@datagrok/bio 2.10.22 → 2.10.24

package/src/utils/sequence-to-mol.ts

@@ -0,0 +1,37 @@
+/* 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';
+
+import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
+import {helm2mol} from './helm-to-molfile';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {checkInputColumnUI} from './check-input-column';
+import {getMonomerLibHelper} from '../package';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+
+export async function sequenceToMolfile(df: DG.DataFrame, macroMolecule: DG.Column, nonlinear: boolean): Promise<void> {
+  if (DG.Func.find({package: 'Chem', name: 'getRdKitModule'}).length === 0) {
+    grok.shell.warning('Transformation to atomic level requires package "Chem" installed.');
+    return;
+  }
+  if (nonlinear) {
+    const seqUh = UnitsHandler.getOrCreate(macroMolecule);
+    if (!seqUh.isHelm())
+      macroMolecule = seqUh.convert(NOTATION.HELM);
+    helm2mol(df, macroMolecule);
+    return;
+  }
+  if (!checkInputColumnUI(macroMolecule, 'To Atomic Level'))
+    return;
+  const monomerLib: IMonomerLib = getMonomerLibHelper().getBioLib();
+  const atomicLevelRes = await _toAtomicLevel(df, macroMolecule, monomerLib);
+  if (atomicLevelRes.col !== null) {
+    df.columns.add(atomicLevelRes.col, true);
+    await grok.data.detectSemanticTypes(df);
+  }
+
+  if (atomicLevelRes.warnings && atomicLevelRes.warnings.length > 0)
+    grok.shell.warning(ui.list(atomicLevelRes.warnings));
+}

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

@@ -152,10 +152,10 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   }
 
   override detach() {
-    if (this.setDataInProgress) return;
     const superDetach = super.detach.bind(this);
     this.detachPromise = this.detachPromise.then(async () => { // detach
       await this.viewPromise;
+      if (this.setDataInProgress) return; // check setDataInProgress synced
       if (this.viewed) {
         await this.destroyView('detach');
         this.viewed = false;
@@ -166,7 +166,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
 
   override onTableAttached() {
     super.onTableAttached();
-    this.setData(this.dataFrame, this.regions);
+    this.setData(this.regions);
   }
 
   public override onPropertyChanged(property: DG.Property | null): void {
@@ -180,7 +180,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
     switch (property.name) {
       case PROPS.regionTypes:
       case PROPS.chains:
-        this.setData(this.dataFrame, this.regions);
+        this.setData(this.regions);
         break;
     }
 
@@ -211,42 +211,66 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
         break;
 
       default:
-        this.setData(this.dataFrame, this.regions); // onPropertyChanged
+        this.setData(this.regions); // onPropertyChanged
         break;
     }
   }
 
   // -- Data --
 
+  // private static viewerCount = 0;
+  // private viewerId: number = ++VdRegionsViewer.viewerCount;
+  // private setDataInCount: number = 0;
+
   // TODO: .onTableAttached is not calling on dataFrame set, onPropertyChanged  also not calling
-  public setData(mlbDf: DG.DataFrame, regions: VdRegion[]) {
-    if (!this.setDataInProgress) this.setDataInProgress = true; else return;
-    _package.logger.debug('Bio: VdRegionsViewer.setData()');
+  public setData(regions: VdRegion[]) {
+    // const setDataInId = ++this.setDataInCount;
+    _package.logger.debug('Bio: VdRegionsViewer.setData(), in, ' +
+      // `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
+      `regions.length = ${regions.length}`
+    );
 
