Cast db_identifier to string in clinical_controls and update publication_identifiers columns; bump Alembic version to 1.14.1

Author: bencap

alembic/versions/a8e345cca190_cast_db_identifier_in_clinical_controls_.py

@@ -0,0 +1,59 @@
+"""cast db_identifier in clinical controls table to a string
+
+Revision ID: a8e345cca190
+Revises: 986b635a697f
+Create Date: 2025-08-20 12:30:05.388503
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "a8e345cca190"
+down_revision = "986b635a697f"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "clinical_controls", "db_identifier", existing_type=sa.INTEGER(), type_=sa.String(), existing_nullable=False
+    )
+    op.alter_column(
+        "publication_identifiers", "title", existing_type=sa.TEXT(), type_=sa.String(), existing_nullable=False
+    )
+    op.alter_column(
+        "publication_identifiers", "abstract", existing_type=sa.TEXT(), type_=sa.String(), existing_nullable=True
+    )
+    op.alter_column(
+        "publication_identifiers",
+        "publication_journal",
+        existing_type=sa.TEXT(),
+        type_=sa.String(),
+        existing_nullable=True,
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "publication_identifiers",
+        "publication_journal",
+        existing_type=sa.String(),
+        type_=sa.TEXT(),
+        existing_nullable=True,
+    )
+    op.alter_column(
+        "publication_identifiers", "abstract", existing_type=sa.String(), type_=sa.TEXT(), existing_nullable=True
+    )
+    op.alter_column(
+        "publication_identifiers", "title", existing_type=sa.String(), type_=sa.TEXT(), existing_nullable=False
+    )
+    op.alter_column(
+        "clinical_controls", "db_identifier", existing_type=sa.String(), type_=sa.INTEGER(), existing_nullable=False
+    )
+    # ### end Alembic commands ###

poetry.lock

@@ -37,11 +37,11 @@ pandas = "~1.4.1"
 pydantic = "~2.10.0"
 python-dotenv = "~0.20.0"
 python-json-logger = "~2.0.7"
-SQLAlchemy = "~2.0.0"
+SQLAlchemy = "~2.0.29"
 ga4gh-va-spec = "~0.4.2"
 
 # Optional dependencies for running this application as a server
-alembic = { version = "~1.7.6", optional = true }
+alembic = { version = "~1.14.0", optional = true }
 alembic-utils = { version = "0.8.1", optional = true }
 arq = { version = "~0.25.0", optional = true }
 authlib = { version = "~1.3.1", optional = true }