Pass machine config from Analyser and MultigridController to Context and related functions (#761)

* Pass machine config from the Analyser to the Context
* Pass 'rsync_basepath' directly to the '_file_transferred_to' and '_atlas_destination' functions
* Pass machine config directly to the 'ensure_dcg_exists' function
* Fixed broken tests

Author: tieneupin

src/murfey/client/analyser.py

@@ -145,7 +145,12 @@ def _find_context(self, file_path: Path) -> bool:
                 )
             )
         ):
-            self._context = CLEMContext("leica", self._basepath, self._token)
+            self._context = CLEMContext(
+                "leica",
+                self._basepath,
+                self._murfey_config,
+                self._token,
+            )
             return True
 
         # -----------------------------------------------------------------------------
@@ -161,7 +166,12 @@ def _find_context(self, file_path: Path) -> bool:
                 and "Sites" in file_path.parts
             )
         ):
-            self._context = FIBContext("autotem", self._basepath, self._token)
+            self._context = FIBContext(
+                "autotem",
+                self._basepath,
+                self._murfey_config,
+                self._token,
+            )
             return True
 
         # Determine if it's from Maps
@@ -173,35 +183,58 @@ def _find_context(self, file_path: Path) -> bool:
                 all(path in file_path.parts for path in ("LayersData", "Layer"))
             )
         ):
-            self._context = FIBContext("maps", self._basepath, self._token)
+            self._context = FIBContext(
+                "maps",
+                self._basepath,
+                self._murfey_config,
+                self._token,
+            )
             return True
 
         # Determine if it's from Meteor
         if (
             # Image metadata stored in "features.json" file
             file_path.name == "features.json" or ()
         ):
-            self._context = FIBContext("meteor", self._basepath, self._token)
+            self._context = FIBContext(
+                "meteor",
+                self._basepath,
+                self._murfey_config,
+                self._token,
+            )
             return True
 
         # -----------------------------------------------------------------------------
         # SXT workflow checks
         # -----------------------------------------------------------------------------
         if file_path.suffix in (".txrm", ".xrm"):
-            self._context = SXTContext("zeiss", self._basepath, self._token)
+            self._context = SXTContext(
+                "zeiss",
+                self._basepath,
+                self._murfey_config,
+                self._token,
+            )
             return True
 
         # -----------------------------------------------------------------------------
         # Tomography and SPA workflow checks
         # -----------------------------------------------------------------------------
         if "atlas" in file_path.parts:
             self._context = AtlasContext(
-                "serialem" if self._serialem else "epu", self._basepath, self._token
+                "serialem" if self._serialem else "epu",
+                self._basepath,
+                self._murfey_config,
+                self._token,
             )
             return True
 
         if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
-            self._context = SPAMetadataContext("epu", self._basepath, self._token)
+            self._context = SPAMetadataContext(
+                "epu",
+                self._basepath,
+                self._murfey_config,
+                self._token,
+            )
             return True
         elif (
             "Batch" in file_path.parts
@@ -210,7 +243,10 @@ def _find_context(self, file_path: Path) -> bool:
             or file_path.name == "Session.dm"
         ):
             self._context = TomographyMetadataContext(
-                "tomo", self._basepath, self._token
+                "tomo",
+                self._basepath,
+                self._murfey_config,
+                self._token,
             )
             return True
 
