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fix to make it work
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@thanhleviet
thanhleviet committed Jan 14, 2025
1 parent ac5c029 commit 422bbdd
Showing 1 changed file with 145 additions and 27 deletions.
172 changes: 145 additions & 27 deletions src/routes/nextseq2k/+page.svelte
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Original file line number Diff line number Diff line change
Expand Up @@ -85,9 +85,34 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
});
}
// Update headerSection with current configuration values
headerSection = [
'[Header],,,',
'FileFormatVersion,2,,',
`RunName,${runName},,`,
'InstrumentPlatform,NextSeq1k2k,,',
'InstrumentType,NextSeq2000,,',
',,,',
'[Reads],,,',
`Read1Cycles,${read1Cycle},,`,
`Read2Cycles,${read2Cycle},,`,
`Index1Cycles,${index1Cycle},,`,
`Index2Cycles,${index2Cycle},,`,
',,,',
'[BCLConvert_Settings],,,',
`SoftwareVersion,${bclVersion},,`,
`BarcodeMismatchesIndex1,${barcodeMismatchesIndex1},,`,
`BarcodeMismatchesIndex2,${barcodeMismatchesIndex2},,`,
`AdapterRead1,${adapterRead1},,`,
`AdapterRead2,${adapterRead2},,`,
`NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,`,
',,,',
'[BCLConvert_Data],,,',
];
// Create the final content
const processedContent = [
getHeaderText(),
...headerSection,
headers.join(','),
...rows.map(row => row.join(','))
].join('\n');
Expand All @@ -107,14 +132,26 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
async function handleFile(uploadedFile: File) {
file = uploadedFile;
// Reset the reverse complement state when loading a new file
// Reset states
error = null;
result = null;
headers = [];
rows = [];
originalRows = [];
reverseComplement2k.set(false);
fileContent = '';
try {
if (file.name.toLowerCase().endsWith('.xlsx') || file.name.toLowerCase().endsWith('.xls')) {
fileContent = await parseExcel(file);
} else {
fileContent = await file.text();
}
if (!fileContent) {
throw new Error('No file content received');
}
await processContent(fileContent);
} catch (e) {
error = e instanceof Error ? e.message : 'An error occurred processing the file';
Expand All @@ -123,51 +160,79 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
async function processContent(content: string) {
try {
const lines = content.split(/\r?\n/).filter(line => line.trim());
if (!content) {
throw new Error('Empty content received');
}
// Define the expected column order
const expectedHeaders = ['Sample_ID', 'Index2', 'Index', 'Sample_Project'];
const lines = content.split(/\r?\n/).filter(line => line.trim());
if (lines.length === 0) {
throw new Error('File appears to be empty');
}
// Check if content has full structure
const hasFullStructure = lines.some(line => line.includes('[Header]'));
if (!hasFullStructure) {
// Parse the input headers
// Simple CSV format - process directly
const inputHeaders = lines[0].split(',').map(header => header.trim());
if (!inputHeaders.length) {
throw new Error('No headers found in the file');
}
// Define required columns (case-insensitive)
const requiredColumns = ['sample_id', 'index2', 'index', 'sample_project'];
const inputHeadersLower = inputHeaders.map(h => h.toLowerCase());
// Create a mapping of current positions to expected positions
// Check for required columns
const missingColumns = requiredColumns.filter(required =>
!inputHeadersLower.includes(required)
);
if (missingColumns.length > 0) {
throw new Error(`Missing required columns: ${missingColumns.join(', ')}`);
}
// Create mapping while preserving original header cases
const headerMap = new Map<number, number>();
expectedHeaders.forEach((expected, expectedIndex) => {
const currentIndex = inputHeaders.findIndex(h =>
h.toLowerCase() === expected.toLowerCase()
);
if (currentIndex !== -1) {
headerMap.set(currentIndex, expectedIndex);
requiredColumns.forEach((required, index) => {
const inputIndex = inputHeadersLower.findIndex(h => h === required);
if (inputIndex !== -1) {
headerMap.set(inputIndex, index);
}
});
// Reorder the data according to expected format
headers = expectedHeaders;
// Use original input headers for the required columns
headers = requiredColumns.map(required => {
const inputIndex = inputHeadersLower.findIndex(h => h === required);
return inputHeaders[inputIndex];
});
originalRows = lines.slice(1)
.filter(line => line.trim())
.map(line => {
const cells = line.split(',').map(cell => cell.trim());
const reorderedCells = new Array(expectedHeaders.length).fill('');
const reorderedCells = new Array(requiredColumns.length).fill('');
headerMap.forEach((newIndex, oldIndex) => {
reorderedCells[newIndex] = cells[oldIndex] || '';
if (cells[oldIndex]) {
reorderedCells[newIndex] = cells[oldIndex];
}
});
return reorderedCells;
});
if (originalRows.length === 0) {
throw new Error('No data rows found in the file');
}
// Generate header section
headerSection = [
'[Header],,,',
`FileFormatVersion,2,,`,
'FileFormatVersion,2,,',
`RunName,${runName},,`,
`InstrumentPlatform,NextSeq1k2k,,`,
`InstrumentType,NextSeq2000,,`,
'InstrumentPlatform,NextSeq1k2k,,',
'InstrumentType,NextSeq2000,,',
',,,',
'[Reads],,,',
`Read1Cycles,${read1Cycle},,`,
Expand All @@ -185,14 +250,17 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
',,,',
'[BCLConvert_Data],,,',
];
} else {
// Process full structure format
// Full structure format
let dataSection = false;
let dataLines: string[] = [];
headerSection = [];
let foundDataSection = false;
for (const line of lines) {
if (line.trim() === '[BCLConvert_Data]') {
if (line.includes('[BCLConvert_Data]')) {
foundDataSection = true;
dataSection = true;
headerSection.push(line);
continue;
Expand All @@ -205,6 +273,14 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
}
}
if (!foundDataSection) {
throw new Error('No [BCLConvert_Data] section found in the file');
}
if (dataLines.length === 0) {
throw new Error('No data found after [BCLConvert_Data] section');
}
headers = dataLines[0].split(',').map(header => header.trim());
originalRows = dataLines.slice(1)
.filter(line => line.trim())
Expand All @@ -214,7 +290,7 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
// Process Sample_ID column
rows = originalRows.map(row => {
const newRow = [...row];
const sampleIdIndex = headers.findIndex(h => h.toLowerCase() === 'sample_id');
const sampleIdIndex = headers.map(h => h.toLowerCase()).indexOf('sample_id');
if (sampleIdIndex !== -1) {
newRow[sampleIdIndex] = replaceSpecialCharacters(row[sampleIdIndex]);
}
Expand Down Expand Up @@ -243,6 +319,31 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
function downloadValidated(removeProject = false) {
if (!headers.length || !rows.length) return;
// Update headerSection with current configuration values
headerSection = [
'[Header],,,',
'FileFormatVersion,2,,',
`RunName,${runName},,`,
'InstrumentPlatform,NextSeq1k2k,,',
'InstrumentType,NextSeq2000,,',
',,,',
'[Reads],,,',
`Read1Cycles,${read1Cycle},,`,
`Read2Cycles,${read2Cycle},,`,
`Index1Cycles,${index1Cycle},,`,
`Index2Cycles,${index2Cycle},,`,
',,,',
'[BCLConvert_Settings],,,',
`SoftwareVersion,${bclVersion},,`,
`BarcodeMismatchesIndex1,${barcodeMismatchesIndex1},,`,
`BarcodeMismatchesIndex2,${barcodeMismatchesIndex2},,`,
`AdapterRead1,${adapterRead1},,`,
`AdapterRead2,${adapterRead2},,`,
`NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,`,
',,,',
'[BCLConvert_Data],,,',
];
let downloadHeaders = [...headers];
let downloadRows = rows.map(row => [...row]);
Expand All @@ -259,7 +360,7 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
}
}
// Create CSV content with original header section
// Create CSV content with updated header section
const csvContent = [
...headerSection,
downloadHeaders.join(','),
Expand Down Expand Up @@ -367,7 +468,6 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,
<li>Note: Index2 sequences can be reverse complemented using the toggle in configuration</li>
</ul>
</div>

