@datagrok/bio 1.10.2 → 1.11.2

package/src/utils/cell-renderer.ts

@@ -2,18 +2,19 @@ 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 {UnknownSeqPalette, UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
+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';
 import {printLeftOrCentered, DrawStyle} from '@datagrok-libraries/bio/src/utils/cell-renderer';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 const undefinedColor = 'rgb(100,100,100)';
 const monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = WebLogo.monomerToShort;
 const gapRenderer = 5;
 
 
-function getPalleteByType(paletteType: string): SeqPalette {
+function getPaletteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
   case 'PT':
     return AminoacidsPalettes.GrokGroups;
@@ -29,6 +30,10 @@ function getPalleteByType(paletteType: string): SeqPalette {
   }
 }
 
+function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number): number {
+  return grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+}
+
 export function processSequence(subParts: string[]): [string[], boolean] {
   const simplified = !subParts.some((amino, index) =>
     amino.length > 1 &&
@@ -57,13 +62,12 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   get defaultWidth(): number { return 230; }
 
   onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    if (gridCell.cell.column.getTag('aligned') !== 'SEQ.MSA') {
+    if (gridCell.cell.column.getTag(UnitsHandler.TAGS.aligned) !== 'SEQ.MSA') {
       return;
     }
     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.gridColumn.left - gridCell.bounds.x);
+    const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x);
     let left = 0;
     let right = maxIndex;
     let found = false;
@@ -108,23 +112,22 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
     cellStyle: DG.GridCellStyle
   ): void {
-    const grid = gridCell.gridRow !== -1 ? gridCell.grid : undefined;
+    const grid = gridCell.gridRow !== -1 ? gridCell.grid : null;
     const cell = gridCell.cell;
-    const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
+    const paletteType = gridCell.cell.column.getTag(C.TAGS.ALPHABET);
     const minDistanceRenderer = 50;
-    w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+    w = getUpdatedWidth(grid, g, x, w);
     g.save();
     g.beginPath();
     g.rect(x, y, w, h);
     g.clip();
     g.font = '12px monospace';
     g.textBaseline = 'top';
-    const s: string = cell.value ?? '';
 
     //TODO: can this be replaced/merged with splitSequence?
     const units = gridCell.cell.column.getTag(DG.TAGS.UNITS);
 
-    const palette = getPalleteByType(paletteType);
+    const palette = getPaletteByType(paletteType);
 
     const separator = gridCell.cell.column.getTag('separator') ?? '';
     const splitLimit = gridCell.bounds.width / 5;
@@ -183,10 +186,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       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;
+      return x1 - minDistanceRenderer - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x) <= gridCell.bounds.width;
+
     });
 
     g.restore();
@@ -225,7 +226,7 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
     g.font = `12px monospace`;
     g.textBaseline = 'top';
 
-    const palette = getPalleteByType(gridCell.tableColumn!.tags[C.TAGS.ALPHABET]);
+    const palette = getPaletteByType(gridCell.tableColumn!.tags[C.TAGS.ALPHABET]);
     const s: string = gridCell.cell.value ? gridCell.cell.value : '-';
     const color = palette.get(s);
 
@@ -261,7 +262,7 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
     const grid = gridCell.grid;
     const cell = gridCell.cell;
 
-    w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+    w = getUpdatedWidth(grid, g, w, x);
     g.save();
     g.beginPath();
     g.rect(x, y, w, h);
@@ -285,7 +286,7 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
 
     let palette: SeqPalette = UnknownSeqPalettes.Color;
     if (units != 'HELM')
-      palette = getPalleteByType(units.substring(units.length - 2));
+      palette = getPaletteByType(units.substring(units.length - 2));
 
     const vShift = 7;
     for (let i = 0; i < subParts1.length; i++) {

package/src/utils/constants.ts

@@ -9,17 +9,13 @@ export enum COLUMNS_NAMES {
   MEAN_DIFFERENCE = 'Mean difference',
 }
 
