@datagrok/bio 2.0.3 → 2.0.4

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 (7) hide show
  1. package/dist/package-test.js +23 -6
  2. package/dist/package.js +6 -5
  3. package/package.json +1 -1
  4. package/src/package.ts +7 -6
  5. package/src/tests/renderers-test.ts +1 -1
  6. package/src/tests/splitters-test.ts +21 -0
  7. package/test-Bio-c5a05867bf79-cba1e171.html +0 -368
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": "2.0.3",
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+ "version": "2.0.4",
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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/package.ts CHANGED
@@ -32,7 +32,7 @@ import {
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  import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
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  import * as C from './utils/constants';
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- import {getFingerprints} from './calculations/fingerprints'
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+ import {getFingerprints} from './calculations/fingerprints';
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  //tags: init
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  export async function initBio() {
@@ -40,8 +40,8 @@ export async function initBio() {
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  //name: fastaSequenceCellRenderer
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  //tags: cellRenderer
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- //meta.cellType: Sequence
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- //meta.columnTags: units=fasta
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+ //meta.cellType: sequence
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+ //meta.columnTags: quality=Macromolecule, units=fasta
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  //output: grid_cell_renderer result
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  export function fastaSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
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  return new MacromoleculeSequenceCellRenderer();
@@ -49,8 +49,8 @@ export function fastaSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
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  //name: separatorSequenceCellRenderer
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  //tags: cellRenderer
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- //meta.cellType: Sequence
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- //meta.columnTags: units=separator
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+ //meta.cellType: sequence
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+ //meta.columnTags: quality=Macromolecule, units=fasta
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  //output: grid_cell_renderer result
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  export function separatorSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
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  return new MacromoleculeSequenceCellRenderer();
@@ -379,6 +379,7 @@ export function monomerCellRenderer(): MonomerCellRenderer {
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  //name: MacromoleculeDifferenceCellRenderer
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  //tags: cellRenderer
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  //meta.cellType: MacromoleculeDifference
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+ //meta.columnTags: quality=MacromoleculeDifference
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  //output: grid_cell_renderer result
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  export function macromoleculeDifferenceCellRenderer(): MacromoleculeDifferenceCellRenderer {
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  return new MacromoleculeDifferenceCellRenderer();
@@ -463,7 +464,7 @@ export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
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  export async function macromoleculesFingerprints(mcol: DG.Column): Promise<Uint8Array[]> {
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  grok.functions.call('Chem:getRdKitModule');
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  const monomers = getHelmMonomers(mcol);
466
- const mols = await grok.functions.call('HELM:getMolFiles', {mcol : mcol});
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+ const mols = await grok.functions.call('HELM:getMolFiles', {mcol: mcol});
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468
 
468
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  return getFingerprints(mols.toList(), monomers);
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  }
package/src/tests/renderers-test.ts CHANGED
@@ -114,7 +114,7 @@ category('renderers', () => {
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  const tw = grok.shell.addTableView(df);
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  await delay(100);
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  const renderer = tw.dataFrame.col('SequencesDiff')?.getTag(DG.TAGS.CELL_RENDERER);
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- if (renderer !== 'MacromoleculeDifferenceCR')
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+ if (renderer !== 'MacromoleculeDifference') // this is value of MacromoleculeDifferenceCR.cellType
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  throw new Error(`Units 'separator', separator '/' and semType 'MacromoleculeDifference' have been ` +
119
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  `manually set on column but after df aws added as table view renderer has been reset to '${renderer}'`);
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  }
package/src/tests/splitters-test.ts CHANGED
@@ -8,6 +8,20 @@ import {splitToMonomers, _package} from '../package';
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  import * as C from '../utils/constants';
9
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  category('splitters', () => {
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+ let tvList: DG.TableView[];
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+ let dfList: DG.DataFrame[];
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+
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+ before(async () => {
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+ await grok.functions.call('Bio:initBio');
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+ tvList = [];
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+ dfList = [];
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+ });
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+
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+ after(async () => {
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+ dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
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+ tvList.forEach((tv: DG.TableView) => tv.close());
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+ });
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+
11
25
  const helm1 = 'PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$';
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13
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  const helm2 = 'PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.N.meK}$$$';
