@datagrok/bio 1.6.0 → 1.7.2

package/src/tests/convert-test.ts

@@ -22,6 +22,10 @@ category('converters', () => {
     fastaRna = 'fastaRna',
     separatorRna = 'separatorRna',
     helmRna = 'helmRna',
+
+    fastaGaps = 'fastaGaps',
+    separatorGaps = 'separatorGaps',
+    helmGaps = 'helmGaps'
   }
 
   const _csvTxts: { [key: string]: string } = {
@@ -69,6 +73,24 @@ U*U*C*A*A*C
 RNA1{R(A)P.R(C)P.R(G)P.R(U)P.R(C)P}$$$
 RNA1{R(C)P.R(A)P.R(G)P.R(U)P.R(G)P.R(U)P}$$$
 RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$
+`,
+
+    fastaGaps: `seq
+FW-PH-EY
+-YNRQWYV-
+MKP---SEYV
+`,
+
+    separatorGaps: `seq
+F/W//P/H//E/Y
+//Y/N/R/Q/W/Y/V//
+M/K/P////S/E/Y/V
+`,
+
+    helmGaps: `seq
+PEPTIDE1{F.W.*.P.H.*.E.Y}$$$
+PEPTIDE1{*.Y.N.R.Q.W.Y.V.*}$$$
+PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
 `,
   };
 
@@ -110,6 +132,7 @@ RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$
     expectArray(resCol.toList(), tgtCol.toList());
   }
 
+  // FASTA tests
   test('testFastaPtToSeparator', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
   });
@@ -130,6 +153,15 @@ RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$
     await _testConvert(Samples.fastaRna, converter(NOTATION.HELM), Samples.helmRna);
   });
 
+  test('testFastaGapsToSeparator', async () => {
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
+  });
+  test('testFastaGapsToHelm', async () => {
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR), Samples.helmGaps);
+  });
+
+
+  // SEPARATOR tests
   test('testSeparatorPtToFasta', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.FASTA), Samples.fastaPt);
   });
@@ -149,4 +181,13 @@ RNA1{R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P}$$$
   test('testSeparatorRnaToHelm', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.HELM), Samples.helmRna);
   });
+  test('testSeparatorGapsToFasta', async () => {
+    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
+  });
+  test('testSeparatorGapsToHelm', async () => {
+    await _testConvert(Samples.separatorGaps, converter(NOTATION.HELM), Samples.helmGaps);
+  });
+
+
+  // HELM tests: TODO
 });

package/src/tests/detectors-test.ts

@@ -104,6 +104,7 @@ MWRSWY-CKHP
     peptidesComplex = 'peptidesComplex',
     fastaCsv = 'fastaCsv',
     fastaFasta = 'fastaFasta',
+    fastaPtCsv = 'fastaPtCsv',
     msaComplex = 'msaComplex',
     helmCsv = 'helmCsv',
     testDemogCsv = 'testDemogCsv',
@@ -114,16 +115,17 @@ MWRSWY-CKHP
   }
 
   const samples: { [key: string]: string } = {
-    'peptidesComplex': 'System:AppData/Bio/samples/peptides_complex_msa.csv',
+    'peptidesComplex': 'System:AppData/Bio/tests/peptides_complex_msa.csv',
     'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
     'fastaFasta': 'System:AppData/Bio/samples/sample_FASTA.fasta',
+    'fastaPtCsv': 'System:AppData/Bio/samples/sample_FASTA_PT.csv',
     'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
     'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
-    'testDemogCsv': 'System:AppData/Bio/samples/testDemog.csv',
-    'testHelmCsv': 'System:AppData/Bio/samples/testHelm.csv',
-    'testIdCsv': 'System:AppData/Bio/samples/id.csv',
-    'testSmilesCsv': 'System:AppData/Bio/samples/testSmiles.csv',
-    'testSmiles2Csv': 'System:AppData/Bio/samples/testSmiles2.csv',
+    'testDemogCsv': 'System:AppData/Bio/tests/testDemog.csv',
+    'testHelmCsv': 'System:AppData/Bio/tests/testHelm.csv',
+    'testIdCsv': 'System:AppData/Bio/tests/id.csv',
+    'testSmilesCsv': 'System:AppData/Bio/tests/testSmiles.csv',
+    'testSmiles2Csv': 'System:AppData/Bio/tests/testSmiles2.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -294,6 +296,10 @@ MWRSWY-CKHP
   test('samplesTestSmiles2NegativeSmiles', async () => {
     await _testNeg(readSamples(Samples.testSmiles2Csv), 'SMILES');
   });
+
+  test('samplesFastaPtPosSequence', async () => {
+    await (_testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT'));
+  });
 });
 
