@datagrok/bio 2.16.8 → 2.17.0

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.16.8",
+  "version": "2.17.0",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,7 +37,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.45.6",
+    "@datagrok-libraries/bio": "^5.45.7",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.2",
     "@datagrok-libraries/ml": "^6.7.4",

package/src/package.ts

@@ -1,3 +1,5 @@
+/* eslint-disable max-params */
+/* eslint-disable max-len */
 /* eslint max-lines: "off" */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
@@ -9,7 +11,7 @@ import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cli
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetrics, KnownMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {IMonomerLib, IMonomerLibBase, IMonomerSet} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
 import {SCORE} from '@datagrok-libraries/bio/src/utils/macromolecule/scoring';
@@ -24,14 +26,13 @@ import {ITSNEOptions, IUMAPOptions} from '@datagrok-libraries/ml/src/multi-colum
 import {generateLongSequence, generateLongSequence2} from '@datagrok-libraries/bio/src/utils/generator';
 import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
-import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+import {RDModule as _RDMoule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 import {MmcrTemps} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
 
 import {getMacromoleculeColumns} from './utils/ui-utils';
 import {MacromoleculeDifferenceCellRenderer, MacromoleculeSequenceCellRenderer,} from './utils/cell-renderer';
-import {MacromoleculeCustomCellRenderer} from './utils/cell-renderer-custom';
 import {VdRegionsViewer} from './viewers/vd-regions-viewer';
 import {SequenceAlignment} from './seq_align';
 import {getEncodedSeqSpaceCol} from './analysis/sequence-space';
@@ -102,52 +103,46 @@ let initBioPromise: Promise<void> | null = null;
 
 //tags: init
 export async function initBio(): Promise<void> {
-  if (initBioPromise === null) {
+  if (initBioPromise === null)
     initBioPromise = initBioInt();
-  }
+
   await initBioPromise;
 }
 
 async function initBioInt() {
   const logPrefix = 'Bio: _package.initBio()';
   _package.logger.debug(`${logPrefix}, start`);
-  let monomerLib!: IMonomerLib;
-  let monomerSets!: IMonomerSet;
-  let rdKitModule!: RDModule;
-  let libHelper!: MonomerLibManager;
   const t1: number = window.performance.now();
-  await Promise.all([
-    (async () => {
-      libHelper = await MonomerLibManager.getInstance();
-      // Fix user lib settings for explicit stuck from a terminated test
-      const libSettings = await getUserLibSettings();
-      if (libSettings.explicit) {
-        libSettings.explicit = [];
-        await setUserLibSettings(libSettings);
-      }
-      libHelper.awaitLoaded(Infinity).then(() => {
-        // Do not wait for monomers and sets loaded
-        return Promise.all([libHelper.loadMonomerLib(), libHelper.loadMonomerSets()]);
-      });
-      monomerLib = libHelper.getMonomerLib();
-      monomerSets = libHelper.getMonomerSets();
-    })(),
-    (async () => {
-      const pkgProps = await _package.getProperties();
-      const bioPkgProps = new BioPackageProperties(pkgProps);
-      _package.properties = bioPkgProps;
-    })(),
-    (async () => { rdKitModule = await getRdKitModule(); })(),
-  ]).finally(() => {
-    const t2: number = window.performance.now();
-    _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
+  // very important that loading should happen in correct order!
+  // first make sure chem and rdkit module are loaded
+  const rdKitModule = await getRdKitModule();
+  // then load package settings
+  const pkgProps = await _package.getProperties();
+  const bioPkgProps = new BioPackageProperties(pkgProps);
+  _package.properties = bioPkgProps;
+  // then load monomer lib
+  const libHelper = await MonomerLibManager.getInstance();
+  // Fix user lib settings for explicit stuck from a terminated test
+  const libSettings = await getUserLibSettings();
+  if (libSettings.explicit) {
+    libSettings.explicit = [];
+    await setUserLibSettings(libSettings);
+  }
+  libHelper.awaitLoaded(Infinity).then(() => {
+    // Do not wait for monomers and sets loaded
+    return Promise.all([libHelper.loadMonomerLib(), libHelper.loadMonomerSets()]);
   });
-  const seqHelper = new SeqHelper(libHelper, rdKitModule);
-  _package.completeInit(seqHelper, monomerLib, monomerSets, rdKitModule);
+  const monomerLib = libHelper.getMonomerLib();
+  const monomerSets = libHelper.getMonomerSets();
+  // finally log
+  const t2: number = window.performance.now();
+  _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
 
   const monomers: string[] = [];
   const logPs: number[] = [];
 
+  const seqHelper = new SeqHelper(libHelper, rdKitModule);
+  _package.completeInit(seqHelper, monomerLib, monomerSets, rdKitModule);
   const series = monomerLib!.getMonomerMolsByPolymerType('PEPTIDE')!;
   Object.keys(series).forEach((symbol) => {
     monomers.push(symbol);
@@ -324,7 +319,7 @@ export function SeqActivityCliffsEditor(call: DG.FuncCall) {
 //meta.columnTags: quality=Macromolecule, units=custom
 //output: grid_cell_renderer result
 export function customSequenceCellRenderer(): DG.GridCellRenderer {
-  return new MacromoleculeCustomCellRenderer();
+  return new MacromoleculeSequenceCellRenderer();
 }
 
