@datagrok/bio 1.0.2 → 1.0.3

package/jest.config.js

@@ -0,0 +1,33 @@
+module.exports = {
+  'roots': [
+    '<rootDir>/src',
+  ],
+  'testMatch': [
+    '**/__jest__/**/*.test.+(ts|tsx)',
+  ],
+  moduleFileExtensions: [
+    'ts',
+    'js',
+  ],
+  'transform': {
+    '^.+\\.(ts|tsx)$': 'ts-jest',
+  },
+  transformIgnorePatterns: ['^.+\\.js$'],
+  globals: {
+    'ts-jest': {
+      'tsconfig': {
+        'target': 'es6',
+        'module': 'es2020',
+      },
+    },
+  },
+  reporters: [
+    'default',
+    [
+      './node_modules/jest-html-reporter',
+      {
+        'includeConsoleLog': true,
+      },
+    ],
+  ],
+};

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.0.2",
+  "version": "1.0.3",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -10,7 +10,8 @@
     "directory": "packages/Bio"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^1.0.2",
+    "@datagrok-libraries/bio": "^2.0.1",
+    "@datagrok-libraries/utils": "^0.4.2",
     "cash-dom": "latest",
     "datagrok-api": "^1.1.5",
     "dayjs": "latest",
@@ -18,10 +19,15 @@
     "typescript": "^4.4.2"
   },
   "devDependencies": {
+    "@types/jest": "^27.0.0",
     "@typescript-eslint/eslint-plugin": "latest",
     "@typescript-eslint/parser": "latest",
     "eslint": "latest",
     "eslint-config-google": "latest",
+    "jest": "^27.0.0",
+    "jest-html-reporter": "^3.5.0",
+    "puppeteer": "latest",
+    "ts-jest": "^27.0.0",
     "webpack": "latest",
     "webpack-cli": "latest"
   },
@@ -39,7 +45,9 @@
     "debug-sequences1-local": "grok publish local --rebuild",
     "release-sequences1-local": "grok publish local --rebuild --release",
     "lint": "eslint \"./src/**/*.ts\"",
-    "lint-fix": "eslint \"./src/**/*.ts\" --fix"
+    "lint-fix": "eslint \"./src/**/*.ts\" --fix",
+    "test": "jest",
+    "test-local": "set HOST=localhost && jest"
   },
   "canEdit": [
     "Developers"

package/src/__jest__/remote.test.ts

@@ -0,0 +1,54 @@
+/**
+ * @jest-environment jsdom
+ */
+
+import * as utils from './test-node';
+import puppeteer from 'puppeteer';
+
+const P_START_TIMEOUT: number = 100000;
+let browser: puppeteer.Browser;
+let page: puppeteer.Page;
+
+beforeAll(async () => {
+  const out = await utils.getBrowserPage(puppeteer);
+  browser = out.browser;
+  page = out.page;
+}, P_START_TIMEOUT);
+
+afterAll(async () => {
+  await browser.close();
+});
+
+it('TEST', async () => {
+  const targetPackage: string = process.env.TARGET_PACKAGE ?? 'Bio';
+  console.log(`Testing ${targetPackage} package`);
+
+  //console.log(require('root-require')('package.json').version);
+  const r = await page.evaluate((targetPackage): Promise<object> => {
+    return new Promise<object>((resolve, reject) => {
+      (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
+        const cStatus = df.columns.byName('success');
+        const cMessage = df.columns.byName('result');
+        const cCat = df.columns.byName('category');
+        const cName = df.columns.byName('name');
+        let failed = false;
+        let report = '';
+        for (let i = 0; i < df.rowCount; i++) {
+          if (!cStatus.get(i)) {
+            report += `${cCat.get(i)}.${cName.get(i)}: ${cMessage.get(i)}\n`;
+            failed = true;
+          }
+        }
+        resolve({report, failed});
+      }).catch((e: any) => reject(e));
+    });
+  }, targetPackage);
+  // @ts-ignore
+  console.log(r.report);
+  // @ts-ignore
+  expect(r.failed).toBe(false);
+}, 100000);
+
+// it('WebLogo.getAlphabetSimilarity', () => {
+//
+// });