-export enum CATEGORIES {
-  OTHER = 'Other',
-  ALL = 'All',
-}
-
 export enum TAGS {
   AAR = 'AAR',
   POSITION = 'Pos',
   SEPARATOR = 'separator',
   SELECTION = 'selection',
   ALPHABET = 'alphabet',
+  ALIGNED = 'aligned',
 }
 
 export enum SEM_TYPES {
@@ -30,6 +26,8 @@ export enum SEM_TYPES {
   MACROMOLECULE = 'Macromolecule',
 }
 
+export const MSA = 'MSA';
+
 export const STATS = 'stats';
 
 export const EMBEDDING_STATUS = 'embeddingStatus';

package/src/utils/convert.ts

@@ -5,7 +5,7 @@ import $ from 'cash-dom';
 
 import {Subscription} from 'rxjs';
 import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 
 let convertDialog: DG.Dialog | null = null;
@@ -42,7 +42,7 @@ export function convert(col: DG.Column): void {
   // set correct visibility on init
   toggleSeparator();
 
-  targetNotationInput.onChanged( () => {
+  targetNotationInput.onChanged(() => {
     toggleSeparator();
   });
 
@@ -85,6 +85,9 @@ export async function convertDo(
   const converter = new NotationConverter(srcCol);
   const newColumn = converter.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);
+
+  // call to calculate 'cell.renderer' tag
   await grok.data.detectSemanticTypes(srcCol.dataFrame);
+
   return newColumn;
 }

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

@@ -9,6 +9,7 @@ import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler'
 import Aioli from '@biowasm/aioli';
 
 import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 /**
  * Converts array of sequences into simple fasta string.
@@ -58,14 +59,14 @@ export async function runKalign(srcCol: DG.Column, isAligned = false, unUsedName
   // units
   const srcUnits = srcCol.getTag(DG.TAGS.UNITS);
   //aligned
-  const srcAligned = srcCol.getTag('aligned');
+  const srcAligned = srcCol.getTag(UnitsHandler.TAGS.aligned);
   const tgtAligned = srcAligned + '.MSA';
   //alphabet
-  const srcAlphabet = srcCol.getTag('alphabet');
+  const srcAlphabet = srcCol.getTag(UnitsHandler.TAGS.alphabet);
 
   tgtCol.setTag(DG.TAGS.UNITS, srcUnits);
-  tgtCol.setTag('aligned', tgtAligned);
-  tgtCol.setTag('alphabet', srcAlphabet);
+  tgtCol.setTag(UnitsHandler.TAGS.aligned, tgtAligned);
+  tgtCol.setTag(UnitsHandler.TAGS.alphabet, srcAlphabet);
   tgtCol.semType = DG.SEMTYPE.MACROMOLECULE;
   return tgtCol;
 }

package/src/utils/sequence-activity-cliffs.ts

@@ -3,18 +3,130 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
+import * as grok from 'datagrok-api/grok';
 
-export async function sequenceGetSimilarities(col: DG.Column, seq: string): Promise<DG.Column | null> {
+export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
   const stringArray = col.toList();
-  const distances = new Array(stringArray.length).fill(0.0);
+  const distances = new Array(stringArray.length).fill(0);
   for (let i = 0; i < stringArray.length; ++i)
-    distances[i] = stringArray[i] ? getSimilarityFromDistance(AvailableMetrics['String']['Levenshtein'](stringArray[i], seq)) : 0;
-  return DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances);
+    distances[i] = stringArray[i] ? AvailableMetrics['String']['Levenshtein'](stringArray[i], seq) : null;
+  return distances;
 }
 
