@datagrok/bio 1.7.7 → 1.7.11

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Files changed (17) hide show
  1. package/detectors.js +22 -7
  2. package/dist/package-test.js +378 -82
  3. package/dist/package.js +276 -62
  4. package/files/tests/testActivityCliffs.csv +311 -0
  5. package/files/tests/testSpgi100.csv +8437 -0
  6. package/files/tests/testUnichemSources.csv +36 -0
  7. package/package.json +2 -2
  8. package/src/package.ts +74 -0
  9. package/src/tests/convert-test.ts +55 -22
  10. package/src/tests/detectors-test.ts +45 -6
  11. package/src/tests/splitters-test.ts +19 -0
  12. package/src/utils/cell-renderer.ts +114 -1
  13. package/src/utils/constants.ts +2 -1
  14. package/src/utils/convert.ts +17 -3
  15. package/src/utils/multiple-sequence-alignment.ts +2 -1
  16. package/src/utils/utils.ts +10 -8
  17. package/{test-Bio-34f75e5127b8-7c42ea4b.html → test-Bio-34f75e5127b8-f542cbde.html} +22 -10
package/src/utils/utils.ts CHANGED
@@ -1,7 +1,10 @@
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  import * as DG from 'datagrok-api/dg';
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  import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
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  import * as grok from 'datagrok-api/grok';
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- import { CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL, RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME } from '../const';
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+ import {
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+ CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL,
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+ RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME
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+ } from '../const';
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8
 
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  export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
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  export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
@@ -50,7 +53,7 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
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  const resultLib = [];
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  for (let i = 0; i < table.rowCount; i++) {
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  const monomer: { [key: string]: string | any } = {};
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- Object.keys(jsonSdfMonomerLibDict).forEach(key => {
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+ Object.keys(jsonSdfMonomerLibDict).forEach((key) => {
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  if (key === MONOMER_SYMBOL) {
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  const monomerSymbol = table.get(jsonSdfMonomerLibDict[key], i);
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  monomer[key] = monomerSymbol === '.' ? table.get(SDF_MONOMER_NAME, i) : monomerSymbol;
@@ -59,21 +62,20 @@ export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
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  const jsonRgroups: any[] = [];
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  rgroups.forEach((g: string) => {
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  const rgroup: { [key: string]: string | any } = {};
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- const altAtom = g.substring(g.lastIndexOf("]") + 1);
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- let radicalNum = g.match(/\[R(\d+)\]/)![1];
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+ const altAtom = g.substring(g.lastIndexOf(']') + 1);
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+ const radicalNum = g.match(/\[R(\d+)\]/)![1];
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  rgroup[CAP_GROUP_SMILES] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
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  rgroup[RGROUP_ALTER_ID] = altAtom === 'H' ? `R${radicalNum}-H` : `R${radicalNum}-OH`;
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  rgroup[CAP_GROUP_NAME] = altAtom === 'H' ? `H` : `OH`;
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  rgroup[RGROUP_LABEL] = `R${radicalNum}`;
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  jsonRgroups.push(rgroup);
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- })
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+ });
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  monomer[key] = jsonRgroups;
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  } else {
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- if((jsonSdfMonomerLibDict as { [key: string]: string | any })[key]) {
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+ if ((jsonSdfMonomerLibDict as { [key: string]: string | any })[key])
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  monomer[key] = table.get((jsonSdfMonomerLibDict as { [key: string]: string | any })[key], i);
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- }
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  }
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- })
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+ });
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  resultLib.push(monomer);
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  }
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  return resultLib;
package/{test-Bio-34f75e5127b8-7c42ea4b.html → test-Bio-34f75e5127b8-f542cbde.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=34f75e5127b8. Commit 7c42ea4b.</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=34f75e5127b8. Commit f542cbde.</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;
@@ -229,11 +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=34f75e5127b8. Commit 7c42ea4b.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-15 17:01:22</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">175.127s</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">165.279s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
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- Test result : Bio.converters.testFastaGapsToSeparator : Error: Units are not specified in column
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- Test result : Bio.converters.testFastaGapsToHelm : Error: Units are not specified in column
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- Test result : Bio.converters.HelmDnaToFasta : Error: Units are not specified in column
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- Test result : Bio.converters.HelmDnaToSeparator : Error: Units are not specified in column
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+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit f542cbde.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-20 17:49:40</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">209.758s</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">199.086s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
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  at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:67:20
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  at Generator.next (&lt;anonymous&gt;)
@@ -304,22 +300,33 @@ Test result : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
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  Test result : Bio.detectors.samplesTestHelmNegativeSmiles : OK
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  Test result : Bio.detectors.samplesTestDemogNegativeAll : OK
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  Test result : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
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+ Test result : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
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  Test result : Bio.detectors.samplesFastaPtPosSequence : OK
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  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.samplesTestUnichemSourcesNegativeSrcUrl : OK
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+ Test result : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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  Test result : Bio.MSA.test_table.is_not_empty : OK
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  Test result : Bio.sequenceSpace.sequenceSpaceOpens : OK
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  Test result : Bio.activityCliffs.activityCliffsOpen : OK
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  Test result : Bio.splitters.helm1 : OK
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  Test result : Bio.splitters.helm2 : OK
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  Test result : Bio.splitters.helm3-multichar : OK
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+ Test result : Bio.splitters.testHelm1 : OK
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+ Test result : Bio.splitters.testHelm2 : OK
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+ Test result : Bio.splitters.testHelm3 : OK
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  Test result : Bio.renderers.afterMsa : OK
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  Test result : Bio.renderers.afterConvert : OK
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  Test result : Bio.converters.testFastaPtToSeparator : OK
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  Test result : Bio.converters.testFastaDnaToSeparator : OK
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  Test result : Bio.converters.testFastaRnaToSeparator : OK
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+ Test result : Bio.converters.testFastaGapsToSeparator : OK
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  Test result : Bio.converters.testFastaPtToHelm : OK
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  Test result : Bio.converters.testFastaDnaToHelm : OK
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  Test result : Bio.converters.testFastaRnaToHelm : OK
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+ Test result : Bio.converters.testFastaGapsToHelm : OK
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  Test result : Bio.converters.testSeparatorPtToFasta : OK
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  Test result : Bio.converters.testSeparatorDnaToFasta : OK
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  Test result : Bio.converters.testSeparatorRnaToFasta : OK
@@ -328,8 +335,13 @@ Test result : Bio.converters.testSeparatorPtToHelm : OK
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  Test result : Bio.converters.testSeparatorDnaToHelm : OK
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  Test result : Bio.converters.testSeparatorRnaToHelm : OK
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  Test result : Bio.converters.testSeparatorGapsToHelm : OK
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- Test result : Bio.converters.HelmRnaToFasta : OK
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- Test result : Bio.converters.HelmPtToFasta : OK
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- Test result : Bio.converters.HelmRnaToSeparator : OK
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- Test result : Bio.converters.HelmPtToSeparator : OK
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+ Test result : Bio.converters.testHelmDnaToFasta : OK
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+ Test result : Bio.converters.testHelmRnaToFasta : OK
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+ Test result : Bio.converters.testHelmPtToFasta : OK
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+ Test result : Bio.converters.testHelmDnaToSeparator : OK
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+ Test result : Bio.converters.testHelmRnaToSeparator : OK
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+ Test result : Bio.converters.testHelmPtToSeparator : OK
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+ Test result : Bio.converters.testHelmLoneRibose : OK
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+ Test result : Bio.converters.testHelmLoneDeoxyribose : OK
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+ Test result : Bio.converters.testHelmLonePhosphorus : OK
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  </pre></div></div></div></div></body></html>