migration bug-fixes

metacatalog_api/db.py

@@ -37,25 +37,11 @@ def get_db_version(session: Session, schema: str = 'public') -> dict:
     return {'db_version': v}
 
 
-def check_db_version(session: Session, schema: str = 'public') -> bool:
-    """Verify that the database version matches the expected version.
-    
-    Args:
-        session: A SQLAlchemy session object
-        
-    Raises:
-        ValueError: If database version doesn't match DB_VERSION constant
-
-    Returns:
-        bool: True if database version matches
-    """
+def has_version_mismatch(session: Session, schema: str = 'public') -> bool:
     remote_db_version = get_db_version(session, schema=schema)['db_version']
     if remote_db_version != DB_VERSION:
-        raise ValueError(
-            f"Database version mismatch. Expected {DB_VERSION}, got {remote_db_version}. "
-            "Please run database migrations to update your schema."
-        )
-    return True
+        return True
+    return False
 
 
 def install(session: Session, schema: str = 'public', populate_defaults: bool = True) -> None:

metacatalog_api/server.py

@@ -10,40 +10,6 @@
 from metacatalog_api.db import DB_VERSION
 
 
-logger = logging.getLogger('uvicorn.error')
-
-# before we initialize the app, we check that the database is installed and up to date
-@asynccontextmanager
-async def lifespan(app: FastAPI):
-    # check if the entries table can be found in the database
-    with core.connect() as session:
-        if not core.db.check_installed(session):
-            logger.info("Database not installed, installing...")
-            core.db.install(session, populate_defaults=True)
-            logger.info("Database installed.")
-
-    # after checking the database, we check the version
-    with core.connect() as session:
-        core.db.check_db_version(session)
-
-    # now we yield the application
-    yield
-
-    # here we can app tear down code - i.e. a log message
-
-# build the base app
-app = FastAPI(lifespan=lifespan)
-
-@app.get('/version')
-def get_version(request: Request):
-    return {
-        "metacatalog_api": __version__,
-        "db_version": DB_VERSION,
-        "hostname": request.url.hostname,
-        "port": request.url.port,
-        "root_path": request.url.path
-    }
-
 class Server(BaseSettings):
     model_config = SettingsConfigDict(
         cli_parse_args=True, 
@@ -54,6 +20,7 @@ class Server(BaseSettings):
     root_path: str = ""
     reload: bool = False
     app_name: str = "explorer"
+    autoupgrade: bool = False
 
     @property
     def uri_prefix(self):
@@ -79,9 +46,48 @@ def cli_cmd(self, asgi_app: str):
         """Start the uvicorn server"""
         uvicorn.run(asgi_app, host=self.host, port=self.port, root_path=self.root_path, reload=self.reload)
 
+logger = logging.getLogger('uvicorn.error')
+
 # create the server object
 server = Server()
 logger.info(server.uri_prefix, server.root_path, server.app_name)
 
+
+# before we initialize the app, we check that the database is installed and up to date
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    # check if the entries table can be found in the database
+    with core.connect() as session:
+        if not core.db.check_installed(session):
+            logger.info("Database not installed, installing...")
+            core.db.install(session, populate_defaults=True)
+            logger.info("Database installed.")
+
+    # after checking the database, we check the version
+    with core.connect() as session:
+            if core.db.has_version_mismatch(session):
+                if server.autoupgrade:
+                    core.migrate_db()
+                else:
+                    raise ValueError(f"Database version mismatch. Expected version {core.db.DB_VERSION}. Please run database migrations to update your schema.")
+
+    # now we yield the application
+    yield
+
+    # here we can app tear down code - i.e. a log message
+
+# build the base app
+app = FastAPI(lifespan=lifespan)
+
+@app.get('/version')
+def get_version(request: Request):
+    return {
+        "metacatalog_api": __version__,
+        "db_version": DB_VERSION,
+        "hostname": request.url.hostname,
+        "port": request.url.port,
+        "root_path": request.url.path
+    }
+
 if __name__ == "__main__":
     print("The main server is not meant to be run directly. Check default_server.py for a sample application")

metacatalog_api/sql/migrate/migration_3.sql

@@ -1,6 +1,6 @@
 -- change the entryGroup types
-ALTER TABLE {schema}.entrygroup_types ALTER COLUMN name type TEXT NOT NULL;
-ALTER TABLE {schema}.entrygroup_types ALTER COLUMN description type TEXT NOT NULL;
+ALTER TABLE {schema}.entrygroup_types ALTER COLUMN name type TEXT;
+ALTER TABLE {schema}.entrygroup_types ALTER COLUMN description type TEXT;
 
 -- add new entry-group types
 INSERT INTO {schema}.entrygroup_types VALUES (5, 'Dataset', 'A Dataset collects different self-contained entries (usually of different variables) that belong together. Other than composites, the single entries are self-contained and can be loaded individually.');