add hack alembic bigserial migration (#208)

* build: bump alembic to v1.18

* add migration to fix borked bigserial cols

Author: bdewilde

migrations/versions/9c67b9d5e01e_fix_borked_bigserial_cols_if_needed.py

@@ -0,0 +1,83 @@
+"""fix-borked-bigserial-cols-if-needed
+
+Revision ID: 9c67b9d5e01e
+Revises: 3143eb18a369
+Create Date: 2026-03-11 13:07:30.838743
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "9c67b9d5e01e"
+down_revision = "3143eb18a369"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    conn = op.get_bind()
+
+    # data_extractions pkey: int8 => bigserial (?)
+    column_default = conn.execute(
+        sa.text(
+            "SELECT column_default FROM information_schema.columns "
+            "WHERE table_name = 'data_extractions' AND column_name = 'id'"
+        )
+    ).scalar()
+    # column_default is null or missing "nextval" if it's plain int8 w/o a sequence default
+    if column_default is None or "nextval" not in column_default:
+        conn.execute(
+            sa.text(
+                "CREATE SEQUENCE IF NOT EXISTS data_extractions_id_seq "
+                "AS bigint OWNED BY data_extractions.id"
+            )
+        )
+        conn.execute(
+            sa.text(
+                "SELECT setval('data_extractions_id_seq', "
+                "(SELECT COALESCE(MAX(id), 1) FROM data_extractions))"
+            )
+        )
+        conn.execute(
+            sa.text(
+                "ALTER TABLE data_extractions "
+                "ALTER COLUMN id SET DEFAULT nextval('data_extractions_id_seq')"
+            )
+        )
+
+    # dedupes pkey: int8 => bigserial (?)
+    column_default = conn.execute(
+        sa.text(
+            "SELECT column_default FROM information_schema.columns "
+            "WHERE table_name = 'dedupes' AND column_name = 'id'"
+        )
+    ).scalar()
+    # column_default is null or missing "nextval" if it's plain int8 w/o a sequence default
+    if column_default is None or "nextval" not in column_default:
+        conn.execute(
+            sa.text(
+                "CREATE SEQUENCE IF NOT EXISTS dedupes_id_seq "
+                "AS bigint OWNED BY dedupes.id"
+            )
+        )
+        conn.execute(
+            sa.text(
+                "SELECT setval('dedupes_id_seq', "
+                "(SELECT COALESCE(MAX(id), 1) FROM dedupes))"
+            )
+        )
+        conn.execute(
+            sa.text(
+                "ALTER TABLE dedupes "
+                "ALTER COLUMN id SET DEFAULT nextval('dedupes_id_seq')"
+            )
+        )
+
+
+def downgrade():
+    # restoring a plain int8 is probably not desirable;
+    # leave downgrade as a no-op or implement as needed
+    pass

pyproject.toml

@@ -14,7 +14,7 @@ classifiers = [
 ]
 requires-python = ">= 3.11"
 dependencies = [
-  "alembic~=1.17.0",
+  "alembic~=1.18.0",
   "apiflask~=3.0.0",
   "arrow~=1.3.0",
   "bibtexparser~=1.4.0",