@datagrok/bio 2.0.6 → 2.0.7

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 (4) hide show
  1. package/dist/package-test.js +29 -7
  2. package/package.json +1 -1
  3. package/src/tests/splitters-test.ts +26 -2
  4. package/test-Bio-7770371320b2-046cde35.html +0 -372
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": "2.0.6",
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+ "version": "2.0.7",
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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/splitters-test.ts CHANGED
@@ -1,10 +1,10 @@
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- import {after, before, category, test, expect, expectArray} from '@datagrok-libraries/utils/src/test';
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+ import {after, before, category, test, expect, expectArray, expectObject} from '@datagrok-libraries/utils/src/test';
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  import * as grok from 'datagrok-api/grok';
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  import * as ui from 'datagrok-api/ui';
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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 {splitToMonomers, _package} from '../package';
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+ import {splitToMonomers, _package, getHelmMonomers} from '../package';
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  import * as C from '../utils/constants';
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  category('splitters', () => {
@@ -87,6 +87,30 @@ category('splitters', () => {
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  splitToMonomers(seqCol);
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  expect(df.columns.names().includes('17'), true);
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  });
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+
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+ test('getHelmMonomers', async () => {
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+ const df: DG.DataFrame = DG.DataFrame.fromCsv(
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+ `HELM,Activity
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+ PEPTIDE1{hHis.N.T}$$$,5.30751
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+ PEPTIDE1{hHis.Aca.Cys_SEt}$$$,5.72388
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+ `);
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+ const expectedMonomerList = ['hHis', 'Aca', 'Cys_SEt', 'N', 'T'];
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+
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+ const helmCol: DG.Column = df.getCol('HELM');
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+ const res = getHelmMonomers(helmCol);
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+
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+ const missed = expectedMonomerList.filter((m) => !res.includes(m));
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+ const unexpected = res.filter((m) => !expectedMonomerList.includes(m));
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+ if (missed.length > 0 || unexpected.length) {
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+ const msgs = [];
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+ if (missed.length > 0)
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+ msgs.push(`Missed monomers ${JSON.stringify(missed)}.`);
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+ if (unexpected.length > 0)
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+ msgs.push(`Unexpected monomers ${JSON.stringify(unexpected)}.`);
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+
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+ throw new Error(msgs.join(' '));
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+ }
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+ });
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  });
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  export async function _testHelmSplitter(src: string, tgt: string[]) {
package/test-Bio-7770371320b2-046cde35.html DELETED
@@ -1,372 +0,0 @@
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- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 046cde35.</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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- 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">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 046cde35.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-16 12:11:55</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">46.232s</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">28.972s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 197 : 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 : 3 : Bio.WebLogo.testPickupPaletteN1 : OK
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- Test result : Success : 1 : Bio.WebLogo.testPickupPaletteN1e : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteAA1 : OK
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- Test result : Success : 1 : Bio.WebLogo.testPickupPaletteX : OK
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- Test result : Success : 0 : 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 : 54 : Bio.detectors.NegativeEmpty : OK
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- Test result : Success : 18 : Bio.detectors.Negative1 : OK
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- Test result : Success : 31 : Bio.detectors.Negative2 : OK
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- Test result : Success : 18 : Bio.detectors.Negative3 : OK
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- Test result : Success : 15 : Bio.detectors.NegativeSmiles : OK
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- Test result : Success : 10 : Bio.detectors.Dna1 : OK
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- Test result : Success : 26 : Bio.detectors.Rna1 : OK
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- Test result : Success : 48 : Bio.detectors.AA1 : OK
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- Test result : Success : 16 : Bio.detectors.MsaDna1 : OK
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- Test result : Success : 9 : Bio.detectors.MsaAA1 : OK
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- Test result : Success : 34 : Bio.detectors.SepDna : OK
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- Test result : Success : 12 : Bio.detectors.SepRna : OK
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- Test result : Success : 14 : Bio.detectors.SepPt : OK
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- Test result : Success : 8 : Bio.detectors.SepUn1 : OK
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- Test result : Success : 13 : Bio.detectors.SepUn2 : OK
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- Test result : Success : 6 : Bio.detectors.SepMsaN1 : OK
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- Test result : Success : 383 : Bio.detectors.SamplesFastaCsvPt : OK
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- Test result : Success : 7 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
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- Test result : Success : 14 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
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- Test result : Success : 48 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
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- Test result : Success : 117 : Bio.detectors.SamplesFastaFastaPt : OK
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- Test result : Success : 707 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
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- Test result : Success : 17 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
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- Test result : Success : 137 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
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- Test result : Success : 162 : Bio.detectors.samplesMsaComplexUn : OK
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- Test result : Success : 24 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
