Add default values to optional fields in SampleUpdate
This commit is contained in:
GotthardG
parent
ac38bc3bb6
commit
0f6759e417
@ -313,6 +313,40 @@ async def download_dewar_label(dewar_id: int, db: Session = Depends(get_db)):
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)
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@router.put("/samples/{sample_id}", response_model=Sample)
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async def update_sample(
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sample_id: int,
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sample_update: SampleUpdate,
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db: Session = Depends(get_db),
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):
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# Log the payload received from the frontend
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logging.info(
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f"Payload received for sample ID {sample_id}: "
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f"{sample_update.dict(exclude_unset=True)}"
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)
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# Query the sample from the database
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sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
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if not sample:
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logging.error(f"Sample with ID {sample_id} not found")
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raise HTTPException(status_code=404, detail="Sample not found")
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# Apply updates
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for key, value in sample_update.dict(exclude_unset=True).items():
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if hasattr(sample, key):
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setattr(sample, key, value)
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# Commit changes to the database
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db.commit()
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db.refresh(sample) # Reload the updated sample object
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# Log the updated sample before returning it
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logging.info(f"Updated sample with ID {sample_id}: {Sample.from_orm(sample)}")
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return Sample.from_orm(sample)
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@router.get("/dewars/{dewar_id}/samples", response_model=Dewar)
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async def get_dewar_samples(dewar_id: int, db: Session = Depends(get_db)):
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# Fetch the Dewar with nested relationships
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@ -374,27 +408,6 @@ async def get_dewar_samples(dewar_id: int, db: Session = Depends(get_db)):
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return Dewar(**dewar_data)
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@router.put("/samples/{sample_id}", response_model=Sample)
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async def update_sample(
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sample_id: int,
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sample_update: SampleUpdate,
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db: Session = Depends(get_db),
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):
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sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
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if not sample:
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raise HTTPException(status_code=404, detail="Sample not found")
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# Apply updates
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for key, value in sample_update.dict(exclude_unset=True).items():
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if hasattr(sample, key):
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setattr(sample, key, value)
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# Save changes
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db.commit()
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db.refresh(sample)
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return Sample.from_orm(sample)
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@router.get("/", response_model=List[DewarSchema])
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async def get_dewars(db: Session = Depends(get_db)):
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try:
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@ -619,12 +619,12 @@ class SlotSchema(BaseModel):
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class SampleUpdate(BaseModel):
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sample_name: Optional[str]
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proteinname: Optional[str]
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priority: Optional[int]
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position: Optional[int]
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comments: Optional[str]
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data_collection_parameters: Optional[DataCollectionParameters]
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sample_name: Optional[str] = None
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proteinname: Optional[str] = None
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priority: Optional[int] = None
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position: Optional[int] = None
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comments: Optional[str] = None
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data_collection_parameters: Optional[DataCollectionParameters] = None
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class Config:
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from_attributes = True
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@ -1,5 +1,5 @@
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import React, { useEffect, useState } from "react";
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import { DataGrid, GridColDef, GridCellEditStopParams } from "@mui/x-data-grid";
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import { DataGrid, GridColDef, GridCellEditStopParams, GridRowModel } from "@mui/x-data-grid";
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import { DewarsService } from "../../openapi";
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interface SampleSpreadsheetProps {
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@ -34,6 +34,24 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
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totalrange,
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transmission,
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dose,
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targetresolution,
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aperture,
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datacollectiontype,
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processingpipeline,
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spacegroupnumber,
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cellparameters,
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rescutkey,
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rescutvalue,
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userresolution,
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pdbid,
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autoprocfull,
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procfull,
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adpenabled,
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noano,
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ffcscampaig,
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trustedhigh,
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autoprocextraparams,
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chiphiangles
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} = sample.data_collection_parameters || {};
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allRows.push({