@@ -63,6 +77,13 @@ category('splitters', () => {
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77
  seqCol.semType = semType;
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78
  seqCol.setTag(C.TAGS.ALIGNED, C.MSA);
65
79
 
80
+ const tv: DG.TableView = grok.shell.addTableView(df);
81
+ // call to calculate 'cell.renderer' tag
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+ await grok.data.detectSemanticTypes(df);
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+
84
+ dfList.push(df);
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+ tvList.push(tv);
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+
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  splitToMonomers(seqCol);
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88
  expect(df.columns.names().includes('17'), true);
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89
  });
package/test-Bio-c5a05867bf79-cba1e171.html DELETED
@@ -1,368 +0,0 @@
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- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=c5a05867bf79. Commit cba1e171.</title><style type="text/css">html,
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- #timestamp {
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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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- @media only screen and (max-width: 720px) {
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- #summary {
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- #summary > div {
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- .summary-total {
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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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- .summary-empty {
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- .test-suitename {
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- .failureMessages {
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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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- flex-grow: 1;
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- font-family: monospace;
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- padding: 0.2rem 0.3rem;
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- font-size: 0.75rem;
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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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- /* CONSOLE LOGS */
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- .suite-consolelog {
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- margin-bottom: 0.25rem;
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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=c5a05867bf79. Commit cba1e171.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-14 17:30:03</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">47.705s</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">32.846s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 4704 : Bio.activityCliffs.activityCliffsOpen : Error: Expected "53 cliffs", got "40869 cliffs"
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- Test result : Failed : 4330 : Bio.activityCliffs.activityCliffsOpenWithEmptyRows : Error: Expected "53 cliffs", got "29143 cliffs"
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- Test result : Failed : 158 : Bio.splitters.splitToMonomers : TypeError: Cannot read properties of undefined (reading 'invalidate')
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- Test result : Failed : 166 : Bio.renderers.setRenderer : Error: Units 'separator', separator '/' and semType 'MacromoleculeDifference' have been manually set on column but after df aws added as table view renderer has been reset to 'sequence'
236
-
237
- at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:68:20
238
- at Generator.next (&lt;anonymous&gt;)
239
- at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
240
- at runMicrotasks (&lt;anonymous&gt;)
241
- 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;)
248
- 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)
251
- 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;)
253
- 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 : 7 : Bio.WebLogo.testGetStats : OK
256
- Test result : Success : 0 : Bio.WebLogo.testGetAlphabetSimilarity : OK
257
- Test result : Success : 3 : Bio.WebLogo.testPickupPaletteN1 : OK
258
- Test result : Success : 1 : Bio.WebLogo.testPickupPaletteN1e : OK
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- Test result : Success : 1 : Bio.WebLogo.testPickupPaletteAA1 : OK
260
- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteX : OK
261
- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerSingle : OK
262
- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerShort : OK
263
- Test result : Success : 1 : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
265
- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
266
- Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
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- Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
268
- Test result : Success : 50 : Bio.detectors.NegativeEmpty : OK
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- Test result : Success : 14 : Bio.detectors.Negative1 : OK
270
- Test result : Success : 28 : Bio.detectors.Negative2 : OK
271
- Test result : Success : 16 : Bio.detectors.Negative3 : OK
272
- Test result : Success : 14 : Bio.detectors.NegativeSmiles : OK
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- Test result : Success : 9 : Bio.detectors.Dna1 : OK
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- Test result : Success : 26 : Bio.detectors.Rna1 : OK
275
- Test result : Success : 31 : Bio.detectors.AA1 : OK
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- Test result : Success : 8 : Bio.detectors.MsaDna1 : OK
277
- Test result : Success : 13 : Bio.detectors.MsaAA1 : OK
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- Test result : Success : 29 : Bio.detectors.SepDna : OK
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- Test result : Success : 18 : Bio.detectors.SepRna : OK
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- Test result : Success : 10 : Bio.detectors.SepPt : OK
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- Test result : Success : 7 : Bio.detectors.SepUn1 : OK
282
- Test result : Success : 26 : Bio.detectors.SepUn2 : OK
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- Test result : Success : 7 : Bio.detectors.SepMsaN1 : OK
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- Test result : Success : 286 : Bio.detectors.SamplesFastaCsvPt : OK
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- Test result : Success : 14 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
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- Test result : Success : 5 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
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- Test result : Success : 36 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
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- Test result : Success : 174 : Bio.detectors.SamplesFastaFastaPt : OK
