Propagate modify time from object to containers

Modifications propagate from:
* data -> entity -> collection
* annotation value -> entity
* relation -> collection

docs/CHANGELOG.rst

@@ -32,6 +32,9 @@ Changed
   authentication backend
 - Use ``keys`` instead of ``scan_iter`` in ``clear`` method of ``redis`` cache,
   since ``scan_iter`` is much slower
+- Modified time propagates from ``Data`` object to ``Entity`` to ``Collection``
+- Modified time propagates from ``AnnotationValue`` to ``Entity``
+- Modified time propagates from ``Relation`` to ``Collection``
 
 
 ===================

resolwe/flow/migrations/0019_alter_annotationpreset_modified_and_more.py

@@ -0,0 +1,53 @@
+# Generated by Django 4.2.7 on 2023-12-06 11:59
+
+from django.db import migrations
+import resolwe.flow.models.base
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("flow", "0018_add_annotationvalue_default_order"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="annotationpreset",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="collection",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="data",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="descriptorschema",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="entity",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="process",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="relation",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="storage",
+            name="modified",
+            field=resolwe.flow.models.base.ModifiedField(auto_now=True, db_index=True),
+        ),
+    ]

resolwe/flow/models/annotations.py

@@ -18,6 +18,7 @@
 
 from django.core.exceptions import ValidationError
 from django.db import models
+from django.utils.timezone import now
 
 from resolwe.flow.models.base import BaseModel
 from resolwe.permissions.models import Permission, PermissionObject
@@ -502,6 +503,8 @@ def save(self, *args, **kwargs):
         if "label" not in self._value:
             self.recompute_label()
         super().save(*args, **kwargs)
+        self.entity.modified = now()
+        self.entity.save(update_fields=["modified"])
 
     def recompute_label(self):
         """Recompute label from value and set it to the model instance."""

resolwe/flow/models/base.py

@@ -16,6 +16,24 @@
 MAX_NAME_LENGTH = 100
 
 
+class ModifiedField(models.DateTimeField):
+    """Custom datetime field.
+
+    When attribute 'skip_auto_now' is set to True, the field is not updated in the
+    pre_save method even if auto_now is set to True. The 'skip_auto_now' is reset
+    on every save to the default value 'False'.
+    """
+
+    def pre_save(self, model_instance, add):
+        """Prepare field for saving."""
+        # When skip_auto_now is set do not generate the new value even is auto_now is
+        # set to True.
+        if getattr(model_instance, "skip_auto_now", False) is True:
+            return getattr(model_instance, self.attname)
+        else:
+            return super().pre_save(model_instance, add)
+
+
 class UniqueSlugError(IntegrityError):
     """The error indicates slug collision."""
 
@@ -85,7 +103,7 @@ class Meta:
     created = models.DateTimeField(auto_now_add=True, db_index=True)
 
     #: modified date and time
-    modified = models.DateTimeField(auto_now=True, db_index=True)
+    modified = ModifiedField(auto_now=True, db_index=True)
 
     #: user that created the entry
     contributor = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.PROTECT)

resolwe/flow/models/data.py

@@ -570,6 +570,16 @@ def save(self, render_name=False, *args, **kwargs):
 
         with transaction.atomic():
             self._perform_save(*args, **kwargs)
+            if self.entity:
+                self.entity.skip_auto_now = True  # type: ignore
+                self.entity.modified = self.modified
+                self.entity.save(update_fields=["modified"])
+                self.entity.skip_auto_now = False  # type: ignore
+            elif self.collection:
+                self.collection.skip_auto_now = True  # type: ignore
+                self.collection.modified = self.modified
+                self.collection.save(update_fields=["modified"])
+                self.collection.skip_auto_now = False  # type: ignore
 
         self._original_output = self.output
 
@@ -621,7 +631,7 @@ def move_to_collection(self, collection):
         self.permission_group = collection.permission_group
         if collection:
             self.tags = collection.tags
-        self.save(update_fields=["tags", "permission_group", "collection"])
+        self.save(update_fields=["tags", "permission_group", "collection", "modified"])
 
     @move_to_container
     def move_to_entity(self, entity):
@@ -635,7 +645,7 @@ def move_to_entity(self, entity):
             else:
                 self.permission_group = entity.permission_group
                 self.tags = entity.tags
-        self.save(update_fields=["permission_group", "entity", "tags"])
+        self.save(update_fields=["permission_group", "entity", "tags", "modified"])
 
     def validate_change_collection(self, collection):
         """Raise validation error if data object cannot change collection."""

resolwe/flow/models/entity.py

@@ -377,6 +377,15 @@ def validate_annotations(self):
         if validation_errors:
             raise ValidationError(validation_errors)
 
+    def save(self, *args, **kwargs):
+        """Propagate the modified time to the collection."""
+        super().save(*args, **kwargs)
+        if self.collection:
+            self.collection.skip_auto_now = True  # type: ignore
+            self.collection.modified = self.modified
+            self.collection.save(update_fields=["modified"])
+            self.collection.skip_auto_now = False  # type: ignore
+
 
 class RelationType(models.Model):
     """Model for storing relation types."""
@@ -501,6 +510,11 @@ def save(self, *args, **kwargs):
                 "`descriptor_schema` must be defined if `descriptor` is given"
             )
         super().save()
+        if self.collection:
+            self.collection.skip_auto_now = True  # type: ignore
+            self.collection.modified = self.modified
+            self.collection.save(update_fields=["modified"])
+            self.collection.skip_auto_now = False  # type: ignore
 
 
 class RelationPartition(models.Model):

resolwe/flow/tests/test_annotations.py

@@ -1,4 +1,5 @@
 # pylint: disable=missing-docstring
+import time
 from typing import Any, Sequence
 
 from django.core.exceptions import ValidationError
@@ -164,6 +165,34 @@ def test_all_fields_included(self):
             self.assertIn(method_name, dir(self))
 
