update IrodsDataRequest handling (#1706), refactor tests

CHANGELOG.rst

@@ -14,8 +14,12 @@ Added
 - **Irodsbackend**
     - ``get_trash_path()`` helper (#1658)
     - iRODS trash statistics for siteinfo (#1658)
+- **Irodsinfo**
+    - ``IrodsEnvRetrieveAPIView`` for retrieving iRODS environment (#1685)
 - **Landingzones**
     - Landing zone updating (#1267)
+    - "Nothing to do" check for landing zone validation and moving (#339)
+    - iRODS path clipboard copying button in iRODS collection list modal (#1282)
 - **Samplesheets**
     - User setting for study and assay table height (#1283)
     - Study table cache disabling (#1639)
@@ -27,6 +31,9 @@ Added
     - Enable ``tumor_normal_dna`` ISA-Tab template (#1697)
     - General iRODS access ticket management for assay collections (#804, #1717)
     - Disabled row delete button tooltips (#1731)
+    - ``IrodsDataRequest`` REST API views (#1588, #1706, #1734, #1735, #1736)
+    - Davrods links in iRODS delete request list (#1339)
+    - Batch accepting and rejecting for iRODS delete requests (#1340)
 - **Taskflowbackend**
     - ``BatchCalculateChecksumTask`` iRODS task (#1634)
     - Automated generation of missing checksums in ``zone_move`` flow (#1634)
@@ -41,10 +48,14 @@ Changed
     - Upgrade to python-irodsclient v1.1.8 (#1538)
 - **Landingzones**
     - Move iRODS object helpers to ``TaskflowTestMixin`` (#1699)
+    - Enable superuser landing zone controls for locked zones (#1607)
+    - Add ``DELETING`` to locked states in UI (#1657)
+    - Query for landing zone status in batch (#1684)
 - **Samplesheets**
     - Sample sheet table viewport background color (#1692)
     - Contract sheet table height to fit content (#1693)
     - Hide additional internal fields from ISA-Tab templates (#1698)
+    - Refactor ``IrodsDataRequest`` model and tests (#1706)
 - **Taskflowbackend**
     - Move iRODS object helpers from ``LandingZoneTaskflowMixin`` (#1699)
     - Move iRODS test cleanup to ``TaskflowTestMixin.clear_irods_test_data()`` (#1722)
@@ -57,13 +68,17 @@ Fixed
     - Batch import tests failing from forbidden obolibrary access (#1694)
 - **Samplesheets**
     - ``perform_project_sync()`` crash with no iRODS collections created (#1687)
+    - iRODS delete request modification UI view permission checks failing for non-creator contributors (#1737)
 
 Removed
 -------
 
+- **Landingzones**
+    - Unused ``data_tables`` references from templates (#1710)
 - **Samplesheets**
     - ``SHEETS_TABLE_HEIGHT`` Django setting (#1283)
     - Duplicate ``IrodsAccessTicketMixin`` from ``test_views_ajax`` (#1703)
+    - ``IRODS_DATA_REQUEST_STATUS_CHOICES`` constant (#1706)
 
 
 v0.13.4 (2023-05-15)

docs_manual/source/api_samplesheets.rst

@@ -15,17 +15,19 @@ API Views
 
 .. autoclass:: IrodsCollsCreateAPIView
 
+.. autoclass:: IrodsDataRequestRetrieveAPIView
+
 .. autoclass:: IrodsDataRequestListAPIView
 
-.. autoclass:: IrodsRequestCreateAPIView
+.. autoclass:: IrodsDataRequestCreateAPIView
 
-.. autoclass:: IrodsRequestUpdateAPIView
+.. autoclass:: IrodsDataRequestUpdateAPIView
 
-.. autoclass:: IrodsRequestDeleteAPIView
+.. autoclass:: IrodsDataRequestDeleteAPIView
 
-.. autoclass:: IrodsRequestAcceptAPIView
+.. autoclass:: IrodsDataRequestAcceptAPIView
 
-.. autoclass:: IrodsRequestRejectAPIView
+.. autoclass:: IrodsDataRequestRejectAPIView
 
 .. autoclass:: SheetImportAPIView
 

samplesheets/forms.py

@@ -26,6 +26,8 @@
     ISATab,
     IrodsAccessTicket,
     IrodsDataRequest,
+    IRODS_REQUEST_STATUS_ACTIVE,
+    IRODS_REQUEST_STATUS_FAILED,
 )
 
