Make shipment fields optional and refactor test scripts.
Updated the `number_of_pucks` and `number_of_samples` fields in the `schemas.py` to be optional for greater flexibility. Simplified the test Jupyter Notebook by restructuring imports and consolidating function calls for better readability and maintainability.
This commit is contained in:
GotthardG
@ -126,7 +126,7 @@ const ShipmentDetails: React.FC<ShipmentDetailsProps> = ({
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throw new Error('Missing required fields');
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}
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const createdDewar = await DewarsService.createDewarDewarsPost(newDewarToPost);
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const createdDewar = await DewarsService.createOrUpdateDewarDewarsPost(selectedShipment.id, newDewarToPost);
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if (createdDewar && selectedShipment) {
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const updatedShipment = await ShipmentsService.addDewarToShipmentShipmentsShipmentIdAddDewarPost(selectedShipment.id, createdDewar.id);
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@ -63,7 +63,6 @@ const SpreadsheetTable = ({
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shipping_date: null,
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arrival_date: null,
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returning_date: null,
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qrcode: 'N/A',
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contact_person_id: selectedShipment?.contact_person?.id,
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return_address_id: selectedShipment?.return_address?.id,
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dewar_name: '',
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@ -236,14 +235,23 @@ const SpreadsheetTable = ({
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'chiphiangles': 31
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};
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const checkIfDewarExists = async (dewarName) => {
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const checkIfDewarExists = async (dewarName: string) => {
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if (!selectedShipment) return null;
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try {
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// Fetch dewars related to the current shipment via API
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const shipDewars = await ShipmentsService.getDewarsByShipmentIdShipmentsShipmentIdDewarsGet(selectedShipment.id);
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return shipDewars.find((d) => d.dewar_name === dewarName);
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// Search for dewar by name within the shipment
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const existingDewar = shipDewars.find((d) => d.dewar_name === dewarName);
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if (existingDewar) {
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console.log(`Dewar "${dewarName}" exists with ID: ${existingDewar.id}`);
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return existingDewar;
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}
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return null;
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} catch (error) {
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console.error('Failed to fetch existing dewars:', error);
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console.error("Failed to fetch existing dewars:", error);
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return null;
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}
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};
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@ -258,75 +266,34 @@ const SpreadsheetTable = ({
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const puckPositionMap = new Map();
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const dewarsToReplace = [];
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const dewarNameIdx = fieldToCol['dewarname'];
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const puckNameIdx = fieldToCol['puckname'];
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const puckTypeIdx = fieldToCol['pucktype'];
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const sampleNameIdx = fieldToCol['crystalname'];
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const proteinNameIdx = fieldToCol['proteinname'];
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const samplePositionIdx = fieldToCol['positioninpuck'];
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const priorityIdx = fieldToCol['priority'];
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const commentsIdx = fieldToCol['comments'];
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for (let rowIndex = 0; rowIndex < data.length; rowIndex++) {
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const row = data[rowIndex];
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if (!row.data) {
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console.error('Row data is missing');
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console.error(`Row ${rowIndex}: Missing or invalid data`);
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continue;
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}
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// Extract values from the appropriate columns
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const dewarName = typeof row.data[dewarNameIdx] === 'string' ? row.data[dewarNameIdx].trim() : null;
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const puckName = row.data[puckNameIdx] !== undefined && row.data[puckNameIdx] !== null ? String(row.data[puckNameIdx]).trim() : null;
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const puckType = typeof row.data[puckTypeIdx] === 'string' ? row.data[puckTypeIdx] : 'Unipuck';
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const sampleName = typeof row.data[sampleNameIdx] === 'string' ? row.data[sampleNameIdx].trim() : null;
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const proteinName = typeof row.data[proteinNameIdx] === 'string' ? row.data[proteinNameIdx].trim() : null;
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const samplePosition = row.data[samplePositionIdx] !== undefined && row.data[samplePositionIdx] !== null ? Number(row.data[samplePositionIdx]) : null;
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const priority = row?.data?.[priorityIdx] ? Number(row.data[priorityIdx]) : null;
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const comments = typeof row.data[commentsIdx] === 'string' ? row.data[commentsIdx].trim() : null;
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// Create data_collection_parameters object
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const dataCollectionParameters = {
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directory: row.data[fieldToCol['directory']],