-export function drawSequences(params: ITooltipAndPanelParams) {
-  params.line.mols.forEach((mol: number, index: number) => {
-    ui.empty(params.hosts[index]);
-    params.hosts[index].append(ui.divText(params.seqCol.get(mol)));
+export async function getSimilaritiesMarix(dim: number, seqCol: DG.Column, df: DG.DataFrame, colName: string, simArr: DG.Column[])
+  : Promise<DG.Column[]> {
+
+  function arrayMin(arr: number[]) {
+    return arr.reduce(function (p, v) {
+      return (p < v ? p : v);
+    });
+  }
+
+  function arrayMax(arr: number[]) {
+    return arr.reduce(function (p, v) {
+      return (p > v ? p : v);
+    });
+  }
+  const distances = new Array(simArr.length).fill(null);
+  let min = Infinity;
+  let max = -Infinity;
+  for (let i = 0; i != dim - 1; ++i) {
+    const seq = seqCol.get(i);
+    df.rows.removeAt(0, 1, false);
+    distances[i] = (await getDistances(df.col(colName)!, seq))!;
+    const newMin = arrayMin(distances[i]);
+    const newMax = arrayMax(distances[i]);
+    if (newMin < min)
+      min = newMin;
+    if (newMax > max)
+      max = newMax;
+  }
+
+  for (let i = 0; i < distances.length; i++) {
+    for (let j = 0; j < distances[i].length; j++) {
+      distances[i][j] = getSimilarityFromDistance((distances[i][j] - min)/(max - min));
+    }
+    simArr[i] = DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances[i]);
+  }
+  return simArr;
+}
+
+export function createTooltipElement(params: ITooltipAndPanelParams): HTMLDivElement {
+  const tooltipElement = ui.divH([]);
+  const columnNames = ui.divV([
+    ui.divText(params.seqCol.name),
+    ui.divText(params.activityCol.name),
+  ]);
+  columnNames.style.fontWeight = 'bold';
+  columnNames.style.display = 'flex';
+  columnNames.style.justifyContent = 'space-between';
+  tooltipElement.append(columnNames);
+  params.line.mols.forEach((molIdx: number, idx: number) => {
+    const activity = ui.divText(params.activityCol.get(molIdx).toFixed(2));
+    activity.style.display = 'flex';
+    activity.style.justifyContent = 'left';
+    activity.style.paddingLeft = '30px';
+    tooltipElement.append(ui.divV([
+      ui.divText(params.seqCol.get(molIdx)),
+      activity,
+    ]));
   });
+  return tooltipElement;
 }
+
+function moleculeInfo(df: DG.DataFrame, idx: number, seqColName: string): HTMLElement {
+  let dict: {[key: string]: string} = {};
+  for (let col of df.columns) {
+    if(col.name !== seqColName) {
+      dict[col.name] = df.get(col.name, idx);
+    }
+  }
+  return ui.tableFromMap(dict);
+}
+
+
+export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivElement {
+  const propPanel = ui.divV([]);
+  const columnNames = ui.divH([
+    ui.divText(params.seqCol.name),
+    ui.divText(params.activityCol.name),
+  ]);
+  columnNames.style.fontWeight = 'bold';
+  columnNames.style.justifyContent = 'space-between';
+  propPanel.append(columnNames);
+  const hosts: HTMLDivElement[] = [];
+  params.line.mols.forEach((molIdx: number, hostIdx: number) => {
+    const activity = ui.divText(params.activityCol.get(molIdx).toFixed(2));
+    activity.style.paddingLeft = '15px';
+    activity.style.paddingLeft = '10px';
+    const molHost = ui.divText(params.seqCol.get(molIdx));
+    if (params.df.currentRowIdx === molIdx) {
+      molHost.style.border = 'solid 1px lightgrey';
+    }
+    //@ts-ignore
+    ui.tooltip.bind(molHost, () => moleculeInfo(params.df, molIdx, params.seqCol.name));
+    molHost.onclick = () => {
+      const obj = grok.shell.o;
+      molHost.style.border = 'solid 1px lightgrey';
+      params.df.currentRowIdx = molIdx;
+      hosts.forEach((h, i) => {
+        if (i !== hostIdx) {
+          h.style.border = '';
+        }
+      })
+      setTimeout(() => {
+        grok.shell.o = obj
+      }, 1000);
+    };
+    propPanel.append(ui.divH([
+      molHost,
+      activity,
+    ]));
+    hosts.push(molHost);
+  });
+  propPanel.append(ui.divH([
+    ui.divText(`Cliff: `, {style: {fontWeight: 'bold', paddingRight: '5px'}}),
+    ui.divText(params.sali!.toFixed(2))
+  ]));
+  return propPanel;
+}

