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Merge pull request #148 from elmedjadjirayane/main
change type for chromosome input in locuszoom and upgrade to version…
2 parents 4a591f1 + c769a6a commit bfcf94c

10 files changed

Lines changed: 147 additions & 56 deletions

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‎packages/locuszoom/.gitignore‎

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@@ -15,4 +15,12 @@ node_modules
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npm-debug.log*
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pnpm-debug.log*
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yarn-debug.log*
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yarn-error.log*
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yarn-error.log*
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# Playwright
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/test-results/
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/playwright-report/
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/blob-report/
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/playwright/.cache/
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/playwright/.auth/
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/.github/

‎packages/locuszoom/e2e/example.spec.js‎

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// @ts-check
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import { test, expect } from '@playwright/test';
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test('Run plot', async ({ page }) => {
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// Test variables
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const URL = 'http://localhost:5173/';
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const CHR_INPUT = 'raya560ne.2.1.2'; // a chromosome
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const POINT = '#lz-plot_association_associationpvalues_-RAYA560NE21261284_TC' // a point in the plot
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const POINT_LOCATOR = page.locator(POINT);
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const PHENO_STAT = '×phenRAYA560NE.2.1.2:61284_T/'; // stats' table for the point
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const PHENO_STAT_TO_CLICK = page.getByText(PHENO_STAT)
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// Test execution
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await page.goto(URL);
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await page.getByRole('button').click();
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await page.getByRole('textbox', { name: 'Please Input' }).nth(1).fill(CHR_INPUT);
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await expect(POINT_LOCATOR).toBeVisible();
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await POINT_LOCATOR.click();
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await PHENO_STAT_TO_CLICK.click();
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await expect(PHENO_STAT_TO_CLICK).toBeVisible();
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await page.getByRole('button', { name: '×' }).click();
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await expect(PHENO_STAT_TO_CLICK).toBeHidden();
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});
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‎packages/locuszoom/package.json‎

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@@ -1,35 +1,38 @@
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{
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"name": "@galaxyproject/locuszoom",
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"version": "0.0.7",
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"type": "module",
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"license": "MIT",
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"files": [
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"static"
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],
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"scripts": {
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"dev": "vite",
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"build": "vite build",
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"preview": "vite preview",
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"prettier": "prettier --config ./prettier.config.js --write 'package.json' '**/*.{js,jsx,ts,tsx,json,css,md,vue}'",
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"test": "vitest --run",
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"test:watch": "vitest --watch",
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"test:ui": "vitest --ui"
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},
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"devDependencies": {
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"@types/node": "^22.9.0",
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"@vitejs/plugin-vue": "^5.0.5",
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"@vitest/ui": "^3.0.9",
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"autoprefixer": "^10.4.19",
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"galaxy-charts": "^0.0.73",
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"galaxy-charts-xml-parser": "^1.0.3",
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"jsdom": "^25.0.1",
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"locuszoom": "^0.14.0",
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"postcss": "^8.4.40",
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"prettier": "^3.3.3",
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"tailwindcss": "^3.4.7",
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"typescript": "^5.5.4",
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"vite": "^6.2.2",
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"vitest": "^3.0.9",
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"vue": "^3.4.31"
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}
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"name": "@galaxyproject/locuszoom",
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"version": "0.0.8",
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"type": "module",
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"license": "MIT",
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"files": [
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"static"
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],
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"scripts": {
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"dev": "vite",
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"build": "vite build",
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"preview": "vite preview",
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"prettier": "prettier --config ./prettier.config.js --write 'package.json' '**/*.{js,jsx,ts,tsx,json,css,md,vue}'",
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"test": "npm run test:unit && npm run test:e2e",
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"test:e2e": "npx playwright test",
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"test:unit": "vitest run",
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"test:watch": "vitest --watch",
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"test:ui": "vitest --ui"
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},
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"devDependencies": {
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"@playwright/test": "^1.58.0",
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"@types/node": "^22.9.0",
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"@vitejs/plugin-vue": "^5.0.5",
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"@vitest/ui": "^3.0.9",
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"autoprefixer": "^10.4.19",
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"galaxy-charts": "^0.0.73",
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"galaxy-charts-xml-parser": "^1.0.3",
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"jsdom": "^25.0.1",
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"locuszoom": "^0.14.0",
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"postcss": "^8.4.40",
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"prettier": "^3.3.3",
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"tailwindcss": "^3.4.7",
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"typescript": "^5.5.4",
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"vite": "^6.2.2",
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"vitest": "^3.0.9",
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"vue": "^3.4.31"
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}
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}

‎packages/locuszoom/playwright.config.js‎

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import { defineConfig } from "@playwright/test";
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export default defineConfig({
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testIgnore: ["src/**"],
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timeout: 120000, // 120 seconds per test
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use: {
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headless: !!process.env.CI,
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},
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snapshotPathTemplate: "{testDir}/test-data/{arg}.png",
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});

