Database migration troubleshooting

This guide is linked from the system info page when WeKnora's startup database migration fails. It covers the most common causes, how to diagnose them, and how to recover without losing data.

If none of these match your situation, jump to Reporting an issue at the bottom.

What "migration failed" means

WeKnora auto-runs golang-migrate migrations on every startup. When a migration fails, the application still finishes starting up (so the UI remains reachable to help you diagnose the problem), but:

• The failing migration is rolled back, leaving the database at the previous version. Any tables / indexes introduced by that migration are not created.
• Downstream features depending on those tables (Wiki ingest, knowledge graph, task queues, …) may silently produce nothing.
• The system info page shows the partial DB version + a red "Migration failed" tag and the captured error.

The cached error message you see in the UI is the same one logged at startup under Database migration failed: .... Recent container logs are the authoritative source — copy them before doing anything destructive.

Common causes

1. Missing PostgreSQL extension

Many migrations require extensions (pg_trgm, vector, pg_search) created by CREATE EXTENSION IF NOT EXISTS. IF NOT EXISTS does not validate that the extension is actually installed — it only checks the catalog. If the extension's shared library is missing or the role lacks CREATE privilege, the statement may succeed in the migration that nominally creates it but a later migration that uses the extension (e.g. building a gin_trgm_ops index) will fail.

Symptoms in the error:

ERROR: operator class "gin_trgm_ops" does not exist for access method "gin"
ERROR: type "vector" does not exist
ERROR: function ... does not exist

Fix:

-- Connect as a superuser (typically `postgres`):
\c your_weknora_database
CREATE EXTENSION IF NOT EXISTS pg_trgm;
CREATE EXTENSION IF NOT EXISTS vector;       -- if RETRIEVE_DRIVER includes pgvector
CREATE EXTENSION IF NOT EXISTS pg_search;    -- only on ParadeDB

-- Verify they are actually loaded:
SELECT extname, extversion FROM pg_extension WHERE extname IN ('pg_trgm','vector','pg_search');

Then restart WeKnora. The next startup will pick up where the failing migration left off.

If CREATE EXTENSION itself errors with "could not open extension control file" or "permission denied", the extension is not installed on your PostgreSQL server — install the corresponding OS package (e.g. postgresql-contrib for pg_trgm) or switch to an image that ships it preinstalled, then retry.

2. Dirty migration state

If a migration crashed partway through (OOM, container kill, network blip) golang-migrate marks the schema as "dirty" at the failing version. By default, WeKnora's startup tries to auto-recover; if you disabled that with AUTO_RECOVER_DIRTY=false you'll see:

database is in dirty state at version N. ...

Fix — use the bundled helpers:

# Check the recorded version
make migrate-version

# Force the version to the last successful migration (N - 1 in the message)
make migrate-force version=<N-1>

# Re-run pending migrations
make migrate-up

After that, restart WeKnora.

Or set AUTO_RECOVER_DIRTY=true (the default in recent versions) and just restart — startup will perform the same force + retry automatically.

3. Insufficient privileges on the database role

Some migrations create extensions or alter shared catalogs, which require either superuser or CREATEROLE / CREATEDB. Errors look like:

ERROR: permission denied to create extension "pg_trgm"
ERROR: must be owner of database ...

Fix: grant the role used by DB_USER the necessary privileges, or pre-create the extensions / objects as a superuser ahead of time, then restart. The migration's CREATE EXTENSION IF NOT EXISTS will then no-op.

4. Out-of-disk during CREATE INDEX

GIN / pgvector indexes can require significant temporary space. Errors:

ERROR: could not extend file ...: No space left on device
ERROR: cannot create temporary tables in transaction

Fix: free disk on the volume backing PGDATA, then restart. The migration will retry the index build.

5. Schema drift from manual edits

If you previously edited tables / columns by hand and a later migration expects the original shape, it will fail with mismatched-type errors. The safest recovery is to align the live schema with the previous successful migration's *.up.sql and then re-run pending migrations.

Generic diagnostic checklist

1. Read the full error: the cached message in the UI is truncated only by your browser scroll — it is the complete golang-migrate error. The container log shows the same content with stack context.
2. Identify the failing migration: the version number in the error (or make migrate-version) points to a file under migrations/versioned/. Open migrations/versioned/<version>_*.up.sql and look for the statement matching the error type (extension, index, function, foreign key, …).
3. Run the failing statement manually against the DB using psql. The error will be far more specific than the migration wrapper's.
4. Fix the underlying cause (install extension, fix privileges, free disk, …), then either:
   • Restart WeKnora and let auto-recovery retry; or
   • Run make migrate-up from a checkout to apply migrations outside the server process.
5. Verify: the system info page should now show the DB version without the "Migration failed" tag, and the previously broken feature (Wiki, KG, …) should start producing output.

Reporting an issue

If you've worked through the checklist and the migration still fails, please open an issue at:

https://github.com/Tencent/WeKnora/issues/new?template=bug_report.yml

Include:

• WeKnora version + commit ID (from the system info page).
• The full error from the system info page (or container logs).
• PostgreSQL version (SELECT version();) and how it was deployed (vanilla, ParadeDB, Aurora, Aliyun RDS, …).
• The output of:
  sqlCopy

  SELECT extname, extversion FROM pg_extension;
  

• Any non-default values of RETRIEVE_DRIVER, AUTO_MIGRATE, and AUTO_RECOVER_DIRTY.

The "Report issue" link on the system info page pre-fills a body with the captured error for you — clicking it is the fastest path.