package/src/__jest__/test-node.ts

@@ -0,0 +1,97 @@
+import * as path from 'path';
+import * as os from 'os';
+import * as fs from 'fs';
+// @ts-ignore
+import * as yaml from 'js-yaml';
+
+const fetch = require('node-fetch');
+
+export async function getToken(url: string, key: string) {
+  const response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
+  const json = await response.json();
+  if (json.isSuccess == true)
+    return json.token;
+  else
+    throw new Error('Unable to login to server. Check your dev key');
+}
+
+export async function getWebUrl(url: string, token: string) {
+  const response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
+  const json = await response.json();
+  return json.settings.webRoot;
+}
+
+const grokDir = path.join(os.homedir(), '.grok');
+const confPath = path.join(grokDir, 'config.yaml');
+
+function mapURL(conf: Config): Indexable {
+  const urls: Indexable = {};
+  for (const server in conf.servers)
+    urls[conf['servers'][server]['url']] = conf['servers'][server];
+
+  return urls;
+}
+
+export function getDevKey(hostKey: string): { url: string, key: string } {
+  const config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
+  let host = hostKey == '' ? config.default : hostKey;
+  host = host.trim();
+  const urls = mapURL(config);
+  let key = '';
+  let url = '';
+  try {
+    let url = new URL(host).href;
+    if (url.endsWith('/')) url = url.slice(0, -1);
+    if (url in urls) key = config['servers'][urls[url]]['key'];
+  } catch (error) {
+    if (config['servers'][host] == null)
+      throw new Error(`Unknown server alias. Please add it to ${confPath}`);
+    url = config['servers'][host]['url'];
+    key = config['servers'][host]['key'];
+  }
+  return {url, key};
+}
+
+export async function getBrowserPage(puppeteer: any): Promise<{ browser: any, page: any }> {
+  let url: string = process.env.HOST ?? '';
+  const cfg = getDevKey(url);
+  url = cfg.url;
+
+  const key = cfg.key;
+  const token = await getToken(url, key);
+  url = await getWebUrl(url, token);
+  console.log(`Using web root: ${url}`);
+
+  const browser = await puppeteer.launch({
+    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
+    ignoreHTTPSErrors: true,
+  });
+
+  const page = await browser.newPage();
+  await page.goto(`${url}/oauth/`);
+  await page.setCookie({name: 'auth', value: token});
+  await page.evaluate((token: any) => {
+    window.localStorage.setItem('auth', token);
+  }, token);
+  await page.goto(url);
+  try {
+    await page.waitForSelector('.grok-preloader');
+    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 100000});
+  } catch (error) {
+    throw error;
+  }
+  return {browser, page};
+}
+
+
+interface Config {
+  servers: {
+    [alias: string]: {
+      url: string,
+      key: string
+    }
+  },
+  default: string,
+}
+
+interface Indexable {[key: string]: any;}

package/src/package-test.ts

@@ -0,0 +1,18 @@
+import * as DG from 'datagrok-api/dg';
+
+import {runTests, tests} from '@datagrok-libraries/utils/src/test';
+
+import './tests/WebLogo.test';
+
+export const _packageTest = new DG.Package();
+export {tests};
+
+//name: test
+//input: string category {optional: true}
+//input: string t {optional: true}
+//output: dataframe result
+//top-menu: Tools | Dev | JS API Tests
+export async function test(category: string, t: string): Promise<DG.DataFrame> {
+  const data = await runTests({category, test: t});
+  return DG.DataFrame.fromObjects(data)!;
+}

package/src/tests/Palettes.test.ts

@@ -0,0 +1,12 @@
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {_testPaletteN, _testPaletteAA} from '@datagrok-libraries/bio/src/tests/palettes.test';
+
+category('Palettes', () => {
+  test('testPaletteN', async () => { _testPaletteN(); });
+  test('testPaletteAA', async () => { _testPaletteAA(); });
+});

