diff --git a/backend/app/models.py b/backend/app/models.py
index dba5758..ad1ebab 100644
--- a/backend/app/models.py
+++ b/backend/app/models.py
@@ -1,4 +1,4 @@
-from sqlalchemy import Column, Integer, String, Date, ForeignKey
+from sqlalchemy import Column, Integer, String, Date, ForeignKey, JSON
from sqlalchemy.orm import relationship
from app.database import Base
from app.calculations import calculate_number_of_pucks, calculate_number_of_samples
@@ -107,6 +107,7 @@ class Sample(Base):
id = Column(Integer, primary_key=True, index=True, autoincrement=True)
sample_name = Column(String, index=True) # Matches `sample_name` in data creation
position = Column(Integer) # Matches `position` in data creation script
+ data_collection_parameters = Column(JSON, nullable=True)
# Foreign keys and relationships
puck_id = Column(Integer, ForeignKey('pucks.id'))
diff --git a/backend/app/routers/dewar.py b/backend/app/routers/dewar.py
index 01e4020..ce20bbd 100644
--- a/backend/app/routers/dewar.py
+++ b/backend/app/routers/dewar.py
@@ -1,9 +1,12 @@
from fastapi import APIRouter, HTTPException, status, Depends
from sqlalchemy.orm import Session, joinedload
from typing import List
-import uuid
+import logging
+from sqlalchemy.exc import SQLAlchemyError
+from pydantic import ValidationError
from app.schemas import Dewar as DewarSchema, DewarCreate, DewarUpdate
-from app.models import Dewar as DewarModel, Puck as PuckModel
+from app.models import Dewar as DewarModel, Puck as PuckModel, \
+ Sample as SampleModel # Assuming SampleModel is defined in models
from app.dependencies import get_db
router = APIRouter()
@@ -17,24 +20,55 @@ async def get_dewars(db: Session = Depends(get_db)):
@router.post("/", response_model=DewarSchema, status_code=status.HTTP_201_CREATED)
async def create_dewar(dewar: DewarCreate, db: Session = Depends(get_db)) -> DewarSchema:
- db_dewar = DewarModel(
- dewar_name=dewar.dewar_name,
- tracking_number=dewar.tracking_number,
- status=dewar.status,
- ready_date=dewar.ready_date,
- shipping_date=dewar.shipping_date,
- arrival_date=dewar.arrival_date,
- returning_date=dewar.returning_date,
- qrcode=dewar.qrcode,
- contact_person_id=dewar.contact_person_id,
- return_address_id=dewar.return_address_id
- )
+ try:
+ db_dewar = DewarModel(
+ dewar_name=dewar.dewar_name,
+ tracking_number=dewar.tracking_number,
+ status=dewar.status,
+ ready_date=dewar.ready_date,
+ shipping_date=dewar.shipping_date,
+ arrival_date=dewar.arrival_date,
+ returning_date=dewar.returning_date,
+ qrcode=dewar.qrcode,
+ contact_person_id=dewar.contact_person_id,
+ return_address_id=dewar.return_address_id
+ )
- db.add(db_dewar)
- db.commit()
- db.refresh(db_dewar)
+ db.add(db_dewar)
+ db.commit()
+ db.refresh(db_dewar)
- return db_dewar
+ for puck_data in dewar.pucks:
+ puck = PuckModel(
+ dewar_id=db_dewar.id,
+ puck_name=puck_data.puck_name,
+ puck_type=puck_data.puck_type,
+ puck_location_in_dewar=puck_data.puck_location_in_dewar,
+ )
+ db.add(puck)
+ db.commit()
+ db.refresh(puck)
+
+ for sample_data in puck_data.samples:
+ sample = SampleModel(
+ puck_id=puck.id,
+ sample_name=sample_data.sample_name,
+ position=sample_data.position,
+ # Ensure only valid attributes are set
+ data_collection_parameters=sample_data.data_collection_parameters,
+ )
+ db.add(sample)
+ db.commit()
+ db.refresh(sample)
+
+ return db_dewar
+
+ except SQLAlchemyError as e:
+ logging.error(f"Database error occurred: {e}")
+ raise HTTPException(status_code=500, detail="Internal server error")
+ except ValidationError as e:
+ logging.error(f"Validation error occurred: {e}")
+ raise HTTPException(status_code=400, detail="Validation error")
@router.get("/{dewar_id}", response_model=DewarSchema)
diff --git a/backend/app/routers/shipment.py b/backend/app/routers/shipment.py
index 6627772..b9869f3 100644
--- a/backend/app/routers/shipment.py
+++ b/backend/app/routers/shipment.py
@@ -9,7 +9,7 @@ from sqlalchemy.exc import SQLAlchemyError
from app.models import Shipment as ShipmentModel, ContactPerson as ContactPersonModel, Address as AddressModel, \
Proposal as ProposalModel, Dewar as DewarModel, Puck as PuckModel, Sample as SampleModel
from app.schemas import ShipmentCreate, UpdateShipmentComments, Shipment as ShipmentSchema, DewarUpdate, \
- ContactPerson as ContactPersonSchema, Sample as SampleSchema, DewarCreate, PuckCreate, SampleCreate
+ ContactPerson as ContactPersonSchema, Sample as SampleSchema, DewarCreate, PuckCreate, SampleCreate, DewarSchema
from app.database import get_db
from app.crud import get_shipments, get_shipment_by_id
@@ -38,6 +38,19 @@ async def fetch_shipments(id: Optional[int] = Query(None), db: Session = Depends
logging.info(f"Shipment ID: {shipment.id}, Shipment Name: {shipment.shipment_name}")
return shipments
+@router.get("/{shipment_id}/dewars", response_model=List[DewarSchema])
+async def get_dewars_by_shipment_id(shipment_id: int, db: Session = Depends(get_db)):
+ shipment = db.query(ShipmentModel).filter(ShipmentModel.id == shipment_id).first()
+ if not shipment:
+ raise HTTPException(status_code=404, detail="Shipment not found")
+
+ dewars = db.query(DewarModel).filter(DewarModel.shipment_id == shipment_id).all()
+ if not dewars:
+ raise HTTPException(status_code=404, detail="No dewars found for this shipment")
+
+ return dewars
+
+
@router.post("", response_model=ShipmentSchema, status_code=status.HTTP_201_CREATED)
async def create_shipment(shipment: ShipmentCreate, db: Session = Depends(get_db)):
@@ -220,58 +233,55 @@ async def update_shipment_comments(shipment_id: int, comments_data: UpdateShipme
@router.post("/{shipment_id}/add_dewar_puck_sample", response_model=ShipmentSchema, status_code=status.HTTP_201_CREATED)
-async def add_dewar_puck_sample_to_shipment(
- shipment_id: int,
- payload: DewarCreate,
- db: Session = Depends(get_db)
-):
+def add_dewar_puck_sample_to_shipment(shipment_id: int, payload: DewarCreate, db: Session = Depends(get_db)):
shipment = db.query(ShipmentModel).filter(ShipmentModel.id == shipment_id).first()
if not shipment:
- logging.error(f"Shipment not found with ID: {shipment_id}")
raise HTTPException(status_code=404, detail="Shipment not found")
try:
- dewar = DewarModel(
- shipment_id=shipment_id,
- dewar_name=payload.dewar_name,
- tracking_number=payload.tracking_number,
- status=payload.status,
- contact_person_id=payload.contact_person_id,
- return_address_id=payload.return_address_id,
- )
- db.add(dewar)
- db.commit()
- db.refresh(dewar)
-
- for puck_data in payload.pucks:
- puck = PuckModel(
- dewar_id=dewar.id,
- puck_name=puck_data.puck_name,
- puck_type=puck_data.puck_type,
- puck_location_in_dewar=puck_data.puck_location_in_dewar,
- )
- db.add(puck)
- db.commit()
- db.refresh(puck)
-
- for sample_data in puck_data.samples:
- sample = SampleModel(
- puck_id=puck.id,
- sample_name=sample_data.sample_name,
- position=sample_data.position,
- data_collection_parameters=sample_data.data_collection_parameters,
- )
- db.add(sample)
+ for dewar_data in payload.dewars:
+ dewar = db.query(DewarModel).filter(DewarModel.dewar_name == dewar_data.dewar_name).first()
+ if dewar:
+ # Update existing dewar
+ dewar.tracking_number = dewar_data.tracking_number
+ dewar.status = dewar_data.status
db.commit()
- db.refresh(sample)
+ else:
+ dewar = DewarModel(
+ shipment_id=shipment_id,
+ dewar_name=dewar_data.dewar_name,
+ tracking_number=dewar_data.tracking_number,
+ status=dewar_data.status,
+ )
+ db.add(dewar)
+ db.commit()
+ db.refresh(dewar)
+
+ for puck_data in dewar_data.pucks:
+ puck = PuckModel(
+ dewar_id=dewar.id,
+ puck_name=puck_data.puck_name,
+ puck_type=puck_data.puck_type,
+ puck_location_in_dewar=puck_data.puck_location_in_dewar,
+ )
+ db.add(puck)
+ db.commit()
+ db.refresh(puck)
+
+ for sample_data in puck_data.samples:
+ sample = SampleModel(
+ puck_id=puck.id,
+ sample_name=sample_data.sample_name,
+ position=sample_data.position,
+ )
+ db.add(sample)
+ db.commit()
+ db.refresh(sample)
db.refresh(shipment)
except SQLAlchemyError as e:
- logging.error(f"Database error occurred: {e}")
- raise HTTPException(status_code=500, detail="Internal server error")
+ raise HTTPException(status_code=500, detail=f"Database error: {e}")
except ValidationError as e:
- logging.error(f"Validation error occurred: {e}")
- raise HTTPException(status_code=400, detail="Validation error")
+ raise HTTPException(status_code=400, detail=f"Validation error: {e}")
- logging.info(f"Successfully added dewar, puck, and sample for shipment ID: {shipment_id}")
- return shipment
+ return shipment
\ No newline at end of file
diff --git a/backend/app/schemas.py b/backend/app/schemas.py
index 0eaf61c..4b17553 100644
--- a/backend/app/schemas.py
+++ b/backend/app/schemas.py
@@ -101,7 +101,8 @@ class Sample(BaseModel):
class SampleCreate(BaseModel):
sample_name: str = Field(..., alias="crystalname")
position: int = Field(..., alias="positioninpuck")
- data_collection_parameters: DataCollectionParameters
+ data_collection_parameters: Optional[DataCollectionParameters] = None
+ results: Optional[Results] = None
class Config:
populate_by_name = True
@@ -115,8 +116,11 @@ class PuckBase(BaseModel):
puck_location_in_dewar: int
-class PuckCreate(PuckBase):
- pass
+class PuckCreate(BaseModel):
+ puck_name: str
+ puck_type: str
+ puck_location_in_dewar: int
+ samples: List[SampleCreate] = []
class PuckUpdate(BaseModel):
@@ -152,6 +156,7 @@ class DewarBase(BaseModel):
qrcode: str
contact_person_id: Optional[int]
return_address_id: Optional[int]
+ pucks: List[PuckCreate] = []
class DewarCreate(DewarBase):
@@ -181,6 +186,17 @@ class DewarUpdate(BaseModel):
contact_person_id: Optional[int] = None
address_id: Optional[int] = None
+class DewarSchema(BaseModel):
+ id: int
+ dewar_name: str
+ tracking_number: str
+ status: str
+ contact_person_id: int
+ return_address_id: int
+
+ class Config:
+ from_attributes = True
+
# Proposal schemas
class Proposal(BaseModel):
diff --git a/frontend/src/components/SpreadsheetTable.tsx b/frontend/src/components/SpreadsheetTable.tsx
index f93992d..017dbc9 100644
--- a/frontend/src/components/SpreadsheetTable.tsx
+++ b/frontend/src/components/SpreadsheetTable.tsx
@@ -11,7 +11,12 @@ import {
TextField,
Typography,
Button,
- Box
+ Box,
+ Dialog,
+ DialogActions,
+ DialogContent,
+ DialogContentText,
+ DialogTitle
} from '@mui/material';
import { SpreadsheetService, ShipmentsService, DewarsService, ApiError } from '../../openapi';
import * as ExcelJS from 'exceljs';
@@ -30,6 +35,9 @@ const SpreadsheetTable = ({
const [editingCell, setEditingCell] = useState({});
const [nonEditableCells, setNonEditableCells] = useState(new Set());
const [isSubmitting, setIsSubmitting] = useState(false);
+ const [showUpdateDialog, setShowUpdateDialog] = useState(false);
+ const [dewarsToReplace, setDewarsToReplace] = useState([]);
+ const [dewarsToCreate, setDewarsToCreate] = useState(new Map());
const initialNewDewarState = {
number_of_pucks: 0,
@@ -44,7 +52,7 @@ const SpreadsheetTable = ({
dewar_name: '',
tracking_number: 'UNKNOWN',
status: 'In preparation',
- pucks: []
+ pucks: [] // Ensure 'pucks' array exists
};
const [newDewar, setNewDewar] = useState(initialNewDewarState);
@@ -141,36 +149,80 @@ const SpreadsheetTable = ({
'dewarname': 0,
'puckname': 1,
'pucktype': 2,
- // Add other fields as needed
+ 'crystalname': 3,
+ 'positioninpuck': 4,
+ 'priority': 5,
+ 'comments': 6,
+ 'directory': 7,
+ 'proteinname': 8,
+ 'oscillation': 9,
+ 'aperture': 10,
+ 'exposure': 11,
+ 'totalrange': 12,
+ 'transmission': 13,
+ 'dose': 14,
+ 'targetresolution': 15,
+ 'datacollectiontype': 16,
+ 'processingpipeline': 17,
+ 'spacegroupnumber': 18,
+ 'cellparameters': 19,
+ 'rescutkey': 20,
+ 'rescutvalue': 21,
+ 'userresolution': 22,
+ 'pdbid': 23,
+ 'autoprocfull': 24,
+ 'procfull': 25,
+ 'adpenabled': 26,
+ 'noano': 27,
+ 'ffcscampaign': 28,
+ 'trustedhigh': 29,
+ 'autoprocextraparams': 30,
+ 'chiphiangles': 31
};
- const createDewarsFromSheet = async (data, contactPerson, returnAddress) => {
+ const checkIfDewarExists = async (dewarName) => {
+ if (!selectedShipment) return null;
+
+ try {
+ const shipDewars = await ShipmentsService.getDewarsByShipmentIdShipmentsShipmentIdDewarsGet(selectedShipment.id);
+ return shipDewars.find((d) => d.dewar_name === dewarName);
+ } catch (error) {
+ console.error('Failed to fetch existing dewars:', error);
+ return null;
+ }
+ };
+
+ const createOrUpdateDewarsFromSheet = async (data, contactPerson, returnAddress) => {
if (!contactPerson?.id || !returnAddress?.id) {
console.error('contact_person_id or return_address_id is missing');
return null;
}
const dewars = new Map();
+ const puckPositionMap = new Map();
+ const dewarsToReplace = [];
const dewarNameIdx = fieldToCol['dewarname'];
const puckNameIdx = fieldToCol['puckname'];
const puckTypeIdx = fieldToCol['pucktype'];
+ const sampleNameIdx = fieldToCol['crystalname'];
+ const samplePositionIdx = fieldToCol['positioninpuck'];
- let puckPositionInDewar = 1;
+ for (let rowIndex = 0; rowIndex < data.length; rowIndex++) {
+ const row = data[rowIndex];
- for (const row of data) {
if (!row.data) {
- console.error(`Row data is missing`);
+ console.error('Row data is missing');
continue;
}
const dewarName = typeof row.data[dewarNameIdx] === 'string' ? row.data[dewarNameIdx].trim() : null;
- const puckName = typeof row.data[puckNameIdx] === 'string' ? row.data[puckNameIdx].trim() : null;
+ const puckName = row.data[puckNameIdx] !== undefined && row.data[puckNameIdx] !== null ? String(row.data[puckNameIdx]).trim() : null;
