar_uuid),
+            'validate_only': True,
+            'file_name_prohibit': 'txt',
+        }
+        flow = self.taskflow.get_flow(
+            irods_backend=self.irods_backend,
+            project=self.project,
+            flow_name='landing_zone_move',
+            flow_data=flow_data,
+        )
+        with self.assertRaisesRegex(Exception, OBJ_NAME):
+            self.build_and_run(flow)
+        self.zone.refresh_from_db()
+        self.assertEqual(self.zone.status, ZONE_STATUS_FAILED)
+
     def test_revert(self):
         """Test reverting landing_zone_move"""
         coll_path = os.path.join(self.zone_path, COLL_NAME)