fix(IPVC-2399): fix gene id back fill migration script, update paths …

[bsgiles73]

This PR fixs the diff between the SqlAlchemy models and database schema detected by Alembic.

Included in this PR:

• update backfill_gene_id script to handle gzipped input files
• update upgrade shell script to used transcript and gene input files added to the repo
• update the Alembic migration, f85dd97bd9f5, to construct foreign key relationship the way Alembic expects, and update gene_symbol to be nullable=False.

To test this PR:

• I started with the uta_20210129b schema
• ran the upgrade script
• then used Alembic to check the diff between the models and schema

Before this PR:

root@lima-rancher-desktop:/opt/repos/uta# alembic --config etc/alembic.ini check
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.autogenerate.compare] Detected NOT NULL on column 'gene.symbol'
INFO  [alembic.autogenerate.compare] Detected removed foreign key (gene_id)(gene_id) on table uta.transcript
INFO  [alembic.autogenerate.compare] Detected added foreign key (gene_id)(gene_id) on table uta.transcript
ERROR [alembic.util.messaging] New upgrade operations detected: [[('modify_nullable', 'uta', 'gene', 'symbol', {'existing_type': TEXT(), 'existing_server_default': False, 'existing_comment': None}, True, False)], ('remove_fk', ForeignKeyConstraint(<sqlalchemy.sql.base.ReadOnlyColumnCollection object at 0x7fad985bad40>, None, name='fk_uta_transcript_gene_gene_id', onupdate='RESTRICT', ondelete='RESTRICT', table=Table('transcript', MetaData(), Column('gene_id', NullType(), ForeignKey('uta.gene.gene_id'), table=<transcript>), schema='uta'))), ('add_fk', ForeignKeyConstraint(<sqlalchemy.sql.base.ReadOnlyColumnCollection object at 0x7fad989162f0>, None, table=Table('transcript', MetaData(), Column('gene_id', NullType(), ForeignKey('uta.gene.gene_id'), table=<transcript>), schema='uta')))]
  FAILED: New upgrade operations detected: [[('modify_nullable', 'uta', 'gene', 'symbol', {'existing_type': TEXT(), 'existing_server_default': False, 'existing_comment': None}, True, False)], ('remove_fk', ForeignKeyConstraint(<sqlalchemy.sql.base.ReadOnlyColumnCollection object at
  0x7fad985bad40>, None, name='fk_uta_transcript_gene_gene_id', onupdate='RESTRICT', ondelete='RESTRICT', table=Table('transcript', MetaData(), Column('gene_id', NullType(), ForeignKey('uta.gene.gene_id'), table=<transcript>), schema='uta'))), ('add_fk',
  ForeignKeyConstraint(<sqlalchemy.sql.base.ReadOnlyColumnCollection object at 0x7fad989162f0>, None, table=Table('transcript', MetaData(), Column('gene_id', NullType(), ForeignKey('uta.gene.gene_id'), table=<transcript>), schema='uta')))]

Using the changes in this PR to revision was needed.

root@lima-rancher-desktop:/opt/repos/uta# alembic --config etc/alembic.ini check
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
No new upgrade operations detected.

[nvta1209]

Nice, this will be useful in a lot of other places

[bsgiles73]

Thanks to @sptaylor!