@datagrok/peptides 1.0.2 → 1.2.0

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Files changed (27) hide show
  1. package/dist/package-test.js +770 -475
  2. package/dist/package.js +914 -490
  3. package/dist/vendors-node_modules_datagrok-libraries_ml_src_workers_dimensionality-reducer_js.js +162 -163
  4. package/package.json +10 -11
  5. package/src/__jest__/remote.test.ts +5 -4
  6. package/src/__jest__/test-node.ts +3 -2
  7. package/src/model.ts +71 -79
  8. package/src/package-test.ts +0 -1
  9. package/src/package.ts +8 -23
  10. package/src/tests/core.ts +13 -3
  11. package/src/tests/peptide-space-test.ts +7 -7
  12. package/src/tests/utils.ts +3 -8
  13. package/src/utils/cell-renderer.ts +5 -5
  14. package/src/utils/constants.ts +1 -1
  15. package/src/utils/invariant-map.ts +163 -0
  16. package/src/utils/misc.ts +10 -28
  17. package/src/utils/{filtering-statistics.ts → statistics.ts} +0 -0
  18. package/src/viewers/sar-viewer.ts +4 -18
  19. package/src/widgets/analyze-peptides.ts +14 -6
  20. package/src/widgets/distribution.ts +22 -21
  21. package/src/widgets/manual-alignment.ts +3 -2
  22. package/src/widgets/{subst-table.ts → mutation-cliffs.ts} +6 -5
  23. package/helm/JSDraw/Pistoia.HELM.js +0 -27
  24. package/logojs-react/index.d.ts +0 -1
  25. package/src/utils/multiple-sequence-alignment.ts +0 -106
  26. package/src/utils/multivariate-analysis.ts +0 -76
  27. package/test-Peptides-4f0c8bae6479-74cbfe68.html +0 -256
package/src/utils/multivariate-analysis.ts DELETED
@@ -1,76 +0,0 @@
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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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-
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- import * as C from './constants';
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-
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- import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
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-
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- export async function callMVA(
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- currentDf: DG.DataFrame,
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- options: {[name: string]: string},
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- sequencesCol: DG.Column,
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- ): Promise<void> {
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- const activityCol = await _scaleColumn(currentDf.getCol(options['activityColumnName']), options['scaling']);
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- const encDf = _encodeSequences(sequencesCol);
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-
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- //TODO: is it correct? Is it needed?
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- _insertColumns(
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- currentDf,
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- [DG.Column.fromList('double', C.COLUMNS_NAMES.ACTIVITY_SCALED, activityCol.toList())],
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- );
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- _insertColumns(currentDf, encDf.columns.toList());
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-
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- const res = await grok.functions.call('MultivariateAnalysis', {
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- table: currentDf,
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- features: encDf.columns.names(),
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- prediction: C.COLUMNS_NAMES.ACTIVITY_SCALED,
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- components: 10,
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- showScores: true,
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- showRegresCoefs: true,
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- });
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- console.log(res);
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- }
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-
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- /**
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- * Encodes a series of sequences into a certain scale.
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- *
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- * @param {string[]} sequencesCol Column containing the sequences.
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- * @return {DG.DataFrame} The data frame with seqences encoded.
