@datagrok/bio 2.10.24 → 2.10.26

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.10.24",
+  "version": "2.10.26",
   "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",
@@ -34,7 +34,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.38.12",
+    "@datagrok-libraries/bio": "^5.38.13",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.49",
     "@datagrok-libraries/tutorials": "^1.3.6",

package/src/package.ts

@@ -73,7 +73,7 @@ import {HelmToMolfileConverter} from './utils/helm-to-molfile';
 import {DIMENSIONALITY_REDUCER_TERMINATE_EVENT}
   from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
 import {Options} from '@datagrok-libraries/utils/src/type-declarations';
-import { sequenceToMolfile } from './utils/sequence-to-mol';
+import {sequenceToMolfile} from './utils/sequence-to-mol';
 
 export const _package = new BioPackage();
 
@@ -515,7 +515,7 @@ export async function sequenceSpaceTopMenu(
         usingSparseMatrix: table.rowCount > 20000},
     };
 
-    const allowedRowCount = methodName === DimReductionMethods.UMAP ? 100000 : 15000;
+    const allowedRowCount = methodName === DimReductionMethods.UMAP ? 500000 : 15000;
     // number of rows which will be processed relatively fast
     const fastRowCount = methodName === DimReductionMethods.UMAP ? 5000 : 2000;
     if (table.rowCount > allowedRowCount) {

package/src/tests/WebLogo-positions-test.ts

@@ -32,7 +32,7 @@ ATC-G-TTGC--
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo')) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 200);
+    }, 300);
     const positions: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -84,7 +84,7 @@ ATC-G-TTGC--
       {'shrinkEmptyTail': true})) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 200);
+    }, 500);
     const positions: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -122,7 +122,7 @@ ATC-G-TTGC--
       {'skipEmptyPositions': true})) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 200);
+    }, 300);
     const resPosList: PI[] = wlViewer['positions'];
 
     const tgtPosList: PI[] = [
@@ -158,7 +158,7 @@ ATC-G-TTGC--
     })) as WebLogoViewer;
     await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
       tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
-    }, 200);
+    }, 300);
     const resPosList: PI[] = wlViewer['positions'];
     const tgtPosList: PI[] = [
       new PI(2, '3', {'C': new PMI(5)}),
@@ -179,6 +179,24 @@ ATC-G-TTGC--
     const countAt1 = countForMonomerAtPosition(df, uh, df.filter, 'G', atPI1);
     expect(countAt1, 5);
   });
+
+  test('empty', async () => {
+    const df: DG.DataFrame = DG.DataFrame.fromColumns([(() => {
+      const col = DG.Column.fromStrings('seq', []);
+      col.setTag(DG.TAGS.SEMTYPE, DG.SEMTYPE.MACROMOLECULE);
+      col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+      col.setTag(bioTAGS.alphabet, ALPHABET.DNA);
+      return col;
+    })()]);
+
+    const tv: DG.TableView = grok.shell.addTableView(df);
+
+    const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo')) as WebLogoViewer;
+    await testEvent(wlViewer.onLayoutCalculated, () => {}, () => {
+      tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
+    }, 300);
+    const resPosList: PI[] = wlViewer['positions'];
+  });
 });
 
 function expectPositionInfo(actualPos: PI, expectedPos: PI): void {

package/src/utils/helm-to-molfile.ts

@@ -2,13 +2,16 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import {MonomerLibHelper} from './monomer-lib';
 
 import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
 import {MolfileHandlerBase} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler-base';
 import {RDMol, RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {HELM_POLYMER_TYPE, HELM_RGROUP_FIELDS} from '@datagrok-libraries/bio/src/utils/const';
-import {errorToConsole} from '@datagrok-libraries/utils';
+
+import {MonomerLibHelper} from './monomer-lib';
+import {errInfo} from './err-info';
+
+import {_package} from '../package';
 
 const enum V2K_CONST {
   MAX_ATOM_COUNT = 999,
@@ -92,8 +95,9 @@ export class HelmToMolfileConverter {
         let result = '';
         try {
           result = this.getPolymerMolfile(helm, pseudoMolfile);
-        } catch (err) {
-          errorToConsole(err);
+        } catch (err: any) {
+          const [errMsg, errStack] = errInfo(err);
+          _package.logger.error(errMsg, undefined, errStack);
         } finally {
           return result;
         }

package/src/viewers/vd-regions-viewer.ts

@@ -12,6 +12,7 @@ import {
 import {FilterSources, IWebLogoViewer, PositionHeight} from '@datagrok-libraries/bio/src/viewers/web-logo';
 
 import {WebLogoViewer, PROPS as wlPROPS} from '../viewers/web-logo-viewer';
+import {errInfo} from '../utils/err-info';
 
 import {_package} from '../package';
 
