From 70f7398d4ec6cc17a104ddfc9f5b71ff813a4efd Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 8 Jan 2024 10:31:49 +0100
Subject: [PATCH 01/33] fix IrodsDataRequestListView webdav urls (#1860),
 refactor

---
 CHANGELOG.rst                              | 10 ++++++++++
 docs_manual/source/conf.py                 |  2 +-
 docs_manual/source/sodar_release_notes.rst |  8 ++++++++
 samplesheets/tests/test_views.py           | 17 ++++++++++------
 samplesheets/views.py                      | 23 ++++++++++------------
 samplesheets/vueapp/package-lock.json      |  4 ++--
 samplesheets/vueapp/package.json           |  2 +-
 7 files changed, 43 insertions(+), 23 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index fd0d1815..5fa50d74 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -5,6 +5,16 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+Unreleased
+==========
+
+Fixed
+-----
+
+- **Samplesheets**
+    - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
+
+
 v0.14.1 (2023-12-12)
 ====================
 
diff --git a/docs_manual/source/conf.py b/docs_manual/source/conf.py
index 4a4a2d27..8360d084 100644
--- a/docs_manual/source/conf.py
+++ b/docs_manual/source/conf.py
@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.14.1'
+release = '0.14.2-WIP'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 14a5af7b..f657ad54 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -8,6 +8,14 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
+v0.14.2 (WIP)
+============
+
+Release for minor updates, maintenance and bug fixes.
+
+- Fix iRODS data request view issues
+
+
 v0.14.1 (2023-12-12)
 ====================
 
diff --git a/samplesheets/tests/test_views.py b/samplesheets/tests/test_views.py
index 989c398d..e463edeb 100644
--- a/samplesheets/tests/test_views.py
+++ b/samplesheets/tests/test_views.py
@@ -1552,10 +1552,10 @@ class TestIrodsDataRequestListView(
 ):
     """Tests for IrodsDataRequestListView"""
 
-    def test_list(self):
-        """Test GET request for listing delete requests"""
+    def test_get(self):
+        """Test IrodsDataRequestListView GET"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
-        request = self.make_irods_request(
+        irods_request = self.make_irods_request(
             project=self.project,
             action=IRODS_REQUEST_ACTION_DELETE,
             path=IRODS_FILE_PATH,
@@ -1571,9 +1571,14 @@ def test_list(self):
             )
         self.assertEqual(response.status_code, 200)
         self.assertEqual(len(response.context['object_list']), 1)
-        self.assertEqual(response.context['object_list'][0], request)
+        context_obj = response.context['object_list'][0]
+        self.assertEqual(context_obj, irods_request)
+        self.assertEqual(
+            context_obj.webdav_url, 'https://127.0.0.1' + IRODS_FILE_PATH
+        )  # Ensure no extra slash is between host and iRODS path
+        self.assertEqual(context_obj.is_collection, False)
 
-    def test_list_as_contributor_by_superuser(self):
+    def test_get_as_contributor_by_superuser(self):
         """Test GET as contibutor with request created by superuser"""
         self.make_irods_request(
             project=self.project,
@@ -1592,7 +1597,7 @@ def test_list_as_contributor_by_superuser(self):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(len(response.context['object_list']), 0)
 
-    def test_list_as_contributor2_by_contributor(self):
+    def test_get_as_contributor2_by_contributor(self):
         """Test GET as contributor2 with request created by contributor"""
         user_contributor2 = self.make_user('user_contributor2')
         self.make_assignment(
diff --git a/samplesheets/views.py b/samplesheets/views.py
index 55a03e46..953d182c 100644
--- a/samplesheets/views.py
+++ b/samplesheets/views.py
@@ -12,6 +12,7 @@
 from cubi_isa_templates import _TEMPLATES as ISA_TEMPLATES
 from irods.exception import CollectionDoesNotExist
 from packaging import version
+from urllib.parse import urljoin
 
 from django.conf import settings
 from django.contrib import messages
@@ -2864,13 +2865,21 @@ class IrodsDataRequestListView(
     template_name = 'samplesheets/irods_requests.html'
     paginate_by = settings.SHEETS_IRODS_REQUEST_PAGINATION
 
+    @classmethod
+    def get_item_extra_data(cls, irods_session, item):
+        if settings.IRODS_WEBDAV_ENABLED:
+            item.webdav_url = urljoin(settings.IRODS_WEBDAV_URL, item.path)
+        else:
+            item.webdav_url = None
+        item.is_collection = irods_session.collections.exists(item.path)
+
     def get_context_data(self, *args, **kwargs):
         context_data = super().get_context_data(*args, **kwargs)
         irods = get_backend_api('omics_irods')
         with irods.get_session() as irods_session:
             if settings.IRODS_WEBDAV_ENABLED:
                 for item in context_data['object_list']:
-                    self.get_extra_item_data(irods_session, item)
+                    self.get_item_extra_data(irods_session, item)
         assign = RoleAssignment.objects.filter(
             project=self.get_project(),
             user=self.request.user,
@@ -2899,18 +2908,6 @@ def get_queryset(self):
         # For regular users, dispaly their own requests regardless of status
         return queryset.filter(user=self.request.user)
 
-    def build_webdav_url(self, item):
-        return '{}/{}'.format(settings.IRODS_WEBDAV_URL, item.path)
-
-    def get_extra_item_data(self, irods_session, item):
-        # Add webdav URL to the item
-        if settings.IRODS_WEBDAV_ENABLED:
-            item.webdav_url = self.build_webdav_url(item)
-        else:
-            item.webdav_url = None
-        # Check if the item is a collection
-        item.is_collection = irods_session.collections.exists(item.path)
-
     def get(self, request, *args, **kwargs):
         irods_backend = get_backend_api('omics_irods')
         if not irods_backend:
diff --git a/samplesheets/vueapp/package-lock.json b/samplesheets/vueapp/package-lock.json
index ee92aecd..90362481 100644
--- a/samplesheets/vueapp/package-lock.json
+++ b/samplesheets/vueapp/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "samplesheets",
-  "version": "0.14.1",
+  "version": "0.14.2-WIP",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "samplesheets",
-      "version": "0.14.1",
+      "version": "0.14.2-WIP",
       "dependencies": {
         "bootstrap-vue": "^2.22.0",
         "core-js": "^3.23.5",
diff --git a/samplesheets/vueapp/package.json b/samplesheets/vueapp/package.json
index 70d4b455..ec7403bc 100644
--- a/samplesheets/vueapp/package.json
+++ b/samplesheets/vueapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "samplesheets",
-  "version": "0.14.1",
+  "version": "0.14.2-WIP",
   "private": true,
   "scripts": {
     "serve": "vue-cli-service serve",

From 3cb7bb640c0891639b6388cecee4e5e52acab882 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 8 Jan 2024 12:17:15 +0100
Subject: [PATCH 02/33] fix IrodsDataRequest superuser update (#1863, #1864),
 refactor

---
 CHANGELOG.rst                                 |   2 +
 .../samplesheets/irods_requests.html          |   2 +-
 samplesheets/tests/test_views_api_taskflow.py |  14 ++
 samplesheets/tests/test_views_taskflow.py     |  48 +++---
 samplesheets/views.py                         | 146 +++++++++---------
 5 files changed, 119 insertions(+), 93 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5fa50d74..2b01279e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,6 +13,8 @@ Fixed
 
 - **Samplesheets**
     - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
+    - Superuser not allowed to edit iRODS request from other users in UI (#1863)
+    - ``IrodsDataRequest`` user changed on object update (#1864)
 
 
 v0.14.1 (2023-12-12)
diff --git a/samplesheets/templates/samplesheets/irods_requests.html b/samplesheets/templates/samplesheets/irods_requests.html
index 779e186f..f8741bec 100644
--- a/samplesheets/templates/samplesheets/irods_requests.html
+++ b/samplesheets/templates/samplesheets/irods_requests.html
@@ -181,7 +181,7 @@ <h3>iRODS Delete Requests</h3>
                       <i class="iconify" data-icon="mdi:cancel"></i> Reject Request
                     </a>
                   {% endif %}
-                  {% if irods_request.user == request.user %}
+                  {% if request.user.is_superuser or irods_request.user == request.user %}
                     {% if irods_request.status == 'ACTIVE' or irods_request.status == 'FAILED' %}
                       <a class="dropdown-item"
                          href="{% url 'samplesheets:irods_request_update' irodsdatarequest=irods_request.sodar_uuid %}">
diff --git a/samplesheets/tests/test_views_api_taskflow.py b/samplesheets/tests/test_views_api_taskflow.py
index 80c19ff4..da68980a 100644
--- a/samplesheets/tests/test_views_api_taskflow.py
+++ b/samplesheets/tests/test_views_api_taskflow.py
@@ -928,6 +928,20 @@ def test_patch(self):
         self.assertEqual(self.request.path, self.obj_path)
         self._assert_tl_count(1)
 
+    def test_patch_superuser(self):
+        """Test PATCH as superuser"""
+        self._assert_tl_count(0)
+        update_data = {'description': IRODS_REQUEST_DESC_UPDATED}
+        response = self.request_knox(
+            self.url, 'PATCH', data=update_data, token=self.get_token(self.user)
+        )
+        self.assertEqual(response.status_code, 200)
+        self.request.refresh_from_db()
+        self.assertEqual(self.request.description, IRODS_REQUEST_DESC_UPDATED)
+        self.assertEqual(self.request.path, self.obj_path)
+        self.assertEqual(self.request.user, self.user_contributor)
+        self._assert_tl_count(1)
+
 
 # NOTE: For TestIrodsDataRequestDestroyAPIView, see test_views_api
 
diff --git a/samplesheets/tests/test_views_taskflow.py b/samplesheets/tests/test_views_taskflow.py
index c8cfc757..260798ec 100644
--- a/samplesheets/tests/test_views_taskflow.py
+++ b/samplesheets/tests/test_views_taskflow.py
@@ -1323,9 +1323,13 @@ def setUp(self):
             user=self.user_contributor,
             description=IRODS_REQUEST_DESC,
         )
+        self.url = reverse(
+            'samplesheets:irods_request_update',
+            kwargs={'irodsdatarequest': self.request.sodar_uuid},
+        )
 
-    def test_update(self):
-        """Test POST request for updating a delete request"""
+    def test_post(self):
+        """Test IrodsDataRequestUpdateView POST"""
         self.assertEqual(IrodsDataRequest.objects.count(), 1)
         self._assert_tl_count(EVENT_UPDATE, 0)
 
@@ -1334,13 +1338,7 @@ def test_update(self):
             'description': IRODS_REQUEST_DESC_UPDATE,
         }
         with self.login(self.user_contributor):
-            response = self.client.post(
-                reverse(
-                    'samplesheets:irods_request_update',
-                    kwargs={'irodsdatarequest': self.request.sodar_uuid},
-                ),
-                update_data,
-            )
+            response = self.client.post(self.url, update_data)
             self.assertRedirects(
                 response,
                 reverse(
@@ -1361,8 +1359,28 @@ def test_update(self):
         self.assertEqual(self.request.description, IRODS_REQUEST_DESC_UPDATE)
         self._assert_tl_count(EVENT_UPDATE, 1)
 
-    def test_post_update_invalid_form_data(self):
-        """Test updating a delete request with invalid form data"""
+    def test_post_superuser(self):
+        """Test POST as superuser"""
+        self.assertEqual(IrodsDataRequest.objects.count(), 1)
+        self._assert_tl_count(EVENT_UPDATE, 0)
+
+        update_data = {
+            'path': self.obj_path,
+            'description': IRODS_REQUEST_DESC_UPDATE,
+        }
+        with self.login(self.user):
+            self.client.post(self.url, update_data)
+
+        self.assertEqual(IrodsDataRequest.objects.count(), 1)
+        self.request.refresh_from_db()
+        self.assertEqual(self.request.path, self.obj_path)
+        self.assertEqual(self.request.description, IRODS_REQUEST_DESC_UPDATE)
+        # Assert user is not updated when superuser updates the request
+        self.assertEqual(self.request.user, self.user_contributor)
+        self._assert_tl_count(EVENT_UPDATE, 1)
+
+    def test_post_invalid_form_data(self):
+        """Test POST with invalid form data"""
         self.assertEqual(IrodsDataRequest.objects.count(), 1)
         self._assert_tl_count(EVENT_UPDATE, 0)
 
@@ -1371,13 +1389,7 @@ def test_post_update_invalid_form_data(self):
             'description': IRODS_REQUEST_DESC_UPDATE,
         }
         with self.login(self.user_contributor):
-            response = self.client.post(
-                reverse(
-                    'samplesheets:irods_request_update',
-                    kwargs={'irodsdatarequest': self.request.sodar_uuid},
-                ),
-                update_data,
-            )
+            response = self.client.post(self.url, update_data)
 
         self.assertEqual(
             response.context['form'].errors['path'][0],
diff --git a/samplesheets/views.py b/samplesheets/views.py
index 953d182c..92b821bb 100644
--- a/samplesheets/views.py
+++ b/samplesheets/views.py
@@ -2381,6 +2381,76 @@ def delete(self, request, *args, **kwargs):
         return super().delete(request, *args, **kwargs)
 
 
+class IrodsDataRequestListView(
+    LoginRequiredMixin,
+    LoggedInPermissionMixin,
+    ProjectPermissionMixin,
+    InvestigationContextMixin,
+    ListView,
+):
+    """View for listing iRODS data requests"""
+
+    model = IrodsDataRequest
+    permission_required = 'samplesheets.edit_sheet'
+    template_name = 'samplesheets/irods_requests.html'
+    paginate_by = settings.SHEETS_IRODS_REQUEST_PAGINATION
+
+    @classmethod
+    def get_item_extra_data(cls, irods_session, item):
+        if settings.IRODS_WEBDAV_ENABLED:
+            item.webdav_url = urljoin(settings.IRODS_WEBDAV_URL, item.path)
+        else:
+            item.webdav_url = None
+        item.is_collection = irods_session.collections.exists(item.path)
+
+    def get_context_data(self, *args, **kwargs):
+        context_data = super().get_context_data(*args, **kwargs)
+        irods = get_backend_api('omics_irods')
+        with irods.get_session() as irods_session:
+            if settings.IRODS_WEBDAV_ENABLED:
+                for item in context_data['object_list']:
+                    self.get_item_extra_data(irods_session, item)
+        assign = RoleAssignment.objects.filter(
+            project=self.get_project(),
+            user=self.request.user,
+            role__name=SODAR_CONSTANTS['PROJECT_ROLE_CONTRIBUTOR'],
+        )
+        context_data['is_contributor'] = bool(assign)
+        context_data['irods_webdav_enabled'] = settings.IRODS_WEBDAV_ENABLED
+        return context_data
+
+    def get_queryset(self):
+        project = self.get_project()
+        queryset = self.model.objects.filter(project=project)
+        # For superusers, owners and delegates,
+        # display active/failed requests from all users
+        if (
+            self.request.user.is_superuser
+            or project.is_delegate(self.request.user)
+            or project.is_owner(self.request.user)
+        ):
+            return queryset.filter(
+                status__in=[
+                    IRODS_REQUEST_STATUS_ACTIVE,
+                    IRODS_REQUEST_STATUS_FAILED,
+                ]
+            )
+        # For regular users, dispaly their own requests regardless of status
+        return queryset.filter(user=self.request.user)
+
+    def get(self, request, *args, **kwargs):
+        irods_backend = get_backend_api('omics_irods')
+        if not irods_backend:
+            messages.error(request, 'iRODS backend not enabled')
+            return redirect(
+                reverse(
+                    'samplesheets:project_sheets',
+                    kwargs={'project': self.get_project().sodar_uuid},
+                )
+            )
+        return super().get(request, *args, **kwargs)
+
+
 class IrodsDataRequestCreateView(
     LoginRequiredMixin,
     LoggedInPermissionMixin,
@@ -2405,6 +2475,7 @@ def form_valid(self, form):
         project = self.get_project()
         # Create database object
         obj = form.save(commit=False)
+        # TODO: These should happen in the form instead (see #1865)
         obj.user = self.request.user
         obj.project = project
         obj.save()
@@ -2456,10 +2527,7 @@ def get_form_kwargs(self):
         return kwargs
 
     def form_valid(self, form):
-        obj = form.save(commit=False)
-        obj.user = self.request.user
-        obj.project = self.get_project()
-        obj.save()
+        obj = form.save()
         self.add_tl_update(obj)
         messages.success(
             self.request,
@@ -2851,76 +2919,6 @@ def post(self, request, *args, **kwargs):
             )
 
 
-class IrodsDataRequestListView(
-    LoginRequiredMixin,
-    LoggedInPermissionMixin,
-    ProjectPermissionMixin,
-    InvestigationContextMixin,
-    ListView,
-):
-    """View for listing iRODS data requests"""
-
-    model = IrodsDataRequest
-    permission_required = 'samplesheets.edit_sheet'
-    template_name = 'samplesheets/irods_requests.html'
-    paginate_by = settings.SHEETS_IRODS_REQUEST_PAGINATION
-
-    @classmethod
-    def get_item_extra_data(cls, irods_session, item):
-        if settings.IRODS_WEBDAV_ENABLED:
-            item.webdav_url = urljoin(settings.IRODS_WEBDAV_URL, item.path)
-        else:
-            item.webdav_url = None
-        item.is_collection = irods_session.collections.exists(item.path)
-
-    def get_context_data(self, *args, **kwargs):
-        context_data = super().get_context_data(*args, **kwargs)
-        irods = get_backend_api('omics_irods')
-        with irods.get_session() as irods_session:
-            if settings.IRODS_WEBDAV_ENABLED:
-                for item in context_data['object_list']:
-                    self.get_item_extra_data(irods_session, item)
-        assign = RoleAssignment.objects.filter(
-            project=self.get_project(),
-            user=self.request.user,
-            role__name=SODAR_CONSTANTS['PROJECT_ROLE_CONTRIBUTOR'],
-        )
-        context_data['is_contributor'] = bool(assign)
-        context_data['irods_webdav_enabled'] = settings.IRODS_WEBDAV_ENABLED
-        return context_data
-
-    def get_queryset(self):
-        project = self.get_project()
-        queryset = self.model.objects.filter(project=project)
-        # For superusers, owners and delegates,
-        # display active/failed requests from all users
-        if (
-            self.request.user.is_superuser
-            or project.is_delegate(self.request.user)
-            or project.is_owner(self.request.user)
-        ):
-            return queryset.filter(
-                status__in=[
-                    IRODS_REQUEST_STATUS_ACTIVE,
-                    IRODS_REQUEST_STATUS_FAILED,
-                ]
-            )
-        # For regular users, dispaly their own requests regardless of status
-        return queryset.filter(user=self.request.user)
-
-    def get(self, request, *args, **kwargs):
-        irods_backend = get_backend_api('omics_irods')
-        if not irods_backend:
-            messages.error(request, 'iRODS backend not enabled')
-            return redirect(
-                reverse(
-                    'samplesheets:project_sheets',
-                    kwargs={'project': self.get_project().sodar_uuid},
-                )
-            )
-        return super().get(request, *args, **kwargs)
-
-
 class SheetRemoteSyncView(
     LoginRequiredMixin,
     LoggedInPermissionMixin,

From 9cdefa9f174bd58063944cfa4734208e06c644a5 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 12 Jan 2024 11:05:11 +0100
Subject: [PATCH 03/33] fix legacy IrodsDataRequest modifying, cosmetic updates
 (#1858, #1862)

---
 CHANGELOG.rst                     |  8 ++++++++
 samplesheets/models.py            |  3 ++-
 samplesheets/tests/test_models.py |  9 +++++++--
 samplesheets/views.py             | 29 +++++++++++++++++------------
 samplesheets/views_ajax.py        |  2 +-
 5 files changed, 35 insertions(+), 16 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 2b01279e..e79df3f4 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -8,6 +8,13 @@ Changelog for the SODAR project. Loosely follows the
 Unreleased
 ==========
 
+Changed
+-------
+
+- **Samplesheets**
+    - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
+    - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
+
 Fixed
 -----
 
@@ -15,6 +22,7 @@ Fixed
     - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
     - Superuser not allowed to edit iRODS request from other users in UI (#1863)
     - ``IrodsDataRequest`` user changed on object update (#1864)
+    - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
 
 
 v0.14.1 (2023-12-12)
diff --git a/samplesheets/models.py b/samplesheets/models.py
index 96d0c5d0..5d939ffc 100644
--- a/samplesheets/models.py
+++ b/samplesheets/models.py
@@ -1381,7 +1381,8 @@ def save(self, *args, **kwargs):
 
     def _validate_action(self):
         """Validate the action field"""
-        if self.action != IRODS_REQUEST_ACTION_DELETE:
+        # Compare against uppercase string to support legacy requests
+        if self.action.upper() != IRODS_REQUEST_ACTION_DELETE:
             raise ValidationError(
                 'This model currently only supports the action "{}"'.format(
                     IRODS_REQUEST_ACTION_DELETE
diff --git a/samplesheets/tests/test_models.py b/samplesheets/tests/test_models.py
index 249544e7..22629a13 100644
--- a/samplesheets/tests/test_models.py
+++ b/samplesheets/tests/test_models.py
@@ -1602,12 +1602,17 @@ def test__repr__(self):
         )
         self.assertEqual(repr(self.request), expected)
 
-    def test_validate_action(self):
-        """Test _validate_action()"""
+    def test_validate_action_move(self):
+        """Test _validate_action() with MOVE status"""
         with self.assertRaises(ValidationError):
             self.request.action = 'MOVE'
             self.request.save()
 
+    def test_validate_action_legacy(self):
+        """Test _validate_action() with legacy lowercase status"""
+        self.request.action = 'delete'
+        self.request.save()  # No exception
+
     def test_validate_status(self):
         """Test _validate_status()"""
         with self.assertRaises(ValidationError):
diff --git a/samplesheets/views.py b/samplesheets/views.py
index 92b821bb..b3550dbf 100644
--- a/samplesheets/views.py
+++ b/samplesheets/views.py
@@ -1161,6 +1161,21 @@ def get_irods_request_objects(self):
             return IrodsDataRequest.objects.none()
         return IrodsDataRequest.objects.filter(sodar_uuid__in=request_ids)
 
+    def add_error_message(self, obj, ex):
+        """
+        Add Django error message for iRODS data request exception.
+
+        :param obj: IrodsDataRequest object
+        :param ex: Exception
+        """
+        ex_msg = '; '.join(ex) if isinstance(ex, list) else str(ex)
+        messages.error(
+            self.request,
+            'Accepting iRODS data request "{}" failed: {}'.format(
+                obj.get_display_name(), ex_msg
+            ),
+        )
+
 
 class SheetRemoteSyncAPI(SheetImportMixin):
     """
@@ -2667,12 +2682,7 @@ def post(self, request, *args, **kwargs):
                 ),
             )
         except Exception as ex:
-            messages.error(
-                self.request,
-                'Accepting iRODS data request "{}" failed: {}'.format(
-                    obj.get_display_name(), ex
-                ),
-            )
+            self.add_error_message(obj, ex)
         return redirect(
             reverse(
                 'samplesheets:irods_requests',
@@ -2766,12 +2776,7 @@ def post(self, request, *args, **kwargs):
                         ),
                     )
                 except Exception as ex:
-                    messages.error(
-                        self.request,
-                        'Accepting iRODS data request "{}" failed: {}'.format(
-                            obj.get_display_name(), ex
-                        ),
-                    )
+                    self.add_error_message(obj, ex)
 
             return redirect(
                 reverse(
diff --git a/samplesheets/views_ajax.py b/samplesheets/views_ajax.py
index 19b2b996..29e806d2 100644
--- a/samplesheets/views_ajax.py
+++ b/samplesheets/views_ajax.py
@@ -1869,7 +1869,7 @@ def post(self, request, *args, **kwargs):
             path=path,
             user=request.user,
             project=project,
-            description='Request created via Ajax API',
+            description='Request created in iRODS file list',
         )
 
         # Create timeline event

From 828d865f1e9b31030088945e12504ee91aa54b61 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 18 Jan 2024 16:29:04 +0100
Subject: [PATCH 04/33] fix ldap tls env var retrieval (#1853)

---
 CHANGELOG.rst                              |  8 ++++++++
 config/settings/base.py                    | 10 ++--------
 docs_manual/source/sodar_release_notes.rst |  3 ++-
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e79df3f4..c671fb1b 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -18,12 +18,20 @@ Changed
 Fixed
 -----
 
+- **General**
+    - Invalid env var retrieval for ``AUTH_LDAP*_START_TLS`` (#1853)
 - **Samplesheets**
     - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
     - Superuser not allowed to edit iRODS request from other users in UI (#1863)
     - ``IrodsDataRequest`` user changed on object update (#1864)
     - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
 
+Removed
+-------
+
+- **General**
+    - LDAP settings ``OPT_X_TLS_REQUIRE_CERT`` workaround (#1853)
+
 
 v0.14.1 (2023-12-12)
 ====================
diff --git a/config/settings/base.py b/config/settings/base.py
index e35435ae..0c7bc439 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -365,14 +365,12 @@
         'last_name': 'sn',
         'email': 'mail',
     }
-    # Temporarily disable cert checking (see issue #1853)
-    ldap.set_option(ldap.OPT_X_TLS_REQUIRE_CERT, ldap.OPT_X_TLS_NEVER)
 
     # Primary LDAP server
     AUTH_LDAP_SERVER_URI = env.str('AUTH_LDAP_SERVER_URI', None)
     AUTH_LDAP_BIND_DN = env.str('AUTH_LDAP_BIND_DN', None)
     AUTH_LDAP_BIND_PASSWORD = env.str('AUTH_LDAP_BIND_PASSWORD', None)
-    AUTH_LDAP_START_TLS = env.str('AUTH_LDAP_START_TLS', False)
+    AUTH_LDAP_START_TLS = env.bool('AUTH_LDAP_START_TLS', False)
     AUTH_LDAP_CA_CERT_FILE = env.str('AUTH_LDAP_CA_CERT_FILE', None)
     AUTH_LDAP_CONNECTION_OPTIONS = {**LDAP_DEFAULT_CONN_OPTIONS}
     if AUTH_LDAP_CA_CERT_FILE:
@@ -383,7 +381,6 @@
     AUTH_LDAP_USER_FILTER = env.str(
         'AUTH_LDAP_USER_FILTER', '(sAMAccountName=%(user)s)'
     )
-
     AUTH_LDAP_USER_SEARCH = LDAPSearch(
         env.str('AUTH_LDAP_USER_SEARCH_BASE', None),
         ldap.SCOPE_SUBTREE,
@@ -394,7 +391,6 @@
     AUTH_LDAP_DOMAIN_PRINTABLE = env.str(
         'AUTH_LDAP_DOMAIN_PRINTABLE', AUTH_LDAP_USERNAME_DOMAIN
     )
-
     AUTHENTICATION_BACKENDS = tuple(
         itertools.chain(
             ('projectroles.auth_backends.PrimaryLDAPBackend',),
@@ -407,7 +403,7 @@
         AUTH_LDAP2_SERVER_URI = env.str('AUTH_LDAP2_SERVER_URI', None)
         AUTH_LDAP2_BIND_DN = env.str('AUTH_LDAP2_BIND_DN', None)
         AUTH_LDAP2_BIND_PASSWORD = env.str('AUTH_LDAP2_BIND_PASSWORD', None)
-        AUTH_LDAP2_START_TLS = env.str('AUTH_LDAP2_START_TLS', False)
+        AUTH_LDAP2_START_TLS = env.bool('AUTH_LDAP2_START_TLS', False)
         AUTH_LDAP2_CA_CERT_FILE = env.str('AUTH_LDAP2_CA_CERT_FILE', None)
         AUTH_LDAP2_CONNECTION_OPTIONS = {**LDAP_DEFAULT_CONN_OPTIONS}
         if AUTH_LDAP2_CA_CERT_FILE:
@@ -418,7 +414,6 @@
         AUTH_LDAP2_USER_FILTER = env.str(
             'AUTH_LDAP2_USER_FILTER', '(sAMAccountName=%(user)s)'
         )
-
         AUTH_LDAP2_USER_SEARCH = LDAPSearch(
             env.str('AUTH_LDAP2_USER_SEARCH_BASE', None),
             ldap.SCOPE_SUBTREE,
@@ -429,7 +424,6 @@
         AUTH_LDAP2_DOMAIN_PRINTABLE = env.str(
             'AUTH_LDAP2_DOMAIN_PRINTABLE', AUTH_LDAP2_USERNAME_DOMAIN
         )
-
         AUTHENTICATION_BACKENDS = tuple(
             itertools.chain(
                 ('projectroles.auth_backends.SecondaryLDAPBackend',),
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index f657ad54..3f191bf1 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -13,7 +13,8 @@ v0.14.2 (WIP)
 
 Release for minor updates, maintenance and bug fixes.
 
-- Fix iRODS data request view issues
+- Fix iRODS data request issues
+- Fix LDAP TLS settings
 
 
 v0.14.1 (2023-12-12)

From ada1d860c1561afc84ade2ab153ba2a3dbe35818 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 19 Jan 2024 09:48:13 +0100
Subject: [PATCH 05/33] upgrade follow-redirects (#1854)

---
 CHANGELOG.rst                         |  2 ++
 samplesheets/vueapp/package-lock.json | 12 ++++++------
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c671fb1b..164815ab 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -11,6 +11,8 @@ Unreleased
 Changed
 -------
 
+- **General**
+    - Upgrade critical Vue app dependencies (#1854)
 - **Samplesheets**
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
diff --git a/samplesheets/vueapp/package-lock.json b/samplesheets/vueapp/package-lock.json
index 90362481..ac9dc64f 100644
--- a/samplesheets/vueapp/package-lock.json
+++ b/samplesheets/vueapp/package-lock.json
@@ -8125,9 +8125,9 @@
       "dev": true
     },
     "node_modules/follow-redirects": {
-      "version": "1.15.3",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.3.tgz",
-      "integrity": "sha512-1VzOtuEM8pC9SFU1E+8KfTjZyMztRsgEfwQl44z8A25uy13jSzTj6dyK2Df52iV0vgHCfBwLhDWevLn95w5v6Q==",
+      "version": "1.15.5",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.5.tgz",
+      "integrity": "sha512-vSFWUON1B+yAw1VN4xMfxgn5fTUiaOzAJCKBwIIgT/+7CuGy9+r+5gITvP62j3RmaD5Ph65UaERdOSRGUzZtgw==",
       "dev": true,
       "funding": [
         {
@@ -23401,9 +23401,9 @@
       "dev": true
     },
     "follow-redirects": {
-      "version": "1.15.3",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.3.tgz",
-      "integrity": "sha512-1VzOtuEM8pC9SFU1E+8KfTjZyMztRsgEfwQl44z8A25uy13jSzTj6dyK2Df52iV0vgHCfBwLhDWevLn95w5v6Q==",
+      "version": "1.15.5",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.5.tgz",
+      "integrity": "sha512-vSFWUON1B+yAw1VN4xMfxgn5fTUiaOzAJCKBwIIgT/+7CuGy9+r+5gITvP62j3RmaD5Ph65UaERdOSRGUzZtgw==",
       "dev": true
     },
     "for-each": {

From e68871971fd7fe2ee1881e324b7b9024880858c8 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 19 Jan 2024 16:59:43 +0100
Subject: [PATCH 06/33] fix zone stats badge display for superusers (#1866)

---
 CHANGELOG.rst                                       | 2 ++
 landingzones/static/landingzones/js/landingzones.js | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 164815ab..c690a080 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -22,6 +22,8 @@ Fixed
 
 - **General**
     - Invalid env var retrieval for ``AUTH_LDAP*_START_TLS`` (#1853)
+- **Landingzones**
+    - Stats badge displayed to superusers for ``DELETED`` zones (#1866)
 - **Samplesheets**
     - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
     - Superuser not allowed to edit iRODS request from other users in UI (#1863)
diff --git a/landingzones/static/landingzones/js/landingzones.js b/landingzones/static/landingzones/js/landingzones.js
index 7cb82c82..299329f2 100644
--- a/landingzones/static/landingzones/js/landingzones.js
+++ b/landingzones/static/landingzones/js/landingzones.js
@@ -62,7 +62,6 @@ var updateZoneStatus = function() {
                         }
                         if (['CREATING', 'NOT CREATED', 'MOVED', 'DELETED'].includes(zoneStatus)) {
                             zoneTr.find('p#sodar-lz-zone-stats-container-' + zoneUuid).hide();
-
                             if (zoneStatus === 'MOVED') {
                                 var statusMovedSpan = zoneTr.find(
                                     'span#sodar-lz-zone-status-moved-' + zoneUuid
@@ -78,7 +77,6 @@ var updateZoneStatus = function() {
                         }
 
                         // Button modification
-                        // if (zoneStatus !== 'ACTIVE' && zoneStatus !== 'FAILED' && isSuperuser) {}
                         if (zoneStatus !== 'ACTIVE' && zoneStatus !== 'FAILED' && !isSuperuser) {
                             zoneTr.find('td.sodar-lz-zone-title').addClass('text-muted');
                             zoneTr.find('td.sodar-lz-zone-assay').addClass('text-muted');
@@ -96,7 +94,9 @@ var updateZoneStatus = function() {
                             zoneTr.find('td.sodar-lz-zone-title').removeClass('text-muted');
                             zoneTr.find('td.sodar-lz-zone-assay').removeClass('text-muted');
                             zoneTr.find('td.sodar-lz-zone-status-info').removeClass('text-muted');
-                            zoneTr.find('p#sodar-lz-zone-stats-container-' + zoneUuid).show();
+                            if (zoneStatus !== 'DELETED') {
+                                zoneTr.find('p#sodar-lz-zone-stats-container-' + zoneUuid).show();
+                            }
                             zoneTr.find('.btn').each(function() {
                                 if ($(this).is('button')) {
                                     $(this).removeAttr('disabled');

From 5483cd4e073ad59c99da18bec81e9bf347a66507 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 26 Jan 2024 10:21:24 +0100
Subject: [PATCH 07/33] update installation docs (#1871)

---
 CHANGELOG.rst                              |  1 +
 docs_manual/source/admin_install.rst       | 53 ++++++++++++++++------
 docs_manual/source/dev_install.rst         |  6 +--
 docs_manual/source/sodar_release_notes.rst |  3 +-
 4 files changed, 45 insertions(+), 18 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c690a080..5af1fa6d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,6 +13,7 @@ Changed
 
 - **General**
     - Upgrade critical Vue app dependencies (#1854)
+    - Update installation documentation (#1871)
 - **Samplesheets**
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
diff --git a/docs_manual/source/admin_install.rst b/docs_manual/source/admin_install.rst
index f65a98a3..d92ce025 100644
--- a/docs_manual/source/admin_install.rst
+++ b/docs_manual/source/admin_install.rst
@@ -31,13 +31,19 @@ Docker Compose network if e.g. you already have a separate iRODS server running.
     - ``traefik``: Reverse proxy for TLS/SSL routing.
     - ``sssd``: System Security Service Daemon for LDAP/AD authentication.
 
+.. note::
+
+    Currently the sodar-docker-compose environment only supports iRODS v4.2.
+    Support for v4.3 is being worked on. iRODS v4.3 will be the default
+    supported version from SODAR v1.0 onwards.
+
 
 Quickstart Guide
 ================
 
 For a guide on how to try out and evaluate SODAR on your Linux workstation, see
 the `README file <https://github.com/bihealth/sodar-docker-compose#readme>`_ of
-the SODAR Docker Compose repository.
+the sodar-docker-compose repository.
 
 
 Installation Guide
@@ -70,7 +76,7 @@ requirements.
 1. Clone the Repository
 -----------------------
 
-Clone the ``sodar-docker-compose`` repository as follows:
+Clone the sodar-docker-compose repository as follows:
 
 .. code-block:: bash
 
@@ -141,7 +147,7 @@ settings. Note that in the Docker Compose environment, settings specific to the
 SODAR web server are prefixed with ``SODAR_*``. This does not include e.g. iRODS
 settings commonly used by multiple components.
 
-For more information on the iRODS settings, see the
+For more information on iRODS settings, see the
 `iRODS documentation <https://docs.irods.org/master/system_overview/configuration/>`_.
 
 Note that for certain settings to take effect, you need to run the Docker
@@ -160,12 +166,12 @@ following command:
     $ ./run.sh
 
 If you have the need to modify the default configuration, you can alternatively
-launch the network with the ``docker-compose up`` command with appropriate
+launch the network with the ``docker compose up`` command with appropriate
 parameters:
 
 .. code-block:: bash
 
-    $ docker-compose -f docker-compose.yml \
+    $ docker compose -f docker-compose.yml \
         -f docker-compose.override.yml.irods \
         -f docker-compose.override.yml.davrods \
         -f docker-compose.override.yml.provided-cert \
@@ -237,29 +243,46 @@ restart. If the network is running in the background, enter the following:
 
 .. code-block:: bash
 
-    $ docker-compose down && docker-compose up -d
+    $ docker compose down && docker compose up -d
 
 For updating all the images to their latest version, run the following:
 
 .. code-block:: bash
 
-    $ docker-compose pull
+    $ docker compose pull
 
 To only update a specific image, you can do the following:
 
 .. code-block:: bash
 
-    $ docker-compose pull IMAGE-NAME
-    $ docker-compose up -d --no-deps --build IMAGE-NAME
+    $ docker compose pull IMAGE-NAME
+    $ docker compose up -d --no-deps --build IMAGE-NAME
 
 Whenever updating your SODAR environment, it is strongly recommend to ensure
-your ``sodar-docker-compose`` repository is up-to-date with the latest version
-with the following command:
+your sodar-docker-compose repository is up-to-date with the latest version with
+the following command:
 
 .. code-block:: bash
 
     $ git pull origin main
 
+The ``main`` branch of the repository will contain the latest release version of
+the environment, which corresponds to the latest SODAR server release. If you
+want to deploy an older version of SODAR than the most recent release, check out
+the corresponding sodar-docker-compose release according to its git tag.
+
+If you are installing the "bleeding edge" development version of SODAR ``dev``
+with the ``dev-0`` tag, you should correspondingly use the ``dev`` branch
+version of sodar-docker-compose. Note that these versions may contain breaking
+changes and/or not yet fully documented features. Deploying the dev version in
+production is generally recommended only for experienced SODAR admins.
+
+.. note::
+
+    SODAR v1.0 will be upgraded to use iRODS 4.3 and Postgres v16. This version
+    may require special steps for upgrading an existing environment. Make sure
+    to refer to the sodar-docker-compose README for instructions.
+
 
 .. _admin_install_advanced_config:
 
@@ -313,7 +336,11 @@ command.
 Deploying in Production
 =======================
 
-This section details issues specific to deploying SODAR in production.
+Deploying the SODAR environment in production is mostly considered out of scope
+for this documentation, as the exact method of deployment depends on your
+organization's infrastructure and practices. The sodar-docker-compose
+environment can be set up for production using e.g. Ansible playbooks. In this
+section we present certain guidelines and recommendations for deployment.
 
 Production Prerequisites
 ------------------------
@@ -321,8 +348,6 @@ Production Prerequisites
 In addition to the :ref:`general prerequisites <admin_install_prerequisites>`,
 we recommend the following for a production deployment of SODAR:
 
-**TODO:** Update these
-
 - Recommended Hardware
     - Memory: 64 GB of RAM
     - CPU: 16 cores
diff --git a/docs_manual/source/dev_install.rst b/docs_manual/source/dev_install.rst
index dd750d2c..0915ad1f 100644
--- a/docs_manual/source/dev_install.rst
+++ b/docs_manual/source/dev_install.rst
@@ -111,7 +111,7 @@ use OpenSSL as demonstrated below. Ensure the file is placed under
 ----------------------------
 
 Copy the file ``env.example.dev`` into ``.env`` to use the default
-``sodar-docker-compose`` configuration for development.
+sodar-docker-compose configuration for development.
 
 .. code-block:: bash
 
@@ -121,7 +121,7 @@ In the case of the development setup, this environment only includes variables
 available to the external SODAR components. The ``sodar-server`` settings will
 be set up in a local ``.env`` file we will describe further on in this document.
 
-5. Bring up the Environment
+5. Bring Up the Environment
 ---------------------------
 
 To run the environment in the development configuration, use the following
@@ -141,7 +141,7 @@ SODAR Server Setup
 With the required external components running in Docker, you can set up and run
 the SODAR Django server and other local components.
 
-1. Set up the Repository
+1. Set Up the Repository
 ------------------------
 
 First, clone the ``sodar-server`` repository and install the OS dependencies
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 3f191bf1..83599b9e 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -9,12 +9,13 @@ list of changes in current and previous releases, see the
 
 
 v0.14.2 (WIP)
-============
+=============
 
 Release for minor updates, maintenance and bug fixes.
 
 - Fix iRODS data request issues
 - Fix LDAP TLS settings
+- Minor updates and bug fixes
 
 
 v0.14.1 (2023-12-12)

From 3a812fd0ccc42f6f715e3d327a4d559a8d318d74 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 29 Jan 2024 16:19:41 +0100
Subject: [PATCH 08/33] add zone assay shortcut collection creation (#1869)

---
 CHANGELOG.rst                              |  6 +++
 docs_manual/source/sodar_release_notes.rst |  1 +
 landingzones/tests/test_views_taskflow.py  | 43 +++++++++++++++++++---
 landingzones/views.py                      | 17 +++++++--
 4 files changed, 58 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5af1fa6d..3272dff6 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -8,6 +8,12 @@ Changelog for the SODAR project. Loosely follows the
 Unreleased
 ==========
 
+Added
+-----
+
+- **Landingzones**
+    - Create assay plugin shortcut collections for zones (#1869)
+
 Changed
 -------
 
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 83599b9e..38a8b6e4 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -13,6 +13,7 @@ v0.14.2 (WIP)
 
 Release for minor updates, maintenance and bug fixes.
 
