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Register atlas tiles with smartem among other related things #863

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d3dc53d
when finding the data collection group need to account for that fact …
d-j-hatton Aug 13, 2026
af2cf52
add smartem atlas tile registration
d-j-hatton Aug 13, 2026
a400086
allow the location of a keycloak configuration file for smartem to be…
d-j-hatton Aug 13, 2026
20a87c0
add motion correction and ctf results registration for smartem
d-j-hatton Aug 13, 2026
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9 changes: 8 additions & 1 deletion src/murfey/server/api/instrument.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,15 @@
from smartem_backend.keycloak_client import KeycloakClient, load_keycloak_config
from smartem_common.schemas import AcquisitionData, MicroscopeData

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down
57 changes: 45 additions & 12 deletions src/murfey/server/api/session_control.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,24 @@
from fastapi.responses import FileResponse
from ispyb.sqlalchemy import AutoProcProgram as ISPyBAutoProcProgram
from pydantic import BaseModel
from sqlalchemy import func
from sqlalchemy import desc, func
from sqlmodel import select

try:
from smartem_agent.fs_parser import EpuParser
from smartem_backend.api_client import SmartEMAPIClient
from smartem_backend.keycloak_client import KeycloakClient, load_keycloak_config
from smartem_common.schemas import AtlasData
from smartem_common.schemas import AtlasTileGridSquarePositionData

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down Expand Up @@ -390,12 +398,23 @@ def register_atlas(
keycloak_client=keycloak_client,
)
grid_uuid = None
atlas_path = None
if atlas_registration_data.tag:
dcg = db.exec(
select(DataCollectionGroup)
.where(DataCollectionGroup.session_id == session_id)
.where(DataCollectionGroup.tag == atlas_registration_data.tag)
).one_or_none()
if dcg is None:
sample = int(
atlas_registration_data.tag.split("Sample")[1].split("/")[0]
)
dcg = db.exec(
select(DataCollectionGroup)
.where(DataCollectionGroup.session_id == session_id)
.where(DataCollectionGroup.sample == sample)
.order_by(desc(DataCollectionGroup.id))
).first()

@stephen-riggs stephen-riggs Aug 13, 2026

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This query could still return nothing, so maybe worth catching that?

grid_uuid = dcg.smartem_grid_uuid
else:
possible_grids = smartem_client.get_acquisition_grids(
Expand All @@ -404,8 +423,9 @@ def register_atlas(
for grid in possible_grids:
if grid.name == atlas_registration_data.name.replace("_atlas", ""):
grid_uuid = grid.uuid
atlas_path = Path(grid.atlas_dir).parent
break
if grid_uuid is not None:
if grid_uuid is not None and atlas_path is not None:
existing_atlas = smartem_client.get_grid_atlas(grid_uuid)
if (
existing_atlas.name == atlas_registration_data.name
Expand All @@ -414,16 +434,29 @@ def register_atlas(
):
# there is a question here of whether the grid should be registered if specified
return
atlas_data = AtlasData(
id=atlas_registration_data.name,
acquisition_date=datetime.now(),
storage_folder=atlas_registration_data.storage_folder,
name=atlas_registration_data.name,
tiles=[],
gridsquare_positions=None,
grid_uuid=grid_uuid,
parser = EpuParser()
atlas_data = parser.parse_atlas_manifest(
str(atlas_path / "Atlas.dm"), grid_uuid
)
atlas_data.acquisition_date = atlas_data.acquisition_date.replace(
tzinfo=None
) # timezone information is not consistently provided so drop it
smartem_client.create_grid_atlas(atlas_data)
registered_squares = smartem_client.get_grid_gridsquares(grid_uuid)
gs_uuid_map = {gs.gridsquare_id: gs.uuid for gs in registered_squares}
for atlastile in atlas_data.tiles:
pos_data_for_tile = []
for gsid, gs_tile_pos in atlastile.gridsquare_positions.items():
for pos in gs_tile_pos:
pos_data_for_tile.append(
AtlasTileGridSquarePositionData(
gridsquare_uuid=gs_uuid_map[gsid],
tile_uuid=atlastile.uuid,
position=pos.position,
size=pos.size,
)
)
smartem_client.link_atlas_tile_and_gridsquares(pos_data_for_tile)
if atlas_registration_data.register_grid:
smartem_client.grid_registered(grid_uuid)
else:
Expand Down
9 changes: 8 additions & 1 deletion src/murfey/server/api/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,15 @@
MicrographManifest as SmartEMMicrographManifest,
)