 export async function _testNeg(readDf: DfReaderFunc, colName: string) {

package/src/utils/cell-renderer.ts

@@ -1,32 +1,36 @@
-import * as C from "./constants";
+import * as C from './constants';
 import * as DG from 'datagrok-api/dg';
-import {AminoacidsPalettes} from "@datagrok-libraries/bio/src/aminoacids";
-import {NucleotidesPalettes} from "@datagrok-libraries/bio/src/nucleotides";
-import {UnknownSeqPalettes} from "@datagrok-libraries/bio/src/unknown";
-import {SplitterFunc, WebLogo} from "@datagrok-libraries/bio/src/viewers/web-logo";
-import {SeqPalette} from "@datagrok-libraries/bio/src/seq-palettes";
+import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
+import {NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
+import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
+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';
 
 const lru = new DG.LruCache<any, any>();
-const undefinedColor =  'rgb(100,100,100)';
+const undefinedColor = 'rgb(100,100,100)';
 
-function getPalleteByType(paletteType: string): SeqPalette  {
+function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
-    case 'PT':
-      return  AminoacidsPalettes.GrokGroups;
-    case 'NT':
-      return  NucleotidesPalettes.Chromatogram
-      // other
-    default:
-      return UnknownSeqPalettes.Color;
+  case 'PT':
+    return AminoacidsPalettes.GrokGroups;
+  case 'NT':
+    return NucleotidesPalettes.Chromatogram;
+  case 'DNA':
+    return NucleotidesPalettes.Chromatogram;
+  case 'RNA':
+    return NucleotidesPalettes.Chromatogram;
+    // other
+  default:
+    return UnknownSeqPalettes.Color;
   }
 }
 
 export function processSequence(subParts: string[]): [string[], boolean] {
   const simplified = !subParts.some((amino, index) =>
-      amino.length > 1 &&
-      index != 0 &&
-      index != subParts.length - 1);
+    amino.length > 1 &&
+    index != 0 &&
+    index != subParts.length - 1);
 
   const text: string[] = [];
   const gap = simplified ? '' : ' ';
@@ -38,6 +42,7 @@ export function processSequence(subParts: string[]): [string[], boolean] {
   });
   return [text, simplified];
 }
+
 /**
  * A function that prints a string aligned to left or centered.
  *
@@ -50,17 +55,18 @@ export function processSequence(subParts: string[]): [string[], boolean] {
  * @param {string} [color=undefinedColor] String color.
  * @param {number} [pivot=0] Pirvot.
  * @param {boolean} [left=false] Is left aligned.
- * @param {boolean} [hideMod=false] Hide amino acid redidue modifications.
  * @param {number} [transparencyRate=0.0] Transparency rate where 1.0 is fully transparent
+ * @param {string} [separator=''] Is separator for sequence.
+ * @param {boolean} [last=false] Is checker if element last or not.
  * @return {number} x coordinate to start printing at.
  */
 function printLeftOrCentered(
-    x: number, y: number, w: number, h: number,
-    g: CanvasRenderingContext2D, s: string, color = undefinedColor,
-    pivot: number = 0, left = false, hideMod = false, transparencyRate: number = 1.0,
-    separator: string = '', last:boolean = false): number {
+  x: number, y: number, w: number, h: number,
+  g: CanvasRenderingContext2D, s: string, color = undefinedColor,
+  pivot: number = 0, left = false, transparencyRate: number = 1.0,
+  separator: string = '', last: boolean = false): number {
   g.textAlign = 'start';
-  let colorPart = s.substring(0);
+  const colorPart = s.substring(0);
   let grayPart = separator;
   if (last) {
     grayPart = '';
@@ -91,14 +97,10 @@ function printLeftOrCentered(
 }
 
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
-
-  get name(): string {return 'macromoleculeSequence';}
-
-  get cellType(): string {return C.SEM_TYPES.Macro_Molecule;}
-
-  get defaultHeight(): number {return 30;}
-
-  get defaultWidth(): number {return 230;}
+  get name(): string { return 'macromoleculeSequence'; }
+  get cellType(): string { return C.SEM_TYPES.Macro_Molecule; }
+  get defaultHeight(): number { return 30; }
+  get defaultWidth(): number { return 230; }
 