+- Add assay plugin shortcut collection creation in landing zones
 - Fix iRODS data request issues
 - Fix LDAP TLS settings
 - Minor updates and bug fixes
diff --git a/landingzones/tests/test_views_taskflow.py b/landingzones/tests/test_views_taskflow.py
index 14562bdc..0826c638 100644
--- a/landingzones/tests/test_views_taskflow.py
+++ b/landingzones/tests/test_views_taskflow.py
@@ -67,6 +67,8 @@
 ZONE_BASE_COLLS = [MISC_FILES_COLL, RESULTS_COLL, TRACK_HUBS_COLL]
 ZONE_PLUGIN_COLLS = ['0815-N1-DNA1', '0815-T1-DNA1']
 ZONE_ALL_COLLS = ZONE_BASE_COLLS + ZONE_PLUGIN_COLLS
+RAW_DATA_COLL = 'RawData'
+MAX_QUANT_COLL = 'MaxQuantResults'
 
 
 class LandingZoneTaskflowMixin:
@@ -239,8 +241,7 @@ def test_create_zone_colls(self):
             'configuration': '',
         }
         with self.login(self.user):
-            response = self.client.post(self.url, values)
-            self.assertRedirects(response, self.redirect_url)
+            self.client.post(self.url, values)
 
         self.assert_zone_count(1)
         zone = LandingZone.objects.first()
@@ -287,8 +288,7 @@ def test_create_zone_colls_plugin(self):
             'configuration': '',
         }
         with self.login(self.user):
-            response = self.client.post(self.url, values)
-            self.assertRedirects(response, self.redirect_url)
+            self.client.post(self.url, values)
 
         self.assert_zone_count(1)
         zone = LandingZone.objects.first()
@@ -304,6 +304,38 @@ def test_create_zone_colls_plugin(self):
             self.assert_irods_access(
                 self.user.username, os.path.join(zone_path, c), IRODS_ACCESS_OWN
             )
+        # These should not be created for this plugin
+        for c in [MAX_QUANT_COLL, RAW_DATA_COLL]:
+            self.assert_irods_coll(zone, c, False)
+
+    def test_create_zone_colls_plugin_shortcuts(self):
+        """Test landingzones creation with shortcut collections in plugin"""
+        self.assertEqual(LandingZone.objects.count(), 0)
+        # Set pep_ms plugin
+        self.assay.measurement_type = {'name': 'protein expression profiling'}
+        self.assay.technology_type = {'name': 'mass spectrometry'}
+        self.assay.save()
+        # NOTE: update_cache() not implemented in this plugin
+
+        values = {
+            'assay': str(self.assay.sodar_uuid),
+            'title_suffix': ZONE_SUFFIX,
+            'description': ZONE_DESC,
+            'create_colls': True,
+            'restrict_colls': False,
+            'configuration': '',
+        }
+        with self.login(self.user):
+            self.client.post(self.url, values)
+
+        self.assert_zone_count(1)
+        zone = LandingZone.objects.first()
+        self.assert_zone_status(zone, ZONE_STATUS_ACTIVE)
+        zone_colls = ZONE_BASE_COLLS + [RAW_DATA_COLL, MAX_QUANT_COLL]
+        for c in zone_colls:
+            self.assert_irods_coll(zone, c, True)
+        for c in ZONE_PLUGIN_COLLS:
+            self.assert_irods_coll(zone, c, False)
 
     # TODO: Test without sodarcache (see issue #1157)
 
@@ -332,8 +364,7 @@ def test_create_zone_colls_plugin_restrict(self):
             'configuration': '',
         }
         with self.login(self.user):
-            response = self.client.post(self.url, values)
-            self.assertRedirects(response, self.redirect_url)
+            self.client.post(self.url, values)
 
         self.assert_zone_count(1)
         zone = LandingZone.objects.first()
diff --git a/landingzones/views.py b/landingzones/views.py
index 0421f19c..53356ed5 100644
--- a/landingzones/views.py
+++ b/landingzones/views.py
@@ -187,6 +187,7 @@ def submit_create(
         colls = []
         if create_colls:
             logger.debug('Creating default landing zone collections..')
+            assay_path = irods_backend.get_path(zone.assay)
             colls = [RESULTS_COLL, MISC_FILES_COLL, TRACK_HUBS_COLL]
             plugin = zone.assay.get_plugin()
             # First try the cache
@@ -199,14 +200,24 @@ def submit_create(
                     project=zone.project,
                 )
                 if cache_obj and cache_obj.data:
-                    assay_path = irods_backend.get_path(zone.assay)
                     colls += [
                         p.replace(assay_path + '/', '')
                         for p in cache_obj.data['paths'].keys()
                     ]
                     logger.debug('Retrieved collections from cache')
-            elif plugin:
-                pass  # TODO: Build tables, get rows directly from plugin?
+            # TODO: If no cache, build tables and get rows directly from plugin?
+            # Add shortcut paths
+            if plugin:
+                shortcuts = plugin.get_shortcuts(zone.assay) or []
+                for s in shortcuts:
+                    path = s.get('path')
+                    if path:
+                        path = path.replace(assay_path + '/', '')
+                    if path and path not in colls:
+                        colls.append(path)
+                        logger.debug(
+                            'Added shorctut collection "{}"'.format(s.get('id'))
+                        )
 
         logger.debug('Collections to be created: {}'.format(', '.join(colls)))
         flow_name = 'landing_zone_create'

From 6be73da3e8e66b18c6b5a46fd064aa4669e5d274 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 1 Feb 2024 16:36:02 +0100
Subject: [PATCH 09/33] fix protocol ref editability for new rows (#1875)

---
 CHANGELOG.rst                   | 1 +
 samplesheets/vueapp/src/App.vue | 9 ++++-----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 3272dff6..d05a5aeb 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -36,6 +36,7 @@ Fixed
     - Superuser not allowed to edit iRODS request from other users in UI (#1863)
     - ``IrodsDataRequest`` user changed on object update (#1864)
     - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
+    - Protocol ref editable for new row if disabled in column config (#1875)
 
 Removed
 -------
diff --git a/samplesheets/vueapp/src/App.vue b/samplesheets/vueapp/src/App.vue
index ce49b0a2..039418c3 100644
--- a/samplesheets/vueapp/src/App.vue
+++ b/samplesheets/vueapp/src/App.vue
@@ -759,7 +759,6 @@ export default {
         let enableNextIdx = null
 
         // If the next node is a material, enable editing its name
-        // Else if it's a process, enable editing for all cells (if available)
         if (nextNodeCls === 'GenericMaterial') {
           const itemType = cols[startIdx].colDef.cellEditorParams.headerInfo.item_type
           const headerType = cols[startIdx].colDef.cellEditorParams.headerInfo.header_type
@@ -810,7 +809,7 @@ export default {
               rowNode.setDataValue(cols[i].colId, value)
             }
           }
-        } else if (nextNodeCls === 'Process') {
+        } else if (nextNodeCls === 'Process') { // Handle process node enabling
           let i = startIdx
           let processActive = false
           let newInit = true
@@ -821,9 +820,10 @@ export default {
             nextColId = cols[i].colId
             const value = this.getDefaultValue(nextColId, gridOptions, newInit, forceEmpty)
             const headerType = cols[i].colDef.cellEditorParams.headerInfo.header_type
+            const fieldEditable = cols[i].colDef.cellRendererParams.fieldEditable
 
             if (headerType === 'protocol') {
-              value.editable = true
+              value.editable = fieldEditable
               if ('uuid_ref' in value && value.uuid_ref) {
                 processActive = true
                 newInit = false
@@ -842,13 +842,12 @@ export default {
             } else {
               // Only allow editing the rest of the cells if protocol is set
               if (processActive) {
-                value.editable = cols[i].colDef.cellRendererParams.fieldEditable
+                value.editable = fieldEditable
               } else value.editable = false
             }
             rowNode.setDataValue(nextColId, value)
             i += 1
           }
-
           // If default protocol or name was filled, enable the next node(s) too
           if (processActive) enableNextIdx = i
         }

From a3409febb0aad015a1a7a536adaa353571795b15 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 5 Feb 2024 17:28:39 +0100
Subject: [PATCH 10/33] update irods object list retrieval (#1882, #1883)

---
 CHANGELOG.rst                              |  7 ++
 irodsbackend/api.py                        | 62 ++++++-----------
 irodsbackend/tests/test_api_taskflow.py    | 77 ++++++----------------
 irodsbackend/views.py                      | 25 +++++--
 samplesheets/plugins.py                    |  4 +-
 samplesheets/studyapps/cancer/utils.py     |  2 +-
 samplesheets/studyapps/germline/plugins.py |  6 +-
 samplesheets/studyapps/germline/utils.py   |  2 +-
 samplesheets/views_ajax.py                 | 16 ++---
 samplesheets/views_api.py                  |  4 +-
 taskflowbackend/flows/landing_zone_move.py | 45 +++++--------
 taskflowbackend/irods_utils.py             | 22 -------
 taskflowbackend/tests/base.py              |  5 +-
 13 files changed, 102 insertions(+), 175 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index d05a5aeb..2d11c62d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -20,9 +20,14 @@ Changed
 - **General**
     - Upgrade critical Vue app dependencies (#1854)
     - Update installation documentation (#1871)
+- **Irodsbackend**
+    - Reduce redundant object queries (#1883)
+    - Change method logic in ``get_objects()`` and ``get_objs_recursively()`` (#1883)
 - **Samplesheets**
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
+- **Taskflowbackend**
+    - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
 
 Fixed
 -----
@@ -43,6 +48,8 @@ Removed
 
 - **General**
     - LDAP settings ``OPT_X_TLS_REQUIRE_CERT`` workaround (#1853)
+- **Taskflowbackend**
+    - ``get_subcoll_obj_paths()`` and ``get_subcoll_paths()`` helpers (#1882)
 
 
 v0.14.1 (2023-12-12)
diff --git a/irodsbackend/api.py b/irodsbackend/api.py
index 34ebb994..f8d53113 100644
--- a/irodsbackend/api.py
+++ b/irodsbackend/api.py
@@ -582,7 +582,7 @@ def get_colls_recursively(cls, coll):
         return [iRODSCollection(coll.manager, row) for row in query]
 
     def get_objs_recursively(
-        self, irods, coll, md5=False, name_like=None, limit=None
+        self, irods, coll, include_md5=False, name_like=None, limit=None
     ):
         """
         Return objects below a coll recursively. Replacement for the
@@ -591,13 +591,13 @@ def get_objs_recursively(
 
         :param irods: iRODSSession object
         :param coll: Collection object
-        :param md5: if True, return .md5 files, otherwise anything but them
+        :param include_md5: if True, include .md5 files
         :param name_like: Filtering of file names (string or list of strings)
-        :param limit: Limit search to n rows (int)
+        :param limit: Limit retrieval to n rows (int)
         :return: List
         """
         ret = []
-        md5_filter = 'LIKE' if md5 else 'NOT LIKE'
+        md5_filter = '' if include_md5 else 'AND data_name NOT LIKE \'%.md5\''
         path_lookup = []
         q_count = 1
 
@@ -607,8 +607,7 @@ def _do_query(irods, nl=None):
                 'r_data_main.modify_ts as modify_ts, coll_name '
                 'FROM r_data_main JOIN r_coll_main USING (coll_id) '
                 'WHERE (coll_name = \'{coll_path}\' '
-                'OR coll_name LIKE \'{coll_path}/%\') '
-                'AND data_name {md5_filter} \'%.md5\''.format(
+                'OR coll_name LIKE \'{coll_path}/%\') {md5_filter}'.format(
                     coll_path=coll.path, md5_filter=md5_filter
                 )
             )
@@ -621,7 +620,8 @@ def _do_query(irods, nl=None):
                         sql += ' OR '
                     sql += 'data_name LIKE \'%{}%\''.format(n)
                 sql += ')'
-            if not md5 and limit:
+            # TODO: Shouldn't we also allow limit if including .md5 files?
+            if not include_md5 and limit:
                 sql += ' LIMIT {}'.format(limit)
 
             # logger.debug('Object list query = "{}"'.format(sql))
@@ -680,21 +680,21 @@ def get_objects(
         self,
         irods,
         path,
-        check_md5=False,
+        include_md5=False,
         include_colls=False,
         name_like=None,
         limit=None,
     ):
         """
-        Return an iRODS object list.
+        Return a flat iRODS object list recursively under a given path.
 
         :param irods: iRODSSession object
         :param path: Full path to iRODS collection
-        :param check_md5: Whether to add md5 checksum file info (bool)
+        :param include_md5: Include .md5 checksum files (bool)
         :param include_colls: Include collections (bool)
         :param name_like: Filtering of file names (string or list of strings)
         :param limit: Limit search to n rows (int)
-        :return: Dict
+        :return: List
         :raise: FileNotFoundError if collection is not found
         """
         try:
@@ -706,43 +706,21 @@ def get_objects(
             if not isinstance(name_like, list):
                 name_like = [name_like]
             name_like = [n.replace('_', '\_') for n in name_like]  # noqa
-        ret = {'irods_data': []}
-        md5_paths = None
-
-        data_objs = self.get_objs_recursively(
-            irods, coll, name_like=name_like, limit=limit
+        ret = self.get_objs_recursively(
+            irods,
+            coll,
+            include_md5=include_md5,
+            name_like=name_like,
+            limit=limit,
         )
-        if data_objs and check_md5:
-            md5_paths = [
-                o['path']
-                for o in self.get_objs_recursively(
-                    irods, coll, md5=True, name_like=name_like
-                )
-            ]
-
-        for o in data_objs:
-            if check_md5:
-                if o['path'] + '.md5' in md5_paths:
-                    o['md5_file'] = True
-                else:
-                    o['md5_file'] = False
-            ret['irods_data'].append(o)
 
         # Add collections if enabled
-        # TODO: Combine into a single query?
+        # TODO: Combine into a single query? (see issues #1440, #1883)
         if include_colls:
             colls = self.get_colls_recursively(coll)
             for c in colls:
-                ret['irods_data'].append(
-                    {
-                        'name': c.name,
-                        'type': 'coll',
-                        'path': c.path,
-                    }
-                )
-            ret['irods_data'] = sorted(
-                ret['irods_data'], key=lambda x: x['path']
-            )
+                ret.append({'name': c.name, 'type': 'coll', 'path': c.path})
+            ret = sorted(ret, key=lambda x: x['path'])
         return ret
 
     @classmethod
diff --git a/irodsbackend/tests/test_api_taskflow.py b/irodsbackend/tests/test_api_taskflow.py
index 3282796f..4a138f0d 100644
--- a/irodsbackend/tests/test_api_taskflow.py
+++ b/irodsbackend/tests/test_api_taskflow.py
@@ -103,18 +103,17 @@ def test_get_objects(self):
         self.irods.data_objects.create(path + '/' + TEST_FILE_NAME)
         self.irods.data_objects.create(path + '/{}.md5'.format(TEST_FILE_NAME))
         obj_list = self.irods_backend.get_objects(
-            self.irods, path, check_md5=True
+            self.irods, path, include_md5=True
         )
         self.assertIsNotNone(obj_list)
-        self.assertEqual(len(obj_list['irods_data']), 1)  # md5 not listed
+        self.assertEqual(len(obj_list), 2)
 
-        obj = obj_list['irods_data'][0]
+        obj = obj_list[0]
         expected = {
             'name': TEST_FILE_NAME,
             'type': 'obj',
             'path': path + '/' + TEST_FILE_NAME,
             'size': 0,
-            'md5_file': True,
             'modify_time': obj['modify_time'],
         }
         self.assertEqual(obj, expected)
@@ -127,10 +126,10 @@ def test_get_objects_with_colls(self):
         self.irods.data_objects.create(path + '/{}.md5'.format(TEST_FILE_NAME))
         self.irods.collections.create(path + '/subcoll')
         obj_list = self.irods_backend.get_objects(
-            self.irods, path, include_colls=True, check_md5=True
+            self.irods, path, include_md5=True, include_colls=True
         )
         self.assertIsNotNone(obj_list)
-        self.assertEqual(len(obj_list['irods_data']), 2)  # md5 not listed
+        self.assertEqual(len(obj_list), 3)
 
         expected = [
             {
@@ -143,11 +142,17 @@ def test_get_objects_with_colls(self):
                 'type': 'obj',
                 'path': path + '/' + TEST_FILE_NAME,
                 'size': 0,
-                'md5_file': True,
-                'modify_time': obj_list['irods_data'][1]['modify_time'],
+                'modify_time': obj_list[1]['modify_time'],
+            },
+            {
+                'name': TEST_FILE_NAME + '.md5',
+                'type': 'obj',
+                'path': path + '/' + TEST_FILE_NAME + '.md5',
+                'size': 0,
+                'modify_time': obj_list[2]['modify_time'],
             },
         ]
-        self.assertEqual(obj_list['irods_data'], expected)
+        self.assertEqual(obj_list, expected)
 
     def test_get_objects_multi(self):
         """Test get_objects() with multiple search terms"""
@@ -161,30 +166,10 @@ def test_get_objects_multi(self):
             self.irods,
             path,
             name_like=[TEST_FILE_NAME, TEST_FILE_NAME2],
-            check_md5=True,
+            include_md5=True,
         )
         self.assertIsNotNone(obj_list)
-        self.assertEqual(len(obj_list['irods_data']), 2)  # md5 not listed
-
-        expected = [
-            {
-                'name': TEST_FILE_NAME,
-                'type': 'obj',
-                'path': path + '/' + TEST_FILE_NAME,
-                'size': 0,
-                'md5_file': True,
-                'modify_time': obj_list['irods_data'][0]['modify_time'],
-            },
-            {
-                'name': TEST_FILE_NAME2,
-                'type': 'obj',
-                'path': path + '/' + TEST_FILE_NAME2,
-                'size': 0,
-                'md5_file': True,
-                'modify_time': obj_list['irods_data'][1]['modify_time'],
-            },
-        ]
-        self.assertEqual(obj_list['irods_data'], expected)
+        self.assertEqual(len(obj_list), 4)
 
     def test_get_objects_long_query(self):
         """Test get_objects() with a long query"""
@@ -212,30 +197,10 @@ def test_get_objects_long_query(self):
             self.irods,
             path,
             name_like=[TEST_FILE_NAME, TEST_FILE_NAME2],
-            check_md5=True,
+            include_md5=True,
         )
         self.assertIsNotNone(obj_list)
-        self.assertEqual(len(obj_list['irods_data']), 2)  # md5 not listed
-
-        expected = [
-            {
-                'name': TEST_FILE_NAME,
-                'type': 'obj',
-                'path': path + '/' + TEST_FILE_NAME,
-                'size': 0,
-                'md5_file': True,
-                'modify_time': obj_list['irods_data'][0]['modify_time'],
-            },
-            {
-                'name': TEST_FILE_NAME2,
-                'type': 'obj',
-                'path': path + '/' + TEST_FILE_NAME2,
-                'size': 0,
-                'md5_file': True,
-                'modify_time': obj_list['irods_data'][1]['modify_time'],
-            },
-        ]
-        self.assertEqual(obj_list['irods_data'], expected)
+        self.assertEqual(len(obj_list), 4)
 
     def test_get_objects_empty_coll(self):
         """Test get_objects() with an empty sample collection"""
@@ -243,7 +208,7 @@ def test_get_objects_empty_coll(self):
         path = self.irods_backend.get_path(self.project) + '/' + SAMPLE_COLL
         obj_list = self.irods_backend.get_objects(self.irods, path)
         self.assertIsNotNone(obj_list)
-        self.assertEqual(len(obj_list['irods_data']), 0)
+        self.assertEqual(len(obj_list), 0)
 
     def test_get_objects_no_coll(self):
         """Test get_objects() with no created collections"""
@@ -258,10 +223,10 @@ def test_get_objects_limit(self):
         self.irods.data_objects.create(path + '/' + TEST_FILE_NAME)
         self.irods.data_objects.create(path + '/' + TEST_FILE_NAME2)
         obj_list = self.irods_backend.get_objects(
-            self.irods, path, check_md5=False, limit=1
+            self.irods, path, include_md5=False, limit=1
         )
         self.assertIsNotNone(obj_list)
-        self.assertEqual(len(obj_list['irods_data']), 1)  # Limited to 1
+        self.assertEqual(len(obj_list), 1)  # Limited to 1
 
     def test_issue_ticket(self):
         """Test issue_ticket()"""
diff --git a/irodsbackend/views.py b/irodsbackend/views.py
index a6bd5e5c..cc5f877b 100644
--- a/irodsbackend/views.py
+++ b/irodsbackend/views.py
@@ -190,18 +190,31 @@ class IrodsObjectListAjaxView(BaseIrodsAjaxView):
     permission_required = 'irodsbackend.view_files'
 
     def get(self, request, *args, **kwargs):
-        md5 = request.GET.get('md5')
-        colls = request.GET.get('colls')
+        check_md5 = bool(int(request.GET.get('md5')))
+        include_colls = bool(int(request.GET.get('colls')))
         # Get files
         try:
             with self.irods_backend.get_session() as irods:
-                ret_data = self.irods_backend.get_objects(
+                objs = self.irods_backend.get_objects(
                     irods,
                     self.path,
-                    check_md5=bool(int(md5)),
-                    include_colls=bool(int(colls)),
+                    include_md5=check_md5,
+                    include_colls=include_colls,
                 )
-            return Response(ret_data, status=200)
+                ret = []
+                md5_paths = []
+                if check_md5:
+                    md5_paths = [
+                        o['path'] for o in objs if o['path'].endswith('.md5')
+                    ]
+                for o in objs:
+                    if o['type'] == 'coll' and include_colls:
+                        ret.append(o)
+                    elif o['type'] == 'obj' and not o['path'].endswith('.md5'):
+                        if check_md5:
+                            o['md5_file'] = o['path'] + '.md5' in md5_paths
+                        ret.append(o)
+            return Response({'irods_data': ret}, status=200)
         except Exception as ex:
             return Response(self._get_detail(ex), status=500)
 
diff --git a/samplesheets/plugins.py b/samplesheets/plugins.py
index 9d81bf58..d4959049 100644
--- a/samplesheets/plugins.py
+++ b/samplesheets/plugins.py
@@ -360,7 +360,7 @@ def _get_search_files(cls, search_terms, user, irods_backend):
         ret = []
         try:
             with irods_backend.get_session() as irods:
-                obj_data = irods_backend.get_objects(
+                obj_list = irods_backend.get_objects(
                     irods=irods,
                     path=irods_backend.get_projects_path(),
                     name_like=search_terms,
@@ -386,7 +386,7 @@ def _get_search_files(cls, search_terms, user, irods_backend):
             for a in Assay.objects.filter(study__in=studies.values())
         }
 
-        for o in obj_data['irods_data']:
+        for o in obj_list:
             project_uuid = irods_backend.get_uuid_from_path(
                 o['path'], obj_type='project'
             )
diff --git a/samplesheets/studyapps/cancer/utils.py b/samplesheets/studyapps/cancer/utils.py
index af161f84..048d2e96 100644
--- a/samplesheets/studyapps/cancer/utils.py
+++ b/samplesheets/studyapps/cancer/utils.py
@@ -28,7 +28,7 @@ def get_library_file_path(assay, library_name, file_type, irods_backend, irods):
     override = get_igv_omit_override(assay.get_project(), file_type)
     try:
         obj_list = irods_backend.get_objects(irods, query_path)
-        for obj in obj_list['irods_data']:
+        for obj in obj_list:
             if obj['name'].lower().endswith(
                 FILE_TYPE_SUFFIXES[file_type]
             ) and check_igv_file_name(obj['name'], file_type, override):
diff --git a/samplesheets/studyapps/germline/plugins.py b/samplesheets/studyapps/germline/plugins.py
index 0655a3ab..d2684f21 100644
--- a/samplesheets/studyapps/germline/plugins.py
+++ b/samplesheets/studyapps/germline/plugins.py
@@ -310,7 +310,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                 study_objs = irods_backend.get_objects(
                     irods, irods_backend.get_path(study)
                 )
-            obj_len = len(study_objs['irods_data'])
+            obj_len = len(study_objs)
             logger.debug(
                 'Query returned {} data object{}'.format(
                     obj_len, 's' if obj_len != 1 else ''
@@ -349,7 +349,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                 if obj_len > 0 and path not in bam_paths[source_name]:
                     bam_paths[source_name] += [
                         o['path']
-                        for o in study_objs['irods_data']
+                        for o in study_objs
                         if o['path'].startswith(path + '/')
                         and o['name'].lower().endswith('bam')
                         and check_igv_file_name(o['name'], 'bam', bam_override)
@@ -365,7 +365,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                 if obj_len > 0 and path not in vcf_paths[vcf_query_id]:
                     vcf_paths[vcf_query_id] += [
                         o['path']
-                        for o in study_objs['irods_data']
+                        for o in study_objs
                         if o['path'].startswith(path + '/')
                         and o['name'].lower().endswith('vcf.gz')
                         and check_igv_file_name(o['name'], 'vcf', vcf_override)
diff --git a/samplesheets/studyapps/germline/utils.py b/samplesheets/studyapps/germline/utils.py
index b1563fb5..3038488e 100644
--- a/samplesheets/studyapps/germline/utils.py
+++ b/samplesheets/studyapps/germline/utils.py
@@ -81,7 +81,7 @@ def _get_val_by_index(row, idx):
         obj_list = None
     if obj_list:
         for query_path in query_paths:
-            for obj in obj_list['irods_data']:
+            for obj in obj_list:
                 if (
                     obj['path'].startswith(query_path + '/')
                     and obj['name']
diff --git a/samplesheets/views_ajax.py b/samplesheets/views_ajax.py
index 29e806d2..066a553f 100644
--- a/samplesheets/views_ajax.py
+++ b/samplesheets/views_ajax.py
@@ -1942,18 +1942,18 @@ def get(self, request, *args, **kwargs):
         # Get files
         try:
             with irods_backend.get_session() as irods:
-                ret_data = irods_backend.get_objects(irods, self.path)
+                obj_list = irods_backend.get_objects(irods, self.path)
         except Exception as ex:
             return Response({'detail': str(ex)}, status=400)
-        for data_obj in ret_data.get('irods_data', []):
-            obj = IrodsDataRequest.objects.filter(
-                path=data_obj['path'], status__in=['ACTIVE', 'FAILED']
+        for o in obj_list:
+            db_obj = IrodsDataRequest.objects.filter(
+                path=o['path'], status__in=['ACTIVE', 'FAILED']
             ).first()
-            data_obj['irods_request_status'] = obj.status if obj else None
-            data_obj['irods_request_user'] = (
-                str(obj.user.sodar_uuid) if obj else None
+            o['irods_request_status'] = db_obj.status if db_obj else None
+            o['irods_request_user'] = (
+                str(db_obj.user.sodar_uuid) if db_obj else None
             )
-        return Response(ret_data, status=200)
+        return Response({'irods_data': obj_list}, status=200)
 
 
 class SheetVersionCompareAjaxView(SODARBaseProjectAjaxView):
diff --git a/samplesheets/views_api.py b/samplesheets/views_api.py
index 88498c8d..0f7537d2 100644
--- a/samplesheets/views_api.py
+++ b/samplesheets/views_api.py
@@ -838,13 +838,13 @@ def get(self, request, *args, **kwargs):
         path = irods_backend.get_sample_path(project)
         try:
             with irods_backend.get_session() as irods:
-                irods_data = irods_backend.get_objects(irods, path)
+                obj_list = irods_backend.get_objects(irods, path)
         except Exception as ex:
             return Response(
                 {'detail': '{}: {}'.format(IRODS_QUERY_ERROR_MSG, ex)},
                 status=status.HTTP_404_NOT_FOUND,
             )
-        return Response(irods_data, status=status.HTTP_200_OK)
+        return Response({'irods_data': obj_list}, status=status.HTTP_200_OK)
 
 
 # TODO: Temporary HACK, should be replaced by proper API view
diff --git a/taskflowbackend/flows/landing_zone_move.py b/taskflowbackend/flows/landing_zone_move.py
index 217266d5..86ed3d5a 100644
--- a/taskflowbackend/flows/landing_zone_move.py
+++ b/taskflowbackend/flows/landing_zone_move.py
@@ -12,10 +12,6 @@
 from landingzones.models import LandingZone
 
 from taskflowbackend.flows.base_flow import BaseLinearFlow
-from taskflowbackend.irods_utils import (
-    get_subcoll_obj_paths,
-    get_subcoll_paths,
-)
 from taskflowbackend.tasks import irods_tasks
 
 
@@ -37,7 +33,6 @@ def validate(self):
         return super().validate()
 
     def build(self, force_fail=False):
-        # Setup
         validate_only = self.flow_data.get('validate_only', False)
         zone = LandingZone.objects.get(sodar_uuid=self.flow_data['zone_uuid'])
         project_group = self.irods_backend.get_user_group_name(self.project)
@@ -54,39 +49,31 @@ def build(self, force_fail=False):
             ),
         )
 
-        # Get landing zone file paths (without .md5 files) from iRODS
-        zone_coll = self.irods.collections.get(zone_path)
-        zone_objects = get_subcoll_obj_paths(zone_coll)
-        zone_objects_nomd5 = list(
-            set(
-                [
-                    p
-                    for p in zone_objects
-                    if p[p.rfind('.') + 1 :].lower() != 'md5'
-                ]
-            )
-        )
-        zone_objects_md5 = list(
-            set([p for p in zone_objects if p not in zone_objects_nomd5])
+        # Get landing zone data object and collection paths from iRODS
+        zone_all = self.irods_backend.get_objects(
+            self.irods, zone_path, include_md5=True, include_colls=True
         )
+        zone_objects = [o['path'] for o in zone_all if o['type'] == 'obj']
+        zone_objects_nomd5 = [
+            p for p in zone_objects if p[p.rfind('.') + 1 :].lower() != 'md5'
+        ]
+        zone_objects_md5 = [
+            p for p in zone_objects if p not in zone_objects_nomd5
+        ]
         file_count = len(zone_objects_nomd5)
         file_count_msg_plural = 's' if file_count != 1 else ''
 
         # Get all collections with root path
         zone_all_colls = [zone_path]
-        zone_all_colls += get_subcoll_paths(zone_coll)
+        zone_all_colls += [o['path'] for o in zone_all if o['type'] == 'coll']
         # Get list of collections containing files (ignore empty colls)
         zone_object_colls = list(set([p[: p.rfind('/')] for p in zone_objects]))
         # Convert these to collections inside sample collection
-        sample_colls = list(
-            set(
-                [
-                    sample_path + '/' + '/'.join(p.split('/')[10:])
-                    for p in zone_object_colls
-                    if len(p.split('/')) > 10
-                ]
-            )
-        )
+        sample_colls = [
+            sample_path + '/' + '/'.join(p.split('/')[10:])
+            for p in zone_object_colls
+            if len(p.split('/')) > 10
+        ]
 
         # print('sample_path: {}'.format(sample_path))                # DEBUG
         # print('zone_objects: {}'.format(zone_objects))              # DEBUG
diff --git a/taskflowbackend/irods_utils.py b/taskflowbackend/irods_utils.py
index bf26b081..58921af1 100644
--- a/taskflowbackend/irods_utils.py
+++ b/taskflowbackend/irods_utils.py
@@ -1,28 +1,6 @@
 """iRODS utilities for the taskflowbackend app"""
 
 
-def get_subcoll_obj_paths(coll):
-    """
-    Return paths to all files within collection and its subcollections
-    recursively.
-    """
-    ret = []
-    for sub_coll in coll.subcollections:
-        ret += get_subcoll_obj_paths(sub_coll)
-    for data_obj in coll.data_objects:
-        ret.append(data_obj.path)
-    return ret
-
-
-def get_subcoll_paths(coll):
-    """Return paths to all subcollections within collection recursively"""
-    ret = []
-    for sub_coll in coll.subcollections:
-        ret.append(sub_coll.path)
-        ret += get_subcoll_paths(sub_coll)
-    return ret
-
-
 def get_batch_role(project, user_name):
     """
     Return role dict for use with e.g. the role_update_irods_batch flow.
diff --git a/taskflowbackend/tests/base.py b/taskflowbackend/tests/base.py
index 16eee450..e8ca67a0 100644
--- a/taskflowbackend/tests/base.py
+++ b/taskflowbackend/tests/base.py
@@ -236,9 +236,8 @@ def clear_irods_test_data(cls):
                     )
             obj_paths = [
                 o['path']
-                for o in irods_backend.get_objs_recursively(irods, trash_coll)
-                + irods_backend.get_objs_recursively(
-                    irods, trash_coll, md5=True
+                for o in irods_backend.get_objs_recursively(
+                    irods, trash_coll, include_md5=True
                 )
             ]
             for path in obj_paths:

From 239f51cc2d5603ca7898733046b1d281ae251c76 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Tue, 6 Feb 2024 17:36:18 +0100
Subject: [PATCH 11/33] fix IRODS_ROOT_PATH issues (#1888, #1889, #1890, #1891)

---
 CHANGELOG.rst                              |   7 ++
 docs_manual/source/admin_settings.rst      |  10 +-
 docs_manual/source/sodar_release_notes.rst |   1 +
 irodsbackend/api.py                        |  33 +++----
 irodsbackend/tests/test_api.py             |  24 ++++-
 taskflowbackend/flows/landing_zone_move.py |   7 +-
 taskflowbackend/tests/base.py              |  23 +++--
 taskflowbackend/tests/test_flows.py        | 110 +++++++++++++++++++++
 8 files changed, 185 insertions(+), 30 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 2d11c62d..04ac04d1 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -11,6 +11,8 @@ Unreleased
 Added
 -----
 
+- **Irodsbackend**
+    - Sanitize and validate ``IRODS_ROOT_PATH`` in ``get_root_path()`` (#1891)
 - **Landingzones**
     - Create assay plugin shortcut collections for zones (#1869)
 
@@ -23,6 +25,7 @@ Changed
 - **Irodsbackend**
     - Reduce redundant object queries (#1883)
     - Change method logic in ``get_objects()`` and ``get_objs_recursively()`` (#1883)
+    - Use ``get_root_path()`` within ``IrodsAPI`` (#1890)
 - **Samplesheets**
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
@@ -34,6 +37,8 @@ Fixed
 
 - **General**
     - Invalid env var retrieval for ``AUTH_LDAP*_START_TLS`` (#1853)
+- **Irodsbackend**
+    - Invalid path returned by ``get_path()`` if ``IRODS_ROOT_PATH`` is set (#1889)
 - **Landingzones**
     - Stats badge displayed to superusers for ``DELETED`` zones (#1866)
 - **Samplesheets**
@@ -42,6 +47,8 @@ Fixed
     - ``IrodsDataRequest`` user changed on object update (#1864)
     - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
     - Protocol ref editable for new row if disabled in column config (#1875)
+- **Taskflowbackend**
+    - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
 
 Removed
 -------
diff --git a/docs_manual/source/admin_settings.rst b/docs_manual/source/admin_settings.rst
index 5a34af63..ec32895a 100644
--- a/docs_manual/source/admin_settings.rst
+++ b/docs_manual/source/admin_settings.rst
@@ -85,7 +85,8 @@ iRODS Settings
 ``IRODS_ZONE``
     iRODS zone (string).
 ``IRODS_ROOT_PATH``
-    iRODS root path, if something else than ``/{IRODS_ZONE}/`` (string).
+    iRODS root path, without the zone. Used if the SODAR projects collection is
+    not intended to be placed directly under ``IRODS_ZONE`` (string).
 ``IRODS_USER``
     Name of iRODS admin user to be used by backend processes (string).
 ``IRODS_PASS``
@@ -108,6 +109,13 @@ iRODS Settings
     Enable local basic auth endpoint for iRODS if an external LDAP/AD server is
     not used (boolean, default: ``False``).
 
+.. warning::
+
+    Changing path settings such as ``IRODS_ROOT_PATH``, ``IRODS_SAMPLE_COLL``
+    and ``IRODS_LANDING_ZONE_COLL`` is **not** recommended on an existing SODAR
+    installation. In that case, manual moving of existing iRODS collections is
+    required or links to iRODS will not work as expected.
+
 Taskflow Backend Settings
 -------------------------
 
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 38a8b6e4..107adb81 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -15,6 +15,7 @@ Release for minor updates, maintenance and bug fixes.
 
 - Add assay plugin shortcut collection creation in landing zones
 - Fix iRODS data request issues
+- Fix IRODS_ROOT_PATH issues
 - Fix LDAP TLS settings
 - Minor updates and bug fixes
 
diff --git a/irodsbackend/api.py b/irodsbackend/api.py
index f8d53113..0314f319 100644
--- a/irodsbackend/api.py
+++ b/irodsbackend/api.py
@@ -194,7 +194,8 @@ def sanitize_path(cls, path):
         """
         Validate and sanitize iRODS path.
 
-        :param path: iRODS collection or data object path (string)
+        :param path: Full or partial iRODS path to collection or data object
+                     (string)
         :raise: ValueError if iRODS path is invalid or unacceptable
         :return: Sanitized iRODS path (string)
         """
@@ -261,7 +262,6 @@ def get_path(cls, obj):
                     obj_class, ', '.join(ACCEPTED_PATH_TYPES)
                 )
             )
-
         if obj_class == 'Project':
             project = obj
         else:
@@ -270,10 +270,8 @@ def get_path(cls, obj):
             raise ValueError('Project not found for given object')
 
         # Base path (project)
-        rp = settings.IRODS_ROOT_PATH
-        path = '/{zone}/projects/{root_prefix}{uuid_prefix}/{uuid}'.format(
-            root_prefix=rp + '/' if rp else '',
-            zone=settings.IRODS_ZONE,
+        path = '{root_path}/projects/{uuid_prefix}/{uuid}'.format(
+            root_path=cls.get_root_path(),
             uuid_prefix=str(project.sodar_uuid)[:2],
             uuid=project.sodar_uuid,
         )
@@ -341,11 +339,16 @@ def get_zone_path(cls, project):
 
     @classmethod
     def get_root_path(cls):
-        """Return the root path for SODAR data"""
-        root_prefix = (
-            '/' + settings.IRODS_ROOT_PATH if settings.IRODS_ROOT_PATH else ''
-        )
-        return '/{}{}'.format(settings.IRODS_ZONE, root_prefix)
+        """Return the SODAR root path in iRODS"""
+        irods_zone = settings.IRODS_ZONE
+        root_path = ''
+        if settings.IRODS_ROOT_PATH:
+            root_path = cls.sanitize_path(settings.IRODS_ROOT_PATH)
+            if root_path.startswith('/' + irods_zone):
+                raise ValueError(
+                    'iRODS zone must not be included in IRODS_ROOT_PATH'
+                )
+        return '/{}{}'.format(irods_zone, root_path)
 
     @classmethod
     def get_projects_path(cls):
@@ -368,13 +371,9 @@ def get_uuid_from_path(cls, path, obj_type):
         :return: String or None
         :raise: ValueError if obj_type is not accepted
         """
-        root_prefix = (
-            settings.IRODS_ROOT_PATH + '/' if settings.IRODS_ROOT_PATH else ''
-        )
         path_regex = {
-            'project': '/{}/'.format(settings.IRODS_ZONE)
-            + root_prefix
-            + 'projects/[a-zA-Z0-9]{2}/(.+?)(?:/|$)',
+            'project': cls.get_root_path()
+            + '/projects/[a-zA-Z0-9]{2}/(.+?)(?:/|$)',
             'study': '/study_(.+?)(?:/|$)',
             'assay': '/assay_(.+?)(?:/|$)',
         }
diff --git a/irodsbackend/tests/test_api.py b/irodsbackend/tests/test_api.py
index 01db8615..553da917 100644
--- a/irodsbackend/tests/test_api.py
+++ b/irodsbackend/tests/test_api.py
@@ -41,6 +41,7 @@
 ZONE_DESC = 'description'
 IRODS_ZONE = settings.IRODS_ZONE
 IRODS_ROOT_PATH = 'sodar/root'
+IRODS_ROOT_PATH_INVALID = 'sodar/../root'
 SAMPLE_COLL = settings.IRODS_SAMPLE_COLL
 LANDING_ZONE_COLL = settings.IRODS_LANDING_ZONE_COLL
 IRODS_ENV = {
@@ -142,9 +143,9 @@ def test_get_path_project(self):
         self.assertEqual(expected, path)
 
     @override_settings(IRODS_ROOT_PATH=IRODS_ROOT_PATH)
-    def test_get_path_project_root_path(self):
+    def test_get_path_project_root(self):
         """Test get_irods_path() with Project object and root path"""
-        expected = '/{zone}/projects/{root_path}/{uuid_prefix}/{uuid}'.format(
+        expected = '/{zone}/{root_path}/projects/{uuid_prefix}/{uuid}'.format(
             zone=IRODS_ZONE,
             root_path=IRODS_ROOT_PATH,
             uuid_prefix=str(self.project.sodar_uuid)[:2],
@@ -230,6 +231,24 @@ def test_get_root_path_with_path(self):
         expected = '/{}/{}'.format(IRODS_ZONE, IRODS_ROOT_PATH)
         self.assertEqual(self.irods_backend.get_root_path(), expected)
 
+    @override_settings(IRODS_ROOT_PATH=IRODS_ROOT_PATH + '/')
+    def test_get_root_path_trailing_slash(self):
+        """Test get_root_path() with root path setting and trailing slash"""
+        expected = '/{}/{}'.format(IRODS_ZONE, IRODS_ROOT_PATH)
+        self.assertEqual(self.irods_backend.get_root_path(), expected)
+
+    @override_settings(IRODS_ROOT_PATH=IRODS_ROOT_PATH_INVALID)
+    def test_get_root_path_invalid(self):
+        """Test get_root_path() with invalid root path"""
+        with self.assertRaises(ValueError):
+            self.irods_backend.get_root_path()
+
+    @override_settings(IRODS_ROOT_PATH=IRODS_ROOT_PATH_INVALID)
+    def test_get_root_path_with_zone(self):
+        """Test get_root_path() with value containing the zone"""
+        with self.assertRaises(ValueError):
+            self.irods_backend.get_root_path()
+
     def test_get_projects_path(self):
         """Test get_projects_path() with default settings"""
         expected = '/{}/projects'.format(IRODS_ZONE)
@@ -262,7 +281,6 @@ def test_get_uuid_from_path_project(self):
     def test_get_uuid_from_path_wrong_type(self):
         """Test get_uuid_from_path() with invalid type (should fail)"""
         path = self.irods_backend.get_path(self.study)
-
         with self.assertRaises(ValueError):
             self.irods_backend.get_uuid_from_path(path, 'investigation')
 
diff --git a/taskflowbackend/flows/landing_zone_move.py b/taskflowbackend/flows/landing_zone_move.py
index 86ed3d5a..95aa5ee5 100644
--- a/taskflowbackend/flows/landing_zone_move.py
+++ b/taskflowbackend/flows/landing_zone_move.py
@@ -68,11 +68,12 @@ def build(self, force_fail=False):
         zone_all_colls += [o['path'] for o in zone_all if o['type'] == 'coll']
         # Get list of collections containing files (ignore empty colls)
         zone_object_colls = list(set([p[: p.rfind('/')] for p in zone_objects]))
-        # Convert these to collections inside sample collection
+        # Convert paths to collections inside sample collection
+        zone_path_len = len(zone_path.split('/'))
         sample_colls = [
-            sample_path + '/' + '/'.join(p.split('/')[10:])
+            sample_path + '/' + '/'.join(p.split('/')[zone_path_len:])
             for p in zone_object_colls
-            if len(p.split('/')) > 10
+            if len(p.split('/')) > zone_path_len
         ]
 
         # print('sample_path: {}'.format(sample_path))                # DEBUG
diff --git a/taskflowbackend/tests/base.py b/taskflowbackend/tests/base.py
index e8ca67a0..2fa8baee 100644
--- a/taskflowbackend/tests/base.py
+++ b/taskflowbackend/tests/base.py
@@ -192,19 +192,30 @@ def clear_irods_test_data(cls):
                 'TASKFLOW_TEST_MODE not True, cleanup command not allowed'
             )
         irods_backend = get_backend_api('omics_irods')
-        projects_root = irods_backend.get_projects_path()
         permanent_users = getattr(
             settings, 'TASKFLOW_TEST_PERMANENT_USERS', DEFAULT_PERMANENT_USERS
         )
         # TODO: Remove stuff from user home collections
 
         with irods_backend.get_session() as irods:
-            # Remove project folders
+            # Remove SODAR project and root collections
+            rm_kwargs = {'recurse': True, 'force': True}
             try:
-                irods.collections.remove(
-                    projects_root, recurse=True, force=True
-                )
-                logger.debug('Removed projects root: {}'.format(projects_root))
+                if settings.IRODS_ROOT_PATH:
+                    sodar_root = '/{}/{}'.format(
+                        settings.IRODS_ZONE,
+                        settings.IRODS_ROOT_PATH.split('/')[0],
+                    )
+                    irods.collections.remove(sodar_root, **rm_kwargs)
+                    logger.debug(
+                        'Removed root collection: {}'.format(sodar_root)
+                    )
+                else:
+                    projects_root = irods_backend.get_projects_path()
+                    irods.collections.remove(projects_root, **rm_kwargs)
+                    logger.debug(
+                        'Removed projects root: {}'.format(projects_root)
+                    )
             except Exception:
                 pass  # This is OK, the root just wasn't there
                 # Remove created user groups and users
diff --git a/taskflowbackend/tests/test_flows.py b/taskflowbackend/tests/test_flows.py
index 85d57c21..5d8454f4 100644
--- a/taskflowbackend/tests/test_flows.py
+++ b/taskflowbackend/tests/test_flows.py
@@ -80,6 +80,7 @@
 UPDATED_TITLE = 'NewTitle'
 UPDATED_DESC = 'updated description'
 SCRIPT_USER_NAME = 'script_user'
+IRODS_ROOT_PATH = 'sodar/root'
 
 
 class TaskflowbackendFlowTestBase(TaskflowViewTestBase):
@@ -996,6 +997,115 @@ def test_move_restrict(self):
         )
 
 
+@override_settings(IRODS_ROOT_PATH=IRODS_ROOT_PATH)
+class TestLandingZoneMoveAltRootPath(
+    LandingZoneMixin,
+    LandingZoneTaskflowMixin,
+    SampleSheetIOMixin,
+    SampleSheetTaskflowMixin,
+    TaskflowbackendFlowTestBase,
+):
+    """Tests for the landing_zone_move flow with IRODS_ROOT_PATH set"""
+
+    def setUp(self):
+        super().setUp()
+        self.project, self.owner_as = self.make_project_taskflow(
+            'NewProject', PROJECT_TYPE_PROJECT, self.category, self.user
+        )
+        self.group_name = self.irods_backend.get_user_group_name(self.project)
+        self.project_path = self.irods_backend.get_path(self.project)
+        # 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()
+        # Create iRODS collections
+        self.make_irods_colls(self.investigation)
+        # Create zone
+        self.zone = self.make_landing_zone(
+            title=ZONE_TITLE,
+            project=self.project,
+            user=self.user,
+            assay=self.assay,
+            description=ZONE_DESC,
+            status=ZONE_STATUS_CREATING,
+        )
+        self.make_zone_taskflow(self.zone)
+        self.sample_path = self.irods_backend.get_path(self.assay)
+        self.zone_path = self.irods_backend.get_path(self.zone)
+        self.group_name = self.irods_backend.get_user_group_name(self.project)
+
+    def test_move_alt_root_path(self):
+        """Test landing_zone_move with IRODS_ROOT_PATH set"""
+        # Assert alt path have been set correctly and returned for all paths
+        root_path = self.irods_backend.get_root_path()
+        self.assertEqual(
+            root_path, '/{}/{}'.format(settings.IRODS_ZONE, IRODS_ROOT_PATH)
+        )
+        self.assertTrue(self.project_path.startswith(root_path))
+        self.assertTrue(self.sample_path.startswith(root_path))
+        self.assertTrue(self.zone_path.startswith(root_path))
+        self.assertEqual(self.irods.collections.exists(self.project_path), True)
+        self.assertEqual(self.irods.collections.exists(self.sample_path), True)
+        self.assertEqual(self.irods.collections.exists(self.zone_path), True)
+
+        self.assertEqual(self.zone.status, ZONE_STATUS_ACTIVE)
+        empty_coll_path = os.path.join(self.zone_path, COLL_NAME)
+        self.irods.collections.create(empty_coll_path)
+        obj_coll_path = os.path.join(self.zone_path, OBJ_COLL_NAME)
+        obj_coll = self.irods.collections.create(obj_coll_path)
+        obj = self.make_irods_object(obj_coll, OBJ_NAME)
+        self.make_irods_md5_object(obj)
+        obj_path = os.path.join(obj_coll_path, OBJ_NAME)
+        sample_obj_path = os.path.join(
+            self.sample_path, OBJ_COLL_NAME, OBJ_NAME
+        )
+
+        self.assertEqual(self.irods.collections.exists(empty_coll_path), True)
+        self.assertEqual(self.irods.collections.exists(obj_coll_path), True)
+        self.assertEqual(self.irods.data_objects.exists(obj_path), True)
+        self.assertEqual(
+            self.irods.data_objects.exists(obj_path + '.md5'), True
+        )
+        self.assertEqual(self.irods.data_objects.exists(sample_obj_path), False)
+        self.assertEqual(
+            self.irods.data_objects.exists(sample_obj_path + '.md5'),
+            False,
+        )
+
+        flow_data = {'zone_uuid': str(self.zone.sodar_uuid)}
+        flow = self.taskflow.get_flow(
+            irods_backend=self.irods_backend,
+            project=self.project,
+            flow_name='landing_zone_move',
+            flow_data=flow_data,
+        )
+        self._build_and_run(flow)
+
+        self.zone.refresh_from_db()
+        self.assertEqual(self.zone.status, ZONE_STATUS_MOVED)
+        self.assertEqual(self.irods.collections.exists(self.zone_path), False)
+        sample_empty_path = os.path.join(self.sample_path, COLL_NAME)
+        # An empty collection should not be created by moving
+        self.assertEqual(
+            self.irods.collections.exists(sample_empty_path), False
+        )
+        self.assertEqual(self.irods.data_objects.exists(sample_obj_path), True)
+        self.assertEqual(
+            self.irods.data_objects.exists(sample_obj_path + '.md5'),
+            True,
+        )
+        self.assert_irods_access(
+            self.group_name,
+            sample_obj_path,
+            self.irods_access_read,
+        )
+        self.assert_irods_access(
+            self.group_name,
+            sample_obj_path + '.md5',
+            self.irods_access_read,
+        )
+
+
 class TestProjectCreate(TaskflowbackendFlowTestBase):
     """Tests for the project_create flow"""
 

From 4039b0cc98adf31be5ecfacf83bc4d5a95029ffc Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 8 Feb 2024 10:23:33 +0100
Subject: [PATCH 12/33] upgrade to django v3.2.24 (#1854)

---
 CHANGELOG.rst         | 1 +
 requirements/base.txt | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 04ac04d1..5b7f6e8e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -20,6 +20,7 @@ Changed
 -------
 
 - **General**
+    - Upgrade to Django v3.2.24 (#1854)
     - Upgrade critical Vue app dependencies (#1854)
     - Update installation documentation (#1871)
 - **Irodsbackend**
diff --git a/requirements/base.txt b/requirements/base.txt
index e5b08299..04fe2731 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -6,7 +6,7 @@ wheel==0.40.0
 setuptools==67.6.0
 
 # Django
-django==3.2.23
+django==3.2.24
 
 # Configuration
 django-environ==0.10.0

From e418362345533bafba7af6a9c5399804ee8bbc54 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 9 Feb 2024 09:12:31 +0100
Subject: [PATCH 13/33] update zone failed status handling in run_flow()
 (#1458)

---
 CHANGELOG.rst          |  1 +
 taskflowbackend/api.py | 17 +++++++++++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5b7f6e8e..7cdbb812 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -32,6 +32,7 @@ Changed
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
 - **Taskflowbackend**
     - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
+    - Set zone status on uncaught errors in ``run_flow()`` (#1458)
 
 Fixed
 -----
diff --git a/taskflowbackend/api.py b/taskflowbackend/api.py
index 6585cf2c..708ff52a 100644
--- a/taskflowbackend/api.py
+++ b/taskflowbackend/api.py
@@ -125,7 +125,7 @@ def run_flow(
         ex_msg = None
         coordinator = None
         lock = None
-        # Get zone if present in flow
+        # Get landing zone if present in flow
         zone = None
         if flow.flow_data.get('zone_uuid'):
             zone = LandingZone.objects.filter(
@@ -185,9 +185,18 @@ def run_flow(
 
         # Raise exception if failed, otherwise return result
         if ex_msg:
-            logger.error(ex_msg)  # TODO: Isn't this redundant?
-            # NOTE: Not providing zone here since it's handled by flow
-            cls._raise_flow_exception(ex_msg, tl_event, None)
+            logger.error(ex_msg)
+            # Provide landing zone if error occurs but status has not been set
+            # (This means a failure has not been properly handled in the flow)
+            ex_zone = None
+            if zone:
+                zone.refresh_from_db()
+                if zone.status not in [
+                    ZONE_STATUS_NOT_CREATED,
+                    ZONE_STATUS_FAILED,
+                ]:
+                    ex_zone = zone
+            cls._raise_flow_exception(ex_msg, tl_event, ex_zone)
         return flow_result
 
     def submit(

From a3100ca7bee226d59c7ee3877534fc804647c1a0 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 9 Feb 2024 11:01:16 +0100
Subject: [PATCH 14/33] fix sheet template creation with slash in id/title
 field (#1896)

