Updated code to reflect type changes of parameters from str to Path and making keys Optional in MachineConfig

Author: tieneupin

src/murfey/server/api/__init__.py

@@ -51,7 +51,7 @@
 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.config import MachineConfig, from_file, settings
+from murfey.util.config import MachineConfig, machine_config_from_file, settings
 from murfey.util.db import (
     AutoProcProgram,
     ClientEnvironment,
@@ -146,19 +146,19 @@ def connections_check():
 def machine_info() -> Optional[MachineConfig]:
     instrument_name = os.getenv("BEAMLINE")
     if settings.murfey_machine_configuration and instrument_name:
-        return from_file(Path(settings.murfey_machine_configuration), instrument_name)[
-            instrument_name
-        ]
+        return machine_config_from_file(
+            Path(settings.murfey_machine_configuration), instrument_name
+        )[instrument_name]
     return None
 
 
 @lru_cache(maxsize=5)
 @router.get("/instruments/{instrument_name}/machine")
 def machine_info_by_name(instrument_name: str) -> Optional[MachineConfig]:
     if settings.murfey_machine_configuration:
-        return from_file(Path(settings.murfey_machine_configuration), instrument_name)[
-            instrument_name
-        ]
+        return machine_config_from_file(
+            Path(settings.murfey_machine_configuration), instrument_name
+        )[instrument_name]
     return None
 
 
@@ -1218,6 +1218,10 @@ async def request_tomography_preprocessing(
         murfey_ids = _murfey_id(appid, db, number=1, close=False)
         if not mrc_out.parent.exists():
             mrc_out.parent.mkdir(parents=True, exist_ok=True)
+        # Handle case when gain reference file is None
+        if not proc_file.gain_ref:
+            log.error("No gain reference file was provided in the ProcessFile object")
+            return proc_file
         zocalo_message: dict = {
             "recipes": ["em-tomo-preprocess"],
             "parameters": {
@@ -1236,7 +1240,9 @@ async def request_tomography_preprocessing(
                 "fm_dose": proc_file.dose_per_frame,
                 "gain_ref": (
                     str(machine_config.rsync_basepath / proc_file.gain_ref)
-                    if proc_file.gain_ref and machine_config.data_transfer_enabled
+                    if proc_file.gain_ref
+                    and machine_config.data_transfer_enabled
+                    and machine_config.rsync_basepath
                     else proc_file.gain_ref
                 ),
                 "fm_int_file": proc_file.eer_fractionation_file,
@@ -1249,7 +1255,7 @@ async def request_tomography_preprocessing(
             _transport_object.send("processing_recipe", zocalo_message)
         else:
             log.error(
-                f"Pe-processing was requested for {sanitise(ppath.name)} but no Zocalo transport object was found"
+                f"Preprocessing was requested for {sanitise(ppath.name)} but no Zocalo transport object was found"
             )
             return proc_file
     else:
@@ -1285,6 +1291,8 @@ def suggest_path(
         raise ValueError(
             "No machine configuration set when suggesting destination path"
         )
+    if not machine_config.rsync_basepath:
+        raise ValueError("No rsync basepath set")
     check_path = machine_config.rsync_basepath / base_path
     check_path_name = check_path.name
     while check_path.exists():
@@ -1366,6 +1374,8 @@ def start_dc(
     machine_config = get_machine_config(instrument_name=instrument_name)[
         instrument_name
     ]
+    if not machine_config.rsync_basepath:
+        raise ValueError("No rsync basepath set")
     log.info(
         f"Starting data collection on microscope {get_microscope(machine_config=machine_config)} "
         f"with basepath {sanitise(str(machine_config.rsync_basepath))} and directory {sanitise(dc_params.image_directory)}"
@@ -1453,8 +1463,10 @@ async def process_gain(
         executables = machine_config.external_executables
     env = machine_config.external_environment
     safe_path_name = secure_filename(gain_reference_params.gain_ref.name)
+    if not machine_config.rsync_basepath:
+        raise ValueError("No rsync basepath set")
     filepath = (
-        Path(machine_config.rsync_basepath)
+        machine_config.rsync_basepath
         / (machine_config.rsync_module or "data")
         / str(datetime.datetime.now().year)
         / secure_filename(visit_name)
@@ -1521,8 +1533,10 @@ async def write_eer_fractionation_file(
             )
         ) / secure_filename(fractionation_params.fractionation_file_name)
     else:
+        if not machine_config.rsync_basepath:
+            raise ValueError("rsync basepath not set")
         file_path = (
-            Path(machine_config.rsync_basepath)
+            machine_config.rsync_basepath
             / (machine_config.rsync_module or "data")
             / str(datetime.datetime.now().year)
             / secure_filename(visit_name)
@@ -1566,8 +1580,10 @@ async def make_gif(
     machine_config = get_machine_config(instrument_name=instrument_name)[
         instrument_name
     ]
+    if not machine_config.rsync_basepath:
+        raise ValueError("rsync basepath not set")
     output_dir = (
-        Path(machine_config.rsync_basepath)
+        machine_config.rsync_basepath
         / (machine_config.rsync_module or "data")
         / secure_filename(year)
         / secure_filename(visit_name)

src/murfey/server/api/spa.py

@@ -20,6 +20,13 @@ def _cryolo_model_path(visit: str, instrument_name: str) -> Path:
     machine_config = get_machine_config(instrument_name=instrument_name)[
         instrument_name
     ]
+    # Raise error if relevant keys weren't set in MachineConfig
+    if not machine_config.rsync_basepath:
+        raise ValueError("Unable to find crYOLO model; rsync_basepath was not set")
+    if not machine_config.default_model:
+        raise ValueError("No default crYOLO model was set")
+
+    # Find user-provided crYOLO model
     if machine_config.model_search_directory:
         visit_directory = (
             machine_config.rsync_basepath
@@ -32,10 +39,14 @@ def _cryolo_model_path(visit: str, instrument_name: str) -> Path:
         )
         if possible_models:
             return sorted(possible_models, key=lambda x: x.stat().st_ctime)[-1]
+
+    # Return default crYOLO model otherwise
     return machine_config.default_model
 