 //name: fastaSequenceCellRenderer
@@ -770,7 +765,7 @@ export function convertDialog() {
 export async function convertSeqNotation(sequence: string, targetNotation: NOTATION, separator?: string): Promise<string | undefined | null> {
   try {
     const col = DG.Column.fromStrings('sequence', [sequence]);
-    const df = DG.DataFrame.fromColumns([col]);
+    const _df = DG.DataFrame.fromColumns([col]);
     const semType = await grok.functions.call('Bio:detectMacromolecule', {col: col});
     if (semType)
       col.semType = semType;
@@ -1216,6 +1211,7 @@ export async function detectMacromoleculeProbe(file: DG.FileInfo, colName: strin
 //name: getSeqHelper
 //output: object result
 export async function getSeqHelper(): Promise<ISeqHelper> {
+  await initBio();
   return _package.seqHelper;
 }
 

package/src/tests/activity-cliffs-tests.ts

@@ -44,7 +44,7 @@ category('activityCliffs', async () => {
   test('activityCliffsOpens', async () => {
     const testData = !DG.Test.isInBenchmark ?
       {fileName: 'tests/100_3_clustests.csv', tgt: {cliffCount: 3}} :
-      {fileName: 'tests/peptides_motif-with-random_10000.csv', tgt: {cliffCount: 53}};
+      {fileName: 'tests/peptides_with_random_motif_1600.csv', tgt: {cliffCount: 64}};
     const actCliffsDf = await readDataframe(testData.fileName);
     const actCliffsTableView = grok.shell.addTableView(actCliffsDf);
 

package/src/tests/sequence-space-test.ts

@@ -16,7 +16,7 @@ category('sequenceSpace', async () => {
   test('sequenceSpaceOpens', async () => {
     const testData = !DG.Test.isInBenchmark ?
       {fileName: 'tests/100_3_clustests.csv'} :
-      {fileName: 'tests/peptides_motif-with-random_10000.csv'};
+      {fileName: 'tests/peptides_with_random_motif_1600.csv'};
     testFastaDf = await readDataframe(testData.fileName);
     testFastaTableView = grok.shell.addTableView(testFastaDf);
     await _testSequenceSpaceReturnsResult(testFastaDf, DimReductionMethods.UMAP, 'sequence');

package/src/utils/cell-renderer-custom.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
@@ -8,6 +9,7 @@ import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {_package} from '../package';
 
+/// NB! UNUSED LEGACY CODE
 export class MacromoleculeCustomCellRenderer extends DG.GridCellRenderer {
   private readonly seqHelper: ISeqHelper;
 
@@ -41,7 +43,7 @@ export class MacromoleculeCustomCellRenderer extends DG.GridCellRenderer {
     back?.onMouseEnter(gridCell, e);
   }
 
-  override onMouseLeave(gridCell: DG.GridCell, e: MouseEvent) {
+  override onMouseLeave(_gridCell: DG.GridCell, _e: MouseEvent) {
     // TODO: We get gridCell from another column here, so we can not get back object from the column rendered.
     ui.tooltip.hide();
     // const back = this.getRendererBack(gridCell);

package/src/utils/cell-renderer.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 /* eslint-disable max-lines */
 /* eslint-disable max-params */
 /* eslint-disable max-lines-per-function */
@@ -22,7 +23,7 @@ import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {execMonomerHoverLinks} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
-import {getGridCellColTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
+import {CellRendererBackBase, getGridCellColTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {MmcrTemps, rendererSettingsChangedState, tempTAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
 
@@ -53,6 +54,7 @@ export function processSequence(subParts: string[]): [string[], boolean] {
   return [text, simplified];
 }
 
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
 type RendererGridCellTemp = {
   [MmcrTemps.monomerPlacer]: MonomerPlacer
 }
@@ -73,21 +75,58 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     this.seqHelper = _package.seqHelper;
   }
 
-  onClick(gridCell: DG.GridCell, _e: MouseEvent): void {
+  getRendererBack(gridCell: DG.GridCell): CellRendererBackBase<string> | null {
+    const [gridCol, tableCol, _temp] = getGridCellColTemp<string, any>(gridCell);
+    if (tableCol.meta.units !== NOTATION.CUSTOM)
+      return _temp.rendererBack;
+    let back: CellRendererBackBase<string> | null = null;
+
+    if (this.seqHelper) {
+      const sh = this.seqHelper.getSeqHandler(tableCol);
+      back = sh.getRendererBack(gridCol, tableCol);
+    }
+    return back;
+  }
+
+  override onClick(gridCell: DG.GridCell, _e: MouseEvent): void {
     const colTemp: TempType = gridCell.cell.column.temp;
     colTemp[tempTAGS.currentWord] = gridCell.cell.value;
     gridCell.grid.invalidate();
+    if (gridCell.cell.column.meta.units === NOTATION.CUSTOM) {
+      const back = this.getRendererBack(gridCell);
+      back?.onClick(gridCell, _e);
+    }
+  }
+
+  override onMouseEnter(gridCell: DG.GridCell, e: MouseEvent) {
+    const back = this.getRendererBack(gridCell);
+    back?.onMouseEnter(gridCell, e);
   }
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    const [gridCol, tableCol, temp] = getGridCellColTemp<string, MonomerPlacer>(gridCell);
-    temp.rendererBack?.onMouseMove(gridCell, e);
+    const back = this.getRendererBack(gridCell);
+    back?.onMouseMove(gridCell, e);
   }
 
