Fixes for MSys2 style paths (#518)

Author: d-j-hatton

src/murfey/client/contexts/spa.py

@@ -431,12 +431,15 @@ def _position_analysis(
                 grid_square_metadata_file,
                 grid_square,
             )
+            metadata_source_as_str = (
+                "/".join(source.parts[:-2])
+                + f"/{environment.visit}/"
+                + source.parts[-2]
+            )
             metadata_source = Path(
-                (
-                    "/".join(source.parts[:-2])
-                    + f"/{environment.visit}/"
-                    + source.parts[-2]
-                )[1:]
+                metadata_source_as_str[1:]
+                if metadata_source_as_str.startswith("//")
+                else metadata_source_as_str
             )
             image_path = (
                 _file_transferred_to(environment, metadata_source, Path(gs.image))
@@ -471,12 +474,15 @@ def _position_analysis(
                     foil_hole,
                     grid_square,
                 )
+                metadata_source_as_str = (
+                    "/".join(source.parts[:-2])
+                    + f"/{environment.visit}/"
+                    + source.parts[-2]
+                )
                 metadata_source = Path(
-                    (
-                        "/".join(source.parts[:-2])
-                        + f"/{environment.visit}/"
-                        + source.parts[-2]
-                    )[1:]
+                    metadata_source_as_str[1:]
+                    if metadata_source_as_str.startswith("//")
+                    else metadata_source_as_str
                 )
                 image_path = (
                     _file_transferred_to(environment, metadata_source, Path(fh.image))

src/murfey/client/contexts/spa_metadata.py

@@ -44,7 +44,7 @@ def _foil_hole_positions(xml_path: Path, grid_square: int) -> Dict[str, FoilHole
             required_key = key
             break
     if not required_key:
-        logger.warning(f"Required key not found for {str(xml_path)}")
+        logger.info(f"Required key not found for {str(xml_path)}")
         return {}
     foil_holes = {}
     for fh_block in serialization_array[required_key]:
@@ -163,10 +163,13 @@ def post_transfer(
                     atlas=Path(partial_path), sample=sample
                 )
                 url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_data_collection_group"
-                dcg_search_dir = "/" + "/".join(
-                    p
-                    for p in transferred_file.parent.parts[1:]
-                    if p != environment.visit
+                dcg_search_dir = "/".join(
+                    p for p in transferred_file.parent.parts if p != environment.visit
+                )
+                dcg_search_dir = (
+                    dcg_search_dir[1:]
+                    if dcg_search_dir.startswith("//")
+                    else dcg_search_dir
                 )
                 dcg_images_dirs = sorted(
                     Path(dcg_search_dir).glob("Images-Disc*"),
@@ -215,11 +218,16 @@ def post_transfer(
         ):
             # Make sure we have a data collection group before trying to register grid square
             url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_data_collection_group"
-            dcg_search_dir = "/" + "/".join(
+            dcg_search_dir = "/".join(
                 p
-                for p in transferred_file.parent.parent.parts[1:]
+                for p in transferred_file.parent.parent.parts
                 if p != environment.visit
             )
+            dcg_search_dir = (
+                dcg_search_dir[1:]
+                if dcg_search_dir.startswith("//")
+                else dcg_search_dir
+            )
             dcg_images_dirs = sorted(
                 Path(dcg_search_dir).glob("Images-Disc*"),
                 key=lambda x: x.stat().st_ctime,
@@ -241,6 +249,8 @@ def post_transfer(
             )
             fh_positions = _foil_hole_positions(transferred_file, int(gs_name))
             source = _get_source(transferred_file, environment=environment)
+            if source is None:
+                return None
             visitless_source_search_dir = str(source).replace(
                 f"/{environment.visit}", ""
             )
@@ -261,12 +271,15 @@ def post_transfer(
                     transferred_file,
                     int(gs_name),
                 )
+                metadata_source_as_str = (
+                    "/".join(source.parts[:-2])
+                    + f"/{environment.visit}/"
+                    + source.parts[-2]
+                )
                 metadata_source = Path(
-                    (
-                        "/".join(Path(visitless_source).parts[:-2])
-                        + f"/{environment.visit}/"
-                        + Path(visitless_source).parts[-2]
-                    )[1:]
+                    metadata_source_as_str[1:]
+                    if metadata_source_as_str.startswith("//")
+                    else metadata_source_as_str
                 )
                 image_path = (
                     _file_transferred_to(

src/murfey/client/multigrid_control.py

@@ -143,7 +143,7 @@ def _start_rsyncer_multigrid(
             source,
             destination,
             force_metadata=self.processing_enabled,
-            analyse=not extra_directory and use_suggested_path and analyse,
+            analyse=analyse,
             remove_files=remove_files,
             tag=tag,
             limited=limited,

src/murfey/instrument_server/__init__.py

@@ -5,6 +5,8 @@
 from rich.logging import RichHandler
 
 import murfey
+from murfey.client import read_config
+from murfey.client.customlogging import CustomHandler
 from murfey.util import LogFilter
 
 logger = logging.getLogger("murfey.instrument_server")
@@ -33,6 +35,14 @@ def run():
     logging.getLogger("fastapi").addHandler(rich_handler)
     logging.getLogger("uvicorn").addHandler(rich_handler)
 
+    ws = murfey.client.websocket.WSApp(
+        server=read_config()["Murfey"].get("server"),
+        id=0,
+    )
+
+    handler = CustomHandler(ws.send)
+    logging.getLogger().addHandler(handler)
+
     logger.info(
         f"Starting Murfey server version {murfey.__version__}, listening on {args.host}:{args.port}"
     )

src/murfey/instrument_server/api.py

@@ -21,7 +21,7 @@
 from murfey.client.multigrid_control import MultigridController
 from murfey.client.rsync import RSyncer
 from murfey.client.watchdir_multigrid import MultigridDirWatcher
-from murfey.util import sanitise, sanitise_nonpath, secure_path
+from murfey.util import posix_path, sanitise, sanitise_nonpath, secure_path
 from murfey.util.instrument_models import MultigridWatcherSpec
 from murfey.util.models import File, Token
 
@@ -291,7 +291,7 @@ def upload_gain_reference(
     ).json()
     cmd = [
         "rsync",
-        safe_gain_path,
+        posix_path(Path(safe_gain_path)),
         f"{urlparse(_get_murfey_url(), allow_fragments=False).hostname}::{machine_config.get('rsync_module', 'data')}/{safe_visit_path}/{safe_destination_dir}/{secure_filename(gain_reference.gain_path.name)}",
     ]
     gain_rsync = subprocess.run(cmd)

src/murfey/util/__init__.py

@@ -74,9 +74,14 @@ def sanitise_nonpath(in_string: str) -> str:
 
 def secure_path(in_path: Path, keep_spaces: bool = False) -> Path:
     if keep_spaces:
-        secured_parts = [
-            secure_filename(p) if " " not in p else p for p in in_path.parts
-        ]
+        secured_parts = []
+        for p, part in enumerate(in_path.parts):
+            if " " in part:
+                secured_parts.append(part)
+            elif ":" in part and not p:
+                secured_parts.append(secure_filename(part) + ":")
+            else:
+                secured_parts.append(secure_filename(part))
     else:
         secured_parts = [
             (