 
@@ -35,6 +37,9 @@
 TPL_DIR_FIELD = '__output_dir'
 
 
+# Mixins and Helpers -----------------------------------------------------------
+
+
 class MultipleFileInput(forms.ClearableFileInput):
     allow_multiple_selected = True
 
@@ -53,6 +58,72 @@ def clean(self, data, initial=None):
         return result
 
 
+class IrodsDataRequestValidateMixin:
+    """Validation helpers for iRODS data requests"""
+
+    def validate_request_path(self, irods_backend, project, instance, path):
+        """
+        Validate path for IrodsAccessRequest.
+
+        :param irods_backend: IrodsAPI object
+        :param project: Project object
+        :param instance: Existing instance in case of update or None
+        :param path: Full iRODS path to a collection or a data object (string)
+        :raises: ValueError if path is incorrect
+        """
+        old_request = IrodsDataRequest.objects.filter(
+            path=path,
+            status__in=[
+                IRODS_REQUEST_STATUS_ACTIVE,
+                IRODS_REQUEST_STATUS_FAILED,
+            ],
+        ).first()
+        if old_request and old_request != instance:
+            raise ValueError(ERROR_MSG_EXISTING)
+
+        path_re = re.compile(
+            '^' + irods_backend.get_projects_path() + '/[0-9a-f]{2}/'
+            '(?P<project_uuid>[0-9a-f-]{36})/'
+            + settings.IRODS_SAMPLE_COLL
+            + '/study_(?P<study_uuid>[0-9a-f-]{36})/'
+            'assay_(?P<assay_uuid>[0-9a-f-]{36})/.+$'
+        )
+        match = re.search(path_re, path)
+        if not match:
+            raise ValueError(ERROR_MSG_INVALID_PATH)
+
+        project_path = irods_backend.get_path(project)
+        if not path.startswith(project_path):
+            raise ValueError('Path does not belong in project')
+
+        try:
+            Study.objects.get(
+                sodar_uuid=match.group('study_uuid'),
+                investigation__project__sodar_uuid=match.group('project_uuid'),
+            )
+        except Study.DoesNotExist:
+            raise ValueError('Study not found in project with UUID')
+        try:
+            Assay.objects.get(
+                sodar_uuid=match.group('assay_uuid'),
+                study__sodar_uuid=match.group('study_uuid'),
+            )
+        except Assay.DoesNotExist:
+            raise ValueError('Assay not found in this project with UUID')
+
+        with irods_backend.get_session() as irods:
+            if path and not (
+                irods.data_objects.exists(path)
+                or irods.collections.exists(path)
+            ):
+                raise ValueError(
+                    'Path to collection or data object doesn\'t exist in iRODS',
+                )
+
+
+# Forms ------------------------------------------------------------------------
+
+
 class SheetImportForm(forms.Form):
     """
     Form for importing an ISA investigation from an ISA-Tab archive or
@@ -154,7 +225,7 @@ def save(self, *args, **kwargs):
 
 
 class SheetTemplateCreateForm(forms.Form):
-    """Form for creating sample sheets from an ISA-Tab template."""
+    """Form for creating sample sheets from an ISA-Tab template"""
 
     @classmethod
     def _get_tsv_data(cls, path, file_names):
@@ -378,84 +449,34 @@ def clean(self):
         return self.cleaned_data
 
 
-class IrodsRequestForm(forms.ModelForm):
-    """Form for the iRODS delete request creation and editing"""
+class IrodsDataRequestForm(IrodsDataRequestValidateMixin, forms.ModelForm):
+    """Form for iRODS data request creation and editing"""
 
     class Meta:
         model = IrodsDataRequest
         fields = ['path', 'description']
 