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oscillation: row.data[fieldToCol['oscillation']] ? parseFloat(row.data[fieldToCol['oscillation']]) : undefined,
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aperture: row.data[fieldToCol['aperture']] ? row.data[fieldToCol['aperture']].trim() : undefined,
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exposure: row.data[fieldToCol['exposure']] ? parseFloat(row.data[fieldToCol['exposure']]) : undefined,
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totalrange: row.data[fieldToCol['totalrange']] ? parseInt(row.data[fieldToCol['totalrange']], 10) : undefined,
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transmission: row.data[fieldToCol['transmission']] ? parseInt(row.data[fieldToCol['transmission']], 10) : undefined,
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dose: row.data[fieldToCol['dose']] ? parseFloat(row.data[fieldToCol['dose']]) : undefined,
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targetresolution: row.data[fieldToCol['targetresolution']] ? parseFloat(row.data[fieldToCol['targetresolution']]) : undefined,
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datacollectiontype: row.data[fieldToCol['datacollectiontype']],
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processingpipeline: row.data[fieldToCol['processingpipeline']],
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spacegroupnumber: row.data[fieldToCol['spacegroupnumber']] ? parseInt(row.data[fieldToCol['spacegroupnumber']], 10) : undefined,
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cellparameters: row.data[fieldToCol['cellparameters']],
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rescutkey: row.data[fieldToCol['rescutkey']],
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rescutvalue: row.data[fieldToCol['rescutvalue']] ? parseFloat(row.data[fieldToCol['rescutvalue']]) : undefined,
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userresolution: row.data[fieldToCol['userresolution']] ? parseFloat(row.data[fieldToCol['userresolution']]) : undefined,
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pdbid: row.data[fieldToCol['pdbid']],
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autoprocfull: row.data[fieldToCol['autoprocfull']] === true,
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procfull: row.data[fieldToCol['procfull']] === true,
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adpenabled: row.data[fieldToCol['adpenabled']] === true,
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noano: row.data[fieldToCol['noano']] === true,
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ffcscampaign: row.data[fieldToCol['ffcscampaign']] === true,
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trustedhigh: row.data[fieldToCol['trustedhigh']] ? parseFloat(row.data[fieldToCol['trustedhigh']]) : undefined,
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autoprocextraparams: row.data[fieldToCol['autoprocextraparams']],
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chiphiangles: row.data[fieldToCol['chiphiangles']] ? parseFloat(row.data[fieldToCol['chiphiangles']]) : undefined,
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};
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const dewarName = sanitizeAndValidateColumn(row, fieldToCol['dewarname'], 'string', 'Dewar Name');
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const puckName = sanitizeAndValidateColumn(row, fieldToCol['puckname'], 'string', 'Puck Name');
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const puckType = sanitizeAndValidateColumn(row, fieldToCol['pucktype'], 'string', 'Unipuck', true); // Default: `Unipuck`
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const sampleName = sanitizeAndValidateColumn(row, fieldToCol['crystalname'], 'string', 'Sample Name');
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if (dewarName && puckName) {
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let dewar;
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if (!dewars.has(dewarName)) {
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// Initialize new dewar object
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dewar = {
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...initialNewDewarState,
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dewar_name: dewarName,
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contact_person_id: contactPerson.id,
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return_address_id: returnAddress.id,
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pucks: []
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pucks: [],
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};
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dewars.set(dewarName, dewar);
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puckPositionMap.set(dewarName, new Map());
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// Check if the dewar exists in the shipment
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// Check if dewar exists using backend
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const existingDewar = await checkIfDewarExists(dewarName);
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if (existingDewar) {
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dewarsToReplace.push(existingDewar);
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@ -335,78 +302,115 @@ const SpreadsheetTable = ({
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dewar = dewars.get(dewarName);
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}
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// Handle puck positions
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let puckPositions = puckPositionMap.get(dewarName);
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if (!puckPositions.has(puckName)) {
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puckPositions.set(puckName, puckPositions.size + 1);
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}
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const puckPosition = puckPositions.get(puckName);
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let puck = dewar.pucks.find(p => p.puck_name === puckName);
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// Create puck and attach it to the dewar
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let puck = dewar.pucks.find((p) => p.puck_name === puckName);
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if (!puck) {
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puck = {
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puck_name: puckName,
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puck_type: puckType,
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puck_location_in_dewar: puckPosition,
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samples: []
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};
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puck = { puck_name: puckName, puck_type: puckType, puck_location_in_dewar: puckPosition, samples: [] };
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dewar.pucks.push(puck);
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}