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- */
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- function _encodeSequences(sequencesCol: DG.Column): DG.DataFrame {
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- const nRows = sequencesCol.length;
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- const nCols = AlignedSequenceEncoder.clean(sequencesCol.get(0)).length;
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- const enc = new AlignedSequenceEncoder('WimleyWhite');
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- const positions = new Array(nCols).fill(0).map((_) => new Float32Array(nRows));
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-
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- for (let j = 0; j < nRows; ++j) {
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- const s = AlignedSequenceEncoder.clean(sequencesCol.get(j));
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- for (let i = 0; i < nCols; ++i)
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- positions[i][j] = enc.encodeLettter(s[i]);
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- }
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- return DG.DataFrame.fromColumns(positions.map(
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- (v, i) => DG.Column.fromFloat32Array((i+1).toString(), v),
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- ));
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- }
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-
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- async function _scaleColumn(column: DG.Column, method: string): Promise<DG.Column> {
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- if (method == 'none')
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- return column;
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-
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-
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- const formula = (method.startsWith('-') ? '0-' : '')+'Log10(${'+column.name+'})';
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- const newCol = await column.applyFormula(formula);
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-
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- if (newCol == null)
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- throw new Error('Column formula returned unexpected null.');
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-
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- return newCol;
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- }
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-
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- function _insertColumns(targetDf: DG.DataFrame, columns: DG.Column[]): DG.DataFrame {
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- for (const col of columns)
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- targetDf.columns.add(col);
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-
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- return targetDf;
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- }
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-
package/test-Peptides-4f0c8bae6479-74cbfe68.html DELETED
@@ -1,256 +0,0 @@
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- <html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit 74cbfe68.</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;
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- margin: 0;
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- padding: 0;
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- color: #333;
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- }
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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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- }
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- header {
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- display: flex;
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- align-items: center;
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- }
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- #title {
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- margin: 0;
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- flex-grow: 1;
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- }
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- #logo {
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- height: 4rem;
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- }
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- #timestamp {
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- color: #777;
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- margin-top: 0.5rem;
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- }
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-
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- /** SUMMARY */
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- #summary {
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- color: #333;
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- margin: 2rem 0;
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- display: flex;
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- font-family: monospace;
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- font-size: 1rem;
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- }
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- #summary > div {
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- margin-right: 2rem;
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- background: #eee;
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- padding: 1rem;
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- min-width: 15rem;
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- }
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- #summary > div:last-child {
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- margin-right: 0;
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- }
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- @media only screen and (max-width: 720px) {
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- #summary {
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- flex-direction: column;
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- }
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- #summary > div {
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- margin-right: 0;
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- margin-top: 2rem;
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- }
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- #summary > div:first-child {
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- margin-top: 0;
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- }
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- }
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-
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- .summary-total {
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- font-weight: bold;
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- margin-bottom: 0.5rem;
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- }
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- .summary-passed {
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- color: #4f8a10;
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- border-left: 0.4rem solid #4f8a10;
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- padding-left: 0.5rem;
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- }
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- .summary-failed,
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- .summary-obsolete-snapshots {
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- color: #d8000c;
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- border-left: 0.4rem solid #d8000c;
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- padding-left: 0.5rem;
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- }
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- .summary-pending {
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- color: #9f6000;
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- border-left: 0.4rem solid #9f6000;
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- padding-left: 0.5rem;
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- }
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- .summary-empty {
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- color: #999;
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- border-left: 0.4rem solid #999;
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- }
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-
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- .test-result {
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- padding: 1rem;
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- margin-bottom: 0.25rem;
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- }
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- .test-result:last-child {
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- border: 0;
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- }
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- .test-result.passed {
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- background-color: #dff2bf;
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- color: #4f8a10;
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- }
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- .test-result.failed {
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- background-color: #ffbaba;
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- color: #d8000c;
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- }
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- .test-result.pending {
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- background-color: #ffdf61;
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- color: #9f6000;
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- }
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-
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- .test-info {
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- display: flex;
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- justify-content: space-between;
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- }
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- .test-suitename {
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- width: 20%;
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- text-align: left;
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- font-weight: bold;
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- word-break: break-word;
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- }
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- .test-title {