 
 @router.get("/sessions/{session_id}/cryolo_model")
 def get_cryolo_model_path(session_id: int, db=murfey_db):
     session = db.exec(select(MurfeySession).where(MurfeySession.id == session_id)).one()
-    return {"model_path": _cryolo_model_path(session.visit, session.instrment_name)}
+    return {
+        "model_path": str(_cryolo_model_path(session.visit, session.instrment_name))
+    }

src/murfey/server/demo_api.py

@@ -40,7 +40,7 @@
 from murfey.server.api import MurfeySessionID
 from murfey.server.api.auth import validate_token
 from murfey.server.murfey_db import murfey_db
-from murfey.util.config import MachineConfig, from_file
+from murfey.util.config import MachineConfig, machine_config_from_file
 from murfey.util.db import (
     AutoProcProgram,
     ClientEnvironment,
@@ -113,7 +113,9 @@ class Settings(BaseSettings):
 machine_config: dict = {}
 if settings.murfey_machine_configuration:
     microscope = get_microscope()
-    machine_config = from_file(Path(settings.murfey_machine_configuration), microscope)
+    machine_config = machine_config_from_file(
+        Path(settings.murfey_machine_configuration), microscope
+    )
 
 
 # This will be the homepage for a given microscope.
@@ -134,19 +136,19 @@ async def root(request: Request):
 def machine_info() -> Optional[MachineConfig]:
     instrument_name = os.getenv("BEAMLINE")
     if settings.murfey_machine_configuration and instrument_name:
-        return from_file(Path(settings.murfey_machine_configuration), instrument_name)[
-            instrument_name
-        ]
+        return machine_config_from_file(
+            Path(settings.murfey_machine_configuration), instrument_name
+        )[instrument_name]
     return None
 
 
 @lru_cache(maxsize=5)
 @router.get("/instruments/{instrument_name}/machine")
 def machine_info_by_name(instrument_name: str) -> Optional[MachineConfig]:
     if settings.murfey_machine_configuration:
-        return from_file(Path(settings.murfey_machine_configuration), instrument_name)[
-            instrument_name
-        ]
+        return machine_config_from_file(
+            Path(settings.murfey_machine_configuration), instrument_name
+        )[instrument_name]
     return None
 
 

src/murfey/server/gain.py

@@ -24,7 +24,7 @@ def _sanitise(gain_path: Path) -> Path:
 async def prepare_gain(
     camera: int,
     gain_path: Path,
-    executables: Dict[str, str],
+    executables: Dict[str, Path],
     env: Dict[str, str],
     rescale: bool = True,
     tag: str = "",
@@ -57,15 +57,15 @@ async def prepare_gain(
         gain_path_mrc = gain_path.with_suffix(".mrc")
         gain_path_superres = gain_path.parent / (gain_path.name + "_superres.mrc")
         dm4_proc = await asyncio.create_subprocess_shell(
-            f"{executables['dm2mrc']} {gain_path} {gain_path_mrc}",
+            f"{str(executables['dm2mrc'])} {gain_path} {gain_path_mrc}",
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
         )
         stdout, stderr = await dm4_proc.communicate()
         if dm4_proc.returncode:
             return None, None
         clip_proc = await asyncio.create_subprocess_shell(
-            f"{executables['clip']} {flip} {secure_path(gain_path_mrc)} {secure_path(gain_path_superres) if rescale else secure_path(gain_out)}",
+            f"{str(executables['clip'])} {flip} {secure_path(gain_path_mrc)} {secure_path(gain_path_superres) if rescale else secure_path(gain_out)}",
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
         )
@@ -74,7 +74,7 @@ async def prepare_gain(
             return None, None
         if rescale:
             newstack_proc = await asyncio.create_subprocess_shell(
-                f"{executables['newstack']} -bin 2 {secure_path(gain_path_superres)} {secure_path(gain_out)}",
+                f"{str(executables['newstack'])} -bin 2 {secure_path(gain_path_superres)} {secure_path(gain_out)}",
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
             )
@@ -88,7 +88,7 @@ async def prepare_gain(
 
 
 async def prepare_eer_gain(
-    gain_path: Path, executables: Dict[str, str], env: Dict[str, str], tag: str = ""
+    gain_path: Path, executables: Dict[str, Path], env: Dict[str, str], tag: str = ""
 ) -> Tuple[Path | None, Path | None]:
     if not executables.get("tif2mrc"):
         return None, None
@@ -98,7 +98,7 @@ async def prepare_eer_gain(
     for k, v in env.items():
         os.environ[k] = v
     mrc_convert = await asyncio.create_subprocess_shell(
-        f"{executables['tif2mrc']} {secure_path(gain_path)} {secure_path(gain_out)}"
+        f"{str(executables['tif2mrc'])} {secure_path(gain_path)} {secure_path(gain_out)}"
     )
     await mrc_convert.communicate()
     if mrc_convert.returncode: