@datagrok/bio 1.9.1 → 1.10.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "1.9.1",
+  "version": "1.10.2",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -14,7 +14,8 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^3.3.1",
+    "@datagrok-libraries/bio": "^4.1.0",
+    "@datagrok-libraries/chem-meta": "1.0.0",
     "@datagrok-libraries/ml": "^4.0.0",
     "@datagrok-libraries/utils": "^1.6.2",
     "cash-dom": "latest",

package/src/package.ts

@@ -24,7 +24,11 @@ import {representationsWidget} from './widgets/representations';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
 import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-utils';
-import {generateManySequences, generateLongSequence} from './tests/test-sequnces-generators';
+import {
+  generateManySequences,
+  generateLongSequence,
+  performanceTest
+} from './tests/test-sequnces-generators';
 
 //tags: init
 export async function initBio() {
@@ -32,39 +36,12 @@ export async function initBio() {
 
 //name: testManySequencesPerformance
 export function testManySequencesPerformance(): void {
-  const startTime: number = Date.now();
-  const csv = generateManySequences();
-  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
-  const col: DG.Column = df.columns.byName('MSA');
-  df.columns.byName('MSA').semType = DG.SEMTYPE.MACROMOLECULE;
-  col.setTag('units', 'separator');
-  col.setTag('aligned', 'SEQ.MSA');
-  col.setTag('alphabet', 'UN');
-  col.setTag('separator', '/');
-  grok.shell.addTableView(df);
-
-  const endTime: number = Date.now();
-  const elapsedTime: number = endTime - startTime;
-  console.log(`Elapsed time: ${elapsedTime}ms`);
-
+  performanceTest(generateManySequences, 'Many sequences');
 }
+
 //name: testLongSequencesPerformance
 export function testLongSequencesPerformance(): void {
-  const startTime: number = Date.now();
-  const csv = generateLongSequence();
-  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
-  const col: DG.Column = df.columns.byName('MSA');
-  df.columns.byName('MSA').semType = DG.SEMTYPE.MACROMOLECULE;
-  col.setTag('units', 'separator');
-  col.setTag('aligned', 'SEQ.MSA');
-  col.setTag('alphabet', 'UN');
-  col.setTag('separator', '/');
-  grok.shell.addTableView(df);
-
-  const endTime: number = Date.now();
-  const elapsedTime: number = endTime - startTime;
-  console.log(`Elapsed time: ${elapsedTime}ms`);
-
+  performanceTest(generateLongSequence, 'Long sequences');
 }
 
 
@@ -200,11 +177,11 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: D
   if (!encodedCol)
     return;
   const embedColsNames = getEmbeddingColsNames(table);
-  const withoutEmptyValues = DG.DataFrame.fromColumns([macroMolecule]).clone();
+  const withoutEmptyValues = DG.DataFrame.fromColumns([encodedCol]).clone();
   const emptyValsIdxs = removeEmptyStringRows(withoutEmptyValues, encodedCol);
 
   const chemSpaceParams = {
-    seqCol: withoutEmptyValues.col(macroMolecule.name)!,
+    seqCol: withoutEmptyValues.col(encodedCol.name)!,
     methodName: methodName,
     similarityMetric: similarityMetric,
     embedAxesNames: embedColsNames

package/src/tests/detectors-test.ts

@@ -199,44 +199,44 @@ MWRSWY-CKHP
   test('NegativeSmiles', async () => { await _testNeg(readCsv('csvDfSmiles', csvDfSmiles), 'col1'); });
 
   test('Dna1', async () => {
-    await _testPos(readCsv('csvDfDna1', csvDfDna1), 'seq', 'fasta', 'SEQ', 'DNA');
+    await _testPos(readCsv('csvDfDna1', csvDfDna1), 'seq', 'fasta', 'SEQ', 'DNA', 4, false);
   });
   test('Rna1', async () => {
-    await _testPos(readCsv('csvDfRna1', csvDfRna1), 'seq', 'fasta', 'SEQ', 'RNA');
+    await _testPos(readCsv('csvDfRna1', csvDfRna1), 'seq', 'fasta', 'SEQ', 'RNA', 4, false);
   });
   test('AA1', async () => {
-    await _testPos(readCsv('csvDfPt1', csvDfPt1), 'seq', 'fasta', 'SEQ', 'PT');
+    await _testPos(readCsv('csvDfPt1', csvDfPt1), 'seq', 'fasta', 'SEQ', 'PT', 20, false);
   });
   test('MsaDna1', async () => {
-    await _testPos(readCsv('csvDfMsaDna1', csvDfMsaDna1), 'seq', 'fasta', 'SEQ.MSA', 'DNA');
+    await _testPos(readCsv('csvDfMsaDna1', csvDfMsaDna1), 'seq', 'fasta', 'SEQ.MSA', 'DNA', 4, false);
   });
 
   test('MsaAA1', async () => {
-    await _testPos(readCsv('csvDfMsaPt1', csvDfMsaPt1), 'seq', 'fasta', 'SEQ.MSA', 'PT');
+    await _testPos(readCsv('csvDfMsaPt1', csvDfMsaPt1), 'seq', 'fasta', 'SEQ.MSA', 'PT', 20, false);
   });
 
   test('SepDna', async () => {
-    await _testPos(readCsv('csvDfSepDna', csvDfSepDna), 'seq', 'separator', 'SEQ', 'DNA', '*');
+    await _testPos(readCsv('csvDfSepDna', csvDfSepDna), 'seq', 'separator', 'SEQ', 'DNA', 4, false, '*');
   });
   test('SepRna', async () => {
-    await _testPos(readCsv('csvDfSepRna', csvDfSepRna), 'seq', 'separator', 'SEQ', 'RNA', '*');
+    await _testPos(readCsv('csvDfSepRna', csvDfSepRna), 'seq', 'separator', 'SEQ', 'RNA', 4, false, '*');
   });
   test('SepPt', async () => {
-    await _testPos(readCsv('csvDfSepPt', csvDfSepPt), 'seq', 'separator', 'SEQ', 'PT', '-');
+    await _testPos(readCsv('csvDfSepPt', csvDfSepPt), 'seq', 'separator', 'SEQ', 'PT', 20, false, '-');
   });
   test('SepUn1', async () => {
-    await _testPos(readCsv('csvDfSepUn1', csvDfSepUn1), 'seq', 'separator', 'SEQ', 'UN', '-');
+    await _testPos(readCsv('csvDfSepUn1', csvDfSepUn1), 'seq', 'separator', 'SEQ', 'UN', 8, true, '-');
   });
   test('SepUn2', async () => {
-    await _testPos(readCsv('csvDfSepUn2', csvDfSepUn2), 'seq', 'separator', 'SEQ', 'UN', '/');
+    await _testPos(readCsv('csvDfSepUn2', csvDfSepUn2), 'seq', 'separator', 'SEQ', 'UN', 9, true, '/');
   });
 
   test('SepMsaN1', async () => {
-    await _testPos(readCsv('csvDfSepMsaDna1', csvDfSepMsaDna1), 'seq', 'separator', 'SEQ.MSA', 'DNA', '-');
+    await _testPos(readCsv('csvDfSepMsaDna1', csvDfSepMsaDna1), 'seq', 'separator', 'SEQ.MSA', 'DNA', 4, false, '-');
   });
 
   test('SamplesFastaCsvPt', async () => {
-    await _testPos(readSamples(Samples.fastaCsv), 'sequence', 'fasta', 'SEQ', 'PT');
+    await _testPos(readSamples(Samples.fastaCsv), 'sequence', 'fasta', 'SEQ', 'PT', 20, false);
   });
   test('SamplesFastaCsvNegativeEntry', async () => {
     await _testNeg(readSamples(Samples.fastaCsv), 'Entry');
@@ -249,7 +249,7 @@ MWRSWY-CKHP
   });
 
   test('SamplesFastaFastaPt', async () => {
-    await _testPos(readSamples(Samples.fastaFasta, readFileFasta), 'sequence', 'fasta', 'SEQ', 'PT');
+    await _testPos(readSamples(Samples.fastaFasta, readFileFasta), 'sequence', 'fasta', 'SEQ', 'PT', 20, false);
   });
 
   // peptidesComplex contains monomers with spaces in AlignedSequence columns, which are forbidden
@@ -267,7 +267,7 @@ MWRSWY-CKHP
   });
 
   test('samplesMsaComplexUn', async () => {
-    await _testPos(readSamples(Samples.msaComplex), 'MSA', 'separator', 'SEQ.MSA', 'UN', '/');
+    await _testPos(readSamples(Samples.msaComplex), 'MSA', 'separator', 'SEQ.MSA', 'UN', 161, true, '/');
   });
   test('samplesMsaComplexNegativeActivity', async () => {
     await _testNeg(readSamples(Samples.msaComplex), 'Activity');
@@ -282,7 +282,7 @@ MWRSWY-CKHP
   });
 
   test('samplesHelmCsvHELM', async () => {
-    await _testPos(readSamples(Samples.helmCsv), 'HELM', 'helm', null, null, null);
+    await _testPos(readSamples(Samples.helmCsv), 'HELM', 'helm', null, null, 160, true, null);
   });
 
   test('samplesHelmCsvNegativeActivity', async () => {
@@ -298,7 +298,7 @@ MWRSWY-CKHP
     await _testNeg(readSamples(Samples.testHelmCsv), 'Test type');
   });
   test('samplesTestHelmPositiveHelmString', async () => {
-    await _testPos(readSamples(Samples.testHelmCsv), 'HELM string', 'helm', null, null, null);
+    await _testPos(readSamples(Samples.testHelmCsv), 'HELM string', 'helm', null, null, 9, true, null);
   });
   test('samplesTestHelmNegativeValid', async () => {
     await _testNeg(readSamples(Samples.testHelmCsv), 'Valid?');
@@ -330,7 +330,7 @@ MWRSWY-CKHP
   });
 
   test('samplesFastaPtPosSequence', async () => {
-    await _testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta', 'SEQ', 'PT');
+    await _testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta', 'SEQ', 'PT', 20, false);
   });
 
   test('samplesTestCerealNegativeCerealName', async () => {
@@ -388,7 +388,8 @@ export async function _testNeg(readDf: DfReaderFunc, colName: string) {
 
 export async function _testPos(
   readDf: DfReaderFunc, colName: string, units: string,
-  aligned: string | null, alphabet: string | null, separator: string | null = null
+  aligned: string | null, alphabet: string | null, alphabetSize: number, alphabetIsMultichar: boolean,
+  separator: string | null = null
 ) {
   const df: DG.DataFrame = await readDf();
   const col: DG.Column = df.col(colName)!;
@@ -405,6 +406,8 @@ export async function _testPos(
     expect(col.getTag('separator'), separator);
 
   const uh = new UnitsHandler(col);
+  expect(uh.getAlphabetSize(), alphabetSize);
+  expect(uh.getAlphabetIsMultichar(), alphabetIsMultichar);
   if (!uh.isHelm()) {
     expect(uh.aligned, aligned);
     expect(uh.alphabet, alphabet);

package/src/tests/test-sequnces-generators.ts

@@ -1,3 +1,6 @@
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
 export function generateManySequences(): string {
   let csvData = `MSA,Activity
 meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me,5.30751`;
@@ -9,14 +12,34 @@ meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr/
 
 export function generateLongSequence(): string {
   let longSequence = `meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr`;
-  for (let i = 0; i < 10 ** 6; i++) {
+  for (let i = 0; i < 10 ** 5; i++) {
     longSequence += `/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/dv`;
   }
   longSequence += `//Phe_4Me,5.30751`;
-  let csvData = `MSA,Activity
-  \n ${longSequence}`;
-  for (let i = 0; i <= 10 ** 2; i++) {
+  let csvData = `MSA,Activity `;
+  for (let i = 0; i <= 10 ** 1 * 4; i++) {
     csvData += `\n ${longSequence}`;
   }
   return csvData;
 }
+export function setTagsMacromolecule(col: DG.Column) {
+  col.semType = DG.SEMTYPE.MACROMOLECULE;
+  col.setTag('units', 'separator');
+  col.setTag('aligned', 'SEQ.MSA');
+  col.setTag('alphabet', 'UN');
+  col.setTag('separator', '/');
+  return col;
+}
+
+export function performanceTest(generateFunc: () => string,testName: string) {
+  const startTime: number = Date.now();
+  const csv = generateFunc();
+  const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
+  const col: DG.Column = df.columns.byName('MSA');
+  setTagsMacromolecule(col);
+  grok.shell.addTableView(df);
+
+  const endTime: number = Date.now();
+  const elapsedTime: number = endTime - startTime;
+  console.log(`Performance test: ${testName}: ${elapsedTime}ms`);
+}

package/src/utils/atomic-works.ts

@@ -1,7 +1,7 @@
 import * as OCL from 'openchemlib/full.js';
 import * as grok from 'datagrok-api/grok';
 
-import {RDModule} from '@datagrok-libraries/bio/src/rdkit-api';
+import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 
 export async function getMacroMol(monomers: any[][]): Promise<string[]> {
   let result: string[] = [];

package/src/utils/cell-renderer.ts

@@ -6,12 +6,13 @@ import {UnknownSeqPalette, UnknownSeqPalettes} from '@datagrok-libraries/bio/src
 import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import * as ui from 'datagrok-api/ui';
-import {printLeftOrCentered} from '@datagrok-libraries/bio/src/utils/cell-renderer';
+import {printLeftOrCentered, DrawStyle} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
 const undefinedColor = 'rgb(100,100,100)';
 const monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = WebLogo.monomerToShort;
 const gapRenderer = 5;
 
+
 function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
   case 'PT':
@@ -62,7 +63,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const maxLengthWordsSum = gridCell.cell.column.temp['bio-sum-maxLengthWords'];
     const maxIndex = gridCell.cell.column.temp['bio-maxIndex'];
     //@ts-ignore
-    const argsX = e.layerX - gridCell.gridColumn.left - ((gridCell.bounds.x < 0) ? gridCell.bounds.x : 0);
+    const argsX = e.layerX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x);
     let left = 0;
     let right = maxIndex;
     let found = false;
@@ -88,7 +89,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const separator = gridCell.cell.column.getTag('separator') ?? '';
     const splitterFunc: SplitterFunc = WebLogo.getSplitter('separator', separator);
     const subParts: string[] = splitterFunc(gridCell.cell.value);
-    ui.tooltip.show(ui.div(subParts[left]), e.x + 16, e.y + 16);
+    (((subParts[left]?.length ?? 0) > 0)) ? ui.tooltip.show(ui.div(subParts[left]), e.x + 16, e.y + 16) : ui.tooltip.hide();
   }
 
