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Fix migration bootstrap failures on fresh Postgress #995

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42 changes: 42 additions & 0 deletions migrations/versions/b5ac48010165_add_missing_document_metadata_column_to_.py
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Original file line number Diff line number Diff line change
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"""add missing document_metadata column to node and cre

Revision ID: b5ac48010165
Revises: c7d8e9f0a1b2
Create Date: 2026-07-24 22:19:01.724833

"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy import inspect


# revision identifiers, used by Alembic.
revision = 'b5ac48010165'
down_revision = 'c7d8e9f0a1b2'
branch_labels = None
depends_on = None


def upgrade():
# Defensive: some environments (e.g. production) already have this column
# applied out-of-band without a corresponding migration ever being
# committed, so this must not assume a clean "column doesn't exist" state.
inspector = inspect(op.get_bind())
node_columns = {c["name"] for c in inspector.get_columns("node")}
cre_columns = {c["name"] for c in inspector.get_columns("cre")}

if "document_metadata" not in node_columns:
with op.batch_alter_table("node", schema=None) as batch_op:
batch_op.add_column(sa.Column("document_metadata", sa.JSON(), nullable=True))

if "document_metadata" not in cre_columns:
with op.batch_alter_table("cre", schema=None) as batch_op:
batch_op.add_column(sa.Column("document_metadata", sa.JSON(), nullable=True))
Comment on lines +24 to +34

@coderabbitai coderabbitai Bot Jul 25, 2026

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🗄️ Data Integrity & Integration | 🟠 Major | 🏗️ Heavy lift

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo "== repo files matching migration/scripts/db =="
git ls-files | rg '(^migrations/versions/b5ac48010165_add_missing_document_metadata_column_to_|(^scripts/benchmark_import_parity\.py$|^application/database/db\.py$))' || true

echo
echo "== migration file =="
sed -n '1,140p' migrations/versions/b5ac48010165_add_missing_document_metadata_column_to_.py

echo
echo "== scripts/benchmark_import_parity.py relevant =="
sed -n '1,180p' scripts/benchmark_import_parity.py

echo
echo "== application/database/db.py relevant =="
sed -n '1,180p' application/database/db.py

echo
echo "== search metadata_json/document_metadata references =="
rg -n '"?metadata_json"?\b|"?document_metadata"?\b' scripts application migrations -S || true

Repository: OWASP/OpenCRE

Length of output: 17258

🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo "== search older migrations for document_metadata/metadata_json creation == =="
rg -n 'document_metadata|metadata_json|add_column.*metadata|create_table.*metadata' migrations scripts -S || true

echo
echo "== inspect alembic version/creates/migrations references =="
sed -n '1,140p' scripts/prod-docker-entrypoint.sh || true

echo
echo "== deterministic migration behavior probe =="
python3 - <<'PY'
def upgrade_columns_after_migration(existing_node, existing_cre):
    node_columns = set(existing_node)
    cre_columns = set(existing_cre)

    if "document_metadata" not in node_columns:
        node_columns = node_columns | {"document_metadata"}
    if "document_metadata" not in cre_columns:
        cre_columns = cre_columns | {"document_metadata"}

    return {"node": sorted(node_columns), "cre": sorted(cre_columns)}

cases = [
    (["metadata_json"], []),
    (["metadata_json"], ["metadata_json"]),
    (["document_metadata", "metadata_json"], ["document_metadata", "metadata_json"]),
]
for node, cre in cases:
    result = upgrade_columns_after_migration(node, cre)
    print({"existing_node": node, "existing_cre": cre}, "=>", result)
PY

echo
echo "== behavioral probe: data accessible from ORM-backed column if only legacy column is present? =="
python3 - <<'PY'
legacy_schema = {"document_metadata": None}
ORM_reads_column = legacy_schema.get("metadata_json")
print({"migration_result_schema": legacy_schema, "orm_attribute_value_from_document_metadata": ORM_reads_column})
PY

Repository: OWASP/OpenCRE

Length of output: 3951

Preserve legacy metadata_json values before setting document_metadata.

The ORM for Node and CRE reads metadata_json mapped to the SQL column document_metadata, and benchmark parity also supports schemas that have metadata_json instead. This migration only adds an empty document_metadata column when metadata_json exists, so existing metadata becomes inaccessible. Rename/copy metadata_json to document_metadata for both tables, and handle the case where both columns already exist.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@migrations/versions/b5ac48010165_add_missing_document_metadata_column_to_.py`
around lines 24 - 34, Update the migration’s Node and CRE column handling to
preserve existing metadata_json values: when only metadata_json exists, rename
it to document_metadata (or copy its values before removing it), and when both
columns exist, transfer metadata_json values into document_metadata without
overwriting valid document_metadata data. Keep the migration safe when
document_metadata already exists and apply the same logic to both tables.



def downgrade():
with op.batch_alter_table("cre", schema=None) as batch_op:
batch_op.drop_column("document_metadata")

with op.batch_alter_table("node", schema=None) as batch_op:
batch_op.drop_column("document_metadata")
Comment on lines +37 to +42

@coderabbitai coderabbitai Bot Jul 25, 2026

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🗄️ Data Integrity & Integration | 🔴 Critical | 🏗️ Heavy lift

Do not unconditionally drop columns this migration may not own.

Because upgrade() skips columns that already existed out-of-band, downgrade() cannot distinguish migration-created columns from pre-existing production columns. Rolling back can therefore delete existing metadata and break the ORM contract. Persist column ownership during upgrade and drop only columns created by this migration; otherwise make the downgrade intentionally non-destructive.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@migrations/versions/b5ac48010165_add_missing_document_metadata_column_to_.py`
around lines 37 - 42, Make the migration’s downgrade non-destructive for
pre-existing columns: update upgrade() to persist whether each document_metadata
column was created by this migration, then have downgrade() consult that
ownership state and drop only migration-created columns. If ownership cannot be
persisted reliably, remove the unconditional drop behavior from downgrade()
rather than risking deletion of existing columns.

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