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Merged
stephen-riggs merged 4 commits into from
Sep 3, 2025
Merged

Explicitly provide tokens in API calls from instrument server #654

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f58e4f7
explcitly provide tokens to interactions from the instrument server t…
d-j-hatton Sep 3, 2025
3041e3b
test fixing
d-j-hatton Sep 3, 2025
2a18961
pass tokens to more places
d-j-hatton Sep 3, 2025
1c8feb7
more test fixing
d-j-hatton Sep 3, 2025
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31 changes: 22 additions & 9 deletions src/murfey/client/analyser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ class Analyser(Observer):
def __init__(
self,
basepath_local: Path,
token: str,
environment: MurfeyInstanceEnvironment | None = None,
force_mdoc_metadata: bool = False,
limited: bool = False,
Expand All @@ -49,6 +50,7 @@ def __init__(
self._batch_store: dict = {}
self._environment = environment
self._force_mdoc_metadata = force_mdoc_metadata
self._token = token
self.parameters_model: (
Type[ProcessingParametersSPA] | Type[ProcessingParametersTomo] | None
) = None
Expand All @@ -60,6 +62,7 @@ def __init__(
self._murfey_config = (
get_machine_config_client(
str(environment.url.geturl()),
self._token,
instrument_name=environment.instrument_name,
demo=environment.demo,
)
Expand Down Expand Up @@ -123,32 +126,34 @@ def _find_context(self, file_path: Path) -> bool:
# CLEM workflow checks
# Look for LIF and XLIF files
if file_path.suffix in (".lif", ".xlif"):
self._context = CLEMContext("leica", self._basepath)
self._context = CLEMContext("leica", self._basepath, self._token)
return True
# Look for TIFF files associated with CLEM workflow
# Leica's autosave mode seems to name the TIFFs in the format
# PostionXX--ZXX--CXX.tif
if all(
pattern in file_path.name for pattern in ("--Z", "--C")
) and file_path.suffix in (".tiff", ".tif"):
self._context = CLEMContext("leica", self._basepath)
self._context = CLEMContext("leica", self._basepath, self._token)
return True

# Tomography and SPA workflow checks
if "atlas" in file_path.parts:
self._context = AtlasContext("epu", self._basepath)
self._context = AtlasContext("epu", self._basepath, self._token)
return True

if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
self._context = SPAMetadataContext("epu", self._basepath)
self._context = SPAMetadataContext("epu", self._basepath, self._token)
return True
elif (
"Batch" in file_path.parts
or "SearchMaps" in file_path.parts
or "Thumbnails" in file_path.parts
or file_path.name == "Session.dm"
):
self._context = TomographyMetadataContext("tomo", self._basepath)
self._context = TomographyMetadataContext(
"tomo", self._basepath, self._token
)
return True

split_file_stem = file_path.stem.split("_")
Expand All @@ -164,7 +169,9 @@ def _find_context(self, file_path: Path) -> bool:
]:
if not self._context:
logger.info("Acquisition software: EPU")
self._context = SPAModularContext("epu", self._basepath)
self._context = SPAModularContext(
"epu", self._basepath, self._token
)
self.parameters_model = ProcessingParametersSPA
return True

Expand All @@ -178,7 +185,9 @@ def _find_context(self, file_path: Path) -> bool:
):
if not self._context:
logger.info("Acquisition software: tomo")
self._context = TomographyContext("tomo", self._basepath)
self._context = TomographyContext(
"tomo", self._basepath, self._token
)
self.parameters_model = ProcessingParametersTomo
return True
return False
Expand Down Expand Up @@ -213,14 +222,18 @@ def _analyse(self):
or transferred_file.name == "EpuSession.dm"
and not self._context
):
self._context = SPAMetadataContext("epu", self._basepath)
self._context = SPAMetadataContext(
"epu", self._basepath, self._token
)
elif (
"Batch" in transferred_file.parts
or "SearchMaps" in transferred_file.parts
or transferred_file.name == "Session.dm"
and not self._context
):
self._context = TomographyMetadataContext("tomo", self._basepath)
self._context = TomographyMetadataContext(
"tomo", self._basepath, self._token
)
self.post_transfer(transferred_file)
else:
dc_metadata = {}
Expand Down
3 changes: 2 additions & 1 deletion src/murfey/client/context.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,9 @@ class Context:
user_params: List[ProcessingParameter] = []
metadata_params: List[ProcessingParameter] = []

def __init__(self, name: str, acquisition_software: str):
def __init__(self, name: str, acquisition_software: str, token: str):
self._acquisition_software = acquisition_software
self._token = token
self.name = name
self.data_collection_parameters: dict = {}