---
 CHANGELOG.rst                    |  1 +
 requirements/base.txt            |  4 ++--
 samplesheets/tests/test_views.py | 29 +++++++++++++++++++++++++++++
 3 files changed, 32 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 7cdbb812..c2560999 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -49,6 +49,7 @@ Fixed
     - ``IrodsDataRequest`` user changed on object update (#1864)
     - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
     - Protocol ref editable for new row if disabled in column config (#1875)
+    - Sheet template creation failure with slash characters in title/ID fields (#1896)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
 
diff --git a/requirements/base.txt b/requirements/base.txt
index 04fe2731..5bca5041 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -102,8 +102,8 @@ pronto==2.5.0  # For OWL conversion
 
 # CUBI ISA-Tab templates
 cookiecutter==2.2.3
-cubi-isa-templates==0.1.1
-# -e git+https://github.com/bihealth/cubi-isa-templates.git@c4139e147fd5db10bd6478460edbbce157abe425#egg=cubi-isa-templates
+# cubi-isa-templates==0.1.1
+-e git+https://github.com/bihealth/cubi-isa-templates.git@d3ebe866f3823d81fdb358042ef7ed4d8b8fd100#egg=cubi-isa-templates
 
 # Taskflow requirements
 tooz==3.0.0
diff --git a/samplesheets/tests/test_views.py b/samplesheets/tests/test_views.py
index e463edeb..65fec757 100644
--- a/samplesheets/tests/test_views.py
+++ b/samplesheets/tests/test_views.py
@@ -120,6 +120,11 @@
 EDIT_NEW_VALUE_STR = 'edited value'
 DUMMY_UUID = 'aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa'
 IRODS_FILE_PATH = '/sodarZone/path/test1.txt'
+TPL_FILE_NAME_FIELDS = [
+    'investigation_title',
+    'investigation_id',
+    'study_title',
+]
 with open(CONFIG_PATH_DEFAULT) as fp:
     CONFIG_DATA_DEFAULT = json.load(fp)
 
@@ -796,6 +801,30 @@ def test_post_batch(self):
             )
             self.project.investigations.first().delete()
 
+    def test_post_batch_file_name_slash(self):
+        """Test POST with slashes in values used for file names"""
+        for t in ISA_TEMPLATES:
+            self.assertIsNone(self.project.investigations.first())
+            post_data = self._get_post_data(t)
+            for k in TPL_FILE_NAME_FIELDS:
+                if k in post_data:
+                    post_data[k] += '/test'
+            with self.login(self.user):
+                response = self.client.post(
+                    reverse(
+                        'samplesheets:template_create',
+                        kwargs={'project': self.project.sodar_uuid},
+                    )
+                    + '?sheet_tpl='
+                    + t.name,
+                    data=post_data,
+                )
+            self.assertEqual(response.status_code, 302, msg=t.name)
+            self.assertIsNotNone(
+                self.project.investigations.first(), msg=t.name
+            )
+            self.project.investigations.first().delete()
+
     def test_post_multiple(self):
         """Test multiple requests to add multiple sample sheets (should fail)"""
         tpl = ISA_TEMPLATES[0]

From a0752e2bb60cb4c16dc1b4338926341cdf19f860 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 12 Feb 2024 17:35:54 +0100
Subject: [PATCH 15/33] upgrade to django-sodar-core v0.13.4-wip (#1899)

---
 CHANGELOG.rst                              | 1 +
 docs_manual/source/sodar_release_notes.rst | 1 +
 requirements/base.txt                      | 4 ++--
 requirements/ldap.txt                      | 4 ++--
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c2560999..129dcf48 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -21,6 +21,7 @@ Changed
 
 - **General**
     - Upgrade to Django v3.2.24 (#1854)
+    - Upgrade to django-sodar-core v0.13.4-WIP (#1899)
     - Upgrade critical Vue app dependencies (#1854)
     - Update installation documentation (#1871)
 - **Irodsbackend**
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 107adb81..939f6137 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -18,6 +18,7 @@ Release for minor updates, maintenance and bug fixes.
 - Fix IRODS_ROOT_PATH issues
 - Fix LDAP TLS settings
 - Minor updates and bug fixes
+- Upgrade to SODAR Core v0.13.4
 
 
 v0.14.1 (2023-12-12)
diff --git a/requirements/base.txt b/requirements/base.txt
index 5bca5041..68bffe44 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -70,8 +70,8 @@ mistune==2.0.5
 django-autocomplete-light==3.9.4
 
 # SODAR Core
-django-sodar-core==0.13.3
-# -e git+https://github.com/bihealth/sodar-core.git@11b666cd03c555d0b95c3de547fe312f93263f29#egg=django-sodar-core
+# django-sodar-core==0.13.3
+-e git+https://github.com/bihealth/sodar-core.git@1117ff87723389be928538b965fe89576687c1a6#egg=django-sodar-core
 
 # Celery
 celery==5.2.7
diff --git a/requirements/ldap.txt b/requirements/ldap.txt
index 5cbb00d9..8960c63d 100644
--- a/requirements/ldap.txt
+++ b/requirements/ldap.txt
@@ -1,5 +1,5 @@
 # Optional LDAP dependencies go here
 -r base.txt
 
-django-auth-ldap==4.1.0
-python-ldap==3.4.3
+django-auth-ldap>=4.6.0, <4.7
+python-ldap>=3.4.4, <3.5

From 465bd5a933e1a3ce4f11f3682a357f8548263225 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 12 Feb 2024 18:01:10 +0100
Subject: [PATCH 16/33] update TASKFLOW_IRODS_CONN_TIMEOUT default value
 (#1900)

---
 CHANGELOG.rst           | 1 +
 config/settings/base.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 129dcf48..61cfb8cf 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -34,6 +34,7 @@ Changed
 - **Taskflowbackend**
     - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
     - Set zone status on uncaught errors in ``run_flow()`` (#1458)
+    - Change ``TASKFLOW_IRODS_CONN_TIMEOUT`` default value to ``960`` (#1900)
 
 Fixed
 -----
diff --git a/config/settings/base.py b/config/settings/base.py
index 0c7bc439..d9df4e87 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -739,7 +739,7 @@ def set_logging(level=None):
 
 # Taskflow backend settings
 # Connection timeout for taskflowbackend flows (other sessions not affected)
-TASKFLOW_IRODS_CONN_TIMEOUT = env.int('TASKFLOW_IRODS_CONN_TIMEOUT', 480)
+TASKFLOW_IRODS_CONN_TIMEOUT = env.int('TASKFLOW_IRODS_CONN_TIMEOUT', 960)
 TASKFLOW_LOCK_RETRY_COUNT = env.int('TASKFLOW_LOCK_RETRY_COUNT', 2)
 TASKFLOW_LOCK_RETRY_INTERVAL = env.int('TASKFLOW_LOCK_RETRY_INTERVAL', 3)
 TASKFLOW_LOCK_ENABLED = True

From e722fd7b76d69d2f5a894080bad483db378574cf Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Tue, 13 Feb 2024 11:29:40 +0100
Subject: [PATCH 17/33] add taskflowbackend settings in siteinfo (#1901)

---
 CHANGELOG.rst              |  2 ++
 taskflowbackend/plugins.py | 10 +++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 61cfb8cf..9016c77f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -15,6 +15,8 @@ Added
     - Sanitize and validate ``IRODS_ROOT_PATH`` in ``get_root_path()`` (#1891)
 - **Landingzones**
     - Create assay plugin shortcut collections for zones (#1869)
+- **Taskflowbackend**
+    - Django settings in siteinfo (#1901)
 
 Changed
 -------
diff --git a/taskflowbackend/plugins.py b/taskflowbackend/plugins.py
index ebf7e671..db0e69f5 100644
--- a/taskflowbackend/plugins.py
+++ b/taskflowbackend/plugins.py
@@ -34,9 +34,14 @@
 
 # Local constants
 APP_NAME = 'taskflowbackend'
-TL_SUBMIT_DESC = 'Job submitted to Taskflow'
 IRODS_CAT_SKIP_MSG = 'Categories are not synchronized into iRODS'
 RANK_FINDER = ROLE_RANKING[PROJECT_ROLE_FINDER]
+TASKFLOW_INFO_SETTINGS = [
+    'TASKFLOW_IRODS_CONN_TIMEOUT',
+    'TASKFLOW_LOCK_RETRY_COUNT',
+    'TASKFLOW_LOCK_RETRY_INTERVAL',
+]
+TL_SUBMIT_DESC = 'Job submitted to Taskflow'
 
 
 class BackendPlugin(ProjectModifyPluginMixin, BackendPluginPoint):
@@ -54,6 +59,9 @@ class BackendPlugin(ProjectModifyPluginMixin, BackendPluginPoint):
     #: Description string
     description = 'SODAR Taskflow backend for iRODS data transactions'
 
+    #: Names of plugin specific Django settings to display in siteinfo
+    info_settings = TASKFLOW_INFO_SETTINGS
+
     # Internal helpers ---------------------------------------------------------
 
     @classmethod

From 9358c8f250c1ff416ec4bd97752190348d7c2648 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Tue, 13 Feb 2024 13:47:51 +0100
Subject: [PATCH 18/33] add landingzones siteinfo statistics (#1898)

---
 CHANGELOG.rst                              |   1 +
 docs_manual/source/sodar_release_notes.rst |   1 +
 landingzones/plugins.py                    |  39 ++++++
 landingzones/tests/test_plugins.py         | 138 +++++++++++++++++++++
 4 files changed, 179 insertions(+)
 create mode 100644 landingzones/tests/test_plugins.py

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 9016c77f..a882fd49 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -15,6 +15,7 @@ Added
     - Sanitize and validate ``IRODS_ROOT_PATH`` in ``get_root_path()`` (#1891)
 - **Landingzones**
     - Create assay plugin shortcut collections for zones (#1869)
+    - Zone statistics for siteinfo (#1898)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
 
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 939f6137..4ea73d0e 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -14,6 +14,7 @@ v0.14.2 (WIP)
 Release for minor updates, maintenance and bug fixes.
 
 - Add assay plugin shortcut collection creation in landing zones
+- Add landing zone statistics in siteinfo
 - Fix iRODS data request issues
 - Fix IRODS_ROOT_PATH issues
 - Fix LDAP TLS settings
diff --git a/landingzones/plugins.py b/landingzones/plugins.py
index ce8a09e8..9a5d78be 100644
--- a/landingzones/plugins.py
+++ b/landingzones/plugins.py
@@ -19,6 +19,8 @@
 
 from landingzones.constants import (
     STATUS_ALLOW_UPDATE,
+    STATUS_BUSY,
+    STATUS_FINISHED,
     ZONE_STATUS_MOVED,
     ZONE_STATUS_DELETED,
 )
@@ -148,6 +150,43 @@ def get_object_link(self, model_str, uuid):
                 'label': obj.get_display_name(),
             }
 
+    def get_statistics(self):
+        """
+        Return app statistics as a dict. Should take the form of
+        {id: {label, value, url (optional), description (optional)}}.
+
+        :return: Dict
+        """
+        return {
+            'zones_total': {
+                'label': 'Total zones',
+                'value': LandingZone.objects.count(),
+            },
+            'zones_active': {
+                'label': 'Active zones',
+                'value': LandingZone.objects.filter(
+                    status__in=STATUS_ALLOW_UPDATE
+                ).count(),
+                'description': 'Landing zones available for use (active or '
+                'failed)',
+            },
+            'zones_finished': {
+                'label': 'Finished zones',
+                'value': LandingZone.objects.filter(
+                    status__in=STATUS_FINISHED
+                ).count(),
+                'description': 'Landing zones finished successfully, deleted '
+                'or not created',
+            },
+            'zones_busy': {
+                'label': 'Busy zones',
+                'value': LandingZone.objects.filter(
+                    status__in=STATUS_BUSY
+                ).count(),
+                'description': 'Landing zones with an ongoing transaction',
+            },
+        }
+
     def get_project_list_value(self, column_id, project, user):
         """
         Return a value for the optional additional project list column specific
diff --git a/landingzones/tests/test_plugins.py b/landingzones/tests/test_plugins.py
new file mode 100644
index 00000000..2af97f2a
--- /dev/null
+++ b/landingzones/tests/test_plugins.py
@@ -0,0 +1,138 @@
+"""Tests for plugins in the landingzones app"""
+
+from test_plus.test import TestCase
+
+# Projectroles dependency
+from projectroles.models import SODAR_CONSTANTS
+from projectroles.plugins import ProjectAppPluginPoint
+from projectroles.tests.test_models import (
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
+)
+
+# Samplesheets dependency
+from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
+
+import landingzones.constants as lc
+from landingzones.tests.test_models import LandingZoneMixin
+
+
+# Local constants
+SHEET_PATH_SMALL2 = SHEET_DIR + 'i_small2.zip'
+
+
+class LandingzonesPluginTestBase(
+    ProjectMixin,
+    RoleMixin,
+    RoleAssignmentMixin,
+    SampleSheetIOMixin,
+    LandingZoneMixin,
+    TestCase,
+):
+    """Base class for landingzones plugin tests"""
+
+    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
+        )
+        # Import investigation
+        self.investigation = self.import_isa_from_file(
+            SHEET_PATH_SMALL2, self.project
+        )
+        self.investigation.irods_status = True
+        self.investigation.save()
+        self.study = self.investigation.studies.first()
+        self.assay = self.study.assays.first()
+        # Get plugin
+        self.plugin = ProjectAppPluginPoint.get_plugin('landingzones')
+
+
+class TestGetStatistics(LandingzonesPluginTestBase):
+    """Tests for get_statistics()"""
+
+    def _make_zone(self, status):
+        self.make_landing_zone(
+            'zone_{}'.format(status.lower()),
+            self.project,
+            self.user_owner,
+            self.assay,
+            status=status,
+        )
+
+    def _assert_stats(self, expected):
+        stats = self.plugin.get_statistics()
+        for k, v in expected.items():
+            self.assertEqual(stats[k]['value'], v)
+
+    def test_get_statistics_active(self):
+        """Test get_statistics() with active zones"""
+        self._make_zone(lc.ZONE_STATUS_ACTIVE)
+        self._make_zone(lc.ZONE_STATUS_FAILED)
+        self._assert_stats(
+            {
+                'zones_total': 2,
+                'zones_active': 2,
+                'zones_finished': 0,
+                'zones_busy': 0,
+            }
+        )
+
+    def test_get_statistics_finished(self):
+        """Test get_statistics() with finished zones"""
+        self._make_zone(lc.ZONE_STATUS_MOVED)
+        self._make_zone(lc.ZONE_STATUS_DELETED)
+        self._assert_stats(
+            {
+                'zones_total': 2,
+                'zones_active': 0,
+                'zones_finished': 2,
+                'zones_busy': 0,
+            }
+        )
+
+    def test_get_statistics_busy(self):
+        """Test get_statistics() with busy zones"""
+        self._make_zone(lc.ZONE_STATUS_MOVING)
+        self._make_zone(lc.ZONE_STATUS_DELETING)
+        self._assert_stats(
+            {
+                'zones_total': 2,
+                'zones_active': 0,
+                'zones_finished': 0,
+                'zones_busy': 2,
+            }
+        )
+
+    def test_get_statistics_mixed(self):
+        """Test get_statistics() with mixed zone statuses"""
+        self._make_zone(lc.ZONE_STATUS_ACTIVE)
+        self._make_zone(lc.ZONE_STATUS_MOVING)
+        self._make_zone(lc.ZONE_STATUS_DELETED)
+        self._assert_stats(
+            {
+                'zones_total': 3,
+                'zones_active': 1,
+                'zones_finished': 1,
+                'zones_busy': 1,
+            }
+        )
+
+    def test_get_statistics_no_zones(self):
+        """Test get_statistics() with no zones"""
+        self._assert_stats(
+            {
+                'zones_total': 0,
+                'zones_active': 0,
+                'zones_finished': 0,
+                'zones_busy': 0,
+            }
+        )

From 1deac6a0990a03a82aec65eaa8f37ef89512fd77 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Wed, 14 Feb 2024 15:02:25 +0100
Subject: [PATCH 19/33] fix and refactor irods stats retrieval (#1327, #1886,
 #1903)

---
 CHANGELOG.rst                                 |   2 +
 docs_manual/source/sodar_release_notes.rst    |   1 +
 .../static/irodsbackend/js/irodsbackend.js    |  54 +--
 .../templatetags/irodsbackend_tags.py         |  13 +-
 irodsbackend/tests/test_views.py              | 414 +-----------------
 irodsbackend/tests/test_views_taskflow.py     | 386 ++++++++++++++++
 irodsbackend/views.py                         |  47 +-
 7 files changed, 435 insertions(+), 482 deletions(-)
 create mode 100644 irodsbackend/tests/test_views_taskflow.py

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a882fd49..69052a98 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -31,6 +31,7 @@ Changed
     - Reduce redundant object queries (#1883)
     - Change method logic in ``get_objects()`` and ``get_objs_recursively()`` (#1883)
     - Use ``get_root_path()`` within ``IrodsAPI`` (#1890)
+    - Refactor ``IrodsStatisticsAjaxView`` and related JQuery (#1903)
 - **Samplesheets**
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
@@ -46,6 +47,7 @@ Fixed
     - Invalid env var retrieval for ``AUTH_LDAP*_START_TLS`` (#1853)
 - **Irodsbackend**
     - Invalid path returned by ``get_path()`` if ``IRODS_ROOT_PATH`` is set (#1889)
+    - Stats badge stuck in updating with non-200 POST status (#1327, #1886)
 - **Landingzones**
     - Stats badge displayed to superusers for ``DELETED`` zones (#1866)
 - **Samplesheets**
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 4ea73d0e..38a1e751 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -18,6 +18,7 @@ Release for minor updates, maintenance and bug fixes.
 - Fix iRODS data request issues
 - Fix IRODS_ROOT_PATH issues
 - Fix LDAP TLS settings
+- Fix iRODS stats badge stuck in "updating"
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.4
 
diff --git a/irodsbackend/static/irodsbackend/js/irodsbackend.js b/irodsbackend/static/irodsbackend/js/irodsbackend.js
index 7a287f7c..f4f9deaa 100644
--- a/irodsbackend/static/irodsbackend/js/irodsbackend.js
+++ b/irodsbackend/static/irodsbackend/js/irodsbackend.js
@@ -2,54 +2,48 @@
  Collection statistics updating function
  ***************************************/
 var updateCollectionStats = function() {
-    var statsPaths = [];
-    var projectUUID = null;
+    var paths = {};
 
     $('span.sodar-irods-stats').each(function () {
-        var currentPath = decodeURIComponent($(this).attr(
-            'data-stats-url').split('=')[1]);
-        if (!projectUUID) {
-            projectUUID = currentPath.split('/')[4];
+        var projectUUID = $(this).attr('data-project-uuid');
+        if (!paths.hasOwnProperty(projectUUID)) {
+            paths[projectUUID] = [];
         }
-        if (!(statsPaths.includes(currentPath))){
-            statsPaths.push(currentPath);
+        var currentPath = $(this).attr('data-stats-path');
+        if (!(paths[projectUUID].includes(currentPath))) {
+            paths[projectUUID].push(currentPath);
         }
     });
 
-    var d = {paths: statsPaths};
-
-    if (projectUUID) {
+    $.each(paths, function(projectUUID, paths) {
         $.ajax({
             url: '/irodsbackend/ajax/stats/' + projectUUID,
             method: 'POST',
             dataType: 'json',
-            data: d,
+            data: {paths: paths},
             contentType: "application/x-www-form-urlencoded; charset=UTF-8",
             traditional: true
         }).done(function (data) {
             $('span.sodar-irods-stats').each(function () {
                 var statsSpan = $(this);
-                var irodsPath = decodeURIComponent(statsSpan.attr(
-                    'data-stats-url')).split('=')[1];
-                var fileSuffix = 's';
-                for (idx in data['coll_objects']) {
-                    if (data['coll_objects'].hasOwnProperty(idx)) {
-                        if (irodsPath === data['coll_objects'][idx]['path']
-                                && data['coll_objects'][idx]['status'] === '200') {
-                            var stats = data['coll_objects'][idx]['stats'];
-                            if (stats['file_count'] === 1) {
-                                fileSuffix = '';
-                            }
-                            statsSpan.text(
-                                stats['file_count'] + ' file' + fileSuffix +
-                                ' ('+ humanFileSize(stats['total_size'], true) + ')');
-                            break;
-                        }
-                    }
+                var path = statsSpan.attr('data-stats-path');
+                var s = 's';
+                if (path in data['irods_stats']) {
+                    var status = data['irods_stats'][path]['status'];
+                    if (status === 200) {
+                        var fileCount = data['irods_stats'][path]['file_count'];
+                        var totalSize = data['irods_stats'][path]['total_size'];
+                        if (fileCount === 1) s = '';
+                        statsSpan.text(
+                            fileCount + ' file' + s +
+                            ' (' + humanFileSize(totalSize, true) + ')');
+                    } else if (status === 404) statsSpan.text('Not found');
+                    else if (status === 403) statsSpan.text('Denied');
+                    else statsSpan.text('Error');
                 }
             });
         });
-    }
+    });
 };
 
 /***************************************
diff --git a/irodsbackend/templatetags/irodsbackend_tags.py b/irodsbackend/templatetags/irodsbackend_tags.py
index 81ce7836..ba95f84f 100644
--- a/irodsbackend/templatetags/irodsbackend_tags.py
+++ b/irodsbackend/templatetags/irodsbackend_tags.py
@@ -1,6 +1,4 @@
 from django import template
-from django.urls import reverse
-from django.utils.http import urlencode
 
 from irodsbackend.api import IrodsAPI
 
@@ -26,18 +24,11 @@ def get_stats_html(irods_path, project):
     :param project: Project object
     :return: String (contains HTML)
     """
-    url_kwargs = {'project': str(project.sodar_uuid)}
-    query_string = {'path': irods_path}
-    url = (
-        reverse('irodsbackend:stats', kwargs=url_kwargs)
-        + '?'
-        + urlencode(query_string)
-    )
     return (
         '<span class="badge badge-pill badge-info sodar-irods-stats" '
-        'data-stats-url="{}">'
+        'data-stats-path="{}" data-project-uuid="{}">'
         '<i class="iconify spin" data-icon="mdi:loading"></i> Updating..'
-        '</span>'.format(url)
+        '</span>'.format(irods_path, project.sodar_uuid)
     )
 
 
diff --git a/irodsbackend/tests/test_views.py b/irodsbackend/tests/test_views.py
index 94576260..175e295e 100644
--- a/irodsbackend/tests/test_views.py
+++ b/irodsbackend/tests/test_views.py
@@ -1,430 +1,18 @@
 """Tests for views in the irodsbackend app"""
 
 import base64
-import os
 
-from irods.test.helpers import make_object
-
-from django.conf import settings
-from django.test import RequestFactory, override_settings
+from django.test import override_settings
 from django.urls import reverse
 
 from test_plus.test import TestCase
 
-# Projectroles dependency
-from projectroles.models import SODAR_CONSTANTS
-
-# Taskflowbackend dependency
-from taskflowbackend.tests.base import TaskflowViewTestBase
-
-
-# SODAR constants
-PROJECT_ROLE_OWNER = SODAR_CONSTANTS['PROJECT_ROLE_OWNER']
-PROJECT_ROLE_DELEGATE = SODAR_CONSTANTS['PROJECT_ROLE_DELEGATE']
-PROJECT_ROLE_CONTRIBUTOR = SODAR_CONSTANTS['PROJECT_ROLE_CONTRIBUTOR']
-PROJECT_ROLE_GUEST = SODAR_CONSTANTS['PROJECT_ROLE_GUEST']
-PROJECT_TYPE_CATEGORY = SODAR_CONSTANTS['PROJECT_TYPE_CATEGORY']
-PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
 
 # Local constants
-IRODS_TEMP_COLL = 'temp'
-IRODS_OBJ_SIZE = 1024
-IRODS_OBJ_CONTENT = ''.join('x' for _ in range(IRODS_OBJ_SIZE))
-IRODS_OBJ_NAME = 'test1.txt'
-IRODS_MD5_NAME = 'test1.txt.md5'
-IRODS_NON_PROJECT_PATH = (
-    '/' + settings.IRODS_ZONE + '/home/' + settings.IRODS_USER
-)
-IRODS_FAIL_COLL = 'xeiJ1Vie'
 LOCAL_USER_NAME = 'local_user'
 LOCAL_USER_PASS = 'password'
 
 
-class IrodsbackendViewTestBase(TaskflowViewTestBase):
-    """Base class for irodsbackend UI view testing"""
-
-    def setUp(self):
-        super().setUp()
-        self.req_factory = RequestFactory()
-        # Init project with owner in taskflow
-        self.project, self.owner_as = self.make_project_taskflow(
-            'TestProject', PROJECT_TYPE_PROJECT, self.category, self.user
-        )
-        # Create test collection in iRODS
-        self.project_path = self.irods_backend.get_path(self.project)
-        self.irods_path = os.path.join(self.project_path, IRODS_TEMP_COLL)
-        self.irods_coll = self.irods.collections.create(self.irods_path)
-
-
-class TestIrodsStatisticsAjaxView(IrodsbackendViewTestBase):
-    """Tests for the landing zone collection statistics Ajax view"""
-
-    def setUp(self):
-        super().setUp()
-        self.post_url = self.irods_backend.get_url(
-            view='stats', project=self.project, method='POST'
-        )
-
-    def test_get_empty_coll(self):
-        """Test GET request for stats on empty iRODS collection"""
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats', project=self.project, path=self.irods_path
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(response.data['file_count'], 0)
-        self.assertEqual(response.data['total_size'], 0)
-
-    def test_get_invalid_coll(self):
-        """Test GET request with invalid collection (should fail)"""
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats', project=self.project, path=self.irods_path
-                )
-                + '%2F..'
-            )
-        self.assertEqual(response.status_code, 400)
-
-    def test_get_coll_obj(self):
-        """Test GET for stats on collection with data object"""
-        # Put data object in iRODS
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats', project=self.project, path=self.irods_path
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(response.data['file_count'], 1)
-        self.assertEqual(response.data['total_size'], IRODS_OBJ_SIZE)
-
-    def test_get_coll_md5(self):
-        """Test GET for stats on collection with data object and md5"""
-        # Put data object in iRODS
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-        # Put MD5 data object in iRODS
-        md5_path = self.irods_path + '/' + IRODS_MD5_NAME
-        make_object(self.irods, md5_path, IRODS_OBJ_CONTENT)  # Not actual md5
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats', project=self.project, path=self.irods_path
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(response.data['file_count'], 1)  # md5 not counted
-        self.assertEqual(response.data['total_size'], IRODS_OBJ_SIZE)
-
-    def test_get_coll_not_found(self):
-        """Test GET for stats on non-existing collection"""
-        fail_path = self.irods_path + '/' + IRODS_FAIL_COLL
-        self.assertEqual(self.irods.collections.exists(fail_path), False)
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats', project=self.project, path=fail_path
-                )
-            )
-        self.assertEqual(response.status_code, 404)
-
-    def test_get_coll_not_in_project(self):
-        """Test GET for stats on collection not belonging to project"""
-        self.assertEqual(
-            self.irods.collections.exists(IRODS_NON_PROJECT_PATH), True
-        )
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats',
-                    project=self.project,
-                    path=IRODS_NON_PROJECT_PATH,
-                )
-            )
-        self.assertEqual(response.status_code, 400)
-
-    def test_get_no_access(self):
-        """Test GET for stats with no access for iRODS collection"""
-        new_user = self.make_user('new_user')
-        self.make_assignment(
-            self.project, new_user, self.role_contributor
-        )  # No taskflow
-        with self.login(new_user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='stats', project=self.project, path=self.irods_path
-                )
-            )
-        self.assertEqual(response.status_code, 403)
-
-    def test_post_empty_coll_stats(self):
-        """Test POST for batch stats on empty iRODS collections"""
-        post_data = {
-            'paths': [self.irods_path, self.irods_path],
-            'md5': ['0', '0'],
-        }
-        with self.login(self.user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(
-                response.data['coll_objects'][idx]['status'], '200'
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['file_count'], 0
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['total_size'], 0
-            )
-
-    def test_post_coll_stats(self):
-        """Test POST for batch stats on collections with data object"""
-        # Put data object in iRODS
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-        post_data = {
-            'paths': [self.irods_path, self.irods_path],
-            'md5': ['0', '0'],
-        }
-        with self.login(self.user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(
-                response.data['coll_objects'][idx]['status'], '200'
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['file_count'], 1
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['total_size'],
-                IRODS_OBJ_SIZE,
-            )
-
-    def test_post_coll_md5_stats(self):
-        """Test POST for batch stats on collections with data object and md5"""
-        # Put data object in iRODS
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-        # Put MD5 data object in iRODS
-        md5_path = self.irods_path + '/' + IRODS_MD5_NAME
-        make_object(self.irods, md5_path, IRODS_OBJ_CONTENT)  # Not actual md5
-        post_data = {
-            'paths': [self.irods_path, self.irods_path],
-            'md5': ['1', '1'],
-        }
-        with self.login(self.user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(
-                response.data['coll_objects'][idx]['status'], '200'
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['file_count'], 1
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['total_size'],
-                IRODS_OBJ_SIZE,
-            )
-
-    def test_post_coll_not_found(self):
-        """Test POST for stats on non-existing collections"""
-        fail_path = self.irods_path + '/' + IRODS_FAIL_COLL
-        self.assertEqual(self.irods.collections.exists(fail_path), False)
-        post_data = {'paths': [fail_path, fail_path], 'md5': ['0', '0']}
-        with self.login(self.user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(
-                response.data['coll_objects'][idx]['status'], '404'
-            )
-            self.assertEqual(response.data['coll_objects'][idx]['stats'], {})
-
-    def test_post_coll_not_in_project(self):
-        """Test POST for stats on collections not belonging to project"""
-        self.assertEqual(
-            self.irods.collections.exists(IRODS_NON_PROJECT_PATH), True
-        )
-        post_data = {
-            'paths': [IRODS_NON_PROJECT_PATH, IRODS_NON_PROJECT_PATH],
-            'md5': ['0', '0'],
-        }
-        with self.login(self.user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(
-                response.data['coll_objects'][idx]['status'], '400'
-            )
-            self.assertEqual(response.data['coll_objects'][idx]['stats'], {})
-
-    def test_post_no_access(self):
-        """Test POST for batch stats with no access for collections"""
-        new_user = self.make_user('new_user')
-        self.make_assignment(
-            self.project, new_user, self.role_contributor
-        )  # No taskflow
-        post_data = {
-            'paths': [self.irods_path, self.irods_path],
-            'md5': ['0', '0'],
-        }
-        with self.login(new_user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(response.data['coll_objects'][idx]['stats'], {})
-
-    def test_post_one_empty_coll(self):
-        """Test POST for batch stats on one (empty) collection"""
-        post_data = {'paths': [self.irods_path], 'md5': ['0']}
-        with self.login(self.user):
-            response = self.client.post(self.post_url, post_data)
-        self.assertEqual(response.status_code, 200)
-        for idx in range(len(response.data['coll_objects'])):
-            self.assertEqual(
-                response.data['coll_objects'][idx]['status'], '200'
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['file_count'], 0
-            )
-            self.assertEqual(
-                response.data['coll_objects'][idx]['stats']['total_size'], 0
-            )
-
-
-class TestIrodsObjectListAjaxView(IrodsbackendViewTestBase):
-    """Tests for the landing zone data object listing Ajax view"""
-
-    def test_get_empty_coll(self):
-        """Test GET for listing an empty collection in iRODS"""
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list',
-                    path=self.irods_path,
-                    project=self.project,
-                    md5=0,
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(len(response.data['irods_data']), 0)
-
-    def test_get_coll_obj(self):
-        """Test GET for listing a collection with a data object"""
-        # Put data object in iRODS
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        data_obj = make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list',
-                    path=self.irods_path,
-                    project=self.project,
-                    md5=0,
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(len(response.data['irods_data']), 1)
-
-        list_obj = response.data['irods_data'][0]
-        self.assertNotIn('md5_file', list_obj)
-        self.assertEqual(data_obj.name, list_obj['name'])
-        self.assertEqual(data_obj.path, list_obj['path'])
-        self.assertEqual(data_obj.size, IRODS_OBJ_SIZE)
-
-    def test_get_coll_md5(self):
-        """Test GET for listing a collection with a data object and md5"""
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-        # Put MD5 data object in iRODS
-        md5_path = self.irods_path + '/' + IRODS_MD5_NAME
-        make_object(self.irods, md5_path, IRODS_OBJ_CONTENT)  # Not actual md5
-
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list',
-                    path=self.irods_path,
-                    project=self.project,
-                    md5=1,
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(len(response.data['irods_data']), 1)  # Still 1
-        self.assertEqual(response.data['irods_data'][0]['md5_file'], True)
-
-    def test_get_coll_md5_no_file(self):
-        """Test GET with md5 set True but no md5 file"""
-        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
-        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
-
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list',
-                    path=self.irods_path,
-                    project=self.project,
-                    md5=1,
-                )
-            )
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(len(response.data['irods_data']), 1)
-        self.assertEqual(response.data['irods_data'][0]['md5_file'], False)
-
-    def test_get_coll_not_found(self):
-        """Test GET for listing a collection which doesn't exist"""
-        fail_path = self.irods_path + '/' + IRODS_FAIL_COLL
-        self.assertEqual(self.irods.collections.exists(fail_path), False)
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list', path=fail_path, project=self.project, md5=0
-                )
-            )
-        self.assertEqual(response.status_code, 404)
-
-    def test_get_coll_not_in_project(self):
-        """Test GET for listing a collection not belonging to project"""
-        self.assertEqual(
-            self.irods.collections.exists(IRODS_NON_PROJECT_PATH), True
-        )
-        with self.login(self.user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list',
-                    path=IRODS_NON_PROJECT_PATH,
-                    project=self.project,
-                    md5=0,
-                )
-            )
-        self.assertEqual(response.status_code, 400)
-
-    def test_get_no_access(self):
-        """Test GET for listing with no acces for the iRODS folder"""
-        new_user = self.make_user('new_user')
-        self.make_assignment(
-            self.project, new_user, self.role_contributor
-        )  # No taskflow
-        with self.login(new_user):
-            response = self.client.get(
-                self.irods_backend.get_url(
-                    view='list',
-                    path=self.irods_path,
-                    project=self.project,
-                    md5=0,
-                )
-            )
-        self.assertEqual(response.status_code, 403)
-
-
 class TestLocalAuthAPIView(TestCase):
     """Tests for LocalAuthAPIView"""
 
diff --git a/irodsbackend/tests/test_views_taskflow.py b/irodsbackend/tests/test_views_taskflow.py
new file mode 100644
index 00000000..af65ed63
--- /dev/null
+++ b/irodsbackend/tests/test_views_taskflow.py
@@ -0,0 +1,386 @@
+"""Tests for views in the irodsbackend app with taskflow enabled"""
+
+import os
+
+from irods.test.helpers import make_object
+
+from django.conf import settings
+from django.test import RequestFactory
+
+# Projectroles dependency
+from projectroles.models import SODAR_CONSTANTS
+
+# Taskflowbackend dependency
+from taskflowbackend.tests.base import TaskflowViewTestBase
+
+
+# SODAR constants
+PROJECT_ROLE_OWNER = SODAR_CONSTANTS['PROJECT_ROLE_OWNER']
+PROJECT_ROLE_DELEGATE = SODAR_CONSTANTS['PROJECT_ROLE_DELEGATE']
+PROJECT_ROLE_CONTRIBUTOR = SODAR_CONSTANTS['PROJECT_ROLE_CONTRIBUTOR']
+PROJECT_ROLE_GUEST = SODAR_CONSTANTS['PROJECT_ROLE_GUEST']
+PROJECT_TYPE_CATEGORY = SODAR_CONSTANTS['PROJECT_TYPE_CATEGORY']
+PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
+
+# Local constants
+IRODS_TEMP_COLL = 'temp'
+IRODS_TEMP_COLL2 = 'temp2'
+IRODS_OBJ_SIZE = 1024
+IRODS_OBJ_CONTENT = ''.join('x' for _ in range(IRODS_OBJ_SIZE))
+IRODS_OBJ_NAME = 'test1.txt'
+IRODS_MD5_NAME = 'test1.txt.md5'
+IRODS_NON_PROJECT_PATH = (
+    '/' + settings.IRODS_ZONE + '/home/' + settings.IRODS_USER
+)
+IRODS_FAIL_COLL = 'xeiJ1Vie'
+
+
+class IrodsbackendViewTestBase(TaskflowViewTestBase):
+    """Base class for irodsbackend UI view testing"""
+
+    def setUp(self):
+        super().setUp()
+        self.req_factory = RequestFactory()
+        # Init project with owner in taskflow
+        self.project, self.owner_as = self.make_project_taskflow(
+            'TestProject', PROJECT_TYPE_PROJECT, self.category, self.user
+        )
+        # Create test collection in iRODS
+        # NOTE: Not fully valid sample paths, needs make_irods_colls() for that
+        self.project_path = self.irods_backend.get_path(self.project)
+        self.irods_path = os.path.join(self.project_path, IRODS_TEMP_COLL)
+        self.irods_coll = self.irods.collections.create(self.irods_path)
+
+
+class TestIrodsStatisticsAjaxView(IrodsbackendViewTestBase):
+    """Tests for the landing zone collection statistics Ajax view"""
+
+    def setUp(self):
+        super().setUp()
+        self.post_url = self.irods_backend.get_url(
+            view='stats', project=self.project, method='POST'
+        )
+
+    def test_get_empty_coll(self):
+        """Test GET request for stats on empty iRODS collection"""
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats', project=self.project, path=self.irods_path
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.data['file_count'], 0)
+        self.assertEqual(response.data['total_size'], 0)
+
+    def test_get_invalid_coll(self):
+        """Test GET request with invalid collection (should fail)"""
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats', project=self.project, path=self.irods_path
+                )
+                + '%2F..'
+            )
+        self.assertEqual(response.status_code, 400)
+
+    def test_get_coll_obj(self):
+        """Test GET for stats on collection with data object"""
+        # Put data object in iRODS
+        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
+        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats', project=self.project, path=self.irods_path
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.data['file_count'], 1)
+        self.assertEqual(response.data['total_size'], IRODS_OBJ_SIZE)
+
+    def test_get_coll_md5(self):
+        """Test GET for stats on collection with data object and md5"""
+        # Put data object in iRODS
+        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
+        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+        # Put MD5 data object in iRODS
+        md5_path = self.irods_path + '/' + IRODS_MD5_NAME
+        make_object(self.irods, md5_path, IRODS_OBJ_CONTENT)  # Not actual md5
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats', project=self.project, path=self.irods_path
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.data['file_count'], 1)  # md5 not counted
+        self.assertEqual(response.data['total_size'], IRODS_OBJ_SIZE)
+
+    def test_get_coll_not_found(self):
+        """Test GET for stats on non-existing collection"""
+        fail_path = self.irods_path + '/' + IRODS_FAIL_COLL
+        self.assertEqual(self.irods.collections.exists(fail_path), False)
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats', project=self.project, path=fail_path
+                )
+            )
+        self.assertEqual(response.status_code, 404)
+
+    def test_get_coll_not_in_project(self):
+        """Test GET for stats on collection not belonging to project"""
+        self.assertEqual(
+            self.irods.collections.exists(IRODS_NON_PROJECT_PATH), True
+        )
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats',
+                    project=self.project,
+                    path=IRODS_NON_PROJECT_PATH,
+                )
+            )
+        self.assertEqual(response.status_code, 400)
+
+    def test_get_no_access(self):
+        """Test GET for stats with no access for iRODS collection"""
+        new_user = self.make_user('new_user')
+        self.make_assignment(
+            self.project, new_user, self.role_contributor
+        )  # No taskflow
+        with self.login(new_user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='stats', project=self.project, path=self.irods_path
+                )
+            )
+        self.assertEqual(response.status_code, 403)
+
+    def test_post_empty_coll(self):
+        """Test POST on empty iRODS collection"""
+        post_data = {'paths': [self.irods_path]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        self.assertEqual(response.status_code, 200)
+        response_data = response.data['irods_stats']
+        self.assertEqual(len(response_data.values()), 1)
+        expected = {
+            self.irods_path: {'status': 200, 'file_count': 0, 'total_size': 0}
+        }
+        self.assertEqual(response_data, expected)
+
+    def test_post_non_empty_coll(self):
+        """Test POST with data object in collection"""
+        obj_path = os.path.join(self.irods_path, IRODS_OBJ_NAME)
+        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+        post_data = {'paths': [self.irods_path]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        expected = {
+            self.irods_path: {
+                'status': 200,
+                'file_count': 1,
+                'total_size': IRODS_OBJ_SIZE,
+            }
+        }
+        self.assertEqual(response.data['irods_stats'], expected)
+
+    def test_post_md5_file(self):
+        """Test POST with .md5 file in collection"""
+        obj_path = os.path.join(self.irods_path, IRODS_OBJ_NAME)
+        obj = make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+        self.make_irods_md5_object(obj)
+        self.assert_irods_obj(
+            os.path.join(self.irods_path, IRODS_OBJ_NAME + '.md5')
+        )
+        post_data = {'paths': [self.irods_path]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        response_data = response.data['irods_stats']
+        self.assertEqual(len(response_data.values()), 1)  # md5 not included
+        expected = {
+            self.irods_path: {
+                'status': 200,
+                'file_count': 1,
+                'total_size': IRODS_OBJ_SIZE,  # md5 file size not included
+            }
+        }
+        self.assertEqual(response_data, expected)
+
+    def test_post_multiple_paths(self):
+        """Test POST with multiple paths"""
+        irods_path_new = os.path.join(self.project_path, IRODS_TEMP_COLL2)
+        self.irods.collections.create(irods_path_new)
+        obj_path = os.path.join(self.irods_path, IRODS_OBJ_NAME)
+        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+        post_data = {'paths': [self.irods_path, irods_path_new]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        expected = {
+            self.irods_path: {
+                'status': 200,
+                'file_count': 1,
+                'total_size': IRODS_OBJ_SIZE,
+            },
+            irods_path_new: {'status': 200, 'file_count': 0, 'total_size': 0},
+        }
+        self.assertEqual(response.data['irods_stats'], expected)
+
+    def test_post_dupe_path(self):
+        """Test POST with duplicate path"""
+        # This should not happen in the UI, but testing in case of view abuse
+        post_data = {'paths': [self.irods_path, self.irods_path]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        # We should only get one result
+        self.assertEqual(len(response.data['irods_stats'].values()), 1)
+
+    def test_post_coll_not_found(self):
+        """Test POST for stats on non-existing collections"""
+        fail_path = os.path.join(self.irods_path, IRODS_FAIL_COLL)
+        self.assertEqual(self.irods.collections.exists(fail_path), False)
+        post_data = {'paths': [fail_path]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        self.assertEqual(response.status_code, 200)
+        expected = {fail_path: {'status': 404}}
+        self.assertEqual(response.data['irods_stats'], expected)
+
+    def test_post_non_project_path(self):
+        """Test POST with path not belonging to project"""
+        self.assertEqual(
+            self.irods.collections.exists(IRODS_NON_PROJECT_PATH), True
+        )
+        post_data = {'paths': [IRODS_NON_PROJECT_PATH]}
+        with self.login(self.user):
+            response = self.client.post(self.post_url, post_data)
+        self.assertEqual(response.status_code, 200)
+        expected = {IRODS_NON_PROJECT_PATH: {'status': 400}}
+        self.assertEqual(response.data['irods_stats'], expected)
+
+
+class TestIrodsObjectListAjaxView(IrodsbackendViewTestBase):
+    """Tests for IrodsObjectListAjaxView"""
+
+    def test_get_empty_coll(self):
+        """Test IrodsObjectListAjaxView GET with empty collection"""
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list',
+                    path=self.irods_path,
+                    project=self.project,
+                    md5=0,
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.data['irods_data']), 0)
+
+    def test_get_data_obj(self):
+        """Test GET with data object"""
+        # Put data object in iRODS
+        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
+        data_obj = make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list',
+                    path=self.irods_path,
+                    project=self.project,
+                    md5=0,
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.data['irods_data']), 1)
+
+        list_obj = response.data['irods_data'][0]
+        self.assertNotIn('md5_file', list_obj)
+        self.assertEqual(data_obj.name, list_obj['name'])
+        self.assertEqual(data_obj.path, list_obj['path'])
+        self.assertEqual(data_obj.size, IRODS_OBJ_SIZE)
+
+    def test_get_md5_file(self):
+        """Test GET with data object and md5 file"""
+        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
+        obj = make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+        # Create MD5 data object in iRODS
+        self.make_irods_md5_object(obj)
+
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list',
+                    path=self.irods_path,
+                    project=self.project,
+                    md5=1,
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.data['irods_data']), 1)  # Still 1
+        self.assertEqual(response.data['irods_data'][0]['md5_file'], True)
+
+    def test_get_md5_no_file(self):
+        """Test GET with md5 set True and no md5 file"""
+        obj_path = self.irods_path + '/' + IRODS_OBJ_NAME
+        make_object(self.irods, obj_path, IRODS_OBJ_CONTENT)
+
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list',
+                    path=self.irods_path,
+                    project=self.project,
+                    md5=1,
+                )
+            )
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(len(response.data['irods_data']), 1)
+        self.assertEqual(response.data['irods_data'][0]['md5_file'], False)
+
+    def test_get_coll_not_found(self):
+        """Test GET with non-existing collection"""
+        fail_path = self.irods_path + '/' + IRODS_FAIL_COLL
+        self.assertEqual(self.irods.collections.exists(fail_path), False)
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list', path=fail_path, project=self.project, md5=0
+                )
+            )
+        self.assertEqual(response.status_code, 404)
+
+    def test_get_coll_not_in_project(self):
+        """Test GET with collection not in project"""
+        self.assertEqual(
+            self.irods.collections.exists(IRODS_NON_PROJECT_PATH), True
+        )
+        with self.login(self.user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list',
+                    path=IRODS_NON_PROJECT_PATH,
+                    project=self.project,
+                    md5=0,
+                )
+            )
+        self.assertEqual(response.status_code, 400)
+
+    def test_get_no_access(self):
+        """Test GET with no access to collection"""
+        new_user = self.make_user('new_user')
+        self.make_assignment(
+            self.project, new_user, self.role_contributor
+        )  # No taskflow
+        with self.login(new_user):
+            response = self.client.get(
+                self.irods_backend.get_url(
+                    view='list',
+                    path=self.irods_path,
+                    project=self.project,
+                    md5=0,
+                )
+            )
+        self.assertEqual(response.status_code, 403)
diff --git a/irodsbackend/views.py b/irodsbackend/views.py
index cc5f877b..c2df8c3c 100644
--- a/irodsbackend/views.py
+++ b/irodsbackend/views.py
@@ -148,40 +148,31 @@ def get(self, *args, **kwargs):
             return Response(self._get_detail(ex), status=500)
 
     def post(self, request, *args, **kwargs):
-        data = {'coll_objects': []}
-        q_dict = request.POST
+        ret = {}
         project_path = self.irods_backend.get_path(self.project)
         try:
             irods = self.irods_backend.get_session_obj()
         except Exception as ex:
             return JsonResponse(self._get_detail(ex), status=500)
-        for path in q_dict.getlist('paths'):
-            if project_path not in path:
-                data['coll_objects'].append(
-                    {'path': path, 'status': '400', 'stats': {}}
-                )
-                break
-            if not self._check_collection_perm(path, request.user, irods):
-                data['coll_objects'].append(
-                    {'path': path, 'status': '403', 'stats': {}}
-                )
-                break
-            try:
-                if not irods.collections.exists(path):
-                    data['coll_objects'].append(
-                        {'path': path, 'status': '404', 'stats': {}}
-                    )
-                else:
-                    ret_data = self.irods_backend.get_object_stats(irods, path)
-                    data['coll_objects'].append(
-                        {'path': path, 'status': '200', 'stats': ret_data}
-                    )
-            except Exception:
-                data['coll_objects'].append(
-                    {'path': path, 'status': '500', 'stats': {}}
-                )
+        for p in request.POST.getlist('paths'):
+            d = {}
+            if not p.startswith(project_path):
+                d['status'] = 400
+            elif not self._check_collection_perm(p, request.user, irods):
+                d['status'] = 403
+            else:
+                try:
+                    if irods.collections.exists(p):
+                        stats = self.irods_backend.get_object_stats(irods, p)
+                        d.update(stats)
+                        d['status'] = 200
+                    else:
+                        d['status'] = 404
+                except Exception:
+                    d['status'] = 500
+            ret[p] = d
         irods.cleanup()
-        return Response(data, status=200)
+        return Response({'irods_stats': ret}, status=200)
 
 
 class IrodsObjectListAjaxView(BaseIrodsAjaxView):

