84 lines
2.6 KiB
JavaScript
84 lines
2.6 KiB
JavaScript
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#!/usr/bin/env node
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const fs = require('fs');
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const path = require('path');
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const projectRoot = path.resolve(__dirname, '..');
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const indexPath = path.join(projectRoot, 'apps', 'web', 'vue3', 'index.html');
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const html = fs.readFileSync(indexPath, 'utf8');
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function assert(condition, message) {
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if (!condition) {
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console.error(`FAIL: ${message}`);
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process.exitCode = 1;
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}
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}
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function countLiteral(needle) {
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return html.split(needle).length - 1;
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}
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const requiredDialogBindings = [
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'confirmParams.fgseaComparison',
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'confirmParams.fgseaMinSize',
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'confirmParams.fgseaMaxSize',
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'confirmParams.fgseaNperm',
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'confirmParams.fgseaSeed',
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'confirmParams.wgcnaMinMean',
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'confirmParams.wgcnaMaxGenes',
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'confirmParams.wgcnaMinModuleSize',
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'confirmParams.wgcnaMergeCutHeight',
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'confirmParams.wgcnaPowers',
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'confirmParams.candidateMaxDegProteins',
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'confirmParams.candidateRunInterproscan',
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'confirmParams.annotationApplications',
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'confirmParams.enrichBackgroundSource',
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'confirmParams.enrichSpecies',
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'confirmParams.enrichKeyType',
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'confirmParams.keggOrganism',
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'confirmParams.topPathways',
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];
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for (const binding of requiredDialogBindings) {
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assert(
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countLiteral(binding) >= 2,
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`${binding} should appear in both parameter confirmation dialog blocks`
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);
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}
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const requiredExecutionAssignments = [
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'requestBody.fgseaComparison',
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'requestBody.fgseaMinSize',
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'requestBody.fgseaMaxSize',
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'requestBody.fgseaNperm',
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'requestBody.fgseaSeed',
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'requestBody.wgcnaMinMean',
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'requestBody.wgcnaMaxGenes',
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'requestBody.wgcnaMinModuleSize',
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'requestBody.wgcnaMergeCutHeight',
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'requestBody.wgcnaPowers',
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'requestBody.candidateMaxDegProteins',
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'requestBody.candidateRunInterproscan',
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'requestBody.annotationApplications',
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'requestBody.enrichBackgroundSource',
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'requestBody.enrichSpecies',
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'requestBody.enrichKeyType',
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'requestBody.keggOrganism',
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'requestBody.topPathways',
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];
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for (const assignment of requiredExecutionAssignments) {
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assert(
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html.includes(assignment),
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`${assignment} should be assigned in applyRnaseqExecutionParams`
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);
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}
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assert(html.includes('topPathways: 20'), 'confirmParams should define topPathways default');
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assert(html.includes('featureCounts raw fragment counts'), 'dialog should state DESeq2 uses featureCounts raw fragment counts');
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assert(html.includes('Salmon/tximport TPM'), 'dialog should state expression plots use Salmon/tximport TPM after bridge QC');
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assert(html.includes('InterProScan'), 'candidate dialog should warn about InterProScan requirements');
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if (!process.exitCode) {
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console.log('RNA-seq confirmation parameter coverage ok');
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}
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