@datagrok/bio 2.0.8 → 2.0.9

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.
Files changed (13) hide show
  1. package/dist/package-test.js +8 -6
  2. package/dist/package.js +6 -4
  3. package/files/{samples → data}/HELMCoreLibrary.json +0 -0
  4. package/files/{samples → data}/sample_FASTA.fasta +0 -0
  5. package/files/{samples → data}/sample_FASTA_DNA.csv +0 -0
  6. package/files/{samples → data}/sample_FASTA_PT.csv +0 -0
  7. package/files/{samples → data}/sample_FASTA_RNA.csv +0 -0
  8. package/files/{samples → data}/sample_HELM_empty_vals.csv +0 -0
  9. package/files/{samples → data}/sample_SEPARATOR_PT.csv +0 -0
  10. package/package.json +2 -2
  11. package/src/package.ts +4 -2
  12. package/src/tests/detectors-test.ts +2 -2
  13. package/test-Bio-7770371320b2-1095ee64.html +0 -374
package/files/{samples → data}/HELMCoreLibrary.json RENAMED
File without changes
package/files/{samples → data}/sample_FASTA.fasta RENAMED
File without changes
package/files/{samples → data}/sample_FASTA_DNA.csv RENAMED
File without changes
package/files/{samples → data}/sample_FASTA_PT.csv RENAMED
File without changes
package/files/{samples → data}/sample_FASTA_RNA.csv RENAMED
File without changes
package/files/{samples → data}/sample_SEPARATOR_PT.csv RENAMED
File without changes
package/package.json CHANGED
@@ -5,7 +5,7 @@
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  "name": "Leonid Stolbov",
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  "email": "lstolbov@datagrok.ai"
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  },
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- "version": "2.0.8",
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+ "version": "2.0.9",
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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",
@@ -14,7 +14,7 @@
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  },
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  "dependencies": {
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  "@biowasm/aioli": ">=2.4.0",
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- "@datagrok-libraries/bio": "^4.3.0",
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+ "@datagrok-libraries/bio": "^4.4.0",
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  "@datagrok-libraries/chem-meta": "1.0.0",
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  "@datagrok-libraries/ml": "^6.2.0",
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  "@datagrok-libraries/utils": "^1.6.2",
package/src/package.ts CHANGED
@@ -315,9 +315,11 @@ export async function compositionAnalysis(): Promise<void> {
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  return;
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  } else if (colList.length > 1) {
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  const colListNames: string [] = colList.map((col) => col.name);
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- const colInput: DG.InputBase = ui.choiceInput('Column', colListNames[0], colListNames);
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+ const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
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+ const colInput: DG.InputBase = ui.choiceInput(
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+ 'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
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  ui.dialog({
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- title: 'R-Groups Analysis',
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+ title: 'Composition Analysis',
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  helpUrl: '/help/domains/bio/macromolecules.md#composition-analysis'
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  })
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  .add(ui.div([
package/src/tests/detectors-test.ts CHANGED
@@ -131,8 +131,8 @@ MWRSWY-CKHP
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  const samples: { [key: string]: string } = {
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  'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
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- 'fastaFasta': 'System:AppData/Bio/samples/sample_FASTA.fasta',
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- 'fastaPtCsv': 'System:AppData/Bio/samples/sample_FASTA_PT.csv',
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+ 'fastaFasta': 'System:AppData/Bio/data/sample_FASTA.fasta',
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+ 'fastaPtCsv': 'System:AppData/Bio/data/sample_FASTA_PT.csv',
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  'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
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  'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
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  'peptidesComplex': 'System:AppData/Bio/tests/peptides_complex_msa.csv',
package/test-Bio-7770371320b2-1095ee64.html DELETED
@@ -1,374 +0,0 @@
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- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1095ee64.</title><style type="text/css">html,
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- body {
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- body {
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- padding: 2rem 1rem;
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- font-size: 0.85rem;
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- }
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- #jesthtml-content {
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- margin: 0 auto;
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- max-width: 70rem;
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- header {
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- display: flex;
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- align-items: center;
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- color: #000;
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- </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1095ee64.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-19 08:10:18</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">40.792s</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">25.775s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 183 : Bio.renderers.setRendererManually : Error: Tag 'cell.renderer' has been manually set to 'MacromoleculeDifference' for column but after df was added as table, tag 'cell.renderer' has reset to 'sequence' instead of manual 'MacromoleculeDifference'.
