Migrate existing submissions to sync templates

Submissions created between the original introduction of the top-level
templates array and now could be in an inconsistent state.

Author: naglepuff

nmdc_server/migrations/versions/ff4e651c3007_migrate_templates.py

@@ -0,0 +1,49 @@
+"""Migrate study templates
+
+Revision ID: ff4e651c3007
+Revises: 317274ad8137
+Create Date: 2024-09-18 17:21:05.171525
+
+"""
+
+from typing import Optional
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "ff4e651c3007"
+down_revision: Optional[str] = "317274ad8137"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    submission_metadata = table(
+        "submission_metadata",
+        column("id", sa.String),
+        column("metadata_submission", JSONB),
+        column("templates", JSONB),
+    )
+
+    connection = op.get_bind()
+    submissions = connection.execute(
+        sa.select([submission_metadata.c.id, submission_metadata.c.metadata_submission])
+    )
+
+    for submission in submissions:
+        templates = submission.metadata_submission.get("templates")
+        if templates:
+            connection.execute(
+                submission_metadata.update()
+                .where(submission_metadata.c.id == submission.id)
+                .values(templates=templates)
+            )
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###