@datagrok/bio 1.7.8 → 1.7.9

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Files changed (5) hide show
  1. package/detectors.js +2 -1
  2. package/dist/package-test.js +13 -11
  3. package/package.json +1 -1
  4. package/src/tests/convert-test.ts +15 -14
  5. package/{test-Bio-34f75e5127b8-cdc230d8.html → test-Bio-34f75e5127b8-0a8a5821.html} +6 -6
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": "1.7.8",
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+ "version": "1.7.9",
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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",
package/src/tests/convert-test.ts CHANGED
@@ -1,9 +1,9 @@
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- import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
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+ import {category, expectArray, test} from '@datagrok-libraries/utils/src/test';
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  import * as grok from 'datagrok-api/grok';
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  import * as DG from 'datagrok-api/dg';
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- import {ConverterFunc, DfReaderFunc} from './types';
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+ import {ConverterFunc} from './types';
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  import {NOTATION, NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
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  // import {mmSemType} from '../const';
@@ -76,21 +76,19 @@ RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$
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  `,
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  fastaGaps: `seq
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- FW-PH-EY
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- -YNRQWYV-
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- MKP---SEYV
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+ FW-PH-EYY
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+ FYNRQWYV-
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+ FKP-Q-SEYV
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  `,
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-
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  separatorGaps: `seq
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- F/W//P/H//E/Y
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- /Y/N/R/Q/W/Y/V/
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- M/K/P////S/E/Y/V
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+ F/W//P/H//E/Y/Y
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+ F/Y/N/R/Q/W/Y/V/
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+ F/K/P//Q//S/E/Y/V
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  `,
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-
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  helmGaps: `seq
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- PEPTIDE1{F.W.*.P.H.*.E.Y}$$$
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- PEPTIDE1{*.Y.N.R.Q.W.Y.V.*}$$$
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- PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
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+ PEPTIDE1{F.W.*.P.H.*.E.Y.Y}$$$
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+ PEPTIDE1{F.Y.N.R.Q.W.Y.V.*}$$$
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+ PEPTIDE1{F.K.P.*.Q.*.S.E.Y.V}$$$
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  `,
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  };
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@@ -113,6 +111,9 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
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  };
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  function converter(tgtNotation: NOTATION, tgtSeparator: string | null = null): ConverterFunc {
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+ if (tgtNotation === NOTATION.SEPARATOR && !tgtSeparator)
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+ throw new Error(`Argument 'separator' is missed for notation '${tgtNotation.toString()}'.`);
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+
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  return function(srcCol: DG.Column): DG.Column {
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  const converter = new NotationConverter(srcCol);
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  const resCol = converter.convert(tgtNotation, tgtSeparator);
@@ -206,7 +207,7 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
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  // helm -> separator
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  test('HelmDnaToSeparator', async () => {
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- await _testConvert(Samples.helmDna, converter(NOTATION.SEPARATOR), Samples.separatorDna);
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+ await _testConvert(Samples.helmDna, converter(NOTATION.SEPARATOR, '/'), Samples.separatorDna);
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  });
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  test('HelmRnaToSeparator', async () => {
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  await _testConvert(Samples.helmRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
package/{test-Bio-34f75e5127b8-cdc230d8.html → test-Bio-34f75e5127b8-0a8a5821.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 cdc230d8.</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 0a8a5821.</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;
@@ -229,14 +229,10 @@ 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 cdc230d8.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-19 10:23:49</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">179.806s</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">168.85s</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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+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0a8a5821.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-19 13:18:04</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">189.946s</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">177.683s</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.splitters.testHelm1 : Error: Expected R(U)P at position 0, got U
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  Test result : Bio.splitters.testHelm2 : Error: Expected R(U)P at position 1, got U
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  Test result : Bio.splitters.testHelm3 : Error: Expected R(U) at position 1, got U)
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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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  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;)
@@ -321,9 +317,11 @@ 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
@@ -332,8 +330,10 @@ 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.HelmDnaToFasta : 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.HelmDnaToSeparator : 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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  </pre></div></div></div></div></body></html>