From c495393cc32dd15667941c4710032ab08d96e760 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Wed, 14 Feb 2024 17:44:16 +0100
Subject: [PATCH 20/33] fix landing zone status update in project detail view
 (#1902)

---
 CHANGELOG.rst                                 |   2 +
 docs_manual/source/sodar_release_notes.rst    |   1 +
 .../static/landingzones/js/landingzones.js    |  10 +-
 .../templates/landingzones/_details_card.html |   7 +-
 .../templates/landingzones/project_zones.html |   6 +-
 landingzones/tests/test_ui.py                 | 156 +++++++++++++++++-
 6 files changed, 163 insertions(+), 19 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 69052a98..c35f9124 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -16,6 +16,7 @@ Added
 - **Landingzones**
     - Create assay plugin shortcut collections for zones (#1869)
     - Zone statistics for siteinfo (#1898)
+    - UI tests for project details card (#1902)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
 
@@ -50,6 +51,7 @@ Fixed
     - Stats badge stuck in updating with non-200 POST status (#1327, #1886)
 - **Landingzones**
     - Stats badge displayed to superusers for ``DELETED`` zones (#1866)
+    - Zone status updating not working in project details card (#1902)
 - **Samplesheets**
     - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
     - Superuser not allowed to edit iRODS request from other users in UI (#1863)
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 38a1e751..349c0e97 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -19,6 +19,7 @@ Release for minor updates, maintenance and bug fixes.
 - Fix IRODS_ROOT_PATH issues
 - Fix LDAP TLS settings
 - Fix iRODS stats badge stuck in "updating"
+- Fix landing zone status updating not working in project details card
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.4
 
diff --git a/landingzones/static/landingzones/js/landingzones.js b/landingzones/static/landingzones/js/landingzones.js
index 299329f2..baa57463 100644
--- a/landingzones/static/landingzones/js/landingzones.js
+++ b/landingzones/static/landingzones/js/landingzones.js
@@ -20,12 +20,10 @@ var updateZoneStatus = function() {
     // Make the POST request to retrieve zone statuses
     if (zoneUuids.length > 0) {
         $.ajax({
-            url: zoneStatusUrl,
+            url: zoneStatusURL,
             method: 'POST',
             dataType: 'JSON',
-            data: {
-                zone_uuids: zoneUuids
-            }
+            data: {zone_uuids: zoneUuids}
         }).done(function(data) {
             $('.sodar-lz-zone-tr-existing').each(function() {
                 var zoneUuid = $(this).attr('data-zone-uuid');
@@ -67,9 +65,7 @@ var updateZoneStatus = function() {
                                     'span#sodar-lz-zone-status-moved-' + zoneUuid
                                 );
                                 statusMovedSpan.html(
-                                    '<p class="mb-0"><a href="' +
-                                    sampleUrl +
-                                    '">' +
+                                    '<p class="mb-0"><a href="' + sampleUrl + '">' +
                                     '<i class="iconify" data-icon="mdi:arrow-right-circle"></i> ' +
                                     'Browse files in sample sheet</a></p>'
                                 );
diff --git a/landingzones/templates/landingzones/_details_card.html b/landingzones/templates/landingzones/_details_card.html
index c53dd9ca..99d2e95a 100644
--- a/landingzones/templates/landingzones/_details_card.html
+++ b/landingzones/templates/landingzones/_details_card.html
@@ -17,16 +17,13 @@
   .sodar-lz-detail-table td:first-child {
     border-left: 0;
   }
-
   .sodar-lz-detail-table thead tr th:nth-child(1) {
     width: 250px;
   }
-
   .sodar-lz-detail-table thead tr th:nth-child(3) {
     white-space: nowrap;
     width: 150px;
   }
-
   /* Responsive modifications */
   @media screen and (max-width: 1000px) {
     .table.sodar-lz-detail-table tr th:nth-child(2) {
@@ -41,6 +38,8 @@
 <!-- Settings for Javascript -->
 <script type="text/javascript">
   window.statusInterval = {{ zone_status_interval }} * 5000;
+  var zoneStatusURL = "{% url 'landingzones:ajax_status' project=project.sodar_uuid %}";
+  var currentUserURL = "{% url 'projectroles:ajax_user_current' %}";
 </script>
 
 <!-- Landingzones Javascript -->
@@ -61,7 +60,7 @@
         {% include 'landingzones/_zone_item.html' with item=zone details_card_mode=True %}
       {% endfor %}
     {% else %}
-      <tr>
+      <tr id="sodar-lz-detail-table-no-zones">
         <td class="bg-faded font-italic text-center" colspan="4">
           No active landing zones found.
         </td>
diff --git a/landingzones/templates/landingzones/project_zones.html b/landingzones/templates/landingzones/project_zones.html
index 833864e3..6a0110f5 100644
--- a/landingzones/templates/landingzones/project_zones.html
+++ b/landingzones/templates/landingzones/project_zones.html
@@ -56,13 +56,11 @@
         display: none;
       }
     }
-
     @media screen and (max-width: 1200px) {
       .table.sodar-lz-table thead tr th:nth-child(1) {
         width: 250px;
       }
     }
-
     @media screen and (max-width: 900px) {
       .table.sodar-lz-table thead tr th:nth-child(2) {
         display: none;
@@ -71,7 +69,6 @@
         display: none;
       }
     }
-
     @media screen and (max-width: 450px) {
       .table.sodar-lz-table thead tr th:nth-child(4) {
         display: none;
@@ -157,8 +154,7 @@ <h3><i class="iconify" data-icon="mdi:briefcase-upload"></i> Landing Zones</h3>
     window.zoneStatusUpdated = false;
     window.statusInterval = {{ zone_status_interval }} * 1000;
     window.irodsShowChecksumCol = true;
-    var zoneStatusUrl = "{% url 'landingzones:ajax_status' project=project.sodar_uuid %}";
-    <!-- Superuser status variable -->
+    var zoneStatusURL = "{% url 'landingzones:ajax_status' project=project.sodar_uuid %}";
     var currentUserURL = "{% url 'projectroles:ajax_user_current' %}";
   </script>
 
diff --git a/landingzones/tests/test_ui.py b/landingzones/tests/test_ui.py
index 63b02fe3..56c6a038 100644
--- a/landingzones/tests/test_ui.py
+++ b/landingzones/tests/test_ui.py
@@ -16,7 +16,11 @@
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
 from samplesheets.tests.test_sheet_config import SheetConfigMixin
 
-from landingzones.constants import ZONE_STATUS_CREATING
+from landingzones.constants import (
+    ZONE_STATUS_CREATING,
+    ZONE_STATUS_ACTIVE,
+    ZONE_STATUS_VALIDATING,
+)
 from landingzones.tests.test_models import LandingZoneMixin
 
 
@@ -27,10 +31,10 @@
 SHEET_PATH = SHEET_DIR + 'i_small.zip'
 
 
-class TestProjectZoneView(
+class LandingZoneUITestBase(
     SampleSheetIOMixin, SheetConfigMixin, LandingZoneMixin, TestUIBase
 ):
-    """ProjectZoneView UI tests"""
+    """Base class for landingzones UI tests"""
 
     investigation = None
     study = None
@@ -57,6 +61,14 @@ def _assert_btn_enabled(self, element, expected=True):
         else:
             self.assertIn('disabled', element.get_attribute('class'))
 
+    def _wait_for_status(self, status_elem, status):
+        """Wait for a specific status in the zone status element"""
+        for i in range(0, 25):
+            if status_elem.text == status:
+                return
+            time.sleep(1.0)
+        raise Exception('Status not changed')
+
     def _wait_for_status_update(self):
         """Wait for JQuery landing zone status updates to finish"""
         for i in range(0, 20):
@@ -75,6 +87,13 @@ def setUp(self):
             self.user_delegate,
             self.user_contributor,
         ]
+
+
+class TestProjectZoneView(LandingZoneUITestBase):
+    """UI tests for ProjectZoneView"""
+
+    def setUp(self):
+        super().setUp()
         self.url = reverse(
             'landingzones:list',
             kwargs={'project': self.project.sodar_uuid},
@@ -285,6 +304,27 @@ def test_render_other_user_no_access(self):
         self.assertEqual(len(zones), 2)
         self._assert_element(By.CLASS_NAME, 'sodar-lz-zone-warn-access', True)
 
+    def test_status_update(self):
+        """Test ProjectZoneView with zone status update"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        contrib_zone = self.make_landing_zone(
+            'contrib_zone',
+            self.project,
+            self.user_contributor,
+            self.assay,
+            status='ACTIVE',
+        )
+        self.login_and_redirect(self.user_contributor, self.url)
+        zone_status = self.selenium.find_element(
+            By.CLASS_NAME, 'sodar-lz-zone-status'
+        )
+        self.assertEqual(zone_status.text, ZONE_STATUS_ACTIVE)
+        contrib_zone.set_status(ZONE_STATUS_VALIDATING)
+        self._wait_for_status(zone_status, ZONE_STATUS_VALIDATING)
+        self.assertEqual(zone_status.text, ZONE_STATUS_VALIDATING)
+
     def test_zone_buttons(self):
         """Test ProjectZoneView zone buttons"""
         self._setup_investigation()
@@ -420,3 +460,113 @@ def test_zone_locked_contributor(self):
                 By.CLASS_NAME, 'sodar-lz-zone-status-info'
             ).get_attribute('class'),
         )
+
+
+class TestProjectDetailView(LandingZoneUITestBase):
+    """UI tests for ProjectDetailView"""
+
+    def setUp(self):
+        super().setUp()
+        self.url = reverse(
+            'projectroles:detail',
+            kwargs={'project': self.project.sodar_uuid},
+        )
+
+    def test_render_no_zones(self):
+        """Test ProjectDetailView with no zones"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        self.login_and_redirect(self.user_owner, self.url)
+        self._assert_element(By.ID, 'sodar-lz-detail-table-no-zones', True)
+        self._assert_element(By.CLASS_NAME, 'sodar-lz-zone-tr-existing', False)
+
+    def test_render_own_zone(self):
+        """Test ProjectDetailView as contributor with own zone"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        contrib_zone = self.make_landing_zone(
+            'contrib_zone', self.project, self.user_contributor, self.assay
+        )
+        self.login_and_redirect(self.user_contributor, self.url)
+        self._assert_element(By.ID, 'sodar-lz-detail-table-no-zones', False)
+        zones = self.selenium.find_elements(
+            By.CLASS_NAME, 'sodar-lz-zone-tr-existing'
+        )
+        self.assertEqual(len(zones), 1)
+        self.assertEqual(
+            zones[0].get_attribute('data-zone-uuid'),
+            str(contrib_zone.sodar_uuid),
+        )
+
+    def test_render_multiple_zones(self):
+        """Test ProjectDetailView as contributor with multiple own zones"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        self.make_landing_zone(
+            'contrib_zone', self.project, self.user_contributor, self.assay
+        )
+        self.make_landing_zone(
+            'contrib_zone2', self.project, self.user_contributor, self.assay
+        )
+        self.login_and_redirect(self.user_contributor, self.url)
+        zones = self.selenium.find_elements(
+            By.CLASS_NAME, 'sodar-lz-zone-tr-existing'
+        )
+        self.assertEqual(len(zones), 2)
+
+    def test_render_other_zone(self):
+        """Test ProjectDetailView as contributor with other user's zone"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        self.make_landing_zone(
+            'owner_zone', self.project, self.user_owner, self.assay
+        )
+        self.login_and_redirect(self.user_contributor, self.url)
+        self._assert_element(By.ID, 'sodar-lz-detail-table-no-zones', True)
+        self._assert_element(By.CLASS_NAME, 'sodar-lz-zone-tr-existing', False)
+
+    def test_render_as_owner(self):
+        """Test ProjectDetailView as owner with own and other zones"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        owner_zone = self.make_landing_zone(
+            'owner_zone', self.project, self.user_owner, self.assay
+        )
+        self.make_landing_zone(
+            'contrib_zone', self.project, self.user_contributor, self.assay
+        )
+        self.login_and_redirect(self.user_owner, self.url)
+        zones = self.selenium.find_elements(
+            By.CLASS_NAME, 'sodar-lz-zone-tr-existing'
+        )
+        self.assertEqual(len(zones), 1)  # Only own zone should be visible
+        self.assertEqual(
+            zones[0].get_attribute('data-zone-uuid'),
+            str(owner_zone.sodar_uuid),
+        )
+
+    def test_update_status(self):
+        """Test ProjectDetailView with zone status update"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        contrib_zone = self.make_landing_zone(
+            'contrib_zone',
+            self.project,
+            self.user_contributor,
+            self.assay,
+            status='ACTIVE',
+        )
+        self.login_and_redirect(self.user_contributor, self.url)
+        zone_status = self.selenium.find_element(
+            By.CLASS_NAME, 'sodar-lz-zone-status'
+        )
+        self.assertEqual(zone_status.text, ZONE_STATUS_ACTIVE)
+        contrib_zone.set_status(ZONE_STATUS_VALIDATING)
+        self._wait_for_status(zone_status, ZONE_STATUS_VALIDATING)
+        self.assertEqual(zone_status.text, ZONE_STATUS_VALIDATING)

From c8f59a717aec099b5a5a2e4557b75ab7d803dd3f Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 16 Feb 2024 15:54:44 +0100
Subject: [PATCH 21/33] upgrade to django-sodar-core v0.13.4 final (#1899)

---
 CHANGELOG.rst                             | 2 +-
 requirements/base.txt                     | 4 ++--
 samplesheets/tests/test_views_taskflow.py | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c35f9124..5055022b 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -25,7 +25,7 @@ Changed
 
 - **General**
     - Upgrade to Django v3.2.24 (#1854)
-    - Upgrade to django-sodar-core v0.13.4-WIP (#1899)
+    - Upgrade to django-sodar-core v0.13.4 (#1899)
     - Upgrade critical Vue app dependencies (#1854)
     - Update installation documentation (#1871)
 - **Irodsbackend**
diff --git a/requirements/base.txt b/requirements/base.txt
index 68bffe44..97b2b90e 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -70,8 +70,8 @@ mistune==2.0.5
 django-autocomplete-light==3.9.4
 
 # SODAR Core
-# django-sodar-core==0.13.3
--e git+https://github.com/bihealth/sodar-core.git@1117ff87723389be928538b965fe89576687c1a6#egg=django-sodar-core
+django-sodar-core==0.13.4
+# -e git+https://github.com/bihealth/sodar-core.git@be012e5536bacf8bfbfe95e3c930324edae0309b#egg=django-sodar-core
 
 # Celery
 celery==5.2.7
diff --git a/samplesheets/tests/test_views_taskflow.py b/samplesheets/tests/test_views_taskflow.py
index 260798ec..70957895 100644
--- a/samplesheets/tests/test_views_taskflow.py
+++ b/samplesheets/tests/test_views_taskflow.py
@@ -20,6 +20,7 @@
 from projectroles.app_settings import AppSettingAPI
 from projectroles.models import SODAR_CONSTANTS
 from projectroles.plugins import get_backend_api
+from projectroles.views import MSG_NO_AUTH
 
 # Appalerts dependency
 from appalerts.models import AppAlert
@@ -2248,8 +2249,7 @@ def test_reject_contributor(self):
             self.assertRedirects(response, reverse('home'))
 
         self.assertEqual(
-            list(get_messages(response.wsgi_request))[-1].message,
-            'User not authorized for requested action.',
+            list(get_messages(response.wsgi_request))[-1].message, MSG_NO_AUTH
         )
         request.refresh_from_db()
         self.assertEqual(request.status, IRODS_REQUEST_STATUS_ACTIVE)

From 814f96012472f427c47e228924737b9788f0a58a Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Mon, 19 Feb 2024 15:46:07 +0100
Subject: [PATCH 22/33] fix uncaught SetAccessTask exceptions (#1906)

---
 CHANGELOG.rst                        |  1 +
 taskflowbackend/tasks/irods_tasks.py | 23 ++++++++++++-----------
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5055022b..2c92553f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -61,6 +61,7 @@ Fixed
     - Sheet template creation failure with slash characters in title/ID fields (#1896)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
+    - Uncaught exceptions in ``SetAccessTask`` (#1906)
 
 Removed
 -------
diff --git a/taskflowbackend/tasks/irods_tasks.py b/taskflowbackend/tasks/irods_tasks.py
index 5f60bc20..e8108d4f 100644
--- a/taskflowbackend/tasks/irods_tasks.py
+++ b/taskflowbackend/tasks/irods_tasks.py
@@ -292,17 +292,21 @@ def execute(
         *args,
         **kwargs
     ):
-        if obj_target:
-            target = self.irods.data_objects.get(path)
-            recursive = False
-        else:
-            target = self.irods.collections.get(path)
-            recursive = recursive
+        try:
+            if obj_target:
+                target = self.irods.data_objects.get(path)
+                recursive = False
+            else:
+                target = self.irods.collections.get(path)
+                recursive = recursive
+            target_access = self.irods.permissions.get(target=target)
+        except Exception as ex:
+            self._raise_irods_exception(ex, path)
 
-        target_access = self.irods.permissions.get(target=target)
         user_access = next(
             (x for x in target_access if x.user_name == user_name), None
         )
+        modifying_data = False
         if (
             user_access
             and user_access.access_name != access_lookup[access_name]
@@ -314,8 +318,6 @@ def execute(
         elif not user_access:
             self.execute_data['access_name'] = 'null'
             modifying_data = True
-        else:
-            modifying_data = False
 
         if modifying_data:
             acl = iRODSAccess(
@@ -327,8 +329,7 @@ def execute(
             try:
                 self.irods.permissions.set(acl, recursive=recursive)
             except Exception as ex:
-                ex_info = user_name
-                self._raise_irods_exception(ex, ex_info)
+                self._raise_irods_exception(ex, user_name)
             self.data_modified = True
         super().execute(*args, **kwargs)
 

From 60e27d3b71a15786450da738adff8d11aa171940 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Tue, 20 Feb 2024 16:35:44 +0100
Subject: [PATCH 23/33] fix landing_zone_create crash with large projects
 (#1905)

---
 CHANGELOG.rst                                |   3 +
 docs_manual/source/sodar_release_notes.rst   |   1 +
 taskflowbackend/flows/landing_zone_create.py |  24 +-
 taskflowbackend/tasks/irods_tasks.py         | 203 +++++++++++++----
 taskflowbackend/tests/test_tasks.py          | 217 ++++++++++++++++++-
 5 files changed, 388 insertions(+), 60 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 2c92553f..5ebbe96c 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -19,6 +19,8 @@ Added
     - UI tests for project details card (#1902)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
+    - ``BatchSetAccessTask`` in iRODS tasks (#1905)
+    - ``IrodsAccessMixin`` task helper mixin (#1905)
 
 Changed
 -------
@@ -62,6 +64,7 @@ Fixed
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)
+    - Crash in ``landing_zone_create`` with large amount of collections (#1905)
 
 Removed
 -------
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 349c0e97..538b1648 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -20,6 +20,7 @@ Release for minor updates, maintenance and bug fixes.
 - Fix LDAP TLS settings
 - Fix iRODS stats badge stuck in "updating"
 - Fix landing zone status updating not working in project details card
+- Fix landing zone creation crash with large amount of created collections
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.4
 
diff --git a/taskflowbackend/flows/landing_zone_create.py b/taskflowbackend/flows/landing_zone_create.py
index 94550cc3..b9a87948 100644
--- a/taskflowbackend/flows/landing_zone_create.py
+++ b/taskflowbackend/flows/landing_zone_create.py
@@ -154,26 +154,30 @@ def build(self, force_fail=False):
                 )
             )
         # Create collections
-        for d in self.flow_data['colls']:
-            coll_path = os.path.join(zone_path, d)
+        if self.flow_data['colls']:
+            colls_full_path = [
+                os.path.join(zone_path, c) for c in self.flow_data['colls']
+            ]
+            coll_count = len(self.flow_data['colls'])
             self.add_task(
-                irods_tasks.CreateCollectionTask(
-                    name='Create collection {}'.format(coll_path),
+                irods_tasks.BatchCreateCollectionsTask(
+                    name='Batch create {} collection{}'.format(
+                        coll_count, 's' if coll_count != 1 else ''
+                    ),
                     irods=self.irods,
-                    inject={'path': coll_path},
+                    inject={'paths': colls_full_path},
                 )
             )
             # Enforce collection access if set
             if self.flow_data['restrict_colls']:
                 self.add_task(
-                    irods_tasks.SetAccessTask(
-                        name='Set user owner access to collection {}'.format(
-                            coll_path
-                        ),
+                    irods_tasks.BatchSetAccessTask(
+                        name='Batch set user owner access to created '
+                        'collections',
                         irods=self.irods,
                         inject={
                             'access_name': 'own',
-                            'path': coll_path,
+                            'paths': colls_full_path,
                             'user_name': zone.user.username,
                             'access_lookup': access_lookup,
                             'irods_backend': self.irods_backend,
diff --git a/taskflowbackend/tasks/irods_tasks.py b/taskflowbackend/tasks/irods_tasks.py
index e8108d4f..ee931927 100644
--- a/taskflowbackend/tasks/irods_tasks.py
+++ b/taskflowbackend/tasks/irods_tasks.py
@@ -26,6 +26,96 @@
 MD5_RE = re.compile(r'([^\w.])')
 
 
+# Mixins -----------------------------------------------------------------------
+
+
+class IrodsAccessMixin:
+    """Mixin for iRODS access helpers"""
+
+    def execute_set_access(
+        self,
+        access_name,
+        path,
+        user_name,
+        access_lookup,
+        obj_target,
+        recursive,
+    ):
+        """
+        Set access for user in a single data object or collection.
+
+        :param access_name: Access level to set (string)
+        :param path: Full iRODS path to collection or data object (string)
+        :param user_name: Name of user or group (string)
+        :param access_lookup: Access level lookup for iRODS compatibility (dict)
+        :param obj_target: Whether target is a data object (boolean)
+        :param recursive: Set collection access recursively if True (boolean)
+        """
+        if not self.execute_data.get('access_names'):
+            self.execute_data['access_names'] = {}
+        if obj_target:
+            target = self.irods.data_objects.get(path)
+            recursive = False
+        else:
+            target = self.irods.collections.get(path)
+            recursive = recursive
+        target_access = self.irods.permissions.get(target=target)
+
+        user_access = next(
+            (x for x in target_access if x.user_name == user_name), None
+        )
+        modifying_data = False
+        if (
+            user_access
+            and user_access.access_name != access_lookup[access_name]
+        ):
+            self.execute_data['access_names'][path] = access_lookup[
+                user_access.access_name
+            ]
+            modifying_data = True
+        elif not user_access:
+            self.execute_data['access_names'][path] = 'null'
+            modifying_data = True
+
+        if modifying_data:
+            acl = iRODSAccess(
+                access_name=access_name,
+                path=path,
+                user_name=user_name,
+                user_zone=self.irods.zone,
+            )
+            self.irods.permissions.set(acl, recursive=recursive)
+            self.data_modified = True  # Access was modified
+
+    def revert_set_access(
+        self,
+        path,
+        user_name,
+        obj_target,
+        recursive,
+    ):
+        """
+        Revert setting access for user in a single collection or data object.
+
+        :param path: Full iRODS path to collection or data object (string)
+        :param user_name: Name of user or group (string)
+        :param obj_target: Whether target is a data object (boolean)
+        :param recursive: Set collection access recursively if True (boolean)
+        """
+        if self.data_modified:
+            acl = iRODSAccess(
+                access_name=self.execute_data['access_names'][path],
+                path=path,
+                user_name=user_name,
+                user_zone=self.irods.zone,
+            )
+            recursive = False if obj_target else recursive
+            self.irods.permissions.set(acl, recursive=recursive)
+
+
+# Base Task --------------------------------------------------------------------
+
+
 class IrodsBaseTask(BaseTask):
     """Base iRODS task"""
 
@@ -51,6 +141,9 @@ def _raise_irods_exception(self, ex, info=None):
         raise Exception(desc)
 
 
+# Tasks ------------------------------------------------------------------------
+
+
 class CreateCollectionTask(IrodsBaseTask):
     """
     Create collection and its parent collections if they doesn't exist (imkdir)
@@ -274,7 +367,7 @@ def revert(self, path, inherit=True, *args, **kwargs):
         '''
 
 
-class SetAccessTask(IrodsBaseTask):
+class SetAccessTask(IrodsAccessMixin, IrodsBaseTask):
     """
     Set user/group access to target (ichmod). If the target is a data object
     (obj_target=True), the recursive argument will be ignored.
@@ -293,44 +386,16 @@ def execute(
         **kwargs
     ):
         try:
-            if obj_target:
-                target = self.irods.data_objects.get(path)
-                recursive = False
-            else:
-                target = self.irods.collections.get(path)
-                recursive = recursive
-            target_access = self.irods.permissions.get(target=target)
-        except Exception as ex:
-            self._raise_irods_exception(ex, path)
-
-        user_access = next(
-            (x for x in target_access if x.user_name == user_name), None
-        )
-        modifying_data = False
-        if (
-            user_access
-            and user_access.access_name != access_lookup[access_name]
-        ):
-            self.execute_data['access_name'] = access_lookup[
-                user_access.access_name
-            ]
-            modifying_data = True
-        elif not user_access:
-            self.execute_data['access_name'] = 'null'
-            modifying_data = True
-
-        if modifying_data:
-            acl = iRODSAccess(
-                access_name=access_name,
-                path=path,
-                user_name=user_name,
-                user_zone=self.irods.zone,
+            self.execute_set_access(
+                access_name,
+                path,
+                user_name,
+                access_lookup,
+                obj_target,
+                recursive,
             )
-            try:
-                self.irods.permissions.set(acl, recursive=recursive)
-            except Exception as ex:
-                self._raise_irods_exception(ex, user_name)
-            self.data_modified = True
+        except Exception as ex:
+            self._raise_irods_exception(ex, user_name)
         super().execute(*args, **kwargs)
 
     def revert(
@@ -345,15 +410,10 @@ def revert(
         *args,
         **kwargs
     ):
-        if self.data_modified:
-            acl = iRODSAccess(
-                access_name=self.execute_data['access_name'],
-                path=path,
-                user_name=user_name,
-                user_zone=self.irods.zone,
-            )
-            recursive = False if obj_target else recursive
-            self.irods.permissions.set(acl, recursive=recursive)
+        try:
+            self.revert_set_access(path, user_name, obj_target, recursive)
+        except Exception:
+            pass  # TODO: Log revert() exceptions?
 
 
 class IssueTicketTask(IrodsBaseTask):
@@ -496,7 +556,53 @@ def revert(self, src_path, dest_path, *args, **kwargs):
             self.irods.data_objects.move(src_path=new_src, dest_path=new_dest)
 
 
-# Batch file tasks -------------------------------------------------------------
+# Batch Tasks ------------------------------------------------------------------
+
+
+class BatchSetAccessTask(IrodsAccessMixin, IrodsBaseTask):
+    """
+    Set user/group access to multiple targets (ichmod). If a target is a data
+    object (obj_target=True), the recursive argument will be ignored.
+    """
+
+    def execute(
+        self,
+        access_name,
+        paths,
+        user_name,
+        access_lookup,
+        irods_backend,
+        obj_target=False,
+        recursive=True,
+        *args,
+        **kwargs
+    ):
+        # NOTE: Exception handling is done within execute_set_access()
+        for path in paths:
+            self.execute_set_access(
+                access_name,
+                path,
+                user_name,
+                access_lookup,
+                obj_target,
+                recursive,
+            )
+        super().execute(*args, **kwargs)
+
+    def revert(
+        self,
+        access_name,
+        paths,
+        user_name,
+        access_lookup,
+        irods_backend,
+        obj_target=False,
+        recursive=True,
+        *args,
+        **kwargs
+    ):
+        for path in paths:
+            self.revert_set_access(path, user_name, obj_target, recursive)
 
 
 class BatchCheckFilesTask(IrodsBaseTask):
@@ -666,6 +772,7 @@ def execute(
                     'Error getting permissions of target "{}"'.format(target),
                 )
 
+            # TODO: Remove repetition, use IrodsAccessMixin
             user_access = next(
                 (x for x in target_access if x.user_name == user_name), None
             )
diff --git a/taskflowbackend/tests/test_tasks.py b/taskflowbackend/tests/test_tasks.py
index 3f5a353a..62f455ef 100644
--- a/taskflowbackend/tests/test_tasks.py
+++ b/taskflowbackend/tests/test_tasks.py
@@ -34,6 +34,7 @@
 NEW_COLL2_NAME = 'test_new2'
 TEST_OBJ_NAME = 'move_obj'
 SUB_COLL_NAME = 'sub'
+SUB_COLL_NAME2 = 'sub2'
 MOVE_COLL_NAME = 'move_coll'
 
 TEST_USER = USER_PREFIX + 'user3'
@@ -860,7 +861,7 @@ def test_execute_twice(self):
         self.assertEqual(user_access.access_name, self.irods_access_read)
 
     def test_revert_created(self):
-        """Test access setting"""
+        """Test reverting created access"""
         self._add_task(
             cls=SetAccessTask,
             name='Set access',
@@ -883,7 +884,7 @@ def test_revert_created(self):
         # self.assertEqual(user_access.access_name, TEST_ACCESS_NULL)
 
     def test_revert_modified(self):
-        """Test access setting reverting after modification"""
+        """Test reverting modified access"""
         self._add_task(
             cls=SetAccessTask,
             name='Set access',
@@ -1607,6 +1608,218 @@ def test_overwrite_failure(self):
 # TODO: Test Checksum verifying
 
 
+class TestBatchSetAccessTask(IRODSTaskTestBase):
+    """Tests for BatchSetAccessTask"""
+
+    def setUp(self):
+        super().setUp()
+        self.sub_coll_path = os.path.join(self.test_coll_path, SUB_COLL_NAME)
+        self.sub_coll_path2 = os.path.join(self.test_coll_path, SUB_COLL_NAME2)
+        self.irods.collections.create(self.sub_coll_path)
+        self.irods.collections.create(self.sub_coll_path2)
+        self.paths = [self.sub_coll_path, self.sub_coll_path2]
+        # Init default user group
+        self.irods.user_groups.create(DEFAULT_USER_GROUP)
+        self.access_lookup = self.irods_backend.get_access_lookup(self.irods)
+
+    def test_execute_read(self):
+        """Test access setting for read"""
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_READ_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+        )
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path, None)
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+        result = self._run_flow()
+
+        self.assertEqual(result, True)
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_read
+        )
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path2, self.irods_access_read
+        )
+
+    def test_execute_write(self):
+        """Test access setting for write/modify"""
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_WRITE_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+        )
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path, None)
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+        result = self._run_flow()
+
+        self.assertEqual(result, True)
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_write
+        )
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path2, self.irods_access_write
+        )
+
+    def test_execute_mixed(self):
+        """Test access setting for both new and previously set access levels"""
+        self._add_task(
+            cls=SetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_READ_IN,
+                'path': self.sub_coll_path,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+        )
+        self._run_flow()
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_read
+        )
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+
+        self.flow = self._init_flow()
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_WRITE_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+        )
+        result = self._run_flow()
+
+        self.assertEqual(result, True)
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_write
+        )
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path2, self.irods_access_write
+        )
+
+    def test_revert_created(self):
+        """Test reverting created access"""
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_READ_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+            force_fail=True,
+        )  # FAIL
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path, None)
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+        result = self._run_flow()
+
+        self.assertNotEqual(result, True)
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path, None)
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+
+    def test_revert_modified(self):
+        """Test reverting modified access"""
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_READ_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+        )
+        self._run_flow()
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_read
+        )
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path2, self.irods_access_read
+        )
+
+        self.flow = self._init_flow()
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_WRITE_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+            force_fail=True,
+        )  # FAIL
+        result = self._run_flow()
+
+        self.assertNotEqual(result, True)
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_read
+        )
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path2, self.irods_access_read
+        )
+
+    def test_revert_mixed(self):
+        """Test reverting access for both new and existing access levels"""
+        self._add_task(
+            cls=SetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_READ_IN,
+                'path': self.sub_coll_path,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+        )
+        self._run_flow()
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_read
+        )
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+
+        self.flow = self._init_flow()
+        self._add_task(
+            cls=BatchSetAccessTask,
+            name='Set access',
+            inject={
+                'access_name': IRODS_ACCESS_WRITE_IN,
+                'paths': self.paths,
+                'user_name': DEFAULT_USER_GROUP,
+                'access_lookup': self.access_lookup,
+                'irods_backend': self.irods_backend,
+            },
+            force_fail=True,
+        )  # FAIL
+        result = self._run_flow()
+
+        self.assertNotEqual(result, True)
+        self.assert_irods_access(
+            DEFAULT_USER_GROUP, self.sub_coll_path, self.irods_access_read
+        )
+        self.assert_irods_access(DEFAULT_USER_GROUP, self.sub_coll_path2, None)
+
+
 class TestBatchCreateCollectionsTask(IRODSTaskTestBase):
     """Tests for BatchCreateCollectionsTask"""
 

From 33534cbd29e98e702b10b674e151bab24af394fb Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 23 Feb 2024 15:52:28 +0100
Subject: [PATCH 24/33] add IrodsDataRequest timeline event extra data (#1912,
 #1913)

---
 CHANGELOG.rst                              |   3 +
 docs_manual/source/sodar_release_notes.rst |   1 +
 samplesheets/tests/test_views_taskflow.py  | 151 ++++++++++++---------
 samplesheets/views.py                      |  67 +++------
 samplesheets/views_ajax.py                 |  10 +-
 samplesheets/views_api.py                  |   6 +-
 6 files changed, 111 insertions(+), 127 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5ebbe96c..f0fc32b4 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -17,6 +17,8 @@ Added
     - Create assay plugin shortcut collections for zones (#1869)
     - Zone statistics for siteinfo (#1898)
     - UI tests for project details card (#1902)
+- **Samplesheets**
+    - ``IrodsDataRequest`` timeline event extra data (#1912)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
     - ``BatchSetAccessTask`` in iRODS tasks (#1905)
@@ -38,6 +40,7 @@ Changed
 - **Samplesheets**
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
+    - Refactor ``IrodsDataRequestModifyMixin`` timeline helpers (#1913)
 - **Taskflowbackend**
     - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
     - Set zone status on uncaught errors in ``run_flow()`` (#1458)
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 538b1648..4af59d98 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -14,6 +14,7 @@ v0.14.2 (WIP)
 Release for minor updates, maintenance and bug fixes.
 
 - Add assay plugin shortcut collection creation in landing zones
+- Add iRODS data request details in timeline events
 - Add landing zone statistics in siteinfo
 - Fix iRODS data request issues
 - Fix IRODS_ROOT_PATH issues
diff --git a/samplesheets/tests/test_views_taskflow.py b/samplesheets/tests/test_views_taskflow.py
index 70957895..3671a7f3 100644
--- a/samplesheets/tests/test_views_taskflow.py
+++ b/samplesheets/tests/test_views_taskflow.py
@@ -1161,10 +1161,10 @@ def setUp(self):
 
 
 class TestIrodsDataRequestCreateView(IrodsDataRequestViewTestBase):
-    """Test IrodsDataRequestCreateView"""
+    """Tests for IrodsDataRequestCreateView"""
 
-    def test_create(self):
-        """Test creating a delete request"""
+    def test_post(self):
+        """Test IrodsDataRequestCreateView POST"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         self._assert_tl_count(EVENT_CREATE, 0)
         self._assert_alert_count(EVENT_CREATE, self.user, 0)
@@ -1195,11 +1195,19 @@ def test_create(self):
         self.assertEqual(obj.path, self.obj_path)
         self.assertEqual(obj.description, IRODS_REQUEST_DESC)
         self._assert_tl_count(EVENT_CREATE, 1)
+        self.assertEqual(
+            ProjectEvent.objects.get(event_name=EVENT_CREATE).extra_data,
+            {
+                'action': IRODS_REQUEST_ACTION_DELETE,
+                'path': obj.path,
+                'description': obj.description,
+            },
+        )
         self._assert_alert_count(EVENT_CREATE, self.user, 1)
         self._assert_alert_count(EVENT_CREATE, self.user_delegate, 1)
 
-    def test_create_trailing_slash(self):
-        """Test creating a delete request with trailing slash in path"""
+    def test_post_trailing_slash(self):
+        """Test POST with trailing slash in path"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         post_data = {
             'path': self.obj_path + '/',
@@ -1231,8 +1239,8 @@ def test_create_trailing_slash(self):
         self.assertEqual(obj.path, self.obj_path)
         self.assertEqual(obj.description, IRODS_REQUEST_DESC)
 
-    def test_create_invalid_form_data(self):
-        """Test creating a delete request with invalid form data"""
+    def test_post_invalid_data(self):
+        """Test POST with invalid form data"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         self._assert_tl_count(EVENT_CREATE, 0)
         self._assert_alert_count(EVENT_CREATE, self.user, 0)
@@ -1257,8 +1265,8 @@ def test_create_invalid_form_data(self):
         self._assert_alert_count(EVENT_CREATE, self.user, 0)
         self._assert_alert_count(EVENT_CREATE, self.user_delegate, 0)
 
-    def test_create_invalid_path_assay_collection(self):
-        """Test creating a delete request with assay path (should fail)"""
+    def test_post_assay_path(self):
+        """Test POST with assay path (should fail)"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         post_data = {'path': self.assay_path, 'description': IRODS_REQUEST_DESC}
 
@@ -1278,7 +1286,7 @@ def test_create_invalid_path_assay_collection(self):
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
 
     def test_create_multiple(self):
-        """Test creating multiple_requests"""
+        """Test POST with multiple requests for same path"""
         path2 = os.path.join(self.assay_path, IRODS_FILE_NAME2)
         self.irods.data_objects.create(path2)
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
@@ -1359,6 +1367,14 @@ def test_post(self):
         self.assertEqual(self.request.path, self.obj_path)
         self.assertEqual(self.request.description, IRODS_REQUEST_DESC_UPDATE)
         self._assert_tl_count(EVENT_UPDATE, 1)
+        self.assertEqual(
+            ProjectEvent.objects.get(event_name=EVENT_UPDATE).extra_data,
+            {
+                'action': IRODS_REQUEST_ACTION_DELETE,
+                'path': self.request.path,
+                'description': self.request.description,
+            },
+        )
 
     def test_post_superuser(self):
         """Test POST as superuser"""
@@ -1406,7 +1422,7 @@ def test_post_invalid_form_data(self):
 class TestIrodsDataRequestDeleteView(
     IrodsDataRequestMixin, IrodsDataRequestViewTestBase
 ):
-    """Tests for IrodsDataRequestUpdateView"""
+    """Tests for IrodsDataRequestDeleteView"""
 
     def setUp(self):
         super().setUp()
@@ -1415,8 +1431,8 @@ def setUp(self):
             kwargs={'project': self.project.sodar_uuid},
         )
 
-    def test_delete_contributor(self):
-        """Test POST request for deleting a request"""
+    def test_post(self):
+        """Test IrodsDataRequestDeleteView POST"""
         # NOTE: We use post() to ensure alerts are created
         with self.login(self.user_contributor):
             self.client.post(self.create_url, self.post_data)
@@ -1448,13 +1464,16 @@ def test_delete_contributor(self):
         )
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         self.assert_irods_obj(self.obj_path)
-        # Create requests should be deleted
         self._assert_tl_count(EVENT_DELETE, 1)
+        self.assertEqual(
+            ProjectEvent.objects.get(event_name=EVENT_DELETE).extra_data, {}
+        )
+        # Create alerts should be deleted
         self._assert_alert_count(EVENT_CREATE, self.user, 0)
         self._assert_alert_count(EVENT_CREATE, self.user_delegate, 0)
 
-    def test_delete_one_of_multiple(self):
-        """Test deleting one of multiple requests"""
+    def test_post_one_of_multiple(self):
+        """Test POST for one of multiple requests"""
         self._assert_tl_count(EVENT_DELETE, 0)
         obj_path2 = os.path.join(self.assay_path, IRODS_FILE_NAME2)
         self.irods.data_objects.create(obj_path2)
@@ -1500,8 +1519,8 @@ def setUp(self):
             kwargs={'project': self.project.sodar_uuid},
         )
 
-    def test_render(self):
-        """Test rendering IrodsDataRequestAcceptView"""
+    def test_get(self):
+        """Test IrodsDataRequestAcceptView GET"""
         self.assert_irods_obj(self.obj_path)
         self.make_irods_request(
             project=self.project,
@@ -1523,8 +1542,8 @@ def test_render(self):
             )
         self.assertEqual(response.context['request_objects'][0], obj)
 
-    def test_render_coll(self):
-        """Test rendering IrodsDataRequestAcceptView with collection request"""
+    def test_get_coll(self):
+        """Test GET with collection request"""
         coll_path = os.path.join(self.assay_path, 'request_coll')
         self.irods.collections.create(coll_path)
         self.assertEqual(self.irods.collections.exists(coll_path), True)
@@ -1547,8 +1566,8 @@ def test_render_coll(self):
             )
         self.assertEqual(response.context['request_objects'][0], request)
 
-    def test_accept(self):
-        """Test accepting a delete request"""
+    def test_post(self):
+        """Test POST to accept delete request"""
         self.assert_irods_obj(self.obj_path)
         with self.login(self.user_contributor):
             self.client.post(self.create_url, self.post_data)
@@ -1589,8 +1608,8 @@ def test_accept(self):
         self._assert_alert_count(EVENT_ACCEPT, self.user_delegate, 0)
         self.assert_irods_obj(self.obj_path, False)
 
-    def test_accept_no_request(self):
-        """Test accepting non-existing delete request"""
+    def test_post_no_request(self):
+        """Test POST with non-existing delete request"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         with self.login(self.user_owner_cat):
             response = self.client.post(
@@ -1602,8 +1621,8 @@ def test_accept_no_request(self):
             )
         self.assertEqual(response.status_code, 404)
 
-    def test_accept_invalid_form_data(self):
-        """Test accepting delete request with invalid form data"""
+    def test_post_invalid_data(self):
+        """Test POST with invalid form data"""
         self.assert_irods_obj(self.obj_path)
         with self.login(self.user_contributor):
             self.client.post(self.create_url, self.post_data)
@@ -1636,8 +1655,8 @@ def test_accept_invalid_form_data(self):
         self._assert_alert_count(EVENT_ACCEPT, self.user_delegate, 0)
         self.assert_irods_obj(self.obj_path)
 
-    def test_accept_owner(self):
-        """Test accepting delete request as owner"""
+    def test_post_as_owner(self):
+        """Test POST as owner"""
         self.assert_irods_obj(self.obj_path)
         request = self.make_irods_request(
             project=self.project,
@@ -1666,8 +1685,8 @@ def test_accept_owner(self):
         self._assert_alert_count(EVENT_ACCEPT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_ACCEPT, self.user_contributor, 1)
 
-    def test_accept_delegate(self):
-        """Test accepting delete request as delegate"""
+    def test_post_delegate(self):
+        """Test POST as delegate"""
         self.assert_irods_obj(self.obj_path)
         request = self.make_irods_request(
             project=self.project,
@@ -1696,8 +1715,8 @@ def test_accept_delegate(self):
         self._assert_alert_count(EVENT_ACCEPT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_ACCEPT, self.user_contributor, 1)
 
-    def test_accept_contributor(self):
-        """Test accepting delete request as contributor"""
+    def test_post_contributor(self):
+        """Test POST as contributor"""
         self.assert_irods_obj(self.obj_path)
         request = self.make_irods_request(
             project=self.project,
@@ -1727,8 +1746,8 @@ def test_accept_contributor(self):
         self._assert_alert_count(EVENT_ACCEPT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_ACCEPT, self.user_contributor, 0)
 
-    def test_accept_one_of_multiple(self):
-        """Test accepting one of multiple requests"""
+    def test_post_one_of_multiple(self):
+        """Test POST for one of multiple requests"""
         obj_path2 = os.path.join(self.assay_path, IRODS_FILE_NAME2)
         self.irods.data_objects.create(obj_path2)
         self.assert_irods_obj(self.obj_path)
@@ -1772,8 +1791,8 @@ def test_accept_one_of_multiple(self):
         self.assert_irods_obj(obj_path2, False)
 
     @override_settings(REDIS_URL=INVALID_REDIS_URL)
-    def test_accept_lock_failure(self):
-        """Test accepting a delete request with project lock failure"""
+    def test_post_lock_failure(self):
+        """Test POST with project lock failure"""
         self.assert_irods_obj(self.obj_path)
         with self.login(self.user_contributor):
             self.client.post(self.create_url, self.post_data)
@@ -1804,8 +1823,8 @@ def test_accept_lock_failure(self):
         self._assert_alert_count(EVENT_CREATE, self.user_delegate, 1)
         self.assert_irods_obj(self.obj_path, True)
 
-    def test_accept_collection(self):
-        """Test accepting a collection request with multiple objects inside"""
+    def test_post_collection(self):
+        """Test POST with multiple objects in collection"""
         coll_path = os.path.join(self.assay_path, 'request_coll')
         obj_path2 = os.path.join(coll_path, IRODS_FILE_NAME)
         self.irods.collections.create(coll_path)
@@ -1858,8 +1877,8 @@ def setUp(self):
             kwargs={'project': self.project.sodar_uuid},
         )
 
-    def test_render(self):
-        """Test rendering IrodsDataRequestAcceptBatchView"""
+    def test_get(self):
+        """Test IrodsDataRequestAcceptBatchView GET"""
         self.assert_irods_obj(self.obj_path)
         self.make_irods_request(
             project=self.project,
@@ -1911,8 +1930,8 @@ def test_render(self):
             IrodsDataRequest.objects.last(),
         )
 
-    def test_render_coll(self):
-        """Test rendering IrodsDataRequestAcceptBatchView for a collection"""
+    def test_get_coll(self):
+        """Test GET with collection"""
         coll_path = os.path.join(self.assay_path, 'request_coll')
         self.irods.collections.create(coll_path)
         self.assertEqual(self.irods.collections.exists(coll_path), True)
@@ -1946,8 +1965,8 @@ def test_render_coll(self):
             response.context['affected_object_paths'][0], coll_path
         )
 
-    def test_accept(self):
-        """Test accepting a delete request"""
+    def test_post(self):
+        """Test POST to accept delete requests"""
         self.assert_irods_obj(self.obj_path)
         self.assert_irods_obj(self.obj_path2)
 
@@ -2014,8 +2033,8 @@ def test_accept(self):
         self.assert_irods_obj(self.obj_path, False)
         self.assert_irods_obj(self.obj_path2, False)
 
-    def test_accept_no_request(self):
-        """Test accepting a delete request that doesn't exist"""
+    def test_post_no_request(self):
+        """Test POST with non-existing delete request"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         with self.login(self.user_owner_cat):
             response = self.client.post(
@@ -2031,8 +2050,8 @@ def test_accept_no_request(self):
             NO_REQUEST_MSG,
         )
 
-    def test_accept_invalid_form_data(self):
-        """Test accepting a delete request with invalid form data"""
+    def test_post_invalid_data(self):
+        """Test POST with invalid form data"""
         self.assert_irods_obj(self.obj_path)
         self.assert_irods_obj(self.obj_path2)
 
@@ -2074,8 +2093,8 @@ def test_accept_invalid_form_data(self):
         self.assert_irods_obj(self.obj_path2)
 
     @override_settings(REDIS_URL=INVALID_REDIS_URL)
-    def test_accept_lock_failure(self):
-        """Test accepting a delete request with redis lock failure"""
+    def test_post_lock_failure(self):
+        """Test POST with project lock failure"""
         self.assert_irods_obj(self.obj_path)
         self.assert_irods_obj(self.obj_path2)
 
@@ -2135,8 +2154,8 @@ def setUp(self):
             kwargs={'project': self.project.sodar_uuid},
         )
 
-    def test_reject_admin(self):
-        """Test rejecting delete request as admin"""
+    def test_get_admin(self):
+        """Test IrodsDataRequestRejectView GET as admin"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         self.assert_irods_obj(self.obj_path)
         self._assert_alert_count(EVENT_REJECT, self.user, 0)
@@ -2178,8 +2197,8 @@ def test_reject_admin(self):
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_contributor, 1)
 
-    def test_reject_owner(self):
-        """Test rejecting delete request as owner"""
+    def test_get_owner(self):
+        """Test GET as owner"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         request = self.make_irods_request(
             project=self.project,
@@ -2203,8 +2222,8 @@ def test_reject_owner(self):
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_contributor, 1)
 
-    def test_reject_delegate(self):
-        """Test rejecting delete request as delegate"""
+    def test_get_delegate(self):
+        """Test GET as delegate"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         request = self.make_irods_request(
             project=self.project,
@@ -2228,8 +2247,8 @@ def test_reject_delegate(self):
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_contributor, 1)
 
-    def test_reject_contributor(self):
-        """Test rejecting delete request as contributor"""
+    def test_get_contributor(self):
+        """Test GET as contributor"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         request = self.make_irods_request(
             project=self.project,
@@ -2257,8 +2276,8 @@ def test_reject_contributor(self):
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_contributor, 0)
 
-    def test_reject_one_of_multiple(self):
-        """Test rejecting one of multiple requests"""
+    def test_get_one_of_multiple(self):
+        """Test GET with one of multiple requests"""
         obj_path2 = os.path.join(self.assay_path, IRODS_FILE_NAME2)
         self.irods.data_objects.create(obj_path2)
         self.assert_irods_obj(self.obj_path)
@@ -2299,8 +2318,8 @@ def test_reject_one_of_multiple(self):
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_contributor, 1)
 
-    def test_reject_no_request(self):
-        """Test rejecting delete request that doesn't exist"""
+    def test_get_no_request(self):
+        """Test GET with non-existing delete request"""
         with self.login(self.user_owner_cat):
             response = self.client.get(
                 reverse(
@@ -2327,8 +2346,8 @@ def setUp(self):
             kwargs={'project': self.project.sodar_uuid},
         )
 
-    def test_reject(self):
-        """Test rejecting delete request"""
+    def test_post(self):
+        """Test IrodsDataRequestRejectBatchView POST"""
         self.assertEqual(IrodsDataRequest.objects.count(), 0)
         self._assert_alert_count(EVENT_REJECT, self.user, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
@@ -2378,8 +2397,8 @@ def test_reject(self):
         self._assert_alert_count(EVENT_REJECT, self.user_delegate, 0)
         self._assert_alert_count(EVENT_REJECT, self.user_contributor, 0)
 
-    def test_reject_no_request(self):
-        """Test rejecting delete request that doesn't exist"""
+    def test_post_no_request(self):
+        """Test POST with non-existing request"""
         with self.login(self.user_owner_cat):
             response = self.client.post(
                 self.reject_url,
diff --git a/samplesheets/views.py b/samplesheets/views.py
index b3550dbf..d2ae8daf 100644
--- a/samplesheets/views.py
+++ b/samplesheets/views.py
@@ -794,43 +794,30 @@ def __init__(self):
 
     # Timeline helpers ---------------------------------------------------------
 
-    def add_tl_create(self, irods_request):
+    def add_tl_event(self, irods_request, action):
         """
-        Create timeline event for iRODS data request creation.
-
-        :param irods_request: IrodsDataRequest object
-        """
-        if not self.timeline:
-            return
-        tl_event = self.timeline.add_event(
-            project=irods_request.project,
-            app_name=APP_NAME,
-            user=irods_request.user,
-            event_name=IRODS_REQUEST_EVENT_CREATE,
-            description='create iRODS data request {irods_request}',
-            status_type='OK',
-        )
-        tl_event.add_object(
-            obj=irods_request,
-            label='irods_request',
-            name=irods_request.get_display_name(),
-        )
-
-    def add_tl_update(self, irods_request):
-        """
-        Create timeline event for iRODS data request update.
+        Create timeline event for iRODS data request modification.
 
