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Refactor dewar and sample handling; improve grid data binding

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Updated Dewar and Sample schemas, added nested relationships, and adjusted API responses for better data handling. Simplified puck normalization, enhanced data grid logic in the frontend, and implemented a PUT endpoint for updating samples. Incremented backend version to 0.1.0a15 and added new HTTP request example.
This commit is contained in:
GotthardG 2025-01-09 13:01:52 +01:00
parent ae20d6112a
commit 9bfcc30981
7 changed files with 188 additions and 124 deletions
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108
backend/app/routers/dewar.py
View File

@ -17,7 +17,12 @@ from app.schemas import (
DewarTypeCreate,
DewarSerialNumber as DewarSerialNumberSchema,
DewarSerialNumberCreate,
Shipment as ShipmentSchema, # Clearer name for schema
Shipment as ShipmentSchema,
Dewar,
SampleUpdate,
Sample,
Puck,
SampleEventResponse, # Clearer name for schema
)
from app.models import (
Dewar as DewarModel,
@ -308,41 +313,86 @@ async def download_dewar_label(dewar_id: int, db: Session = Depends(get_db)):
)
@router.get("/dewars/{dewar_id}/samples", response_model=dict)
@router.get("/dewars/{dewar_id}/samples", response_model=Dewar)
async def get_dewar_samples(dewar_id: int, db: Session = Depends(get_db)):
# Fetch Dewar, associated Pucks, and Samples
# Fetch the Dewar with nested relationships
dewar = db.query(DewarModel).filter(DewarModel.id == dewar_id).first()
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
pucks = db.query(PuckModel).filter(PuckModel.dewar_id == dewar.id).all()
data = {"dewar": {"id": dewar.id, "dewar_name": dewar.dewar_name}, "pucks": []}
for puck in pucks:
samples = db.query(SampleModel).filter(SampleModel.puck_id == puck.id).all()
data["pucks"].append(
{
"id": puck.id,
"name": puck.puck_name,
"type": puck.puck_type,
"samples": [
{
"id": sample.id,
"position": sample.position,
"dewar_name": dewar.dewar_name,
"sample_name": sample.sample_name,
"priority": sample.priority,
"comments": sample.comments,
"proteinname": sample.proteinname,
**(sample.data_collection_parameters or {}),
}
for sample in samples
# Explicitly map nested relationships
dewar_data = {
"id": dewar.id,
"dewar_name": dewar.dewar_name,
"tracking_number": dewar.tracking_number,
"status": dewar.status,
"number_of_pucks": len(dewar.pucks), # Calculate number of pucks
"number_of_samples": sum(
len(puck.samples) for puck in dewar.pucks
), # Calculate total samples
"ready_date": dewar.ready_date,
"shipping_date": dewar.shipping_date,
"arrival_date": dewar.arrival_date,
"returning_date": dewar.returning_date,
"contact_person_id": dewar.contact_person.id if dewar.contact_person else None,
"return_address_id": dewar.return_address.id if dewar.return_address else None,
"shipment_id": dewar.shipment_id,
"contact_person": dewar.contact_person,
"return_address": dewar.return_address,
"pucks": [
Puck(
id=puck.id,
puck_name=puck.puck_name,
puck_type=puck.puck_type,
puck_location_in_dewar=puck.puck_location_in_dewar,
dewar_id=dewar.id,
samples=[
Sample(
id=sample.id,
sample_name=sample.sample_name,
position=sample.position,
puck_id=sample.puck_id,
crystalname=getattr(sample, "crystalname", None),
proteinname=getattr(sample, "proteinname", None),
positioninpuck=getattr(sample, "positioninpuck", None),
priority=sample.priority,
comments=sample.comments,
data_collection_parameters=sample.data_collection_parameters,
events=[
SampleEventResponse.from_orm(event)
for event in sample.events
],
)
for sample in puck.samples
],
}
)
)
for puck in dewar.pucks
],
}
return data
# Return the Pydantic Dewar model
return Dewar(**dewar_data)
@router.put("/samples/{sample_id}", response_model=Sample)
async def update_sample(
sample_id: int,
sample_update: SampleUpdate,
db: Session = Depends(get_db),
):
sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
if not sample:
raise HTTPException(status_code=404, detail="Sample not found")
# Apply updates
for key, value in sample_update.dict(exclude_unset=True).items():
if hasattr(sample, key):
setattr(sample, key, value)
# Save changes
db.commit()
db.refresh(sample)
return Sample.from_orm(sample)
@router.get("/", response_model=List[DewarSchema])

