@datagrok/bio 2.0.31 → 2.0.33
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/package-test.js +379 -139
- package/dist/package.js +326 -113
- package/files/libraries/HELMCoreLibrary.json +18218 -0
- package/package.json +3 -3
- package/src/analysis/sequence-activity-cliffs.ts +18 -0
- package/src/analysis/sequence-space.ts +18 -3
- package/src/calculations/monomerLevelMols.ts +1 -1
- package/src/package.ts +221 -20
- package/src/tests/activity-cliffs-tests.ts +21 -6
- package/src/tests/activity-cliffs-utils.ts +1 -1
- package/src/tests/similarity-diversity-tests.ts +35 -19
- package/test-Bio-3afbd4014fa1-15e7930e.html +389 -0
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit 15e7930e.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-04 14:02:19</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 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 summary-empty">0 passed</div><div class="summary-failed">1 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">45.144s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">28.346s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 234 : Bio.splitters.splitToMonomers : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of undefined (reading 'forEach')
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Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of undefined (reading 'endsWith')
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Test result : Failed : 359 : Bio.renderers.rendererMacromoleculeFasta : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 254 : Bio.renderers.rendererMacromoleculeSeparator : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 96 : Bio.renderers.rendererMacromoleculeDifference : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 545 : Bio.renderers.afterMsa : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 352 : Bio.renderers.afterConvert : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 104 : Bio.renderers.selectRendererBySemType : TypeError: Cannot read properties of undefined (reading 'push')
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Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of undefined (reading 'forEach')
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Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of undefined (reading 'endsWith')
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at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:70:20
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at Generator.next (<anonymous>)
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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 (<anonymous>)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></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.<anonymous> (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
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at Generator.next (<anonymous>)
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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
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at Generator.next (<anonymous>)
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at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
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at new Promise (<anonymous>)
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at Object.<anonymous>.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
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at Object.<anonymous> (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
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at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
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at new Promise (<anonymous>)</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:68:11
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at Generator.next (<anonymous>)
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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 (<anonymous>)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Bio.Palettes.testPaletteN : OK
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Test result : Success : 1 : Bio.Palettes.testPaletteAA : OK
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Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
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Test result : Success : 273 : Bio.detectors.NegativeEmpty : OK
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Test result : Success : 34 : Bio.detectors.Negative1 : OK
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Test result : Success : 36 : Bio.detectors.Negative2 : OK
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Test result : Success : 31 : Bio.detectors.Negative3 : OK
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Test result : Success : 44 : Bio.detectors.NegativeSmiles : OK
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Test result : Success : 24 : Bio.detectors.Dna1 : OK
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Test result : Success : 37 : Bio.detectors.Rna1 : OK
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Test result : Success : 38 : Bio.detectors.AA1 : OK
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Test result : Success : 23 : Bio.detectors.MsaDna1 : OK
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Test result : Success : 46 : Bio.detectors.MsaAA1 : OK
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Test result : Success : 21 : Bio.detectors.SepDna : OK
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Test result : Success : 22 : Bio.detectors.SepRna : OK
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Test result : Success : 24 : Bio.detectors.SepPt : OK
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Test result : Success : 19 : Bio.detectors.SepUn1 : OK
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Test result : Success : 18 : Bio.detectors.SepUn2 : OK
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Test result : Success : 29 : Bio.detectors.SepMsaN1 : OK
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Test result : Success : 1790 : Bio.detectors.SamplesFastaCsvPt : OK
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282
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+
Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
|
|
283
|
+
Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
|
|
284
|
+
Test result : Success : 137 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
|
|
285
|
+
Test result : Success : 335 : Bio.detectors.SamplesFastaFastaPt : OK
|
|
286
|
+
Test result : Success : 1536 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
|
|
287
|
+
Test result : Success : 41 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
|
|
288
|
+
Test result : Success : 239 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
|
|
289
|
+
Test result : Success : 340 : Bio.detectors.samplesMsaComplexUn : OK
|
|
290
|
+
Test result : Success : 65 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
|
|
291
|
+
Test result : Success : 241 : Bio.detectors.samplesIdCsvNegativeID : OK
|
|
292
|
+
Test result : Success : 222 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
|
|
293
|
+
Test result : Success : 217 : Bio.detectors.samplesHelmCsvHELM : OK
|
|
294
|
+
