@datagrok/bio 1.7.19 → 1.7.22

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Files changed (8) hide show
  1. package/detectors.js +24 -12
  2. package/dist/package-test.js +12 -4
  3. package/dist/package.js +5 -4
  4. package/files/tests/testAlertCollection.csv +1252 -0
  5. package/package.json +6 -2
  6. package/src/package.ts +6 -5
  7. package/src/tests/detectors-test.ts +9 -0
  8. package/{test-Bio-4f0c8bae6479-ddc1ded2.html → test-Bio-4f0c8bae6479-dd77efbc.html} +5 -2
package/package.json CHANGED
@@ -2,7 +2,7 @@
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  "name": "@datagrok/bio",
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  "beta": false,
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  "friendlyName": "Bio",
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- "version": "1.7.19",
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+ "version": "1.7.22",
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  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
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  "repository": {
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  "type": "git",
@@ -60,7 +60,11 @@
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  "Developers"
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  ],
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  "sources": [
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- "css/helm.css"
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+ "css/helm.css",
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+ "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js",
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+ "helm/JSDraw/Scilligence.JSDraw2.Lite.js",
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+ "helm/JSDraw/Scilligence.JSDraw2.Resources.js",
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+ "helm/JSDraw/Pistoia.HELM-uncompressed.js"
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  ],
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  "category": "Bioinformatics"
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  }
package/src/package.ts CHANGED
@@ -26,17 +26,18 @@ import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
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  import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
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-
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  //tags: init
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  export async function initBio(): Promise<void> {
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  // apparently HELMWebEditor requires dojo to be initialized first
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- if (DG.Func.find({package: 'Helm', name: 'initHelm'}) != null) {
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- grok.functions.call('Helm:initHelp');
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- }
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+ const funcList: DG.Func[] = DG.Func.find({package: 'Helm', name: 'initHelm'});
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+ console.debug(`Bio: initBio() funcList.length = ${funcList.length}`);
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+ if (funcList.length === 1)
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+ await grok.functions.call('Helm:initHelp');
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+
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  return new Promise((resolve, reject) => {
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  // @ts-ignore
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  dojo.ready(function() { resolve(null); });
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- });
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+ });
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  }
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  //name: Lru
package/src/tests/detectors-test.ts CHANGED
@@ -125,6 +125,7 @@ MWRSWY-CKHP
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  testSpgi100 = 'testSpgi100',
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  testUnichemSources = 'testUnichemSources',
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  testDmvOffices = 'testDmvOffices',
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+ testAlertCollection = 'testAlertCollection',
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  }
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  const samples: { [key: string]: string } = {
@@ -145,6 +146,7 @@ MWRSWY-CKHP
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  'testSpgi100': 'System:AppData/Bio/tests/testSpgi100.csv',
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  'testUnichemSources': 'System:AppData/Bio/tests/testUnichemSources.csv',
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  'testDmvOffices': 'System:AppData/Bio/tests/testDmvOffices.csv',
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+ 'testAlertCollection': 'System:AppData/Bio/tests/testAlertCollection.csv',
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  };
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  const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -342,6 +344,9 @@ MWRSWY-CKHP
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  test('samplesTestSpgi100NegativePrimaryScaffoldName', async () => {
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  await _testNeg(readSamples(Samples.testSpgi100), 'Primary Scaffold Name');
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  });
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+ test('samplesTestSpgi100NegativeSampleName', async () => {
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+ await _testNeg(readSamples(Samples.testSpgi100), 'Sample Name');
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+ });
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  test('samplesTestUnichemSourcesNegativeSrcUrl', async () => {
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  await _testNeg(readSamples(Samples.testUnichemSources), 'src_url');
@@ -356,6 +361,10 @@ MWRSWY-CKHP
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  test('samplesTestDmvOfficesNegativeCity', async () => {
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  await _testNeg(readSamples(Samples.testDmvOffices), 'City');
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  });
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+
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+ test('samplesTestAlertCollectionNegativeSmarts', async () => {
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+ await _testNeg(readSamples(Samples.testAlertCollection), 'smarts');
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+ });
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  });
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  export async function _testNeg(readDf: DfReaderFunc, colName: string) {
package/{test-Bio-4f0c8bae6479-ddc1ded2.html → test-Bio-4f0c8bae6479-dd77efbc.html} RENAMED
@@ -1,4 +1,4 @@
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- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit ddc1ded2.</title><style type="text/css">html,
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+ <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit dd77efbc.</title><style type="text/css">html,
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  body {
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  font-family: Arial, Helvetica, sans-serif;
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  font-size: 1rem;
@@ -229,7 +229,7 @@ header {
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  font-size: 1rem;
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  padding: 0 0.5rem;
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  }
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- </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit ddc1ded2.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-01 11:56:39</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">225.198s</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">209.26s</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)
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+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit dd77efbc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-01 14:54:31</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">230.253s</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">213.793s</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)
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  at Generator.next (&lt;anonymous&gt;)
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  at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
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  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
@@ -242,6 +242,7 @@ header {
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  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:65:11
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  at Generator.next (&lt;anonymous&gt;)
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  at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
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+ at runMicrotasks (&lt;anonymous&gt;)
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  at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Bio.WebLogo.testGetStats : OK
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  Test result : Bio.WebLogo.testGetAlphabetSimilarity : OK
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  Test result : Bio.WebLogo.testPickupPaletteN1 : OK
@@ -300,10 +301,12 @@ Test result : Bio.detectors.samplesTestCerealNegativeCerealName : OK
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  Test result : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
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  Test result : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
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  Test result : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
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+ Test result : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
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  Test result : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
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  Test result : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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  Test result : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
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  Test result : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
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+ Test result : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
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  Test result : Bio.MSA.isCorrect : OK
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  Test result : Bio.MSA.isCorrectLong : OK
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  Test result : Bio.sequenceSpace.sequenceSpaceOpens : OK