@@ -153,15 +154,18 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
 
   override detach() {
     const superDetach = super.detach.bind(this);
-    this.detachPromise = this.detachPromise.then(async () => { // detach
-      await this.viewPromise;
+    this.viewPromise = this.viewPromise.then(async () => { // detach
       if (this.setDataInProgress) return; // check setDataInProgress synced
       if (this.viewed) {
         await this.destroyView('detach');
         this.viewed = false;
       }
       superDetach();
-    });
+    })
+      .catch((err: any) => {
+        const [errMsg, errStack] = errInfo(err);
+        _package.logger.error(errMsg, undefined, errStack);
+      });
   }
 
   override onTableAttached() {
@@ -247,9 +251,6 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
           this.viewed = false;
         }
 
-        await this.detachPromise;
-        // Wait whether this.dataFrame assigning has called detach() before continue set data and build view
-
         // -- Data --
         this.regions = regions;
 
@@ -261,10 +262,9 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
           this.viewed = true;
         }
       } catch (err: any) {
-        const errMsg = err instanceof Error ? err.message : err.toString();
-        const stack = err instanceof Error ? err.stack : undefined;
+        const [errMsg, errStack] = errInfo(err);
         grok.shell.error(errMsg);
-        _package.logger.error(errMsg, undefined, stack);
+        _package.logger.error(errMsg, undefined, errStack);
       } finally {
         // _package.logger.debug('Bio: VdRegionsViewer.setData(), finally, ' +
         //   `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
@@ -277,7 +277,6 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   // -- View --
 
   private viewPromise: Promise<void> = Promise.resolve();
-  private detachPromise: Promise<void> = Promise.resolve();
   private setDataInProgress: boolean = false;
 
   private host: HTMLElement | null = null;

package/src/viewers/web-logo-viewer.ts

@@ -415,7 +415,6 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
           this.viewed = false;
         }
 
-        await this.detachPromise;
         this.updateSeqCol();
 
         if (!this.viewed) {
@@ -435,7 +434,6 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   // -- View --
 
   private viewPromise: Promise<void> = Promise.resolve();
-  private detachPromise: Promise<void> = Promise.resolve();
   private setDataInProgress: boolean = false;
   private viewSubs: Unsubscribable[] = [];
 
@@ -834,15 +832,18 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.detach(), `);
 
     const superDetach = super.detach.bind(this);
-    this.detachPromise = this.detachPromise.then(async () => { // detach
-      await this.viewPromise;
+    this.viewPromise = this.viewPromise.then(async () => { // detach
       if (this.setDataInProgress) return; // check setDataInProgress synced
       if (this.viewed) {
         await this.destroyView();
         this.viewed = false;
       }
       superDetach();
-    });
+    })
+      .catch((err: any) => {
+        const [errMsg, errStack] = errInfo(err);
+        _package.logger.error(errMsg, undefined, errStack);
+      });
   }
 
   private _onSizeChanged: Subject<void> = new Subject<void>();
@@ -910,7 +911,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   }
 
   /** Render WebLogo sensitive to changes in params of rendering
-   *@param {WlRenderLevel} recalcLevel - indicates that need to recalculate data for rendering
+   *@param {WlRenderLevel} renderLevel - indicates that need to recalculate data for rendering
    */
   protected async renderInt(renderLevel: WlRenderLevel): Promise<void> {
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.renderInt( renderLevel=${renderLevel} ), ` +
@@ -958,7 +959,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     };
 
     /** Calculate layout of monomers on screen (canvas) based on freqs, required to handle mouse events */
-    const calculateLayoutInt = (dpr: number, positionLabelsHeight: number): void => {
+    const calculateLayoutInt = (firstPos: number, lastPos: number, dpr: number, positionLabelsHeight: number): void => {
       _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.calculateLayoutInt(), start `);
 
       const absoluteMaxHeight = this.canvas.height - positionLabelsHeight * dpr;
@@ -967,7 +968,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
         grok.shell.error('WebLogo: alphabet is undefined.');
       const alphabetSizeLog = Math.log2(alphabetSize);
 