Test result : Success : 28 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
|
|
295
|
+
Test result : Success : 213 : Bio.detectors.samplesTestHelmNegativeID : OK
|
|
296
|
+
Test result : Success : 23 : Bio.detectors.samplesTestHelmNegativeTestType : OK
|
|
297
|
+
Test result : Success : 10 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
|
|
298
|
+
Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeValid : OK
|
|
299
|
+
Test result : Success : 19 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
|
|
300
|
+
Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
|
|
301
|
+
Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
|
|
302
|
+
Test result : Success : 1437 : Bio.detectors.samplesTestDemogNegativeAll : OK
|
|
303
|
+
Test result : Success : 698 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
|
|
304
|
+
Test result : Success : 185 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
|
|
305
|
+
Test result : Success : 136 : Bio.detectors.samplesFastaPtPosSequence : OK
|
|
306
|
+
Test result : Success : 162 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
|
|
307
|
+
Test result : Success : 216 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
|
|
308
|
+
Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
|
|
309
|
+
Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
|
|
310
|
+
Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
|
|
311
|
+
Test result : Success : 210 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
|
|
312
|
+
Test result : Success : 9 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
|
|
313
|
+
Test result : Success : 192 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
|
|
314
|
+
Test result : Success : 28 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
|
|
315
|
+
Test result : Success : 168 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
|
|
316
|
+
Test result : Success : 2670 : Bio.MSA.isCorrect : OK
|
|
317
|
+
Test result : Success : 124 : Bio.MSA.isCorrectLong : OK
|
|
318
|
+
Test result : Success : 1279 : Bio.sequenceSpace.sequenceSpaceOpens : OK
|
|
319
|
+
Test result : Success : 596 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
|
|
320
|
+
Test result : Success : 836 : Bio.activityCliffs.activityCliffsOpens : OK
|
|
321
|
+
Test result : Success : 868 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
|
|
322
|
+
Test result : Success : 1 : Bio.splitters.fastaMulti : OK
|
|
323
|
+
Test result : Success : 1 : Bio.splitters.helm1 : OK
|
|
324
|
+
Test result : Success : 0 : Bio.splitters.helm2 : OK
|
|
325
|
+
Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
|
|
326
|
+
Test result : Success : 0 : Bio.splitters.testHelm1 : OK
|
|
327
|
+
Test result : Success : 1 : Bio.splitters.testHelm2 : OK
|
|
328
|
+
Test result : Success : 0 : Bio.splitters.testHelm3 : OK
|
|
329
|
+
Test result : Success : 1 : Bio.splitters.getHelmMonomers : OK
|
|
330
|
+
Test result : Success : 109 : Bio.renderers.long sequence performance : OK
|
|
331
|
+
Test result : Success : 918 : Bio.renderers.many sequence performance : OK
|
|
332
|
+
Test result : Success : 0 : Bio.renderers.setRendererManually : GROK-11212
|
|
333
|
+
Test result : Success : 6 : Bio.converters.testFastaPtToSeparator : OK
|
|
334
|
+
Test result : Success : 5 : Bio.converters.testFastaDnaToSeparator : OK
|
|
335
|
+
Test result : Success : 4 : Bio.converters.testFastaRnaToSeparator : OK
|
|
336
|
+
Test result : Success : 5 : Bio.converters.testFastaGapsToSeparator : OK
|
|
337
|
+
Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
|
|
338
|
+
Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
|
|
339
|
+
Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
|
|
340
|
+
Test result : Success : 1 : Bio.converters.testFastaGapsToHelm : OK
|
|
341
|
+
Test result : Success : 0 : Bio.converters.testSeparatorPtToFasta : OK
|
|
342
|
+
Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
|
|
343
|
+
Test result : Success : 1 : Bio.converters.testSeparatorRnaToFasta : OK
|
|
344
|
+
Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
|
|
345
|
+
Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
|
|
346
|
+
Test result : Success : 1 : Bio.converters.testSeparatorDnaToHelm : OK
|
|
347
|
+
Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
|
|
348
|
+
Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
|
|
349
|
+
Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
|
|
350
|
+
Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
|
|
351
|
+
Test result : Success : 1 : Bio.converters.testHelmPtToFasta : OK
|
|
352
|
+
Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
|
|
353
|
+
Test result : Success : 1 : Bio.converters.testHelmRnaToSeparator : OK
|
|
354
|
+
Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
|
|
355
|
+
Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
|
|
356
|
+
Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
|
|
357
|
+
Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
|
|
358
|
+
Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
|
|
359
|
+
Test result : Success : 1 : Bio.fastaFileHandler.testExtraSpaces : OK
|
|
360
|
+
Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
|
|
361
|
+
Test result : Success : 1 : Bio.fastaExport.wrapSequenceSingle : OK
|
|
362
|
+
Test result : Success : 0 : Bio.fastaExport.wrapSequenceMulti : OK
|
|
363
|
+
Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest1 : OK
|
|
364
|
+
Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest2 : OK
|
|
365
|
+
Test result : Success : 2 : Bio.bio.testGetStatsHelm1 : OK
|
|
366
|
+
Test result : Success : 1 : Bio.bio.testGetStatsN1 : OK
|
|
367
|
+
Test result : Success : 1 : Bio.bio.testGetAlphabetSimilarity : OK
|
|
368
|
+
Test result : Success : 1 : Bio.bio.testPickupPaletteN1 : OK
|
|
369
|
+
Test result : Success : 2 : Bio.bio.testPickupPaletteN1e : OK
|
|
370
|
+
Test result : Success : 1 : Bio.bio.testPickupPaletteAA1 : OK
|
|
371
|
+
Test result : Success : 2 : Bio.bio.testPickupPaletteX : OK
|
|
372
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerSingle : OK
|
|
373
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
|
|
374
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
|
|
375
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
|
|
376
|
+
Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
|
|
377
|
+
Test result : Success : 140 : Bio.WebLogo-positions.allPositions : OK
|
|
378
|
+
Test result : Success : 120 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
|
|
379
|
+
Test result : Success : 132 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
|
|
380
|
+
Test result : Success : 3 : Bio.checkInputColumn.testMsaPos : OK
|
|
381
|
+
Test result : Success : 1 : Bio.checkInputColumn.testMsaNegHelm : OK
|
|
382
|
+
Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
|
|
383
|
+
Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
|
|
384
|
+
Test result : Success : 484 : Bio.similarity/diversity.similaritySearchViewer : OK
|
|
385
|
+
Test result : Success : 356 : Bio.similarity/diversity.diversitySearchViewer : OK
|
|
386
|
+
Test result : Success : 231 : Bio.substructureFilters.fasta : OK
|
|
387
|
+
Test result : Success : 420 : Bio.substructureFilters.separator : OK
|
|
388
|
+
Test result : Success : 1913 : Bio.substructureFilters.helm : OK
|
|
389
|
+
</pre></div></div></div></div></body></html>
|