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- Test result : Success : 83 : Bio.detectors.samplesIdCsvNegativeID : OK
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- Test result : Success : 165 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
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- Test result : Success : 235 : Bio.detectors.samplesHelmCsvHELM : OK
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- Test result : Success : 16 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
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- Test result : Success : 139 : Bio.detectors.samplesTestHelmNegativeID : OK
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- Test result : Success : 19 : Bio.detectors.samplesTestHelmNegativeTestType : OK
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- Test result : Success : 5 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
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- Test result : Success : 8 : Bio.detectors.samplesTestHelmNegativeValid : OK
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- Test result : Success : 7 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
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- Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
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- Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
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- Test result : Success : 733 : Bio.detectors.samplesTestDemogNegativeAll : OK
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- Test result : Success : 380 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
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- Test result : Success : 113 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
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- Test result : Success : 126 : Bio.detectors.samplesFastaPtPosSequence : OK
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- Test result : Success : 158 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
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- Test result : Success : 229 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
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- Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
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- Test result : Success : 14 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
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- Test result : Success : 6 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
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- Test result : Success : 160 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
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- Test result : Success : 8 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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- Test result : Success : 136 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
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- Test result : Success : 7 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
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- Test result : Success : 184 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
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- Test result : Success : 932 : Bio.MSA.isCorrect : OK
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- Test result : Success : 293 : Bio.MSA.isCorrectLong : OK
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- Test result : Success : 1441 : Bio.sequenceSpace.sequenceSpaceOpens : OK
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- Test result : Success : 7627 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
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- Test result : Success : 1467 : Bio.activityCliffs.activityCliffsOpen : OK
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- Test result : Success : 1356 : 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 : 0 : Bio.splitters.helm3-multichar : OK
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- Test result : Success : 0 : Bio.splitters.testHelm1 : OK
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- Test result : Success : 0 : Bio.splitters.testHelm2 : OK
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- Test result : Success : 0 : Bio.splitters.testHelm3 : OK
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- Test result : Success : 518 : Bio.splitters.splitToMonomers : OK
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- Test result : Success : 157 : Bio.renderers.long sequence performance : OK
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- Test result : Success : 1230 : Bio.renderers.many sequence performance : OK
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- Test result : Success : 372 : Bio.renderers.rendererMacromoleculeFasta : OK
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- Test result : Success : 289 : Bio.renderers.rendererMacromoleculeSeparator : OK
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- Test result : Success : 126 : Bio.renderers.rendererMacromoleculeDifference : OK
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- Test result : Success : 812 : Bio.renderers.afterMsa : OK
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- Test result : Success : 351 : Bio.renderers.afterConvert : OK
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- Test result : Success : 178 : Bio.renderers.selectRendererBySemType : OK
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- Test result : Success : 5 : Bio.converters.testFastaPtToSeparator : OK
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- Test result : Success : 5 : Bio.converters.testFastaDnaToSeparator : OK
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- Test result : Success : 13 : Bio.converters.testFastaRnaToSeparator : OK
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- Test result : Success : 5 : Bio.converters.testFastaGapsToSeparator : OK
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- Test result : Success : 3 : Bio.converters.testFastaPtToHelm : OK
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- Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
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- Test result : Success : 11 : 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
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- Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorPtToHelm : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorRnaToHelm : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
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- Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
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- Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
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- Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
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- Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
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- Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
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- Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
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- Test result : Success : 3 : Bio.converters.testHelmLoneRibose : OK
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- Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
361
- Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
362
- Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
363
- Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
364
- Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
365
- Test result : Success : 116 : Bio.WebLogo-positions.allPositions : OK
366
- Test result : Success : 126 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
367
- Test result : Success : 100 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
368
- Test result : Success : 4 : Bio.checkInputColumn.testMsaPos : OK
369
- Test result : Success : 1 : Bio.checkInputColumn.testMsaNegHelm : OK
370
- Test result : Success : 2 : Bio.checkInputColumn.testMsaNegUN : OK
371
- Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
372
- </pre></div></div></div></div></body></html>