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// Add sample to puck
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const sample = {
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sample_name: sampleName,
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proteinname: proteinName,
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position: samplePosition,
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priority: priority,
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comments: comments,
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data_collection_parameters: dataCollectionParameters, // Attach the parameters
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results: null // Placeholder for results field
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position: sanitizeIntColumn(row, fieldToCol['positioninpuck'], 'Sample Position'),
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proteinname: sanitizeAndValidateColumn(row, fieldToCol['proteinname'], 'string', 'Protein Name'),
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priority: sanitizeIntColumn(row, fieldToCol['priority'], 'Priority'),
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comments: sanitizeAndValidateColumn(row, fieldToCol['comments'], 'string', 'Comments', true),
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data_collection_parameters: collectDataParameters(row), // Consolidate data parameters
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};
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if (isNaN(sample.position)) {
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console.error(`Invalid sample position for sample ${sample.sample_name} in puck ${puckName}`);
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} else {
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puck.samples.push(sample);
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}
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puck.samples.push(sample);
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} else {
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if (!dewarName) {
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console.error(`Dewar name is missing in row ${rowIndex}`);
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}
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if (!puckName) {
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console.error(`Puck name is missing in row ${rowIndex}`);
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}
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console.error(`Row ${rowIndex} is missing required fields for dewar/puck creation.`);
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}
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}
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const dewarsArray = Array.from(dewars.values());
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// Save dewars array for later use in handleConfirmUpdate
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// Save for update dialog control
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setDewarsToCreate(dewars);
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if (dewarsArray.length > 0 && dewarsToReplace.length > 0) {
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setDewarsToReplace(dewarsToReplace);
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setShowUpdateDialog(true);
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} else {
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} else if (dewarsArray.length > 0) {
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await handleDewarCreation(dewarsArray);
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}
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};
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const sanitizeAndValidateColumn = (row, colIndex, type, columnName, isOptional = false) => {
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const value = row?.data?.[colIndex];
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const sanitizedValue = type === 'string' ? value?.trim() : value;
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if (!sanitizedValue && !isOptional) {
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console.error(`${columnName} is missing or invalid.`);
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return null;
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}
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if (type === 'number' && isNaN(sanitizedValue)) {
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console.error(`${columnName} is not a valid number.`);
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}
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return sanitizedValue;
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};
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// Utility to sanitize integer columns
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const sanitizeIntColumn = (row, colIndex, columnName) => {
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const rawValue = row?.data?.[colIndex];
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const intValue = parseInt(rawValue, 10);
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if (isNaN(intValue)) {
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console.error(`${columnName} is not a valid integer.`);
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}
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return intValue;
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};
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// Consolidate data collection parameters
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const collectDataParameters = (row) => ({
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directory: sanitizeAndValidateColumn(row, fieldToCol['directory'], 'string', 'Directory', true),
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oscillation: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['oscillation'], 'number', 'Oscillation', true)),
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aperture: sanitizeAndValidateColumn(row, fieldToCol['aperture'], 'string', 'Aperture', true),
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exposure: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['exposure'], 'number', 'Exposure', true)),
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totalrange: sanitizeIntColumn(row, fieldToCol['totalrange'], 'Total Range'),
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transmission: sanitizeIntColumn(row, fieldToCol['transmission'], 'Transmission'),
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dose: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['dose'], 'number', 'Dose', true)),
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targetresolution: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['targetresolution'], 'number', 'Target Resolution', true)),
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datacollectiontype: sanitizeAndValidateColumn(row, fieldToCol['datacollectiontype'], 'string', 'Data Collection Type', true),
