feat(IPVC-2280): add codon_table to transcript + migration

[sptaylor]

This PR adds codon_table to the Transcript model and adds a migration. By setting server_default to 1, all existing transcripts will be assigned 1 during the migration.

Note: I did not add codon_table to any of the views. I'd be happy to add that to my migration if we want to update any views.

Because alembic can be a bit finicky, here are the steps I used to successfully apply and validate the migration:

docker build --target uta -t uta-update .
docker compose up -d uta-update
docker-compose exec uta-update bash
root@lima-rancher-desktop:/opt/repos/uta# alembic -c etc/alembic.ini history
edadb97f6502 -> cc51f50ae896 (head), add sqlalchemy model for assocacs
<base> -> edadb97f6502, initial state
root@lima-rancher-desktop:/opt/repos/uta# alembic -c etc/alembic.ini upgrade head
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
root@lima-rancher-desktop:/opt/repos/uta# alembic -c etc/alembic.ini revision --autogenerate -m "add codon_table to Transcript"
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.autogenerate.compare] Detected add column 'uta.transcript.codon_table'
  Generating /opt/repos/uta/src/alembic/versions/a697b584f699_add_codon_table_to_transcript.py ...  done
root@lima-rancher-desktop:/opt/repos/uta# alembic -c etc/alembic.ini upgrade head
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.runtime.migration] Running upgrade cc51f50ae896 -> a697b584f699, add codon_table to Transcript
root@lima-rancher-desktop:/opt/repos/uta# uta --conf=etc/global.conf --conf=etc/[email protected] shell
INFO:uta.cli:loaded etc/global.conf
INFO:uta.cli:loaded etc/[email protected]
INFO:uta.cli:connecting to postgresql://uta_admin@localhost/uta
INFO:uta:connected to postgresql://uta_admin@localhost/uta
Python 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.23.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from sqlalchemy.orm import Session
   ...: from sqlalchemy import create_engine
   ...: from uta.models import *

In [2]:  engine = create_engine("postgresql://uta_admin:@localhost/uta")
   ...: connection = engine.connect()
   ...: session = Session(bind=connection)
   ...:  t = session.query(Transcript).filter(Transcript.ac == 'NM_007297.4').first()  # BRCA1

In [3]: t.codon_table
Out[3]: 1

Confirmed outside of the shell as well:

(uta-venv2) ➜  uta git:(IPVC-2280) ✗ alembic -c etc/alembic.ini history
cc51f50ae896 -> a697b584f699 (head), add codon_table to Transcript
edadb97f6502 -> cc51f50ae896, add sqlalchemy model for assocacs
<base> -> edadb97f6502, initial state
(uta-venv2) ➜  uta git:(IPVC-2280) ✗ alembic -c etc/alembic.ini upgrade head
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
(uta-venv2) ➜  uta git:(IPVC-2280) ✗  psql "postgresql://uta_admin:@localhost/uta"

psql (14.3, server 14.9 (Debian 14.9-1.pgdg120+1))
Type "help" for help.

uta=> set search_path = uta;
SET
uta=> select * from transcript limit 10;
       ac        | origin_id |   hgnc   | cds_start_i | cds_end_i |             cds_md5              |           added            | codon_table
-----------------+-----------+----------+-------------+-----------+----------------------------------+----------------------------+-------------
 ENST00000596924 |        10 | A1BG     |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000263100 |        10 | A1BG     |          62 |      1550 | 80dcb3d1bc2d2154d109dfa1287b561e | 2015-08-25 23:59:17.412518 |           1
 ENST00000595014 |        10 | A1BG     |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000598345 |        10 | A1BG     |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000600966 |        10 | A1BG     |           0 |       917 | 8c35c193d0252d7b0003d70ca5b1ea5a | 2015-08-25 23:59:17.412518 |           1
 ENST00000594950 |        10 | A1BG-AS1 |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000593374 |        10 | A1BG-AS1 |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000599728 |        10 | A1BG-AS1 |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000593960 |        10 | A1BG-AS1 |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
 ENST00000600379 |        10 | A1BG-AS1 |             |           |                                  | 2015-08-25 23:59:17.412518 |           1
(10 rows)

[bsgiles73]

Looks good to me. Thanks for the README documentation for Alembic