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@ -53,7 +71,24 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
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totalRange: totalrange || null,
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transmission: transmission || null,
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dose: dose || null,
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dataCollectionParameters: sample.data_collection_parameters || {}, // Ensure this is never undefined
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targetresolution: targetresolution || null,
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aperture: aperture || null,
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datacollectiontype: datacollectiontype || null,
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processingpipeline: processingpipeline || null,
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spacegroupnumber: spacegroupnumber || null,
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cellparameters: cellparameters || {},
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rescutkey: rescutkey || null,
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rescutvalue: rescutvalue || null,
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userresolution: userresolution || null,
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pdbid: pdbid || null,
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autoprocfull: autoprocfull || null,
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procfull: procfull || null,
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adpenabled: adpenabled || null,
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noano: noano || null,
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ffcscampaig: ffcscampaig || null,
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trustedhigh: trustedhigh || null,
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autoprocextraparams: autoprocextraparams || {},
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chiphiangles: chiphiangles || null,
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});
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});
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});
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@ -62,30 +97,38 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
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// Define columns for the grid
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setColumns([
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{ field: "dewarName", headerName: "Dewar Name", width: 150, editable: false },
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{ field: "puckName", headerName: "Puck Name", width: 150 },
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{ field: "puckType", headerName: "Puck Type", width: 150 },
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{ field: "crystalName", headerName: "Crystal Name", width: 200, editable: true },
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{ field: "proteinName", headerName: "Protein Name", width: 200, editable: true },
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{ field: "dewarName", headerName: "Dewar Name", width: 150, editable: false }, // not editable for now
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{ field: "puckName", headerName: "Puck Name", width: 150, editable: false }, // not editable for now
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{ field: "puckType", headerName: "Puck Type", width: 150, editable: false }, // not editable for now
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{ field: "crystalName", headerName: "Crystal Name", width: 200, editable: false }, // not editable for now
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{ field: "proteinName", headerName: "Protein Name", width: 200, editable: false }, // not editable for now
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{ field: "position", headerName: "Position", width: 100, editable: true, type: "number" },
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{ field: "priority", headerName: "Priority", width: 100, editable: true, type: "number" },
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{ field: "comments", headerName: "Comments", width: 300, editable: true },
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{ field: "directory", headerName: "Directory", width: 200 },
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{ field: "directory", headerName: "Directory", width: 200, editable: true },
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{ field: "oscillation", headerName: "Oscillation", width: 150, editable: true, type: "number" },
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{ field: "exposure", headerName: "Exposure", width: 150, editable: true, type: "number" },
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{ field: "totalRange", headerName: "Total Range", width: 150, editable: true, type: "number" },
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{ field: "transmission", headerName: "Transmission", width: 150, editable: true, type: "number" },
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{ field: "dose", headerName: "Dose", width: 150, editable: true, type: "number" },
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{
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field: "dataCollectionParameters",
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headerName: "Data Collection Parameters (Raw)",
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width: 300,
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valueGetter: (params) =>
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params.row?.dataCollectionParameters
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? JSON.stringify(params.row.dataCollectionParameters)
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: "N/A", // Fallback if undefined
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editable: false,
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},
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{ field: "targetresolution", headerName: "Target Resolution", width: 150, editable: true, type: "number" },
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{ field: "aperture", headerName: "Aperture", width: 150, editable: true },
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{ field: "datacollectiontype", headerName: "Data Collection Type", width: 200, editable: true },
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{ field: "processingpipeline", headerName: "Processing Pipeline", width: 200, editable: true },
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{ field: "spacegroupnumber", headerName: "Space Group Number", width: 200, editable: true },
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{ field: "cellparameters", headerName: "Cell Parameters", width: 300, editable: true },
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{ field: "rescutkey", headerName: "ResCut Key", width: 150, editable: true },
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{ field: "rescutvalue", headerName: "ResCut Value", width: 150, editable: true, editable: true },
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{ field: "userresolution", headerName: "User Resolution", width: 150, editable: true, editable: true },
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{ field: "pdbid", headerName: "PDB ID", width: 150, editable: true },
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{ field: "autoprocfull", headerName: "AutoProc Full", width: 200, editable: true },
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{ field: "procfull", headerName: "Proc Full", width: 200, editable: true },
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{ field: "adpenabled", headerName: "ADP Enabled", width: 150, editable: true },
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{ field: "noano", headerName: "No Anomalous", width: 150, editable: true },
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{ field: "ffcscampaig", headerName: "FFCS Campaign", width: 150, editable: true },
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{ field: "trustedhigh", headerName: "Trusted High", width: 150, editable: true },
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{ field: "autoprocextraparams", headerName: "AutoProc Extra Params", width: 300, editable: true },
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{ field: "chiphiangles", headerName: "Chi Phi Angles", width: 150, editable: true },