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-
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- at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:68:20
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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></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
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- at Generator.next (&lt;anonymous&gt;)
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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 (&lt;anonymous&gt;)
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- at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
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- at Object.&lt;anonymous&gt; (/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 (&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:66:11
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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 : Success : 6 : Bio.WebLogo.testGetStats : OK
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- Test result : Success : 0 : Bio.WebLogo.testGetAlphabetSimilarity : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteN1 : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteN1e : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteAA1 : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteX : OK
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- Test result : Success : 1 : Bio.WebLogo.monomerToText.longMonomerSingle : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerShort : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
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- Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
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- Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
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- Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
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- Test result : Success : 49 : Bio.detectors.NegativeEmpty : OK
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- Test result : Success : 15 : Bio.detectors.Negative1 : OK
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- Test result : Success : 22 : Bio.detectors.Negative2 : OK
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- Test result : Success : 16 : Bio.detectors.Negative3 : OK
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- Test result : Success : 14 : Bio.detectors.NegativeSmiles : OK
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- Test result : Success : 9 : Bio.detectors.Dna1 : OK
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- Test result : Success : 26 : Bio.detectors.Rna1 : OK
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- Test result : Success : 41 : Bio.detectors.AA1 : OK
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- Test result : Success : 26 : Bio.detectors.MsaDna1 : OK
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- Test result : Success : 20 : Bio.detectors.MsaAA1 : OK
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- Test result : Success : 40 : Bio.detectors.SepDna : OK
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- Test result : Success : 21 : Bio.detectors.SepRna : OK
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- Test result : Success : 17 : Bio.detectors.SepPt : OK
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- Test result : Success : 15 : Bio.detectors.SepUn1 : OK
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- Test result : Success : 19 : Bio.detectors.SepUn2 : OK
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- Test result : Success : 18 : Bio.detectors.SepMsaN1 : OK
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- Test result : Success : 653 : Bio.detectors.SamplesFastaCsvPt : OK
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- Test result : Success : 17 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
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- Test result : Success : 20 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
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- Test result : Success : 89 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
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- Test result : Success : 417 : Bio.detectors.SamplesFastaFastaPt : OK
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- Test result : Success : 1139 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
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- Test result : Success : 28 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
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- Test result : Success : 211 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
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- Test result : Success : 285 : Bio.detectors.samplesMsaComplexUn : OK
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- Test result : Success : 38 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
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- Test result : Success : 212 : Bio.detectors.samplesIdCsvNegativeID : OK
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- Test result : Success : 242 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
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- Test result : Success : 208 : Bio.detectors.samplesHelmCsvHELM : OK
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- Test result : Success : 13 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
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- Test result : Success : 248 : Bio.detectors.samplesTestHelmNegativeID : OK
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- Test result : Success : 15 : Bio.detectors.samplesTestHelmNegativeTestType : OK
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- Test result : Success : 9 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
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- Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeValid : OK
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- Test result : Success : 5 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
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- Test result : Success : 8 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
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- Test result : Success : 16 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
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- Test result : Success : 1095 : Bio.detectors.samplesTestDemogNegativeAll : OK
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- Test result : Success : 889 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
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- Test result : Success : 274 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
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- Test result : Success : 273 : Bio.detectors.samplesFastaPtPosSequence : OK
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- Test result : Success : 216 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
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- Test result : Success : 348 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
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- Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
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- Test result : Success : 14 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
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- Test result : Success : 29 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
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- Test result : Success : 231 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
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- Test result : Success : 5 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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- Test result : Success : 219 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
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- Test result : Success : 24 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
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- Test result : Success : 249 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
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- Test result : Success : 1661 : Bio.MSA.isCorrect : OK
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- Test result : Success : 306 : Bio.MSA.isCorrectLong : OK
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- Test result : Success : 1216 : Bio.sequenceSpace.sequenceSpaceOpens : OK
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- Test result : Success : 4269 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
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- Test result : Success : 947 : Bio.activityCliffs.activityCliffsOpen : OK
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- Test result : Success : 853 : Bio.activityCliffs.activityCliffsOpenWithEmptyRows : OK
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- Test result : Success : 1 : Bio.splitters.helm1 : OK
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- Test result : Success : 1 : Bio.splitters.helm2 : OK
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- Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
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- Test result : Success : 1 : Bio.splitters.testHelm1 : OK
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- Test result : Success : 1 : Bio.splitters.testHelm2 : OK
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- Test result : Success : 1 : Bio.splitters.testHelm3 : OK
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- Test result : Success : 335 : Bio.splitters.splitToMonomers : OK
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- Test result : Success : 2 : Bio.splitters.getHelmMonomers : OK
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- Test result : Success : 93 : Bio.renderers.long sequence performance : OK
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- Test result : Success : 676 : Bio.renderers.many sequence performance : OK
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- Test result : Success : 269 : Bio.renderers.rendererMacromoleculeFasta : OK
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- Test result : Success : 218 : Bio.renderers.rendererMacromoleculeSeparator : OK
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- Test result : Success : 72 : Bio.renderers.rendererMacromoleculeDifference : OK
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- Test result : Success : 534 : Bio.renderers.afterMsa : OK
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- Test result : Success : 238 : Bio.renderers.afterConvert : OK
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- Test result : Success : 207 : Bio.renderers.selectRendererBySemType : OK
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- Test result : Success : 6 : Bio.converters.testFastaPtToSeparator : OK
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- Test result : Success : 10 : Bio.converters.testFastaDnaToSeparator : OK
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- Test result : Success : 6 : Bio.converters.testFastaRnaToSeparator : OK
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- Test result : Success : 5 : Bio.converters.testFastaGapsToSeparator : OK
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- Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
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- Test result : Success : 1 : Bio.converters.testFastaDnaToHelm : OK
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- Test result : Success : 1 : Bio.converters.testFastaRnaToHelm : OK
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- Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
349
- Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
350
- Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
351
- Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
352
- Test result : Success : 1 : Bio.converters.testSeparatorDnaToHelm : OK
353
- Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
354
- Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
355
- Test result : Success : 0 : Bio.converters.testHelmDnaToFasta : OK
356
- Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
357
- Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
358
- Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
359
- Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
360
- Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
361
- Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
362
- Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
363
- Test result : Success : 1 : Bio.converters.testHelmLonePhosphorus : OK
364
- Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
365
- Test result : Success : 1 : Bio.fastaFileHandler.testExtraSpaces : OK
366
- Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
367
- Test result : Success : 111 : Bio.WebLogo-positions.allPositions : OK
368
- Test result : Success : 116 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
369
- Test result : Success : 126 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
370
- Test result : Success : 8 : Bio.checkInputColumn.testMsaPos : OK
371
- Test result : Success : 2 : Bio.checkInputColumn.testMsaNegHelm : OK
372
- Test result : Success : 2 : Bio.checkInputColumn.testMsaNegUN : OK
373
- Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
374
- </pre></div></div></div></div></body></html>