14
backend/app/routers/puck.py
View File

@ -34,8 +34,7 @@ def normalize_puck_name(name: str) -> str:
"""
Normalize a puck_name to remove special characters and ensure consistent formatting.
"""
name = str(name).strip().replace(" ", "_").upper()
name = re.sub(r"[^A-Z0-9]", "", name) # Remove special characters
name = re.sub(r"[^A-Z0-9]", "", name.upper()) # Remove special characters
return name
@ -50,22 +49,11 @@ async def set_tell_positions(
):
results = []
# Helper function to normalize puck names for database querying
def normalize_puck_name(name: str) -> str:
return str(name).strip().replace(" ", "_").upper()
if not pucks:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
detail="Payload cannot be empty. Provide at least one puck.",
)
# Retrieve all pucks in the database with their most recent
# `tell_position_set` event
all_pucks_with_last_event = (
db.query(PuckModel, PuckEventModel)
.outerjoin(PuckEventModel, PuckEventModel.puck_id == PuckModel.id)
.filter(PuckEventModel.event_type == "tell_position_set")
.order_by(PuckEventModel.puck_id, PuckEventModel.timestamp.desc())
.all()
)

20
backend/app/schemas.py
View File

@ -423,7 +423,10 @@ class Sample(BaseModel):
priority: Optional[int] = None
comments: Optional[str] = None
data_collection_parameters: Optional[DataCollectionParameters]
events: List[SampleEventCreate] = []
events: List[SampleEventResponse] = []
class Config:
from_attributes = True
class SampleCreate(BaseModel):
@ -501,6 +504,9 @@ class DewarBase(BaseModel):
return_address_id: Optional[int]
pucks: List[PuckCreate] = []
class Config:
from_attributes = True
class DewarCreate(DewarBase):
pass
@ -612,6 +618,18 @@ class SlotSchema(BaseModel):
from_attributes = True
class SampleUpdate(BaseModel):
sample_name: Optional[str]
proteinname: Optional[str]
priority: Optional[int]
position: Optional[int]
comments: Optional[str]
data_collection_parameters: Optional[DataCollectionParameters]
class Config:
from_attributes = True
class SetTellPosition(BaseModel):
puck_name: str
segment: Optional[str] = Field(

4
backend/main.py
View File

@ -139,8 +139,8 @@ def on_startup():
load_slots_data(db)
else: # dev or test environments
print(f"{environment.capitalize()} environment: Regenerating database.")
Base.metadata.drop_all(bind=engine)
Base.metadata.create_all(bind=engine)
# Base.metadata.drop_all(bind=engine)
# Base.metadata.create_all(bind=engine)
if environment == "dev":
from app.database import load_sample_data