         :param irods_request: IrodsDataRequest object
+        :param action: 'create', 'update' or 'delete' (string)
         """
         if not self.timeline:
             return
+        extra_data = {}
+        if action in ['create', 'update']:
+            extra_data = {
+                'action': irods_request.action,
+                'path': irods_request.path,
+                'description': irods_request.description,
+            }
         tl_event = self.timeline.add_event(
             project=irods_request.project,
             app_name=APP_NAME,
             user=irods_request.user,
-            event_name=IRODS_REQUEST_EVENT_UPDATE,
-            description='update iRODS data request {irods_request}',
+            event_name='irods_request_{}'.format(action),
+            description=action + ' iRODS data request {irods_request}',
             status_type='OK',
+            extra_data=extra_data,
         )
         tl_event.add_object(
             obj=irods_request,
@@ -838,28 +825,6 @@ def add_tl_update(self, irods_request):
             name=irods_request.get_display_name(),
         )
 
-    def add_tl_delete(self, irods_request):
-        """
-        Create timeline event for iRODS data request deletion.
-
-        :param irods_request: IrodsDataRequest object
-        """
-        if not self.timeline:
-            return
-        tl_event = self.timeline.add_event(
-            project=irods_request.project,
-            app_name=APP_NAME,
-            user=irods_request.user,
-            event_name=IRODS_REQUEST_EVENT_DELETE,
-            description='delete iRODS data request {irods_request}',
-            status_type='OK',
-        )
-        tl_event.add_object(
-            obj=irods_request,
-            label='irods_request',
-            name=str(irods_request),
-        )
-
     # App Alert Helpers --------------------------------------------------------
 
     def add_alerts_create(self, project, app_alerts=None):
@@ -2495,7 +2460,7 @@ def form_valid(self, form):
         obj.project = project
         obj.save()
         # Create timeline event
-        self.add_tl_create(obj)
+        self.add_tl_event(obj, 'create')
         # Add app alerts to owners/delegates
         self.add_alerts_create(project)
         messages.success(
@@ -2543,7 +2508,7 @@ def get_form_kwargs(self):
 
     def form_valid(self, form):
         obj = form.save()
-        self.add_tl_update(obj)
+        self.add_tl_event(obj, 'update')
         messages.success(
             self.request,
             'iRODS data request "{}" updated.'.format(obj.get_display_name()),
@@ -2582,7 +2547,7 @@ def has_permission(self):
 
     def get_success_url(self):
         # Add timeline event
-        self.add_tl_delete(self.object)
+        self.add_tl_event(self.object, 'delete')
         # Handle project alerts
         self.handle_alerts_deactivate(self.object)
         messages.success(self.request, 'iRODS data request deleted.')
diff --git a/samplesheets/views_ajax.py b/samplesheets/views_ajax.py
index 066a553f..a2c79e40 100644
--- a/samplesheets/views_ajax.py
+++ b/samplesheets/views_ajax.py
@@ -1873,7 +1873,7 @@ def post(self, request, *args, **kwargs):
         )
 
         # Create timeline event
-        self.add_tl_create(irods_request)
+        self.add_tl_event(irods_request, 'create')
         # Add app alerts to owners/delegates
         self.add_alerts_create(project)
         return Response(
@@ -1911,16 +1911,12 @@ def post(self, request, *args, **kwargs):
             )
 
         # Add timeline event
-        self.add_tl_delete(irods_request)
+        self.add_tl_event(irods_request, 'delete')
         # Handle project alerts
         self.handle_alerts_deactivate(irods_request)
         irods_request.delete()
         return Response(
-            {
-                'detail': 'ok',
-                'status': None,
-                'user': None,
-            },
+            {'detail': 'ok', 'status': None, 'user': None},
             status=200,
         )
 
diff --git a/samplesheets/views_api.py b/samplesheets/views_api.py
index 0f7537d2..5506515a 100644
--- a/samplesheets/views_api.py
+++ b/samplesheets/views_api.py
@@ -588,7 +588,7 @@ class IrodsDataRequestCreateAPIView(
     def perform_create(self, serializer):
         serializer.save()
         # Create timeline event
-        self.add_tl_create(serializer.instance)
+        self.add_tl_event(serializer.instance, 'create')
         # Add app alerts to owners/delegates
         self.add_alerts_create(serializer.instance.project)
 
@@ -620,7 +620,7 @@ def perform_update(self, serializer):
             raise PermissionDenied
         serializer.save()
         # Add timeline event
-        self.add_tl_update(serializer.instance)
+        self.add_tl_event(serializer.instance, 'update')
 
 
 class IrodsDataRequestDestroyAPIView(
@@ -647,7 +647,7 @@ def perform_destroy(self, instance):
             raise PermissionDenied
         instance.delete()
         # Add timeline event
-        self.add_tl_delete(instance)
+        self.add_tl_event(instance, 'delete')
         # Handle project alerts
         self.handle_alerts_deactivate(instance)
 

From 5cf31c7a1e9b97da041e8b6562ab1bb86067e8e3 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Wed, 28 Feb 2024 16:22:13 +0100
Subject: [PATCH 25/33] add cram support (#1908, #1914)

---
 CHANGELOG.rst                                 |   3 +
 config/settings/base.py                       |   4 +-
 docs_manual/source/admin_settings.rst         |   2 +-
 docs_manual/source/ext_tool_igv_opening.rst   |   8 +-
 docs_manual/source/introduction.rst           |   2 +-
 docs_manual/source/metadata_advanced.rst      |  13 +-
 docs_manual/source/sodar_release_notes.rst    |  12 ++
 docs_manual/source/ui_project_update.rst      |   6 +-
 samplesheets/plugins.py                       |   8 +-
 samplesheets/studyapps/cancer/plugins.py      |   8 +-
 .../cancer/tests/test_plugins_taskflow.py     | 199 ++++++++++++++++--
 samplesheets/studyapps/cancer/utils.py        |  13 +-
 samplesheets/studyapps/germline/plugins.py    |  17 +-
 .../germline/tests/test_plugins_taskflow.py   | 153 +++++++++++++-
 samplesheets/studyapps/germline/utils.py      |   8 +-
 samplesheets/studyapps/tests/test_utils.py    |  35 ++-
 samplesheets/studyapps/utils.py               |  36 +++-
 samplesheets/tests/test_utils.py              |  20 +-
 18 files changed, 470 insertions(+), 77 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f0fc32b4..08fc022c 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -19,6 +19,8 @@ Added
     - UI tests for project details card (#1902)
 - **Samplesheets**
     - ``IrodsDataRequest`` timeline event extra data (#1912)
+    - CRAM file support in study apps (#1908)
+    - ``check_igv_file_suffix()`` helper in ``studyapps.utils`` (#1908)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
     - ``BatchSetAccessTask`` in iRODS tasks (#1905)
@@ -64,6 +66,7 @@ Fixed
     - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
     - Protocol ref editable for new row if disabled in column config (#1875)
     - Sheet template creation failure with slash characters in title/ID fields (#1896)
+    - ``get_pedigree_file_path()`` used in cancer study app tests (#1914)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)
diff --git a/config/settings/base.py b/config/settings/base.py
index d9df4e87..813a8c01 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -807,11 +807,11 @@ def set_logging(level=None):
 # Remote sample sheet sync interval in minutes
 SHEETS_SYNC_INTERVAL = env.int('SHEETS_SYNC_INTERVAL', 5)
 
-# BAM file name suffixes to omit from study shortcuts and IGV session generation
+# BAM/CRAM file name suffixes to omit from study shortcuts and IGV sessions
 SHEETS_IGV_OMIT_BAM = env.list(
     'SHEETS_IGV_OMIT_BAM', default=['dragen_evidence.bam']
 )
-# VCF file name suffixes to omit from study shortcuts and IGV session generation
+# VCF file name suffixes to omit from study shortcuts and IGV sessions
 SHEETS_IGV_OMIT_VCF = env.list(
     'SHEETS_IGV_OMIT_VCF', default=['cnv.vcf.gz', 'ploidy.vcf.gz', 'sv.vcf.gz']
 )
diff --git a/docs_manual/source/admin_settings.rst b/docs_manual/source/admin_settings.rst
index ec32895a..016e7e60 100644
--- a/docs_manual/source/admin_settings.rst
+++ b/docs_manual/source/admin_settings.rst
@@ -193,7 +193,7 @@ Sample Sheets Settings
 ``SHEETS_SYNC_INTERVAL``
     Interval for remote sheet synchronization in minutes (integer).
 ``SHEETS_IGV_OMIT_BAM``
-    BAM file name suffixes to omit from study shortcuts and IGV session
+    BAM and CRAM file name suffixes to omit from study shortcuts and IGV session
     generation.
 ``SHEETS_IGV_OMIT_VCF``
     VCF file name suffixes to omit from study shortcuts and IGV session
diff --git a/docs_manual/source/ext_tool_igv_opening.rst b/docs_manual/source/ext_tool_igv_opening.rst
index 8512e4b2..f5bd2b61 100644
--- a/docs_manual/source/ext_tool_igv_opening.rst
+++ b/docs_manual/source/ext_tool_igv_opening.rst
@@ -35,8 +35,8 @@ The IGV session can be opened replacing the currently open session in IGV.
 Another option is to merge the session into the currently open one with the
 button displaying a plus icon.
 
-BAM and VCF files can be similarly loaded into the currently open IGV session by
-clicking the corresponding button with a plus icon.
+BAM/CRAM and VCF files can be similarly loaded into the currently open IGV
+session by clicking the corresponding button with a plus icon.
 
 .. image:: _static/ext_tool_igv/IGV_Study_Shortcuts.png
     :width: 75%
@@ -49,8 +49,8 @@ Obtaining File URLs
 You can also obtain URLs into the SODAR file serving sub system.
 
 The donor or pedigree names in the IGV links window depicted above link directly
-to the BAM and VCF files in the file serving sub system. Right-click the link
-and use the "copy link location" context menu entry to copy the File URL.
+to the BAM/CRAM and VCF files in the file serving sub system. Right-click the
+link and use the "copy link location" context menu entry to copy the File URL.
 
 You can then open this link in IGV using the "File" > "Load from URL" command.
 Paste the URL that you just copied into the "File URL" field of the window that
diff --git a/docs_manual/source/introduction.rst b/docs_manual/source/introduction.rst
index e03b93ae..2bc1cee6 100644
--- a/docs_manual/source/introduction.rst
+++ b/docs_manual/source/introduction.rst
@@ -81,7 +81,7 @@ Notable Features
     * Sample sheet generation from templates
     * Sample sheet editing and version control
     * Sample sheet export in ISA-Tab and Excel formats
-    * Automated iRODS shortcut generation for e.g. BAM/VCF files
+    * Automated iRODS shortcut generation for BAM/CRAM/VCF files
     * Automated Integrative Genomics Viewer (IGV) session file generation and
       merging
     * Track hub management for UCSC Genome Browser integration
diff --git a/docs_manual/source/metadata_advanced.rst b/docs_manual/source/metadata_advanced.rst
index a5c0cd5a..774b0701 100644
--- a/docs_manual/source/metadata_advanced.rst
+++ b/docs_manual/source/metadata_advanced.rst
@@ -26,11 +26,13 @@ SODAR currently supports the following study configurations:
 - **Cancer**
     * Indended for: Cancer studies
     * Configuration: ``bih_cancer``
-    * Provides: **sample specific** shortcuts to the latest BAM and VCF files.
+    * Provides: **sample specific** shortcuts to the latest BAM/CRAM and VCF
+      files.
 - **Germline**
     * Indended for: Germline studies
     * Configuration: ``bih_germline``
-    * Provides: **pedigree specific** shortcuts to the latest BAM and VCF files.
+    * Provides: **pedigree specific** shortcuts to the latest BAM/CRAM and VCF
+      files.
 
 If the configuration is not specified or is not known to SODAR, the shortcut
 column will not be visible.
@@ -44,11 +46,12 @@ Placement of files in subcollections under the row-specific collection does not
 affect study shortcuts or IGV session inclusion. This also means files can be
 freely organized within desired subcollections.
 
-If there is need to omit BAM or VCF files with certain file name patterns from
-shortcuts and IGV sessions, file name suffixes can be defined in the
+If there is need to omit BAM/CRAM or VCF files with certain file name patterns
+from shortcuts and IGV sessions, file name suffixes can be defined in the
 :ref:`project update view <ui_project_update>`. Administrators can also define
 site-wide file suffixes to omit via :ref:`Django settings <admin_settings>`
-under ``SHEETS_IGV_OMIT_BAM`` and ``SHEETS_IGV_OMIT_VCF``.
+under ``SHEETS_IGV_OMIT_BAM`` (also affects CRAM files) and
+``SHEETS_IGV_OMIT_VCF``.
 
 
 Assay iRODS Data Linking
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 4af59d98..97409657 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -13,6 +13,7 @@ v0.14.2 (WIP)
 
 Release for minor updates, maintenance and bug fixes.
 
+- Add CRAM file support for cancer/germline study links and IGV sessions
 - Add assay plugin shortcut collection creation in landing zones
 - Add iRODS data request details in timeline events
 - Add landing zone statistics in siteinfo
@@ -25,6 +26,17 @@ Release for minor updates, maintenance and bug fixes.
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.4
 
+Migration Guide
+---------------
+
+CRAM File Support
+    This release adds support for CRAM files. They are linked in studies and IGV
+    sessions similar to BAM files. If your project contains CRAM files uploaded
+    prior to this release, you will have to run :guilabel:`Update Sheet Cache`
+    in the Sample Sheets app to enable the files in study links and generated
+    IGV sessions. Alternatively, an administrator can run the ``synccache``
+    management command to update all projects or a specific project.
+
 
 v0.14.1 (2023-12-12)
 ====================
diff --git a/docs_manual/source/ui_project_update.rst b/docs_manual/source/ui_project_update.rst
index 7161e970..5f387d3b 100644
--- a/docs_manual/source/ui_project_update.rst
+++ b/docs_manual/source/ui_project_update.rst
@@ -53,9 +53,9 @@ Token for Sheet Synchronization
 IGV session genome
     Genome used in generating IGV session files for the project. The name needs
     to be in a format accepted by IGV. Affects cancer and germline projects.
-BAM files to omit from IGV sessions
-    Comma separated list of BAM file suffixes to omit from IGV sessions.
-    Overrides site-wide setting, affects cancer and germline projects.
+BAM and CRAM files to omit from IGV sessions
+    Comma separated list of BAM and CRAM file suffixes to omit from IGV
+    sessions. Overrides site-wide setting, affects cancer and germline projects.
 VCF files to omit from IGV sessions
     Comma separated list of VCF file suffixes to omit from IGV sessions.
     Overrides site-wide setting, affects cancer and germline projects.
diff --git a/samplesheets/plugins.py b/samplesheets/plugins.py
index d4959049..b689fe5f 100644
--- a/samplesheets/plugins.py
+++ b/samplesheets/plugins.py
@@ -213,12 +213,12 @@ class ProjectAppPlugin(
         'igv_omit_bam': {
             'scope': SODAR_CONSTANTS['APP_SETTING_SCOPE_PROJECT'],
             'type': 'STRING',
-            'label': 'BAM files to omit from IGV sessions',
+            'label': 'BAM and CRAM files to omit from IGV sessions',
             'default': '',
             'placeholder': ', '.join(settings.SHEETS_IGV_OMIT_BAM),
-            'description': 'Comma separated list of BAM file suffixes to omit '
-            'from generated IGV sessions. Overrides site-wide setting, affects '
-            'cancer and germline projects.',
+            'description': 'Comma separated list of BAM and CRAM file suffixes '
+            'to omit from generated IGV sessions. Overrides site-wide setting, '
+            'affects cancer and germline projects.',
             'user_modifiable': True,
         },
         'igv_omit_vcf': {
diff --git a/samplesheets/studyapps/cancer/plugins.py b/samplesheets/studyapps/cancer/plugins.py
index 039acd83..05c77016 100644
--- a/samplesheets/studyapps/cancer/plugins.py
+++ b/samplesheets/studyapps/cancer/plugins.py
@@ -85,8 +85,8 @@ def get_shortcut_column(self, study, study_tables):
                 'files': {
                     'type': 'modal',
                     'icon': 'mdi:folder-open-outline',
-                    'title': 'View links to BAM, VCF and IGV session files '
-                    'for the case',
+                    'title': 'View links to BAM/CRAM, VCF and IGV session '
+                    'files for the case',
                 },
             },
             'data': [],
@@ -172,7 +172,7 @@ def get_shortcut_links(self, study, study_tables, **kwargs):
             'title': 'Case-Wise Links for {}'.format(case_id),
             'data': {
                 'session': {'title': 'IGV Session File', 'files': []},
-                'bam': {'title': 'BAM Files', 'files': []},
+                'bam': {'title': 'BAM/CRAM Files', 'files': []},
                 'vcf': {'title': 'VCF Files', 'files': []},
             },
         }
@@ -190,7 +190,7 @@ def _add_lib_path(library_name, file_type):
                         'extra_links': [
                             {
                                 'label': 'Add {} file to IGV'.format(
-                                    file_type.upper()
+                                    'BAM/CRAM' if file_type == 'bam' else 'VCF'
                                 ),
                                 'icon': 'mdi:plus-thick',
                                 'url': get_igv_irods_url(path, merge=True),
diff --git a/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py b/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py
index ac4604a9..e85f30cc 100644
--- a/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py
+++ b/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py
@@ -3,6 +3,7 @@
 import os
 
 from django.conf import settings
+from django.test import override_settings
 from django.urls import reverse
 
 # Projectroles dependency
@@ -18,7 +19,7 @@
 from samplesheets.tests.test_models import SampleSheetModelMixin
 from samplesheets.tests.test_views_taskflow import SampleSheetTaskflowMixin
 from samplesheets.plugins import SampleSheetStudyPluginPoint
-from samplesheets.studyapps.germline.utils import get_pedigree_file_path
+from samplesheets.studyapps.cancer.utils import get_library_file_path
 from samplesheets.studyapps.utils import get_igv_session_url
 
 
@@ -143,6 +144,28 @@ def test_get_shortcut_column_files(self):
             self.assertEqual(sc['data'][i]['igv']['enabled'], False)
             self.assertEqual(sc['data'][i]['files']['enabled'], False)
 
+    def test_get_shortcut_column_cram(self):
+        """Test get_shortcut_column() with CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID_NORMAL)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.irods.data_objects.create(vcf_path)
+
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sc = self.plugin.get_shortcut_column(self.study, study_tables)
+
+        self.assertEqual(sc['data'][0]['igv']['enabled'], True)
+        self.assertEqual(sc['data'][0]['files']['enabled'], True)
+        for i in range(1, 4):
+            self.assertEqual(sc['data'][i]['igv']['enabled'], False)
+            self.assertEqual(sc['data'][i]['files']['enabled'], False)
+
     def test_get_shortcut_links(self):
         """Test get_shortcut_links() with no cache item or files"""
         study_tables = self.tb.build_study_tables(self.study)
@@ -197,21 +220,84 @@ def test_get_shortcut_links_files(self):
         self.assertEqual(
             sl['data']['bam']['files'][0]['url'],
             settings.IRODS_WEBDAV_URL
-            + get_pedigree_file_path('bam', self.source, study_tables),
+            + get_library_file_path(
+                self.assay,
+                LIBRARY_ID_NORMAL,
+                'bam',
+                self.irods_backend,
+                self.irods,
+            ),
+        )
+        self.assertEqual(
+            sl['data']['vcf']['files'][0]['url'],
+            settings.IRODS_WEBDAV_URL
+            + get_library_file_path(
+                self.assay,
+                LIBRARY_ID_NORMAL,
+                'vcf',
+                self.irods_backend,
+                self.irods,
+            ),
+        )
+
+    def test_get_shortcut_links_cram(self):
+        """Test get_shortcut_links() with CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID_NORMAL)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.irods.data_objects.create(vcf_path)
+
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, case=[SOURCE_ID_NORMAL]
+        )
+
+        self.assertEqual(len(sl['data']['session']['files']), 1)
+        self.assertEqual(len(sl['data']['bam']['files']), 1)
+        self.assertEqual(len(sl['data']['vcf']['files']), 1)
+        self.assertEqual(
+            sl['data']['session']['files'][0]['url'],
+            reverse(
+                'samplesheets.studyapps.cancer:igv',
+                kwargs={'genericmaterial': self.source.sodar_uuid},
+            ),
+        )
+        self.assertEqual(
+            sl['data']['bam']['files'][0]['url'],
+            settings.IRODS_WEBDAV_URL
+            + get_library_file_path(
+                self.assay,
+                LIBRARY_ID_NORMAL,
+                'bam',
+                self.irods_backend,
+                self.irods,
+            ),
         )
         self.assertEqual(
             sl['data']['vcf']['files'][0]['url'],
             settings.IRODS_WEBDAV_URL
-            + get_pedigree_file_path('vcf', self.source, study_tables),
+            + get_library_file_path(
+                self.assay,
+                LIBRARY_ID_NORMAL,
+                'vcf',
+                self.irods_backend,
+                self.irods,
+            ),
         )
 
     def test_get_shortcut_links_multiple(self):
         """Test get_shortcut_links() with multiple BAM/VCF files"""
         self.irods.collections.create(self.source_path)
-        bam_path = os.path.join(
-            self.source_path, '{}_test_2022-11-06.bam'.format(SAMPLE_ID_NORMAL)
+        cram_path = os.path.join(
+            self.source_path, '{}_test_2022-11-06.cram'.format(SAMPLE_ID_NORMAL)
         )
-        bam_path2 = os.path.join(
+        bam_path = os.path.join(
             self.source_path, '{}_test_2022-11-07.bam'.format(SAMPLE_ID_NORMAL)
         )
         vcf_path = os.path.join(
@@ -222,8 +308,8 @@ def test_get_shortcut_links_multiple(self):
             self.source_path,
             '{}_test.vcf_2022-11-07.vcf.gz'.format(SAMPLE_ID_NORMAL),
         )
+        self.irods.data_objects.create(cram_path)
         self.irods.data_objects.create(bam_path)
-        self.irods.data_objects.create(bam_path2)
         self.irods.data_objects.create(vcf_path)
         self.irods.data_objects.create(vcf_path2)
 
@@ -237,14 +323,12 @@ def test_get_shortcut_links_multiple(self):
         # Only the most recent bam and vcf should be returned
         self.assertEqual(len(sl['data']['bam']['files']), 1)
         self.assertEqual(len(sl['data']['vcf']['files']), 1)
-        self.assertTrue(
-            sl['data']['bam']['files'][0]['url'].endswith(bam_path2)
-        )
+        self.assertTrue(sl['data']['bam']['files'][0]['url'].endswith(bam_path))
         self.assertTrue(
             sl['data']['vcf']['files'][0]['url'].endswith(vcf_path2)
         )
 
-    def test_get_shortcut_links_bam(self):
+    def test_get_shortcut_links_bam_only(self):
         """Test get_shortcut_links() with BAM file only"""
         self.irods.collections.create(self.source_path)
         bam_path = os.path.join(
@@ -260,7 +344,23 @@ def test_get_shortcut_links_bam(self):
         self.assertEqual(len(sl['data']['bam']['files']), 1)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    def test_get_shortcut_links_vcf(self):
+    def test_get_shortcut_links_cram_only(self):
+        """Test get_shortcut_links() with CRAM file only"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, case=[SOURCE_ID_NORMAL]
+        )
+        self.assertEqual(len(sl['data']['session']['files']), 1)
+        self.assertEqual(len(sl['data']['bam']['files']), 1)
+        self.assertEqual(len(sl['data']['vcf']['files']), 0)
+
+    def test_get_shortcut_links_vcf_only(self):
         """Test get_shortcut_links() with VCF file only"""
         self.irods.collections.create(self.source_path)
         vcf_path = os.path.join(
@@ -332,12 +432,24 @@ def test_get_shortcut_links_files_omit(self):
         self.assertEqual(
             sl['data']['bam']['files'][0]['url'],
             settings.IRODS_WEBDAV_URL
-            + get_pedigree_file_path('bam', self.source, study_tables),
+            + get_library_file_path(
+                self.assay,
+                LIBRARY_ID_NORMAL,
+                'bam',
+                self.irods_backend,
+                self.irods,
+            ),
         )
         self.assertEqual(
             sl['data']['vcf']['files'][0]['url'],
             settings.IRODS_WEBDAV_URL
-            + get_pedigree_file_path('vcf', self.source, study_tables),
+            + get_library_file_path(
+                self.assay,
+                LIBRARY_ID_NORMAL,
+                'vcf',
+                self.irods_backend,
+                self.irods,
+            ),
         )
 
     def test_get_shortcut_links_files_omit_only(self):
@@ -360,6 +472,23 @@ def test_get_shortcut_links_files_omit_only(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
+    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
+    def test_get_shortcut_links_files_omit_only_cram(self):
+        """Test get_shortcut_links() with omittable CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path_omit = os.path.join(
+            self.source_path, '{}_omit.cram'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(cram_path_omit)
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, case=[SOURCE_ID_NORMAL]
+        )
+        self.assertEqual(len(sl['data']['session']['files']), 0)
+        self.assertEqual(len(sl['data']['bam']['files']), 0)
+        self.assertEqual(len(sl['data']['vcf']['files']), 0)
+
     def test_get_shortcut_links_files_omit_override(self):
         """Test get_shortcut_links() with project-specific omit override"""
         app_settings.set(
@@ -425,6 +554,27 @@ def test_update_cache_files(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
+    def test_update_cache_files_cram(self):
+        """Test update_cache() with CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID_NORMAL)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.irods.data_objects.create(vcf_path)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        self.assertEqual(ci['bam'][CASE_IDS[0]], cram_path)
+        self.assertEqual(ci['vcf'][CASE_IDS[0]], vcf_path)
+        for i in range(1, len(CASE_IDS) - 1):
+            self.assertEqual(ci['bam'][CASE_IDS[i]], None)
+            self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
+
     def test_update_cache_files_omit(self):
         """Test update_cache() with omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
@@ -458,7 +608,6 @@ def test_update_cache_files_omit(self):
     def test_update_cache_files_omit_only(self):
         """Test update_cache() with only omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
-        # Create omittable files which come before real ones alphabetically
         bam_path_omit = os.path.join(
             self.source_path, '{}_dragen_evidence.bam'.format(SAMPLE_ID_NORMAL)
         )
@@ -475,6 +624,26 @@ def test_update_cache_files_omit_only(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
+    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
+    def test_update_cache_files_omit_only_cram(self):
+        """Test update_cache() with omittable CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path_omit = os.path.join(
+            self.source_path, '{}_omit.cram'.format(SAMPLE_ID_NORMAL)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(cram_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        for i in range(0, len(CASE_IDS) - 1):
+            self.assertEqual(ci['bam'][CASE_IDS[i]], None)
+            self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
+
     def test_update_cache_files_omit_override(self):
         """Test update_cache() with project-specific omit override"""
         app_settings.set(
diff --git a/samplesheets/studyapps/cancer/utils.py b/samplesheets/studyapps/cancer/utils.py
index 048d2e96..a5c38c75 100644
--- a/samplesheets/studyapps/cancer/utils.py
+++ b/samplesheets/studyapps/cancer/utils.py
@@ -4,8 +4,8 @@
 
 from samplesheets.studyapps.utils import (
     get_igv_omit_override,
+    check_igv_file_suffix,
     check_igv_file_name,
-    FILE_TYPE_SUFFIXES,
 )
 from samplesheets.utils import get_latest_file_path
 
@@ -13,11 +13,11 @@
 def get_library_file_path(assay, library_name, file_type, irods_backend, irods):
     """
     Return iRODS path for the most recent file of type "bam" or "vcf"
-    linked to the library.
+    linked to the library. CRAM files are included in "bam" searches.
 
     :param assay: Assay object
     :param library_name: Library name (string)
-    :param file_type: String ("bam" or "vcf")
+    :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
     :param irods_backend: IrodsAPI object
     :param irods: IRODSSession object
     :return: String
@@ -29,9 +29,10 @@ def get_library_file_path(assay, library_name, file_type, irods_backend, irods):
     try:
         obj_list = irods_backend.get_objects(irods, query_path)
         for obj in obj_list:
-            if obj['name'].lower().endswith(
-                FILE_TYPE_SUFFIXES[file_type]
-            ) and check_igv_file_name(obj['name'], file_type, override):
+            obj_name = obj['name'].lower()
+            if check_igv_file_suffix(
+                obj_name, file_type
+            ) and check_igv_file_name(obj_name, file_type, override):
                 file_paths.append(obj['path'])
     except Exception:
         pass
diff --git a/samplesheets/studyapps/germline/plugins.py b/samplesheets/studyapps/germline/plugins.py
index d2684f21..3e90f83a 100644
--- a/samplesheets/studyapps/germline/plugins.py
+++ b/samplesheets/studyapps/germline/plugins.py
@@ -15,6 +15,7 @@
 from samplesheets.rendering import SampleSheetTableBuilder
 from samplesheets.studyapps.utils import (
     get_igv_omit_override,
+    check_igv_file_suffix,
     check_igv_file_name,
     get_igv_session_url,
     get_igv_irods_url,
@@ -86,8 +87,8 @@ def get_shortcut_column(self, study, study_tables):
                 'files': {
                     'type': 'modal',
                     'icon': 'mdi:folder-open-outline',
-                    'title': 'View links to pedigree BAM, VCF and IGV session '
-                    'files',
+                    'title': 'View links to pedigree BAM/CRAM, VCF and IGV '
+                    'session files',
                 },
             },
             'data': [],
@@ -179,7 +180,7 @@ def get_shortcut_links(self, study, study_tables, **kwargs):
             'title': 'Pedigree-Wise Links for {}'.format(query_id),
             'data': {
                 'session': {'title': 'IGV Session File', 'files': []},
-                'bam': {'title': 'BAM Files', 'files': []},
+                'bam': {'title': 'BAM/CRAM Files', 'files': []},
                 'vcf': {'title': 'VCF File', 'files': []},
             },
         }
@@ -197,7 +198,7 @@ def get_shortcut_links(self, study, study_tables, **kwargs):
                 project=study.get_project(),
             )
 
-        # BAM links
+        # BAM/CRAM links
         for source in sources:
             # Use cached value if present
             if cache_item and source.name in cache_item.data['bam']:
@@ -211,10 +212,10 @@ def get_shortcut_links(self, study, study_tables, **kwargs):
                     {
                         'label': source.name,
                         'url': webdav_url + bam_path,
-                        'title': 'Download BAM file',
+                        'title': 'Download BAM/CRAM file',
                         'extra_links': [
                             {
-                                'label': 'Add BAM file to IGV',
+                                'label': 'Add BAM/CRAM file to IGV',
                                 'icon': 'mdi:plus-thick',
                                 'url': get_igv_irods_url(bam_path, merge=True),
                             }
@@ -342,7 +343,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                 source_name = row[0]['value']
                 if source_name not in bam_paths:
                     bam_paths[source_name] = []
-                # Add BAM objects
+                # Add BAM/CRAM objects
                 path = assay_plugin.get_row_path(
                     row, assay_table, assay, assay_path
                 )
@@ -351,7 +352,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                         o['path']
                         for o in study_objs
                         if o['path'].startswith(path + '/')
-                        and o['name'].lower().endswith('bam')
+                        and check_igv_file_suffix(o['name'], 'bam')
                         and check_igv_file_name(o['name'], 'bam', bam_override)
                     ]
                 row_fam = row[fam_idx]['value']
diff --git a/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py b/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
index db4e8f89..7fc66a7a 100644
--- a/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
+++ b/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
@@ -3,6 +3,7 @@
 import os
 
 from django.conf import settings
+from django.test import override_settings
 from django.urls import reverse
 
 # Projectroles dependency
@@ -140,6 +141,29 @@ def test_get_shortcut_column_files(self):
             self.assertEqual(sc['data'][i]['igv']['enabled'], False)
             self.assertEqual(sc['data'][i]['files']['enabled'], False)
 
+    def test_get_shortcut_column_cram_file(self):
+        """Test get_shortcut_column() with cache item and CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.irods.data_objects.create(vcf_path)
+
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sc = self.plugin.get_shortcut_column(self.study, study_tables)
+
+        for i in range(0, 2):
+            self.assertEqual(sc['data'][i]['igv']['enabled'], True)
+            self.assertEqual(sc['data'][i]['files']['enabled'], True)
+        for i in range(3, 5):
+            self.assertEqual(sc['data'][i]['igv']['enabled'], False)
+            self.assertEqual(sc['data'][i]['files']['enabled'], False)
+
     def test_get_shortcut_column_parent_vcf(self):
         """Test get_shortcut_column() with VCF file in a parent's collection"""
         self.irods.collections.create(self.parent_path)
@@ -266,14 +290,53 @@ def test_get_shortcut_links_files(self):
             + get_pedigree_file_path('vcf', self.source, study_tables),
         )
 
+    def test_get_shortcut_links_files_cram(self):
+        """Test get_shortcut_links() with CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.irods.data_objects.create(vcf_path)
+
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, family=[FAMILY_ID]
+        )
+
+        self.assertEqual(len(sl['data']['session']['files']), 1)
+        self.assertEqual(len(sl['data']['bam']['files']), 1)
+        self.assertEqual(len(sl['data']['vcf']['files']), 1)
+        self.assertEqual(
+            sl['data']['session']['files'][0]['url'],
+            reverse(
+                'samplesheets.studyapps.germline:igv',
+                kwargs={'genericmaterial': self.source.sodar_uuid},
+            ),
+        )
+        self.assertEqual(
+            sl['data']['bam']['files'][0]['url'],
+            settings.IRODS_WEBDAV_URL
+            + get_pedigree_file_path('bam', self.source, study_tables),
+        )
+        self.assertEqual(
+            sl['data']['vcf']['files'][0]['url'],
+            settings.IRODS_WEBDAV_URL
+            + get_pedigree_file_path('vcf', self.source, study_tables),
+        )
+
     def test_get_shortcut_links_multiple(self):
         """Test get_shortcut_links() with multiple BAM/VCF files"""
         self.irods.collections.create(self.source_path)
         bam_path = os.path.join(
             self.source_path, '{}_test_2022-11-06.bam'.format(SAMPLE_ID)
         )
-        bam_path2 = os.path.join(
-            self.source_path, '{}_test_2022-11-07.bam'.format(SAMPLE_ID)
+        cram_path = os.path.join(
+            self.source_path, '{}_test_2022-11-07.cram'.format(SAMPLE_ID)
         )
         vcf_path = os.path.join(
             self.source_path, '{}_test.vcf_2022-11-06.vcf.gz'.format(FAMILY_ID)
@@ -282,7 +345,7 @@ def test_get_shortcut_links_multiple(self):
             self.source_path, '{}_test.vcf_2022-11-07.vcf.gz'.format(FAMILY_ID)
         )
         self.irods.data_objects.create(bam_path)
-        self.irods.data_objects.create(bam_path2)
+        self.irods.data_objects.create(cram_path)
         self.irods.data_objects.create(vcf_path)
         self.irods.data_objects.create(vcf_path2)
 
@@ -293,17 +356,17 @@ def test_get_shortcut_links_multiple(self):
         )
 
         self.assertEqual(len(sl['data']['session']['files']), 1)
-        # Only the most recent bam and vcf should be returned
+        # Only the most recent bam/cram and vcf should be returned
         self.assertEqual(len(sl['data']['bam']['files']), 1)
         self.assertEqual(len(sl['data']['vcf']['files']), 1)
         self.assertTrue(
-            sl['data']['bam']['files'][0]['url'].endswith(bam_path2)
+            sl['data']['bam']['files'][0]['url'].endswith(cram_path)
         )
         self.assertTrue(
             sl['data']['vcf']['files'][0]['url'].endswith(vcf_path2)
         )
 
-    def test_get_shortcut_links_bam(self):
+    def test_get_shortcut_links_bam_only(self):
         """Test get_shortcut_links() with BAM file only"""
         self.irods.collections.create(self.source_path)
         bam_path = os.path.join(
@@ -319,7 +382,23 @@ def test_get_shortcut_links_bam(self):
         self.assertEqual(len(sl['data']['bam']['files']), 1)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    def test_get_shortcut_links_vcf(self):
+    def test_get_shortcut_links_cram_only(self):
+        """Test get_shortcut_links() with CRAM file only"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, family=[FAMILY_ID]
+        )
+        self.assertEqual(len(sl['data']['session']['files']), 1)
+        self.assertEqual(len(sl['data']['bam']['files']), 1)
+        self.assertEqual(len(sl['data']['vcf']['files']), 0)
+
+    def test_get_shortcut_links_vcf_only(self):
         """Test get_shortcut_links() with VCF file only"""
         self.irods.collections.create(self.source_path)
         vcf_path = os.path.join(
@@ -419,6 +498,28 @@ def test_get_shortcut_links_files_omit_only(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
+    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
+    def test_get_shortcut_links_files_omit_cram(self):
+        """Test get_shortcut_links() with omittable CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path_omit = os.path.join(
+            self.source_path, '{}_omit.cram'.format(SAMPLE_ID)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(cram_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, family=[FAMILY_ID]
+        )
+        self.assertEqual(len(sl['data']['session']['files']), 0)
+        self.assertEqual(len(sl['data']['bam']['files']), 0)
+        self.assertEqual(len(sl['data']['vcf']['files']), 0)
+
     def test_get_shortcut_links_files_omit_override(self):
         """Test get_shortcut_links() with project-specific omit override"""
         app_settings.set(
@@ -483,6 +584,25 @@ def test_update_cache_files(self):
         self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path)
         self.assertIsNone(ci['vcf'][FAMILY_ID2])
 
+    def test_update_cache_files_cram(self):
+        """Test update_cache() with CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path = os.path.join(
+            self.source_path, '{}_test.cram'.format(SAMPLE_ID)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(cram_path)
+        self.irods.data_objects.create(vcf_path)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        self.assertEqual(ci['bam'][self.source.name], cram_path)
+        self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path)
+        self.assertIsNone(ci['vcf'][FAMILY_ID2])
+
     def test_update_cache_files_omit(self):
         """Test update_cache() with omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
@@ -530,6 +650,25 @@ def test_update_cache_files_omit_only(self):
         self.assertIsNone(ci['bam'][self.source.name])
         self.assertIsNone(ci['vcf'][FAMILY_ID])
 
+    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
+    def test_update_cache_files_omit_only_cram(self):
+        """Test update_cache() with omittable CRAM file in iRODS"""
+        self.irods.collections.create(self.source_path)
+        cram_path_omit = os.path.join(
+            self.source_path, '{}_omit.cram'.format(SAMPLE_ID)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(cram_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        self.assertIsNone(ci['bam'][self.source.name])
+        self.assertIsNone(ci['vcf'][FAMILY_ID])
+
     def test_update_cache_files_omit_override(self):
         """Test update_cache() with project-specific omit override"""
         app_settings.set(
diff --git a/samplesheets/studyapps/germline/utils.py b/samplesheets/studyapps/germline/utils.py
index 3038488e..1c526d3f 100644
--- a/samplesheets/studyapps/germline/utils.py
+++ b/samplesheets/studyapps/germline/utils.py
@@ -9,7 +9,7 @@
 from samplesheets.studyapps.utils import (
     get_igv_omit_override,
     check_igv_file_name,
-    FILE_TYPE_SUFFIXES,
+    check_igv_file_suffix,
 )
 from samplesheets.utils import get_index_by_header
 
@@ -22,7 +22,7 @@ def get_pedigree_file_path(file_type, source, study_tables):
     Return iRODS path for the most recent file of type "bam" or "vcf"
     linked to the source.
 
-    :param file_type: String ("bam" or "vcf")
+    :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
     :param source: GenericMaterial of type SOURCE
     :param study_tables: Render study tables
     :return: String
@@ -84,9 +84,7 @@ def _get_val_by_index(row, idx):
             for obj in obj_list:
                 if (
                     obj['path'].startswith(query_path + '/')
-                    and obj['name']
-                    .lower()
-                    .endswith(FILE_TYPE_SUFFIXES[file_type])
+                    and check_igv_file_suffix(obj['name'], file_type)
                     and check_igv_file_name(obj['name'], file_type, override)
                 ):
                     file_paths.append(obj['path'])
diff --git a/samplesheets/studyapps/tests/test_utils.py b/samplesheets/studyapps/tests/test_utils.py
index a485d999..3eacfaaf 100644
--- a/samplesheets/studyapps/tests/test_utils.py
+++ b/samplesheets/studyapps/tests/test_utils.py
@@ -14,7 +14,7 @@
 from projectroles.tests.test_models import ProjectMixin, RoleAssignmentMixin
 
 from samplesheets.plugins import IGV_DEFAULT_GENOME
-from samplesheets.studyapps.utils import get_igv_xml
+from samplesheets.studyapps.utils import check_igv_file_suffix, get_igv_xml
 from samplesheets.tests.test_io import SampleSheetIOMixin
 
 
@@ -41,6 +41,39 @@ def setUp(self):
         )
 
 
+class TestCheckIGVFileSuffix(TestCase):
+    """Tests for check_igv_file_suffix()"""
+
+    def test_check_bam(self):
+        """Test checking with BAM type and valid name"""
+        self.assertTrue(check_igv_file_suffix('test.bam', 'bam'))
+
+    def test_check_bam_invalid_name(self):
+        """Test checking with BAM type and invalid name"""
+        self.assertFalse(check_igv_file_suffix('test.vcf', 'bam'))
+
+    def test_check_bam_cram(self):
+        """Test checking with BAM type and CRAM name"""
+        self.assertTrue(check_igv_file_suffix('test.cram', 'bam'))
+
+    def test_check_bam_uppercase(self):
+        """Test checking with BAM type and uppercase name"""
+        self.assertTrue(check_igv_file_suffix('TEST.BAM', 'bam'))
+
+    def test_check_vcf(self):
+        """Test checking with VCF type and valid name"""
+        self.assertTrue(check_igv_file_suffix('test.vcf.gz', 'vcf'))
+
+    def test_check_vcf_no_gz(self):
+        """Test checking with VCF type and name without .gz suffix"""
+        self.assertFalse(check_igv_file_suffix('test.vcf', 'vcf'))
+
+    def test_check_invalid_type(self):
+        """Test checking with invalid_type"""
+        with self.assertRaises(ValueError):
+            check_igv_file_suffix('test.bam', 'INVALID')
+
+
 class TestGetIGVXML(TestStudyAppUtilsBase):
     """Tests for get_igv_xml()"""
 
diff --git a/samplesheets/studyapps/utils.py b/samplesheets/studyapps/utils.py
index cb486841..335aa49a 100644
--- a/samplesheets/studyapps/utils.py
+++ b/samplesheets/studyapps/utils.py
@@ -17,6 +17,7 @@
 # Constants
 IGV_URL_BASE = 'http://127.0.0.1:60151'
 FILE_TYPE_SUFFIXES = {'bam': '.bam', 'vcf': '.vcf.gz'}
+FILE_TYPE_SUFFIX_CRAM = '.cram'  # Special case grouped together with bam
 INVALID_TYPE_MSG = 'Invalid value for file_type'
 
 
@@ -26,7 +27,7 @@ def get_igv_omit_override(project, file_type):
     method to avoid redundant database queries.
 
