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newline at end of file diff --git a/src/ell/stores/migrations/env.py b/src/ell/stores/migrations/env.py new file mode 100644 index 000000000..aa284ef50 --- /dev/null +++ b/src/ell/stores/migrations/env.py @@ -0,0 +1,92 @@ +from logging.config import fileConfig + +from sqlalchemy import engine_from_config +from sqlalchemy import pool + +from alembic import context +from sqlmodel import SQLModel +from ell.types.studio import * + + +# this is the Alembic Config object, which provides +# access to the values within the .ini file in use. +config = context.config + +# Interpret the config file for Python logging. +# This line sets up loggers basically. +if config.config_file_name is not None: + fileConfig(config.config_file_name) + + +# add your model's MetaData object here +# for 'autogenerate' support +# from myapp import mymodel +# target_metadata = mymodel.Base.metadata +target_metadata = SQLModel.metadata + +# other values from the config, defined by the needs of env.py, +# can be acquired: +# my_important_option = config.get_main_option("my_important_option") +# ... etc. + + +def run_migrations_offline() -> None: + """Run migrations in 'offline' mode. + + This configures the context with just a URL + and not an Engine, though an Engine is acceptable + here as well. By skipping the Engine creation + we don't even need a DBAPI to be available. + + Calls to context.execute() here emit the given string to the + script output. + + """ + url = config.get_main_option("sqlalchemy.url") + version_table = config.get_main_option("version_table", "ell_alembic_version") + + context.configure( + url=url, + target_metadata=target_metadata, + literal_binds=True, + dialect_opts={"paramstyle": "named"}, + compare_type=True, + compare_server_default=True, + render_as_batch=True, + as_sql=True, + version_table=version_table + ) + + with context.begin_transaction(): + context.run_migrations() + + +def run_migrations_online() -> None: + """Run migrations in 'online' mode. + + In this scenario we need to create an Engine + and associate a connection with the context. + + """ + connectable = engine_from_config( + config.get_section(config.config_ini_section, {}), + prefix="sqlalchemy.", + poolclass=pool.NullPool, + ) + + with connectable.connect() as connection: + version_table = config.get_main_option("version_table", "ell_alembic_version") + context.configure( + connection=connection, + target_metadata=target_metadata, + version_table=version_table + ) + + with context.begin_transaction(): + context.run_migrations() + + +if context.is_offline_mode(): + run_migrations_offline() +else: + run_migrations_online() diff --git a/src/ell/stores/migrations/make.py b/src/ell/stores/migrations/make.py new file mode 100644 index 000000000..6193aea60 --- /dev/null +++ b/src/ell/stores/migrations/make.py @@ -0,0 +1,32 @@ +import argparse +from sqlalchemy import create_engine +from ell.stores.sql import get_alembic_config +from alembic import command + +def main(): + parser = argparse.ArgumentParser(description='Create a new database migration') + parser.add_argument('message', help='Migration message/description') + + args = parser.parse_args() + + # Create temporary directory for SQLite database + import tempfile + from pathlib import Path + + with tempfile.TemporaryDirectory() as tmpdir: + db_path = Path(tmpdir) / "temp.db" + engine = create_engine(f"sqlite:///{db_path}") + alembic_cfg = get_alembic_config(str(engine.url)) + + # First, upgrade to head to get to latest migration state + command.upgrade(alembic_cfg, "head") + + # Now generate new migration + command.revision(alembic_cfg, + message=args.message, + autogenerate=True) + + print(f"✨ Created new migration with message: {args.message}") + +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/src/ell/stores/migrations/script.py.mako b/src/ell/stores/migrations/script.py.mako new file mode 100644 index 000000000..fbc4b07dc --- /dev/null +++ b/src/ell/stores/migrations/script.py.mako @@ -0,0 +1,26 @@ +"""${message} + +Revision ID: ${up_revision} +Revises: ${down_revision | comma,n} +Create Date: ${create_date} + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +${imports if imports else ""} + +# revision identifiers, used by Alembic. +revision: str = ${repr(up_revision)} +down_revision: Union[str, None] = ${repr(down_revision)} +branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)} +depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)} + + +def upgrade() -> None: + ${upgrades if upgrades else "pass"} + + +def downgrade() -> None: + ${downgrades if downgrades else "pass"} diff --git a/src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py b/src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py new file mode 100644 index 000000000..0e8192e58 --- /dev/null +++ b/src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py @@ -0,0 +1,30 @@ +"""correcting incorrect unique constraint specification + +Revision ID: 17ff4eaabe85 +Revises: 4524fb60d23e +Create Date: 2024-11-18 21:08:45.321668+00:00 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '17ff4eaabe85' +down_revision: Union[str, None] = '4524fb60d23e' +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.create_unique_constraint('uq_serializedlmp_version_number_name', 'serializedlmp', ['version_number', 'name']) + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.drop_constraint('uq_serializedlmp_version_number_name', 'serializedlmp', type_='unique') + # ### end Alembic commands ### diff --git a/src/ell/stores/migrations/versions/4524fb60d23e_initial_ell_sql_schema.py