   /**
    * Cell renderer function.
@@ -113,32 +115,32 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
    * @memberof AlignedSequenceCellRenderer
    */
   render(
-      g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-      cellStyle: DG.GridCellStyle,
+    g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
+    cellStyle: DG.GridCellStyle
   ): void {
-    const grid = gridCell.grid;
+    const grid = gridCell.gridRow !== -1 ? gridCell.grid : undefined;
     const cell = gridCell.cell;
     const tag = gridCell.cell.column.getTag(DG.TAGS.UNITS);
     if (tag === 'HELM') {
-      let host = ui.div([], { style: { width: `${w}px`, height: `${h}px`}});
+      const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
       host.setAttribute('dataformat', 'helm');
       host.setAttribute('data', gridCell.cell.value);
       gridCell.element = host;
       //@ts-ignore
-      var canvas = new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
-      var formula = canvas.getFormula(true);
+      const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
+      const formula = canvas.getFormula(true);
       if (!formula) {
         gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
       } else {
         gridCell.element = host;
-        var molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
-        var coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
-        var molfile = canvas.getMolfile();
-        var result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
+        const molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
+        const coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
+        const molfile = canvas.getMolfile();
+        const result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
         lru.set(gridCell.cell.value, result);
       }
     } else {
-      const [type, subtype, paletteType] =  gridCell.cell.column.getTag(DG.TAGS.UNITS).split(":");
+      const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
       w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
       g.save();
       g.beginPath();
@@ -154,12 +156,10 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       const palette = getPalleteByType(paletteType);
 
       const separator = gridCell.cell.column.getTag('separator') ?? '';
-      const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator') );// splitter,
+      const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator'));
 
-      const subParts:string[] =  splitterFunc(cell.value);
+      const subParts: string[] = splitterFunc(cell.value);
       // console.log(subParts);
-
-      const textSize = g.measureText(subParts.join(''));
       let x1 = x;
       let color = undefinedColor;
       subParts.forEach((amino, index) => {
@@ -169,7 +169,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         if (index === subParts.length - 1) {
           last = true;
         }
-        x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, false, 1.0, separator, last);
+        x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0,  separator, last);
       });
 
       g.restore();

package/src/utils/multiple-sequence-alignment.ts

@@ -4,7 +4,6 @@ import * as DG from 'datagrok-api/dg';
 import Aioli from '@biowasm/aioli';
 
 import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
-import * as C from './constants';
 
 /**
  * Converts array of sequences into simple fasta string.

package/src/utils/notation-converter.ts

@@ -13,6 +13,12 @@ export class NotationConverter {
   private _sourceColumn: DG.Column; // the column to be converted
   private _sourceUnits: string; // units, of the form fasta:SEQ:NT, etc.
   private _sourceNotation: NOTATION; // current notation (without :SEQ:NT, etc.)
+  private _defaultGapSymbol: string;
+  private _defaultGapSymbolsDict = {
+    helm: '*',
+    separator: '',
+    fasta: '-',
+  };
 
   private get sourceUnits(): string { return this._sourceUnits; }
 
@@ -20,6 +26,16 @@ export class NotationConverter {
 
   public get sourceNotation(): NOTATION { return this._sourceNotation; }
 
+  public get defaultGapSymbol(): string { return this._defaultGapSymbol; }
+
+  public get separator(): string {
+    const separator = this.sourceColumn.getTag('separator');
+    if (separator !== null)
+      return separator;
+    else
+      throw new Error('Separator not set');
+  }
+
   public isFasta(): boolean { return this.sourceNotation === NOTATION.FASTA; }
 
