Merge pull request #46 from princeton-ddss/43-migrate-database-on-sta…

…rt-up

43 migrate database on start up

.gitignore

@@ -89,7 +89,6 @@ target/
 # Database
 *.sqlite
 *.sqlite3
-src/migrations
 
 # GitHub pages
 site/

src/app/__init__.py

@@ -13,6 +13,7 @@
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from litestar import Litestar, get, post, put, delete
+from litestar.utils.module_loader import module_to_os_path
 from litestar.datastructures import State
 from litestar.dto import DTOConfig, DataclassDTO
 from advanced_alchemy.extensions.litestar import (
@@ -401,14 +402,18 @@ async def get_image_details():
 
 session_config = AsyncSessionConfig(expire_on_commit=False)
 
+BASE_DIR = module_to_os_path("app")
+
 db_config = SQLAlchemyAsyncConfig(
-    connection_string="sqlite+aiosqlite:///app.sqlite",
+    connection_string=(
+        f"sqlite+aiosqlite:///{blackfish_config.BLACKFISH_HOME_DIR}/app.sqlite"
+    ),
     metadata=UUIDAuditBase.metadata,
     create_all=True,
     alembic_config=AlembicAsyncConfig(
         version_table_name="ddl_version",
-        script_config="migrations/alembic.ini",
-        script_location="migrations",
+        script_config=f"{BASE_DIR}/db/migrations/alembic.ini",
+        script_location=f"{BASE_DIR}/db/migrations",
     ),
 )
 

src/app/cli/__main__.py

@@ -14,7 +14,8 @@
     update_profile,
     delete_profile,
 )
-from app.config import config, SlurmRemote
+from app.config import config
+from app.logger import logger
 
 """
 The CLI serves as a client to access the API from as well as performing
@@ -91,71 +92,36 @@ def start(reload: bool, profile: str) -> None:  # pragma: no cover
     "Start the blackfish app."
 
     import uvicorn
+    from advanced_alchemy.extensions.litestar.alembic import AlembicCommands
+    from sqlalchemy.exc import OperationalError
+
     from app import __file__
+    from app import app
 
     if not os.path.isdir(config.BLACKFISH_HOME_DIR):
         click.echo("Home directory not found. Have you run `blackfish init`?")
         return
 
-    if profile is None:
-        # TODO: migrate_db()
-        # TODO: update models table
-        uvicorn.run(
-            "app:app",
-            host=config.BLACKFISH_HOST,
-            port=config.BLACKFISH_PORT,
-            log_level="info",
-            app_dir=os.path.abspath(os.path.join(__file__, "..", "..")),
-            reload_dirs=os.path.abspath(os.path.join(__file__, "..")),
-            reload=reload,
-        )
-        # _ = subprocess.check_output(
-        #     [
-        #         sys.executable,
-        #         "-m",
-        #         "uvicorn",
-        #         "--host",
-        #         config.BLACKFISH_HOST,
-        #         "--port",
-        #         str(config.BLACKFISH_PORT),
-        #         "--log-level",
-        #         "info",
-        #         "--reload",
-        #         "--app-dir",
-        #         os.path.abspath(os.path.join(app.__file__, "..", "..")),
-        #         "app:app",
-        #     ]
-        # )
-        # _ = subprocess.check_output(
-        #     [
-        #         "litestar",
-        #         "--app-dir",
-        #         os.path.abspath(os.path.join(app.__file__, "..", "..")),
-        #         "run",
-        #         "--reload"
-        #     ]
-        # )
-    else:
-        # TODO: running Blackfish remotely
-        profile = config.BLACKFISH_PROFILES[profile]
-        if isinstance(profile, SlurmRemote):
-            raise NotImplementedError
-            # _ = subprocess.check_output(
-            #     [
-            #         "ssh",
-            #         f"{profile['user']}@{profile['host']}",
-            #         "uvicorn",
-            #         "--port",
-            #         profile['port'],
-            #         "--log-level",
-            #         "info",
-            #         "--reload",
-            #         reload,
-            #     ]
-            # )
+    alembic_commands = AlembicCommands(app=app)
+
+    try:
+        logger.info("Upgrading database...")
+        alembic_commands.upgrade()
+    except OperationalError as e:
+        if e.args == ("(sqlite3.OperationalError) table service already exists",):
+            logger.info("Database is already up-to-date. Skipping.")
         else:
-            raise NotImplementedError
-        raise NotImplementedError
+            logger.error(f"Failed to upgrade database: {e}")
+
+    uvicorn.run(
+        "app:app",
+        host=config.BLACKFISH_HOST,
+        port=config.BLACKFISH_PORT,
+        log_level="info",
+        app_dir=os.path.abspath(os.path.join(__file__, "..", "..")),
+        reload_dirs=os.path.abspath(os.path.join(__file__, "..")),
+        reload=reload,
+    )
 
 
 # blackfish run [OPTIONS] COMMAND

src/app/db/migrations/versions/2024-09-17_v0.1.0_6f8469490c8e.py

@@ -0,0 +1,90 @@
+# type: ignore
+"""v0.1.0
+
+Revision ID: 6f8469490c8e
+Revises: 57e64d3a65ea
+Create Date: 2024-09-17 14:57:00.346660+00:00
+
+"""
+from __future__ import annotations
+
+import warnings
+from typing import TYPE_CHECKING
+
+import sqlalchemy as sa
+from alembic import op
+from advanced_alchemy.types import (
+    EncryptedString,
+    EncryptedText,
+    GUID,
+    ORA_JSONB,
+    DateTimeUTC,
+)
+
+if TYPE_CHECKING:
+    pass
+
+__all__ = [
+    "downgrade",
+    "upgrade",
+    "schema_upgrades",
+    "schema_downgrades",
+    "data_upgrades",
+    "data_downgrades",
+]
+
+sa.GUID = GUID
+sa.DateTimeUTC = DateTimeUTC
+sa.ORA_JSONB = ORA_JSONB
+sa.EncryptedString = EncryptedString
+sa.EncryptedText = EncryptedText
+
+# revision identifiers, used by Alembic.
+revision = "6f8469490c8e"
+down_revision = "57e64d3a65ea"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=UserWarning)
+        with op.get_context().autocommit_block():
+            schema_upgrades()
+            data_upgrades()
+
+
+def downgrade() -> None:
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=UserWarning)
+        with op.get_context().autocommit_block():
+            data_downgrades()
+            schema_downgrades()
+
+
+def schema_upgrades() -> None:
+    """schema upgrade migrations go here."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("service", schema=None) as batch_op:
+        batch_op.alter_column("user", existing_type=sa.VARCHAR(), nullable=True)
+        batch_op.alter_column("port", existing_type=sa.INTEGER(), nullable=True)
+
+    # ### end Alembic commands ###
+
+
+def schema_downgrades() -> None:
+    """schema downgrade migrations go here."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("service", schema=None) as batch_op:
+        batch_op.alter_column("port", existing_type=sa.INTEGER(), nullable=False)
+        batch_op.alter_column("user", existing_type=sa.VARCHAR(), nullable=False)
+
+    # ### end Alembic commands ###
+
+
+def data_upgrades() -> None:
+    """Add any optional data upgrade migrations here!"""
+
+
+def data_downgrades() -> None:
+    """Add any optional data downgrade migrations here!"""