-  override onMouseLeave(gridCell: DG.GridCell, e: MouseEvent) {
+  override onMouseLeave(gridCell: DG.GridCell, _e: MouseEvent) {
     execMonomerHoverLinks(gridCell, null);
   }
 
+  override onDoubleClick(gridCell: DG.GridCell, e: MouseEvent) {
+    const back = this.getRendererBack(gridCell);
+    back?.onDoubleClick(gridCell, e);
+  }
+
+  override onKeyDown(gridCell: DG.GridCell, e: KeyboardEvent) {
+    const back = this.getRendererBack(gridCell);
+    back?.onKeyDown(gridCell, e);
+  }
+
+  override onKeyPress(gridCell: DG.GridCell, e: KeyboardEvent) {
+    const back = this.getRendererBack(gridCell);
+    back?.onKeyPress(gridCell, e);
+  }
+
   /**
    * Cell renderer function.
    *
@@ -99,11 +138,11 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
    * @param {DG.GridCell} gridCell Grid cell.
    * @param {DG.GridCellStyle} _cellStyle Cell style.
    */
-  render(
+  renderInt(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
     _cellStyle: DG.GridCellStyle
   ): void {
-    const logPrefix: string = 'MacromoleculeSequenceCellRenderer.render()';
+    const _logPrefix: string = 'MacromoleculeSequenceCellRenderer.render()';
 
     const [gridCol, tableCol, temp] =
       getGridCellColTemp<string, MonomerPlacer>(gridCell);
@@ -111,7 +150,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const tableColTemp: TempType = tableCol.temp;
     const sh = this.seqHelper.getSeqHandler(tableCol);
 
-    let gapLength = 0;
+    const gapLength = 0;
     const msaGapLength = 8;
 
     // Cell renderer settings
@@ -140,6 +179,15 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     seqColTemp.render(g, x, y, w, h, gridCell, _cellStyle);
   }
+
+  override render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, cellStyle: DG.GridCellStyle): void {
+    if (gridCell.cell.column?.meta?.units === NOTATION.CUSTOM) {
+      const back = this.getRendererBack(gridCell);
+      back?.render(g, x, y, w, h, gridCell, cellStyle);
+      return;
+    }
+    this.renderInt(g, x, y, w, h, gridCell, cellStyle);
+  }
 }
 
 export class MacromoleculeDifferenceCellRendererBack extends CellRendererWithMonomerLibBackBase {
@@ -151,7 +199,7 @@ export class MacromoleculeDifferenceCellRendererBack extends CellRendererWithMon
   }
 
   render(g: CanvasRenderingContext2D,
-    x: number, y: number, w: number, h: number, gridCell: DG.GridCell, cellStyle: DG.GridCellStyle
+    x: number, y: number, w: number, h: number, gridCell: DG.GridCell, _cellStyle: DG.GridCellStyle
   ): void {
     const dpr = window.devicePixelRatio;
     const grid = gridCell.grid;
@@ -172,7 +220,7 @@ export class MacromoleculeDifferenceCellRendererBack extends CellRendererWithMon
     drawMoleculeDifferenceOnCanvas(g, x, y, w, h, subParts1, subParts2, biotype, this.monomerLib, undefined, undefined);
   }
 
-  async awaitRendered(timeout: number = 10000, reason: string = `${timeout} timeout`): Promise<void> {
+  async awaitRendered(timeout: number = 10000, _reason: string = `${timeout} timeout`): Promise<void> {
     return Promise.resolve();
   }
 
@@ -258,15 +306,15 @@ export function drawMoleculeDifferenceOnCanvas(
       const amino2 = subParts2[i];
 
       let color1 = undefinedColor;
-      if (monomerLib) {
+      if (monomerLib)
         color1 = monomerLib.getMonomerTextColor(biotype, amino1);
-      }
+
 
       if (amino1 != amino2) {
         let color2 = undefinedColor;
-        if (monomerLib) {
+        if (monomerLib)
           color2 = monomerLib.getMonomerTextColor(biotype, amino2);
-        }
+
         const subX0 = printLeftOrCentered(g, amino1, updatedX, updatedY - vShift, w, h,
           {color: color1, pivot: 0, left: true});
         const subX1 = printLeftOrCentered(g, amino2, updatedX, updatedY + vShift, w, h,