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]);
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} catch (error) {
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console.error("Error fetching dewar samples:", error);
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@ -98,19 +141,112 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
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// Handle cell editing to persist changes to the backend
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const handleCellEditStop = async (params: GridCellEditStopParams) => {
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const { id, field, value } = params;
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// Validation to ensure we have valid data from the cell edit
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if (!id || !field || value === undefined) {
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console.error("Invalid edit inputs");
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console.error("Invalid edit inputs:", { id, field, value });
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return;
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}
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// Fetch the current row data (old state) based on its ID
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const updatedRow = rows.find((row) => row.id === id);
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if (!updatedRow) {
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console.error("Row not found for ID:", id);
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return;
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}
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// Create the updated sample, force-overwriting the changed cell value
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const updatedSample = {
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...updatedRow, // Include other fields from the existing row
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[field]: value, // Explicitly overwrite the updated field with new value
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};
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console.log("Payload sent to the backend:", updatedSample); // Log fixed payload
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try {
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// Call the update_sample API endpoint
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await DewarsService.updateSampleSampleIdPut(id as number, {
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[field]: value,
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});
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console.log("Sample updated successfully");
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// Optimistically update UI for better experience
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setRows((prevRows) =>
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prevRows.map((row) =>
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row.id === id ? { ...row, [field]: value } : row
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)
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);
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// API call to persist changes
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await DewarsService.updateSampleDewarsSamplesSampleIdPut(Number(id), updatedSample);
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console.log(`Sample with ID ${id} successfully updated.`);
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} catch (error) {
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console.error(`Error updating sample (id: ${id}):`, error);
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console.error(`Failed to update sample with ID ${id}:`, error);
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// Revert optimistic update on error
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setRows((prevRows) =>
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prevRows.map((row) => (row.id === id ? updatedRow : row))
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);
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}
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};
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const processRowUpdate = async (newRow: GridRowModel, oldRow: GridRowModel) => {
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try {
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console.log("Old row:", oldRow); // Log the original row
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console.log("Updated row:", newRow); // Log the updated data from the grid
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// Reconstruct 'data_collection_parameters' from the flat table structure
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const updatedDataCollectionParameters = {
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...(oldRow.data_collection_parameters || {}), // Preserve old values
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directory: newRow.directory ?? oldRow.data_collection_parameters?.directory,
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oscillation: newRow.oscillation ?? oldRow.data_collection_parameters?.oscillation,
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exposure: newRow.exposure ?? oldRow.data_collection_parameters?.exposure,
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totalrange: newRow.totalRange ?? oldRow.data_collection_parameters?.totalrange,
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transmission: newRow.transmission ?? oldRow.data_collection_parameters?.transmission,
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dose: newRow.dose ?? oldRow.data_collection_parameters?.dose,
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targetresolution: newRow.targetresolution ?? oldRow.data_collection_parameters?.targetresolution,
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aperture: newRow.aperture ?? oldRow.data_collection_parameters?.aperture,
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datacollectiontype: newRow.datacollectiontype ?? oldRow.data_collection_parameters?.datacollectiontype,
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processingpipeline: newRow.processingpipeline ?? oldRow.data_collection_parameters?.processingpipeline,
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spacegroupnumber: newRow.spacegroupnumber ?? oldRow.data_collection_parameters?.spacegroupnumber,
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//cellparameters: newRow.cellparameters ?? oldRow.data_collection_parameters?.cellparameters,
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rescutkey: newRow.rescutkey ?? oldRow.data_collection_parameters?.rescutkey,
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rescutvalue: newRow.rescutvalue ?? oldRow.data_collection_parameters?.rescutvalue,
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userresolution: newRow.userresolution ?? oldRow.data_collection_parameters?.userresolution,
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pdbid: newRow.pdbid ?? oldRow.data_collection_parameters?.pdbid,
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autoprocfull: newRow.autoprocfull ?? oldRow.data_collection_parameters?.autoprocfull,
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procfull: newRow.procfull ?? oldRow.data_collection_parameters?.procfull,
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adpenabled: newRow.adpenabled ?? oldRow.data_collection_parameters?.adpenabled,
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noano: newRow.noano ?? oldRow.data_collection_parameters?.noano,
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ffcscampaig: newRow.ffcscampaig ?? oldRow.data_collection_parameters?.ffcscampaig,
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trustedhigh: newRow.trustedhigh ?? oldRow.data_collection_parameters?.trustedhigh,
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//autoprocextraparams: newRow.autoprocextraparams ?? oldRow.data_collection_parameters?.autoprocextraparams,
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chiphiangles: newRow.chiphiangles ?? oldRow.data_collection_parameters?.chiphiangles,
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};