const puckType = typeof row.data[puckTypeIdx] === 'string' ? row.data[puckTypeIdx] : 'Unipuck';
+ const sampleName = typeof row.data[sampleNameIdx] === 'string' ? row.data[sampleNameIdx].trim() : null;
+ const samplePosition = row.data[samplePositionIdx] !== undefined && row.data[samplePositionIdx] !== null ? Number(row.data[samplePositionIdx]) : null;
- console.log(`Processing Dewar: ${dewarName}, Puck: ${puckName}, Type: ${puckType}`);
-
- if (dewarName) {
+ if (dewarName && puckName) {
let dewar;
if (!dewars.has(dewarName)) {
dewar = {
@@ -181,44 +233,116 @@ const SpreadsheetTable = ({
pucks: []
};
dewars.set(dewarName, dewar);
- puckPositionInDewar = 1;
- console.log(`Created new dewar: ${dewarName}`);
+ puckPositionMap.set(dewarName, new Map());
+
+ // Check if the dewar exists in the shipment
+ const existingDewar = await checkIfDewarExists(dewarName);
+ if (existingDewar) {
+ dewarsToReplace.push(existingDewar);
+ }
} else {
dewar = dewars.get(dewarName);
- puckPositionInDewar++;
- console.log(`Found existing dewar: ${dewarName}`);
}
- const puck = {
- puck_name: puckName || 'test', // Fixed puck name
- puck_type: puckType || 'Unipuck', // Fixed puck type
- puck_position_in_dewar: puckPositionInDewar
- };
- dewar.pucks.push(puck);
+ let puckPositions = puckPositionMap.get(dewarName);
+ if (!puckPositions.has(puckName)) {
+ puckPositions.set(puckName, puckPositions.size + 1);
+ }
+ const puckPosition = puckPositions.get(puckName);
- console.log(`Added puck: ${JSON.stringify(puck)}`);
+ let puck = dewar.pucks.find(p => p.puck_name === puckName);
+ if (!puck) {
+ puck = {
+ puck_name: puckName,
+ puck_type: puckType,
+ puck_location_in_dewar: puckPosition,
+ samples: []
+ };
+ dewar.pucks.push(puck);
+ }
+
+ const sample = {
+ sample_name: sampleName,
+ position: samplePosition,
+ results: null // Placeholder for results field
+ };
+
+ if (isNaN(sample.position)) {
+ console.error(`Invalid sample position for sample ${sample.sample_name} in puck ${puckName}`);
+ } else {
+ puck.samples.push(sample);
+ }
} else {
- console.error('Dewar name is missing in the row');
+ if (!dewarName) {
+ console.error(`Dewar name is missing in row ${rowIndex}`);
+ }
+ if (!puckName) {
+ console.error(`Puck name is missing in row ${rowIndex}`);
+ }
}
}
const dewarsArray = Array.from(dewars.values());
+
+ // Save dewars array for later use in handleConfirmUpdate
+ setDewarsToCreate(dewars);
+
+ if (dewarsArray.length > 0 && dewarsToReplace.length > 0) {
+ setDewarsToReplace(dewarsToReplace);
+ setShowUpdateDialog(true);
+ } else {
+ await handleDewarCreation(dewarsArray);
+ }
+ };
+
+ const handleConfirmUpdate = async () => {
+ if (dewarsToReplace.length === 0) return;
+
+ try {
+ for (const dewar of dewarsToReplace) {
+ await DewarsService.deleteDewarDewarsDewarIdDelete(dewar.id);
+ }
+ const dewarsArray = Array.from(dewarsToCreate.values());
+ await handleDewarCreation(dewarsArray);
+ console.log('Dewars replaced successfully');
+ } catch (error) {
+ console.error('Error replacing dewar', error);
+ if (error instanceof ApiError && error.body) {
+ console.error('Validation errors:', error.body.detail);
+ } else {
+ console.error('Unexpected error:', error);
+ }
+ }
+ setShowUpdateDialog(false);
+ setDewarsToReplace([]);
+ setDewarsToCreate(new Map());
+ };
+
+ const handleCancelUpdate = () => {
+ setShowUpdateDialog(false);