<!-- Upload Section -->
<div class="bg-white rounded-lg shadow p-4">
<DragAndDrop
Expand Down Expand Up @@ -608,15 +708,33 @@ NoLaneSplitting,${noLaneSplitting ? 'TRUE' : 'FALSE'},,

<!-- Error Message -->
{#if error}
<div class="rounded-lg bg-red-50 p-4 shadow ring-1 ring-red-900/5">
<p class="text-red-600">{error}</p>
<div class="bg-red-50 border-l-4 border-red-400 p-4 mb-4">
<div class="flex">
<div class="flex-shrink-0">
<svg class="h-5 w-5 text-red-400" viewBox="0 0 20 20" fill="currentColor">
<path fill-rule="evenodd" d="M10 18a8 8 0 100-16 8 8 0 000 16zM8.707 7.293a1 1 0 00-1.414 1.414L8.586 10l-1.293 1.293a1 1 0 101.414 1.414L10 11.414l1.293 1.293a1 1 0 001.414-1.414L11.414 10l1.293-1.293a1 1 0 00-1.414-1.414L10 8.586 8.707 7.293z" clip-rule="evenodd" />
</svg>
</div>
<div class="ml-3">
<h3 class="text-sm font-medium text-red-800">
Error Processing File
</h3>
<div class="mt-2 text-sm text-red-700">
<p>{error}</p>
{#if error === 'No data section found in the file'}
<p class="mt-1">Please ensure your file contains the required [BCLConvert_Data] section or is in the correct CSV format with the required columns.</p>
{/if}
</div>
</div>
</div>
</div>
{/if}

<!-- Table Section -->
<div class="rounded-lg bg-white shadow ring-1 ring-gray-900/5">
<div class="px-4 py-2 border-b border-gray-200">
<h2 class="text-sm font-semibold text-gray-900">Sample Sheet Content</h2>
<p class="text-xs text-gray-500">Headers: {headers.length}, Rows: {rows.length}</p>
</div>
<Table {headers} {rows} />
</div>
Expand Down

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