@datagrok/bio 2.1.11 → 2.4.2

package/jest.config.js

@@ -1,33 +0,0 @@
-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/src/__jest__/remote.test.ts

@@ -1,77 +0,0 @@
-/**
- * @jest-environment jsdom
- */
-
-import * as utils from './test-node';
-import puppeteer from 'puppeteer';
-
-const P_START_TIMEOUT: number = 3600000;
-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();
-});
-
-expect.extend({
-  checkOutput(received, expected, context) {
-    if (received === expected) {
-      return {
-        message: () => context,
-        pass: true
-      };
-    } else {
-      return {
-        message: () => context,
-        pass: false
-      };
-    }
-  }
-});
-
-it('TEST', async () => {
-  const targetPackage: string = process.env.TARGET_PACKAGE ?? 'Bio';
-  console.log(`Testing ${targetPackage} package`);
-
-  let 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 cSkipped = df.columns.byName('skipped');
-        const cMessage = df.columns.byName('result');
-        const cCat = df.columns.byName('category');
-        const cName = df.columns.byName('name');
-        const cTime = df.columns.byName('ms');
-        let failed = false;
-        let skipReport = '';
-        let passReport = '';
-        let failReport = '';
-        for (let i = 0; i < df.rowCount; i++) {
-          if (cStatus.get(i)) {
-            if (cSkipped.get(i)) {
-              skipReport += `Test result : Skipped : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-            } else {
-              passReport += `Test result : Success : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-            }
-          } else {
-            failed = true;
-            failReport += `Test result : Failed : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-          }
-        }
-        resolve({failReport, skipReport, passReport, failed});
-      }).catch((e: any) => reject(e));
-    });
-  }, targetPackage);
-  // @ts-ignore
-  console.log(r.passReport);
-  // @ts-ignore
-  console.log(r.skipReport);
-  // @ts-ignore
-  expect(r.failed).checkOutput(false, r.failReport);
-}, 7200000);

package/src/__jest__/test-node.ts

@@ -1,98 +0,0 @@
-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: ${url}`);
-
-  const browser = await puppeteer.launch({
-    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
-    ignoreHTTPSErrors: true,
-  });
-
-  const page = await browser.newPage();
-  await page.setDefaultNavigationTimeout(0);
-  await page.goto(`${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', { timeout: 1800000 });
-    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 3600000});
-  } catch (error) {
-    throw error;
-  }
-  return {browser, page};
-}
-
-
-interface Config {
-  servers: {
-    [alias: string]: {
-      url: string,
-      key: string
-    }
-  },
-  default: string,
-}
-
-interface Indexable {[key: string]: any;}

