add general irods access ticket support (#804), refactor tests

CHANGELOG.rst

@@ -22,6 +22,7 @@ Added
     - Enable ``stem_cell_core_bulk`` ISA-Tab template (#1697)
     - Enable ``stem_cell_core_sc`` ISA-Tab template (#1697)
     - Enable ``tumor_normal_dna`` ISA-Tab template (#1697)
+    - General iRODS access ticket management for assay collections (#804)
 - **Taskflowbackend**
     - ``BatchCalculateChecksumTask`` iRODS task (#1634)
     - Automated generation of missing checksums in ``zone_move`` flow (#1634)
@@ -54,6 +55,7 @@ Removed
 
 - **Samplesheets**
     - ``SHEETS_TABLE_HEIGHT`` Django setting (#1283)
+    - Duplicate ``IrodsAccessTicketMixin`` from ``test_views_ajax`` (#1703)
 
 
 v0.13.4 (2023-05-15)

docs_manual/source/sodar_release_notes.rst

@@ -13,6 +13,7 @@ v0.14.0 (WIP)
 
 Major feature update.
 
+- Add general read-only iRODS access tickets for assay collections
 - Add support for additional sample sheet templates
 - Add landing zone updating
 - Add automated checksum calculation in landing zone validation and moving

samplesheets/forms.py

@@ -279,48 +279,24 @@ def save(self):
 
 
 class IrodsAccessTicketForm(forms.ModelForm):
-    """Form for the irods access ticket creation and editing."""
+    """Form for the irods access ticket creation and editing"""
 
     class Meta:
         model = IrodsAccessTicket
         fields = ('path', 'label', 'date_expires')
 
-    def __init__(self, *args, **kwargs):
+    def __init__(self, project=None, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        from samplesheets.views import TRACK_HUBS_COLL
-
-        # Add selection to path field
-        irods_backend = get_backend_api('omics_irods')
-        assays = Assay.objects.filter(
-            study__investigation__project=kwargs['initial']['project']
-        )
-        if irods_backend:
-            with irods_backend.get_session() as irods:
-                choices = [
-                    (
-                        track_hub.path,
-                        "{} / {}".format(
-                            assay.get_display_name(), track_hub.name
-                        ),
-                    )
-                    for assay in assays
-                    for track_hub in irods_backend.get_child_colls(
-                        irods,
-                        os.path.join(
-                            irods_backend.get_path(assay), TRACK_HUBS_COLL
-                        ),
-                    )
-                ]
+        if self.instance.pk:
+            self.project = self.instance.get_project()
         else:
-            choices = []
-
-        # Hide path in update or make it a dropdown with available track hubs
-        # on creation
+            self.project = project
+        # Update path help and hide in update
+        path_help = 'Full path to iRODS collection within an assay'
+        self.fields['path'].help_text = path_help
         if self.instance.path:
             self.fields['path'].widget = forms.widgets.HiddenInput()
-        else:
-            self.fields['path'].widget = forms.widgets.Select(choices=choices)
-
+            self.fields['path'].required = False
         # Add date input widget to expiry date field
         self.fields['date_expires'].label = 'Expiry date'
         self.fields['date_expires'].widget = forms.widgets.DateInput(
@@ -329,6 +305,51 @@ def __init__(self, *args, **kwargs):
 