   /**
@@ -110,6 +111,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const grid = gridCell.gridRow !== -1 ? gridCell.grid : undefined;
     const cell = gridCell.cell;
     const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
+    const minDistanceRenderer = 50;
     w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
     g.save();
     g.beginPath();
@@ -125,15 +127,16 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const palette = getPalleteByType(paletteType);
 
     const separator = gridCell.cell.column.getTag('separator') ?? '';
-    const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, separator);
+    const splitLimit = gridCell.bounds.width / 5;
+    const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, separator, gridCell.bounds.width / 5);
 
 
     const maxLengthOfMonomer = 8;
 
     let maxLengthWords: any = {};
-    if (gridCell.cell.column.getTag('.calculatedCellRender') !== 'exist') {
+    if (gridCell.cell.column.getTag('.calculatedCellRender') !== splitLimit.toString()) {
       let samples = 0;
-      while (samples < Math.max(Math.min(gridCell.cell.column.length, 100), gridCell.cell.column.length / 100)) {
+      while (samples < Math.min(gridCell.cell.column.length, 100)) {
         let column = gridCell.cell.column.get(samples);
         let subParts: string[] = splitterFunc(column);
         subParts.forEach((amino, index) => {
@@ -163,7 +166,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         'bio-maxIndex': maxLengthWords['bio-maxIndex'],
         'bio-maxLengthWords': maxLengthWords
       };
-      gridCell.cell.column.setTag('.calculatedCellRender', 'exist');
+      gridCell.cell.column.setTag('.calculatedCellRender', splitLimit.toString());
     } else {
       maxLengthWords = gridCell.cell.column.temp['bio-maxLengthWords'];
     }
@@ -171,15 +174,19 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const subParts: string[] = splitterFunc(cell.value);
     let x1 = x;
     let color = undefinedColor;
-    let drawStyle = 'classic';
-    if (gridCell.cell.column.getTag('aligned').includes('MSA')) {
-      drawStyle = 'msa';
+    let drawStyle = DrawStyle.classic;
+    if (gridCell.cell.column.getTag('aligned').includes('MSA') && gridCell.cell.column.getTag('units') === 'separator') {
+      drawStyle = DrawStyle.MSA;
     }
-    subParts.forEach((amino, index) => {
+    subParts.every((amino, index) => {
       color = palette.get(amino);
       g.fillStyle = undefinedColor;
       let last = index === subParts.length - 1;
       x1 = printLeftOrCentered(x1, y, w, h, g, monomerToShortFunction(amino, maxLengthOfMonomer), color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell);
+      if (x1 - minDistanceRenderer - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x) > gridCell.bounds.width) {
+        return false;
+      }
+      return true;
     });
 
     g.restore();

package/src/utils/sequence-space.ts

@@ -12,7 +12,9 @@ export interface ISequenceSpaceResult {
 }
 
 export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<ISequenceSpaceResult> {
-  let preparedData: any;
+
+// code deprecated since seqCol is encoded
+/*    let preparedData: any;
   if (!(spaceParams.seqCol!.tags[DG.TAGS.UNITS] === 'HELM')) {
     const sep = spaceParams.seqCol.getTag('separator');
     const sepFinal = sep ? sep === '.' ? '\\\.' : sep : '-';
@@ -23,10 +25,10 @@ export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<
       preparedData = spaceParams.seqCol.toList().map((v: string) => v.replace(regex, '')) as string[];
   } else {
     preparedData = spaceParams.seqCol.toList();
-  }
+  }  */
 
   const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
-    preparedData,
+    spaceParams.seqCol.toList(),
     spaceParams.methodName,
     spaceParams.similarityMetric as StringMetrics | BitArrayMetrics,
     spaceParams.options);

package/{test-Bio-fe2f9610d4ed-cdfe422f.html → test-Bio-eb4783c07294-0aa1538b.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=fe2f9610d4ed. Commit cdfe422f.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=eb4783c07294. Commit 0aa1538b.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=fe2f9610d4ed. Commit cdfe422f.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-01 07:04:31</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 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">1 passed</div><div class="summary-failed summary-empty">0 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">46.104s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">27.903s</div></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)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=eb4783c07294. Commit 0aa1538b.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-02 13:13:34</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 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">1 passed</div><div class="summary-failed summary-empty">0 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">45.182s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">30.315s</div></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)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
     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