smartem_backend.api_server

Members

acknowledge_instruction	HTTP endpoint for instruction acknowledgements with database persistence
agent_heartbeat	Agent heartbeat endpoint to update connection health status.
check_database_health	Check database connectivity and basic functionality
check_rabbitmq_health	Check RabbitMQ connectivity
close_managed_session	Close a session using the connection manager
create_acquisition	Create a new acquisition
create_acquisition_grid	Create a new grid for a specific acquisition
create_atlas_tile_for_atlas	Create a new tile for a specific atlas
create_foilhole_micrograph	Create a new micrograph for a specific foil hole
create_grid_atlas	Create a new atlas for a grid
create_grid_gridsquare	Create a new grid square for a specific grid
create_gridsquare_foilhole	Create a new foil hole for a specific grid square
create_managed_session	Create a session using the connection manager
create_prediction_model
create_quality_prediction
create_test_instruction	Debug endpoint to create test instructions
create_test_session	Debug endpoint to create test sessions
delete_acquisition	Delete an acquisition
delete_atlas	Delete an atlas by publishing to RabbitMQ
delete_atlas_tile	Delete an atlas tile by publishing to RabbitMQ
delete_foilhole	Delete a foil hole by publishing to RabbitMQ
delete_grid	Delete a grid by publishing to RabbitMQ
delete_gridsquare	Delete a grid square by publishing to RabbitMQ
delete_micrograph	Delete a micrograph by publishing to RabbitMQ
delete_prediction_model
get_acquisition	Get a single acquisition by ID
get_acquisition_grids	Get all grids for a specific acquisition
get_acquisitions	Get all acquisitions
get_active_connections	Debug endpoint to view active agent connections
get_active_sessions	Debug endpoint to view all active sessions
get_atlas	Get a single atlas by ID
get_atlas_tile	Get a single atlas tile by ID
get_atlas_tiles	Get all atlas tiles
get_atlas_tiles_by_atlas	Get all tiles for a specific atlas
get_atlases	Get all atlases
get_connection_stats	Get real-time connection and session statistics
get_db
get_foilhole	Get a single foil hole by ID
get_foilhole_micrographs	Get all micrographs for a specific foil hole
get_foilhole_quality_prediction_time_series_for_gridsquare	Get time ordered predictions for all models that provide them for this square
get_foilhole_quality_prediction_time_series_for_gridsquare_for_metric	Get time ordered predictions for all models that provide them for this square
get_foilholes	Get all foil holes
get_grid	Get a single grid by ID
get_grid_atlas	Get the atlas for a specific grid
get_grid_atlas_image	Get a single grid by ID
get_grid_gridsquares	Get all grid squares for a specific grid
get_grid_latent_representation
get_grid_predictions
get_grids	Get all grids
get_gridsquare	Get a single grid square by ID
get_gridsquare_foilhole_quality_predictions
get_gridsquare_foilholes	Get all foil holes for a specific grid square
get_gridsquare_image	Get a single grid square by ID
get_gridsquare_quality_prediction_time_series	Get time ordered predictions for all models that provide them for this square
get_gridsquare_quality_predictions
get_gridsquares	Get all grid squares
get_health	Health check endpoint with actual connectivity checks
get_latent_rep
get_micrograph	Get a single micrograph by ID
get_micrographs	Get all micrographs
get_model_weights_for_grid	Get time series of model weights for grid
get_overall_prediction_for_gridsquare
get_prediction_for_grid
get_prediction_for_gridsquare
get_prediction_model
get_prediction_models
get_quality_metrics
get_session_instructions	Debug endpoint to view instructions for a session
get_square_latent_rep
get_status	Get API status and configuration information
get_suggested_square_collections
grid_registered	All squares on a grid have been registered at low mag
gridsquare_registered	All holes on a grid square have been registered at square mag
lifespan	Manage application lifespan events.
link_atlas_tile_to_gridsquare	Connect a grid square to a tile with its position information
link_atlas_tile_to_gridsquares	Connect mutliple grid squares to a tile with its position information
log_requests
stream_instructions	SSE endpoint for streaming instructions to agents for a specific session
update_acquisition	Update an acquisition
update_atlas	Update an atlas
update_atlas_tile	Update an atlas tile
update_foilhole	Update a foil hole
update_grid	Update a grid
update_gridsquare	Update a grid square
update_micrograph	Update a micrograph
update_prediction_model

smartem_backend.api_server.lifespan(app: FastAPI)

Manage application lifespan events.

smartem_backend.api_server.check_database_health()

Check database connectivity and basic functionality

smartem_backend.api_server.check_rabbitmq_health()

Check RabbitMQ connectivity

smartem_backend.api_server.get_status()

Get API status and configuration information

smartem_backend.api_server.get_health()

Health check endpoint with actual connectivity checks

smartem_backend.api_server.get_acquisitions(db: Session = Depends(get_db))

Get all acquisitions

smartem_backend.api_server.create_acquisition(acquisition: AcquisitionCreateRequest, db: Session = Depends(get_db))

Create a new acquisition

smartem_backend.api_server.get_acquisition(acquisition_uuid: str, db: Session = Depends(get_db))

Get a single acquisition by ID

smartem_backend.api_server.update_acquisition(acquisition_uuid: str, acquisition: AcquisitionUpdateRequest, db: Session = Depends(get_db))

Update an acquisition

smartem_backend.api_server.delete_acquisition(acquisition_uuid: str, db: Session = Depends(get_db))

Delete an acquisition

smartem_backend.api_server.get_grids(db: Session = Depends(get_db))

Get all grids

smartem_backend.api_server.get_grid(grid_uuid: str, db: Session = Depends(get_db))

Get a single grid by ID

smartem_backend.api_server.update_grid(grid_uuid: str, grid: GridUpdateRequest, db: Session = Depends(get_db))

Update a grid

smartem_backend.api_server.delete_grid(grid_uuid: str, db: Session = Depends(get_db))

Delete a grid by publishing to RabbitMQ

smartem_backend.api_server.get_acquisition_grids(acquisition_uuid: str, db: Session = Depends(get_db))

Get all grids for a specific acquisition

smartem_backend.api_server.create_acquisition_grid(acquisition_uuid: str, grid: GridCreateRequest, db: Session = Depends(get_db))

Create a new grid for a specific acquisition

smartem_backend.api_server.grid_registered(grid_uuid: str) → bool

All squares on a grid have been registered at low mag

smartem_backend.api_server.get_atlases(db: Session = Depends(get_db))

Get all atlases

smartem_backend.api_server.get_atlas(atlas_uuid: str, db: Session = Depends(get_db))

Get a single atlas by ID

smartem_backend.api_server.update_atlas(atlas_uuid: str, atlas: AtlasUpdateRequest, db: Session = Depends(get_db))

Update an atlas

smartem_backend.api_server.delete_atlas(atlas_uuid: str, db: Session = Depends(get_db))

Delete an atlas by publishing to RabbitMQ

smartem_backend.api_server.get_grid_atlas(grid_uuid: str, db: Session = Depends(get_db))

Get the atlas for a specific grid

smartem_backend.api_server.create_grid_atlas(grid_uuid: str, atlas: AtlasCreateRequest, db: Session = Depends(get_db))

Create a new atlas for a grid

smartem_backend.api_server.get_atlas_tiles(db: Session = Depends(get_db))

Get all atlas tiles

smartem_backend.api_server.get_atlas_tile(tile_uuid: str, db: Session = Depends(get_db))

Get a single atlas tile by ID

smartem_backend.api_server.update_atlas_tile(tile_uuid: str, tile: AtlasTileUpdateRequest, db: Session = Depends(get_db))

Update an atlas tile

smartem_backend.api_server.delete_atlas_tile(tile_uuid: str, db: Session = Depends(get_db))

Delete an atlas tile by publishing to RabbitMQ

smartem_backend.api_server.get_atlas_tiles_by_atlas(atlas_uuid: str, db: Session = Depends(get_db))

Get all tiles for a specific atlas

smartem_backend.api_server.create_atlas_tile_for_atlas(atlas_uuid: str, tile: AtlasTileCreateRequest, db: Session = Depends(get_db))

Create a new tile for a specific atlas

smartem_backend.api_server.link_atlas_tile_to_gridsquare(tile_uuid: str, gridsquare_uuid: str, gridsquare_position: GridSquarePositionRequest, db: Session = Depends(get_db))

Connect a grid square to a tile with its position information

smartem_backend.api_server.link_atlas_tile_to_gridsquares(tile_uuid: str, gridsquare_positions: list[GridSquarePositionRequest], db: Session = Depends(get_db))

Connect mutliple grid squares to a tile with its position information

smartem_backend.api_server.get_gridsquares(db: Session = Depends(get_db))

Get all grid squares

smartem_backend.api_server.get_gridsquare(gridsquare_uuid: str, db: Session = Depends(get_db))

Get a single grid square by ID

smartem_backend.api_server.update_gridsquare(gridsquare_uuid: str, gridsquare: GridSquareUpdateRequest, db: Session = Depends(get_db))

Update a grid square

smartem_backend.api_server.delete_gridsquare(gridsquare_uuid: str, db: Session = Depends(get_db))

Delete a grid square by publishing to RabbitMQ

smartem_backend.api_server.get_grid_gridsquares(grid_uuid: str, db: Session = Depends(get_db))

Get all grid squares for a specific grid

smartem_backend.api_server.create_grid_gridsquare(grid_uuid: str, gridsquare: GridSquareCreateRequest, db: Session = Depends(get_db))

Create a new grid square for a specific grid

smartem_backend.api_server.gridsquare_registered(gridsquare_uuid: str, count: int | None = None, db: Session = Depends(get_db)) → bool

