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LLeMbas/src/lembas/db/migrations.py
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Jaroslav Beneš 2f978d84d1 Add nullable columns without a default
Deploying knowledge bases showed the migration runner doing the wrong thing:

    ALTER TABLE "documents" ADD COLUMN "base_id" VARCHAR(32) DEFAULT ''

`base_id` is nullable and its absent value is NULL, but the runner derived a
default from the column type and backfilled every existing row with the empty
string. Nothing then matched `base_id IS NULL`, so the startup sweep that files
pre-bases documents into a default base would have skipped all of them and the
documents would have stayed invisible.

Nobody lost anything -- the live instance had no documents yet -- but the fault
is general: any nullable column added from here would arrive as "" rather than
NULL, and every "is this set?" check would be wrong about the rows that predate
it. So a default is now emitted only for NOT NULL columns, where SQLite requires
one.

The sweep also accepts "" as meaning unfiled, since a deployment that upgraded
through the previous release has rows holding it.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-07-21 20:03:01 +02:00

233 lines
9.7 KiB
Python

"""Additive schema synchronisation.
This project has no Alembic, by design: it is SQLite-only and the schema is
created at startup. That was fine until the first live instance had data in it,
at which point adding a column to a model stopped being free -- ``create_all``
only creates missing *tables*, so a new column silently never appears and every
query mentioning it fails.
What this module does instead is derive the migration from the models: compare
each table's declared columns against what the database actually has, and
``ALTER TABLE ... ADD COLUMN`` for whatever is missing. That covers new tables
and new columns, which is essentially every schema change this project makes.
What it deliberately does NOT do:
* rename, drop or retype a column
* add a PRIMARY KEY or UNIQUE constraint to an existing table
* backfill anything requiring application logic
SQLite cannot do most of those with ALTER TABLE anyway; they need the
create-copy-swap dance. Anything in that category is a hand-written job and
should be added to MANUAL_STEPS below so it is at least visible.
"""
from __future__ import annotations
import logging
from typing import Any
from sqlalchemy import Engine, inspect, text
from sqlalchemy.schema import Column, Table
from lembas.db.base import Base
log = logging.getLogger(__name__)
# Schema changes that this module cannot perform. Kept as documentation so a
# failure has somewhere to point rather than being a mystery.
MANUAL_STEPS: list[str] = []
def _literal_default(column: Column) -> str | None:
"""A SQL literal to backfill an existing row's new column with.
SQLite refuses to add a NOT NULL column without a default, and refuses a
non-constant default. Python-side defaults (``default=dict``,
``default=utcnow``) are callables and cannot be expressed in DDL, so the
value is derived from the column type instead. New rows still get the real
Python default; this only fills the rows that already exist.
"""
default = column.default
if default is not None and not default.is_callable and not default.is_clause_element:
value: Any = default.arg
if isinstance(value, bool):
return "1" if value else "0"
if isinstance(value, (int, float)):
return str(value)
if isinstance(value, str):
escaped = value.replace("'", "''")
return f"'{escaped}'"
affinity = column.type.__class__.__name__.upper()
if "JSON" in affinity:
# MutableList columns must start as [] and MutableDict as {}; guessing
# wrong makes the first read blow up rather than return empty.
python_type = getattr(column.type, "python_type", None)
return "'[]'" if python_type is list else "'{}'"
if "BOOL" in affinity:
return "0"
if any(token in affinity for token in ("INT", "FLOAT", "NUMERIC", "DECIMAL")):
return "0"
if "DATE" in affinity or "TIME" in affinity:
return "CURRENT_TIMESTAMP"
if any(token in affinity for token in ("STRING", "TEXT", "VARCHAR", "CHAR")):
return "''"
return None
def _add_column_sql(table: Table, column: Column, dialect) -> str | None:
type_sql = column.type.compile(dialect)
default = _literal_default(column)
if not column.nullable and default is None:
log.error(
"cannot add NOT NULL column %s.%s: no usable default. Add it by hand.",
table.name,
column.name,
)
return None
parts = [f'ALTER TABLE "{table.name}" ADD COLUMN "{column.name}" {type_sql}']
if not column.nullable:
# SQLite refuses a NOT NULL column with no default, so existing rows
# have to be given something. That is the only reason a default is
# emitted at all.
parts.append("NOT NULL")
parts.append(f"DEFAULT {default}")
# A nullable column gets no default on purpose. Backfilling one would give
# existing rows a value the model does not consider absent -- an added
# foreign key would arrive as "" rather than NULL, and every "is this set?"
# check downstream would be wrong about rows that predate it.
return " ".join(parts)