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down
3 changes: 3 additions & 0 deletions src/murfey/util/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -261,6 +261,9 @@ class Security(BaseModel):
session_token_timeout: Optional[int] = None
allow_origins: list[str] = ["*"]

# SmartEM keycloak config file
smartem_keycloak_config: str = ""

# RabbitMQ settings
rabbitmq_credentials: Path
feedback_queue: str = "murfey_feedback"
Expand Down
28 changes: 25 additions & 3 deletions src/murfey/workflows/spa/ctf_estimation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,25 @@
try:
from smartem_backend.api_client import SmartEMAPIClient
from smartem_backend.keycloak_client import KeycloakClient, load_keycloak_config
from smartem_backend.model.http_request import MicrographUpdateRequest
from smartem_backend.model.http_response import MicrographResponse
from smartem_backend.model.http_request import (
CtfEstimationRegisteredRequest,
MicrographUpdateRequest,
)
from smartem_backend.model.http_response import (
MicrographResponse,
ProcessingFeedbackPublishResponse,
)
from smartem_common.entity_status import MicrographStatus

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down Expand Up @@ -55,6 +68,15 @@ def ctf_estimated(message: dict, murfey_db: Session) -> dict[str, bool]:
update,
MicrographResponse,
)
registered_request = CtfEstimationRegisteredRequest(
quality=True, metric_name="ctfmaxresolution"
) # True is a placeholder until we figure out the best way to calculate this
smartem_client._request(
"post",
f"micrographs/{movie.smartem_uuid}/ctf_estimation/registered",
registered_request,
ProcessingFeedbackPublishResponse,
)
except Exception:
logger.warning(
"Failed to emit CTF estimation complete event to smartem",
Expand Down
9 changes: 8 additions & 1 deletion src/murfey/workflows/spa/flush_spa_preprocess.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,15 @@
GridSquareMetadata as SmartEMGridSquareMetadata,
)

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down
28 changes: 25 additions & 3 deletions src/murfey/workflows/spa/motion_correction.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,25 @@
try:
from smartem_backend.api_client import SmartEMAPIClient
from smartem_backend.keycloak_client import KeycloakClient, load_keycloak_config
from smartem_backend.model.http_request import MicrographUpdateRequest
from smartem_backend.model.http_response import MicrographResponse
from smartem_backend.model.http_request import (
MicrographUpdateRequest,
MotionCorrectionRegisteredRequest,
)
from smartem_backend.model.http_response import (
MicrographResponse,
ProcessingFeedbackPublishResponse,
)
from smartem_common.entity_status import MicrographStatus

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down Expand Up @@ -57,6 +70,15 @@ def motion_corrected(message: dict, murfey_db: Session) -> dict[str, bool]:
update,
MicrographResponse,
)
registered_request = MotionCorrectionRegisteredRequest(
quality=True, metric_name="motioncorrection"
) # True is a placeholder until we figure out the best way to calculate this
smartem_client._request(
"post",
f"micrographs/{movie.smartem_uuid}/motion_correction/registered",
registered_request,
ProcessingFeedbackPublishResponse,
)
except Exception:
logger.warning(
"Failed to emit motion correction complete event to smartem",
Expand Down
9 changes: 8 additions & 1 deletion src/murfey/workflows/spa/picking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,15 @@
from smartem_backend.model.http_response import MicrographResponse
from smartem_common.entity_status import MicrographStatus

from murfey.util.config import get_security_config

keycloak_client = KeycloakClient(
load_keycloak_config(Path(os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION") or ""))
load_keycloak_config(
Path(
os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
or get_security_config().smartem_keycloak_config
)
)
)
SMARTEM_ACTIVE = True
except ImportError:
Expand Down