@@ -228,7 +264,10 @@ def _find_context(self, file_path: Path) -> bool:
                 if not self._context:
                     logger.info("Acquisition software: EPU")
                     self._context = SPAModularContext(
-                        "epu", self._basepath, self._token
+                        "epu",
+                        self._basepath,
+                        self._murfey_config,
+                        self._token,
                     )
                 self.parameters_model = ProcessingParametersSPA
                 return True
@@ -244,7 +283,10 @@ def _find_context(self, file_path: Path) -> bool:
                 if not self._context:
                     logger.info("Acquisition software: tomo")
                     self._context = TomographyContext(
-                        "tomo", self._basepath, self._token
+                        "tomo",
+                        self._basepath,
+                        self._murfey_config,
+                        self._token,
                     )
                     self.parameters_model = ProcessingParametersTomo
                 return True
@@ -281,7 +323,10 @@ def _analyse(self):
                     and not self._context
                 ):
                     self._context = SPAMetadataContext(
-                        "epu", self._basepath, self._token
+                        "epu",
+                        self._basepath,
+                        self._murfey_config,
+                        self._token,
                     )
                 elif (
                     "Batch" in transferred_file.parts
@@ -290,7 +335,10 @@ def _analyse(self):
                     and not self._context
                 ):
                     self._context = TomographyMetadataContext(
-                        "tomo", self._basepath, self._token
+                        "tomo",
+                        self._basepath,
+                        self._murfey_config,
+                        self._token,
                     )
                 self.post_transfer(transferred_file)
             else:

src/murfey/client/context.py

@@ -8,27 +8,25 @@
 import xmltodict
 
 from murfey.client.instance_environment import MurfeyInstanceEnvironment, SampleInfo
-from murfey.util.client import capture_post, get_machine_config_client
+from murfey.util.client import capture_post
 
 logger = logging.getLogger("murfey.client.context")
 
 
 def _file_transferred_to(
-    environment: MurfeyInstanceEnvironment, source: Path, file_path: Path, token: str
+    environment: MurfeyInstanceEnvironment,
+    source: Path,
+    file_path: Path,
+    rsync_basepath: Path,
 ):
-    machine_config = get_machine_config_client(
-        str(environment.url.geturl()),
-        token,
-        instrument_name=environment.instrument_name,
-    )
     if environment.visit in environment.default_destinations[source]:
         return (
-            Path(machine_config.get("rsync_basepath", ""))
+            rsync_basepath
             / Path(environment.default_destinations[source])
             / file_path.relative_to(source)  # need to strip out the rsync_module name
         )
     return (
-        Path(machine_config.get("rsync_basepath", ""))
+        rsync_basepath
         / Path(environment.default_destinations[source])
         / environment.visit
         / file_path.relative_to(source)
@@ -52,22 +50,19 @@ def _get_source(file_path: Path, environment: MurfeyInstanceEnvironment) -> Path
 
 
 def _atlas_destination(
-    environment: MurfeyInstanceEnvironment, source: Path, token: str
+    environment: MurfeyInstanceEnvironment,
+    source: Path,
+    rsync_basepath: Path,
 ) -> Path:
-    machine_config = get_machine_config_client(
-        str(environment.url.geturl()),
-        token,
-        instrument_name=environment.instrument_name,
-    )
     for i, destination_part in enumerate(
         Path(environment.default_destinations[source]).parts
     ):
         if destination_part == environment.visit:
-            return Path(machine_config.get("rsync_basepath", "")) / "/".join(
+            return rsync_basepath / "/".join(
                 Path(environment.default_destinations[source]).parent.parts[: i + 1]
             )
     return (
-        Path(machine_config.get("rsync_basepath", ""))
+        rsync_basepath
         / Path(environment.default_destinations[source]).parent
         / environment.visit
     )
@@ -77,6 +72,7 @@ def ensure_dcg_exists(
     collection_type: str,
     metadata_source: Path,
     environment: MurfeyInstanceEnvironment,
+    machine_config: dict,
     token: str,
 ) -> str | None:
     """Create  a data collection group"""
@@ -183,7 +179,11 @@ def ensure_dcg_exists(
                 "experiment_type_id": experiment_type_id,
                 "tag": dcg_tag,
                 "atlas": str(
-                    _atlas_destination(environment, session_file.parent, token)
+                    _atlas_destination(
+                        environment,
+                        session_file.parent,
+                        Path(machine_config.get("rsync_basepath", "")),
+                    )
                     / environment.samples[metadata_source].atlas.parent
                     / atlas_xml_path.with_suffix(".jpg").name
                 ).replace("//", "/"),