# --- Full-text search --------------------------------------------------------
# The library stores are searched rather than listed, and LIKE over a few
# hundred documents ranks nothing and matches badly. SQLite ships FTS5, so the
# index costs no dependency and works offline like everything else here.
#
# These are the one part of the schema this module's model-diffing cannot
# derive: an FTS5 virtual table is not a SQLAlchemy model, has no columns to
# compare, and needs triggers to stay in step with the table it shadows. So it
# is written out -- but written out *idempotently*, with IF NOT EXISTS
# throughout, which keeps it the same kind of thing as the column sync: run it
# at every startup and it converges.
#
# `content=` makes each index external-content: the text is not stored twice,
# and the triggers below are what the FTS5 documentation calls for to keep an
# external-content index correct through updates and deletes.
FTS_INDEXES: tuple[tuple[str, str, tuple[str, ...]], ...] = (
("documents_fts", "documents", ("title", "description", "extracted_text")),
("notes_fts", "notes", ("title", "body")),
("skills_fts", "skills", ("name", "description", "body")),
)
def _fts_statements(index: str, table: str, columns: tuple[str, ...]) -> list[str]:
# `id` rides along UNINDEXED so a match can be turned straight back into an
# ORM row. The alternative is joining on rowid, which SQLAlchemy models do
# not expose and which changes under VACUUM.
columns = ("id", *columns)
column_list = ", ".join(columns)
declared = ", ".join(
f"{name} UNINDEXED" if name == "id" else name for name in columns
)
new_values = ", ".join(f"new.{name}" for name in columns)
old_values = ", ".join(f"old.{name}" for name in columns)
return [
f"CREATE VIRTUAL TABLE IF NOT EXISTS {index} USING fts5("
f"{declared}, content='{table}', content_rowid='rowid')",
# 'delete' rows carry the old values because an external-content index
# cannot look them up itself once the source row has gone.
f"""CREATE TRIGGER IF NOT EXISTS {index}_ai AFTER INSERT ON {table} BEGIN
INSERT INTO {index}(rowid, {column_list}) VALUES (new.rowid, {new_values});
END""",
f"""CREATE TRIGGER IF NOT EXISTS {index}_ad AFTER DELETE ON {table} BEGIN
INSERT INTO {index}({index}, rowid, {column_list})
VALUES ('delete', old.rowid, {old_values});
END""",
f"""CREATE TRIGGER IF NOT EXISTS {index}_au AFTER UPDATE ON {table} BEGIN
INSERT INTO {index}({index}, rowid, {column_list})
VALUES ('delete', old.rowid, {old_values});
INSERT INTO {index}(rowid, {column_list}) VALUES (new.rowid, {new_values});
END""",
]
def ensure_fts(engine: Engine) -> list[str]:
"""Create the search indexes and their triggers if they are missing.
Returns the indexes it created. A failure here is logged and swallowed:
search degrading to "finds nothing" is bad, but it is much better than the
application refusing to start.
"""
created: list[str] = []
inspector = inspect(engine)
known = set(inspector.get_table_names())
with engine.begin() as connection:
for index, table, columns in FTS_INDEXES:
if table not in known:
continue
fresh = index not in known
for statement in _fts_statements(index, table, columns):
connection.execute(text(statement))
if fresh:
# Backfill anything already in the table. Only on creation --
# the triggers keep it current from then on.
column_list = ", ".join(("id", *columns))
connection.execute(
text(
f"INSERT INTO {index}(rowid, {column_list}) "
f"SELECT rowid, {column_list} FROM {table}"
)
)
created.append(index)
return created
def sync_schema(engine: Engine) -> list[str]:
"""Bring the database up to the declared schema. Returns what it changed."""
import lembas.db.models # noqa: F401 (registers every table on the metadata)
changes: list[str] = []
inspector = inspect(engine)
known_tables = set(inspector.get_table_names())
for table in Base.metadata.sorted_tables:
if table.name not in known_tables:
changes.append(f"create table {table.name}")
# Creates anything missing; existing tables are left alone.
Base.metadata.create_all(bind=engine)
inspector = inspect(engine)
with engine.begin() as connection:
for table in Base.metadata.sorted_tables:
existing = {col["name"] for col in inspector.get_columns(table.name)}
for column in table.columns:
if column.name in existing:
continue
statement = _add_column_sql(table, column, engine.dialect)
if statement is None:
continue
connection.execute(text(statement))
changes.append(f"add column {table.name}.{column.name}")
log.info("schema: %s", statement)
try:
for index in ensure_fts(engine):
changes.append(f"create search index {index}")
except Exception: # noqa: BLE001 - search is not worth refusing to start over
log.exception("could not create the full-text search indexes")
if changes:
log.info("schema synchronised: %d change(s)", len(changes))
for step in MANUAL_STEPS:
log.warning("manual schema step still required: %s", step)
return changes