 
+class TestModifiedPropagated(TestCase):
+    def test_modified_propagated(self):
+        """Test modify propagates to entity."""
+        entity = Entity.objects.create(contributor=self.contributor)
+        annotation_group = AnnotationGroup.objects.create(
+            name="group", label="Annotation group", sort_order=1
+        )
+        field = AnnotationField.objects.create(
+            name="field name",
+            label="field label",
+            type=AnnotationType.STRING.value,
+            sort_order=1,
+            group=annotation_group,
+        )
+
+        old_modified = entity.modified
+        time.sleep(0.1)
+        value = AnnotationValue.objects.create(entity=entity, value="Test", field=field)
+        entity.refresh_from_db()
+        self.assertGreater(entity.modified, old_modified)
+        old_modified = entity.modified
+        time.sleep(0.1)
+        value.value = "New value"
+        value.save()
+        entity.refresh_from_db()
+        self.assertGreater(entity.modified, old_modified)
+
+
 class TestOrderEntityByAnnotations(TestCase):
     """Test ordering Entities by annotation values."""
 

resolwe/flow/tests/test_models.py

@@ -1,6 +1,7 @@
 # pylint: disable=missing-docstring,too-many-lines
 import os
 import shutil
+import time
 from datetime import timedelta
 from unittest.mock import MagicMock, PropertyMock, patch
 
@@ -310,6 +311,39 @@ def test_dependencies_list(self):
             {d.kind for d in third.parents_dependency.all()}, {DataDependency.KIND_IO}
         )
 
+    def test_modified_propagated(self):
+        """Test modified field is propagated to the entity and collection."""
+        process = Process.objects.create(contributor=self.contributor)
+        data = Data.objects.create(contributor=self.contributor, process=process)
+        collection = Collection.objects.create(contributor=self.contributor)
+        entity = Entity.objects.create(
+            contributor=self.contributor, collection=collection
+        )
+        old_modified = data.modified
+        old_collection_modified = collection.modified
+        data.move_to_collection(collection)
+        time.sleep(0.1)
+        data.refresh_from_db()
+        collection.refresh_from_db()
+        self.assertGreater(data.modified, old_modified)
+        self.assertGreater(data.modified, old_collection_modified)
+        self.assertEqual(collection.modified, data.modified)
+
+        data = Data.objects.create(contributor=self.contributor, process=process)
+        old_modified = data.modified
+        old_entity_modified = entity.modified
+        old_collection_modified = collection.modified
+        time.sleep(0.1)
+        data.move_to_entity(entity)
+        data.refresh_from_db()
+        collection.refresh_from_db()
+        entity.refresh_from_db()
+        self.assertGreater(data.modified, old_modified)
+        self.assertGreater(data.modified, old_collection_modified)
+        self.assertGreater(data.modified, old_entity_modified)
+        self.assertEqual(collection.modified, data.modified)
+        self.assertEqual(entity.modified, data.modified)
+
 
 class EntityModelTest(TestCase):
     def setUp(self):
@@ -330,6 +364,21 @@ def setUp(self):
             name="Test data", contributor=self.contributor, process=self.process
         )
 
+    def test_modified_propagated(self):
+        """Test modified field is propagated to the entity and collection."""
+        collection = Collection.objects.create(contributor=self.contributor)
+        entity = Entity.objects.create(
+            contributor=self.contributor, collection=collection
+        )
+        old_entity_modified = entity.modified
+        entity.name = "New name"
+        time.sleep(0.1)
+        entity.save()
+        entity.refresh_from_db()
+        collection.refresh_from_db()
+        self.assertGreater(entity.modified, old_entity_modified)
+        self.assertEqual(collection.modified, entity.modified)
+
     def test_delete_data(self):
         # Create another Data object and add it to the same Entity.
         data_2 = Data.objects.create(
@@ -1728,3 +1777,5 @@ def test_referenced_mix(self):
         refs.remove("jsonout.txt")
         refs.remove("stdout.txt")
         self.assertSetEqual(set(refs), {"file1", "file2"})
+        self.assertSetEqual(set(refs), {"file1", "file2"})
+        self.assertSetEqual(set(refs), {"file1", "file2"})

resolwe/flow/tests/test_relations.py

@@ -1,5 +1,6 @@
 # pylint: disable=missing-docstring
 import os
+import time
 
 from django.apps import apps
 from django.contrib.auth.models import AnonymousUser
@@ -122,6 +123,17 @@ def setUp(self):
         )
         self.collection.set_permission(Permission.VIEW, AnonymousUser())
 
+    def test_modified_propagated(self):
+        """Test modified date propagetes to collection."""
+        old_modified = self.collection.modified
+        time.sleep(0.1)
+        self.relation_group.contributor = self.user
+        self.relation_group.save()
+        self.collection.refresh_from_db()
+        self.relation_group.refresh_from_db()
+        self.assertGreater(self.collection.modified, old_modified)
+        self.assertEqual(self.relation_group.modified, self.collection.modified)
+
     def test_prefetch(self):
         self.relation_group.delete()
         self.relation_series.delete()