b/src/ell/stores/migrations/versions/4524fb60d23e_initial_ell_sql_schema.py new file mode 100644 index 000000000..3f918eb5f --- /dev/null +++ b/src/ell/stores/migrations/versions/4524fb60d23e_initial_ell_sql_schema.py @@ -0,0 +1,107 @@ +"""Initial ell sql schema + +Revision ID: 4524fb60d23e +Revises: +Create Date: 2024-11-14 10:51:49.545417 +""" +from alembic import op +import sqlalchemy as sa +from sqlalchemy import Column, JSON, TIMESTAMP, Float, String, Integer, ForeignKey, Boolean +import enum + +from ell.types.lmp import LMPType + +# revision identifiers, used by Alembic. +revision = '4524fb60d23e' +down_revision = None +branch_labels = None +depends_on = None + +def upgrade() -> None: + # Create SerializedLMP table first (as it's referenced by others) + op.create_table( + 'serializedlmp', + sa.Column('lmp_id', String(), nullable=False), + sa.Column('name', String(), nullable=False), + sa.Column('source', String(), nullable=False), + sa.Column('dependencies', String(), nullable=False), + sa.Column('created_at', TIMESTAMP(timezone=True), nullable=False), + sa.Column('lmp_type', sa.Enum(LMPType, name='lmptype'), nullable=False), + sa.Column('api_params', JSON, nullable=True), + sa.Column('initial_free_vars', JSON, nullable=True), + sa.Column('initial_global_vars', JSON, nullable=True), + sa.Column('num_invocations', Integer(), nullable=True, default=None), + sa.Column('commit_message', String(), nullable=True), + sa.Column('version_number', Integer(), nullable=True), + sa.PrimaryKeyConstraint('lmp_id') + ) + op.create_index('ix_serializedlmp_name', 'serializedlmp', ['name']) + op.create_index('ix_serializedlmp_created_at', 'serializedlmp', ['created_at']) + + # Create SerializedLMPUses table + op.create_table( + 'serializedlmpuses', + sa.Column('lmp_user_id', String(), nullable=False), + sa.Column('lmp_using_id', String(), nullable=False), + sa.ForeignKeyConstraint(['lmp_user_id'], ['serializedlmp.lmp_id']), + sa.ForeignKeyConstraint(['lmp_using_id'], ['serializedlmp.lmp_id']), + sa.PrimaryKeyConstraint('lmp_user_id', 'lmp_using_id') + ) + op.create_index('ix_serializedlmpuses_lmp_user_id', 'serializedlmpuses', ['lmp_user_id']) + op.create_index('ix_serializedlmpuses_lmp_using_id', 'serializedlmpuses', ['lmp_using_id']) + + # Create Invocation table + op.create_table( + 'invocation', + sa.Column('id', String(), nullable=False), + sa.Column('lmp_id', String(), nullable=False), + sa.Column('latency_ms', Float(), nullable=False), + sa.Column('prompt_tokens', Integer(), nullable=True), + sa.Column('completion_tokens', Integer(), nullable=True), + sa.Column('state_cache_key', String(), nullable=True), + sa.Column('created_at', TIMESTAMP(timezone=True), nullable=False), + sa.Column('used_by_id', String(), nullable=True), + sa.ForeignKeyConstraint(['lmp_id'], ['serializedlmp.lmp_id']), + sa.ForeignKeyConstraint(['used_by_id'], ['invocation.id']), + sa.PrimaryKeyConstraint('id') + ) + op.create_index('ix_invocation_lmp_id', 'invocation', ['lmp_id']) + op.create_index('ix_invocation_used_by_id', 'invocation', ['used_by_id']) + op.create_index('ix_invocation_created_at_latency_ms', 'invocation', ['created_at', 'latency_ms']) + op.create_index('ix_invocation_created_at_tokens', 'invocation', ['created_at', 'prompt_tokens', 'completion_tokens']) + op.create_index('ix_invocation_lmp_id_created_at', 'invocation', ['lmp_id', 'created_at']) + + # Create InvocationContents table + op.create_table( + 'invocationcontents', + sa.Column('invocation_id', String(), nullable=False), + sa.Column('params', JSON, nullable=True), + sa.Column('results', JSON, nullable=True), + sa.Column('invocation_api_params', JSON, nullable=True), + sa.Column('global_vars', JSON, nullable=True), + sa.Column('free_vars', JSON, nullable=True), + sa.Column('is_external', Boolean(), nullable=False), + sa.ForeignKeyConstraint(['invocation_id'], ['invocation.id']), + sa.PrimaryKeyConstraint('invocation_id') + ) + op.create_index('ix_invocationcontents_invocation_id', 'invocationcontents', ['invocation_id']) + + # Create InvocationTrace table + op.create_table( + 'invocationtrace', + sa.Column('invocation_consumer_id', String(), nullable=False), + sa.Column('invocation_consuming_id', String(), nullable=False), + sa.ForeignKeyConstraint(['invocation_consumer_id'], ['invocation.id']), + sa.ForeignKeyConstraint(['invocation_consuming_id'], ['invocation.id']), + sa.PrimaryKeyConstraint('invocation_consumer_id', 'invocation_consuming_id') + ) + op.create_index('ix_invocationtrace_invocation_consumer_id', 'invocationtrace', ['invocation_consumer_id']) + op.create_index('ix_invocationtrace_invocation_consuming_id', 'invocationtrace', ['invocation_consuming_id']) + +def downgrade() -> None: + # Drop tables in correct order (reverse of creation) + op.drop_table('invocationtrace') + op.drop_table('invocationcontents') + op.drop_table('invocation') + op.drop_table('serializedlmpuses') + op.drop_table('serializedlmp') \ No newline at end of file diff --git a/src/ell/stores/sql.py b/src/ell/stores/sql.py index 3000ef02b..e8fcb3aba 100644 --- a/src/ell/stores/sql.py +++ b/src/ell/stores/sql.py @@ -1,5 +1,6 @@ from datetime import datetime, timedelta import os +from pathlib import Path from typing import Any, Optional, Dict, List, Set from sqlmodel import Session, SQLModel, create_engine, select import ell.stores.store @@ -10,13 +11,90 @@ import gzip import json +from alembic import command +from alembic.config import Config +from sqlalchemy import inspect + +import logging + +logger = logging.getLogger(__name__) + +def get_alembic_config(engine_url: str) -> Config: + """Create Alembic config