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processingpipeline: sanitizeAndValidateColumn(row, fieldToCol['processingpipeline'], 'string', 'Processing Pipeline', true),
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spacegroupnumber: sanitizeIntColumn(row, fieldToCol['spacegroupnumber'], 'Space Group Number'),
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cellparameters: sanitizeAndValidateColumn(row, fieldToCol['cellparameters'], 'string', 'Cell Parameters', true),
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rescutkey: sanitizeAndValidateColumn(row, fieldToCol['rescutkey'], 'string', 'Resolution Cut Key', true),
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rescutvalue: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['rescutvalue'], 'number', 'Resolution Cut Value', true)),
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userresolution: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['userresolution'], 'number', 'User Resolution', true)),
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pdbid: sanitizeAndValidateColumn(row, fieldToCol['pdbid'], 'string', 'PDB ID', true),
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autoprocfull: row.data[fieldToCol['autoprocfull']] === true,
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procfull: row.data[fieldToCol['procfull']] === true,
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adpenabled: row.data[fieldToCol['adpenabled']] === true,
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noano: row.data[fieldToCol['noano']] === true,
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ffcscampaign: row.data[fieldToCol['ffcscampaign']] === true,
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trustedhigh: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['trustedhigh'], 'number', 'Trusted High', true)),
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autoprocextraparams: sanitizeAndValidateColumn(row, fieldToCol['autoprocextraparams'], 'string', 'Autoproc Extra Params', true),
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chiphiangles: parseFloat(sanitizeAndValidateColumn(row, fieldToCol['chiphiangles'], 'number', 'Chi/Phi Angles', true)),
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});
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const handleConfirmUpdate = async () => {
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if (dewarsToReplace.length === 0) return;
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try {
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for (const dewar of dewarsToReplace) {
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await DewarsService.deleteDewarDewarsDewarIdDelete(dewar.id);
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}
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const dewarsArray = Array.from(dewarsToCreate.values());
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await handleDewarCreation(dewarsArray);
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await handleDewarCreation(dewarsArray); // Updated logic handles replacement
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console.log('Dewars replaced successfully');
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} catch (error) {
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console.error('Error replacing dewar', error);
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if (error instanceof ApiError && error.body) {
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console.error('Validation errors:', error.body.detail);
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} else {
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console.error('Unexpected error:', error);
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}
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console.error('Error replacing dewars:', error);
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}
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setShowUpdateDialog(false);
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setDewarsToReplace([]);
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@ -419,30 +423,18 @@ const SpreadsheetTable = ({
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setDewarsToCreate(new Map());
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};
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const handleDewarCreation = async (dewarsArray) => {
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const handleDewarCreation = async (dewarsArray: any[]) => {
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for (const dewar of dewarsArray) {
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try {
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if (!dewar.pucks || dewar.pucks.length === 0) {
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console.error(`Dewar ${dewar.dewar_name} does not have any pucks.`);
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continue;
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}
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// Prepare payload and exclude number_of_pucks before sending
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const { number_of_pucks, number_of_samples, ...payload } = dewar;
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const createdDewar = await DewarsService.createDewarDewarsPost(dewar);
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// Call the backend to create or update dewars
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await DewarsService.createOrUpdateDewarDewarsPost(selectedShipment.id, payload);
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if (createdDewar && selectedShipment) {
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await ShipmentsService.addDewarToShipmentShipmentsShipmentIdAddDewarPost(
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selectedShipment.id,
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createdDewar.id
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);
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console.log(`Dewar ${createdDewar.dewar_name} with ID ${createdDewar.id} created and added to the shipment.`);
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}
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console.log(`Dewar "${dewar.dewar_name}" processed successfully.`);
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} catch (error) {
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console.error('Error adding dewar', error);
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if (error instanceof ApiError && error.body) {
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console.error('Validation errors:', error.body.detail);
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} else {
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console.error('Unexpected error:', error);
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}
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console.error("Error creating/updating dewar:", error);
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}
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}
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};
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Block a user