src/murfey/client/contexts/atlas.py

@@ -12,9 +12,16 @@
 
 
 class AtlasContext(Context):
-    def __init__(self, acquisition_software: str, basepath: Path, token: str):
+    def __init__(
+        self,
+        acquisition_software: str,
+        basepath: Path,
+        machine_config: dict,
+        token: str,
+    ):
         super().__init__("Atlas", acquisition_software, token)
         self._basepath = basepath
+        self._machine_config = machine_config
 
     def post_transfer(
         self,
@@ -69,7 +76,9 @@ def post_transfer_epu(
             source = _get_source(transferred_file, environment)
             if source:
                 transferred_atlas_name = _atlas_destination(
-                    environment, source, self._token
+                    environment,
+                    source,
+                    Path(self._machine_config.get("rsync_basepath", "")),
                 ) / transferred_file.relative_to(source.parent)
                 capture_post(
                     base_url=str(environment.url.geturl()),
@@ -91,7 +100,9 @@ def post_transfer_epu(
             if source:
                 atlas_mrc = transferred_file.with_suffix(".mrc")
                 transferred_atlas_jpg = _atlas_destination(
-                    environment, source, self._token
+                    environment,
+                    source,
+                    Path(self._machine_config.get("rsync_basepath", "")),
                 ) / atlas_mrc.relative_to(source.parent).with_suffix(".jpg")
 
                 with open(transferred_file, "rb") as atlas_xml:

src/murfey/client/contexts/clem.py

@@ -12,28 +12,23 @@
 
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
-from murfey.util.client import capture_post, get_machine_config_client
+from murfey.util.client import capture_post
 
 # Create logger object
 logger = logging.getLogger("murfey.client.contexts.clem")
 
 
 def _file_transferred_to(
-    environment: MurfeyInstanceEnvironment, source: Path, file_path: Path, token: str
+    environment: MurfeyInstanceEnvironment,
+    source: Path,
+    file_path: Path,
+    rsync_basepath: Path,
 ) -> Optional[Path]:
     """
     Returns the Path of the transferred file on the DLS file system.
     """
-    machine_config = get_machine_config_client(
-        str(environment.url.geturl()),
-        token,
-        instrument_name=environment.instrument_name,
-    )
-
     # Construct destination path
-    base_destination = Path(machine_config.get("rsync_basepath", "")) / Path(
-        environment.default_destinations[source]
-    )
+    base_destination = rsync_basepath / Path(environment.default_destinations[source])
     # Add visit number to the path if it's not present in default destination
     if environment.visit not in environment.default_destinations[source]:
         base_destination = base_destination / environment.visit
@@ -87,9 +82,16 @@ def _find_elements_recursively(
 
 
 class CLEMContext(Context):
-    def __init__(self, acquisition_software: str, basepath: Path, token: str):
+    def __init__(
+        self,
+        acquisition_software: str,
+        basepath: Path,
+        machine_config: dict,
+        token: str,
+    ):
         super().__init__("CLEM", acquisition_software, token)
         self._basepath = basepath
+        self._machine_config = machine_config
         # CLEM contexts for "auto-save" acquisition mode
         self._tiff_series: Dict[str, List[str]] = {}  # {Series name : TIFF path list}
         self._series_metadata: Dict[str, str] = {}  # {Series name : Metadata file path}
@@ -125,7 +127,7 @@ def post_transfer(
                 environment=environment,
                 source=source,
                 file_path=transferred_file,
-                token=self._token,
+                rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")),
             )
             if not destination_file:
                 logger.warning(
@@ -301,7 +303,7 @@ def post_transfer(
                 environment=environment,
                 source=source,
                 file_path=transferred_file,
-                token=self._token,
+                rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")),
             )
             if not destination_file:
                 logger.warning(