programmatically""" + alembic_cfg = Config() + migrations_dir = Path(__file__).parent / "migrations" + + alembic_cfg.set_main_option("script_location", str(migrations_dir)) + alembic_cfg.set_main_option("sqlalchemy.url", str(engine_url)) + alembic_cfg.set_main_option("version_table", "ell_alembic_version") + alembic_cfg.set_main_option("timezone", "UTC") + + return alembic_cfg + +def init_or_migrate_database(engine) -> None: + """Initialize or migrate database with ELL schema + + Handles three cases: + 1. Existing database with our tables but no Alembic -> stamp with initial migration + 2. Database with Alembic -> upgrade to head + 3. New/empty database or database without our tables -> create tables and stamp with head + + Args: + engine_or_url: SQLAlchemy engine or database URL string + """ + inspector = inspect(engine) + + # Check database state + our_tables_v1 = {'serializedlmp', 'invocation', 'invocationcontents', + 'invocationtrace', 'serializedlmpuses'} + existing_tables = set(inspector.get_table_names()) + has_our_tables = bool(our_tables_v1 & existing_tables) # Intersection + has_alembic = 'ell_alembic_version' in existing_tables + + alembic_cfg = get_alembic_config(engine.url) + + try: + if has_our_tables and not has_alembic: + # Case 1: Existing database with our tables but no Alembic + # This is likely a database from version <= 0.14 + logger.info("Found existing ell tables without Alembic. Stamping with initial migration.") + + + command.stamp(alembic_cfg, "4524fb60d23e") + # Verify table was created + after_tables = set(inspect(engine).get_table_names()) + # import code; code.interact(local=dict(globals(), **locals())) + # Check if version table has our stamp + with engine.connect() as connection: + version_result = connection.execute(text("SELECT version_num FROM ell_alembic_version")).first() + if not version_result or version_result[0] != "4524fb60d23e": + raise RuntimeError("Failed to stamp database - version table empty or incorrect version") + + + elif has_alembic: + # Case 2: Database has Alembic - run any pending migrations + command.upgrade(alembic_cfg, "head") + + else: + # Case 3: New database or database without our tables + # Create all tables according to current schema + SQLModel.metadata.create_all(engine) + # Stamp with latest migration + command.stamp(alembic_cfg, "head") + + except Exception as e: + logger.error(f"Failed to initialize/migrate database: {e}") + raise + + class SQLStore(ell.stores.store.Store): def __init__(self, db_uri: str, blob_store: Optional[ell.stores.store.BlobStore] = None): + # XXX: Use Serialization serialzie_object in incoming PR. self.engine = create_engine(db_uri, json_serializer=lambda obj: json.dumps(pydantic_ltype_aware_cattr.unstructure(obj), sort_keys=True, default=repr, ensure_ascii=False)) - SQLModel.metadata.create_all(self.engine) + init_or_migrate_database(self.engine) self.open_files: Dict[str, Dict[str, Any]] = {} super().__init__(blob_store) diff --git a/src/ell/stores/studio.py b/src/ell/stores/studio.py index f02f68ed7..048e7f7af 100644 --- a/src/ell/stores/studio.py +++ b/src/ell/stores/studio.py @@ -17,6 +17,7 @@ from typing import Any, List, Optional from sqlmodel import Field, SQLModel, Relationship, JSON, Column from sqlalchemy import Index, func +import sqlalchemy as sa from typing import TypeVar, Any @@ -90,6 +91,10 @@ class Config: table_name = "serializedlmp" unique_together = [("version_number", "name")] + __table_args__ = ( + sa.UniqueConstraint('version_number', 'name', name='uq_serializedlmp_version_number_name'), + ) + class InvocationTrace(SQLModel, table=True): invocation_consumer_id: str = Field(foreign_key="invocation.id", primary_key=True, index=True) invocation_consuming_id: str = Field(foreign_key="invocation.id", primary_key=True, index=True) diff --git a/src/ell/studio/config.py b/src/ell/studio/config.py index 851c9c5e5..e56a834d7 100644 --- a/src/ell/studio/config.py +++ b/src/ell/studio/config.py @@ -37,4 +37,4 @@ def create( # This intends to honor the default we had set in the CLI storage_dir = os.getcwd() - return cls(pg_connection_string=pg_connection_string, storage_dir=storage_dir) \ No newline at end of file + return cls(pg_connection_string=pg_connection_string, storage_dir=storage_dir) diff --git a/tests/test_migrations.py b/tests/test_migrations.py new file mode 100644 index 000000000..c362c0b1a --- /dev/null +++ b/tests/test_migrations.py @@ -0,0 +1,183 @@ +import os +import tempfile +from pathlib import Path +import pytest +from sqlalchemy import inspect, MetaData, create_engine, text +from sqlmodel import SQLModel + +from ell.stores.sql import init_or_migrate_database, get_alembic_config +from alembic import command +from alembic.config import Config + +def get_table_metadata(engine, exclude_tables=None): + """Helper to get table metadata in a consistent format""" + inspector = inspect(engine) + metadata = {} + exclude_tables = exclude_tables or set() + + for table_name in inspector.get_table_names(): + if table_name in exclude_tables: + continue + + columns = {col['name']: { + 'type': str(col['type']), + 'nullable': col['nullable'], + 'default': col['default'], + 'primary_key': col['primary_key'] + } for col in inspector.get_columns(table_name)} + + foreign_keys = [ + {'referred_table': fk['referred_table'], + 'referred_columns': fk['referred_columns'], + 'constrained_columns': fk['constrained_columns']} + for fk in inspector.get_foreign_keys(table_name) + ] + + indexes = [ + {'name': idx['name'], + 'columns': idx['column_names'], + 'unique': idx['unique']} + for idx in inspector.get_indexes(table_name) + ] + + # Add unique constraints + unique_constraints = [ + {'name': const['name'], + 'columns': const['column_names']} + for const in inspector.get_unique_constraints(table_name) + ] + + metadata[table_name] = { + 'columns': columns, + 'foreign_keys': foreign_keys, + 'indexes': indexes, + 'unique_constraints': unique_constraints + } + + return metadata + +@pytest.fixture +def temp_db_url(): + """Create a temporary SQLite database URL""" + with tempfile.TemporaryDirectory() as tmpdir: + db_path = Path(tmpdir) / "test.db" + yield f"sqlite:///{db_path}" + +def test_empty_db_migration(temp_db_url): + """Test migrating an empty database creates same schema as SQLModel metadata""" + # Create engine for empty database + engine = create_engine(temp_db_url) + + # Initialize database using migrations + init_or_migrate_database(engine) + + # Get schema created by migrations, excluding alembic version table + migrated_metadata = get_table_metadata(engine, exclude_tables={'ell_alembic_version'}) + + # Create new empty database + engine2 = create_engine(temp_db_url.replace("test.db", "test2.db")) + + # Create schema using SQLModel metadata + SQLModel.metadata.create_all(engine2) + + # Get schema created by SQLModel + sqlmodel_metadata = get_table_metadata(engine2) + + # Compare schemas + assert migrated_metadata == sqlmodel_metadata + +def test_existing_tables_no_alembic(temp_db_url): + """Test database with existing tables but no alembic version table""" + engine = create_engine(temp_db_url) + + # Create tables using SQLModel + SQLModel.metadata.create_all(engine) + + # Initialize/migrate database + init_or_migrate_database(engine) + + # Verify alembic version table exists and has correct version + inspector = inspect(engine) + assert 'ell_alembic_version' in inspector.get_table_names() + + with engine.connect() as conn: + result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) + version = result.scalar() + assert version == "4524fb60d23e" # Initial migration version + +def test_multiple_migrations(temp_db_url): + """Test running multiple migrations in sequence""" + engine = create_engine(temp_db_url) + + # Get alembic config + alembic_cfg = get_alembic_config(str(engine.url)) + + # Start with empty database + init_or_migrate_database(engine) + + # Verify we're at head revision + with engine.connect() as conn: + result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) + version = result.scalar() + assert version == "4524fb60d23e" + + # Downgrade to base + command.downgrade(alembic_cfg, "base") + + # Verify no version + with engine.connect() as conn: + result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) + version = result.scalar() + assert version is None + + # Upgrade to head again + command.upgrade(alembic_cfg, "head") + + # Verify back at head + with engine.connect() as conn: + result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) + version = result.scalar() + assert version == "4524fb60d23e" + +def test_migration_idempotency(temp_db_url): + """Test that running migrations multiple times is idempotent""" + engine = create_engine(temp_db_url) + + # Initial migration + init_or_migrate_database(engine) + initial_metadata = get_table_metadata(engine) + + # Run migration again + init_or_migrate_database(engine) + final_metadata = get_table_metadata(engine) + + # Verify schemas are identical + assert initial_metadata == final_metadata + +def test_pure_migration_matches_metadata(temp_db_url): + """ + Test that running just the initial migration (without SQLModel.metadata) + creates the same schema as SQLModel.metadata + """ + # Create first empty database for migration + engine1 = create_engine(temp_db_url) + + # Get alembic config and run just the initial migration + alembic_cfg = get_alembic_config(str(engine1.url)) + command.upgrade(alembic_cfg, "4524fb60d23e") # Run initial migration only + # Upgrade to head to ensure we're on latest version + command.upgrade(alembic_cfg, "head") + + # Get schema created by migration + migration_metadata = get_table_metadata(engine1, exclude_tables={'ell_alembic_version'}) + + # Create second empty database for SQLModel metadata + engine2 = create_engine(temp_db_url.replace("test.db", "test2.db")) + + # Create tables using SQLModel metadata + SQLModel.metadata.create_all(engine2) + + # Get schema created by SQLModel + sqlmodel_metadata = get_table_metadata(engine2) + + assert migration_metadata == sqlmodel_metadata From 193e9630ababc66390a3c6a9e97cb3748c6dd268 Mon Sep 17 00:00:00 2001 From: William Guss Date: Mon, 18 Nov 2024 17:00:37 -0800 Subject: [PATCH 2/8] passing tests for multiple versions --- src/ell/stores/migrations/script.py.mako | 1 + ...correcting_incorrect_unique_constraint_.py | 30 ------------------- src/ell/stores/studio.py | 6 ++-- tests/test_migrations.py | 10 +++---- 4 files changed, 8 insertions(+), 39 deletions(-) delete mode 100644 src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py diff --git a/src/ell/stores/migrations/script.py.mako b/src/ell/stores/migrations/script.py.mako index fbc4b07dc..6ce335109 100644 --- a/src/ell/stores/migrations/script.py.mako +++ b/src/ell/stores/migrations/script.py.mako @@ -9,6 +9,7 @@ from typing import Sequence, Union from alembic import op import sqlalchemy as sa +import sqlmodel ${imports if imports else ""} # revision identifiers, used by Alembic. diff --git a/src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py b/src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py deleted file mode 100644 index 0e8192e58..000000000 --- a/src/ell/stores/migrations/versions/17ff4eaabe85_correcting_incorrect_unique_constraint_.py +++ /dev/null @@ -1,30 +0,0 @@ -"""correcting incorrect unique constraint specification - -Revision ID: 17ff4eaabe85 -Revises: 4524fb60d23e -Create Date: 2024-11-18 21:08:45.321668+00:00 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '17ff4eaabe85' -down_revision: Union[str, None] = '4524fb60d23e' -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.create_unique_constraint('uq_serializedlmp_version_number_name', 'serializedlmp', ['version_number', 'name']) - # ### end Alembic commands ### - - -def downgrade() -> None: - # ### commands auto generated by Alembic - please adjust! ### - op.drop_constraint('uq_serializedlmp_version_number_name', 'serializedlmp', type_='unique') - # ### end Alembic commands ### diff --git a/src/ell/stores/studio.py b/src/ell/stores/studio.py index 048e7f7af..3d6aa1ed7 100644 --- a/src/ell/stores/studio.py +++ b/src/ell/stores/studio.py @@ -86,14 +86,12 @@ class SerializedLMP(SerializedLMPBase, table=True): secondaryjoin="SerializedLMP.lmp_id==SerializedLMPUses.lmp_user_id", ), ) - + class Config: table_name = "serializedlmp" + # XXX: THis is not a real constraint. unique_together = [("version_number", "name")] - __table_args__ = ( - sa.UniqueConstraint('version_number', 'name', name='uq_serializedlmp_version_number_name'), - ) class InvocationTrace(SQLModel, table=True): invocation_consumer_id: str = Field(foreign_key="invocation.id", primary_key=True, index=True) diff --git a/tests/test_migrations.py b/tests/test_migrations.py index c362c0b1a..a50f85766 100644 --- a/tests/test_migrations.py +++ b/tests/test_migrations.py @@ -119,7 +119,7 @@ def test_multiple_migrations(temp_db_url): with engine.connect() as conn: result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) version = result.scalar() - assert version == "4524fb60d23e" + assert version # Downgrade to base command.downgrade(alembic_cfg, "base") @@ -127,8 +127,8 @@ def test_multiple_migrations(temp_db_url): # Verify no version with engine.connect() as conn: result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) - version = result.scalar() - assert version is None + first_version = result.scalar() + assert first_version is None # Upgrade to head again command.upgrade(alembic_cfg, "head") @@ -136,8 +136,8 @@ def test_multiple_migrations(temp_db_url): # Verify back at head with engine.connect() as conn: result = conn.execute(text("SELECT version_num FROM ell_alembic_version")) - version = result.scalar() - assert version == "4524fb60d23e" + new_version = result.scalar() + assert version == new_version def test_migration_idempotency(temp_db_url): """Test that running migrations multiple times is idempotent""" From dbf6f755ff43e4666dfe96629f4c6b53595559be Mon Sep 17 00:00:00 2001 From: William Guss Date: Mon, 18 Nov 2024 17:01:16 -0800 Subject: [PATCH 3/8] deleting datasets --- .../dataset/37/a6/259cc0c1dae299a7866489dff0bd | Bin 53 -> 0 bytes .../dataset/b0/30/006b792b14d36006781226b8568c | Bin 101 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 examples/logdir/dataset/37/a6/259cc0c1dae299a7866489dff0bd delete mode 100644 examples/logdir/dataset/b0/30/006b792b14d36006781226b8568c diff --git a/examples/logdir/dataset/37/a6/259cc0c1dae299a7866489dff0bd b/examples/logdir/dataset/37/a6/259cc0c1dae299a7866489dff0bd deleted file mode 100644 index fdc68081be5e4494f0c3c37cbb08bd8b088023be..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 53 zcmb2|=HS?EX`0UT-^kQ5IoTlDFeNe7$kH;=+``Pv#KJNqEzKY)h2gaJ*^`V6{(nxZ JvM?|(006X15ElRd diff --git a/examples/logdir/dataset/b0/30/006b792b14d36006781226b8568c b/examples/logdir/dataset/b0/30/006b792b14d36006781226b8568c deleted file mode 100644 index b52b711307aca475a24cab2fc745aaa15c4fb8e6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 101 zcmb2|=HS?BX`0UT-@w2u$=uQ?$WsFAZs4Y% z4mX3TOrMIiiiN$6req~&mx^pyU3k)8|Csvwnc Date: Mon, 18 Nov 2024 17:13:43 -0800 Subject: [PATCH 4/8] raedme --- .gitignore | 1 + src/ell/stores/migrations/README | 49 +++++++++++++++++++++++++++++++- src/ell/stores/sql.py | 16 ++++++----- 3 files changed, 58 insertions(+), 8 deletions(-) diff --git a/.gitignore b/.gitignore index 8c728acef..e2063d8c3 100644 --- a/.gitignore +++ b/.gitignore @@ -39,6 +39,7 @@ wheels/ share/python-wheels/ *.egg-info/ .installed.cfg +dataset/* *.egg MANIFEST diff --git a/src/ell/stores/migrations/README b/src/ell/stores/migrations/README index 98e4f9c44..4be64decb 100644 --- a/src/ell/stores/migrations/README +++ b/src/ell/stores/migrations/README @@ -1 +1,48 @@ -Generic single-database configuration. \ No newline at end of file +# ell Database Migrations + +This directory contains the database migration utilities for ell's SQL storage backend. The migration system uses Alembic to handle schema changes and version control for the database. + +## Overview + +The migration system handles: +- Initial schema creation +- Schema updates and changes +- Version tracking of database changes +- Automatic migration detection and application + +## Key Components + +- `versions/`: Contains individual migration scripts +- `env.py`: Alembic environment configuration +- `script.py.mako`: Template for generating new migrations +- `make.py`: Utility script for creating new migrations + +## Usage + +### Creating a New Migration +```bash +python -m ell.stores.migrations.make "your migration message" +``` + +This will: +1. Create a temporary SQLite database +2. Detect schema changes +3. Generate a new migration file in the versions directory + +### Applying Migrations + +Migrations are automatically handled by the `init_or_migrate_database()` function in `ell.stores.sql`. When initializing an ell store, it will: + +1. Check for existing