159
frontend/src/components/SampleSpreadsheetGrid.tsx
View File

@ -18,83 +18,79 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
}
const fetchSamples = async () => {
try {
const response = await DewarsService.getDewarSamplesDewarsDewarsDewarIdSamplesGet(dewarId);
const dewarData = response; // Assume response is already in correct structure
try {
const response = await DewarsService.getDewarSamplesDewarsDewarsDewarIdSamplesGet(dewarId);
console.log("Response from backend:", response);
const dewarData = response; // Assume response is already in correct structure
// Transform pucks and samples into rows for the grid
const allRows = [];
dewarData.pucks.forEach((puck: any) => {
puck.samples.forEach((sample: any) => {
allRows.push({
id: sample.id,
puckId: puck.id,
puckName: puck.name,
puckType: puck.type,
dewarName: dewarData.dewar.dewar_name,
position: sample.position,
crystalName: sample.sample_name,
proteinName: sample.proteinname,
priority: sample.priority,
comments: sample.comments,
directory: sample.directory,
oscillation: sample.oscillation,
aperture: sample.aperture,
exposure: sample.exposure,
totalRange: sample.totalrange,
transmission: sample.transmission,
dose: sample.dose,
targetResolution: sample.targetresolution,
datacollectiontype: sample.datacollectiontype,
processingpipeline: sample.processingpipeline,
spacegroupnumber: sample.spacegroupnumber,
cellparameters: sample.cellparameters,
rescutkey: sample.rescutkey,
//rescutvalues: sample.rescutvalues,
pdbid: sample.pdbid,
autoprocfull: sample.autoprocfull,
procfull: sample.procfull,
adpenabled: sample.adpenabled,
noano: sample.noano,
ffcscampaign: sample.ffcscampaign,
// Transform pucks and samples into rows for the grid
const allRows: any[] = [];
dewarData.pucks.forEach((puck: any) => {
puck.samples.forEach((sample: any) => {
const {
directory,
oscillation,
exposure,
totalrange,
transmission,
dose,
} = sample.data_collection_parameters || {};
allRows.push({
id: sample.id,
puckId: puck.id,
puckName: puck.puck_name,
puckType: puck.puck_type,
dewarName: dewarData.dewar_name,
position: sample.position,
crystalName: sample.sample_name,
proteinName: sample.proteinname,
priority: sample.priority,
comments: sample.comments,
directory: directory || null,
oscillation: oscillation || null,
exposure: exposure || null,
totalRange: totalrange || null,
transmission: transmission || null,
dose: dose || null,
dataCollectionParameters: sample.data_collection_parameters || {}, // Ensure this is never undefined
});
});
});
});
});
setRows(allRows);
console.log("All rows for DataGrid:", allRows);
setRows(allRows);
setColumns([
{ field: "dewarName", headerName: "Dewar Name", width: 150, editable: false },
{ field: "puckName", headerName: "Puck Name", width: 150 },
{ field: "puckType", headerName: "Puck Type", width: 150 },
{ field: "crystalName", headerName: "Crystal Name", width: 200, editable: true },
{ field: "proteinName", headerName: "Protein Name", width: 200, editable: true },
{ field: "position", headerName: "Position", width: 100, editable: true, type: "number" },
{ field: "priority", headerName: "Priority", width: 100, editable: true, type: "number" },
{ field: "comments", headerName: "Comments", width: 300, editable: true },
{ field: "directory", headerName: "Directory", width: 200 },
{ field: "oscillation", headerName: "Oscillation", width: 150, editable: true, type: "number" },
{ field: "aperture", headerName: "Aperture", width: 150, editable: true, type: "number" },
{ field: "exposure", headerName: "Exposure", width: 150, editable: true, type: "number" },
{ field: "totalRange", headerName: "Total Range", width: 150, editable: true, type: "number" },
{ field: "transmission", headerName: "Transmission", width: 150, editable: true, type: "number" },
{ field: "dose", headerName: "Dose", width: 150, editable: true, type: "number" },
{ field: "targetResolution", headerName: "Target Resolution", width: 200, editable: true, type: "number" },
{ field: "datacollectiontype", headerName: "Data Collection Type", width: 200 },
{ field: "processingpipeline", headerName: "Processing Pipeline", width: 200 },
{ field: "spacegroupnumber", headerName: "Space Group Number", width: 150, type: "number" },
{ field: "cellparameters", headerName: "Cell Parameters", width: 200 },
{ field: "rescutkey", headerName: "Rescut Key", width: 150 },
{ field: "pdbid", headerName: "PDB ID", width: 150 },
{ field: "autoprocfull", headerName: "Auto Proc Full", width: 150 },
{ field: "procfull", headerName: "Proc Full", width: 150 },
{ field: "adpenabled", headerName: "ADP Enabled", width: 150, editable: true, type: "boolean" },
{ field: "noano", headerName: "No Ano", width: 150, editable: true, type: "boolean" },
{ field: "ffcscampaign", headerName: "FFCS Campaign", width: 200 },
]);
} catch (error) {
console.error("Error fetching dewar samples:", error);
}
};
// Define columns for the grid
setColumns([
{ field: "dewarName", headerName: "Dewar Name", width: 150, editable: false },
{ field: "puckName", headerName: "Puck Name", width: 150 },
{ field: "puckType", headerName: "Puck Type", width: 150 },
{ field: "crystalName", headerName: "Crystal Name", width: 200, editable: true },
{ field: "proteinName", headerName: "Protein Name", width: 200, editable: true },
{ field: "position", headerName: "Position", width: 100, editable: true, type: "number" },
{ field: "priority", headerName: "Priority", width: 100, editable: true, type: "number" },
{ field: "comments", headerName: "Comments", width: 300, editable: true },
{ field: "directory", headerName: "Directory", width: 200 },
{ field: "oscillation", headerName: "Oscillation", width: 150, editable: true, type: "number" },
{ field: "exposure", headerName: "Exposure", width: 150, editable: true, type: "number" },
{ field: "totalRange", headerName: "Total Range", width: 150, editable: true, type: "number" },
{ field: "transmission", headerName: "Transmission", width: 150, editable: true, type: "number" },
{ field: "dose", headerName: "Dose", width: 150, editable: true, type: "number" },
{
field: "dataCollectionParameters",
headerName: "Data Collection Parameters (Raw)",
width: 300,
valueGetter: (params) =>
params.row?.dataCollectionParameters
? JSON.stringify(params.row.dataCollectionParameters)
: "N/A", // Fallback if undefined
editable: false,
},
]);
} catch (error) {
console.error("Error fetching dewar samples:", error);
}
};
fetchSamples();
}, [dewarId]);
@ -102,12 +98,19 @@ const SampleSpreadsheet: React.FC<SampleSpreadsheetProps> = ({ dewarId }) => {
// Handle cell editing to persist changes to the backend
const handleCellEditStop = async (params: GridCellEditStopParams) => {
const { id, field, value } = params;
if (!id || !field || value === undefined) {
console.error("Invalid edit inputs");
return;
}
try {
// Example: Replace with a proper OpenAPI call if available
await DewarsService.updateSampleData(id as number, { [field]: value }); // Assuming this exists
console.log("Updated successfully");
// Call the update_sample API endpoint
await DewarsService.updateSampleSampleIdPut(id as number, {
[field]: value,
});
console.log("Sample updated successfully");
} catch (error) {
console.error("Error saving data:", error);
console.error(`Error updating sample (id: ${id}):`, error);
}
};

2
pyproject.toml
View File

@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "aareDB"
version = "0.1.0a14"
version = "0.1.0a15"
description = "Backend for next gen sample management system"
authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
license = {text = "MIT"}

5
req.http Normal file
View File

@ -0,0 +1,5 @@
### GET request to example server
PUT https://127.0.0.1:8000/pucks/set-tell-positions
###