package/src/utils/sequence-space.ts

@@ -16,7 +16,7 @@ export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<
 // code deprecated since seqCol is encoded
 /*    let preparedData: any;
   if (!(spaceParams.seqCol!.tags[DG.TAGS.UNITS] === 'HELM')) {
-    const sep = spaceParams.seqCol.getTag('separator');
+    const sep = spaceParams.seqCol.getTag(UnitsHandler.TAGS.separator);
     const sepFinal = sep ? sep === '.' ? '\\\.' : sep : '-';
     const regex = new RegExp(sepFinal, 'g');
     if (Object.keys(AvailableMetrics['String']).includes(spaceParams.similarityMetric))

package/src/utils/utils.ts

@@ -5,6 +5,7 @@ import {
   CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, MONOMER_SYMBOL,
   RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME
 } from '../const';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
 export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
@@ -16,7 +17,7 @@ export function encodeMonomers(col: DG.Column): DG.Column | null {
   let encodeSymbol = MONOMER_ENCODE_MIN;
   const monomerSymbolDict: { [key: string]: number } = {};
   const units = col.tags[DG.TAGS.UNITS];
-  const sep = col.getTag('separator');
+  const sep = col.getTag(UnitsHandler.TAGS.separator);
   const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, sep);
   const encodedStringArray = [];
   for (let i = 0; i < col.length; ++i) {
@@ -25,7 +26,7 @@ export function encodeMonomers(col: DG.Column): DG.Column | null {
     monomers.forEach((m) => {
       if (!monomerSymbolDict[m]) {
         if (encodeSymbol > MONOMER_ENCODE_MAX) {
-          grok.shell.error(`Not enougth symbols to encode monomers`);
+          grok.shell.error(`Not enough symbols to encode monomers`);
           return null;
         }
         monomerSymbolDict[m] = encodeSymbol;