tables +2. Apply any pending migrations +3. Initialize new databases with the latest schema + +## Migration Files + +Each migration file contains: +- Unique revision ID +- Dependencies on other migrations +- `upgrade()` function for applying changes +- `downgrade()` function for reverting changes + +For examples, see the existing migrations in the `versions/` directory. \ No newline at end of file diff --git a/src/ell/stores/sql.py b/src/ell/stores/sql.py index e8fcb3aba..22f3dd451 100644 --- a/src/ell/stores/sql.py +++ b/src/ell/stores/sql.py @@ -52,31 +52,34 @@ def init_or_migrate_database(engine) -> None: has_alembic = 'ell_alembic_version' in existing_tables alembic_cfg = get_alembic_config(engine.url) - try: if has_our_tables and not has_alembic: # Case 1: Existing database with our tables but no Alembic # This is likely a database from version <= 0.14 - logger.info("Found existing ell tables without Alembic. Stamping with initial migration.") - + logger.debug("Found existing tables but no Alembic - stamping with initial migration") command.stamp(alembic_cfg, "4524fb60d23e") # Verify table was created after_tables = set(inspect(engine).get_table_names()) - # import code; code.interact(local=dict(globals(), **locals())) + logger.debug(f"Tables after stamp: {after_tables}") + # Check if version table has our stamp with engine.connect() as connection: version_result = connection.execute(text("SELECT version_num FROM ell_alembic_version")).first() if not version_result or version_result[0] != "4524fb60d23e": raise RuntimeError("Failed to stamp database - version table empty or incorrect version") + logger.debug(f"Successfully stamped database with version {version_result[0]}") - - elif has_alembic: + has_alembic = True + + if has_alembic: # Case 2: Database has Alembic - run any pending migrations + logger.debug("Running any pending Alembic migrations") command.upgrade(alembic_cfg, "head") else: # Case 3: New database or database without our tables + logger.debug("New database detected - creating schema and stamping with latest migration") # Create all tables according to current schema SQLModel.metadata.create_all(engine) # Stamp with latest migration @@ -85,7 +88,6 @@ def init_or_migrate_database(engine) -> None: except Exception as e: logger.error(f"Failed to initialize/migrate database: {e}") raise - class SQLStore(ell.stores.store.Store): def __init__(self, db_uri: str, blob_store: Optional[ell.stores.store.BlobStore] = None): From 7adbe02b4e388bd6bcbb4a5af4d75eb2bcbf166f Mon Sep 17 00:00:00 2001 From: William Guss Date: Mon, 18 Nov 2024 17:14:12 -0800 Subject: [PATCH 5/8] no database --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index e2063d8c3..60e511a4a 100644 --- a/.gitignore +++ b/.gitignore @@ -313,3 +313,4 @@ static/ *.db-shm *.db-wal .aider* +examples/logdir From a8b88d295368d052535ca0bca64e848350fc9a39 Mon Sep 17 00:00:00 2001 From: William Guss Date: Mon, 18 Nov 2024 17:18:16 -0800 Subject: [PATCH 6/8] moving and cleaning things --- src/ell/stores/migrations/__init__.py | 80 +++++++++++++++++++++++++++ src/ell/stores/migrations/env.py | 3 + src/ell/stores/migrations/make.py | 2 +- src/ell/stores/sql.py | 75 +------------------------ tests/test_migrations.py | 2 +- 5 files changed, 86 insertions(+), 76 deletions(-) create mode 100644 src/ell/stores/migrations/__init__.py diff --git a/src/ell/stores/migrations/__init__.py b/src/ell/stores/migrations/__init__.py new file mode 100644 index 000000000..14602592c --- /dev/null +++ b/src/ell/stores/migrations/__init__.py @@ -0,0 +1,80 @@ + +from alembic import command +from alembic.config import Config +from sqlalchemy import inspect, text +from pathlib import Path + +from sqlmodel import Session, SQLModel, create_engine, select +import logging + +logger = logging.getLogger(__name__) + +def get_alembic_config(engine_url: str) -> Config: + """Create Alembic config programmatically""" + alembic_cfg = Config() + migrations_dir = Path(__file__).parent + + alembic_cfg.set_main_option("script_location", str(migrations_dir)) + alembic_cfg.set_main_option("sqlalchemy.url", str(engine_url)) + alembic_cfg.set_main_option("version_table", "ell_alembic_version") + alembic_cfg.set_main_option("timezone", "UTC") + + return alembic_cfg + +def init_or_migrate_database(engine) -> None: + """Initialize or migrate database with ELL schema + + Handles three cases: + 1. Existing database with our tables but no Alembic -> stamp with initial migration + 2. Database with Alembic -> upgrade to head + 3. New/empty database or database without our tables -> create tables and stamp with head + + Args: + engine_or_url: SQLAlchemy engine or database URL string + """ + inspector = inspect(engine) + + # Check database state + our_tables_v1 = {'serializedlmp', 'invocation', 'invocationcontents', + 'invocationtrace', 'serializedlmpuses'} + existing_tables = set(inspector.get_table_names()) + has_our_tables = bool(our_tables_v1 & existing_tables) # Intersection + has_alembic = 'ell_alembic_version' in existing_tables + + alembic_cfg = get_alembic_config(engine.url) + try: + if has_our_tables and not has_alembic: + # Case 1: Existing database with our tables but no Alembic + # This is likely a database from version <= 0.14 + logger.debug("Found existing tables but no Alembic - stamping with initial migration") + + command.stamp(alembic_cfg, "4524fb60d23e") + # Verify table was created + after_tables = set(inspect(engine).get_table_names()) + logger.debug(f"Tables after stamp: {after_tables}") + + # Check if version table has our stamp + with engine.connect() as connection: + version_result = connection.execute(text("SELECT version_num FROM ell_alembic_version")).first() + if not version_result or version_result[0] != "4524fb60d23e": + raise RuntimeError("Failed to stamp database - version table empty or incorrect version") + logger.debug(f"Successfully stamped database with version {version_result[0]}") + + has_alembic = True + + if has_alembic: + # Case 2: Database has Alembic - run any pending migrations + logger.debug("Running any pending Alembic migrations") + command.upgrade(alembic_cfg, "head") + + else: + # Case 3: New database or database without our tables + logger.debug("New database detected - creating schema and stamping with latest migration") + # Create all tables according to current schema + SQLModel.metadata.create_all(engine) + # Stamp with latest migration + command.stamp(alembic_cfg, "head") + + except Exception as e: + logger.error(f"Failed to initialize/migrate database: {e}") + raise diff --git a/src/ell/stores/migrations/env.py b/src/ell/stores/migrations/env.py index aa284ef50..bf2dc98e2 100644 --- a/src/ell/stores/migrations/env.py +++ b/src/ell/stores/migrations/env.py @@ -42,6 +42,7 @@ def run_migrations_offline() -> None: script output. """ + #XXX: These are currently untested and unused. url = config.get_main_option("sqlalchemy.url") version_table = config.get_main_option("version_table", "ell_alembic_version") @@ -68,6 +69,8 @@ def run_migrations_online() -> None: and associate a connection with the context. """ + + #XXX: These are currently untested and unused. connectable = engine_from_config( config.get_section(config.config_ini_section, {}), prefix="sqlalchemy.", diff --git a/src/ell/stores/migrations/make.py b/src/ell/stores/migrations/make.py index 6193aea60..fec1aaac3 100644 --- a/src/ell/stores/migrations/make.py +++ b/src/ell/stores/migrations/make.py @@ -1,6 +1,6 @@ import argparse from sqlalchemy import create_engine -from ell.stores.sql import get_alembic_config +from ell.stores.migrations import get_alembic_config from alembic import command def main(): diff --git a/src/ell/stores/sql.py b/src/ell/stores/sql.py index 22f3dd451..ebfbb9ab5 100644 --- a/src/ell/stores/sql.py +++ b/src/ell/stores/sql.py @@ -3,6 +3,7 @@ from pathlib import Path from typing import Any, Optional, Dict, List, Set from sqlmodel import Session, SQLModel, create_engine, select +from ell.stores.migrations import init_or_migrate_database import ell.stores.store from sqlalchemy.sql import text from ell.stores.studio import InvocationTrace, SerializedLMP, Invocation @@ -11,84 +12,10 @@ import gzip import json -from alembic import command -from alembic.config import Config -from sqlalchemy import inspect - import logging logger = logging.getLogger(__name__) -def get_alembic_config(engine_url: str) -> Config: - """Create Alembic config programmatically""" - alembic_cfg = Config() - migrations_dir = Path(__file__).parent / "migrations" - - alembic_cfg.set_main_option("script_location", str(migrations_dir)) - alembic_cfg.set_main_option("sqlalchemy.url", str(engine_url)) - alembic_cfg.set_main_option("version_table", "ell_alembic_version") - alembic_cfg.set_main_option("timezone", "UTC") - - return alembic_cfg - -def init_or_migrate_database(engine) -> None: - """Initialize or migrate database with ELL schema - - Handles three cases: - 1. Existing database with our tables but no Alembic -> stamp with initial migration - 2. Database with Alembic -> upgrade to head - 3. New/empty database or database without our tables -> create tables and stamp with head - - Args: - engine_or_url: SQLAlchemy engine or database URL string - """ - inspector = inspect(engine) - - # Check database state - our_tables_v1 = {'serializedlmp', 'invocation', 'invocationcontents', - 'invocationtrace', 'serializedlmpuses'} - existing_tables = set(inspector.get_table_names()) - has_our_tables = bool(our_tables_v1 & existing_tables) # Intersection - has_alembic = 'ell_alembic_version' in existing_tables - - alembic_cfg = get_alembic_config(engine.url) - try: - if has_our_tables and not has_alembic: - # Case 1: Existing database with our tables but no Alembic - # This is likely a database from version <= 0.14 - logger.debug("Found existing tables but no Alembic - stamping with initial migration") - - command.stamp(alembic_cfg, "4524fb60d23e") - # Verify table was created - after_tables = set(inspect(engine).get_table_names()) - logger.debug(f"Tables after stamp: {after_tables}") - - # Check if version table has our stamp - with engine.connect() as connection: - version_result = connection.execute(text("SELECT version_num FROM ell_alembic_version")).first() - if not version_result or version_result[0] != "4524fb60d23e": - raise RuntimeError("Failed to stamp database - version table empty or incorrect version") - logger.debug(f"Successfully stamped database with version {version_result[0]}") - - has_alembic = True - - if has_alembic: - # Case 2: Database has Alembic - run any pending migrations - logger.debug("Running any pending Alembic migrations") - command.upgrade(alembic_cfg, "head") - - else: - # Case 3: New database or database without our tables - logger.debug("New database detected - creating schema and stamping with latest migration") - # Create all tables according to current schema - SQLModel.metadata.create_all(engine) - # Stamp with latest migration - command.stamp(alembic_cfg, "head") - - except Exception as e: - logger.error(f"Failed to initialize/migrate database: {e}") - raise - class SQLStore(ell.stores.store.Store): def __init__(self, db_uri: str, blob_store: Optional[ell.stores.store.BlobStore] = None): # XXX: Use Serialization serialzie_object