     def clean(self):
         irods_backend = get_backend_api('omics_irods')
+        # Validate path (only if creating)
+        if not self.instance.pk:
+            try:
+                self.cleaned_data['path'] = irods_backend.sanitize_path(
+                    self.cleaned_data['path']
+                )
+            except Exception as ex:
+                self.add_error('path', 'Invalid iRODS path: {}'.format(ex))
+                return self.cleaned_data
+            # Ensure path is within project
+            if not self.cleaned_data['path'].startswith(
+                irods_backend.get_path(self.project)
+            ):
+                self.add_error('path', 'Path is not within the project')
+                return self.cleaned_data
+            # Ensure path is within a project assay
+            match = re.search(
+                r'/assay_([0-9a-f]{8}-([0-9a-f]{4}-){3}[0-9a-f]{12})',
+                self.cleaned_data['path'],
+            )
+            if not match:
+                self.add_error('path', 'Not a valid assay path')
+                return self.cleaned_data
+            else:
+                try:
+                    # Set assay if successful
+                    self.cleaned_data['assay'] = Assay.objects.get(
+                        study__investigation__project=self.project,
+                        sodar_uuid=match.group(1),
+                    )
+                except ObjectDoesNotExist:
+                    self.add_error('path', 'Assay not found in project')
+                    return self.cleaned_data
+            # Ensure path is a collection
+            with irods_backend.get_session() as irods:
+                if not irods.collections.exists(self.cleaned_data['path']):
+                    self.add_error(
+                        'path',
+                        'Path does not point to a collection or the collection '
+                        'doesn\'t exist',
+                    )
+                    return self.cleaned_data
+        else:  # Do not allow editing path
+            self.cleaned_data['path'] = self.instance.path
+
         # Check if expiry date is in the past
         if (
             self.cleaned_data.get('date_expires')
@@ -337,28 +358,15 @@ def clean(self):
             self.add_error(
                 'date_expires', 'Expiry date in the past not allowed'
             )
-        # Check path validity
-        try:
-            self.cleaned_data['path'] = irods_backend.sanitize_path(
-                self.cleaned_data['path']
-            )
-        except Exception as ex:
-            self.add_error('path', 'Invalid iRODS path: {}'.format(ex))
-            return self.cleaned_data
-        # Check if path corresponds to a track hub path
-        match = re.search(
-            r'/assay_([0-9a-f]{8}-([0-9a-f]{4}-){3}[0-9a-f]{12})/',
-            self.cleaned_data['path'],
-        )
-        if not match:
-            self.add_error('path', 'Not a valid TrackHubs path')
-        else:
-            try:
-                self.cleaned_data['assay'] = Assay.objects.get(
-                    sodar_uuid=match.group(1)
-                )
-            except ObjectDoesNotExist:
-                self.add_error('path', 'Assay not found')
+
+        # Check if unexpired ticket already exists for path
+        if (
+            not self.instance.pk
+            and IrodsAccessTicket.objects.filter(
+                path=self.cleaned_data['path']
+            ).first()
+        ):
+            self.add_error('path', 'Ticket for path already exists')
         return self.cleaned_data
 
 

samplesheets/migrations/0020_update_irodsaccessticket.py

@@ -0,0 +1,47 @@
+# Generated by Django 3.2.19 on 2023-06-13 10:29
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+import django.db.models.manager
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('samplesheets', '0019_alter_isatab_date_created'),
+    ]
+
+    operations = [
+        migrations.AlterModelManagers(
+            name='irodsaccessticket',
+            managers=[
+                ('active_objects', django.db.models.manager.Manager()),
+            ],
+        ),
+        migrations.RemoveField(
+            model_name='irodsaccessticket',
+            name='project',
+        ),
+        migrations.AlterField(
+            model_name='irodsaccessticket',
+            name='assay',
+            field=models.ForeignKey(blank=True, help_text='Assay in which the ticket belongs (optional)', null=True, on_delete=django.db.models.deletion.CASCADE, related_name='irods_access_tickets', to='samplesheets.assay'),
+        ),
+        migrations.AlterField(
+            model_name='irodsaccessticket',
+            name='date_expires',
+            field=models.DateTimeField(blank=True, help_text='DateTime of ticket expiration (leave unset to never expire)', null=True),
+        ),
+        migrations.AlterField(
+            model_name='irodsaccessticket',
+            name='study',
+            field=models.ForeignKey(help_text='Study in which the ticket belongs', on_delete=django.db.models.deletion.CASCADE, related_name='irods_access_tickets', to='samplesheets.study'),
+        ),
+        migrations.AlterField(
+            model_name='irodsaccessticket',
+            name='user',
+            field=models.ForeignKey(help_text='User that created the ticket', null=True, on_delete=django.db.models.deletion.CASCADE, related_name='irods_access_tickets', to=settings.AUTH_USER_MODEL),
+        ),
+    ]

samplesheets/models.py

@@ -1116,44 +1116,23 @@ def get_queryset(self):
 
 
 class IrodsAccessTicket(models.Model):
-    """
-    Model for managing tickets in irods
-    """
-
-    class Meta:
-        ordering = ['-date_created']
-
-    objects = models.Manager()
-    active_objects = IrodsAccessTicketActiveManager()
-
-    #: Internal UUID for the object
-    sodar_uuid = models.UUIDField(
-        default=uuid.uuid4, unique=True, help_text='SODAR UUID for the object'
-    )
-
-    #: Project the ticket belongs to
-    project = models.ForeignKey(
-        Project,
-        related_name='irods_access_ticket',
-        help_text='Project the ticket belongs to',
-        on_delete=models.CASCADE,
-    )
+    """Model for managing access tickets in iRODS"""
 