package/test-Bio-f1ac5a5eade4-a0f7e8c0.html

@@ -0,0 +1,261 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=f1ac5a5eade4. Commit a0f7e8c0.</title><style type="text/css">html,
+body {
+  font-family: Arial, Helvetica, sans-serif;
+  font-size: 1rem;
+  margin: 0;
+  padding: 0;
+  color: #333;
+}
+body {
+  padding: 2rem 1rem;
+  font-size: 0.85rem;
+}
+#jesthtml-content {
+  margin: 0 auto;
+  max-width: 70rem;
+}
+header {
+  display: flex;
+  align-items: center;
+}
+#title {
+  margin: 0;
+  flex-grow: 1;
+}
+#logo {
+  height: 4rem;
+}
+#timestamp {
+  color: #777;
+  margin-top: 0.5rem;
+}
+
+/** SUMMARY */
+#summary {
+  color: #333;
+  margin: 2rem 0;
+  display: flex;
+  font-family: monospace;
+  font-size: 1rem;
+}
+#summary > div {
+  margin-right: 2rem;
+  background: #eee;
+  padding: 1rem;
+  min-width: 15rem;
+}
+#summary > div:last-child {
+  margin-right: 0;
+}
+@media only screen and (max-width: 720px) {
+  #summary {
+    flex-direction: column;
+  }
+  #summary > div {
+    margin-right: 0;
+    margin-top: 2rem;
+  }
+  #summary > div:first-child {
+    margin-top: 0;
+  }
+}
+
+.summary-total {
+  font-weight: bold;
+  margin-bottom: 0.5rem;
+}
+.summary-passed {
+  color: #4f8a10;
+  border-left: 0.4rem solid #4f8a10;
+  padding-left: 0.5rem;
+}
+.summary-failed,
+.summary-obsolete-snapshots {
+  color: #d8000c;
+  border-left: 0.4rem solid #d8000c;
+  padding-left: 0.5rem;
+}
+.summary-pending {
+  color: #9f6000;
+  border-left: 0.4rem solid #9f6000;
+  padding-left: 0.5rem;
+}
+.summary-empty {
+  color: #999;
+  border-left: 0.4rem solid #999;
+}
+
+.test-result {
+  padding: 1rem;
+  margin-bottom: 0.25rem;
+}
+.test-result:last-child {
+  border: 0;
+}
+.test-result.passed {
+  background-color: #dff2bf;
+  color: #4f8a10;
+}
+.test-result.failed {
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.test-result.pending {
+  background-color: #ffdf61;
+  color: #9f6000;
+}
+
+.test-info {
+  display: flex;
+  justify-content: space-between;
+}
+.test-suitename {
+  width: 20%;
+  text-align: left;
+  font-weight: bold;
+  word-break: break-word;
+}
+.test-title {
+  width: 40%;
+  text-align: left;
+  font-style: italic;
+}
+.test-status {
+  width: 20%;
+  text-align: right;
+}
+.test-duration {
+  width: 10%;
+  text-align: right;
+  font-size: 0.75rem;
+}
+
+.failureMessages {
+  padding: 0 1rem;
+  margin-top: 1rem;
+  border-top: 1px dashed #d8000c;
+}
+.failureMessages.suiteFailure {
+  border-top: none;
+}
+.failureMsg {
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+
+.suite-container {
+  margin-bottom: 2rem;
+}
+.suite-info {
+  padding: 1rem;
+  background-color: #eee;
+  color: #777;
+  display: flex;
+  align-items: center;
+  margin-bottom: 0.25rem;
+}
+.suite-info .suite-path {
+  word-break: break-all;
+  flex-grow: 1;
+  font-family: monospace;
+  font-size: 1rem;
+}
+.suite-info .suite-time {
+  margin-left: 0.5rem;
+  padding: 0.2rem 0.3rem;
+  font-size: 0.75rem;
+}
+.suite-info .suite-time.warn {
+  background-color: #d8000c;
+  color: #fff;
+}
+
+/* CONSOLE LOGS */
+.suite-consolelog {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #efefef;
+}
+.suite-consolelog-header {
+  font-weight: bold;
+}
+.suite-consolelog-item {
+  padding: 0.5rem;
+}
+.suite-consolelog-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-consolelog-item-origin {
+  color: #777;
+  font-weight: bold;
+}
+.suite-consolelog-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+
+/* OBSOLETE SNAPSHOTS */
+.suite-obsolete-snapshots {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.suite-obsolete-snapshots-header {
+  font-weight: bold;
+}
+.suite-obsolete-snapshots-item {
+  padding: 0.5rem;
+}
+.suite-obsolete-snapshots-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-obsolete-snapshots-item-message {
+  color: #000;
+  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=f1ac5a5eade4. Commit a0f7e8c0.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-08 10:03:50</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">10.76s</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">0s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Unknown server alias. Please add it to /home/runner/.grok/config.yaml
+    at getDevKey (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:48:13)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:57:15)
+    at Generator.next (&lt;anonymous&gt;)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:31:71
+    at new Promise (&lt;anonymous&gt;)
+    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:27:12)
+    at Object.getBrowserPage (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:94:12)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:13:27
+    at Generator.next (&lt;anonymous&gt;)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
+    at new Promise (&lt;anonymous&gt;)
+    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:12:22
+    at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
+    at new Promise (&lt;anonymous&gt;)
+    at callAsyncCircusFn (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:316:10)
+    at _callCircusHook (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/run.js:181:40)
+    at _runTestsForDescribeBlock (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/run.js:47:7)
+    at run (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/run.js:25:3)
+    at runAndTransformResultsToJestFormat (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/legacy-code-todo-rewrite/jestAdapterInit.js:170:21)
+    at jestAdapter (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/legacy-code-todo-rewrite/jestAdapter.js:82:19)
+    at runTestInternal (/home/runner/work/public/public/packages/Bio/node_modules/jest-runner/build/runTest.js:389:16)
+    at runTest (/home/runner/work/public/public/packages/Bio/node_modules/jest-runner/build/runTest.js:475:34)
+    at TestRunner.runTests (/home/runner/work/public/public/packages/Bio/node_modules/jest-runner/build/index.js:101:12)
+    at TestScheduler.scheduleTests (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/TestScheduler.js:333:13)
+    at runJest (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/runJest.js:404:19)
+    at _run10000 (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/cli/index.js:320:7)
+    at runCLI (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/cli/index.js:173:3)
+    at Object.run (/home/runner/work/public/public/packages/Bio/node_modules/jest-cli/build/cli/index.js:155:37)</pre></div></div></div></div></div></body></html>

package/src/utils/split-to-monomers.ts

@@ -1,8 +0,0 @@
-/* Do not change these import lines to match external modules in webpack configuration */
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-export function splitToMonomers() {
-
-}