Expand Down
7 changes: 4 additions & 3 deletions src/murfey/client/contexts/atlas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@


class AtlasContext(Context):
def __init__(self, acquisition_software: str, basepath: Path):
super().__init__("Atlas", acquisition_software)
def __init__(self, acquisition_software: str, basepath: Path, token: str):
super().__init__("Atlas", acquisition_software, token)
self._basepath = basepath

def post_transfer(
Expand All @@ -36,12 +36,13 @@ def post_transfer(
source = _get_source(transferred_file, environment)
if source:
transferred_atlas_name = _atlas_destination(
environment, source, transferred_file
environment, source, transferred_file, self._token
) / transferred_file.relative_to(source.parent)
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="make_atlas_jpg",
token=self._token,
session_id=environment.murfey_session,
data={"path": str(transferred_atlas_name)},
)
Expand Down
13 changes: 10 additions & 3 deletions src/murfey/client/contexts/clem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,14 @@


def _file_transferred_to(
environment: MurfeyInstanceEnvironment, source: Path, file_path: Path
environment: MurfeyInstanceEnvironment, source: Path, file_path: Path, token: str
) -> 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,
demo=environment.demo,
)
Expand Down Expand Up @@ -89,8 +90,8 @@ def _find_elements_recursively(


class CLEMContext(Context):
def __init__(self, acquisition_software: str, basepath: Path):
super().__init__("CLEM", acquisition_software)
def __init__(self, acquisition_software: str, basepath: Path, token: str):
super().__init__("CLEM", acquisition_software, token)
self._basepath = basepath
# CLEM contexts for "auto-save" acquisition mode
self._tiff_series: Dict[str, List[str]] = {} # {Series name : TIFF path list}
Expand Down Expand Up @@ -128,6 +129,7 @@ def post_transfer(
environment=environment,
source=source,
file_path=transferred_file,
token=self._token,
)
if not destination_file:
logger.warning(
Expand Down Expand Up @@ -320,6 +322,7 @@ def post_transfer(
environment=environment,
source=source,
file_path=transferred_file,
token=self._token,
)
if not destination_file:
logger.warning(
Expand Down Expand Up @@ -356,6 +359,7 @@ def register_lif_file(
base_url=str(environment.url.geturl()),
router_name="clem.router",
function_name="register_lif_file",
token=self._token,
session_id=environment.murfey_session,
data={"lif_file": quote(str(lif_file), safe="")},
)
Expand All @@ -381,6 +385,7 @@ def process_lif_file(
base_url=str(environment.url.geturl()),
router_name="clem.router",
function_name="process_raw_lifs",
token=self._token,
session_id=environment.murfey_session,
data={"lif_file": quote(str(lif_file), safe="")},
)
Expand All @@ -404,6 +409,7 @@ def register_tiff_file(
base_url=str(environment.url.geturl()),
router_name="clem.router",
function_name="register_tiff_file",
token=self._token,
session_id=environment.murfey_session,
data={"tiff_file": quote(str(tiff_file), safe="")},
)
Expand All @@ -429,6 +435,7 @@ def process_tiff_series(
base_url=str(environment.url.geturl()),
router_name="clem.router",
function_name="process_raw_tiffs",
token=self._token,
session_id=environment.murfey_session,
data=tiff_dataset,
)
Expand Down
5 changes: 3 additions & 2 deletions src/murfey/client/contexts/fib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ def _number_from_name(name: str) -> int:


class FIBContext(Context):
def __init__(self, acquisition_software: str, basepath: Path):
super().__init__("FIB", acquisition_software)
def __init__(self, acquisition_software: str, basepath: Path, token: str):
super().__init__("FIB", acquisition_software, token)
self._basepath = basepath
self._milling: Dict[int, List[MillingProgress]] = {}
self._lamellae: Dict[int, Lamella] = {}
Expand Down Expand Up @@ -95,6 +95,7 @@ def post_transfer(
base_url=str(environment.url.geturl()),
router_name="workflow.correlative_router",
function_name="make_gif",
token=self._token,
year=datetime.now().year,
visit_name=environment.visit,
session_id=environment.murfey_session,
Expand Down
26 changes: 20 additions & 6 deletions src/murfey/client/contexts/spa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,10 +26,11 @@


def _file_transferred_to(
environment: MurfeyInstanceEnvironment, source: Path, file_path: Path
environment: MurfeyInstanceEnvironment, source: Path, file_path: Path, token: str
):
machine_config = get_machine_config_client(
str(environment.url.geturl()),
token,
instrument_name=environment.instrument_name,
demo=environment.demo,
)
Expand Down Expand Up @@ -111,8 +112,8 @@ class SPAModularContext(Context):
ProcessingParameter("motion_corr_binning", "Motion Correction Binning"),
]

def __init__(self, acquisition_software: str, basepath: Path):
super().__init__("SPA", acquisition_software)
def __init__(self, acquisition_software: str, basepath: Path, token: str):
super().__init__("SPA", acquisition_software, token)
self._basepath = basepath
self._processing_job_stash: dict = {}
self._foil_holes: Dict[int, List[int]] = {}
Expand Down Expand Up @@ -229,6 +230,7 @@ def gather_metadata(
base_url=str(environment.url.geturl()),
router_name="session_control.router",
function_name="machine_info_by_instrument",
token=self._token,
instrument_name=environment.instrument_name,
)
if server_config_response is None:
Expand Down Expand Up @@ -302,6 +304,7 @@ def _position_analysis(
base_url=str(environment.url.geturl()),
router_name="session_info.router",
function_name="get_dc_groups",
token=self._token,
session_id=environment.murfey_session,
)
.json()
Expand Down Expand Up @@ -339,14 +342,17 @@ def _position_analysis(
else metadata_source_as_str
)
image_path = (
_file_transferred_to(environment, metadata_source, Path(gs.image))
_file_transferred_to(
environment, metadata_source, Path(gs.image), self._token
)
if gs.image
else ""
)
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_grid_square",
token=self._token,
session_id=environment.murfey_session,
gsid=grid_square,
data={
Expand Down Expand Up @@ -385,14 +391,17 @@ def _position_analysis(
else metadata_source_as_str
)
image_path = (
_file_transferred_to(environment, metadata_source, Path(fh.image))
_file_transferred_to(
environment, metadata_source, Path(fh.image), self._token
)
if fh.image
else ""
)
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_foil_hole",
token=self._token,
session_id=environment.murfey_session,
gs_name=grid_square,
data={
Expand All @@ -416,6 +425,7 @@ def _position_analysis(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_foil_hole",
token=self._token,
session_id=environment.murfey_session,
gs_name=grid_square,
data={
Expand Down Expand Up @@ -444,6 +454,7 @@ def post_transfer(
if environment:
machine_config = get_machine_config_client(
str(environment.url.geturl()),
self._token,
instrument_name=environment.instrument_name,
demo=environment.demo,
)
Expand All @@ -470,13 +481,14 @@ def post_transfer(

if environment:
file_transferred_to = _file_transferred_to(
environment, source, transferred_file
environment, source, transferred_file, self._token
)
if not environment.movie_counters.get(str(source)):
movie_counts_get = capture_get(
base_url=str(environment.url.geturl()),
router_name="session_control.router",
function_name="count_number_of_movies",
token=self._token,
)
if movie_counts_get is not None:
environment.movie_counters[str(source)] = count(
Expand All @@ -493,6 +505,7 @@ def post_transfer(
base_url=str(environment.url.geturl()),
router_name="file_io_instrument.router",
function_name="write_eer_fractionation_file",
token=self._token,
visit_name=environment.visit,
session_id=environment.murfey_session,
data={
Expand Down Expand Up @@ -552,6 +565,7 @@ def post_transfer(
base_url=str(environment.url.geturl()),
router_name="workflow.spa_router",
function_name="request_spa_preprocessing",
token=self._token,
visit_name=environment.visit,
session_id=environment.murfey_session,
data={
Expand Down
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