package/src/tests/WebLogo.test.ts

@@ -0,0 +1,132 @@
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {Nucleotides, NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
+import {Aminoacids, AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
+import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
+import {UnknownSeqPalette} from '@datagrok-libraries/bio/src/unknown';
+
+category('WebLogo', () => {
+  test('testGetAlphabetSimilarity', async () => { _testGetAlphabetSimilarity(); });
+
+  test('testPickupPaletteN1', async () => { _testPickupPaletteN1(); });
+  test('testPickupPaletteAA1', async () => { _testPickupPaletteAA1(); });
+
+  // dfAA2 is too similar to nucleotides
+  // test('testPickupPaletteAA2', async () => {
+  //   _testPickupPaletteAA2();
+  // });
+});
+
+const dfN1: DG.DataFrame = DG.DataFrame.fromCsv(
+  `seq
+'ACGT'
+'CAGT'
+'TTCA'
+`);
+
+/** 2 - is an error monomer
+ * This sequence set should be classified as nucleotides sequences.
+ * Small error, not similar to amino acids.
+ */
+const dfN1e: DG.DataFrame = DG.DataFrame.fromCsv(
+  `seq
+ACGT
+CAGT
+TTC2
+`);
+
+/** Pure amino acids sequence */
+const dfAA1: DG.DataFrame = DG.DataFrame.fromCsv(
+  `seq
+FWPHWYV
+YNRQWYV
+MKPSWYV
+`);
+
+/** A - alanine, G - glycine, T -= threonine, C - cysteine, W - tryptophan
+ * This sequence set should be detected as amino acids more than nucleotides.
+ */
+const dfAA2: DG.DataFrame = DG.DataFrame.fromCsv(
+  `seq
+AGTC
+AGTC
+AGTCW
+`);
+
+/** This sequence set should be recognized as unknown. */
+const dfX: DG.DataFrame = DG.DataFrame.fromCsv(
+  `seq
+XZJ{}2
+5Z4733
+3Z6></
+675687
+`);
+
+export function _testGetAlphabetFreqs() {
+  const seqCol: DG.Column = dfN1.col('seq')!;
+  const mFreq = WebLogo.getAlphabetFreqs(seqCol);
+
+  expectObject(mFreq, {
+    'A': 3,
+    'C': 3,
+    'G': 2,
+    'T': 4
+  });
+}
+
+export function _testGetAlphabetSimilarity() {
+  const freq: { [m: string]: number } = {
+    'A': 2041,
+    'C': 3015,
+    'G': 3015,
+    'T': 2048,
+    '-': 1000
+  };
+  const alphabet: Set<string> = new Set(Object.keys(Nucleotides.Names));
+  const res = WebLogo.getAlphabetSimilarity(freq, alphabet);
+
+  expect(res > 0.6, true);
+}
+
+export function _testPickupPaletteN1() {
+  const seqCol: DG.Column = dfN1.col('seq')!;
+  const cp = WebLogo.pickUpPalette(seqCol);
+
+  expect(cp instanceof NucleotidesPalettes, true);
+}
+
+export function _testPickupPaletteAA1() {
+  const seqCol: DG.Column = dfAA1.col('seq')!;
+  const cp = WebLogo.pickUpPalette(seqCol);
+
+  expect(cp instanceof AminoacidsPalettes, true);
+}
+
+export function _testPickupPaletteAA2() {
+  const seqCol: DG.Column = dfAA2.col('seq')!;
+  const cp = WebLogo.pickUpPalette(seqCol);
+
+  expect(cp instanceof AminoacidsPalettes, true);
+}
+
+export function _testPickupPaletteAll() {
+  const seqColN1: DG.Column = dfN1.col('seq')!;
+  const seqColAA1: DG.Column = dfAA1.col('seq')!;
+  const seqColAA2: DG.Column = dfAA2.col('seq')!;
+  const seqColX: DG.Column = dfX.col('seq')!;
+
+  const cpN1: SeqPalette = WebLogo.pickUpPalette(seqColN1);
+  const cpAA1: SeqPalette = WebLogo.pickUpPalette(seqColAA1);
+  const cpAA2: SeqPalette = WebLogo.pickUpPalette(seqColAA2);
+  const cpX: SeqPalette = WebLogo.pickUpPalette(seqColX);
+
+  expect(cpN1 instanceof NucleotidesPalettes, true);
+  expect(cpAA1 instanceof AminoacidsPalettes, true);
+  expect(cpAA2 instanceof AminoacidsPalettes, true);
+  expect(cpX instanceof UnknownSeqPalette, true);
+}