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- width: 40%;
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- text-align: left;
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- font-style: italic;
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- }
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- .test-status {
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- width: 20%;
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- text-align: right;
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- }
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- .test-duration {
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- width: 10%;
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- text-align: right;
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- font-size: 0.75rem;
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- }
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-
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- .failureMessages {
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- padding: 0 1rem;
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- margin-top: 1rem;
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- border-top: 1px dashed #d8000c;
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- }
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- .failureMessages.suiteFailure {
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- border-top: none;
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- }
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- .failureMsg {
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- white-space: pre-wrap;
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- white-space: -moz-pre-wrap;
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- white-space: -pre-wrap;
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- white-space: -o-pre-wrap;
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- word-wrap: break-word;
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- }
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-
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- .suite-container {
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- margin-bottom: 2rem;
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- }
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- .suite-info {
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- padding: 1rem;
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- background-color: #eee;
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- color: #777;
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- display: flex;
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- align-items: center;
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- margin-bottom: 0.25rem;
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- }
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- .suite-info .suite-path {
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- word-break: break-all;
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- flex-grow: 1;
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- font-family: monospace;
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- font-size: 1rem;
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- }
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- .suite-info .suite-time {
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- margin-left: 0.5rem;
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- padding: 0.2rem 0.3rem;
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- font-size: 0.75rem;
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- }
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- .suite-info .suite-time.warn {
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- background-color: #d8000c;
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- color: #fff;
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- }
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-
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- /* CONSOLE LOGS */
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- .suite-consolelog {
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- margin-bottom: 0.25rem;
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- padding: 1rem;
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- background-color: #efefef;
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- }
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- .suite-consolelog-header {
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- font-weight: bold;
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- }
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- .suite-consolelog-item {
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- padding: 0.5rem;
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- }
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- .suite-consolelog-item pre {
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- margin: 0.5rem 0;
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- white-space: pre-wrap;
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- white-space: -moz-pre-wrap;
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- white-space: -pre-wrap;
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- white-space: -o-pre-wrap;
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- word-wrap: break-word;
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- }
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- .suite-consolelog-item-origin {
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- color: #777;
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- font-weight: bold;
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- }
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- .suite-consolelog-item-message {
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- color: #000;
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- font-size: 1rem;
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- padding: 0 0.5rem;
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- }
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-
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- /* OBSOLETE SNAPSHOTS */
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- .suite-obsolete-snapshots {
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- margin-bottom: 0.25rem;
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- padding: 1rem;
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- background-color: #ffbaba;
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- color: #d8000c;
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- }
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- .suite-obsolete-snapshots-header {
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- font-weight: bold;
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- }
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- .suite-obsolete-snapshots-item {
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- padding: 0.5rem;
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- }
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- .suite-obsolete-snapshots-item pre {
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- margin: 0.5rem 0;
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- white-space: pre-wrap;
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- white-space: -moz-pre-wrap;
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- white-space: -pre-wrap;
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- white-space: -o-pre-wrap;
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- word-wrap: break-word;
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- }
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- .suite-obsolete-snapshots-item-message {
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- color: #000;
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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">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit 74cbfe68.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-04 13:00:12</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/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">122.36s</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">100.002s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
233
- Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
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- at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:1)
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- at Runtime._execModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1646:24)
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- at Runtime._loadModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1185:12)
237
- at Runtime.requireModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1009:12)
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- at jestAdapter (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/legacy-code-todo-rewrite/jestAdapter.js:79:13)
239
- at runTestInternal (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runner/build/runTest.js:389:16)
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- at runTest (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runner/build/runTest.js:475:34)
241
- at TestRunner.runTests (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runner/build/index.js:101:12)
242
- at TestScheduler.scheduleTests (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/TestScheduler.js:333:13)
243
- at runJest (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/runJest.js:404:19)
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- at _run10000 (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/cli/index.js:320:7)
245
- at runCLI (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/cli/index.js:173:3)
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- at Object.run (/home/runner/work/public/public/packages/Peptides/node_modules/jest-cli/build/cli/index.js:155:37)</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/Peptides/src/__jest__/test-node.ts:62:11)
247
- at Generator.next (&lt;anonymous&gt;)
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- at fulfilled (/home/runner/work/public/public/packages/Peptides/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/Peptides/src/__jest__/remote.test.ts:40:11
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- at Generator.next (&lt;anonymous&gt;)
251
- at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:34:71
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- at new Promise (&lt;anonymous&gt;)
253
- at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:30:12)
254
- at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:23)
255
- at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/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 Peptides package</pre></div></div></div></div></body></html>