‎packages/locuszoom/public/locuszoom.xml‎

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<input>
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<label>Select a chromosome</label>
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<name>chromosome</name>
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<type>integer</type>
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<min>1</min>
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<value>1</value>
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<type>string</type>
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</input>
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<input>
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<label>Select start position</label>
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<param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/1.gwas_tabix.gz" ftype="gwas_tabix.gz" />
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</test>
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</tests>
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<help format="markdown"><![CDATA[
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<help format="markdown"><![CDATA[
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# What is LocusZoom?
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LocusZoom is a specialized tool designed to create interactive Manhattan plots for visualizing results from genome-wide association studies (GWAS).
@@ -117,5 +115,5 @@ For more information:
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Boughton, A. P. et al. LocusZoom.js: interactive and embeddable visualization of genetic association study results. Bioinformatics (2021) doi:10.1093/bioinformatics/btab186.
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]]></help>
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]]> </help>
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</visualization>

‎packages/locuszoom/src/Plugin.vue‎

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@@ -10,6 +10,11 @@ LocusZoom.use(LzTabixSource);
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const TabixUrlSource = LocusZoom.Adapters.get("TabixUrlSource");
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// Test files paths
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const BGZIP_PRIMARY_DATASET_PATH = "http://localhost:5173/test-data/weird.gwas_bgzip";
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const TABIX_SECONDARY_DATASET_PATH = "http://localhost:5173/test-data/weird.gwas_bgzip.tbi";
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// Patch URLFetchable prototype by accessing it through a reader instance
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let hasURLFetchablePrototypeBeenPatched = false;
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const errorMessage = ref("");
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// Functions to retrieve URLs
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function getPrimaryURL(root,primaryID) {
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if (primaryID==="__test__"){
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return BGZIP_PRIMARY_DATASET_PATH;
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}
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else {
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return `${root}api/datasets/${primaryID}/display`;
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}
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}
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function getSecondaryURL(root,primaryID, secondaryID) {
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if (primaryID==="__test__"){
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return TABIX_SECONDARY_DATASET_PATH;
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}
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else {
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return `${root}api/datasets/${secondaryID}/display`;
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}
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}
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function render() {
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const bgzipURL = getPrimaryURL(props.root,props.datasetId);
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const tabixURL = getSecondaryURL(props.root,props.datasetId, props.settings.tabix?.id);
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const id = props.settings.tabix?.id;
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const chrIn = props.settings.chromosome;
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const startIn = props.settings.start;
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const is_neg_log_pvalue = props.settings.is_neg_log_pvalue;
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const beta_col = props.settings.beta_col;
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const stderr_beta_col = props.settings.stderr_beta_col;
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if (!id) {
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if (tabixURL.includes("/api/datasets/undefined/display")) {
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errorMessage.value = "Please select a Tabix file.";
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return;
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}
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let data_sources = new LocusZoom.DataSources().add("assoc", [
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"TabixUrlSource",
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{
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url_data: `${props.root}api/datasets/${props.datasetId}/display`,
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url_tbi: `${props.root}api/datasets/${id}/display`,
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url_data: bgzipURL,
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url_tbi: tabixURL,
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parser_func: gwasParser,
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overfetch: 0,
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},

‎packages/locuszoom/src/main.js‎

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// Construct the incoming data object with mock configuration and data
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const dataIncoming = {
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visualization_config: {
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dataset_id: "b620c45fba703209", // id of primary_dataset.bgzip
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dataset_id: process.env.dataset_id || "__test__", // id of primary_dataset.bgzip
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// Placeholder for additional visualization settings
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settings: {
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tabix: { id: "abd164196b68b912" }, // id of secondary_dataset.tbi
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tabix: {}, // id of secondary_dataset.tbi
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},
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},
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// Parse and load the visualization XML configuration

‎packages/locuszoom/test-data/weird.gwas_bgzip‎

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‎packages/locuszoom/test-data/weird.gwas_bgzip.tbi‎

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‎packages/locuszoom/yarn.lock‎

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"@babel/helper-validator-identifier" "^7.24.7"
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to-fast-properties "^2.0.0"
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"@esbuild/darwin-arm64@0.25.1":
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"@esbuild/linux-x64@0.25.1":
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version "0.25.1"
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resolved "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.25.1.tgz"
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"@hapi/hoek@^9.0.0":
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version "9.3.0"
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"@playwright/test@^1.58.0":
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dependencies:
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playwright "1.58.0"
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"@polka/url@^1.0.0-next.24":
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version "1.0.0-next.28"
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resolved "https://registry.npmjs.org/@polka/url/-/url-1.0.0-next.28.tgz"
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"@rollup/rollup-darwin-arm64@4.35.0":
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version "4.35.0"
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"@types/estree@^1.0.0", "@types/estree@1.0.6":
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version "1.0.6"
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resolved "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz"
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integrity sha512-OO0pH2lK6a0hZnAdau5ItzHPI6pUlvI7jMVnxUQRtw4owF2wk8lOSabtGDCTP4Ggrg2MbGnWO9X8K1t4+fGMDw==
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fsevents@~2.3.2, fsevents@~2.3.3:
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function-bind@^1.1.2:
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version "1.1.2"
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resolved "https://registry.npmjs.org/function-bind/-/function-bind-1.1.2.tgz"
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"jszlib@git+https://github.com/dasmoth/jszlib.git#4e562c7":
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version "0.2.1"
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just-clone@^3.2.1:
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version "3.2.1"
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playwright-core@1.58.0:
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version "1.58.0"
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playwright@1.58.0:
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dependencies:
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playwright-core "1.58.0"
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optionalDependencies:
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fsevents "2.3.2"
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postcss-import@^15.1.0:
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version "15.1.0"
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resolved "https://registry.npmjs.org/postcss-import/-/postcss-import-15.1.0.tgz"

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