feat: initial commit

docs_manual/source/api_samplesheets.rst

@@ -15,6 +15,16 @@ API Views
 
 .. autoclass:: IrodsCollsCreateAPIView
 
+.. autoclass:: IrodsAccessTicketListAPIView
+
+.. autoclass:: IrodsAccessTicketRetrieveAPIView
+
+.. autoclass:: IrodsAccessTicketCreateAPIView
+
+.. autoclass:: IrodsAccessTicketUpdateAPIView
+
+.. autoclass:: IrodsAccessTicketDeleteAPIView
+
 .. autoclass:: IrodsDataRequestRetrieveAPIView
 
 .. autoclass:: IrodsDataRequestListAPIView

samplesheets/serializers.py

@@ -1,5 +1,9 @@
 """API view model serializers for the samplesheets app"""
 
+import re
+
+from django.core.exceptions import ObjectDoesNotExist
+from django.utils import timezone
 from rest_framework import serializers
 
 # Projectroles dependency
@@ -11,7 +15,13 @@
 )
 
 from samplesheets.forms import IrodsDataRequestValidateMixin
-from samplesheets.models import Investigation, Study, Assay, IrodsDataRequest
+from samplesheets.models import (
+    Investigation,
+    Study,
+    Assay,
+    IrodsDataRequest,
+    IrodsAccessTicket,
+)
 
 
 class AssaySerializer(SODARNestedListSerializer):
@@ -130,3 +140,127 @@ def create(self, validated_data):
         validated_data['project'] = self.context['project']
         validated_data['user'] = self.context['request'].user
         return super().create(validated_data)
+
+
+class IrodsAccessTicketSerializer(serializers.ModelSerializer):
+    """Serializer for the IrodsAccessTicket model"""
+
+    is_active = serializers.SerializerMethodField()
+
+    class Meta:
+        model = IrodsAccessTicket
+        fields = [
+            'study',
+            'assay',
+            'ticket',
+            'path',
+            'user',
+            'date_created',
+            'date_expires',
+            'label',
+            'sodar_uuid',
+            'is_active',
+        ]
+
+    def get_is_active(self, obj):
+        if not obj.date_expires:
+            return True
+        return obj.date_expires > timezone.now()
+
+    def get_read_only_fields(self):
+        return [
+            'study',
+            'assay',
+            'ticket',
+            'path',
+            'user',
+            'date_created',
+            'is_active',
+            'sodar_uuid',
+        ]
+
+    def validate(self, attrs):
+        irods_backend = get_backend_api('omics_irods')
+        # Validate path (only if creating)
+        if not self.instance:
+            project = self.context['project']
+            try:
+                attrs['path'] = irods_backend.sanitize_path(attrs['path'])
+            except Exception as ex:
+                raise serializers.ValidationError(
+                    {'path': 'Invalid iRODS path: {}'.format(ex)}
+                )
+            # Ensure path is within project
+            if not attrs['path'].startswith(irods_backend.get_path(project)):
+                raise serializers.ValidationError(
+                    {'path': 'Path is not within the project'}
+                )
+            # Ensure path is a collection
+            with irods_backend.get_session() as irods:
+                if not irods.collections.exists(attrs['path']):
+                    raise serializers.ValidationError(
+                        {
+                            'path': 'Path does not point to a collection or the'
+                            ' collection doesn\'t exist'
+                        }
+                    )
+            # 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})',
+                attrs['path'],
+            )
+            if not match:
+                raise serializers.ValidationError(
+                    {'path': 'Not a valid assay path'}
+                )
+            else:
+                try:
+                    # Set assay if successful
+                    attrs['assay'] = Assay.objects.get(
+                        study__investigation__project=project,
+                        sodar_uuid=match.group(1),
+                    )
+                except ObjectDoesNotExist:
+                    raise serializers.ValidationError(
+                        {'path': 'Assay not found in project'}
+                    )
+            # Ensure path is not assay root
+            if attrs['path'] == irods_backend.get_path(attrs['assay']):
+                raise serializers.ValidationError(
+                    {
+                        'path': 'Ticket creation for assay root path is not allowed'
+                    }
+                )
+
+            # Add study from assay
+            attrs['study'] = attrs['assay'].study
+            # Add empty ticket
+            attrs['ticket'] = ''
+            # Add user from context
+            attrs['user'] = self.context['user']
+        else:  # Update
+            attrs['path'] = self.instance.path
+            attrs['assay'] = self.instance.assay
+            attrs['study'] = self.instance.study
+            attrs['ticket'] = self.instance.ticket
+            attrs['user'] = self.instance.user
+
+            # Check if expiry date is in the past
+        if (
+            attrs.get('date_expires')
+            and attrs.get('date_expires') <= timezone.now()
+        ):
+            raise serializers.ValidationError(
+                {'date_expires': 'Expiry date in the past not allowed'}
+            )
+
+            # Check if unexpired ticket already exists for path
+        if (
+            not self.instance
+            and IrodsAccessTicket.objects.filter(path=attrs['path']).first()
+        ):
+            raise serializers.ValidationError(
+                {'path': 'Ticket for path already exists'}
+            )
+
+        return attrs