Add command line tool for updating Murfey database tables (#205)

setup.cfg

@@ -37,6 +37,7 @@ console_scripts =
     murfey.simulate = murfey.cli.dummy:run
     murfey.transfer = murfey.cli.transfer:run
     murfey.sessions = murfey.cli.db_sessions:run
+    murfey.create_db = murfey.cli.create_db:run
 
 [options.extras_require]
 server =

src/murfey/cli/create_db.py

@@ -0,0 +1,36 @@
+import argparse
+import os
+
+from murfey.util.db import clear, setup
+
+
+def run():
+    parser = argparse.ArgumentParser(
+        description="Generate the necessary tables for the Murfey database"
+    )
+
+    parser.add_argument(
+        "--no-clear",
+        dest="clear",
+        default=True,
+        action="store_false",
+        help="Do not clear current database tables before creating specified tables",
+    )
+    parser.add_argument(
+        "-m",
+        "--microscope",
+        dest="microscope",
+        type=str,
+        default="",
+        help="Microscope as specified in the Murfey machine configuration",
+    )
+
+    args = parser.parse_args()
+    if args.microscope:
+        os.environ["BEAMLINE"] = args.microscope
+
+    from murfey.server.murfey_db import url
+
+    if args.clear:
+        clear(url())
+    setup(url())

src/murfey/util/db.py

@@ -1,5 +1,6 @@
 from typing import List, Optional
 
+import sqlalchemy
 from sqlmodel import Field, Relationship, SQLModel, create_engine
 
 
@@ -341,3 +342,11 @@ class Class3D(SQLModel, table=True):  # type: ignore
 def setup(url: str):
     engine = create_engine(url)
     SQLModel.metadata.create_all(engine)
+
+
+def clear(url: str):
+    engine = create_engine(url)
+    metadata = sqlalchemy.MetaData(engine)
+    metadata.reflect()
+
+    metadata.drop_all(engine)