package/test-Bio-91c83d8913ff-bb573307.html

@@ -1,392 +0,0 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit bb573307.</title><style type="text/css">html,
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit bb573307.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-30 16:25:48</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">49.92s</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">35.236s</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:40:11
-    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:38:23)
-    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:72:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
-    at runMicrotasks (&lt;anonymous&gt;)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
-Test result : Success : 1 : Bio.Palettes.testPaletteAA : OK
-Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
-Test result : Success : 228 : Bio.detectors.NegativeEmpty : OK
-Test result : Success : 36 : Bio.detectors.Negative1 : OK
-Test result : Success : 33 : Bio.detectors.Negative2 : OK
-Test result : Success : 38 : Bio.detectors.Negative3 : OK
-Test result : Success : 586 : Bio.detectors.NegativeSmiles : OK
-Test result : Success : 56 : Bio.detectors.Dna1 : OK
-Test result : Success : 28 : Bio.detectors.Rna1 : OK
-Test result : Success : 42 : Bio.detectors.AA1 : OK
-Test result : Success : 35 : Bio.detectors.MsaDna1 : OK
-Test result : Success : 38 : Bio.detectors.MsaAA1 : OK
-Test result : Success : 27 : Bio.detectors.SepDna : OK
-Test result : Success : 25 : Bio.detectors.SepRna : OK
-Test result : Success : 38 : Bio.detectors.SepPt : OK
-Test result : Success : 18 : Bio.detectors.SepUn1 : OK
-Test result : Success : 17 : Bio.detectors.SepUn2 : OK
-Test result : Success : 18 : Bio.detectors.SepMsaN1 : OK
-Test result : Success : 674 : Bio.detectors.SamplesFastaCsvPt : OK
-Test result : Success : 24 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
-Test result : Success : 21 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
-Test result : Success : 56 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
-Test result : Success : 345 : Bio.detectors.SamplesFastaFastaPt : OK
-Test result : Success : 1174 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
-Test result : Success : 7 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
-Test result : Success : 22 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
-Test result : Success : 360 : Bio.detectors.samplesMsaComplexUn : OK
-Test result : Success : 14 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
-Test result : Success : 239 : Bio.detectors.samplesIdCsvNegativeID : OK
-Test result : Success : 248 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
-Test result : Success : 275 : Bio.detectors.samplesHelmCsvHELM : OK
-Test result : Success : 12 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
-Test result : Success : 246 : Bio.detectors.samplesTestHelmNegativeID : OK
-Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeTestType : OK
-Test result : Success : 18 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
-Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeValid : OK
-Test result : Success : 15 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
-Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
-Test result : Success : 18 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
-Test result : Success : 966 : Bio.detectors.samplesTestDemogNegativeAll : OK
-Test result : Success : 332 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
-Test result : Success : 138 : Bio.detectors.samplesTestSmilesShortNegativeSmiles : OK
-Test result : Success : 166 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
-Test result : Success : 144 : Bio.detectors.samplesFastaPtPosSequence : OK
-Test result : Success : 141 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
-Test result : Success : 221 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
-Test result : Success : 10 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
-Test result : Success : 6 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
-Test result : Success : 6 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
-Test result : Success : 196 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
-Test result : Success : 5 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
-Test result : Success : 183 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
-Test result : Success : 16 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
-Test result : Success : 166 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
-Test result : Success : 249 : Bio.detectors.samplesTestSpgiNegativeVals : OK
-Test result : Success : 13 : Bio.detectorsBenchmark.separatorDnaShorts50Few50 : OK
-Test result : Success : 10007 : Bio.detectorsBenchmark.separatorDnaShorts50Many1E6 : OK
-Test result : Success : 1882 : Bio.MSA.isCorrect : OK
-Test result : Success : 152 : Bio.MSA.isCorrectLong : OK
-Test result : Success : 1316 : Bio.sequenceSpace.sequenceSpaceOpens : OK
-Test result : Success : 600 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
-Test result : Success : 921 : Bio.activityCliffs.activityCliffsOpens : OK
-Test result : Success : 1014 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