in incoming PR. diff --git a/tests/test_migrations.py b/tests/test_migrations.py index a50f85766..ebb0cf190 100644 --- a/tests/test_migrations.py +++ b/tests/test_migrations.py @@ -5,7 +5,7 @@ from sqlalchemy import inspect, MetaData, create_engine, text from sqlmodel import SQLModel -from ell.stores.sql import init_or_migrate_database, get_alembic_config +from ell.stores.migrations import init_or_migrate_database, get_alembic_config from alembic import command from alembic.config import Config From 852cf5c418e73764decceae6216ceb4c3630002f Mon Sep 17 00:00:00 2001 From: William Guss Date: Mon, 18 Nov 2024 17:20:31 -0800 Subject: [PATCH 7/8] udpating pyproject toml with alembic optional dependecy --- poetry.lock | 60 +++++++++++++++++++++++++++++++++++++++++--------- pyproject.toml | 1 + 2 files changed, 50 insertions(+), 11 deletions(-) diff --git a/poetry.lock b/poetry.lock index 11eb7ed99..86afded79 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,6 +11,25 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] +[[package]] +name = "alembic" +version = "1.14.0" +description = "A database migration tool for SQLAlchemy." +optional = true +python-versions = ">=3.8" +files = [ + {file = "alembic-1.14.0-py3-none-any.whl", hash = "sha256:99bd884ca390466db5e27ffccff1d179ec5c05c965cfefc0607e69f9e411cb25"}, + {file = "alembic-1.14.0.tar.gz", hash = "sha256:b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b"}, +] + +[package.dependencies] +Mako = "*" +SQLAlchemy = ">=1.3.0" +typing-extensions = ">=4" + +[package.extras] +tz = ["backports.zoneinfo"] + [[package]] name = "annotated-types" version = "0.7.0" @@ -625,13 +644,13 @@ files = [ [[package]] name = "httpcore" -version = "1.0.6" +version = "1.0.7" description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" files = [ - {file = "httpcore-1.0.6-py3-none-any.whl", hash = "sha256:27b59625743b85577a8c0e10e55b50b5368a4f2cfe8cc7bcfa9cf00829c2682f"}, - {file = "httpcore-1.0.6.tar.gz", hash = "sha256:73f6dbd6eb8c21bbf7ef8efad555481853f5f6acdeaff1edb0694289269ee17f"}, + {file = "httpcore-1.0.7-py3-none-any.whl", hash = "sha256:a3fff8f43dc260d5bd363d9f9cf1830fa3a458b332856f34282de498ed420edd"}, + {file = "httpcore-1.0.7.tar.gz", hash = "sha256:8551cb62a169ec7162ac7be8d4817d561f60e08eaa485234898414bb5a8a0b4c"}, ] [package.dependencies] @@ -916,6 +935,25 @@ files = [ {file = "jiter-0.7.1.tar.gz", hash = "sha256:448cf4f74f7363c34cdef26214da527e8eeffd88ba06d0b80b485ad0667baf5d"}, ] +[[package]] +name = "mako" +version = "1.3.6" +description = "A super-fast templating language that borrows the best ideas from the existing templating languages." +optional = true +python-versions = ">=3.8" +files = [ + {file = "Mako-1.3.6-py3-none-any.whl", hash = "sha256:a91198468092a2f1a0de86ca92690fb0cfc43ca90ee17e15d93662b4c04b241a"}, + {file = "mako-1.3.6.tar.gz", hash = "sha256:9ec3a1583713479fae654f83ed9fa8c9a4c16b7bb0daba0e6bbebff50c0d983d"}, +] + +[package.dependencies] +MarkupSafe = ">=0.9.2" + +[package.extras] +babel = ["Babel"] +lingua = ["lingua"] +testing = ["pytest"] + [[package]] name = "markdown-it-py" version = "3.0.0" @@ -2080,13 +2118,13 @@ telegram = ["requests"] [[package]] name = "typer" -version = "0.13.0" +version = "0.13.1" description = "Typer, build great CLIs. Easy to code. Based on Python type hints." optional = true python-versions = ">=3.7" files = [ - {file = "typer-0.13.0-py3-none-any.whl", hash = "sha256:d85fe0b777b2517cc99c8055ed735452f2659cd45e451507c76f48ce5c1d00e2"}, - {file = "typer-0.13.0.tar.gz", hash = "sha256:f1c7198347939361eec90139ffa0fd8b3df3a2259d5852a0f7400e476d95985c"}, + {file = "typer-0.13.1-py3-none-any.whl", hash = "sha256:5b59580fd925e89463a29d363e0a43245ec02765bde9fb77d39e5d0f29dd7157"}, + {file = "typer-0.13.1.tar.gz", hash = "sha256:9d444cb96cc268ce6f8b94e13b4335084cef4c079998a9f4851a90229a3bd25c"}, ] [package.dependencies] @@ -2393,14 +2431,14 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", type = ["pytest-mypy"] [extras] -all = ["anthropic", "fastapi", "groq", "sqlmodel", "uvicorn"] +all = ["alembic", "anthropic", "fastapi", "groq", "sqlmodel", "uvicorn"] anthropic = ["anthropic"] groq = ["groq"] -postgres = ["psycopg2", "sqlmodel"] -sqlite = ["sqlmodel"] -studio = ["fastapi", "sqlmodel", "uvicorn"] +postgres = ["alembic", "psycopg2", "sqlmodel"] +sqlite = ["alembic", "sqlmodel"] +studio = ["alembic", "fastapi", "sqlmodel", "uvicorn"] [metadata] lock-version = "2.0" python-versions = ">=3.9" -content-hash = "cda598b413c36ec9c4b7ca2091e0eec61c45db0ed75962d0456197fc25a91b1d" +content-hash = "edacdfbe26e995a2e7ea2844c917e2a42c9f3e347b26a19c48405128ba9a187e" diff --git a/pyproject.toml b/pyproject.toml index 687fe743b..eb9d23663 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,6 +47,7 @@ sqlmodel = { version = ">=0.0.21, <0.1.0", optional = true } fastapi = { version = "^0.111.1", optional = true } uvicorn = { version = "^0.30.3", optional = true } +alembic = { version = "^1.14.0", optional = true } [tool.poetry.group.dev.dependencies] pytest = "^8.3.2" sphinx = "<8.0.0" From db4db0649393a4251f1aa9bb774383c95dcad4ac Mon Sep 17 00:00:00 2001 From: William Guss Date: Mon, 18 Nov 2024 17:24:00 -0800 Subject: [PATCH 8/8] . --- src/ell/stores/migrations/env.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ell/stores/migrations/env.py b/src/ell/stores/migrations/env.py index bf2dc98e2..fcfa72a99 100644 --- a/src/ell/stores/migrations/env.py +++ b/src/ell/stores/migrations/env.py @@ -5,7 +5,6 @@ from alembic import context from sqlmodel import SQLModel -from ell.types.studio import * # this is the Alembic Config object, which provides