     this.viewPromise = this.viewPromise.then(async () => { // setData
-      if (this.viewed) {
-        await this.destroyView('setData');
-        this.viewed = false;
-      }
-    }).then(async () => {
-      await this.detachPromise;
-      // Wait whether this.dataFrame assigning has called detach() before continue set data and build view
-
-      // -- Data --
-      this.regions = regions;
-      if (this.dataFrame.dart !== mlbDf.dart) this.dataFrame = mlbDf; // causes detach and onTableAttached
-    }).then(async () => {
-      if (!this.viewed) {
-        await this.buildView('setData');
-        this.viewed = true;
+      // _package.logger.debug('Bio: VdRegionsViewer.setData(), in sync, ' +
+      //   `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
+      //   `regions.length = ${regions.length}`);
+      if (!this.setDataInProgress) this.setDataInProgress = true; else return; // check setDataInProgress synced
+      // _package.logger.debug('Bio: VdRegionsViewer.setData(), start, ' +
+      //   `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
+      //   `regions.length = ${regions.length}`);
+      try {
+        if (this.viewed) {
+          // _package.logger.debug('Bio: VdRegionsViewer.setData(), destroyView, ' +
+          //   `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
+          //   `regions.length = ${regions.length}`);
+          await this.destroyView('setData');
+          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;
+
+        if (!this.viewed) {
+          // _package.logger.debug('Bio: VdRegionsViewer.setData(), buildView, ' +
+          //   `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
+          //   `regions.length = ${regions.length}`);
+          await this.buildView('setData');
+          this.viewed = true;
+        }
+      } catch (err: any) {
+        const errMsg = err instanceof Error ? err.message : err.toString();
+        const stack = err instanceof Error ? err.stack : undefined;
+        grok.shell.error(errMsg);
+        _package.logger.error(errMsg, undefined, stack);
+      } finally {
+        // _package.logger.debug('Bio: VdRegionsViewer.setData(), finally, ' +
+        //   `viewerId = ${this.viewerId}, setDataInId = ${setDataInId}, ` +
+        //   `regions.length = ${regions.length}`);
+        this.setDataInProgress = false;
       }
-    }).catch((err: any) => {
-      const errMsg = err instanceof Error ? err.message : err.toString();
-      const stack = err instanceof Error ? err.stack : undefined;
-      grok.shell.error(errMsg);
-      _package.logger.error(errMsg, undefined, stack);
-    }).finally(() => {
-      this.setDataInProgress = false;
     });
   }
 
@@ -266,7 +290,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   private async destroyView(purpose: string): Promise<void> {
     // TODO: Unsubscribe from and remove all view elements
     _package.logger.debug(`Bio: VdRegionsViewer.destroyView( mainLayout = ${!this.mainLayout ? 'none' : 'value'} ), ` +
-      `purpose = '${purpose}'`);
+      `purpose = '${purpose}', this.regions.length = ${this.regions.length}`);
     if (this.filterSourceInput) {
       //
       ui.empty(this.filterSourceInput.root);
@@ -284,7 +308,8 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   }
 
   private async buildView(purpose: string): Promise<void> {
-    _package.logger.debug(`Bio: VdRegionsViewer.buildView() begin, ` + `purpose = '${purpose}'`);
+    _package.logger.debug(`Bio: VdRegionsViewer.buildView() begin, ` +
+      `purpose = '${purpose}', this.regions.length = ${this.regions.length}`);
 
     const regionsFiltered: VdRegion[] = this.regions.filter((r: VdRegion) => this.regionTypes.includes(r.type));
     const orderList: number[] = Array.from(new Set(regionsFiltered.map((r) => r.order))).sort();

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

@@ -18,6 +18,8 @@ import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {intToHtmlA} from '@datagrok-libraries/utils/src/color';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 
+import {errInfo} from '../utils/err-info';
+
 import {_package} from '../package';
 
 declare global {
@@ -403,25 +405,30 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   // -- Data --
 
   setData(): void {
-    if (!this.setDataInProgress) this.setDataInProgress = true; else return;
-    _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.setData() `);
-
+    _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.setData(), in`);
     this.viewPromise = this.viewPromise.then(async () => { // setData
-      if (this.viewed) {
-        await this.destroyView();
-        this.viewed = false;
-      }
-    }).then(async () => {
-      await this.detachPromise;
-
-      this.updateSeqCol();
-    }).then(async () => {
-      if (!this.viewed) {
-        await this.buildView();
-        this.viewed = true;
+      if (!this.setDataInProgress) this.setDataInProgress = true; else return; // check setDataInProgress synced
+      try {
+        if (this.viewed) {
+          this.renderRequestSub.unsubscribe();
+          await this.destroyView();
+          this.viewed = false;
+        }
+
+        await this.detachPromise;
+        this.updateSeqCol();
+
+        if (!this.viewed) {
+          await this.buildView(); //requests rendering
+          this.viewed = true;
+        }
+      } catch (err: any) {
+        const [errMsg, errStack] = errInfo(err);
+        grok.shell.error(errMsg);
+        _package.logger.error(errMsg, undefined, errStack);
+      } finally {
+        this.setDataInProgress = false;
       }
-    }).finally(() => {
-      this.setDataInProgress = false;
     });
   }
 