     :param project: Project object
-    :param file_type: String ("bam" or "vcf")
+    :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
     :return: List or None
     """
     ft = file_type.lower()
@@ -40,19 +41,37 @@ def get_igv_omit_override(project, file_type):
     return None
 
 
+def check_igv_file_suffix(file_name, file_type):
+    """
+    Check if file name corresponds to the specified file type.
+
+    :param file_name: String
+    :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
+    :raise: ValueError if file_type is incorrect
+    :return: Boolean (True if suffix matches the file type)
+    """
+    if file_type.lower() not in ['bam', 'vcf']:
+        raise ValueError(INVALID_TYPE_MSG)
+    fn = file_name.lower()  # Just in case suffix is in upper case
+    return (
+        fn.endswith(FILE_TYPE_SUFFIXES[file_type])
+        or file_type == 'bam'
+        and fn.endswith(FILE_TYPE_SUFFIX_CRAM)
+    )
+
+
 def check_igv_file_name(file_name, file_type, override=None):
     """
     Check if file is acceptable for IGV session inclusion. Returns False if
     suffix is found in env vars of omittable files.
 
     :param file_name: String
-    :param file_type: String ("bam" or "vcf")
+    :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
     :param override: File suffixes to override site-wide setting (list or None)
     :raise: ValueError if file_type is incorrect
     :return: Boolean (True if name is OK)
     """
-    ft = file_type.lower()
-    if ft not in ['bam', 'vcf']:
+    if file_type.lower() not in ['bam', 'vcf']:
         raise ValueError(INVALID_TYPE_MSG)
     fn = file_name.lower()
     if override:
@@ -79,10 +98,7 @@ def get_igv_session_url(source, app_name, merge=False):
         '{}:igv'.format(app_name), kwargs={'genericmaterial': source.sodar_uuid}
     )
     return '{}/load?merge={}&file={}{}.xml'.format(
-        IGV_URL_BASE,
-        str(merge).lower(),
-        file_prefix,
-        file_url,
+        IGV_URL_BASE, str(merge).lower(), file_prefix, file_url
     )
 
 
@@ -104,7 +120,7 @@ def get_igv_xml(project, bam_urls, vcf_urls, vcf_title, request, string=True):
     Build IGV session XML file.
 
     :param project: Project object
-    :param bam_urls: BAM file URLs (dict {name: url})
+    :param bam_urls: BAM/CRAM file URLs (dict {name: url})
     :param vcf_urls: VCF file URLs (dict {name: url})
     :param vcf_title: VCF title to prefix to VCF title strings (string)
     :param request: Django request
@@ -164,7 +180,7 @@ def get_igv_xml(project, bam_urls, vcf_urls, vcf_title, request, string=True):
                 'windowFunction': 'count',
             },
         )
-    # BAM panels
+    # BAM/CRAM panels
     for bam_name, bam_url in bam_urls.items():
         # Generating unique panel name with hashlib
         xml_bam_panel = ET.SubElement(
diff --git a/samplesheets/tests/test_utils.py b/samplesheets/tests/test_utils.py
index c103fa17..86bb60fa 100644
--- a/samplesheets/tests/test_utils.py
+++ b/samplesheets/tests/test_utils.py
@@ -27,6 +27,7 @@
     compare_inv_replace,
     get_webdav_url,
     get_ext_link_labels,
+    get_latest_file_path,
 )
 from samplesheets.tests.test_io import (
     SampleSheetIOMixin,
@@ -52,6 +53,9 @@
 ]
 IRODS_TICKET_STR = 'ooChaa1t'
 EXT_LINK_PATH_INVALID = '/tmp/NON_EXISTING_EXT_LINK_FILE.json'
+BAM_PATH = '/sodarZone/coll_z/file_2023-02-28.bam'
+BAM_PATH2 = '/sodarZone/coll_x/file_2023-03-01.bam'
+CRAM_PATH = '/sodarZone/coll_y/file_2023-02-29.cram'
 
 
 class SamplesheetsUtilsTestBase(
@@ -289,6 +293,20 @@ def test_get(self):
 
     @override_settings(SHEETS_EXTERNAL_LINK_PATH=EXT_LINK_PATH_INVALID)
     def test_get_default(self):
-        """Test retrievint default labels"""
+        """Test retrieving default labels"""
         labels = get_ext_link_labels()
         self.assertEqual(labels, DEFAULT_EXTERNAL_LINK_LABELS)
+
+
+class TestGetLatestFilePath(SamplesheetsUtilsTestBase):
+    """Tests for get_latest_file_path()"""
+
+    def test_get_bam(self):
+        """Test retrieval with two BAM paths"""
+        self.assertEqual(get_latest_file_path([BAM_PATH, BAM_PATH2]), BAM_PATH2)
+
+    def test_get_mixed(self):
+        """Test retrieval with mixed BAM and CRAM paths"""
+        self.assertEqual(
+            get_latest_file_path([BAM_PATH, BAM_PATH2, CRAM_PATH]), BAM_PATH2
+        )

From e1360a7badc863c30f80e282aee5233f63c35f1e Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 29 Feb 2024 12:00:15 +0100
Subject: [PATCH 26/33] fix finished zone status updating (#1909)

---
 CHANGELOG.rst                       |  2 ++
 landingzones/tasks_taskflow.py      | 12 ++++---
 taskflowbackend/api.py              | 36 +++++++++++++++-----
 taskflowbackend/tests/test_flows.py | 51 ++++++++++++++++++++++++++++-
 4 files changed, 87 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 08fc022c..a78abdbc 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -59,6 +59,7 @@ Fixed
 - **Landingzones**
     - Stats badge displayed to superusers for ``DELETED`` zones (#1866)
     - Zone status updating not working in project details card (#1902)
+    - Modifying finished lock status allowed in ``SetLandingZoneStatusTask`` (#1909)
 - **Samplesheets**
     - Invalid WebDAV URLs generated in ``IrodsDataRequestListView`` (#1860)
     - Superuser not allowed to edit iRODS request from other users in UI (#1863)
@@ -71,6 +72,7 @@ Fixed
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)
     - Crash in ``landing_zone_create`` with large amount of collections (#1905)
+    - Finished landing zone status modified by lock exception (#1909)
 
 Removed
 -------
diff --git a/landingzones/tasks_taskflow.py b/landingzones/tasks_taskflow.py
index 71911796..875fee5b 100644
--- a/landingzones/tasks_taskflow.py
+++ b/landingzones/tasks_taskflow.py
@@ -19,6 +19,7 @@
 
 from landingzones.constants import (
     STATUS_BUSY,
+    STATUS_FINISHED,
     ZONE_STATUS_FAILED,
     ZONE_STATUS_NOT_CREATED,
     ZONE_STATUS_MOVED,
@@ -381,10 +382,13 @@ def execute(
         *args,
         **kwargs
     ):
-        self.set_status(
-            landing_zone, flow_name, status, status_info, extra_data
-        )
-        self.data_modified = True
+        # Prevent setting status if already finished (see #1909)
+        landing_zone.refresh_from_db()
+        if landing_zone.status not in STATUS_FINISHED:
+            self.set_status(
+                landing_zone, flow_name, status, status_info, extra_data
+            )
+            self.data_modified = True
         super().execute(*args, **kwargs)
 
     def revert(
diff --git a/taskflowbackend/api.py b/taskflowbackend/api.py
index 708ff52a..60a47d36 100644
--- a/taskflowbackend/api.py
+++ b/taskflowbackend/api.py
@@ -8,6 +8,7 @@
     ZONE_STATUS_NOT_CREATED,
     ZONE_STATUS_CREATING,
     ZONE_STATUS_FAILED,
+    STATUS_FINISHED,
 )
 from landingzones.models import LandingZone
 
@@ -62,6 +63,29 @@ def _raise_flow_exception(cls, ex_msg, tl_event=None, zone=None):
         # TODO: Create app alert for failure if async (see #1499)
         raise cls.FlowSubmitException(ex_msg)
 
+    @classmethod
+    def _raise_lock_exception(cls, ex_msg, tl_event=None, zone=None):
+        """
+        Raise exception specifically for project lock errors. Updates the status
+        of the landing zone only if zone has not yet been finished by a
+        concurrent taskflow.
+
+        :param ex_msg: Exception message (string)
+        :param tl_event: Timeline event or None
+        :param zone: LandingZone object or None
+        :raise: FlowSubmitException
+        """
+        lock_zone = None
+        if zone:
+            zone.refresh_from_db()
+            if zone.status not in STATUS_FINISHED:
+                lock_zone = zone  # Exclude zone if already finished (see #1909)
+        cls._raise_flow_exception(
+            LOCK_FAIL_MSG + ': ' + str(ex_msg),
+            tl_event,
+            lock_zone,
+        )
+
     @classmethod
     def get_flow(
         cls,
@@ -137,10 +161,8 @@ def run_flow(
             # Acquire lock
             coordinator = lock_api.get_coordinator()
             if not coordinator:
-                cls._raise_flow_exception(
-                    LOCK_FAIL_MSG + ': Failed to retrieve lock coordinator',
-                    tl_event,
-                    zone,
+                cls._raise_lock_exception(
+                    'Failed to retrieve lock coordinator', tl_event, zone
                 )
             else:
                 lock_id = str(project.sodar_uuid)
@@ -148,11 +170,7 @@ def run_flow(
                 try:
                     lock_api.acquire(lock)
                 except Exception as ex:
-                    cls._raise_flow_exception(
-                        LOCK_FAIL_MSG + ': {}'.format(ex),
-                        tl_event,
-                        zone,
-                    )
+                    cls._raise_lock_exception(str(ex), tl_event, zone)
         else:
             logger.info('Lock not required (flow.require_lock=False)')
 
diff --git a/taskflowbackend/tests/test_flows.py b/taskflowbackend/tests/test_flows.py
index 5d8454f4..130f3a84 100644
--- a/taskflowbackend/tests/test_flows.py
+++ b/taskflowbackend/tests/test_flows.py
@@ -81,6 +81,7 @@
 UPDATED_DESC = 'updated description'
 SCRIPT_USER_NAME = 'script_user'
 IRODS_ROOT_PATH = 'sodar/root'
+INVALID_REDIS_URL = 'redis://127.0.0.1:6666/0'
 
 
 class TaskflowbackendFlowTestBase(TaskflowViewTestBase):
@@ -454,7 +455,7 @@ def setUp(self):
         self.make_irods_colls(self.investigation)
 
     def test_delete(self):
-        """Test landing_zone_delete with an empty landing zone"""
+        """Test landing_zone_delete with empty landing zone"""
         zone = self.make_landing_zone(
             title=ZONE_TITLE,
             project=self.project,
@@ -561,6 +562,54 @@ def test_delete_files_restrict(self):
         self.assertEqual(self.irods.data_objects.exists(obj_path), False)
         self.assertEqual(self.irods.collections.exists(zone_path), False)
 
+    def test_delete_finished(self):
+        """Test landing_zone_delete with finished zone"""
+        # NOTE: This may happen with concurrent requests. See #1909, #1910
+        zone = self.make_landing_zone(
+            title=ZONE_TITLE,
+            project=self.project,
+            user=self.user,
+            assay=self.assay,
+            description=ZONE_DESC,
+            status=ZONE_STATUS_DELETED,
+        )
+        # Do not create in taskflow
+        self.assertEqual(zone.status, ZONE_STATUS_DELETED)
+        flow_data = {'zone_uuid': str(zone.sodar_uuid)}
+        flow = self.taskflow.get_flow(
+            irods_backend=self.irods_backend,
+            project=self.project,
+            flow_name='landing_zone_delete',
+            flow_data=flow_data,
+        )
+        self._build_and_run(flow)
+        zone.refresh_from_db()
+        # This should still be deleted, not failed
+        self.assertEqual(zone.status, ZONE_STATUS_DELETED)
+
+    @override_settings(REDIS_URL=INVALID_REDIS_URL)
+    def test_delete_finished_lock_failure(self):
+        """Test landing_zone_delete with finished zone and lock failure"""
+        zone = self.make_landing_zone(
+            title=ZONE_TITLE,
+            project=self.project,
+            user=self.user,
+            assay=self.assay,
+            description=ZONE_DESC,
+            status=ZONE_STATUS_DELETED,
+        )
+        self.assertEqual(zone.status, ZONE_STATUS_DELETED)
+        flow_data = {'zone_uuid': str(zone.sodar_uuid)}
+        flow = self.taskflow.get_flow(
+            irods_backend=self.irods_backend,
+            project=self.project,
+            flow_name='landing_zone_delete',
+            flow_data=flow_data,
+        )
+        self._build_and_run(flow)
+        zone.refresh_from_db()
+        self.assertEqual(zone.status, ZONE_STATUS_DELETED)
+
 
 class TestLandingZoneMove(
     LandingZoneMixin,

From e5a66d38df8278ddae91623b39068c043b56aeab Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Wed, 6 Mar 2024 15:51:06 +0100
Subject: [PATCH 27/33] add igv omit setting path and glob pattern support
 (#1923, #1924, #1925)

---
 CHANGELOG.rst                                 |   5 +
 config/settings/base.py                       |   9 +-
 config/settings/test.py                       |   4 +-
 docs_manual/source/sodar_release_notes.rst    |   1 +
 docs_manual/source/ui_project_update.rst      |  22 ++-
 samplesheets/plugins.py                       |  24 ++--
 samplesheets/studyapps/cancer/plugins.py      |   5 +-
 .../cancer/tests/test_plugins_taskflow.py     |  88 +++++++++---
 samplesheets/studyapps/cancer/utils.py        |  11 +-
 samplesheets/studyapps/germline/plugins.py    |  24 ++--
 .../germline/tests/test_plugins_taskflow.py   |  89 +++++++++---
 samplesheets/studyapps/germline/utils.py      |   8 +-
 samplesheets/studyapps/tests/test_utils.py    | 136 +++++++++++++++++-
 samplesheets/studyapps/utils.py               |  44 +++---
 14 files changed, 361 insertions(+), 109 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a78abdbc..5cf243a5 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -21,6 +21,8 @@ Added
     - ``IrodsDataRequest`` timeline event extra data (#1912)
     - CRAM file support in study apps (#1908)
     - ``check_igv_file_suffix()`` helper in ``studyapps.utils`` (#1908)
+    - Path checking for IGV omit settings (#1923)
+    - Glob pattern support for IGV omit settings (#1923)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
     - ``BatchSetAccessTask`` in iRODS tasks (#1905)
@@ -43,6 +45,8 @@ Changed
     - Improve Django messages for ``IrodsDataRequest`` exceptions (#1858)
     - Change ``IrodsDataRequest`` description if created in Ajax view (#1862)
     - Refactor ``IrodsDataRequestModifyMixin`` timeline helpers (#1913)
+    - Rename ``get_igv_omit_override()`` to ``get_igv_omit_list()`` (#1924)
+    - Rename ``check_igv_file_name()`` to ``check_igv_file_path()`` (#1923)
 - **Taskflowbackend**
     - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
     - Set zone status on uncaught errors in ``run_flow()`` (#1458)
@@ -68,6 +72,7 @@ Fixed
     - Protocol ref editable for new row if disabled in column config (#1875)
     - Sheet template creation failure with slash characters in title/ID fields (#1896)
     - ``get_pedigree_file_path()`` used in cancer study app tests (#1914)
+    - IGV omit settings not correctly set on project creation (#1925)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)
diff --git a/config/settings/base.py b/config/settings/base.py
index 813a8c01..091a5791 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -807,13 +807,14 @@ def set_logging(level=None):
 # Remote sample sheet sync interval in minutes
 SHEETS_SYNC_INTERVAL = env.int('SHEETS_SYNC_INTERVAL', 5)
 
-# BAM/CRAM file name suffixes to omit from study shortcuts and IGV sessions
+# BAM/CRAM file path glob patterns to omit from study shortcuts and IGV sessions
 SHEETS_IGV_OMIT_BAM = env.list(
-    'SHEETS_IGV_OMIT_BAM', default=['dragen_evidence.bam']
+    'SHEETS_IGV_OMIT_BAM', default=['*dragen_evidence.bam']
 )
-# VCF file name suffixes to omit from study shortcuts and IGV sessions
+# VCF file path glob patterns to omit from study shortcuts and IGV sessions
 SHEETS_IGV_OMIT_VCF = env.list(
-    'SHEETS_IGV_OMIT_VCF', default=['cnv.vcf.gz', 'ploidy.vcf.gz', 'sv.vcf.gz']
+    'SHEETS_IGV_OMIT_VCF',
+    default=['*cnv.vcf.gz', '*ploidy.vcf.gz', '*sv.vcf.gz'],
 )
 
 # Landingzones app settings
diff --git a/config/settings/test.py b/config/settings/test.py
index 76566c48..93410ead 100644
--- a/config/settings/test.py
+++ b/config/settings/test.py
@@ -107,8 +107,8 @@
 SHEETS_EXTERNAL_LINK_PATH = os.path.join(
     ROOT_DIR, 'samplesheets/tests/config/ext_links.json'
 )
-SHEETS_IGV_OMIT_BAM = ['dragen_evidence.bam']
-SHEETS_IGV_OMIT_VCF = ['cnv.vcf.gz', 'ploidy.vcf.gz', 'sv.vcf.gz']
+SHEETS_IGV_OMIT_BAM = ['*dragen_evidence.bam']
+SHEETS_IGV_OMIT_VCF = ['*cnv.vcf.gz', '*ploidy.vcf.gz', '*sv.vcf.gz']
 
 # Landingzones app settings
 LANDINGZONES_TRIGGER_ENABLE = True
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index 97409657..f5ccc1d7 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -14,6 +14,7 @@ v0.14.2 (WIP)
 Release for minor updates, maintenance and bug fixes.
 
 - Add CRAM file support for cancer/germline study links and IGV sessions
+- Add path glob pattern support for IGV session BAM/VCF omit settings
 - Add assay plugin shortcut collection creation in landing zones
 - Add iRODS data request details in timeline events
 - Add landing zone statistics in siteinfo
diff --git a/docs_manual/source/ui_project_update.rst b/docs_manual/source/ui_project_update.rst
index 5f387d3b..24f0ab5b 100644
--- a/docs_manual/source/ui_project_update.rst
+++ b/docs_manual/source/ui_project_update.rst
@@ -53,12 +53,22 @@ Token for Sheet Synchronization
 IGV session genome
     Genome used in generating IGV session files for the project. The name needs
     to be in a format accepted by IGV. Affects cancer and germline projects.
-BAM and CRAM files to omit from IGV sessions
-    Comma separated list of BAM and CRAM file suffixes to omit from IGV
-    sessions. Overrides site-wide setting, affects cancer and germline projects.
-VCF files to omit from IGV sessions
-    Comma separated list of VCF file suffixes to omit from IGV sessions.
-    Overrides site-wide setting, affects cancer and germline projects.
+BAM and CRAM paths to omit from IGV sessions
+    Comma-separated list of iRODS path glob patterns for omitting BAM and CRAM
+    files from IGV sessions and study shortcuts. Overrides site-wide setting,
+    affects cancer and germline projects. You can input paths to subcollections
+    under project sample data as well as file names. Using wildcards like ``*``
+    and ``?`` is permitted. Providing full iRODS paths is not necessary: each
+    pattern is assumed to start with a ``*`` wildcard. An empty setting means no
+    files or collections are excluded. You need to run
+    :guilabel:`Update Sheet Cache` in the Sample Sheet application for changes
+    to take effect.
+VCF paths to omit from IGV sessions
+    Comma-separated list of iRODS path glob patterns for omitting VCF files from
+    IGV sessions and study shortcuts. Overrides site-wide setting, affects
+    cancer and germline projects. Behaves similarly to the related BAM/CRAM
+    setting. You need to run :guilabel:`Update Sheet Cache` in the Sample Sheet
+    application for changes to take effect.
 IP Restrict
     Restrict project access to specific IP addresses if this is set.
 IP Allow List
diff --git a/samplesheets/plugins.py b/samplesheets/plugins.py
index b689fe5f..f93aead4 100644
--- a/samplesheets/plugins.py
+++ b/samplesheets/plugins.py
@@ -213,23 +213,23 @@ class ProjectAppPlugin(
         'igv_omit_bam': {
             'scope': SODAR_CONSTANTS['APP_SETTING_SCOPE_PROJECT'],
             'type': 'STRING',
-            'label': 'BAM and CRAM files to omit from IGV sessions',
-            'default': '',
-            'placeholder': ', '.join(settings.SHEETS_IGV_OMIT_BAM),
-            'description': 'Comma separated list of BAM and CRAM file suffixes '
-            'to omit from generated IGV sessions. Overrides site-wide setting, '
-            'affects cancer and germline projects.',
+            'label': 'BAM and CRAM paths to omit from IGV sessions',
+            'default': ', '.join(settings.SHEETS_IGV_OMIT_BAM),
+            'description': 'Comma-separated list of iRODS path glob patterns '
+            'for omitting BAM and CRAM files from IGV sessions and study '
+            'shortcuts. Overrides site-wide setting, affects cancer and '
+            'germline projects. Update sheet cache after updating this value.',
             'user_modifiable': True,
         },
         'igv_omit_vcf': {
             'scope': SODAR_CONSTANTS['APP_SETTING_SCOPE_PROJECT'],
             'type': 'STRING',
-            'label': 'VCF files to omit from IGV sessions',
-            'default': '',
-            'placeholder': ', '.join(settings.SHEETS_IGV_OMIT_VCF),
-            'description': 'Comma separated list of VCF file suffixes to omit '
-            'from generated IGV sessions. Overrides site-wide setting, affects '
-            'cancer and germline projects.',
+            'label': 'VCF paths to omit from IGV sessions',
+            'default': ', '.join(settings.SHEETS_IGV_OMIT_VCF),
+            'description': 'Comma-separated list of iRODS path glob patterns '
+            'for omitting VCF files from IGV sessions and study shortcuts. '
+            'Overrides site-wide setting, affects cancer and germline '
+            'projects. Update sheet cache after updating this value.',
             'user_modifiable': True,
         },
     }
diff --git a/samplesheets/studyapps/cancer/plugins.py b/samplesheets/studyapps/cancer/plugins.py
index 05c77016..169f6f41 100644
--- a/samplesheets/studyapps/cancer/plugins.py
+++ b/samplesheets/studyapps/cancer/plugins.py
@@ -18,10 +18,7 @@
     get_latest_file_path,
 )
 from samplesheets.studyapps.utils import get_igv_session_url, get_igv_irods_url
-from samplesheets.utils import (
-    get_isa_field_name,
-    get_last_material_index,
-)
+from samplesheets.utils import get_isa_field_name, get_last_material_index
 
 
 logger = logging.getLogger(__name__)
diff --git a/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py b/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py
index e85f30cc..8634c0cf 100644
--- a/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py
+++ b/samplesheets/studyapps/cancer/tests/test_plugins_taskflow.py
@@ -3,7 +3,6 @@
 import os
 
 from django.conf import settings
-from django.test import override_settings
 from django.urls import reverse
 
 # Projectroles dependency
@@ -392,7 +391,7 @@ def test_get_shortcut_links_invalid(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    def test_get_shortcut_links_files_omit(self):
+    def test_get_shortcut_links_omit(self):
         """Test get_shortcut_links() with omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         # Create omittable files which come before real ones alphabetically
@@ -452,7 +451,7 @@ def test_get_shortcut_links_files_omit(self):
             ),
         )
 
-    def test_get_shortcut_links_files_omit_only(self):
+    def test_get_shortcut_links_omit_only(self):
         """Test get_shortcut_links() with only omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         bam_path_omit = os.path.join(
@@ -472,9 +471,37 @@ def test_get_shortcut_links_files_omit_only(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
-    def test_get_shortcut_links_files_omit_only_cram(self):
+    def test_get_shortcut_links_omit_only_empty_overrides(self):
+        """Test get_shortcut_links() with empty project overrides"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '', project=self.project
+        )
+        app_settings.set(
+            'samplesheets', 'igv_omit_vcf', '', project=self.project
+        )
+        self.irods.collections.create(self.source_path)
+        bam_path_omit = os.path.join(
+            self.source_path, '{}_dragen_evidence.bam'.format(SAMPLE_ID_NORMAL)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(bam_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, case=[SOURCE_ID_NORMAL]
+        )
+        self.assertEqual(len(sl['data']['session']['files']), 1)
+        self.assertEqual(len(sl['data']['bam']['files']), 1)
+        self.assertEqual(len(sl['data']['vcf']['files']), 1)
+
+    def test_get_shortcut_links_omit_only_cram(self):
         """Test get_shortcut_links() with omittable CRAM file in iRODS"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '*omit.cram', project=self.project
+        )
         self.irods.collections.create(self.source_path)
         cram_path_omit = os.path.join(
             self.source_path, '{}_omit.cram'.format(SAMPLE_ID_NORMAL)
@@ -489,18 +516,18 @@ def test_get_shortcut_links_files_omit_only_cram(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    def test_get_shortcut_links_files_omit_override(self):
+    def test_get_shortcut_links_omit_override(self):
         """Test get_shortcut_links() with project-specific omit override"""
         app_settings.set(
             'samplesheets',
             'igv_omit_bam',
-            'test.bam, xxx.bam',
+            '*test.bam,*xxx.bam',
             project=self.project,
         )
         app_settings.set(
             'samplesheets',
             'igv_omit_vcf',
-            'test.vcf.gz, yyy.vcf.gz',
+            '*test.vcf.gz,*yyy.vcf.gz',
             project=self.project,
         )
         self.irods.collections.create(self.source_path)
@@ -554,7 +581,7 @@ def test_update_cache_files(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
-    def test_update_cache_files_cram(self):
+    def test_update_cache_cram(self):
         """Test update_cache() with CRAM file in iRODS"""
         self.irods.collections.create(self.source_path)
         cram_path = os.path.join(
@@ -575,7 +602,7 @@ def test_update_cache_files_cram(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
-    def test_update_cache_files_omit(self):
+    def test_update_cache_omit(self):
         """Test update_cache() with omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         # Create omittable files which come before real ones alphabetically
@@ -605,7 +632,7 @@ def test_update_cache_files_omit(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
-    def test_update_cache_files_omit_only(self):
+    def test_update_cache_omit_only(self):
         """Test update_cache() with only omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         bam_path_omit = os.path.join(
@@ -624,9 +651,38 @@ def test_update_cache_files_omit_only(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
-    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
-    def test_update_cache_files_omit_only_cram(self):
+    def test_update_cache_omit_only_empty_overrides(self):
+        """Test update_cache() with empty project overrides"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '', project=self.project
+        )
+        app_settings.set(
+            'samplesheets', 'igv_omit_vcf', '', project=self.project
+        )
+        self.irods.collections.create(self.source_path)
+        bam_path_omit = os.path.join(
+            self.source_path, '{}_dragen_evidence.bam'.format(SAMPLE_ID_NORMAL)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(SAMPLE_ID_NORMAL)
+        )
+        self.irods.data_objects.create(bam_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        self.assertEqual(ci['bam'][CASE_IDS[0]], bam_path_omit)
+        self.assertEqual(ci['vcf'][CASE_IDS[0]], vcf_path_omit)
+        for i in range(1, len(CASE_IDS) - 1):
+            self.assertEqual(ci['bam'][CASE_IDS[i]], None)
+            self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
+
+    def test_update_cache_omit_only_cram(self):
         """Test update_cache() with omittable CRAM file in iRODS"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '*omit.cram', project=self.project
+        )
         self.irods.collections.create(self.source_path)
         cram_path_omit = os.path.join(
             self.source_path, '{}_omit.cram'.format(SAMPLE_ID_NORMAL)
@@ -644,18 +700,18 @@ def test_update_cache_files_omit_only_cram(self):
             self.assertEqual(ci['bam'][CASE_IDS[i]], None)
             self.assertEqual(ci['vcf'][CASE_IDS[i]], None)
 
-    def test_update_cache_files_omit_override(self):
+    def test_update_cache_omit_override(self):
         """Test update_cache() with project-specific omit override"""
         app_settings.set(
             'samplesheets',
             'igv_omit_bam',
-            'test.bam, xxx.bam',
+            '*test.bam,*xxx.bam',
             project=self.project,
         )
         app_settings.set(
             'samplesheets',
             'igv_omit_vcf',
-            'test.vcf.gz, yyy.vcf.gz',
+            '*test.vcf.gz,*yyy.vcf.gz',
             project=self.project,
         )
         self.irods.collections.create(self.source_path)
diff --git a/samplesheets/studyapps/cancer/utils.py b/samplesheets/studyapps/cancer/utils.py
index a5c38c75..89c9c536 100644
--- a/samplesheets/studyapps/cancer/utils.py
+++ b/samplesheets/studyapps/cancer/utils.py
@@ -3,9 +3,9 @@
 import os
 
 from samplesheets.studyapps.utils import (
-    get_igv_omit_override,
+    get_igv_omit_list,
     check_igv_file_suffix,
-    check_igv_file_name,
+    check_igv_file_path,
 )
 from samplesheets.utils import get_latest_file_path
 
@@ -25,14 +25,13 @@ def get_library_file_path(assay, library_name, file_type, irods_backend, irods):
     assay_path = irods_backend.get_path(assay)
     query_path = os.path.join(assay_path, library_name)
     file_paths = []
-    override = get_igv_omit_override(assay.get_project(), file_type)
+    omit_list = get_igv_omit_list(assay.get_project(), file_type)
     try:
         obj_list = irods_backend.get_objects(irods, query_path)
         for obj in obj_list:
-            obj_name = obj['name'].lower()
             if check_igv_file_suffix(
-                obj_name, file_type
-            ) and check_igv_file_name(obj_name, file_type, override):
+                obj['name'].lower(), file_type
+            ) and check_igv_file_path(obj['path'], omit_list):
                 file_paths.append(obj['path'])
     except Exception:
         pass
diff --git a/samplesheets/studyapps/germline/plugins.py b/samplesheets/studyapps/germline/plugins.py
index 3e90f83a..9041b873 100644
--- a/samplesheets/studyapps/germline/plugins.py
+++ b/samplesheets/studyapps/germline/plugins.py
@@ -13,21 +13,20 @@
 from samplesheets.models import Investigation, Study, GenericMaterial
 from samplesheets.plugins import SampleSheetStudyPluginPoint
 from samplesheets.rendering import SampleSheetTableBuilder
+from samplesheets.studyapps.germline.utils import (
+    get_pedigree_file_path,
+    get_families,
+    get_family_sources,
+)
 from samplesheets.studyapps.utils import (
-    get_igv_omit_override,
+    get_igv_omit_list,
     check_igv_file_suffix,
-    check_igv_file_name,
+    check_igv_file_path,
     get_igv_session_url,
     get_igv_irods_url,
 )
 from samplesheets.utils import get_index_by_header
 
-from samplesheets.studyapps.germline.utils import (
-    get_pedigree_file_path,
-    get_families,
-    get_family_sources,
-)
-
 
 logger = logging.getLogger(__name__)
 table_builder = SampleSheetTableBuilder()
@@ -36,7 +35,6 @@
 
 # SODAR constants
 PROJECT_TYPE_PROJECT = SODAR_CONSTANTS['PROJECT_TYPE_PROJECT']
-
 # Local constants
 APP_NAME = 'samplesheets.studyapps.germline'
 
@@ -323,8 +321,8 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
             logger.error('Error querying for study objects: {}'.format(ex))
 
         project = study.get_project()
-        bam_override = get_igv_omit_override(project, 'bam')
-        vcf_override = get_igv_omit_override(project, 'vcf')
+        bam_omit_list = get_igv_omit_list(project, 'bam')
+        vcf_omit_list = get_igv_omit_list(project, 'vcf')
 
         for assay in study.assays.all():
             assay_plugin = assay.get_plugin()
@@ -353,7 +351,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                         for o in study_objs
                         if o['path'].startswith(path + '/')
                         and check_igv_file_suffix(o['name'], 'bam')
-                        and check_igv_file_name(o['name'], 'bam', bam_override)
+                        and check_igv_file_path(o['path'], bam_omit_list)
                     ]
                 row_fam = row[fam_idx]['value']
                 # Add VCF objects
@@ -369,7 +367,7 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                         for o in study_objs
                         if o['path'].startswith(path + '/')
                         and o['name'].lower().endswith('vcf.gz')
-                        and check_igv_file_name(o['name'], 'vcf', vcf_override)
+                        and check_igv_file_path(o['path'], vcf_omit_list)
                     ]
 
         # Update data
diff --git a/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py b/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
index 7fc66a7a..01776764 100644
--- a/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
+++ b/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
@@ -3,7 +3,6 @@
 import os
 
 from django.conf import settings
-from django.test import override_settings
 from django.urls import reverse
 
 # Projectroles dependency
@@ -290,7 +289,7 @@ def test_get_shortcut_links_files(self):
             + get_pedigree_file_path('vcf', self.source, study_tables),
         )
 
-    def test_get_shortcut_links_files_cram(self):
+    def test_get_shortcut_links_cram(self):
         """Test get_shortcut_links() with CRAM file in iRODS"""
         self.irods.collections.create(self.source_path)
         cram_path = os.path.join(
@@ -430,7 +429,7 @@ def test_get_shortcut_links_invalid(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    def test_get_shortcut_links_files_omit(self):
+    def test_get_shortcut_links_omit(self):
         """Test get_shortcut_links() with omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         bam_path = os.path.join(
@@ -477,7 +476,7 @@ def test_get_shortcut_links_files_omit(self):
             + get_pedigree_file_path('vcf', self.source, study_tables),
         )
 
-    def test_get_shortcut_links_files_omit_only(self):
+    def test_get_shortcut_links_omit_only(self):
         """Test get_shortcut_links() with only omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         bam_path_omit = os.path.join(
@@ -498,9 +497,38 @@ def test_get_shortcut_links_files_omit_only(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
-    def test_get_shortcut_links_files_omit_cram(self):
+    def test_get_shortcut_links_omit_only_empty_overrides(self):
+        """Test get_shortcut_links() with empty project overrides"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '', project=self.project
+        )
+        app_settings.set(
+            'samplesheets', 'igv_omit_vcf', '', project=self.project
+        )
+        self.irods.collections.create(self.source_path)
+        bam_path_omit = os.path.join(
+            self.source_path, '{}_dragen_evidence.bam'.format(SAMPLE_ID)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(bam_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+
+        self.plugin.update_cache(self.cache_name, self.project)
+        study_tables = self.tb.build_study_tables(self.study)
+        sl = self.plugin.get_shortcut_links(
+            self.study, study_tables, family=[FAMILY_ID]
+        )
+        self.assertEqual(len(sl['data']['session']['files']), 1)
+        self.assertEqual(len(sl['data']['bam']['files']), 1)
+        self.assertEqual(len(sl['data']['vcf']['files']), 1)
+
+    def test_get_shortcut_links_omit_cram(self):
         """Test get_shortcut_links() with omittable CRAM file in iRODS"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '*omit.cram', project=self.project
+        )
         self.irods.collections.create(self.source_path)
         cram_path_omit = os.path.join(
             self.source_path, '{}_omit.cram'.format(SAMPLE_ID)
@@ -520,18 +548,18 @@ def test_get_shortcut_links_files_omit_cram(self):
         self.assertEqual(len(sl['data']['bam']['files']), 0)
         self.assertEqual(len(sl['data']['vcf']['files']), 0)
 
-    def test_get_shortcut_links_files_omit_override(self):
+    def test_get_shortcut_links_omit_override(self):
         """Test get_shortcut_links() with project-specific omit override"""
         app_settings.set(
             'samplesheets',
             'igv_omit_bam',
-            'test.bam, xxx.bam',
+            '*test.bam,*xxx.bam',
             project=self.project,
         )
         app_settings.set(
             'samplesheets',
             'igv_omit_vcf',
-            'test.vcf.gz, yyy.vcf.gz',
+            '*test.vcf.gz,*yyy.vcf.gz',
             project=self.project,
         )
         self.irods.collections.create(self.source_path)
@@ -584,7 +612,7 @@ def test_update_cache_files(self):
         self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path)
         self.assertIsNone(ci['vcf'][FAMILY_ID2])
 
-    def test_update_cache_files_cram(self):
+    def test_update_cache_cram(self):
         """Test update_cache() with CRAM file in iRODS"""
         self.irods.collections.create(self.source_path)
         cram_path = os.path.join(
@@ -603,7 +631,7 @@ def test_update_cache_files_cram(self):
         self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path)
         self.assertIsNone(ci['vcf'][FAMILY_ID2])
 
-    def test_update_cache_files_omit(self):
+    def test_update_cache_omit(self):
         """Test update_cache() with omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         # Create omittable files which come before real ones alphabetically
@@ -631,7 +659,7 @@ def test_update_cache_files_omit(self):
         self.assertEqual(ci['bam'][self.source.name], bam_path)
         self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path)
 
-    def test_update_cache_files_omit_only(self):
+    def test_update_cache_omit_only(self):
         """Test update_cache() with only omittable files in iRODS"""
         self.irods.collections.create(self.source_path)
         bam_path_omit = os.path.join(
@@ -650,9 +678,36 @@ def test_update_cache_files_omit_only(self):
         self.assertIsNone(ci['bam'][self.source.name])
         self.assertIsNone(ci['vcf'][FAMILY_ID])
 
-    @override_settings(SHEETS_IGV_OMIT_BAM=['omit.cram'])
-    def test_update_cache_files_omit_only_cram(self):
+    def test_update_cache_omit_only_empty_overrides(self):
+        """Test update_cache() with empty project overrides"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '', project=self.project
+        )
+        app_settings.set(
+            'samplesheets', 'igv_omit_vcf', '', project=self.project
+        )
+        self.irods.collections.create(self.source_path)
+        bam_path_omit = os.path.join(
+            self.source_path, '{}_dragen_evidence.bam'.format(SAMPLE_ID)
+        )
+        vcf_path_omit = os.path.join(
+            self.source_path, '{}_cnv.vcf.gz'.format(FAMILY_ID)
+        )
+        self.irods.data_objects.create(bam_path_omit)
+        self.irods.data_objects.create(vcf_path_omit)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        # Omitted files should not be returned
+        self.assertEqual(ci['bam'][self.source.name], bam_path_omit)
+        self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path_omit)
+
+    def test_update_cache_omit_only_cram(self):
         """Test update_cache() with omittable CRAM file in iRODS"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '*omit.cram', project=self.project
+        )
         self.irods.collections.create(self.source_path)
         cram_path_omit = os.path.join(
             self.source_path, '{}_omit.cram'.format(SAMPLE_ID)
@@ -669,18 +724,18 @@ def test_update_cache_files_omit_only_cram(self):
         self.assertIsNone(ci['bam'][self.source.name])
         self.assertIsNone(ci['vcf'][FAMILY_ID])
 
-    def test_update_cache_files_omit_override(self):
+    def test_update_cache_omit_override(self):
         """Test update_cache() with project-specific omit override"""
         app_settings.set(
             'samplesheets',
             'igv_omit_bam',
-            'test.bam, xxx.bam',
+            '*test.bam,*xxx.bam',
             project=self.project,
         )
         app_settings.set(
             'samplesheets',
             'igv_omit_vcf',
-            'test.vcf.gz, yyy.vcf.gz',
+            '*test.vcf.gz,*yyy.vcf.gz',
             project=self.project,
         )
         self.irods.collections.create(self.source_path)
diff --git a/samplesheets/studyapps/germline/utils.py b/samplesheets/studyapps/germline/utils.py
index 1c526d3f..69d4ced6 100644
--- a/samplesheets/studyapps/germline/utils.py
+++ b/samplesheets/studyapps/germline/utils.py
@@ -7,8 +7,8 @@
 
 from samplesheets.models import GenericMaterial
 from samplesheets.studyapps.utils import (
-    get_igv_omit_override,
-    check_igv_file_name,
+    get_igv_omit_list,
+    check_igv_file_path,
     check_igv_file_suffix,
 )
 from samplesheets.utils import get_index_by_header
@@ -32,7 +32,7 @@ def get_pedigree_file_path(file_type, source, study_tables):
         raise Exception('iRODS Backend not available')
 
     query_paths = []
-    override = get_igv_omit_override(source.study.get_project(), file_type)
+    omit_list = get_igv_omit_list(source.study.get_project(), file_type)
 
     def _get_val_by_index(row, idx):
         return row[idx]['value'] if idx else None
@@ -85,7 +85,7 @@ def _get_val_by_index(row, idx):
                 if (
                     obj['path'].startswith(query_path + '/')
                     and check_igv_file_suffix(obj['name'], file_type)
-                    and check_igv_file_name(obj['name'], file_type, override)
+                    and check_igv_file_path(obj['path'], omit_list)
                 ):
                     file_paths.append(obj['path'])
                     logger.debug('Added path: {}'.format(obj['path']))
diff --git a/samplesheets/studyapps/tests/test_utils.py b/samplesheets/studyapps/tests/test_utils.py
index 3eacfaaf..57f1a772 100644
--- a/samplesheets/studyapps/tests/test_utils.py
+++ b/samplesheets/studyapps/tests/test_utils.py
@@ -14,13 +14,22 @@
 from projectroles.tests.test_models import ProjectMixin, RoleAssignmentMixin
 
 from samplesheets.plugins import IGV_DEFAULT_GENOME
-from samplesheets.studyapps.utils import check_igv_file_suffix, get_igv_xml
+from samplesheets.studyapps.utils import (
+    get_igv_omit_list,
+    check_igv_file_suffix,
+    check_igv_file_path,
+    get_igv_xml,
+)
 from samplesheets.tests.test_io import SampleSheetIOMixin
 
 
 app_settings = AppSettingAPI()
 
 
+# Local constants
+INVALID_FILE_TYPE = 'INVALID_TYPE'
+
+
 class TestStudyAppUtilsBase(
     ProjectMixin, RoleAssignmentMixin, SampleSheetIOMixin, TestCase
 ):
@@ -41,7 +50,78 @@ def setUp(self):
         )
 
 
-class TestCheckIGVFileSuffix(TestCase):
+class TestGetIGVOmitList(TestStudyAppUtilsBase):
+    """Tests for get_igv_omit_list()"""
+
+    def test_get(self):
+        """Test get_igv_omit_list()"""
+        self.assertEqual(
+            get_igv_omit_list(self.project, 'bam'), ['*dragen_evidence.bam']
+        )
+        self.assertEqual(
+            get_igv_omit_list(self.project, 'vcf'),
+            ['*cnv.vcf.gz', '*ploidy.vcf.gz', '*sv.vcf.gz'],
+        )
+
+    def test_get_invalid_file_type(self):
+        """Test get_igv_omit_list() with invalid file type"""
+        with self.assertRaises(ValueError):
+            get_igv_omit_list(self.project, INVALID_FILE_TYPE)
+
+    def test_get_no_preceeding_asterisk(self):
+        """Test get_igv_omit_list() without preceeding asterisk"""
+        # NOTE: We can't use override_settings here
+        app_settings.set(
+            'samplesheets',
+            'igv_omit_bam',
+            'dragen_evidence.bam',
+            project=self.project,
+        )
+        app_settings.set(
+            'samplesheets', 'igv_omit_vcf', 'cnv.vcf.gz', project=self.project
+        )
+        self.assertEqual(
+            get_igv_omit_list(self.project, 'bam'), ['*dragen_evidence.bam']
+        )
+        self.assertEqual(
+            get_igv_omit_list(self.project, 'vcf'), ['*cnv.vcf.gz']
+        )
+
+    def test_get_mixed_preceeding_asterisks(self):
+        """Test get_igv_omit_list() with mixed preceeding asterisk"""
+        app_settings.set(
+            'samplesheets',
+            'igv_omit_bam',
+            '*xxx.bam,yyy.bam',
+            project=self.project,
+        )
+        app_settings.set(
+            'samplesheets',
+            'igv_omit_vcf',
+            '*xxx.vcf.gz,yyy.vcf.gz',
+            project=self.project,
+        )
+        self.assertEqual(
+            get_igv_omit_list(self.project, 'bam'), ['*xxx.bam', '*yyy.bam']
+        )
+        self.assertEqual(
+            get_igv_omit_list(self.project, 'vcf'),
+            ['*xxx.vcf.gz', '*yyy.vcf.gz'],
+        )
+
+    def test_get_empty_setting(self):
+        """Test get_igv_omit_list() with empty setting values"""
+        app_settings.set(
+            'samplesheets', 'igv_omit_bam', '', project=self.project
+        )
+        app_settings.set(
+            'samplesheets', 'igv_omit_vcf', '', project=self.project
+        )
+        self.assertEqual(get_igv_omit_list(self.project, 'bam'), [])
+        self.assertEqual(get_igv_omit_list(self.project, 'vcf'), [])
+
+
+class TestCheckIGVFileSuffix(TestCase):  # TestStudyAppUtilsBase not needed
     """Tests for check_igv_file_suffix()"""
 
     def test_check_bam(self):
@@ -74,6 +154,58 @@ def test_check_invalid_type(self):
             check_igv_file_suffix('test.bam', 'INVALID')
 
 
+class TestCheckIGVFilePath(TestCase):
+    """Tests for check_igv_file_path()"""
+
+    def test_path(self):
+        """Test check_igv_file_path()"""
+        path = 'xxx/yyy.bam'
+        omit_list = ['*zzz.bam']
+        self.assertTrue(check_igv_file_path(path, omit_list))
+
+    def test_path_omit_file(self):
+        """Test check_igv_file_path() with file name in omit list"""
+        path = 'xxx/yyy.bam'
+        omit_list = ['*yyy.bam']
+        self.assertFalse(check_igv_file_path(path, omit_list))
+
+    def test_path_empty_list(self):
+        """Test check_igv_file_path() with empty omit list"""
+        path = 'xxx/yyy.bam'
+        omit_list = []
+        self.assertTrue(check_igv_file_path(path, omit_list))
+
+    def test_path_omit_multiple(self):
+        """Test check_igv_file_path() with multiple patterns"""
+        path = 'xxx/yyy.bam'
+        omit_list = ['*yyy.bam', '*zzz.bam']
+        self.assertFalse(check_igv_file_path(path, omit_list))
+
+    def test_path_omit_no_math(self):
+        """Test check_igv_file_path() with multiple non-matching patterns"""
+        path = 'xxx/yyy.bam'
+        omit_list = ['*aaa.bam', '*bbb.bam']
+        self.assertTrue(check_igv_file_path(path, omit_list))
+
+    def test_path_omit_case(self):
+        """Test check_igv_file_path() with file name in different case"""
+        path = 'xxx/YYY.BAM'
+        omit_list = ['*yyy.bam']
+        self.assertFalse(check_igv_file_path(path, omit_list))
+
+    def test_path_omit_collections(self):
+        """Test check_igv_file_path() with matching collections"""
+        path = '000/aaa/bbb/yyy.bam'
+        omit_list = ['*/aaa/bbb/*']
+        self.assertFalse(check_igv_file_path(path, omit_list))
+
+    def test_path_omit_collections_middle(self):
+        """Test check_igv_file_path() with partial collection match"""
+        path = '000/aaa/bbb/yyy.bam'
+        omit_list = ['*/aaa/*/yyy.bam']
+        self.assertFalse(check_igv_file_path(path, omit_list))
+
+
 class TestGetIGVXML(TestStudyAppUtilsBase):
     """Tests for get_igv_xml()"""
 
diff --git a/samplesheets/studyapps/utils.py b/samplesheets/studyapps/utils.py
index 335aa49a..cebf5ae2 100644
--- a/samplesheets/studyapps/utils.py
+++ b/samplesheets/studyapps/utils.py
@@ -3,6 +3,7 @@
 import hashlib
 
 from lxml import etree as ET
+from pathlib import PurePosixPath
 
 from django.conf import settings
 from django.urls import reverse
@@ -21,24 +22,27 @@
 INVALID_TYPE_MSG = 'Invalid value for file_type'
 
 
-def get_igv_omit_override(project, file_type):
+def get_igv_omit_list(project, file_type):
     """
-    Get IGV omit override setting for a project. NOTE: Added as a separate
-    method to avoid redundant database queries.
+    Get list of IGV omit glob patterns for a specific file type in a project.
+    NOTE: Added as a separate method to avoid redundant database queries.
 