   public isSeparator(): boolean { return this.sourceNotation === NOTATION.SEPARATOR; }
@@ -42,34 +58,15 @@ export class NotationConverter {
   /**
    * @return {NOTATION}     Notation associated with the units type
    */
-  private determineSourceNotation(): NOTATION {
+  private getSourceNotation(): NOTATION {
     if (this.sourceUnits.toLowerCase().startsWith('fasta'))
       return NOTATION.FASTA;
     else if (this.sourceUnits.toLowerCase().startsWith('separator'))
       return NOTATION.SEPARATOR;
-    else
-      // TODO: handle possible exceptions
+    else if (this.sourceUnits.toLowerCase().startsWith('helm'))
       return NOTATION.HELM;
-  }
-
-  /**
-   * Determine the separator used in SEPARATOR column
-   *
-   * @return {string} The detected separator
-   */
-  private determineSeparator(): string {
-    //   TODO: figure out how to determine the separator efficiently
-    const col = this.sourceColumn;
-    let i = 0;
-    const re = /[^a-z]/;
-    while (i < col.length) {
-      const molecule = col.get(i);
-      const foundSeparator = molecule.toLowerCase().match(re);
-      if (foundSeparator)
-        return foundSeparator[0];
-      i++;
-    }
-    throw new Error('No separators found');
+    else
+      throw new Error('The column has units that do not correspond to any notation');
   }
 
   /**
@@ -86,7 +83,7 @@ export class NotationConverter {
     const newColName = col.dataFrame.columns.getUnusedName(name);
     // dummy code
     const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill(''));
-    newColumn.semType = 'Macromolecule';
+    newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
     newColumn.setTag(
       DG.TAGS.UNITS,
       this.sourceUnits.replace(
@@ -98,6 +95,7 @@ export class NotationConverter {
     if (this.toFasta(targetNotation)) {
       newColumn.setTag(
         DG.TAGS.CELL_RENDERER,
+        // TODO: replace by the enumeration value
         'Macromolecule');
     }
     return newColumn;
@@ -128,19 +126,12 @@ export class NotationConverter {
     return newColumn;
   }
 
-  /**
-   * Convert a Macromolecule column from FASTA to HELM
-   *
-   * @param {string} fastaGapSymbol   Optional fasta gap symbol
-   * @param {string} helmGapSymbol    Optional helm gap symbol
-   * @return {DG.Column}              A new column in HELM notation
-   */
-  private convertFastaToHelm(
-    fastaGapSymbol: string = '-',
-    helmGapSymbol: string = '*'
-  ): DG.Column {
-    // a function splitting FASTA sequence into an array of monomers
-    const splitterAsFasta = WebLogo.splitterAsFasta;
+  private convertToHelm(sourceGapSymbol: string | null = null) {
+    if (sourceGapSymbol === null)
+      sourceGapSymbol = this.defaultGapSymbol;
+    // A function splitting a sequence into an array of monomers according to
+    // its notation
+    const splitter = WebLogo.getSplitterForColumn(this.sourceColumn);
 
     const prefix = (this.isDna()) ? 'DNA1{' :
       (this.isRna()) ? 'RNA1{' :
@@ -158,19 +149,17 @@ export class NotationConverter {
     const newColumn = this.getNewColumn(NOTATION.HELM);
     // assign the values to the empty column
     newColumn.init((idx: number) => {
-      const fastaPolymer = this.sourceColumn.get(idx);
-      const fastaMonomersArray = splitterAsFasta(fastaPolymer);
+      const sourcePolymer = this.sourceColumn.get(idx);
+      const sourceMonomersArray = splitter(sourcePolymer);
       const helmArray = [prefix];
       let firstIteration = true;
-      for (let i = 0; i < fastaMonomersArray.length; i++) {
-        if (fastaMonomersArray[i] === fastaGapSymbol) {
-          // TODO: verify the correctness of gap symbols handling
-          helmArray.push(helmGapSymbol);
-        } else {
-          const dot = firstIteration ? '' : '.';
-          const item = [dot, leftWrapper, fastaMonomersArray[i], rightWrapper];
-          helmArray.push(item.join(''));
-        }
+      for (let i = 0; i < sourceMonomersArray.length; i++) {
+        const dot = firstIteration ? '' : '.';
+        let token = sourceMonomersArray[i];
+        if (token === sourceGapSymbol)
+          token = this._defaultGapSymbolsDict.helm;
+        const item = [dot, leftWrapper, token, rightWrapper];
+        helmArray.push(item.join(''));
         firstIteration = false;
       }
       helmArray.push(postfix);
@@ -210,12 +199,12 @@ export class NotationConverter {
     // conversion
     // * consider automatic determining the separator
 
-    // if (separator === null)
-    //   separator = this.determineSeparator();
+    if (separator === null)
+      separator = this.separator;
 