All holes on a grid square have been registered at square mag

smartem_backend.api_server.get_foilholes(db: Session = Depends(get_db))

Get all foil holes

smartem_backend.api_server.get_foilhole(foilhole_uuid: str, db: Session = Depends(get_db))

Get a single foil hole by ID

smartem_backend.api_server.update_foilhole(foilhole_uuid: str, foilhole: FoilHoleUpdateRequest, db: Session = Depends(get_db))

Update a foil hole

smartem_backend.api_server.delete_foilhole(foilhole_uuid: str, db: Session = Depends(get_db))

Delete a foil hole by publishing to RabbitMQ

smartem_backend.api_server.get_gridsquare_foilholes(gridsquare_uuid: str, on_square_only: bool = False, db: Session = Depends(get_db))

Get all foil holes for a specific grid square

smartem_backend.api_server.create_gridsquare_foilhole(gridsquare_uuid: str, foilholes: list[FoilHoleCreateRequest], db: Session = Depends(get_db))

Create a new foil hole for a specific grid square

smartem_backend.api_server.get_micrographs(db: Session = Depends(get_db))

Get all micrographs

smartem_backend.api_server.get_micrograph(micrograph_uuid: str, db: Session = Depends(get_db))

Get a single micrograph by ID

smartem_backend.api_server.update_micrograph(micrograph_uuid: str, micrograph: MicrographUpdateRequest, db: Session = Depends(get_db))

Update a micrograph

smartem_backend.api_server.delete_micrograph(micrograph_uuid: str, db: Session = Depends(get_db))

Delete a micrograph by publishing to RabbitMQ

smartem_backend.api_server.get_foilhole_micrographs(foilhole_uuid: str, db: Session = Depends(get_db))

Get all micrographs for a specific foil hole

smartem_backend.api_server.create_foilhole_micrograph(foilhole_uuid: str, micrograph: MicrographCreateRequest, db: Session = Depends(get_db))

Create a new micrograph for a specific foil hole

async smartem_backend.api_server.stream_instructions(agent_id: str, session_id: str, db: Session = Depends(get_db)) → EventSourceResponse

SSE endpoint for streaming instructions to agents for a specific session

async smartem_backend.api_server.acknowledge_instruction(agent_id: str, session_id: str, instruction_id: str, acknowledgement: AgentInstructionAcknowledgement, db: Session = Depends(get_db)) → AgentInstructionAcknowledgementResponse

HTTP endpoint for instruction acknowledgements with database persistence

async smartem_backend.api_server.agent_heartbeat(agent_id: str, session_id: str, db: Session = Depends(get_db))

Agent heartbeat endpoint to update connection health status.

Parameters:

• agent_id – The agent identifier

• session_id – The session identifier

• db – Database session

Returns:

Heartbeat response with status and timestamp

async smartem_backend.api_server.get_active_connections(db: Session = Depends(get_db))

Debug endpoint to view active agent connections

async smartem_backend.api_server.get_session_instructions(session_id: str, db: Session = Depends(get_db))

Debug endpoint to view instructions for a session

async smartem_backend.api_server.get_active_sessions(db: Session = Depends(get_db))

Debug endpoint to view all active sessions

async smartem_backend.api_server.get_connection_stats()

Get real-time connection and session statistics

async smartem_backend.api_server.create_managed_session(session_data: dict)

Create a session using the connection manager

async smartem_backend.api_server.close_managed_session(session_id: str)

Close a session using the connection manager

async smartem_backend.api_server.create_test_instruction(session_id: str, instruction_data: dict, db: Session = Depends(get_db))

Debug endpoint to create test instructions

async smartem_backend.api_server.create_test_session(session_data: dict, db: Session = Depends(get_db))

Debug endpoint to create test sessions

smartem_backend.api_server.get_model_weights_for_grid(grid_uuid: str, db: Session = Depends(get_db))

Get time series of model weights for grid

smartem_backend.api_server.get_gridsquare_quality_prediction_time_series(gridsquare_uuid: str, db: Session = Depends(get_db))

Get time ordered predictions for all models that provide them for this square

smartem_backend.api_server.get_foilhole_quality_prediction_time_series_for_gridsquare(gridsquare_uuid: str, db: Session = Depends(get_db))

Get time ordered predictions for all models that provide them for this square

smartem_backend.api_server.get_foilhole_quality_prediction_time_series_for_gridsquare_for_metric(metric_name: str, gridsquare_uuid: str, db: Session = Depends(get_db))

Get time ordered predictions for all models that provide them for this square

smartem_backend.api_server.get_grid_atlas_image(grid_uuid: str, x: int | None = None, y: int | None = None, w: int | None = None, h: int | None = None, db: Session = Depends(get_db))

Get a single grid by ID

smartem_backend.api_server.get_gridsquare_image(gridsquare_uuid: str, db: Session = Depends(get_db))

Get a single grid square by ID