+ setDewarsToReplace([]);
+ setDewarsToCreate(new Map());
+ };
+
+ const handleDewarCreation = async (dewarsArray) => {
for (const dewar of dewarsArray) {
try {
- // Call to create the dewar
- const createdDewar = await DewarsService.createDewarDewarsPost(dewar);
- console.log(`Created dewar: ${createdDewar.id}`);
+ if (!dewar.pucks || dewar.pucks.length === 0) {
+ console.error(`Dewar ${dewar.dewar_name} does not have any pucks.`);
+ continue;
+ }
+
+ const createdDewar = await DewarsService.createDewarDewarsPost(dewar);
- // Add dewar to the shipment if created successfully
if (createdDewar && selectedShipment) {
await ShipmentsService.addDewarToShipmentShipmentsShipmentIdAddDewarPost(
selectedShipment.id,
createdDewar.id
);
- console.log(`Added dewar to shipment: ${createdDewar.id}`);
+ console.log(`Dewar ${createdDewar.dewar_name} with ID ${createdDewar.id} created and added to the shipment.`);
}
} catch (error) {
- console.error(`Error adding dewar`, error);
+ console.error('Error adding dewar', error);
if (error instanceof ApiError && error.body) {
console.error('Validation errors:', error.body.detail);
} else {
@@ -226,8 +350,6 @@ const SpreadsheetTable = ({
}
}
}
-
- return dewarsArray;
};
const handleSubmit = async () => {
@@ -241,18 +363,12 @@ const SpreadsheetTable = ({
setIsSubmitting(true);
console.log('All data is valid. Proceeding with submission...');
- const processedDewars = await createDewarsFromSheet(
+ await createOrUpdateDewarsFromSheet(
raw_data,
selectedShipment?.contact_person,
selectedShipment?.return_address
);
- if (processedDewars && processedDewars.length > 0) {
- console.log('Dewars processed successfully.');
- } else {
- console.error('No valid dewars were created.');
- }
-
setIsSubmitting(false);
} else {
console.log('There are validation errors in the dataset. Please correct them before submission.');
@@ -270,22 +386,12 @@ const SpreadsheetTable = ({
});
});
- const buffer = await workbook.xlsx.writeBuffer();
- const blob = new Blob([buffer], { type: 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' });
-
- saveAs(blob, 'corrected_data.xlsx');
+ workbook.xlsx.writeBuffer().then((buffer) => {
+ const blob = new Blob([buffer], { type: 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' });
+ saveAs(blob, 'corrected_spreadsheet.xlsx');
+ });
};
- useEffect(() => {
- console.log('Raw data:', raw_data);
- console.log('Errors:', localErrors);
- console.log('Headers:', headers);
- }, [raw_data, localErrors, headers]);
-
- if (!raw_data || !headers) {
- return Loading...
;
- }
-
return (
@@ -323,21 +429,25 @@ const SpreadsheetTable = ({
return (
- setEditingCell({ ...editingCell, [`${rowIndex}-${colIndex}`]: e.target.value })}
- onKeyDown={(e) => {
- if (e.key === "Enter") {
- handleCellEdit(rowIndex, colIndex);
- }
- }}
- onBlur={() => handleCellBlur(rowIndex, colIndex)}
- error={isInvalid}
- fullWidth
- variant="outlined"
- size="small"
- disabled={isReadonly}
- />
+ {isInvalid ? (
+ setEditingCell({ ...editingCell, [`${rowIndex}-${colIndex}`]: e.target.value })}
+ onKeyDown={(e) => {
+ if (e.key === "Enter") {
+ handleCellEdit(rowIndex, colIndex);
+ }
+ }}
+ onBlur={() => handleCellBlur(rowIndex, colIndex)}
+ error={isInvalid}
+ fullWidth
+ variant="outlined"
+ size="small"
+ disabled={isReadonly}
+ />
+ ) : (
+ cellValue
+ )}
);
@@ -346,6 +456,28 @@ const SpreadsheetTable = ({
))}
+
+
);
};