     // a function splitting FASTA sequence into an array of monomers
     //const splitterAsSeparator = WebLogo.getSplitterWithSeparator(separator);
-    const splitter = WebLogo.getSplitterForColumn(this._sourceColumn);
+    const splitter = WebLogo.getSplitterForColumn(this.sourceColumn);
 
     const newColumn = this.getNewColumn(NOTATION.FASTA);
     // assign the values to the empty column
@@ -241,47 +230,6 @@ export class NotationConverter {
     return newColumn;
   }
 
-  private convertSeparatorToHelm(fastaGapSymbol: string = '-', helmGapSymbol: string = '*'): DG.Column {
-    // a function splitting FASTA sequence into an array of monomers
-    const splitter = WebLogo.getSplitterForColumn(this._sourceColumn);
-
-    const prefix = (this.isDna()) ? 'DNA1{' :
-      (this.isRna()) ? 'RNA1{' :
-        (this.isPeptide()) ? 'PEPTIDE1{' :
-          'Unknown'; // this case should be handled as exceptional
-
-    if (prefix === 'Unknown')
-      throw new Error('Neither peptide, nor nucleotide');
-
-    const postfix = '}$$$';
-    const leftWrapper = (this.isDna()) ? 'D(' :
-      (this.isRna()) ? 'R(' : ''; // no wrapper for peptides
-    const rightWrapper = (this.isDna() || this.isRna()) ? ')P' : ''; // no wrapper for peptides
-
-    const newColumn = this.getNewColumn(NOTATION.HELM);
-    // assign the values to the empty column
-    newColumn.init((idx: number) => {
-      const fastaPolymer = this.sourceColumn.get(idx);
-      const fastaMonomersArray = splitter(fastaPolymer);
-      const helmArray = [prefix];
-      let firstIteration = true;
-      for (let i = 0; i < fastaMonomersArray.length; i++) {
-        if (fastaMonomersArray[i] === fastaGapSymbol) {
-          // TODO: verify the correctness of gap symbols handling
-          helmArray.push(helmGapSymbol);
-        } else {
-          const dot = firstIteration ? '' : '.';
-          const item = [dot, leftWrapper, fastaMonomersArray[i], rightWrapper];
-          helmArray.push(item.join(''));
-        }
-        firstIteration = false;
-      }
-      helmArray.push(postfix);
-      return helmArray.join('');
-    });
-    return newColumn;
-  }
-
   private convertHelmToFasta(): DG.Column {
     // TODO: implementation
     return this.getNewColumn(NOTATION.FASTA);
@@ -307,12 +255,10 @@ export class NotationConverter {
 
     if (this.isFasta() && this.toSeparator(targetNotation) && tgtSeparator !== null)
       return this.convertFastaToSeparator(tgtSeparator);
-    else if (this.isFasta() && this.toHelm(targetNotation))
-      return this.convertFastaToHelm();
+    else if ((this.isFasta() || this.isSeparator()) && this.toHelm(targetNotation))
+      return this.convertToHelm();
     else if (this.isSeparator() && this.toFasta(targetNotation))
       return this.convertSeparatorToFasta(tgtSeparator!);
-    else if (this.isSeparator() && this.toHelm(targetNotation))
-      return this.convertSeparatorToHelm();
     else if (this.isHelm() && this.toFasta(targetNotation))
       return this.convertHelmToFasta();
     else
@@ -321,7 +267,14 @@ export class NotationConverter {
 
   public constructor(col: DG.Column) {
     this._sourceColumn = col;
-    this._sourceUnits = this._sourceColumn.tags[DG.TAGS.UNITS];
-    this._sourceNotation = this.determineSourceNotation();
+    const units = this._sourceColumn.tags[DG.TAGS.UNITS];
+    if (units !== null)
+      this._sourceUnits = units;
+    else
+      throw new Error('Units are not specified in column');
+    this._sourceNotation = this.getSourceNotation();
+    this._defaultGapSymbol = (this.isFasta()) ? this._defaultGapSymbolsDict.fasta :
+      (this.isHelm()) ? this._defaultGapSymbolsDict.helm :
+        this._defaultGapSymbolsDict.separator;
   }
 }

package/{test-Bio-34f75e5127b8-95c6fae9.html → test-Bio-34f75e5127b8-ac96da52.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 95c6fae9.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit ac96da52.</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=34f75e5127b8. Commit 95c6fae9.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-12 11:55:44</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">112.789s</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.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit ac96da52.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-13 09:24:48</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">110.354s</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">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
 Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:1)
     at Runtime._execModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1646:24)