-      for (let jPos = Math.floor(this.slider.min); jPos <= Math.floor(this.slider.max); ++jPos) {
+      for (let jPos = firstPos; jPos <= lastPos; ++jPos) {
         if (!(jPos in this.positions)) {
           console.warn(`Bio: WebLogoViewer<${this.viewerId}>.render.calculateLayoutInt() ` +
             `this.positions.length = ${this.positions.length}, jPos = ${jPos}`);
@@ -998,41 +999,48 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     const positionLabelsHeight = this.showPositionLabels ? POSITION_LABELS_HEIGHT : 0;
     if (renderLevel >= WlRenderLevel.Freqs) calculateFreqsInt();
     this.calcLayout(dpr); // after _skipEmptyPositions
-    if (this.positions.length === 0 || this.startPosition === -1 || this.endPosition === -1) return;
-    if (renderLevel >= WlRenderLevel.Layout) calculateLayoutInt(window.devicePixelRatio, positionLabelsHeight);
+    if ( /* this.positions.length === 0 || */ this.startPosition === -1 /* || this.endPosition === -1*/) return;
+    const firstPos: number = Math.max(Math.floor(this.slider.min), 0);
+    const lastPos: number = Math.min(this.positions.length - 1, Math.floor(this.slider.max));
+    if (renderLevel >= WlRenderLevel.Layout)
+      calculateLayoutInt(firstPos, lastPos, window.devicePixelRatio, positionLabelsHeight);
 
     const g = this.canvas.getContext('2d');
     if (!g) return;
-
-    const length: number = this.Length;
-    g.resetTransform();
-    g.fillStyle = intToHtmlA(this.backgroundColor);
-    g.fillRect(0, 0, this.canvas.width, this.canvas.height);
-    g.textBaseline = this.textBaseline;
-
-    //#region Plot positionNames
-    const positionFontSize = 10 * dpr;
-    g.resetTransform();
-    g.fillStyle = 'black';
-    g.textAlign = 'center';
-    g.font = `${positionFontSize.toFixed(1)}px Roboto, Roboto Local, sans-serif`;
-    const posNameMaxWidth = Math.max(...this.positions.map((pos) => g.measureText(pos.name).width));
-    const hScale = posNameMaxWidth < (this._positionWidth * dpr - 2) ? 1 :
-      (this._positionWidth * dpr - 2) / posNameMaxWidth;
-
-    if (positionLabelsHeight > 0) {
-      renderPositionLabels(g, dpr, hScale, this._positionWidthWithMargin, this._positionWidth,
-        this.positions, this.slider.min, this.slider.max);
-    }
-    //#endregion Plot positionNames
-    const fontStyle = '16px Roboto, Roboto Local, sans-serif';
-    // Hacks to scale uppercase characters to target rectangle
-    const uppercaseLetterAscent = 0.25;
-    const uppercaseLetterHeight = 12.2;
-    for (let jPos = Math.floor(this.slider.min); jPos <= Math.floor(this.slider.max); jPos++) {
-      this.positions[jPos].render(g, (m) => { return this.unitsHandler!.isGap(m); },
-        fontStyle, uppercaseLetterAscent, uppercaseLetterHeight,
-        /* this._positionWidthWithMargin, firstVisiblePosIdx,*/ this.cp);
+    g.save();
+    try {
+      const length: number = this.Length;
+      g.resetTransform();
+      g.fillStyle = intToHtmlA(this.backgroundColor);
+      g.fillRect(0, 0, this.canvas.width, this.canvas.height);
+      g.textBaseline = this.textBaseline;
+
+      //#region Plot positionNames
+      const positionFontSize = 10 * dpr;
+      g.resetTransform();
+      g.fillStyle = 'black';
+      g.textAlign = 'center';
+      g.font = `${positionFontSize.toFixed(1)}px Roboto, Roboto Local, sans-serif`;
+      const posNameMaxWidth = Math.max(...this.positions.map((pos) => g.measureText(pos.name).width));
+      const hScale = posNameMaxWidth < (this._positionWidth * dpr - 2) ? 1 :
+        (this._positionWidth * dpr - 2) / posNameMaxWidth;
+
+      if (positionLabelsHeight > 0 && this.positions.length > 0) {
+        renderPositionLabels(g, dpr, hScale, this._positionWidthWithMargin, this._positionWidth,
+          this.positions, this.slider.min, this.slider.max);
+      }
+      //#endregion Plot positionNames
+      const fontStyle = '16px Roboto, Roboto Local, sans-serif';
+      // Hacks to scale uppercase characters to target rectangle
+      const uppercaseLetterAscent = 0.25;
+      const uppercaseLetterHeight = 12.2;
+      for (let jPos = firstPos; jPos <= lastPos; jPos++) {
+        this.positions[jPos].render(g, (m) => { return this.unitsHandler!.isGap(m); },
+          fontStyle, uppercaseLetterAscent, uppercaseLetterHeight,
+          /* this._positionWidthWithMargin, firstVisiblePosIdx,*/ this.cp);
+      }
+    } finally {
+      g.restore();
     }
 
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.renderInt( recalcLevel=${renderLevel} ), end`);