-Test result : Success : 1 : Bio.splitters.fastaMulti : OK
-Test result : Success : 1 : Bio.splitters.helm1 : OK
-Test result : Success : 1 : Bio.splitters.helm2 : OK
-Test result : Success : 0 : Bio.splitters.helm3-multichar : OK
-Test result : Success : 0 : Bio.splitters.testHelm1 : OK
-Test result : Success : 0 : Bio.splitters.testHelm2 : OK
-Test result : Success : 1 : Bio.splitters.testHelm3 : OK
-Test result : Success : 393 : Bio.splitters.splitToMonomers : OK
-Test result : Success : 2 : Bio.splitters.getHelmMonomers : OK
-Test result : Success : 90 : Bio.renderers.long sequence performance  : OK
-Test result : Success : 665 : Bio.renderers.many sequence performance : OK
-Test result : Success : 397 : Bio.renderers.rendererMacromoleculeFasta : OK
-Test result : Success : 269 : Bio.renderers.rendererMacromoleculeSeparator : OK
-Test result : Success : 100 : Bio.renderers.rendererMacromoleculeDifference : OK
-Test result : Success : 560 : Bio.renderers.afterMsa : OK
-Test result : Success : 395 : Bio.renderers.afterConvert : OK
-Test result : Success : 223 : Bio.renderers.selectRendererBySemType : OK
-Test result : Success : 7 : Bio.converters.testFastaPtToSeparator : OK
-Test result : Success : 6 : Bio.converters.testFastaDnaToSeparator : OK
-Test result : Success : 6 : Bio.converters.testFastaRnaToSeparator : OK
-Test result : Success : 7 : Bio.converters.testFastaGapsToSeparator : OK
-Test result : Success : 4 : Bio.converters.testFastaPtToHelm : OK
-Test result : Success : 3 : Bio.converters.testFastaDnaToHelm : OK
-Test result : Success : 3 : Bio.converters.testFastaRnaToHelm : OK
-Test result : Success : 3 : Bio.converters.testFastaGapsToHelm : OK
-Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
-Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
-Test result : Success : 1 : Bio.converters.testSeparatorRnaToFasta : OK
-Test result : Success : 1 : Bio.converters.testSeparatorGapsToFasta : OK
-Test result : Success : 1 : Bio.converters.testSeparatorPtToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
-Test result : Success : 1 : Bio.converters.testSeparatorRnaToHelm : OK
-Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
-Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
-Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
-Test result : Success : 1 : Bio.converters.testHelmPtToFasta : OK
-Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
-Test result : Success : 1 : Bio.converters.testHelmRnaToSeparator : OK
-Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
-Test result : Success : 4 : Bio.converters.testHelmLoneRibose : OK
-Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
-Test result : Success : 3 : Bio.converters.testHelmLonePhosphorus : OK
-Test result : Success : 1 : Bio.fastaFileHandler.testNormalFormatting : OK
-Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
-Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
-Test result : Success : 1 : Bio.fastaExport.wrapSequenceSingle : OK
-Test result : Success : 0 : Bio.fastaExport.wrapSequenceMulti : OK
-Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest1 : OK
-Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest2 : OK
-Test result : Success : 1 : Bio.bio.testGetStatsHelm1 : OK
-Test result : Success : 1 : Bio.bio.testGetStatsN1 : OK
-Test result : Success : 0 : Bio.bio.testGetAlphabetSimilarity : OK
-Test result : Success : 1 : Bio.bio.testPickupPaletteN1 : OK
-Test result : Success : 1 : Bio.bio.testPickupPaletteN1e : OK
-Test result : Success : 2 : Bio.bio.testPickupPaletteAA1 : OK
-Test result : Success : 1 : Bio.bio.testPickupPaletteX : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerSingle : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
-Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
-Test result : Success : 154 : Bio.WebLogo-positions.allPositions : OK
-Test result : Success : 123 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
-Test result : Success : 127 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
-Test result : Success : 4 : Bio.checkInputColumn.testMsaPos : OK
-Test result : Success : 2 : Bio.checkInputColumn.testMsaNegHelm : OK
-Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
-Test result : Success : 0 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
-Test result : Success : 476 : Bio.similarity/diversity.similaritySearchViewer : OK
-Test result : Success : 350 : Bio.similarity/diversity.diversitySearchViewer : OK
-Test result : Success : 257 : Bio.substructureFilters.fasta : OK
-Test result : Success : 434 : Bio.substructureFilters.separator : OK
-</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:74:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
-    at runMicrotasks (&lt;anonymous&gt;)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Skipped : 0 : Bio.detectorsBenchmark.fastaDnaShorts50Few50 : #1192
-Test result : Skipped : 0 : Bio.detectorsBenchmark.fastaDnaShorts50Many1E6 : #1192
-Test result : Skipped : 0 : Bio.detectorsBenchmark.fastaDnaLong1e6Few50 : #1192
-Test result : Skipped : 0 : Bio.detectorsBenchmark.separatorDnaLong1e6Few50 : #1192
-Test result : Skipped : 0 : Bio.renderers.setRendererManually : GROK-11212
-Test result : Skipped : 0 : Bio.substructureFilters.helm : #1206
-</pre></div></div></div></div></body></html>