     :param project: Project object
     :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
-    :return: List or None
+    :return: List (appends * in front of each path if missing)
     """
     ft = file_type.lower()
     if ft not in ['bam', 'vcf']:
         raise ValueError(INVALID_TYPE_MSG)
-    setting = app_settings.get(
+    setting_val = app_settings.get(
         'samplesheets', 'igv_omit_{}'.format(ft), project=project
     )
-    if setting:
-        return [s.strip() for s in setting.split(',')]
-    return None
+    if not setting_val:
+        return []
+    return [
+        '{}{}'.format('*' if not s.strip().startswith('*') else '', s.strip())
+        for s in setting_val.split(',')
+    ]
 
 
 def check_igv_file_suffix(file_name, file_type):
@@ -60,24 +64,18 @@ def check_igv_file_suffix(file_name, file_type):
     )
 
 
-def check_igv_file_name(file_name, file_type, override=None):
+def check_igv_file_path(path, omit_list):
     """
-    Check if file is acceptable for IGV session inclusion. Returns False if
-    suffix is found in env vars of omittable files.
+    Check if file path is acceptable for IGV session inclusion. Returns False if
+    pattern is found in IGV omit settings.
 
-    :param file_name: String
-    :param file_type: String ("bam" or "vcf", "bam" is also used for CRAM)
-    :param override: File suffixes to override site-wide setting (list or None)
-    :raise: ValueError if file_type is incorrect
-    :return: Boolean (True if name is OK)
+    :param path: Full or partial iRODS path (string)
+    :param omit_list: List of path glob patterns to omit (list)
+    :return: Boolean (True if path is OK)
     """
-    if file_type.lower() not in ['bam', 'vcf']:
-        raise ValueError(INVALID_TYPE_MSG)
-    fn = file_name.lower()
-    if override:
-        return not any([s.lower() for s in override if fn.endswith(s)])
-    ol = getattr(settings, 'SHEETS_IGV_OMIT_' + file_type.upper(), [])
-    return not any([s.lower() for s in ol if fn.endswith(s)])
+    return not any(
+        [p for p in omit_list if PurePosixPath(path.lower()).match(p.lower())]
+    )
 
 
 def get_igv_session_url(source, app_name, merge=False):

From 288da3ec71b6e5dbd4163abaaf162c45e8da7bbd Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 7 Mar 2024 10:34:53 +0100
Subject: [PATCH 28/33] fix germline study cache update with no family column
 (#1921)

---
 CHANGELOG.rst                                 |  1 +
 samplesheets/studyapps/germline/plugins.py    |  7 +++--
 .../germline/tests/test_plugins_taskflow.py   | 26 +++++++++++++++++++
 3 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5cf243a5..50069b87 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -73,6 +73,7 @@ Fixed
     - Sheet template creation failure with slash characters in title/ID fields (#1896)
     - ``get_pedigree_file_path()`` used in cancer study app tests (#1914)
     - IGV omit settings not correctly set on project creation (#1925)
+    - Germline study cache build crash with no family column (#1921)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)
diff --git a/samplesheets/studyapps/germline/plugins.py b/samplesheets/studyapps/germline/plugins.py
index 9041b873..995805c1 100644
--- a/samplesheets/studyapps/germline/plugins.py
+++ b/samplesheets/studyapps/germline/plugins.py
@@ -353,11 +353,10 @@ def _update_study_cache(cls, study, user, cache_backend, irods_backend):
                         and check_igv_file_suffix(o['name'], 'bam')
                         and check_igv_file_path(o['path'], bam_omit_list)
                     ]
-                row_fam = row[fam_idx]['value']
                 # Add VCF objects
-                if row_fam:
-                    vcf_query_id = row_fam
-                else:
+                if fam_idx and row[fam_idx].get('value'):
+                    vcf_query_id = row[fam_idx]['value']
+                else:  # If family column isn't present/filled, use source name
                     vcf_query_id = source_name
                 if vcf_query_id not in vcf_paths:
                     vcf_paths[vcf_query_id] = []
diff --git a/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py b/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
index 01776764..ee960a0b 100644
--- a/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
+++ b/samplesheets/studyapps/germline/tests/test_plugins_taskflow.py
@@ -13,6 +13,7 @@
 # Taskflowbackend dependency
 from taskflowbackend.tests.base import TaskflowViewTestBase
 
+from samplesheets.models import GenericMaterial
 from samplesheets.rendering import SampleSheetTableBuilder
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
 from samplesheets.tests.test_models import SampleSheetModelMixin
@@ -763,3 +764,28 @@ def test_update_cache_omit_override(self):
         # Omitted files should not be returned
         self.assertEqual(ci['bam'][self.source.name], bam_path_omit)
         self.assertEqual(ci['vcf'][FAMILY_ID], vcf_path_omit)
+
+    def test_update_cache_no_family(self):
+        """Test update_cache() with no family characteristic in source"""
+        # Clear the family characteristics and header
+        for m in GenericMaterial.objects.filter(
+            study=self.study, item_type='SOURCE'
+        ):
+            m.characteristics.pop('Family')
+            m.headers.remove('Characteristics[Family]')
+            m.save()
+        self.irods.collections.create(self.source_path)
+        bam_path = os.path.join(
+            self.source_path, '{}_test.bam'.format(SAMPLE_ID)
+        )
+        vcf_path = os.path.join(
+            self.source_path, '{}_test.vcf.gz'.format(SAMPLE_ID)
+        )
+        self.irods.data_objects.create(bam_path)
+        self.irods.data_objects.create(vcf_path)
+        self.plugin.update_cache(self.cache_name, self.project)
+        ci = self.cache_backend.get_cache_item(
+            APP_NAME, self.cache_name, self.project
+        ).data
+        self.assertEqual(ci['bam'][self.source.name], bam_path)
+        self.assertEqual(ci['vcf'][self.source.name], vcf_path)

From 5b9c8179b1a414020346131122790dea2c18c2bb Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 7 Mar 2024 11:25:54 +0100
Subject: [PATCH 29/33] upgrade to cubi-isa-templates==0.1.2 (#1854)

---
 CHANGELOG.rst         | 1 +
 requirements/base.txt | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 50069b87..06b1c676 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -35,6 +35,7 @@ Changed
     - Upgrade to Django v3.2.24 (#1854)
     - Upgrade to django-sodar-core v0.13.4 (#1899)
     - Upgrade critical Vue app dependencies (#1854)
+    - Upgrade to cubi-isa-templates v0.1.2 (#1854)
     - Update installation documentation (#1871)
 - **Irodsbackend**
     - Reduce redundant object queries (#1883)
diff --git a/requirements/base.txt b/requirements/base.txt
index 97b2b90e..ffa20142 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -102,8 +102,8 @@ pronto==2.5.0  # For OWL conversion
 
 # CUBI ISA-Tab templates
 cookiecutter==2.2.3
-# cubi-isa-templates==0.1.1
--e git+https://github.com/bihealth/cubi-isa-templates.git@d3ebe866f3823d81fdb358042ef7ed4d8b8fd100#egg=cubi-isa-templates
+cubi-isa-templates==0.1.2
+# -e git+https://github.com/bihealth/cubi-isa-templates.git@d3ebe866f3823d81fdb358042ef7ed4d8b8fd100#egg=cubi-isa-templates
 
 # Taskflow requirements
 tooz==3.0.0

From c7d29950e53c7dda6914ac8e3abf6ff5aa0ef670 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Wed, 13 Mar 2024 16:13:42 +0100
Subject: [PATCH 30/33] fix named process pooling and renaming issues (#1904)

---
 CHANGELOG.rst                                 |   1 +
 ...> i_small_assay_insert_pool_material.json} |   0
 .../i_small_assay_insert_pool_process.json    | 124 ++++++++++
 samplesheets/tests/test_views_ajax.py         | 230 ++++++++++--------
 samplesheets/views_ajax.py                    |  14 +-
 samplesheets/vueapp/src/App.vue               |  68 ++++--
 .../src/components/editors/DataCellEditor.vue |  37 +--
 .../components/renderers/RowEditRenderer.vue  |  12 +-
 .../vueapp/tests/unit/DataCellEditor.spec.js  |  48 ++++
 9 files changed, 374 insertions(+), 160 deletions(-)
 rename samplesheets/tests/edit/{i_small_assay_insert_pool.json => i_small_assay_insert_pool_material.json} (100%)
 create mode 100644 samplesheets/tests/edit/i_small_assay_insert_pool_process.json

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 06b1c676..3c7c7733 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -48,6 +48,7 @@ Changed
     - Refactor ``IrodsDataRequestModifyMixin`` timeline helpers (#1913)
     - Rename ``get_igv_omit_override()`` to ``get_igv_omit_list()`` (#1924)
     - Rename ``check_igv_file_name()`` to ``check_igv_file_path()`` (#1923)
+    - Named process pooling and renaming in sheet editor (#1904)
 - **Taskflowbackend**
     - Optimize ``landing_zone_move`` iRODS path retrieval (#1882)
     - Set zone status on uncaught errors in ``run_flow()`` (#1458)
diff --git a/samplesheets/tests/edit/i_small_assay_insert_pool.json b/samplesheets/tests/edit/i_small_assay_insert_pool_material.json
similarity index 100%
rename from samplesheets/tests/edit/i_small_assay_insert_pool.json
rename to samplesheets/tests/edit/i_small_assay_insert_pool_material.json
diff --git a/samplesheets/tests/edit/i_small_assay_insert_pool_process.json b/samplesheets/tests/edit/i_small_assay_insert_pool_process.json
new file mode 100644
index 00000000..6bb7de85
--- /dev/null
+++ b/samplesheets/tests/edit/i_small_assay_insert_pool_process.json
@@ -0,0 +1,124 @@
+{
+  "study": "11111111-1111-1111-1111-111111111111",
+  "assay": "22222222-2222-2222-2222-222222222222",
+  "nodes": [
+    {
+      "cells": [
+        {
+          "uuid": "11111111-1111-1111-5555-000000000000",
+          "obj_cls": "GenericMaterial",
+          "value": "0818-N1"
+        }
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "library preparation",
+          "uuid_ref": "22222222-2222-2222-bbbb-000000000000",
+          "header_name": "Protocol",
+          "header_type": "protocol",
+          "header_field": "col10",
+          "obj_cls": "Process"
+        }
+      ],
+      "headers": [
+        "Protocol REF"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "0818-N1-DNA1",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col11",
+          "obj_cls": "GenericMaterial",
+          "item_type": "MATERIAL"
+        }
+      ],
+      "headers": [
+        "Library Name"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": "22222222-2222-2222-2222-000000000003",
+          "value": "nucleic acid sequencing",
+          "obj_cls": "Process"
+        }
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "0818-N1-DNA1-WES1-R1.fastq.qz",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col14",
+          "obj_cls": "GenericMaterial",
+          "item_type": "DATA"
+        }
+      ],
+      "headers": [
+        "Raw Data File"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "0818-N1-DNA1-WES1-R2.fastq.qz",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col15",
+          "obj_cls": "GenericMaterial",
+          "item_type": "DATA"
+        }
+      ],
+      "headers": [
+        "Raw Data File"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "somatic variant calling-2",
+          "unit": "",
+          "header_name": "Data Transformation Name",
+          "header_type": "process_name",
+          "header_field": "col16",
+          "obj_cls": "Process"
+        }
+      ],
+      "headers": [
+        "Data Transformation Name"
+      ]
+    },
+    {
+      "cells": [
+        {
+          "uuid": null,
+          "value": "new-somatic.vcf.gz",
+          "unit": "",
+          "header_name": "Name",
+          "header_type": "name",
+          "header_field": "col17",
+          "obj_cls": "GenericMaterial",
+          "item_type": "DATA"
+        }
+      ],
+      "headers": [
+        "Derived Data File"
+      ]
+    }
+  ]
+}
\ No newline at end of file
diff --git a/samplesheets/tests/test_views_ajax.py b/samplesheets/tests/test_views_ajax.py
index 156c6c49..2a7a8ba0 100644
--- a/samplesheets/tests/test_views_ajax.py
+++ b/samplesheets/tests/test_views_ajax.py
@@ -76,7 +76,12 @@
 STUDY_INSERT_PATH = EDIT_DIR + 'i_small_study_insert.json'
 ASSAY_INSERT_PATH = EDIT_DIR + 'i_small_assay_insert.json'
 ASSAY_INSERT_SPLIT_PATH = EDIT_DIR + 'i_small_assay_insert_split.json'
-ASSAY_INSERT_POOL_PATH = EDIT_DIR + 'i_small_assay_insert_pool.json'
+ASSAY_INSERT_POOL_MATERIAL_PATH = os.path.join(
+    EDIT_DIR, 'i_small_assay_insert_pool_material.json'
+)
+ASSAY_INSERT_POOL_PROCESS_PATH = os.path.join(
+    EDIT_DIR, 'i_small_assay_insert_pool_process.json'
+)
 STUDY_DELETE_PATH = EDIT_DIR + 'i_small_study_delete.json'
 ASSAY_DELETE_PATH = EDIT_DIR + 'i_small_assay_delete.json'
 EDIT_SOURCE_NAME = '0818'
@@ -184,7 +189,7 @@ def setUp(self):
         self.assay = self.study.assays.first()
 
     def test_get(self):
-        """Test GET for context retrieval with sample sheets"""
+        """Test SheetContextAjaxView GET"""
         with self.login(self.user):
             response = self.client.get(
                 reverse(
@@ -289,8 +294,8 @@ def test_get(self):
         }
         self.assertEqual(response_data, expected)
 
-    def test_no_sheets(self):
-        """Test context retrieval without sample sheets"""
+    def test_get_no_sheets(self):
+        """Test GET without sample sheets"""
         self.investigation.active = False
         self.investigation.save()
 
@@ -345,7 +350,7 @@ def test_no_sheets(self):
 
     # TODO: Test anonymous request and irods_webdav_enabled
 
-    def test_delegate_min_owner(self):
+    def test_get_delegate_min_owner(self):
         """Test GET as delegate with owner minimum role"""
         app_settings.set(
             APP_NAME,
@@ -363,7 +368,7 @@ def test_delegate_min_owner(self):
         self.assertEqual(response.status_code, 200)
         self.assertFalse(json.loads(response.json())['perms']['edit_config'])
 
-    def test_delegate_min_delegate(self):
+    def test_get_delegate_min_delegate(self):
         """Test GET as delegate with delegate minimum role"""
         app_settings.set(
             APP_NAME,
@@ -381,7 +386,7 @@ def test_delegate_min_delegate(self):
         self.assertEqual(response.status_code, 200)
         self.assertTrue(json.loads(response.json())['perms']['edit_config'])
 
-    def test_irods_request_alert_owner(self):
+    def test_get_irods_request_alert_owner(self):
         """Test GET with active iRODS request alert as owner"""
         self.investigation.irods_status = True
         self.investigation.save()
@@ -413,7 +418,7 @@ def test_irods_request_alert_owner(self):
             ),
         )
 
-    def test_irods_request_alert_contributor(self):
+    def test_get_irods_request_alert_contributor(self):
         """Test GET with active iRODS request alert as contributor"""
         self.investigation.irods_status = True
         self.investigation.save()
@@ -440,7 +445,7 @@ def test_irods_request_alert_contributor(self):
         response_data = json.loads(response.data)
         self.assertEqual(len(response_data['alerts']), 0)
 
-    def test_inherited_owner(self):
+    def test_get_inherited_owner(self):
         """Test GET as inherited owner"""
         # Set up category owner
         user_cat = self.make_user('user_cat')
@@ -477,7 +482,7 @@ def setUp(self):
         self.cache_args = [APP_NAME, self.cache_name, self.project]
 
     def test_get(self):
-        """Test study tables retrieval"""
+        """Test StudyTablesAjaxView GET"""
         with self.login(self.user):
             response = self.client.get(
                 reverse(
@@ -513,7 +518,7 @@ def test_get(self):
         self.assertNotIn('edit_context', ret_data)
 
     def test_get_edit(self):
-        """Test study tables retrieval with edit mode enabled"""
+        """Test GET with edit mode enabled"""
         with self.login(self.user):
             response = self.client.get(
                 reverse(
@@ -549,7 +554,7 @@ def test_get_edit(self):
         self.assertIsNotNone(ret_data['edit_context']['protocols'])
 
     def test_get_study_cache(self):
-        """Test cached study table creation on retrieval"""
+        """Test GET for cached study table creation on retrieval"""
         self.assertIsNone(self.cache_backend.get_cache_item(*self.cache_args))
         self.assertEqual(JSONCacheItem.objects.count(), 0)
         with self.login(self.user):
@@ -566,7 +571,7 @@ def test_get_study_cache(self):
         self.assertEqual(JSONCacheItem.objects.count(), 1)
 
     def test_get_study_cache_existing(self):
-        """Test retrieval with existing cached study tables"""
+        """Test GET with existing cached study tables"""
         study_tables = table_builder.build_study_tables(self.study)
         cache_name = STUDY_TABLE_CACHE_ITEM.format(study=self.study.sodar_uuid)
         self.cache_backend.set_cache_item(
@@ -602,7 +607,7 @@ def setUp(self):
         self.assay = self.study.assays.first()
 
     def test_get(self):
-        """Test study links retrieval without plugin"""
+        """Test StudyLinksAjaxView GET without plugin"""
         with self.login(self.user):
             response = self.client.get(
                 reverse(
@@ -623,7 +628,7 @@ def setUp(self):
         self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
 
     def test_get(self):
-        """Test study tables retrieval"""
+        """Test SheetWarningsAjaxView GET"""
         with self.login(self.user):
             response = self.client.get(
                 reverse(
@@ -640,19 +645,6 @@ def test_get(self):
 class TestSheetCellEditAjaxView(SamplesheetsViewTestBase):
     """Tests for SheetCellEditAjaxView"""
 
-    def setUp(self):
-        super().setUp()
-        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
-        self.study = self.investigation.studies.first()
-        # Set up POST data
-        self.values = {'updated_cells': []}
-        # Set up helpers
-        self.cache_backend = get_backend_api('sodar_cache')
-        self.cache_name = STUDY_TABLE_CACHE_ITEM.format(
-            study=self.study.sodar_uuid
-        )
-        self.cache_args = [APP_NAME, self.cache_name, self.project]
-
     @classmethod
     def _convert_ontology_value(cls, value):
         """
@@ -668,8 +660,21 @@ def _convert_ontology_value(cls, value):
             value['unit'] = None
         return value
 
-    def test_edit_name(self):
-        """Test editing the name of a material"""
+    def setUp(self):
+        super().setUp()
+        self.investigation = self.import_isa_from_file(SHEET_PATH, self.project)
+        self.study = self.investigation.studies.first()
+        # Set up POST data
+        self.values = {'updated_cells': []}
+        # Set up helpers
+        self.cache_backend = get_backend_api('sodar_cache')
+        self.cache_name = STUDY_TABLE_CACHE_ITEM.format(
+            study=self.study.sodar_uuid
+        )
+        self.cache_args = [APP_NAME, self.cache_name, self.project]
+
+    def test_post_material_name(self):
+        """Test SheetCellEditAjaxView POST with material name"""
         obj = GenericMaterial.objects.get(study=self.study, name='0816')
         new_name = '0816aaa'
         self.values['updated_cells'].append(
@@ -694,8 +699,8 @@ def test_edit_name(self):
         obj.refresh_from_db()
         self.assertEqual(obj.name, new_name)
 
-    def test_edit_name_empty(self):
-        """Test setting an empty material name (should fail)"""
+    def test_post_material_name_empty(self):
+        """Test POST with empty material name (should fail)"""
         obj = GenericMaterial.objects.get(study=self.study, name='0816')
         self.values['updated_cells'].append(
             {
@@ -719,8 +724,8 @@ def test_edit_name_empty(self):
         obj.refresh_from_db()
         self.assertEqual(obj.name, '0816')
 
-    def test_edit_performer(self):
-        """Test editing the performer of a process"""
+    def test_post_performer(self):
+        """Test POST with process performer"""
         obj = Process.objects.filter(study=self.study, assay=None).first()
         value = 'Alice Example <alice@example.com>'
         self.values['updated_cells'].append(
@@ -745,8 +750,8 @@ def test_edit_performer(self):
         obj.refresh_from_db()
         self.assertEqual(obj.performer, value)
 
-    def test_edit_perform_date(self):
-        """Test editing the perform date of a process"""
+    def test_post_perform_date(self):
+        """Test POST with process perform date"""
         obj = Process.objects.filter(study=self.study, assay=None).first()
         value = '2020-07-07'
         self.values['updated_cells'].append(
@@ -771,8 +776,8 @@ def test_edit_perform_date(self):
         obj.refresh_from_db()
         self.assertEqual(obj.perform_date.strftime('%Y-%m-%d'), value)
 
-    def test_edit_perform_date_empty(self):
-        """Test editing the perform date of a process with an empty date"""
+    def test_post_perform_date_empty(self):
+        """Test POST with empty process perform date"""
         obj = Process.objects.filter(study=self.study, assay=None).first()
         value = ''
         self.values['updated_cells'].append(
@@ -797,8 +802,8 @@ def test_edit_perform_date_empty(self):
         obj.refresh_from_db()
         self.assertIsNone(obj.perform_date)
 
-    def test_edit_perform_date_invalid(self):
-        """Test editing the perform date of a process with an invalid date"""
+    def test_post_perform_date_invalid(self):
+        """Test POST with invalid perform date (should fail)"""
         obj = Process.objects.filter(study=self.study, assay=None).first()
         og_date = obj.perform_date
         value = '2020-11-31'
@@ -824,8 +829,8 @@ def test_edit_perform_date_invalid(self):
         obj.refresh_from_db()
         self.assertEqual(obj.perform_date, og_date)
 
-    def test_edit_characteristics_str(self):
-        """Test editing a characteristics string value in a material"""
+    def test_post_characteristics_str(self):
+        """Test POST with material characteristics string value"""
         obj = GenericMaterial.objects.get(study=self.study, name='0816')
         header_name = 'organism'
         self.assertNotEqual(
@@ -858,8 +863,8 @@ def test_edit_characteristics_str(self):
             {'unit': None, 'value': EDIT_NEW_VALUE_STR},
         )
 
-    def test_edit_param_values_str(self):
-        """Test editing a parameter values string value in a process"""
+    def test_post_param_values_str(self):
+        """Test POST with process parameter values string value"""
         obj = Process.objects.filter(study=self.study, assay=None).first()
         header_name = 'instrument'
         self.assertNotEqual(
@@ -892,8 +897,8 @@ def test_edit_param_values_str(self):
             {'unit': None, 'value': EDIT_NEW_VALUE_STR},
         )
 
-    def test_edit_protocol(self):
-        """Test editing the protocol reference of a process"""
+    def test_post_protocol(self):
+        """Test POST with process protocol reference"""
         obj = Process.objects.filter(
             study=self.study, unique_name__icontains='sample collection'
         ).first()
@@ -926,8 +931,8 @@ def test_edit_protocol(self):
         obj.refresh_from_db()
         self.assertEqual(obj.protocol, new_protocol)
 
-    def test_edit_process_name(self):
-        """Test editing the name of a process"""
+    def test_post_process_name(self):
+        """Test POST with process name"""
         obj = Process.objects.filter(
             study=self.study, unique_name__icontains='sample collection'
         ).first()
@@ -960,8 +965,8 @@ def test_edit_process_name(self):
         self.assertEqual(obj.name, name)
         self.assertEqual(obj.name_type, name_type)
 
-    def test_edit_ontology_term(self):
-        """Test editing an ontology term with a single term"""
+    def test_post_ontology_term(self):
+        """Test POST with single ontology term"""
         obj = GenericMaterial.objects.get(study=self.study, name='0817')
         name = 'organism'
         self.assertEqual(obj.characteristics[name], EMPTY_ONTOLOGY_VAL)
@@ -1000,8 +1005,8 @@ def test_edit_ontology_term(self):
             obj.characteristics[name], self._convert_ontology_value(value)
         )
 
-    def test_edit_ontology_term_replace(self):
-        """Test replacing an existing ontology term"""
+    def test_post_ontology_term_replace(self):
+        """Test POST to replace existing ontology term"""
         obj = GenericMaterial.objects.get(study=self.study, name='0815')
         name = 'organism'
         og_value = {
@@ -1047,8 +1052,8 @@ def test_edit_ontology_term_replace(self):
             obj.characteristics[name], self._convert_ontology_value(value)
         )
 
-    def test_edit_ontology_term_list(self):
-        """Test editing an ontology term with a list of terms"""
+    def test_post_ontology_term_list(self):
+        """Test POST with list of ontology terms"""
         obj = GenericMaterial.objects.get(study=self.study, name='0817')
         name = 'organism'
         value = [
@@ -1093,8 +1098,8 @@ def test_edit_ontology_term_list(self):
             obj.characteristics[name], self._convert_ontology_value(value)
         )
 
-    def test_edit_ontology_term_empty(self):
-        """Test editing an ontology term with an empty value"""
+    def test_post_ontology_term_empty(self):
+        """Test POST with empty ontology term value"""
         obj = GenericMaterial.objects.get(study=self.study, name='0815')
         name = 'organism'
         og_value = {
@@ -1128,8 +1133,8 @@ def test_edit_ontology_term_empty(self):
         obj.refresh_from_db()
         self.assertEqual(obj.characteristics[name], EMPTY_ONTOLOGY_VAL)
 
-    def test_edit_ontology_term_ref(self):
-        """Test ontology source ref updating when editing term value"""
+    def test_post_ontology_term_ref(self):
+        """Test POST for ontology source ref updating when editing term value"""
         # Set up ontology
         obo_doc = fastobo.load(OBO_PATH)
         ontology = OBOFormatOntologyIO().import_obo(
@@ -1203,8 +1208,8 @@ def test_edit_ontology_term_ref(self):
         }
         self.assertEqual(ref, expected)
 
-    def test_edit_study_cache(self):
-        """Test editing with cached study tables"""
+    def test_post_study_cache(self):
+        """Test POST with cached study tables"""
         # Create cache item
         study_tables = table_builder.build_study_tables(self.study)
         cache_name = STUDY_TABLE_CACHE_ITEM.format(study=self.study.sodar_uuid)
@@ -1258,8 +1263,8 @@ def setUp(self):
         self.study = self.investigation.studies.first()
         self.values = {'updated_cells': []}
 
-    def test_edit_extract_label_string(self):
-        """Test updating the extract label field with a string value"""
+    def test_post_extract_label_string(self):
+        """Test SheetCellEditAjaxView POST with extract label and string value"""
         label = 'New label'
         name_type = th.LABELED_EXTRACT_NAME
         obj = GenericMaterial.objects.get(
@@ -1316,8 +1321,8 @@ def setUp(self):
         )
         self.cache_args = [APP_NAME, self.cache_name, self.project]
 
-    def test_insert_study_row(self):
-        """Test inserting a new row into a study"""
+    def test_post_study_row(self):
+        """Test SheetRowInsertAjaxView POST with study row"""
         self.assertIsNone(
             GenericMaterial.objects.filter(
                 study=self.study, name='0818'
@@ -1378,8 +1383,8 @@ def test_insert_study_row(self):
         self.assertEqual(sample.characteristics['status']['value'], '0')
         self.assertEqual(sample.factor_values['treatment']['value'], 'yes')
 
-    def test_insert_assay_row(self):
-        """Test inserting a new row into an assay"""
+    def test_post_assay_row(self):
+        """Test POST with assay row"""
         # Insert study row
         response = self.insert_row(path=STUDY_INSERT_PATH)
         self.assertEqual(response.status_code, 200)
@@ -1430,8 +1435,8 @@ def test_insert_assay_row(self):
         for i in range(len(node_names) - 1):
             self.assertIn([node_names[i], node_names[i + 1]], self.assay.arcs)
 
-    def test_insert_assay_row_split(self):
-        """Test inserting a row with splitting into an assay"""
+    def test_post_assay_row_split(self):
+        """Test POST with assay row and splitting"""
         # Insert study and assay rows
         self.insert_row(path=STUDY_INSERT_PATH)
         sample = GenericMaterial.objects.get(
@@ -1458,8 +1463,8 @@ def test_insert_assay_row_split(self):
         )
         self.assertEqual(len(self.assay.arcs), arc_count + 1)
 
-    def test_insert_assay_row_pool(self):
-        """Test inserting a row with pooling into an assay"""
+    def test_post_assay_row_pool_material(self):
+        """Test POST with assay row and pooling by data file material"""
         self.insert_row(path=STUDY_INSERT_PATH)
         sample = GenericMaterial.objects.get(
             study=self.study, name=EDIT_SAMPLE_NAME
@@ -1472,7 +1477,7 @@ def test_insert_assay_row_pool(self):
         mat_count = GenericMaterial.objects.filter(assay=self.assay).count()
         proc_count = Process.objects.filter(assay=self.assay).count()
         arc_count = len(self.assay.arcs)
-        response = self.insert_row(path=ASSAY_INSERT_POOL_PATH)
+        response = self.insert_row(path=ASSAY_INSERT_POOL_MATERIAL_PATH)
 
         self.assertEqual(response.status_code, 200)
         self.assay.refresh_from_db()
@@ -1485,10 +1490,37 @@ def test_insert_assay_row_pool(self):
         )
         self.assertEqual(len(self.assay.arcs), arc_count + 7)
 
+    def test_post_assay_row_pool_process(self):
+        """Test POST with assay row and pooling by named process"""
+        self.insert_row(path=STUDY_INSERT_PATH)
+        sample = GenericMaterial.objects.get(
+            study=self.study, name=EDIT_SAMPLE_NAME
+        )
+        sample.sodar_uuid = EDIT_SAMPLE_UUID
+        sample.save()
+        self.insert_row(path=ASSAY_INSERT_PATH)
+
+        self.update_assay_row_uuids(update_sample=False)
+        mat_count = GenericMaterial.objects.filter(assay=self.assay).count()
+        proc_count = Process.objects.filter(assay=self.assay).count()
+        arc_count = len(self.assay.arcs)
+        response = self.insert_row(path=ASSAY_INSERT_POOL_PROCESS_PATH)
+
+        self.assertEqual(response.status_code, 200)
+        self.assay.refresh_from_db()
+        self.assertEqual(
+            GenericMaterial.objects.filter(assay=self.assay).count(),
+            mat_count + 4,
+        )
+        self.assertEqual(
+            Process.objects.filter(assay=self.assay).count(), proc_count + 1
+        )
+        self.assertEqual(len(self.assay.arcs), arc_count + 7)
+
     # TODO: Test ontology ref updating
 
-    def test_insert_study_cache(self):
-        """Test inserting new row with cached study tables"""
+    def test_post_study_cache(self):
+        """Test POST with cached study tables"""
         study_tables = table_builder.build_study_tables(self.study)
         cache_name = STUDY_TABLE_CACHE_ITEM.format(study=self.study.sodar_uuid)
         self.cache_backend.set_cache_item(
@@ -1552,8 +1584,8 @@ def setUp(self):
         )
         self.cache_args = [APP_NAME, self.cache_name, self.project]
 
-    def test_delete_assay_row(self):
-        """Test row deletion from assay"""
+    def test_post_assay_row(self):
+        """Test SheetRowDeleteAjaxView POST with assay row"""
         response = self.delete_row(ASSAY_DELETE_PATH)
         self.assertEqual(response.status_code, 200)
         self.assay.refresh_from_db()
@@ -1568,8 +1600,8 @@ def test_delete_assay_row(self):
         for n in self.row_names:
             self.assertNotIn(n, target_nodes)
 
-    def test_delete_study_row(self):
-        """Test row deletion from study"""
+    def test_post_study_row(self):
+        """Test POST with study row"""
         # First delete the assay row
         response = self.delete_row(ASSAY_DELETE_PATH)
         self.assertEqual(response.status_code, 200)
@@ -1593,8 +1625,8 @@ def test_delete_study_row(self):
             ).first()
         )
 
-    def test_delete_study_row_in_use(self):
-        """Test study row deletion with sample used in asssay (should fail)"""
+    def test_post_study_row_in_use(self):
+        """Test POST with study row containing sample used in asssay (should fail)"""
         response = self.delete_row(STUDY_DELETE_PATH)
         self.assertEqual(response.status_code, 500)
         self.assertIsNotNone(
@@ -1615,8 +1647,8 @@ def test_delete_study_row_in_use(self):
 
     # TODO: Test deletion with splitting/pooling
 
-    def test_delete_assay_row_study_cache(self):
-        """Test row deletion from assay with cached study tables"""
+    def test_post_assay_row_study_cache(self):
+        """Test POST with assay row and cached study tables"""
         study_tables = table_builder.build_study_tables(self.study)
         cache_name = STUDY_TABLE_CACHE_ITEM.format(study=self.study.sodar_uuid)
         self.cache_backend.set_cache_item(
@@ -1771,8 +1803,8 @@ def setUp(self):
         )
         self.cache_args = [APP_NAME, self.cache_name, self.project]
 
-    def test_update_study_column(self):
-        """Test posting a study column update"""
+    def test_post_study_column(self):
+        """Test SheetEditConfigAjaxView POST with study column"""
         sheet_config = app_settings.get(
             APP_NAME, 'sheet_config', project=self.project
         )
@@ -1823,8 +1855,8 @@ def test_update_study_column(self):
             1,
         )
 
-    def test_superuser_min_owner(self):
-        """Test updating as superuser with minimum role of owner"""
+    def test_post_superuser_min_owner(self):
+        """Test POST as superuser with minimum role of owner"""
         edit_config_min_role = app_settings.get(
             APP_NAME, 'edit_config_min_role', project=self.project
         )
@@ -1842,8 +1874,8 @@ def test_superuser_min_owner(self):
             )
         self.assertEqual(response.status_code, 200)
 
-    def test_owner_min_owner(self):
-        """Test updating as owner with minimum=owner"""
+    def test_post_owner_min_owner(self):
+        """Test POST as owner with minimum=owner"""
         edit_config_min_role = app_settings.get(
             APP_NAME, 'edit_config_min_role', project=self.project
         )
@@ -1861,8 +1893,8 @@ def test_owner_min_owner(self):
             )
         self.assertEqual(response.status_code, 200)
 
-    def test_delegate_min_owner(self):
-        """Test updating as delegate with minimum=owner (should fail)"""
+    def test_post_delegate_min_owner(self):
+        """Test POST as delegate with minimum=owner (should fail)"""
         edit_config_min_role = app_settings.get(
             APP_NAME, 'edit_config_min_role', project=self.project
         )
@@ -1884,8 +1916,8 @@ def test_delegate_min_owner(self):
             'User not allowed to modify column config',
         )
 
-    def test_contributor_min_owner(self):
-        """Test updating as contributor with minimum=owner (should fail)"""
+    def test_post_contributor_min_owner(self):
+        """Test POST as contributor with minimum=owner (should fail)"""
         edit_config_min_role = app_settings.get(
             APP_NAME, 'edit_config_min_role', project=self.project
         )
@@ -1907,8 +1939,8 @@ def test_contributor_min_owner(self):
             'User not allowed to modify column config',
         )
 
-    def test_inherited_owner(self):
-        """Test updating as inherited owner"""
+    def test_post_inherited_owner(self):
+        """Test POST as inherited owner"""
         with self.login(self.user_cat):
             response = self.client.post(
                 reverse(
@@ -1920,8 +1952,8 @@ def test_inherited_owner(self):
             )
         self.assertEqual(response.status_code, 200)
 
-    def test_update_study_cache(self):
-        """Test posting a study column update with cached study tables"""
+    def test_post_study_cache(self):
+        """Test POST with study column and cached study tables"""
         study_tables = table_builder.build_study_tables(self.study)
         cache_name = STUDY_TABLE_CACHE_ITEM.format(study=self.study.sodar_uuid)
         self.cache_backend.set_cache_item(
@@ -1983,7 +2015,7 @@ def setUp(self):
         self.study_config = self.display_config['studies'][self.s_uuid]
 
     def test_post(self):
-        """Test updating the sheet configuration"""
+        """Test StudyDisplayConfigAjaxView POST"""
         self.assertEqual(
             self.study_config['nodes'][0]['fields'][2]['visible'], True
         )
@@ -2013,7 +2045,7 @@ def test_post(self):
         )
 
     def test_post_default(self):
-        """Test updating along with the default configuration"""
+        """Test POST with default configuration"""
         self.assertEqual(
             self.study_config['nodes'][0]['fields'][2]['visible'], True
         )
@@ -2048,7 +2080,7 @@ def test_post_default(self):
         self.assertEqual(updated_config, default_config)
 
     def test_post_no_change(self):
-        """Test posting with no updates"""
+        """Test POST with no updates"""
         with self.login(self.user):
             response = self.client.post(
                 reverse(
@@ -2099,7 +2131,7 @@ def setUp(self):
         self.isa2.save()
 
     def test_get(self):
-        """Test GET returning diff data"""
+        """Test SheetVersionCompareAjaxView GET returning diff data"""
         expected = {
             'studies': {
                 's_small2.txt': [
diff --git a/samplesheets/views_ajax.py b/samplesheets/views_ajax.py
index a2c79e40..17ce0ad3 100644
--- a/samplesheets/views_ajax.py
+++ b/samplesheets/views_ajax.py
@@ -999,10 +999,11 @@ def _get_name(cls, node):
         """
         if node['cells'][0]['obj_cls'] == 'Process':
             for cell in node['cells']:
-                if cell['header_type'] == 'process_name':
+                if cell.get('header_type') == 'process_name':
                     return cell['value']
         else:  # Material
             return node['cells'][0]['value']
+        return None
 
     @classmethod
     def _add_node_attr(cls, node_obj, cell):
@@ -1191,8 +1192,15 @@ def _insert_row(self, row):
             )
         )
 
+        # TODO: We create duplicate rows with named processes, fix!
+
         # Check if we'll need to consider collapsing of unnamed nodes
-        if len([n for n in row['nodes'] if not self._get_name(n)]) > 0:
+        # (References to existing nodes with UUID will not have to be collapsed)
+        if [
+            n
+            for n in row['nodes']
+            if not n['cells'][0].get('uuid') and not self._get_name(n)
+        ]:
             logger.debug('Unnamed node(s) in row, will attempt collapsing')
             collapse = True
             try:
@@ -1390,6 +1398,8 @@ def post(self, request, *args, **kwargs):
                 except Exception as ex:
                     return Response({'detail': str(ex)}, status=500)
             except Exception as ex:
+                if settings.DEBUG:
+                    raise (ex)
                 return Response({'detail': str(ex)}, status=500)
         return Response(self.ok_data, status=200)
 
diff --git a/samplesheets/vueapp/src/App.vue b/samplesheets/vueapp/src/App.vue
index 039418c3..d649b61c 100644
--- a/samplesheets/vueapp/src/App.vue
+++ b/samplesheets/vueapp/src/App.vue
@@ -765,12 +765,12 @@ export default {
           let value = this.getDefaultValue(nextColId, gridOptions, true)
 
           // If default name suffix is set, fill name, enable node and continue
+          // TODO: Remove repetition with named process (see below)
           if (headerType === 'name' &&
               !(['SOURCE', 'DATA'].includes(itemType)) &&
               value.value) {
             value.value = this.getNamePrefix(rowNode, cols, startIdx) + value.value
             let createNew = true
-
             // Check if name already appears in column, update UUID if found
             gridOptions.api.forEachNode(function (r) {
               if (r.data[nextColId].value === value.value) {
@@ -778,7 +778,6 @@ export default {
                 value.uuid = r.data[nextColId].uuid
               }
             })
-
             value.newInit = false
             value.editable = true
             rowNode.setDataValue(nextColId, value)
@@ -831,12 +830,30 @@ export default {
               } else forceEmpty = true
             } else if (headerType === 'process_name') {
               // Fill process name with default suffix if set
+              // TODO: Remove repetition with material name
               const namePrefix = this.getNamePrefix(rowNode, cols, i)
               if (namePrefix && value.value) {
                 value.value = namePrefix + value.value
+                let createNew = true
+                // Check if name already appears in column, update UUID if found
+                gridOptions.api.forEachNode(function (r) {
+                  if (r.data[nextColId].value === value.value) {
+                    createNew = false
+                    value.uuid = r.data[nextColId].uuid
+                  }
+                })
                 newInit = false
                 value.newInit = false
                 processActive = true
+                rowNode.setDataValue(nextColId, value)
+                this.handleNodeUpdate(
+                  value,
+                  cols[i],
+                  rowNode,
+                  gridOptions,
+                  gridUuid,
+                  createNew)
+                return
               } else value.value = '' // HACK: Reset default value if not filled
               value.editable = true // Process name should always be editable
             } else {
@@ -859,14 +876,13 @@ export default {
     },
 
     handleNodeUpdate (
-      firstCellValue, column, rowNode, gridOptions, gridUuid, createNew
+      nameCellValue, column, rowNode, gridOptions, gridUuid, createNew
     ) {
       // console.log('handleNodeUpdate() called; colId=' + column.colId) // DEBUG
       const gridApi = gridOptions.api
       const columnApi = gridOptions.columnApi
-      const firstColId = column.colId // ID of the identifying node column
+      const nameColId = column.colId // ID of the identifying node column
       let assayMode = false
-
       if (gridUuid in this.sodarContext.studies[this.currentStudyUuid].assays) {
         assayMode = true
       }
@@ -878,23 +894,22 @@ export default {
         const studyCols = studyOptions.columnApi.getColumns()
         let studyCopyRow = null
         const sampleColId = this.sampleColId
-
         // Get sample row from study table
         studyApi.forEachNode(function (rowNode) {
           if (!studyCopyRow &&
-              rowNode.data[sampleColId].uuid === firstCellValue.uuid_ref) {
+              rowNode.data[sampleColId].uuid === nameCellValue.uuid_ref) {
             studyCopyRow = rowNode
           }
         })
-
-        // Fill in preceeding nodes
+        // Fill in preceeding nodes for sample
         for (let i = 1; i < this.sampleIdx; i++) {
           // TODO: Create a generic helper for copying
           const copyColId = studyCols[i].colId
           const copyData = Object.assign(studyCopyRow.data[copyColId])
           copyData.newRow = true
           copyData.newInit = false
-          copyData.editable = columnApi.getColumn(copyColId).colDef.cellRendererParams.fieldEditable
+          copyData.editable = columnApi.getColumn(
+            copyColId).colDef.cellRendererParams.fieldEditable
           rowNode.setDataValue(copyColId, copyData)
         }
       }
@@ -908,55 +923,64 @@ export default {
       let groupId = parent.groupId
       if (groupId === '1' && this.sourceColSpan > 1) groupId = '2'
       let startIdx
-
       for (let i = 1; i < cols.length - 1; i++) {
-        if (cols[i].colId === firstColId) {
+        if (cols[i].colId === nameColId) {
           startIdx = i + 1
           break
         }
       }
-
       for (let i = startIdx; i < cols.length - 1; i++) {
         const col = cols[i]
         // NOTE: Must use originalParent to work with hidden columns
         if (col.originalParent.groupId === groupId) {
           nodeCols.push(col)
-        } else if (col.colId !== firstColId &&
+        } else if (col.colId !== nameColId &&
               col.originalParent.groupId !== groupId) {
           nextNodeStartIdx = i
           break
         }
       }
 
-      // IF node is new THEN fill out other cells with default/empty values
+      // If the node is new, fill out other cells with default/empty values
       if (createNew) {
         for (let i = 0; i < nodeCols.length; i++) {
           const newColId = nodeCols[i].colId
           const value = this.getDefaultValue(nodeCols[i].colId, gridOptions)
           rowNode.setDataValue(newColId, value)
         }
-      } else { // ELSE set UUIDs and update cell values (only in the same table)
+      } else { // Else set UUIDs and update cell values (only in the same table)
         let copyRowNode = null
         gridApi.forEachNode(function (rowNode) {
-          if (!copyRowNode && rowNode.data[firstColId].value === firstCellValue.value) {
+          if (!copyRowNode &&
+              rowNode.data[nameColId].value === nameCellValue.value) {
             copyRowNode = rowNode
           }
         })
-
         for (let i = 0; i < nodeCols.length; i++) {
           const copyColId = nodeCols[i].colId
           const copyData = Object.assign(copyRowNode.data[copyColId])
           copyData.newInit = false
-          copyData.editable = columnApi.getColumn(copyColId).colDef.cellRendererParams.fieldEditable
+          copyData.editable = columnApi.getColumn(
+            copyColId).colDef.cellRendererParams.fieldEditable
           rowNode.setDataValue(copyColId, copyData)
         }
       }
+      // When updating protocol name column, update preceeding protocol UUID
+      if (startIdx > 2) {
+        const headerType = column.colDef.cellEditorParams.headerInfo.header_type
+        const prevCol = cols[startIdx - 2]
+        const prevHeaderType = prevCol.colDef.cellEditorParams.headerInfo.header_type
+        if (headerType === 'process_name' &&
+            prevHeaderType === 'protocol' &&
+            cols[startIdx - 2].originalParent.groupId === groupId) {
+          rowNode.data[prevCol.colId].uuid = rowNode.data[nameColId].uuid
+        }
+      }
 
