Merge branch 'feat/database-version-control' into feat/metadata

database.py

@@ -165,9 +165,9 @@ def __init__(self, mercury_db_path: str, user_db_path: str):
         print("Open db at ", mercury_db_path)
         version = mercury_db.execute("SELECT value FROM config WHERE key = 'version'").fetchone()
         if version is None:
-            mercury_db.execute("INSERT INTO config (key, value) VALUES ('version', ?)", (__version__,))
-        else:
-            if version[0] != __version__:
+            print("Can not determine database version.")
+            exit(1)
+        elif version[0] != __version__:
                 print("Database version mismatch. Please migrate the database.")
                 exit(1)
         mercury_db.execute("CREATE TABLE IF NOT EXISTS annotations (\

ingester.py

@@ -116,7 +116,7 @@ def prepare_db(self):
             f"CREATE VIRTUAL TABLE IF NOT EXISTS chunks USING vec0(chunk_id INTEGER PRIMARY KEY, text TEXT, text_type TEXT, sample_id INTEGER, char_offset INTEGER, chunk_offset INTEGER, embedding float[{self.embedding_dimension}])"
         )
         self.db.execute(
-            "CREATE TABLE IF NOT EXISTS config (key TEXT PRIMARY KEY, value TEXT)"
+            "CREATE TABLE IF NOT EXISTS config (key TEXT PRIMARY KEY UNIQUE , value TEXT)"
         )
         self.db.execute(
             "CREATE TABLE IF NOT EXISTS sample_meta (sample_id INTEGER PRIMARY KEY, json_meta TEXT)"

migration/database_version_control.py

@@ -0,0 +1,27 @@
+import argparse
+import sqlite3
+
+
+class Migrator:
+    def __init__(self, db_path):
+        conn = sqlite3.connect(db_path)
+        self.conn = conn
+        version = self.conn.execute("SELECT count(*) FROM config WHERE key = 'version'").fetchone()
+        if version[0] != 0:
+            print("Can not migrate database with existing version")
+            exit(0)
+
+    def migrate(self):
+        self.conn.execute("ALTER TABLE config RENAME TO config_old")
+        self.conn.execute("CREATE TABLE config(key TEXT PRIMARY KEY UNIQUE , value TEXT)")
+        self.conn.execute("INSERT INTO config SELECT key, value FROM config_old")
+        self.conn.execute("INSERT INTO config VALUES ('version', '0.1.0')")
+        self.conn.commit()
+        print("Migration completed")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Migrate the database to 0.1.0")
+    parser.add_argument("--db_path", help="Path to the database", default="../mercury.sqlite")
+    args = parser.parse_args()
+    migrator = Migrator(args.db_path)
+    migrator.migrate()