work on e2e tests

Niema-Lab · Sep 26, 2023 · b54161f · b54161f
1 parent 14aa817
commit b54161f
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Showing 4 changed files with 27 additions and 6 deletions.
diff --git a/.github/workflows/playwright.yml b/.github/workflows/playwright.yml
@@ -26,6 +26,6 @@ jobs:
     - uses: actions/upload-artifact@v3
       if: always()
       with:
-        name: playwright-report
+        name: benchmarks
         path: e2e/results/
         retention-days: 30
diff --git a/e2e/tests/pageload.spec.ts b/e2e/tests/pageload.spec.ts
@@ -1,6 +1,5 @@
 import { test, expect } from '@playwright/test';
 import fs from 'fs';
-
 let errors: string[] = [];
 
 test.beforeEach(async ({ page }) => {
@@ -27,13 +26,35 @@ const downloadFile = async (page, identifier: string, location: string) => {
 	await download.saveAs(location + download.suggestedFilename());
 }
 
-
 test('run example data', async ({ page, browserName }) => {
+	test.setTimeout(15000);
 	await page.getByTestId('load-example-data').click();
 	await page.getByTestId('run').click();
-	await expect(page.getByTestId('output-text')).toHaveValue(/Done! Time Elapsed:/);
+
+	await expect(page.getByTestId('output-text')).toHaveValue(/Done! Time Elapsed:/, { timeout: 10000 });
 	const timeElapsed = (await page.getByTestId('duration-text').textContent())?.replace(/[^0-9\.]/g, '') ?? '-1';
 	await expect(parseFloat(timeElapsed)).toBeGreaterThan(0);
 	await downloadFile(page, 'Download', 'e2e/results/' + browserName + '/example/');
 	fs.appendFileSync('e2e/results/' + browserName + '/example/time.txt', timeElapsed);
+});
+
+const runBenchmark = async (page, browserName: string, alignmentFiles: string[], referenceFile, downloadedLocation: string, runTimeout: number) => {
+	test.setTimeout(runTimeout + 15000);
+	await page.getByTestId('alignment-files').setInputFiles(...alignmentFiles);
+	await page.getByTestId('reference-file').setInputFiles(referenceFile);
+	await page.getByTestId('run').click();
+
+	await expect(page.getByTestId('output-text')).toHaveValue(/Done! Time Elapsed:/, { timeout: runTimeout });
+	const timeElapsed = (await page.getByTestId('duration-text').textContent())?.replace(/[^0-9\.]/g, '') ?? '-1';
+	await expect(parseFloat(timeElapsed)).toBeGreaterThan(0);
+	await downloadFile(page, 'Download Consensus FASTA', 'e2e/results/' + browserName + '/' + downloadedLocation + '/');
+	fs.appendFileSync('e2e/results/' + browserName + '/' + downloadedLocation + '/time.txt', timeElapsed);
+}
+
+test('run example data - uploaded', async ({ page, browserName }) => {
+	await runBenchmark(page, browserName, ['./public/data/example.bam'], './public/data/NC_045512.2.fas', 'example-uploaded', 10000);
+});
+
+test('run large data set', async ({ page, browserName }) => {
+	await runBenchmark(page, browserName, ['./public/data/reads.fastq.gz'], './public/data/NC_045512.2.fas', 'large dataset', 240000);
 });
diff --git a/public/data/reads.fastq.gz b/public/data/reads.fastq.gz
diff --git a/src/App.jsx b/src/App.jsx
@@ -706,7 +706,7 @@ export class App extends Component {
 						<div id="input-content">
 							<div className="d-flex flex-column mb-4">
 								<label htmlFor="alignment-files" className="form-label">Upload Input Reads File(s) (BAM, SAM, FASTQ(s))<span className="text-danger"> *</span></label>
-								<input className={`form-control ${!this.state.alignmentFilesValid && 'is-invalid'}`} type="file" multiple accept=".sam,.bam,.fastq,.fastq.gz,.fq,.fq.gz" id="alignment-files" onChange={this.uploadAlignmentFiles} />
+								<input className={`form-control ${!this.state.alignmentFilesValid && 'is-invalid'}`} type="file" multiple accept=".sam,.bam,.fastq,.fastq.gz,.fq,.fq.gz" id="alignment-files" data-testid="alignment-files" onChange={this.uploadAlignmentFiles} />
 								{this.state.alignmentFiles === 'EXAMPLE_DATA' &&
 									<p className="mt-2 mb-0"><strong>Using Loaded Example file: <a
 										href={`${import.meta.env.BASE_URL || ''}${EXAMPLE_ALIGNMENT_FILE}`}
@@ -760,7 +760,7 @@ export class App extends Component {
 							<div className="d-flex flex-column mb-4">
 								<label htmlFor="reference-file" className="form-label">Reference File (FASTA)<span className="text-danger"> *</span></label>
 								<div className="input-group">
-									<input className={`form-control ${!this.state.refFileValid && 'is-invalid'}`} type="file" id="reference-file" onChange={this.uploadRefFile} />
+									<input className={`form-control ${!this.state.refFileValid && 'is-invalid'}`} type="file" id="reference-file" data-testid="reference-file" onChange={this.uploadRefFile} />
 									<button className="btn btn-outline-danger" type="button" id="reference-file-addon" onClick={this.clearRefFile}><i className="bi bi-trash"></i></button>
 								</div>
 							</div>