Merge pull request #839 from ImageMarkup/fix-licenses

isic/ingest/migrations/0049_alter_accession_blob_size_alter_accession_height_and_more.py

@@ -0,0 +1,93 @@
+# Generated by Django 4.1.13 on 2024-02-13 16:56
+
+from django.db import migrations, models
+import django.db.models.deletion
+from django.db.models.expressions import OuterRef, Subquery
+
+
+def set_copyright_license(apps, schema_editor):
+    Accession = apps.get_model("ingest", "Accession")
+
+    Accession.objects.filter(copyright_license="").update(
+        copyright_license=Subquery(
+            Accession.objects.filter(id=OuterRef("id"))
+            .annotate(default_copyright_license=models.F("cohort__default_copyright_license"))
+            .values("default_copyright_license")[:1]
+        )
+    )
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("ingest", "0048_metadatafile_validation_completed_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="accession",
+            name="blob_size",
+            field=models.PositiveBigIntegerField(
+                blank=True, default=None, editable=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="height",
+            field=models.PositiveIntegerField(blank=True, null=True),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="lesion",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="accessions",
+                to="ingest.lesion",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="metadata",
+            field=models.JSONField(blank=True, default=dict),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="patient",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="accessions",
+                to="ingest.patient",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="thumbnail_256_size",
+            field=models.PositiveIntegerField(blank=True, default=None, editable=False, null=True),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="unstructured_metadata",
+            field=models.JSONField(blank=True, default=dict),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="width",
+            field=models.PositiveIntegerField(blank=True, null=True),
+        ),
+        migrations.AlterField(
+            model_name="accession",
+            name="zip_upload",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="accessions",
+                to="ingest.zipupload",
+            ),
+        ),
+        migrations.RunPython(set_copyright_license),
+    ]

isic/ingest/models/accession.py

@@ -155,7 +155,7 @@ class Meta(CreationSortedTimeStampedModel.Meta):
         blank=True, max_length=24, help_text="The image_id from Girder.", db_index=True
     )
     zip_upload = models.ForeignKey(
-        ZipUpload, on_delete=models.CASCADE, null=True, related_name="accessions"
+        ZipUpload, on_delete=models.CASCADE, null=True, blank=True, related_name="accessions"
     )
     cohort = models.ForeignKey(Cohort, on_delete=models.CASCADE, related_name="accessions")
 
@@ -174,25 +174,27 @@ class Meta(CreationSortedTimeStampedModel.Meta):
     # WHERE blob_name IN (...) queries
     blob_name = models.CharField(max_length=255, db_index=True, editable=False, blank=True)
     # blob_size/width/height are nullable unless status is succeeded
-    blob_size = models.PositiveBigIntegerField(null=True, default=None, editable=False)
-    width = models.PositiveIntegerField(null=True)
-    height = models.PositiveIntegerField(null=True)
+    blob_size = models.PositiveBigIntegerField(null=True, blank=True, default=None, editable=False)
+    width = models.PositiveIntegerField(null=True, blank=True)
+    height = models.PositiveIntegerField(null=True, blank=True)
 
     status = models.CharField(
         choices=AccessionStatus.choices, max_length=20, default=AccessionStatus.CREATING
     )
 
     thumbnail_256 = S3FileField(blank=True)
-    thumbnail_256_size = models.PositiveIntegerField(null=True, default=None, editable=False)
+    thumbnail_256_size = models.PositiveIntegerField(
+        null=True, blank=True, default=None, editable=False
+    )
 
-    metadata = models.JSONField(default=dict)
-    unstructured_metadata = models.JSONField(default=dict)
+    metadata = models.JSONField(default=dict, blank=True)
+    unstructured_metadata = models.JSONField(default=dict, blank=True)
 
     lesion = models.ForeignKey(
-        Lesion, on_delete=models.SET_NULL, null=True, related_name="accessions"
+        Lesion, on_delete=models.SET_NULL, null=True, blank=True, related_name="accessions"
     )
     patient = models.ForeignKey(
-        Patient, on_delete=models.SET_NULL, null=True, related_name="accessions"
+        Patient, on_delete=models.SET_NULL, null=True, blank=True, related_name="accessions"
     )
 
     objects = AccessionQuerySet.as_manager()

isic/ingest/models/zip_upload.py

@@ -101,6 +101,8 @@ def extract(self):
                         accession = Accession.from_blob(zip_item)
                         accession.creator = self.creator
                         accession.cohort = self.cohort
+                        accession.copyright_license = accession.cohort.default_copyright_license
+                        accession.full_clean(validate_constraints=False)
                         self.accessions.add(accession, bulk=False)
 
                 self.accessions.update(status=AccessionStatus.CREATED)

isic/ingest/services/accession/__init__.py

@@ -8,6 +8,7 @@
 from isic.ingest.tasks import accession_generate_blob_task
 
 
+# Note: this method isn't used when creating accessions as part of a zip extraction.
 def accession_create(
     *,
     creator: User,
@@ -26,14 +27,16 @@ def accession_create(
     if isinstance(original_blob, S3PlaceholderFile):
         original_blob = original_blob.name
 
-    accession = Accession.objects.create(
+    accession = Accession(
         creator=creator,
         cohort=cohort,
         copyright_license=cohort.default_copyright_license,
         original_blob=original_blob,
         original_blob_name=original_blob_name,
         original_blob_size=original_blob_size,
     )
+    accession.full_clean(validate_constraints=False)
+    accession.save()
 
     accession_generate_blob_task.delay(accession.pk)
 

isic/ingest/tests/test_accession.py

@@ -43,6 +43,8 @@ def test_accession_without_zip_upload(user, jpg_blob, cohort):
     accession = Accession.from_blob(jpg_blob)
     accession.creator = user
     accession.cohort = cohort
+    accession.copyright_license = cohort.default_copyright_license
+    accession.full_clean(validate_constraints=False)
     accession.save()
 
 
@@ -99,6 +101,7 @@ def test_accession_upload_invalid_cohort(
 def test_accession_mutable_before_publish(user, accession_factory):
     accession = accession_factory(image=None)
     accession.update_metadata(user, {"foo": "bar"})
+    accession.full_clean(validate_constraints=False)
     accession.save()