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// Assemble the final payload
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const payload = {
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...oldRow, // Include all original fields
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...newRow, // Overwrite or add updated fields
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data_collection_parameters: updatedDataCollectionParameters, // Include the merged/validated structure
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};
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console.log("Final payload sent to backend:", payload);
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// Optimistically update the UI
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setRows((prevRows) =>
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prevRows.map((row) =>
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row.id === newRow.id ? { ...row, ...payload } : row
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)
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);
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// Send the payload to the backend
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await DewarsService.updateSampleDewarsSamplesSampleIdPut(Number(newRow.id), payload);
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console.log(`Successfully updated sample with ID ${newRow.id}.`);
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return payload; // Return the updated row
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} catch (error) {
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console.error(`Failed to update sample with ID ${newRow.id}:`, error);
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// On failure, revert to the old row
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return oldRow;
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}
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};
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@ -120,7 +256,7 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
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rows={rows}
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columns={columns}
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pageSize={10}
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onCellEditStop={handleCellEditStop}
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processRowUpdate={processRowUpdate} // Exclusively handle updates
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/>
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</div>
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);
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@ -3506,8 +3506,8 @@
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-01-09T19:33:01.143326Z",
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"start_time": "2025-01-09T19:33:01.128023Z"
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"end_time": "2025-01-09T19:41:14.264895Z",
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"start_time": "2025-01-09T19:41:14.245643Z"
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}
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},
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"cell_type": "code",
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@ -3518,9 +3518,9 @@
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" api_instance = aareDBclient.SamplesApi(api_client)\n",
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"\n",
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" # Define the sample ID and event payload using the expected model\n",
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" sample_id = 260\n",
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" sample_id = 261\n",
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" event_payload = SampleEventCreate(\n",
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" event_type=\"Unmounted\" # Replace with actual event type if different\n",
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" event_type=\"Failed\" # Replace with actual event type if different\n",
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" )\n",
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"\n",
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" try:\n",
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@ -3543,7 +3543,7 @@
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"text": [
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"The response of post_sample_event:\n",
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"\n",
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"SampleEventResponse(id=417, sample_id=260, event_type='Unmounted', timestamp=datetime.datetime(2025, 1, 9, 20, 33, 1))\n"
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"SampleEventResponse(id=418, sample_id=261, event_type='Failed', timestamp=datetime.datetime(2025, 1, 9, 20, 41, 14))\n"
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]
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},
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{
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@ -3555,13 +3555,13 @@
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]
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}
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],
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"execution_count": 67
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"execution_count": 70
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},
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{
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-01-09T19:33:04.470152Z",
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"start_time": "2025-01-09T19:33:04.454152Z"
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"end_time": "2025-01-09T19:41:23.052434Z",
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"start_time": "2025-01-09T19:41:23.036108Z"
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}
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},
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"cell_type": "code",
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@ -3573,7 +3573,7 @@
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"\n",
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" try:\n",
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" # Get the last sample event\n",
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" last_event_response = api_instance.get_last_sample_event_samples_samples_sample_id_events_last_get(260)\n",
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" last_event_response = api_instance.get_last_sample_event_samples_samples_sample_id_events_last_get(261)\n",
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" print(\"The response of get_last_sample_event:\\n\")\n",
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" pprint(last_event_response)\n",
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"\n",
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@ -3588,7 +3588,7 @@
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"text": [
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"The response of get_last_sample_event:\n",
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"\n",
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"SampleEventResponse(id=417, sample_id=260, event_type='Unmounted', timestamp=datetime.datetime(2025, 1, 9, 20, 33, 1))\n"
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"SampleEventResponse(id=418, sample_id=261, event_type='Failed', timestamp=datetime.datetime(2025, 1, 9, 20, 41, 14))\n"
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]
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},
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{
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@ -3600,7 +3600,7 @@
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]
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}
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],
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"execution_count": 68
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"execution_count": 71
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}
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],
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"metadata": {
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|
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