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Fixes for SmartEM integration #777

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Merged
d-j-hatton merged 3 commits into from
Apr 7, 2026
+25 −8
Merged

Fixes for SmartEM integration #777

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bb68168
perform basic smartem atlas registration for epu acquisition
d-j-hatton Mar 27, 2026
156b822
rather than register a smartem atlas when the atlas is seen push this…
d-j-hatton Mar 30, 2026
c9aa896
minor fixes for smartem integration
d-j-hatton Apr 7, 2026
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9 changes: 8 additions & 1 deletion src/murfey/client/contexts/atlas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,14 @@ def post_transfer_serialem(
data={
"name": transferred_file.stem,
"acquisition_uuid": environment.acquisition_uuid,
"storage_folder": str(source),
"storage_folder": str(
_atlas_destination(
environment,
source,
Path(self._machine_config.get("rsync_basepath", "")),
)
/ "atlas"
),
},
)

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1 change: 1 addition & 0 deletions src/murfey/client/contexts/spa_metadata.py
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Expand Up @@ -164,6 +164,7 @@ def post_transfer(
"name": f"{environment.visit}-sample-{environment.samples[images_disc].sample}",
"acquisition_uuid": environment.acquisition_uuid,
"register_grid": True,
"tag": dcg_tag,
},
)

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23 changes: 16 additions & 7 deletions src/murfey/server/api/session_control.py
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Original file line number Diff line number Diff line change
Expand Up @@ -362,6 +362,7 @@ class AtlasRegistration(BaseModel):
acquisition_uuid: str
storage_folder: str = ""
register_grid: bool = False
tag: str = ""


@spa_router.post("/sessions/{session_id}/register_atlas")
Expand All @@ -379,14 +380,22 @@ def register_atlas(
smartem_client = SmartEMAPIClient(
base_url=machine_config.smartem_api_url, logger=logger
)
possible_grids = smartem_client.get_acquisition_grids(
atlas_registration_data.acquisition_uuid
)
grid_uuid = None
for grid in possible_grids:
if grid.name == atlas_registration_data.name.replace("_atlas", ""):
grid_uuid = grid.uuid
break
if atlas_registration_data.tag:
dcg = murfey_db.exec(
select(DataCollectionGroup)
.where(DataCollectionGroup.session_id == session_id)
.where(DataCollectionGroup.tag == atlas_registration_data.tag)
).one_or_none()
grid_uuid = dcg.smartem_grid_uuid
else:
possible_grids = smartem_client.get_acquisition_grids(
atlas_registration_data.acquisition_uuid
)
for grid in possible_grids:
if grid.name == atlas_registration_data.name.replace("_atlas", ""):
grid_uuid = grid.uuid
break
if grid_uuid is not None:
atlas_data = AtlasData(
id=atlas_registration_data.name,
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