package/test-Bio-e702a345ac13-fb65a774.html

@@ -0,0 +1,245 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=e702a345ac13. Commit fb65a774.</title><style type="text/css">html,
+body {
+  font-family: Arial, Helvetica, sans-serif;
+  font-size: 1rem;
+  margin: 0;
+  padding: 0;
+  color: #333;
+}
+body {
+  padding: 2rem 1rem;
+  font-size: 0.85rem;
+}
+#jesthtml-content {
+  margin: 0 auto;
+  max-width: 70rem;
+}
+header {
+  display: flex;
+  align-items: center;
+}
+#title {
+  margin: 0;
+  flex-grow: 1;
+}
+#logo {
+  height: 4rem;
+}
+#timestamp {
+  color: #777;
+  margin-top: 0.5rem;
+}
+
+/** SUMMARY */
+#summary {
+  color: #333;
+  margin: 2rem 0;
+  display: flex;
+  font-family: monospace;
+  font-size: 1rem;
+}
+#summary > div {
+  margin-right: 2rem;
+  background: #eee;
+  padding: 1rem;
+  min-width: 15rem;
+}
+#summary > div:last-child {
+  margin-right: 0;
+}
+@media only screen and (max-width: 720px) {
+  #summary {
+    flex-direction: column;
+  }
+  #summary > div {
+    margin-right: 0;
+    margin-top: 2rem;
+  }
+  #summary > div:first-child {
+    margin-top: 0;
+  }
+}
+
+.summary-total {
+  font-weight: bold;
+  margin-bottom: 0.5rem;
+}
+.summary-passed {
+  color: #4f8a10;
+  border-left: 0.4rem solid #4f8a10;
+  padding-left: 0.5rem;
+}
+.summary-failed,
+.summary-obsolete-snapshots {
+  color: #d8000c;
+  border-left: 0.4rem solid #d8000c;
+  padding-left: 0.5rem;
+}
+.summary-pending {
+  color: #9f6000;
+  border-left: 0.4rem solid #9f6000;
+  padding-left: 0.5rem;
+}
+.summary-empty {
+  color: #999;
+  border-left: 0.4rem solid #999;
+}
+
+.test-result {
+  padding: 1rem;
+  margin-bottom: 0.25rem;
+}
+.test-result:last-child {
+  border: 0;
+}
+.test-result.passed {
+  background-color: #dff2bf;
+  color: #4f8a10;
+}
+.test-result.failed {
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.test-result.pending {
+  background-color: #ffdf61;
+  color: #9f6000;
+}
+
+.test-info {
+  display: flex;
+  justify-content: space-between;
+}
+.test-suitename {
+  width: 20%;
+  text-align: left;
+  font-weight: bold;
+  word-break: break-word;
+}
+.test-title {
+  width: 40%;
+  text-align: left;
+  font-style: italic;
+}
+.test-status {
+  width: 20%;
+  text-align: right;
+}
+.test-duration {
+  width: 10%;
+  text-align: right;
+  font-size: 0.75rem;
+}
+
+.failureMessages {
+  padding: 0 1rem;
+  margin-top: 1rem;
+  border-top: 1px dashed #d8000c;
+}
+.failureMessages.suiteFailure {
+  border-top: none;
+}
+.failureMsg {
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+
+.suite-container {
+  margin-bottom: 2rem;
+}
+.suite-info {
+  padding: 1rem;
+  background-color: #eee;
+  color: #777;
+  display: flex;
+  align-items: center;
+  margin-bottom: 0.25rem;
+}
+.suite-info .suite-path {
+  word-break: break-all;
+  flex-grow: 1;
+  font-family: monospace;
+  font-size: 1rem;
+}
+.suite-info .suite-time {
+  margin-left: 0.5rem;
+  padding: 0.2rem 0.3rem;
+  font-size: 0.75rem;
+}
+.suite-info .suite-time.warn {
+  background-color: #d8000c;
+  color: #fff;
+}
+
+/* CONSOLE LOGS */
+.suite-consolelog {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #efefef;
+}
+.suite-consolelog-header {
+  font-weight: bold;
+}
+.suite-consolelog-item {
+  padding: 0.5rem;
+}
+.suite-consolelog-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-consolelog-item-origin {
+  color: #777;
+  font-weight: bold;
+}
+.suite-consolelog-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+
+/* OBSOLETE SNAPSHOTS */
+.suite-obsolete-snapshots {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.suite-obsolete-snapshots-header {
+  font-weight: bold;
+}
+.suite-obsolete-snapshots-item {
+  padding: 0.5rem;
+}
+.suite-obsolete-snapshots-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-obsolete-snapshots-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=e702a345ac13. Commit fb65a774.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-06-06 08:15:45</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">18.503s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">6.9s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:24:11
+    at Generator.next (&lt;anonymous&gt;)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
+    at new Promise (&lt;anonymous&gt;)
+    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:23)
+    at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:47:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>

package/webpack.config.js

@@ -1,9 +1,15 @@
 const path = require('path');
+const packageName = path.parse(require('./package.json').name).name.toLowerCase().replace(/-/g, '');
 
 module.exports = {
   mode: 'development',
   entry: {
-    package: './src/package.ts',
+    package: ['./src/package.ts'],
+    test: {
+      filename: 'package-test.js',
+      library: {type: 'var', name: `${packageName}_test`},
+      import: './src/package-test.ts',
+    },
   },
   resolve: {
     fallback: {'url': false},