Flyway: non-empty schema without metadata table

Found non-empty schema "public" without metadata table! Use init() or set initOnMigrate to true to initialize the metadata table.

I'm using Postgres 9.2 with Postgis 2.0. This means that by default when I create a new database there will be a table created in public schema called spatial_ref_sys.

When I run flyway migrate on this database, I get the above error. Running init seems to create the public.schema_version table and mark version 1 as SUCCEDED without actually running the the migration file. I've also tried combinations of initOnMigrate with no success. Flyway is not configured to manage any schemas.

Any ideas on how I can run a migration in this scenario?

Solution

The title is somewhat contradictory, as the database is indeed not virgin as you installed, through the PostGIS extension, a number of objects in the public schema.

You can either

set flyway.schemas to a new schema, say my_app, which will then be created automatically by Flyway. Your application should then use this one instead of public (recommended)
set flyway.baselineOnMigrate to true or invoke flyway.baseline() against the public schema. This will work, but public will then contain a mix of both your application objects and the PostGIS objects