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

README.md

@@ -342,3 +342,18 @@ Example:
 ```
 sbin/uta-update $(pwd)/ncbi-data $(pwd)/seqrepo-data $(pwd)/uta-build uta_20210129b 2024-02-20
 ```
+
+## Migrations
+UTA uses alembic to manage database migrations. To auto-generate a migration:
+```
+alembic -c etc/alembic.ini revision --autogenerate -m "description of the migration"
+```
+This will create a migration script in the alembic/versions directory.
+Adjust the upgrade and downgrade function definitions. To apply the migration:
+```
+alembic -c etc/alembic.ini upgrade head
+```
+To reverse a migration, use `downgrade` with the number of steps to reverse. For example, to reverse the last: 
+```
+alembic -c etc/alembic.ini downgrade -1
+```

src/alembic/versions/a697b584f699_add_codon_table_to_transcript.py

@@ -0,0 +1,30 @@
+"""add codon_table to Transcript
+
+Revision ID: a697b584f699
+Revises: cc51f50ae896
+Create Date: 2024-04-08 17:27:41.570024
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = 'a697b584f699'
+down_revision: Union[str, None] = 'cc51f50ae896'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('transcript', sa.Column('codon_table', sa.Integer(), server_default='1', nullable=False), schema='uta')
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('transcript', 'codon_table', schema='uta')
+    # ### end Alembic commands ###

src/uta/models.py

@@ -130,6 +130,7 @@ class Transcript(Base):
     cds_md5 = sa.Column(sa.Text, index=True)
     added = sa.Column(
         sa.DateTime, default=datetime.datetime.now(), nullable=False)
+    codon_table = sa.Column(sa.Integer, nullable=False, server_default='1')  # 1 = standard, 2 = mitochondrial
 
     # relationships:
     origin = sao.relationship("Origin", backref="transcripts")