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- Test result : Success : 620 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
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- Test result : Success : 15 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
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- Test result : Success : 131 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
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- Test result : Success : 307 : Bio.detectors.samplesMsaComplexUn : OK
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- Test result : Success : 41 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
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- Test result : Success : 184 : Bio.detectors.samplesIdCsvNegativeID : OK
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- Test result : Success : 277 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
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- Test result : Success : 222 : Bio.detectors.samplesHelmCsvHELM : OK
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- Test result : Success : 28 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
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- Test result : Success : 184 : Bio.detectors.samplesTestHelmNegativeID : OK
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- Test result : Success : 17 : Bio.detectors.samplesTestHelmNegativeTestType : OK
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- Test result : Success : 19 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
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- Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeValid : OK
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- Test result : Success : 9 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
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- Test result : Success : 22 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
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- Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
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- Test result : Success : 1075 : Bio.detectors.samplesTestDemogNegativeAll : OK
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- Test result : Success : 549 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
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- Test result : Success : 187 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
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- Test result : Success : 197 : Bio.detectors.samplesFastaPtPosSequence : OK
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- Test result : Success : 173 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
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- Test result : Success : 438 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
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- Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
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- Test result : Success : 13 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
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- Test result : Success : 12 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
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- Test result : Success : 241 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
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- Test result : Success : 47 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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- Test result : Success : 401 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
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- Test result : Success : 6 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
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- Test result : Success : 260 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
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- Test result : Success : 1668 : Bio.MSA.isCorrect : OK
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- Test result : Success : 211 : Bio.MSA.isCorrectLong : OK
321
- Test result : Success : 1295 : Bio.sequenceSpace.sequenceSpaceOpens : OK
322
- Test result : Success : 7563 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
323
- Test result : Success : 1 : Bio.splitters.helm1 : OK
324
- Test result : Success : 1 : Bio.splitters.helm2 : OK
325
- Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
326
- Test result : Success : 1 : Bio.splitters.testHelm1 : OK
327
- Test result : Success : 1 : Bio.splitters.testHelm2 : OK
328
- Test result : Success : 1 : Bio.splitters.testHelm3 : OK
329
- Test result : Success : 67 : Bio.renderers.long sequence performance : OK
330
- Test result : Success : 603 : Bio.renderers.many sequence performance : OK
331
- Test result : Success : 378 : Bio.renderers.afterMsa : OK
332
- Test result : Success : 227 : Bio.renderers.afterConvert : OK
333
- Test result : Success : 7 : Bio.converters.testFastaPtToSeparator : OK
334
- Test result : Success : 5 : Bio.converters.testFastaDnaToSeparator : OK
335
- Test result : Success : 11 : Bio.converters.testFastaRnaToSeparator : OK
336
- Test result : Success : 4 : Bio.converters.testFastaGapsToSeparator : OK
337
- Test result : Success : 3 : Bio.converters.testFastaPtToHelm : OK
338
- Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
339
- Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
340
- Test result : Success : 2 : Bio.converters.testFastaGapsToHelm : OK
341
- Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
342
- Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
343
- Test result : Success : 1 : Bio.converters.testSeparatorRnaToFasta : OK
344
- Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
345
- Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
346
- Test result : Success : 2 : Bio.converters.testSeparatorDnaToHelm : OK
347
- Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
348
- Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
349
- Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
350
- Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
351
- Test result : Success : 1 : Bio.converters.testHelmPtToFasta : OK
352
- Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
353
- Test result : Success : 1 : Bio.converters.testHelmRnaToSeparator : OK
354
- Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
355
- Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
356
- Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
357
- Test result : Success : 3 : Bio.converters.testHelmLonePhosphorus : OK
358
- Test result : Success : 1 : Bio.fastaFileHandler.testNormalFormatting : OK
359
- Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
360
- Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
361
- Test result : Success : 104 : Bio.WebLogo-positions.allPositions : OK
362
- Test result : Success : 97 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
363
- Test result : Success : 93 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
364
- Test result : Success : 22 : Bio.checkInputColumn.testMsaPos : OK
365
- Test result : Success : 3 : Bio.checkInputColumn.testMsaNegHelm : OK
366
- Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
367
- Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
368
- </pre></div></div></div></div></body></html>