alembic

backend/alembic/versions/397feb4e1315_update_json_keys_caseinfo.py

@@ -0,0 +1,95 @@
+"""Update JSON keys in caseinfo table
+
+Revision ID: 397feb4e1315
+Revises: 850ccab0221d
+Create Date: 2024-02-14 12:42:36.371531+01:00
+
+"""
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "397feb4e1315"
+down_revision = "850ccab0221d"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # Convert diseases and hpo_terms columns to jsonb if they aren't already
+    op.execute("ALTER TABLE caseinfo ALTER COLUMN diseases TYPE jsonb USING diseases::jsonb")
+    op.execute("ALTER TABLE caseinfo ALTER COLUMN hpo_terms TYPE jsonb USING hpo_terms::jsonb")
+
+    # Update the diseases jsonb structure
+    op.execute(
+        """
+        UPDATE caseinfo
+        SET diseases = (
+            SELECT jsonb_agg(
+                jsonb_build_object(
+                    'omimId', value->'omim_id',
+                    'name', value->'name'
+                )
+            )
+            FROM jsonb_array_elements(diseases)
+        )
+        WHERE diseases IS NOT NULL
+    """
+    )
+
+    # Update the hpo_terms jsonb structure
+    op.execute(
+        """
+        UPDATE caseinfo
+        SET hpo_terms = (
+            SELECT jsonb_agg(
+                jsonb_build_object(
+                    'termId', value->'term_id',
+                    'name', value->'name'
+                )
+            )
+            FROM jsonb_array_elements(hpo_terms)
+        )
+        WHERE hpo_terms IS NOT NULL
+    """
+    )
+
+
+def downgrade():
+    # Note: The downgrade logic here assumes the only keys were 'omimId', 'termId', and 'name'.
+    # If there were other keys or if the original structure was different, adjust accordingly.
+
+    # Revert the diseases jsonb structure update
+    op.execute(
+        """
+        UPDATE caseinfo
+        SET diseases = (
+            SELECT jsonb_agg(
+                jsonb_build_object(
+                    'omim_id', value->'omimId',
+                    'name', value->'name'
+                )
+            )
+            FROM jsonb_array_elements(diseases)
+        )
+        WHERE diseases IS NOT NULL
+    """
+    )
+
+    # Revert the hpo_terms jsonb structure update
+    op.execute(
+        """
+        UPDATE caseinfo
+        SET hpo_terms = (
+            SELECT jsonb_agg(
+                jsonb_build_object(
+                    'term_id', value->'termId',
+                    'name', value->'name'
+                )
+            )
+            FROM jsonb_array_elements(hpo_terms)
+        )
+        WHERE hpo_terms IS NOT NULL
+    """
+    )