       // Enable the next node(s), if we are initializing node for the 1st time
       if (nextNodeStartIdx) {
         this.enableNextNodes(rowNode, gridOptions, gridUuid, nextNodeStartIdx)
       }
-
       // Redraw row node for all changes to be displayed
       gridApi.redrawRows({ rows: [rowNode] })
     },
@@ -1031,7 +1055,6 @@ export default {
               if (this.sourceColSpan > 1) lastSourceGroupIdx = 2 // 2nd source group
               const lastSourceGroupId = cols[lastSourceGroupIdx].originalParent.groupId
               let groupId = cols[1].originalParent.groupId
-
               // Modify starting index and group id for assay table updating
               if (assayMode) {
                 startIdx = this.sampleIdx
@@ -1046,13 +1069,11 @@ export default {
                 value.newInit = false
                 value.editable = cols[i].colDef.cellRendererParams.fieldEditable
                 rowNode.setDataValue(cols[i].colId, value)
-
                 // Save sample info if new sample was added in study
                 if (!assayMode && cols[i].colId === this.sampleColId) {
                   sampleUuid = data.node_uuids[nodeIdx]
                   sampleName = rowNode.data[cols[i].colId].value
                 }
-
                 if (i < cols.length - 2 &&
                     groupId !== cols[i + 1].originalParent.groupId &&
                     cols[i + 1].originalParent.groupId !== lastSourceGroupId) {
@@ -1090,7 +1111,6 @@ export default {
               console.log('Row insert status: ' + data.detail) // DEBUG
               this.showNotification('Insert Failed', 'danger', 1000)
             }
-
             finishCallback()
             this.updatingRow = false
           }
diff --git a/samplesheets/vueapp/src/components/editors/DataCellEditor.vue b/samplesheets/vueapp/src/components/editors/DataCellEditor.vue
index 63afc5d0..500323eb 100644
--- a/samplesheets/vueapp/src/components/editors/DataCellEditor.vue
+++ b/samplesheets/vueapp/src/components/editors/DataCellEditor.vue
@@ -88,6 +88,7 @@ export default Vue.extend({
       nameValues: [],
       nameUuids: {},
       sampleColId: null,
+      nameColumn: false,
       destroyCalled: false // HACK for issue #869
     }
   },
@@ -138,7 +139,7 @@ export default Vue.extend({
       return ''
     },
     getValidState () {
-      if (this.headerInfo.header_type === 'name') { // Name is a special case
+      if (this.nameColumn) { // Name is a special case
         // TODO: Cleanup/simplify
         // NOTE: Empty value is allowed for DATA materials
         if ((this.editValue.length === 0 &&
@@ -233,7 +234,6 @@ export default Vue.extend({
   created () {
     this.app = this.params.app
     this.gridOptions = this.app.getGridOptionsByUuid(this.params.gridUuid)
-
     // Cancel editing if editingCell is true
     if (this.app.editingCell) {
       this.editAllowed = false
@@ -248,18 +248,18 @@ export default Vue.extend({
       this.isValueArray = true
       this.editValue = this.editValue.join('; ')
     }
-
     if (this.value.value) {
       this.ogEditValue = Object.assign(this.value.value)
     } else {
       this.ogEditValue = null
     }
-
     this.headerInfo = this.params.headerInfo
     this.renderInfo = this.params.renderInfo
     this.editConfig = this.params.editConfig
     this.sampleColId = this.params.sampleColId
-
+    if (['name', 'process_name'].includes(this.headerInfo.header_type)) {
+      this.nameColumn = true
+    }
     // console.log('Edit colId/field: ' + this.params.colDef.field) // DEBUG
 
     // Set up unit value
@@ -322,7 +322,7 @@ export default Vue.extend({
     }
 
     // Special setup for the name column
-    if (this.headerInfo.header_type === 'name') {
+    if (this.nameColumn) {
       if (this.value.newRow) this.containerTitle = 'Enter name of new or existing node'
       else this.containerTitle = 'Rename node'
       // If name, get other current values for comparison in validation
@@ -360,20 +360,6 @@ export default Vue.extend({
           this.value.value[i] = this.value.value[i].trim()
         }
       }
-      // Check if we're in a named process without a protocol
-      let namedProcess = false
-      if (this.headerInfo.header_type === 'process_name') {
-        namedProcess = true
-        const groupId = this.params.column.originalParent.groupId
-        const cols = this.gridOptions.columnApi.getColumns()
-        for (let i = 1; i < cols.length - 1; i++) {
-          if (cols[i].originalParent.groupId === groupId &&
-              cols[i].colDef.cellEditorParams.headerInfo.header_type === 'protocol') {
-            namedProcess = false
-            break
-          }
-        }
-      }
 
       // Reject invalid value
       if (!this.valid) {
@@ -385,7 +371,7 @@ export default Vue.extend({
       }
 
       // Confirm renaming node into an existing node and overwriting values
-      if ((this.headerInfo.header_type === 'name' || namedProcess) &&
+      if ((this.nameColumn) &&
           this.value.newRow &&
           this.ogEditValue &&
           this.nameValues.includes(this.editValue)) {
@@ -402,12 +388,11 @@ export default Vue.extend({
       }
 
       // Proceed with setting values and saving
-      if ((this.headerInfo.header_type === 'name' || namedProcess) &&
-            (!this.value.uuid || this.value.newRow)) {
+      if (this.nameColumn && (!this.value.uuid || this.value.newRow)) {
         // Set UUID if we are referring to an existing node (only if material)
-        if (!namedProcess && this.nameValues.includes(this.value.value)) {
+        if (this.nameValues.includes(this.value.value)) {
           this.value.uuid = this.nameUuids[this.value.value]
-        } else if (!namedProcess) {
+        } else {
           // Clear UUID in case user switched from existing to new while editing
           this.value.uuid = null
         }
@@ -419,6 +404,7 @@ export default Vue.extend({
         else this.value.unit = this.editUnit
 
         // Handle updating/initiating node
+        // TODO: Ensure this works also if setting process name value to empty
         this.app.handleNodeUpdate(
           this.value,
           this.params.column,
@@ -434,7 +420,6 @@ export default Vue.extend({
         // Update cell (only if we already have the UUID!)
         if (this.value.uuid) {
           this.app.handleCellEdit(this.getUpdateData(), true)
-
           // If a sample has been renamed, update sample list for assay
           if (this.headerInfo.header_type === 'name' &&
               this.params.colDef.field === this.sampleColId) {
diff --git a/samplesheets/vueapp/src/components/renderers/RowEditRenderer.vue b/samplesheets/vueapp/src/components/renderers/RowEditRenderer.vue
index 62062a91..2afe0908 100644
--- a/samplesheets/vueapp/src/components/renderers/RowEditRenderer.vue
+++ b/samplesheets/vueapp/src/components/renderers/RowEditRenderer.vue
@@ -313,23 +313,17 @@ export default Vue.extend({
       let groupId = cols[startIdx].originalParent.groupId
       let fieldIdx = 0 // Field index within node
       let nodeCells = []
-      let nodeClass
+      // let nodeClass
       let nodeStartIdx = startIdx
 
       for (let i = startIdx; i < cols.length - 1; i++) {
-        if (fieldIdx === 0) {
-          nodeStartIdx = i
-          nodeClass = cols[i].colDef.cellEditorParams.headerInfo.obj_cls
-        }
-
+        if (fieldIdx === 0) nodeStartIdx = i
         // Add cells for new nodes, only the first node for existing ones
-        if (nodeClass === 'Process' ||
-            fieldIdx === 0 ||
+        if (fieldIdx === 0 ||
             (!this.rowNode.data[cols[i].colId].uuid &&
             !(this.assayMode && inSampleNode))) {
           nodeCells.push(this.getCellData(cols[i]))
         }
-
         if (i === cols.length - 1 ||
             groupId !== cols[i + 1].originalParent.groupId) {
           groupId = cols[i + 1].originalParent.groupId
diff --git a/samplesheets/vueapp/tests/unit/DataCellEditor.spec.js b/samplesheets/vueapp/tests/unit/DataCellEditor.spec.js
index 3a7902bd..f658190b 100644
--- a/samplesheets/vueapp/tests/unit/DataCellEditor.spec.js
+++ b/samplesheets/vueapp/tests/unit/DataCellEditor.spec.js
@@ -1,6 +1,7 @@
 import { createLocalVue, mount } from '@vue/test-utils'
 import {
   studyUuid,
+  assayUuid,
   copy,
   getAppStub,
   getSheetTableComponents,
@@ -819,6 +820,53 @@ describe('DataCellEditor.vue', () => {
     expect(wrapper.find('.sodar-ss-data').text()).toBe('-')
   })
 
+  it('updates value in process assay name column', async () => {
+    const value = '0815-N1-DNA1-WES1-UPDATED'
+    const table = copy(studyTablesOneCol).tables.assays[assayUuid]
+    table.field_header[0] = studyTablesEdit.tables.assays[assayUuid].field_header[13]
+    table.table_data[0][0] = copy(studyTablesEdit).tables.assays[assayUuid].table_data[0][13]
+    const wrapper = mountSheetTable({
+      table: table,
+      editStudyConfig: {
+        nodes: [{ fields: [studyEditConfig.assays[assayUuid].nodes[2].fields[1]] }]
+      }
+    })
+    await waitAG(wrapper)
+    await waitRAF()
+
+    await wrapper.find('.sodar-ss-data-cell').trigger('dblclick')
+    const input = wrapper.find('.ag-cell-edit-input')
+    input.element.value = value
+    await input.trigger('input')
+    await gridOptions.api.stopEditing()
+    expect(wrapper.find('.ag-cell-edit-input').exists()).toBe(false)
+    expect(wrapper.find('.sodar-ss-data').text()).toBe(value)
+  })
+
+  it('updates process assay name column with empty value', async () => {
+    const value = '' // NOTE: For named processes this IS allowed
+    const table = copy(studyTablesOneCol).tables.assays[assayUuid]
+    table.field_header[0] = studyTablesEdit.tables.assays[assayUuid].field_header[13]
+    table.table_data[0][0] = copy(studyTablesEdit).tables.assays[assayUuid].table_data[0][13]
+    const wrapper = mountSheetTable({
+      table: table,
+      editStudyConfig: {
+        nodes: [{ fields: [studyEditConfig.assays[assayUuid].nodes[2].fields[1]] }]
+      }
+    })
+    await waitAG(wrapper)
+    await waitRAF()
+
+    await wrapper.find('.sodar-ss-data-cell').trigger('dblclick')
+    const input = wrapper.find('.ag-cell-edit-input')
+    input.element.value = value
+    await input.trigger('input')
+    await gridOptions.api.stopEditing()
+    expect(wrapper.find('.ag-cell-edit-input').exists()).toBe(false)
+    expect(wrapper.find('.sodar-ss-data').text()).toBe('-') // Empty value
+  })
+
+  // TODO: Test renaming to assay name already existing in table for new/old row
   // TODO: Test update propagation for multiple rows
   // TODO: Test value updating for new rows
 })

From b0c0775fcc798a0d93ece6cd5fa4d6d808d27395 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Thu, 14 Mar 2024 13:43:09 +0100
Subject: [PATCH 31/33] fix assay table source name editing after row insert
 (#1928)

---
 CHANGELOG.rst                              |  1 +
 docs_manual/source/sodar_release_notes.rst |  1 +
 samplesheets/vueapp/src/App.vue            | 10 ++++++++--
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 3c7c7733..e919a646 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -76,6 +76,7 @@ Fixed
     - ``get_pedigree_file_path()`` used in cancer study app tests (#1914)
     - IGV omit settings not correctly set on project creation (#1925)
     - Germline study cache build crash with no family column (#1921)
+    - Source name editing failing in assay table after row insert (#1928)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index f5ccc1d7..a9f1b039 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -24,6 +24,7 @@ Release for minor updates, maintenance and bug fixes.
 - Fix iRODS stats badge stuck in "updating"
 - Fix landing zone status updating not working in project details card
 - Fix landing zone creation crash with large amount of created collections
+- Fix multiple sheet editor issues
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.4
 
diff --git a/samplesheets/vueapp/src/App.vue b/samplesheets/vueapp/src/App.vue
index d649b61c..50d271a7 100644
--- a/samplesheets/vueapp/src/App.vue
+++ b/samplesheets/vueapp/src/App.vue
@@ -1055,10 +1055,16 @@ export default {
               if (this.sourceColSpan > 1) lastSourceGroupIdx = 2 // 2nd source group
               const lastSourceGroupId = cols[lastSourceGroupIdx].originalParent.groupId
               let groupId = cols[1].originalParent.groupId
-              // Modify starting index and group id for assay table updating
-              if (assayMode) {
+
+              if (assayMode) { // Assay table modifications
+                // Modify starting index and group id for assay table
                 startIdx = this.sampleIdx
                 groupId = cols[startIdx].originalParent.groupId
+                // Update newRow for source cells
+                for (let i = 1; i < startIdx; i++) {
+                  const value = rowNode.data[cols[i].colId]
+                  value.newRow = false
+                }
               }
 
               // Set cell data to match an existing row

From 863b1b8edb6d0eabbcb98249ce91682fa853a5a1 Mon Sep 17 00:00:00 2001
From: Harald Wilhelmi <harald@hwwey.de>
Date: Thu, 14 Mar 2024 13:55:17 +0100
Subject: [PATCH 32/33] add django settings for reverse proxy setup (#1917)

Co-authored-by: Harald Wilhelmi <harald.wilhelmi@uni-heidelberg.de>
---
 config/settings/base.py       | 1 +
 config/settings/production.py | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/config/settings/base.py b/config/settings/base.py
index 091a5791..459da0b6 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -35,6 +35,7 @@
 # ------------------------------------------------------------------------------
 # Hosts/domain names that are valid for this site
 ALLOWED_HOSTS = env.list('DJANGO_ALLOWED_HOSTS', default=['*'])
+USE_X_FORWARDED_HOST = env.bool('DJANGO_USE_X_FORWARDED_HOST', False)
 
 # APP CONFIGURATION
 # ------------------------------------------------------------------------------
diff --git a/config/settings/production.py b/config/settings/production.py
index 9d86f543..961a3268 100644
--- a/config/settings/production.py
+++ b/config/settings/production.py
@@ -43,6 +43,9 @@
 )
 CSRF_COOKIE_SECURE = True
 CSRF_COOKIE_HTTPONLY = True
+CSRF_TRUSTED_ORIGINS = env.list('DJANGO_CSRF_TRUSTED_ORIGINS', default=[])
+CSRF_COOKIE_DOMAIN = env.str('DJANGO_CSRF_COOKIE_DOMAIN', default=None)
+
 X_FRAME_OPTIONS = 'DENY'
 
 INSTALLED_APPS += ['gunicorn']

From b38e158896c83610a667cc7a2edd7c432bccc306 Mon Sep 17 00:00:00 2001
From: Mikko Nieminen <mikko.nieminen@bih-charite.de>
Date: Fri, 15 Mar 2024 10:26:22 +0100
Subject: [PATCH 33/33] cleanup and prepare v0.14.2 release (#1861)

---
 CHANGELOG.rst                                 |  8 +-
 config/settings/base.py                       |  7 +-
 config/settings/local.py                      |  4 +-
 config/settings/production.py                 |  8 +-
 docs_manual/source/api_documentation.rst      |  2 +-
 docs_manual/source/api_examples.rst           |  4 +-
 docs_manual/source/api_irodsinfo.rst          |  2 +-
 docs_manual/source/api_landingzones.rst       |  2 +-
 docs_manual/source/api_samplesheets.rst       |  2 +-
 docs_manual/source/conf.py                    |  4 +-
 docs_manual/source/dev_guide.rst              | 10 +-
 docs_manual/source/sodar_release_notes.rst    |  4 +-
 landingzones/tests/test_ui.py                 | 70 ++++++++++++++
 landingzones/views.py                         | 19 +---
 landingzones/views_ajax.py                    |  4 -
 landingzones/views_api.py                     |  1 -
 requirements/base.txt                         |  2 +-
 .../samplesheets/samplesheet_import_form.html | 16 +---
 samplesheets/views.py                         | 33 ++-----
 samplesheets/views_ajax.py                    |  4 +-
 samplesheets/views_api.py                     |  2 -
 samplesheets/vueapp/package-lock.json         |  4 +-
 samplesheets/vueapp/package.json              |  2 +-
 samplesheets/vueapp/src/App.vue               |  3 +-
 taskflowbackend/flows/landing_zone_delete.py  |  2 +-
 taskflowbackend/flows/landing_zone_move.py    |  2 +-
 taskflowbackend/tests/test_flows.py           | 96 +++++++------------
 27 files changed, 163 insertions(+), 154 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e919a646..cc256490 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -5,12 +5,14 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
-Unreleased
-==========
+v0.14.2 (2024-03-15)
+====================
 
 Added
 -----
 
+- **General**
+    - Django settings for reverse proxy setup (#1917)
 - **Irodsbackend**
     - Sanitize and validate ``IRODS_ROOT_PATH`` in ``get_root_path()`` (#1891)
 - **Landingzones**
@@ -32,7 +34,7 @@ Changed
 -------
 
 - **General**
-    - Upgrade to Django v3.2.24 (#1854)
+    - Upgrade to Django v3.2.25 (#1854)
     - Upgrade to django-sodar-core v0.13.4 (#1899)
     - Upgrade critical Vue app dependencies (#1854)
     - Upgrade to cubi-isa-templates v0.1.2 (#1854)
diff --git a/config/settings/base.py b/config/settings/base.py
index 459da0b6..6fec8a55 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -22,7 +22,7 @@
 env = environ.Env()
 
 # .env file, should load only in development environment
-READ_DOT_ENV_FILE = env.bool('DJANGO_READ_DOT_ENV_FILE', default=False)
+READ_DOT_ENV_FILE = env.bool('DJANGO_READ_DOT_ENV_FILE', False)
 
 if READ_DOT_ENV_FILE:
     # Operating System Environment variables have precedence over variables
@@ -157,7 +157,7 @@
 # See: https://docs.djangoproject.com/en/3.2/ref/settings/#databases
 # Uses django-environ to accept uri format
 # See: https://django-environ.readthedocs.io/en/latest/#supported-types
-DATABASES = {'default': env.db('DATABASE_URL', default='postgres:///sodar')}
+DATABASES = {'default': env.db('DATABASE_URL', 'postgres:///sodar')}
 DATABASES['default']['ATOMIC_REQUESTS'] = False
 
 # Set default auto field (for Django 3.2+)
@@ -607,7 +607,7 @@ def set_logging(level=None):
 
 
 # General API settings
-SODAR_API_DEFAULT_VERSION = '0.14.1'
+SODAR_API_DEFAULT_VERSION = '0.14.2'
 SODAR_API_ALLOWED_VERSIONS = [
     '0.7.0',
     '0.7.1',
@@ -628,6 +628,7 @@ def set_logging(level=None):
     '0.13.4',
     '0.14.0',
     '0.14.1',
+    '0.14.2',
 ]
 SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'
 SODAR_API_DEFAULT_HOST = env.url(
diff --git a/config/settings/local.py b/config/settings/local.py
index 74ce43d2..7ffc301b 100644
--- a/config/settings/local.py
+++ b/config/settings/local.py
@@ -16,7 +16,7 @@
 
 # DEBUG
 # ------------------------------------------------------------------------------
-DEBUG = env.bool('DJANGO_DEBUG', default=True)
+DEBUG = env.bool('DJANGO_DEBUG', True)
 TEMPLATES[0]['OPTIONS']['debug'] = DEBUG
 
 # SECRET CONFIGURATION
@@ -53,7 +53,7 @@
 
 # django-debug-toolbar
 # ------------------------------------------------------------------------------
-ENABLE_DEBUG_TOOLBAR = env.bool('ENABLE_DEBUG_TOOLBAR', default=True)
+ENABLE_DEBUG_TOOLBAR = env.bool('ENABLE_DEBUG_TOOLBAR', True)
 
 if ENABLE_DEBUG_TOOLBAR:
     MIDDLEWARE += ['debug_toolbar.middleware.DebugToolbarMiddleware']
diff --git a/config/settings/production.py b/config/settings/production.py
index 961a3268..af45a4b9 100644
--- a/config/settings/production.py
+++ b/config/settings/production.py
@@ -28,15 +28,15 @@
 SECURE_HSTS_SECONDS = 60
 
 SECURE_HSTS_INCLUDE_SUBDOMAINS = env.bool(
-    'DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS', default=True
+    'DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS', True
 )
 SECURE_CONTENT_TYPE_NOSNIFF = env.bool(
-    'DJANGO_SECURE_CONTENT_TYPE_NOSNIFF', default=True
+    'DJANGO_SECURE_CONTENT_TYPE_NOSNIFF', True
 )
 SECURE_BROWSER_XSS_FILTER = True
 SESSION_COOKIE_SECURE = True
 SESSION_COOKIE_HTTPONLY = True
-SECURE_SSL_REDIRECT = env.bool('DJANGO_SECURE_SSL_REDIRECT', default=True)
+SECURE_SSL_REDIRECT = env.bool('DJANGO_SECURE_SSL_REDIRECT', True)
 SECURE_REDIRECT_EXEMPT = env.list(
     'DJANGO_SECURE_REDIRECT_EXEMPT',
     default=['/taskflow/', r'^irodsbackend/api/auth$'],
@@ -44,7 +44,7 @@
 CSRF_COOKIE_SECURE = True
 CSRF_COOKIE_HTTPONLY = True
 CSRF_TRUSTED_ORIGINS = env.list('DJANGO_CSRF_TRUSTED_ORIGINS', default=[])
-CSRF_COOKIE_DOMAIN = env.str('DJANGO_CSRF_COOKIE_DOMAIN', default=None)
+CSRF_COOKIE_DOMAIN = env.str('DJANGO_CSRF_COOKIE_DOMAIN', None)
 
 X_FRAME_OPTIONS = 'DENY'
 
diff --git a/docs_manual/source/api_documentation.rst b/docs_manual/source/api_documentation.rst
index b3dbf395..0c421193 100644
--- a/docs_manual/source/api_documentation.rst
+++ b/docs_manual/source/api_documentation.rst
@@ -45,7 +45,7 @@ expected version.
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.2
 
 Specific sections of the SODAR API may require their own accept header. See the
 exact header requirement in the respective documentation on each section of the
diff --git a/docs_manual/source/api_examples.rst b/docs_manual/source/api_examples.rst
index 9b8ce3bf..205e0052 100644
--- a/docs_manual/source/api_examples.rst
+++ b/docs_manual/source/api_examples.rst
@@ -41,9 +41,9 @@ the SODAR API:
     # Token authorization header (required)
     auth_header = {'Authorization': 'token {}'.format(api_token)}
     # Use core_headers for project management API endpoints
-    core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.3'}
+    core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.4'}
     # Use sodar_headers for sample sheet and landing zone API endpoints
-    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.14.1'}
+    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.14.2'}
 
 .. note::
 
diff --git a/docs_manual/source/api_irodsinfo.rst b/docs_manual/source/api_irodsinfo.rst
index a2e936fb..3234e4d3 100644
--- a/docs_manual/source/api_irodsinfo.rst
+++ b/docs_manual/source/api_irodsinfo.rst
@@ -22,4 +22,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.1
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.2
diff --git a/docs_manual/source/api_landingzones.rst b/docs_manual/source/api_landingzones.rst
index a28ba97a..024e27f4 100644
--- a/docs_manual/source/api_landingzones.rst
+++ b/docs_manual/source/api_landingzones.rst
@@ -32,4 +32,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.1
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.2
diff --git a/docs_manual/source/api_samplesheets.rst b/docs_manual/source/api_samplesheets.rst
index c91fca3b..401166c6 100644
--- a/docs_manual/source/api_samplesheets.rst
+++ b/docs_manual/source/api_samplesheets.rst
@@ -68,4 +68,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.14.1
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.2
diff --git a/docs_manual/source/conf.py b/docs_manual/source/conf.py
index 8360d084..a604f6d4 100644
--- a/docs_manual/source/conf.py
+++ b/docs_manual/source/conf.py
@@ -22,11 +22,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'SODAR'
-copyright = '2018-2023, BIH Core Unit Bioinformatics'
+copyright = '2018-2024, BIH Core Unit Bioinformatics'
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.14.2-WIP'
+release = '0.14.2'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs_manual/source/dev_guide.rst b/docs_manual/source/dev_guide.rst
index 067c9526..c106065a 100644
--- a/docs_manual/source/dev_guide.rst
+++ b/docs_manual/source/dev_guide.rst
@@ -16,12 +16,14 @@ for development and is always the latest "bleeding edge" version of SODAR. The
 
 When naming your work branches, prefix them with the issue ID, preferably
 followed by a verb depicting the action: "add", "update", "fix", "remove",
-"refactor", "upgrade", "deprecate" or something else if none of these ar
-applicable.
+"refactor", "upgrade", "deprecate" or something else if none of these are
+applicable. If a relevant issue does not exist yet, please create one in the
+repository's issue tracker. This will make changes and pull requests much easier
+to track.
 
 The rest of the branch name should *concisely* represent the change. It is not
 necessary (and often not recommended) to include the entire name of the issue
-as they may be verbose.
+as they may be overly verbose.
 
 If a branch and pull request tackles multiple issues at once, including the ID
 of the most major issue is enough.
@@ -49,7 +51,7 @@ Pull Requests
 Please add the related issue ID(s) to the title of your pull request and ensure
 the pull request is set against the ``dev`` branch.
 
-It is strongly recommended to use descriptive commit messages even in work
+It is strongly recommended to use descriptive commit messages even for work
 commits that are to be squashed in merging. This will aid the review process.
 
 Before submitting a pull request for review, ensure the following:
diff --git a/docs_manual/source/sodar_release_notes.rst b/docs_manual/source/sodar_release_notes.rst
index a9f1b039..d8b3d215 100644
--- a/docs_manual/source/sodar_release_notes.rst
+++ b/docs_manual/source/sodar_release_notes.rst
@@ -8,8 +8,8 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
-v0.14.2 (WIP)
-=============
+v0.14.2 (2024-03-15)
+====================
 
 Release for minor updates, maintenance and bug fixes.
 
diff --git a/landingzones/tests/test_ui.py b/landingzones/tests/test_ui.py
index 56c6a038..637cf1be 100644
--- a/landingzones/tests/test_ui.py
+++ b/landingzones/tests/test_ui.py
@@ -20,6 +20,7 @@
     ZONE_STATUS_CREATING,
     ZONE_STATUS_ACTIVE,
     ZONE_STATUS_VALIDATING,
+    ZONE_STATUS_DELETED,
 )
 from landingzones.tests.test_models import LandingZoneMixin
 
@@ -325,6 +326,75 @@ def test_status_update(self):
         self._wait_for_status(zone_status, ZONE_STATUS_VALIDATING)
         self.assertEqual(zone_status.text, ZONE_STATUS_VALIDATING)
 
+    def test_stats_deleted_owner(self):
+        """Test ProjectZoneView stats badge on DELETED zone as owner"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        zone = self.make_landing_zone(
+            'contrib_zone',
+            self.project,
+            self.user_contributor,
+            self.assay,
+            status=ZONE_STATUS_ACTIVE,
+        )
+        self.login_and_redirect(self.user_contributor, self.url)
+
+        zone_status = self.selenium.find_element(
+            By.CLASS_NAME, 'sodar-lz-zone-status'
+        )
+        zone_status_info = self.selenium.find_element(
+            By.CLASS_NAME, 'sodar-lz-zone-status-info'
+        )
+        self._wait_for_status(zone_status, ZONE_STATUS_ACTIVE)
+        self.assertTrue(
+            zone_status_info.find_element(
+                By.CLASS_NAME, 'sodar-irods-stats'
+            ).is_displayed()
+        )
+        # Update status to deleted, stats badge should no longer be rendered
+        zone.set_status(ZONE_STATUS_DELETED)
+        self._wait_for_status(zone_status, ZONE_STATUS_DELETED)
+        self.assertFalse(
+            zone_status_info.find_element(
+                By.CLASS_NAME, 'sodar-irods-stats'
+            ).is_displayed()
+        )
+
+    def test_stats_deleted_superuser(self):
+        """Test ProjectZoneView stats badge on DELETED zone as superuser"""
+        self._setup_investigation()
+        self.investigation.irods_status = True
+        self.investigation.save()
+        zone = self.make_landing_zone(
+            'contrib_zone',
+            self.project,
+            self.user_contributor,
+            self.assay,
+            status=ZONE_STATUS_ACTIVE,
+        )
+        self.login_and_redirect(self.superuser, self.url)
+
+        zone_status = self.selenium.find_element(
+            By.CLASS_NAME, 'sodar-lz-zone-status'
+        )
+        zone_status_info = self.selenium.find_element(
+            By.CLASS_NAME, 'sodar-lz-zone-status-info'
+        )
+        self._wait_for_status(zone_status, ZONE_STATUS_ACTIVE)
+        self.assertTrue(
+            zone_status_info.find_element(
+                By.CLASS_NAME, 'sodar-irods-stats'
+            ).is_displayed()
+        )
+        zone.set_status(ZONE_STATUS_DELETED)
+        self._wait_for_status(zone_status, ZONE_STATUS_DELETED)
+        self.assertFalse(
+            zone_status_info.find_element(
+                By.CLASS_NAME, 'sodar-irods-stats'
+            ).is_displayed()
+        )
+
     def test_zone_buttons(self):
         """Test ProjectZoneView zone buttons"""
         self._setup_investigation()
diff --git a/landingzones/views.py b/landingzones/views.py
index 53356ed5..1308d69c 100644
--- a/landingzones/views.py
+++ b/landingzones/views.py
@@ -32,7 +32,6 @@
     STATUS_ALLOW_UPDATE,
     STATUS_FINISHED,
     STATUS_INFO_DELETE_NO_COLL,
-    ZONE_STATUS_OK,
     ZONE_STATUS_DELETED,
 )
 from landingzones.forms import LandingZoneForm
@@ -174,9 +173,7 @@ def submit_create(
             )
             tl_event.add_object(obj=zone, label='zone', name=zone.title)
             tl_event.add_object(
-                obj=zone.user,
-                label='user',
-                name=zone.user.username,
+                obj=zone.user, label='user', name=zone.user.username
             )
             tl_event.add_object(
                 obj=zone.assay, label='assay', name=zone.assay.get_name()
@@ -268,15 +265,11 @@ def update_zone(self, zone, request=None):
                 user=user,
                 event_name='zone_update',
                 description=description,
-                status_type=ZONE_STATUS_OK,
+                status_type='OK',
                 extra_data=tl_extra,
             )
             tl_event.add_object(obj=zone, label='zone', name=zone.title)
-            tl_event.add_object(
-                obj=user,
-                label='user',
-                name=user.username,
-            )
+            tl_event.add_object(obj=user, label='user', name=user.username)
             tl_event.add_object(
                 obj=zone.assay, label='assay', name=zone.assay.get_name()
             )
@@ -329,11 +322,7 @@ def submit_delete(self, zone):
         if zone_exists:  # Submit with taskflow
             flow_name = 'landing_zone_delete'
             flow_data = self.get_flow_data(
-                zone,
-                flow_name,
-                {
-                    'zone_uuid': str(zone.sodar_uuid),
-                },
+                zone, flow_name, {'zone_uuid': str(zone.sodar_uuid)}
             )
             taskflow.submit(
                 project=project,
diff --git a/landingzones/views_ajax.py b/landingzones/views_ajax.py
index 6e02698f..2979c115 100644
--- a/landingzones/views_ajax.py
+++ b/landingzones/views_ajax.py
@@ -24,21 +24,17 @@ def check_zone_permission(self, zone, user):
     def post(self, request, *args, **kwargs):
         zone_uuids = request.data.getlist('zone_uuids[]')
         project = self.get_project()
-
         # Filter landing zones based on UUIDs and project
         zones = LandingZone.objects.filter(
             sodar_uuid__in=zone_uuids, project=project
         )
-
         status_dict = {}
         for zone in zones:
             # Check permissions
             if not self.check_zone_permission(zone, self.request.user):
                 continue
-
             status_dict[str(zone.sodar_uuid)] = {
                 'status': zone.status,
                 'status_info': zone.status_info,
             }
-
         return Response(status_dict, status=200)
diff --git a/landingzones/views_api.py b/landingzones/views_api.py
index 57836422..3dda7365 100644
--- a/landingzones/views_api.py
+++ b/landingzones/views_api.py
@@ -280,7 +280,6 @@ def perform_update(self, serializer):
         if not self._validate_update_fields(serializer):
             # Should raise 400 Bad Request
             raise ValidationError('{}Invalid update fields'.format(ex_msg))
-
         # If all is OK, go forward with object update and taskflow submission
         super().perform_update(serializer)
         try:
diff --git a/requirements/base.txt b/requirements/base.txt
index ffa20142..a77640a9 100644
--- a/requirements/base.txt
+++ b/requirements/base.txt
@@ -6,7 +6,7 @@ wheel==0.40.0
 setuptools==67.6.0
 
 # Django
-django==3.2.24
+django==3.2.25
 
 # Configuration
 django-environ==0.10.0
diff --git a/samplesheets/templates/samplesheets/samplesheet_import_form.html b/samplesheets/templates/samplesheets/samplesheet_import_form.html
index 2b2bec86..de71ee98 100644
--- a/samplesheets/templates/samplesheets/samplesheet_import_form.html
+++ b/samplesheets/templates/samplesheets/samplesheet_import_form.html
@@ -91,17 +91,11 @@ <h3>
            href="{% url 'samplesheets:project_sheets' project=project.sodar_uuid %}">
           <i class="iconify" data-icon="mdi:arrow-left-circle"></i> Cancel
         </a>
-        {% if replace_sheets %}
-          <button type="submit" class="btn btn-primary sodar-btn-submit-once"
-                  id="sodar-ss-btn-import-submit">
-            <i class="iconify" data-icon="mdi:refresh"></i> Replace
-          </button>
-        {% else %}
-          <button type="submit" class="btn btn-primary sodar-btn-submit-once"
-                  id="sodar-ss-btn-import-submit">
-            <i class="iconify" data-icon="mdi:upload"></i> Import
-          </button>
-        {% endif %}
+        <button type="submit" class="btn btn-primary sodar-btn-submit-once"
+                id="sodar-ss-btn-import-submit">
+          <i class="iconify" data-icon="mdi:upload"></i>
+          {% if replace_sheets %}Replace{% else %}Import{% endif %}
+        </button>
       </div>
     </div>
   </form>
diff --git a/samplesheets/views.py b/samplesheets/views.py
index d2ae8daf..27272413 100644
--- a/samplesheets/views.py
+++ b/samplesheets/views.py
@@ -686,15 +686,10 @@ def create_colls(self, investigation, request=None, sync=False):
             'ticket_str': ticket_str,
         }
         taskflow.submit(
-            project=project,
-            flow_name='sheet_colls_create',
-            flow_data=flow_data,
+            project=project, flow_name='sheet_colls_create', flow_data=flow_data
         )
         app_settings.set(
-            APP_NAME,
-            'public_access_ticket',
-            ticket_str,
-            project=project,
+            APP_NAME, 'public_access_ticket', ticket_str, project=project
         )
         if tl_event:
             tl_event.set_status('OK')
@@ -1472,12 +1467,8 @@ def get_context_data(self, *args, **kwargs):
     def get_form_kwargs(self):
         """Pass kwargs to form"""
         kwargs = super().get_form_kwargs()
-        kwargs.update(
-            {
-                'project': self.get_project(),
-                'sheet_tpl': self._get_sheet_template(),
-            }
-        )
+        kwargs['project'] = self.get_project()
+        kwargs['sheet_tpl'] = self._get_sheet_template()
         return kwargs
 
     def form_valid(self, form):
@@ -1744,9 +1735,7 @@ def post(self, request, *args, **kwargs):
                 tl_event.set_status('SUBMIT')
             try:
                 taskflow.submit(
-                    project=project,
-                    flow_name='sheet_delete',
-                    flow_data={},
+                    project=project, flow_name='sheet_delete', flow_data={}
                 )
             except taskflow.FlowSubmitException as ex:
                 delete_success = False
@@ -2184,17 +2173,14 @@ def post(self, request, **kwargs):
                     status_type='OK',
                 )
                 tl_event.add_object(
-                    obj=sv,
-                    label='isatab',
-                    name=sv.get_full_name(),
+                    obj=sv, label='isatab', name=sv.get_full_name()
                 )
 
         context['sheet_versions'].delete()
         messages.success(
             request,
             'Deleted {} sample sheet version{}.'.format(
-                version_count,
-                's' if version_count != 1 else '',
+                version_count, 's' if version_count != 1 else ''
             ),
         )
         return redirect(
@@ -2840,10 +2826,7 @@ def post(self, request, *args, **kwargs):
         try:
             batch = self.get_irods_request_objects()
             if not batch:
-                messages.error(
-                    self.request,
-                    NO_REQUEST_MSG,
-                )
+                messages.error(self.request, NO_REQUEST_MSG)
                 return redirect(
                     reverse(
                         'samplesheets:irods_requests',
diff --git a/samplesheets/views_ajax.py b/samplesheets/views_ajax.py
index 17ce0ad3..cab0f0a7 100644
--- a/samplesheets/views_ajax.py
+++ b/samplesheets/views_ajax.py
@@ -544,9 +544,7 @@ def _get_display_config(self, investigation, user, sheet_config=None):
                 'using default..'.format(user.username)
             )
             display_config = app_settings.get(
-                APP_NAME,
-                'display_config_default',
-                project=project,
+                APP_NAME, 'display_config_default', project=project
             )
 
         # If default display configuration is not found, build it
diff --git a/samplesheets/views_api.py b/samplesheets/views_api.py
index 5506515a..7b50f8ef 100644
--- a/samplesheets/views_api.py
+++ b/samplesheets/views_api.py
@@ -185,14 +185,12 @@ def get(self, request, *args, **kwargs):
         ).first()
         if not investigation:
             raise NotFound()
-
         export_format = 'json'
         if self.request.get_full_path() == reverse(
             'samplesheets:api_export_zip',
             kwargs={'project': project.sodar_uuid},
         ):
             export_format = 'zip'
-
         try:
             return self.get_isa_export(project, request, export_format)
         except Exception as ex:
diff --git a/samplesheets/vueapp/package-lock.json b/samplesheets/vueapp/package-lock.json
index ac9dc64f..2d26489c 100644
--- a/samplesheets/vueapp/package-lock.json
+++ b/samplesheets/vueapp/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "samplesheets",
-  "version": "0.14.2-WIP",
+  "version": "0.14.2",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "samplesheets",
-      "version": "0.14.2-WIP",
+      "version": "0.14.2",
       "dependencies": {
         "bootstrap-vue": "^2.22.0",
         "core-js": "^3.23.5",
diff --git a/samplesheets/vueapp/package.json b/samplesheets/vueapp/package.json
index ec7403bc..c3f264f6 100644
--- a/samplesheets/vueapp/package.json
+++ b/samplesheets/vueapp/package.json
@@ -1,6 +1,6 @@
 {
   "name": "samplesheets",
-  "version": "0.14.2-WIP",
+  "version": "0.14.2",
   "private": true,
   "scripts": {
     "serve": "vue-cli-service serve",
diff --git a/samplesheets/vueapp/src/App.vue b/samplesheets/vueapp/src/App.vue
index 50d271a7..497698d5 100644
--- a/samplesheets/vueapp/src/App.vue
+++ b/samplesheets/vueapp/src/App.vue
@@ -1062,8 +1062,7 @@ export default {
                 groupId = cols[startIdx].originalParent.groupId
                 // Update newRow for source cells
                 for (let i = 1; i < startIdx; i++) {
-                  const value = rowNode.data[cols[i].colId]
-                  value.newRow = false
+                  rowNode.data[cols[i].colId].newRow = false
                 }
               }
 
diff --git a/taskflowbackend/flows/landing_zone_delete.py b/taskflowbackend/flows/landing_zone_delete.py
index 39fa04ed..373e9ea6 100644
--- a/taskflowbackend/flows/landing_zone_delete.py
+++ b/taskflowbackend/flows/landing_zone_delete.py
@@ -54,7 +54,7 @@ def build(self, force_fail=False):
                 inject={'path': zone_path},
             )
         )
-        # Set zone status to DELETING
+        # Set zone status to DELETED
         self.add_task(
             lz_tasks.SetLandingZoneStatusTask(
                 name='Set landing zone status to DELETED',
diff --git a/taskflowbackend/flows/landing_zone_move.py b/taskflowbackend/flows/landing_zone_move.py
index 95aa5ee5..9e40d771 100644
--- a/taskflowbackend/flows/landing_zone_move.py
+++ b/taskflowbackend/flows/landing_zone_move.py
@@ -16,7 +16,7 @@
 
 
 SAMPLE_COLL = settings.IRODS_SAMPLE_COLL
-ZONE_INFO_CALC = 'Finding and calculating missing checksums in iRODS'
+ZONE_INFO_CALC = 'Calculating missing checksums in iRODS'
 ZONE_INFO_VALIDATE = 'Validating {count} file{plural}'
 ZONE_INFO_READ_ONLY = ', write access disabled'
 
diff --git a/taskflowbackend/tests/test_flows.py b/taskflowbackend/tests/test_flows.py
index 130f3a84..d455ec73 100644
--- a/taskflowbackend/tests/test_flows.py
+++ b/taskflowbackend/tests/test_flows.py
@@ -670,8 +670,7 @@ def test_move(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), False)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            False,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), False
         )
 
         flow_data = {'zone_uuid': str(self.zone.sodar_uuid)}
@@ -694,18 +693,13 @@ def test_move(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), True)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            True,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), True
         )
         self.assert_irods_access(
-            self.group_name,
-            sample_obj_path,
-            self.irods_access_read,
+            self.group_name, sample_obj_path, self.irods_access_read
         )
         self.assert_irods_access(
-            self.group_name,
-            sample_obj_path + '.md5',
-            self.irods_access_read,
+            self.group_name, sample_obj_path + '.md5', self.irods_access_read
         )
 
     def test_move_no_checksum(self):
@@ -728,8 +722,7 @@ def test_move_no_checksum(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), False)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            False,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), False
         )
         self.assertIsNone(obj.replicas[0].checksum)
 
@@ -748,8 +741,7 @@ def test_move_no_checksum(self):
         self.assertEqual(self.irods.collections.exists(self.zone_path), False)
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), True)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            True,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), True
         )
         obj = self.irods.data_objects.get(sample_obj_path)  # Reload object
         self.assertIsNotNone(obj.replicas[0].checksum)
@@ -821,8 +813,7 @@ def test_move_coll_exists(self):
         sample_obj_path = os.path.join(self.sample_path, COLL_NAME, OBJ_NAME)
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), True)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            True,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), True
         )
 
     def test_move_obj_exists(self):
@@ -958,8 +949,7 @@ def test_revert(self):
         sample_obj_path = os.path.join(self.sample_path, COLL_NAME, OBJ_NAME)
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), False)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            False,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), False
         )
         self.assert_irods_access(
             self.user.username, zone_coll, IRODS_ACCESS_OWN
@@ -1006,8 +996,7 @@ def test_move_restrict(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), False)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            False,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), False
         )
 
         flow_data = {'zone_uuid': str(new_zone.sodar_uuid)}
@@ -1031,18 +1020,13 @@ def test_move_restrict(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), True)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            True,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), True
         )
         self.assert_irods_access(
-            self.group_name,
-            sample_obj_path,
-            self.irods_access_read,
+            self.group_name, sample_obj_path, self.irods_access_read
         )
         self.assert_irods_access(
-            self.group_name,
-            sample_obj_path + '.md5',
-            self.irods_access_read,
+            self.group_name, sample_obj_path + '.md5', self.irods_access_read
         )
 
 
@@ -1117,8 +1101,7 @@ def test_move_alt_root_path(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), False)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            False,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), False
         )
 
         flow_data = {'zone_uuid': str(self.zone.sodar_uuid)}
@@ -1140,18 +1123,13 @@ def test_move_alt_root_path(self):
         )
         self.assertEqual(self.irods.data_objects.exists(sample_obj_path), True)
         self.assertEqual(
-            self.irods.data_objects.exists(sample_obj_path + '.md5'),
-            True,
+            self.irods.data_objects.exists(sample_obj_path + '.md5'), True
         )
         self.assert_irods_access(
-            self.group_name,
-            sample_obj_path,
-            self.irods_access_read,
+            self.group_name, sample_obj_path, self.irods_access_read
         )
         self.assert_irods_access(
-            self.group_name,
-            sample_obj_path + '.md5',
-            self.irods_access_read,
+            self.group_name, sample_obj_path + '.md5', self.irods_access_read
         )
 
 
@@ -1200,12 +1178,10 @@ def test_create(self):
             self.irods_backend.get_path(project)
         )
         self.assertEqual(
-            project_coll.metadata.get_one('title').value,
-            project.title,
+            project_coll.metadata.get_one('title').value, project.title
         )
         self.assertEqual(
-            project_coll.metadata.get_one('description').value,
-            META_EMPTY_VALUE,
+            project_coll.metadata.get_one('description').value, META_EMPTY_VALUE
         )
         self.assertEqual(
             project_coll.metadata.get_one('parent_uuid').value,
@@ -1234,12 +1210,10 @@ def test_update_metadata(self):
         self.assertNotEqual(self.project.description, UPDATED_DESC)
         project_coll = self.irods.collections.get(self.project_path)
         self.assertEqual(
-            project_coll.metadata.get_one('title').value,
-            self.project.title,
+            project_coll.metadata.get_one('title').value, self.project.title
         )
         self.assertEqual(
-            project_coll.metadata.get_one('description').value,
-            META_EMPTY_VALUE,
+            project_coll.metadata.get_one('description').value, META_EMPTY_VALUE
         )
 
         self.project.title = UPDATED_TITLE
@@ -1256,12 +1230,10 @@ def test_update_metadata(self):
 
         project_coll = self.irods.collections.get(self.project_path)
         self.assertEqual(
-            project_coll.metadata.get_one('title').value,
-            UPDATED_TITLE,
+            project_coll.metadata.get_one('title').value, UPDATED_TITLE
         )
         self.assertEqual(
-            project_coll.metadata.get_one('description').value,
-            UPDATED_DESC,
+            project_coll.metadata.get_one('description').value, UPDATED_DESC
         )
 
     def test_update_parent(self):
@@ -1339,7 +1311,10 @@ def test_enable_access(self):
         )
         self.assert_irods_access(PUBLIC_GROUP, self.sample_path, None)
 
-        flow_data = {'path': self.sample_path, 'access': True}
+        flow_data = {
+            'path': self.sample_path,
+            'access': True,
+        }
         flow = self.taskflow.get_flow(
             irods_backend=self.irods_backend,
             project=self.project,
@@ -1370,7 +1345,10 @@ def test_disable_access(self):
             PUBLIC_GROUP, self.sample_path, self.irods_access_read
         )
 
-        flow_data = {'path': self.sample_path, 'access': False}
+        flow_data = {
+            'path': self.sample_path,
+            'access': False,
+        }
         flow = self.taskflow.get_flow(
             irods_backend=self.irods_backend,
             project=self.project,
@@ -1393,7 +1371,10 @@ def test_revert(self):
         )
         self.assert_irods_access(PUBLIC_GROUP, self.sample_path, None)
 
-        flow_data = {'path': self.sample_path, 'access': True}
+        flow_data = {
+            'path': self.sample_path,
+            'access': True,
+        }
         flow = self.taskflow.get_flow(
             irods_backend=self.irods_backend,
             project=self.project,
@@ -1834,12 +1815,11 @@ def test_delete(self):
                 project=self.project, active=True
             ).first()
         )
-        flow_data = {}
         flow = self.taskflow.get_flow(
             irods_backend=self.irods_backend,
             project=self.project,
             flow_name='sheet_delete',
-            flow_data=flow_data,
+            flow_data={},
         )
         self.assertEqual(type(flow), SheetDeleteFlow)
         self._build_and_run(flow)
@@ -1859,12 +1839,11 @@ def test_delete_colls(self):
         self.make_irods_colls(self.investigation)
         self.assertEqual(self.irods.collections.exists(self.sample_path), True)
 
-        flow_data = {}
         flow = self.taskflow.get_flow(
             irods_backend=self.irods_backend,
             project=self.project,
             flow_name='sheet_delete',
-            flow_data=flow_data,
+            flow_data={},
         )
         self.assertEqual(type(flow), SheetDeleteFlow)
         self._build_and_run(flow)
@@ -1898,12 +1877,11 @@ def test_delete_zone(self):
         zone_path = self.irods_backend.get_path(zone)
         self.assertEqual(self.irods.collections.exists(zone_path), True)
 
-        flow_data = {}
         flow = self.taskflow.get_flow(
             irods_backend=self.irods_backend,
             project=self.project,
             flow_name='sheet_delete',
-            flow_data=flow_data,
+            flow_data={},
         )
         self.assertEqual(type(flow), SheetDeleteFlow)
         self._build_and_run(flow)