-    def __init__(self, *args, **kwargs):
+    def __init__(self, project=None, *args, **kwargs):
         super().__init__(*args, **kwargs)
+        if project:
+            self.project = Project.objects.filter(sodar_uuid=project).first()
         self.fields['description'].required = False
 
     def clean(self):
         cleaned_data = super().clean()
         irods_backend = get_backend_api('omics_irods')
-        # Remove trailing slashes as irodspython client does not recognize
-        # this as a collection
-        cleaned_data['path'] = cleaned_data['path'].rstrip('/')
-
-        old_request = IrodsDataRequest.objects.filter(
-            path=cleaned_data['path'], status__in=['ACTIVE', 'FAILED']
-        ).first()
-        if old_request and old_request != self.instance:
-            self.add_error('path', ERROR_MSG_EXISTING)
-            return cleaned_data
-
-        path_re = re.compile(
-            '^' + irods_backend.get_projects_path() + '/[0-9a-f]{2}/'
-            '(?P<project_uuid>[0-9a-f-]{36})/'
-            + settings.IRODS_SAMPLE_COLL
-            + '/study_(?P<study_uuid>[0-9a-f-]{36})/'
-            'assay_(?P<assay_uuid>[0-9a-f-]{36})/.+$'
-        )
-        match = re.search(
-            path_re,
-            cleaned_data['path'],
-        )
-        if not match:
-            self.add_error('path', ERROR_MSG_INVALID_PATH)
-        else:
-            try:
-                cleaned_data['project'] = Project.objects.get(
-                    sodar_uuid=match.group('project_uuid')
-                )
-            except Project.DoesNotExist:
-                self.add_error('path', 'Project not found')
-            try:
-                Study.objects.get(
-                    sodar_uuid=match.group('study_uuid'),
-                    investigation__project__sodar_uuid=match.group(
-                        'project_uuid'
-                    ),
-                )
-            except Study.DoesNotExist:
-                self.add_error('path', 'Study not found in project with UUID')
-            try:
-                Assay.objects.get(
-                    sodar_uuid=match.group('assay_uuid'),
-                    study__sodar_uuid=match.group('study_uuid'),
-                )
-            except Assay.DoesNotExist:
-                self.add_error(
-                    'path', 'Assay not found in this project with UUID'
-                )
-
-        with irods_backend.get_session() as irods:
-            if 'path' in cleaned_data and not (
-                irods.data_objects.exists(cleaned_data['path'])
-                or irods.collections.exists(cleaned_data['path'])
-            ):
-                self.add_error(
-                    'path',
-                    'Path to collection or data object doesn\'t exist in iRODS',
-                )
+        cleaned_data['path'] = irods_backend.sanitize_path(cleaned_data['path'])
+        try:
+            self.validate_request_path(
+                irods_backend, self.project, self.instance, cleaned_data['path']
+            )
+        except Exception as ex:
+            self.add_error('path', str(ex))
         return cleaned_data
 
 
-class IrodsRequestAcceptForm(forms.Form):
-    """Form accepting an iRODS delete request."""
+class IrodsDataRequestAcceptForm(forms.Form):
+    """Form for accepting an iRODS data request"""
 
     confirm = forms.BooleanField(required=True)
 
@@ -468,7 +489,7 @@ def __init__(self, *args, **kwargs):
 
 
 class SheetVersionEditForm(forms.ModelForm):
-    """Form for editing a saved ISA-Tab version of the sample sheets."""
+    """Form for editing a saved ISA-Tab version of sample sheets"""
 
     class Meta:
         model = ISATab

samplesheets/migrations/0021_update_irodsdatarequest.py

@@ -0,0 +1,40 @@
+# Generated by Django 3.2.19 on 2023-07-27 13:52
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('projectroles', '0028_populate_finder_role'),
+        ('samplesheets', '0020_update_irodsaccessticket'),
+    ]
+
+    operations = [
+        migrations.AlterModelManagers(
+            name='irodsaccessticket',
+            managers=[
+            ],
+        ),
+        migrations.AlterField(
+            model_name='irodsdatarequest',
+            name='action',
+            field=models.CharField(default='DELETE', help_text='Action to be performed', max_length=64),
+        ),
+        migrations.AlterField(
+            model_name='irodsdatarequest',
+            name='description',
+            field=models.CharField(blank=True, help_text='Request description (optional)', max_length=1024, null=True),
+        ),
+        migrations.AlterField(
+            model_name='irodsdatarequest',
+            name='project',
+            field=models.ForeignKey(help_text='Project to which the iRODS data request belongs', on_delete=django.db.models.deletion.CASCADE, related_name='irods_data_request', to='projectroles.project'),
+        ),
+        migrations.AlterField(
+            model_name='irodsdatarequest',
+            name='status',
+            field=models.CharField(default='ACTIVE', help_text='Status of the request', max_length=16),
+        ),
+    ]