issue SACGF/variantgrid_private#2926

classification/management/commands/classification_set_legacy_allele_origin.py

@@ -0,0 +1,67 @@
+from django.core.management import BaseCommand
+from django.db.models import Q
+
+from classification.enums import SubmissionSource
+from classification.models import Classification, SpecialEKeys
+from library.guardian_utils import admin_bot
+from library.utils import Value
+
+
+class Command(BaseCommand):
+    @staticmethod
+    def _update_allele_origin(user, qs, old_value, allele_origin_value, allele_origin_confirmation_value):
+        note = f"Auto set from '{old_value}' (legacy)"
+
+        patch = {
+            SpecialEKeys.ALLELE_ORIGIN: {"value": allele_origin_value, "note": note},
+            'allele_origin_confirmation': {"value": allele_origin_confirmation_value, "note": note},
+        }
+
+        classification_ids = []
+        for classification in qs:
+            classification_ids.append(classification.pk)
+
+            # keep track of if there are outstanding changes before we patch the value
+            # as we don't want to publish changes a user hasn't published yet
+            has_outstanding_changes = classification.has_outstanding_changes()
+            classification.patch_value(
+                patch=patch,
+                user=user,
+                source=SubmissionSource.FORM, # set this to form so as to not make it immutable
+                # leave_existing_values=True, # safety just in case you set this on a record that already has allele origin
+                save=True
+            )
+            if not has_outstanding_changes:
+                # by not providing share level, it will default to publishing at the existing share level
+                classification.publish_latest(user=user)
+
+        if classification_ids:
+            print(f"Updated allele_origin from {old_value} => {allele_origin_value}")
+            print(", ".join(classification_ids))
+
+
+    def handle(self, *args, **options):
+        raise ValueError("Don't run this - haven't confirmed it's the right thing to do yet. "
+                         "See https://github.com/SACGF/variantgrid_private/issues/2926")
+
+        user = admin_bot()
+        # Only alter ones that are from this system (not external)
+        qs_internal = Classification.objects.filter(lab__external=False)
+
+        Q_OLD_VALUE_NEW_VALUE = [
+            (Q(evidence__allele_origin__isnull=True), "blank", "germline"),
+            (Q(evidence__allele_origin__value="likely_germline"), "likely_germline", "germline"),
+            # It was decided to handle these manually - https://github.com/SACGF/variantgrid_private/issues/2926
+            #(Q(evidence__allele_origin__value="unknown"), "unknown", "germline"),
+            #(Q(evidence__allele_origin__value="other"), "other", "germline"),
+            #(Q(evidence__allele_origin__value="tested_inconclusive"), "tested_inconclusive", "germline"),
+            (Q(evidence__allele_origin__value="likely_somatic"), "likely_somatic", "somatic"),
+        ]
+
+        for q, old_value, allele_origin_value in Q_OLD_VALUE_NEW_VALUE:
+            qs = qs_internal.filter(q)
+            self._update_allele_origin(user, qs,
+                                       old_value=old_value,
+                                       allele_origin_value=allele_origin_value,
+                                       allele_origin_confirmation_value="unconfirmed")
+