Moved 'sanitise()' and 'sanitise_path()' from 'murfey.server.__init__' to 'murfey.util.__init__'

Author: tieneupin

src/murfey/server/__init__.py

@@ -40,7 +40,6 @@
 )
 from sqlalchemy.orm.exc import ObjectDeletedError
 from sqlmodel import Session, create_engine, select
-from werkzeug.utils import secure_filename
 from workflows import Error as WorkflowsError
 from workflows.transport.pika_transport import PikaTransport
 
@@ -49,7 +48,7 @@
 import murfey.util.db as db
 from murfey.server.ispyb import ISPyBSession, get_session_id
 from murfey.server.murfey_db import url  # murfey_db
-from murfey.util import LogFilter
+from murfey.util import LogFilter, sanitise
 from murfey.util.config import (
     MachineConfig,
     get_hostname,
@@ -94,14 +93,6 @@ class JobIDs(NamedTuple):
     appid: int
 
 
-def sanitise(in_string: str) -> str:
-    return in_string.replace("\r\n", "").replace("\n", "")
-
-
-def sanitise_path(in_path: Path) -> Path:
-    return Path("/".join(secure_filename(p) for p in in_path.parts))
-
-
 def get_angle(tilt_file_name: str) -> float:
     for p in Path(tilt_file_name).name.split("_"):
         if "." in p:

src/murfey/server/api/auth.py

@@ -16,8 +16,8 @@
 from pydantic import BaseModel
 from sqlmodel import Session, create_engine, select
 
-from murfey.server import sanitise
 from murfey.server.murfey_db import murfey_db, url
+from murfey.util import sanitise
 from murfey.util.config import get_security_config
 from murfey.util.db import MurfeyUser as User
 from murfey.util.db import Session as MurfeySession

src/murfey/server/api/bootstrap.py

@@ -29,7 +29,8 @@
 from fastapi.responses import FileResponse, HTMLResponse, StreamingResponse
 
 import murfey
-from murfey.server import get_machine_config, respond_with_template
+from murfey.server import respond_with_template
+from murfey.util.config import get_machine_config
 
 tag = {
     "name": "bootstrap",

src/murfey/server/api/file_manip.py

@@ -8,11 +8,10 @@
 from sqlmodel import select
 from werkzeug.utils import secure_filename
 
-from murfey.server import sanitise
 from murfey.server.api.auth import MurfeySessionID, validate_token
 from murfey.server.gain import Camera, prepare_eer_gain, prepare_gain
 from murfey.server.murfey_db import murfey_db
-from murfey.util import secure_path
+from murfey.util import sanitise, secure_path
 from murfey.util.config import get_machine_config
 from murfey.util.db import Session, SessionProcessingParameters
 from murfey.util.eer import num_frames

src/murfey/server/api/instrument.py

@@ -12,7 +12,6 @@
 from sqlmodel import select
 from werkzeug.utils import secure_filename
 
-from murfey.server import sanitise
 from murfey.server.api.auth import (
     MurfeySessionID,
     create_access_token,
@@ -21,7 +20,7 @@
     validate_token,
 )
 from murfey.server.murfey_db import murfey_db
-from murfey.util import secure_path
+from murfey.util import sanitise, secure_path
 from murfey.util.config import get_machine_config
 from murfey.util.db import RsyncInstance, Session, SessionProcessingParameters
 from murfey.util.models import File, MultigridWatcherSetup

src/murfey/server/api/prometheus.py

@@ -4,9 +4,9 @@
 from sqlmodel import select
 
 import murfey.server.prometheus as prom
-from murfey.server import sanitise
 from murfey.server.api.auth import validate_token
 from murfey.server.murfey_db import murfey_db
+from murfey.util import sanitise
 from murfey.util.db import RsyncInstance
 from murfey.util.models import RsyncerInfo
 

src/murfey/server/api/session_control.py

@@ -17,7 +17,7 @@
     from murfey.server.ispyb import DB
 except ImportError:
     DB = None
-from murfey.server import _transport_object, sanitise
+from murfey.server import _transport_object
 from murfey.server.api.auth import MurfeySessionID, validate_token
 from murfey.server.api.shared import get_foil_hole as _get_foil_hole
 from murfey.server.api.shared import (
@@ -33,6 +33,7 @@
     remove_session_by_id,
 )
 from murfey.server.murfey_db import murfey_db
+from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config
 from murfey.util.db import (
     AutoProcProgram,

src/murfey/server/api/session_info.py

@@ -12,13 +12,7 @@
 
 import murfey.server.ispyb
 import murfey.server.websocket as ws
-from murfey.server import (
-    _transport_object,
-    get_hostname,
-    get_microscope,
-    sanitise,
-    templates,
-)
+from murfey.server import _transport_object, get_hostname, get_microscope, templates
 from murfey.server.api.auth import MurfeySessionID, validate_token
 from murfey.server.api.shared import get_foil_hole as _get_foil_hole
 from murfey.server.api.shared import (
@@ -34,6 +28,7 @@
     remove_session_by_id,
 )
 from murfey.server.murfey_db import murfey_db
+from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config
 from murfey.util.db import (
     ClientEnvironment,

src/murfey/server/api/shared.py

@@ -7,8 +7,7 @@
 from werkzeug.utils import secure_filename
 
 import murfey.server.prometheus as prom
-from murfey.server import sanitise
-from murfey.util import safe_run
+from murfey.util import safe_run, sanitise
 from murfey.util.config import MachineConfig, from_file, get_machine_config, settings
 from murfey.util.db import (
     DataCollection,

src/murfey/server/api/workflow.py

@@ -33,12 +33,12 @@
     get_angle,
     get_job_ids,
     get_tomo_proc_params,
-    sanitise,
 )
 from murfey.server.api.auth import MurfeySessionID, validate_token
 from murfey.server.api.spa import _cryolo_model_path
 from murfey.server.ispyb import DB, get_proposal_id
 from murfey.server.murfey_db import murfey_db
+from murfey.util import sanitise
 from murfey.util.config import get_machine_config
 from murfey.util.db import (
     AutoProcProgram,