Integrate alembic and add hg38 DB schema as initial revision

[oltionchampari]

This PR depeneds on datavisyn/tdp_core#292

Closes #64

Summary

• Integrated alembic according to the instructions in https://wiki.datavisyn.io/tdp/extension-points/db-migration.
• Exported the hg_38 schema from the postgres 12 database and imported it in the upgrade function to be executed as the initial revision.
• Tested running db-migration:upgrade:head:tdp_publicdb both in a postgres 10-alpine container and and postgres 12.1 container. In both cases the schema gets imported and the tdp_publicdb_alembic_version table with the current revision ID gets created in the public schema.

The following script to create the tdp_publicdb_alembic_version table needs to be executed in the hg_38 postgres 12.1 database so the alembic upgrade command does not try to upgrade it.

CREATE TABLE public.tdp_publicdb_alembic_version
(
    version_num character varying(32) COLLATE pg_catalog."default" NOT NULL,
    CONSTRAINT tdp_publicdb_alembic_version_pkc PRIMARY KEY (version_num)
)
WITH (
    OIDS = FALSE
)
TABLESPACE pg_default;

ALTER TABLE public.tdp_publicdb_alembic_version
    OWNER to publicdb;

INSERT INTO public.tdp_publicdb_alembic_version(version_num)
	VALUES('b477004c3673');

• Already tested the above script in a 12 and 10 postgres container.

To test

1. Switch tdp_core branch to the mp/291_db_migration (necessary since the alembic integration is not yet in the develop branch). --> merged into develop
2. Create a postgres12.1 container and a matching pgadmin container in your docker-compose.yml file.
3. Open pgadmin on the browser and add ordino and postgres users/roles.
4. Execute alembic command db-migration:upgrade:head:tdp_publicdb.
5. Check if the schema looks okay and also that the table tdp_publicdb_alembic_version has been created.

[thinkh]

Just a minor request to add a comment to the commented line.

[oltionchampari]

Running the first alembic revision in an empty database produces the below error when querying the data.

This error can be fixed by refreshing the view right after creating it:

REFRESH MATERIALIZED VIEW cellline.mutationalburden;

Source: scenic-views/scenic#184

[thinkh]

Thanks for the integration and testing. I ran a test now and it works well. 👍