     #: Study the ticket belongs to
     study = models.ForeignKey(
         Study,
-        related_name='irods_access_ticket',
-        help_text='Study the ticket belongs to',
+        related_name='irods_access_tickets',
+        help_text='Study in which the ticket belongs',
         on_delete=models.CASCADE,
     )
 
     #: Assay the ticket belongs to (optional)
     assay = models.ForeignKey(
         Assay,
-        related_name='irods_access_ticket',
+        related_name='irods_access_tickets',
         null=True,
         blank=True,
-        help_text='Assay the ticket belongs to (optional)',
+        help_text='Assay in which the ticket belongs (optional)',
         on_delete=models.CASCADE,
     )
 
@@ -1178,7 +1157,7 @@ class Meta:
     #: User that created the ticket
     user = models.ForeignKey(
         AUTH_USER_MODEL,
-        related_name='irods_access_ticket',
+        related_name='irods_access_tickets',
         null=True,
         help_text='User that created the ticket',
         on_delete=models.CASCADE,
@@ -1193,11 +1172,50 @@ class Meta:
     date_expires = models.DateTimeField(
         null=True,
         blank=True,
-        help_text='DateTime of ticket expiration (leave unset to never '
-        'expire; click x on righthand-side of field to unset)',
+        help_text='DateTime of ticket expiration (leave unset to never expire)',
+    )
+
+    #: SODAR UUID for the object
+    sodar_uuid = models.UUIDField(
+        default=uuid.uuid4, unique=True, help_text='SODAR UUID for the object'
     )
 
-    def get_track_hub_name(self):
+    #: Standard manager
+    objects = models.Manager()
+
+    #: Active objects manager
+    active_objects = IrodsAccessTicketActiveManager()
+
+    class Meta:
+        ordering = ['-date_created']
+
+    def __str__(self):
+        return '{} / {} / {} / {}'.format(
+            self.study.investigation.project.title,
+            self.assay.get_display_name(),
+            self.get_coll_name(),
+            self.get_label(),
+        )
+
+    def __repr__(self):
+        values = (
+            self.study.investigation.project.title,
+            self.assay.get_display_name(),
+            self.get_coll_name(),
+            self.get_label(),
+        )
+        return 'IrodsAccessTicket({})'.format(
+            ', '.join(repr(v) for v in values)
+        )
+
+    def get_project(self):
+        return self.study.investigation.project
+
+    @classmethod
+    def get_project_filter_key(cls):
+        return 'study__investigation__project'
+
+    def get_coll_name(self):
         return os.path.basename(self.path)
 
     def get_date_created(self):
@@ -1215,13 +1233,13 @@ def get_display_name(self):
         assay_name = ''
         if (
             Assay.objects.filter(
-                study__investigation__project=self.project
+                study__investigation__project=self.study.investigation.project
             ).count()
             > 1
         ):
             assay_name = '{} / '.format(self.assay.get_display_name())
         return '{}{} / {}'.format(
-            assay_name, self.get_track_hub_name(), self.get_label()
+            assay_name, self.get_coll_name(), self.get_label()
         )
 
     def get_webdav_link(self):
@@ -1234,25 +1252,6 @@ def get_webdav_link(self):
     def is_active(self):
         return self.date_expires is None or self.date_expires >= timezone.now()
 
-    def __str__(self):
-        return '{} / {} / {} / {}'.format(
-            self.project.title,
-            self.assay.get_display_name(),
-            self.get_track_hub_name(),
-            self.get_label(),
-        )
-
-    def __repr__(self):
-        values = (
-            self.project.title,
-            self.assay.get_display_name(),
-            self.get_track_hub_name(),
-            self.get_label(),
-        )
-        return 'IrodsAccessTicket({})'.format(
-            ', '.join(repr(v) for v in values)
-        )
-
 
 class IrodsDataRequest(models.Model):
     """