@@ -450,6 +457,8 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     const dataFrameTxt: string = this.dataFrame ? 'data' : 'null';
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.buildView( dataFrame = ${dataFrameTxt} ) start`);
     const dpr = window.devicePixelRatio;
+    this.viewSubs.push(DG.debounce(this.renderRequest)
+      .subscribe(this.renderRequestOnDebounce.bind(this)));
 
     this.helpUrl = '/help/visualize/viewers/web-logo.md';
 
@@ -508,7 +517,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   private rootOnSizeChanged(): void {
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.rootOnSizeChanged(), start `);
 
-    this.render(WlRenderLevel.Layout, 'rootOnSizeChanged').then(() => {});
+    this.render(WlRenderLevel.Layout, 'rootOnSizeChanged');
   }
 
   /** Assigns {@link seqCol} and {@link cp} based on {@link sequenceColumnName} and calls {@link render}().
@@ -571,7 +580,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       this.positionNames.includes(this.endPositionName)) ?
       this.positionNames.indexOf(this.endPositionName) : (maxLength - 1);
 
-    this.render(WlRenderLevel.Freqs, 'updatePositions').then(() => {});
+    this.render(WlRenderLevel.Freqs, 'updatePositions');
   }
 
   private getFilter(): DG.BitSet {
@@ -801,11 +810,11 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       case PROPS.verticalAlignment:
       case PROPS.positionMargin:
       case PROPS.positionMarginState:
-        this.render(WlRenderLevel.Layout, `onPropertyChanged(${property.name})`).then(() => {});
+        this.render(WlRenderLevel.Layout, `onPropertyChanged(${property.name})`);
         break;
 
       case PROPS.backgroundColor:
-        this.render(WlRenderLevel.Render, `onPropertyChanged(${property.name})`).then(() => {});
+        this.render(WlRenderLevel.Render, `onPropertyChanged(${property.name})`);
         break;
     }
   }
@@ -822,12 +831,12 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
 
   /** Remove all handlers when table is a detach  */
   public override async detach() {
-    if (this.setDataInProgress) return;
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.detach(), `);
 
     const superDetach = super.detach.bind(this);
     this.detachPromise = this.detachPromise.then(async () => { // detach
       await this.viewPromise;
+      if (this.setDataInProgress) return; // check setDataInProgress synced
       if (this.viewed) {
         await this.destroyView();
         this.viewed = false;
@@ -888,12 +897,24 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   }
 
   /** default value of RecalcLevel.Freqs is for recalc from the scratch at the beginning */
-  private renderLevelRequested: WlRenderLevel = WlRenderLevel.Freqs;
+  private requestedRenderLevel: WlRenderLevel = WlRenderLevel.Freqs;
+  private readonly renderRequest: Subject<WlRenderLevel> = new Subject<WlRenderLevel>();
+  private renderRequestSub: Unsubscribable;
 
   /** Renders requested repeatedly will be performed once on window.requestAnimationFrame() */
-  render(recalcLevel: WlRenderLevel, reason: string): Promise<void> {
+  render(renderLevel: WlRenderLevel, reason: string): void {
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>` +
-      `.render( recalcLevelVal=${recalcLevel}, reason='${reason}' )`);
+      `.render( recalcLevelVal=${renderLevel}, reason='${reason}' )`);
+    this.requestedRenderLevel = Math.max(this.requestedRenderLevel, renderLevel);
+    this.renderRequest.next(this.requestedRenderLevel);
+  }
+
+  /** Render WebLogo sensitive to changes in params of rendering
+   *@param {WlRenderLevel} recalcLevel - indicates that need to recalculate data for rendering
+   */
+  protected async renderInt(renderLevel: WlRenderLevel): Promise<void> {
+    _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.renderInt( renderLevel=${renderLevel} ), ` +
+      `start `);
 
     /** Calculate freqs of monomers */
     const calculateFreqsInt = (): void => {
@@ -960,85 +981,70 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       this._onLayoutCalculated.next();
     };
 
-    /** Render WebLogo sensitive to changes in params of rendering
-     *@param {WlRenderLevel} recalcLevel - indicates that need to recalculate data for rendering
-     */
-    const renderInt = (recalcLevel: WlRenderLevel) => {
-      _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.renderInt( recalcLevel=${recalcLevel} ), ` +
-        `start `);
-      if (this.msgHost) {
-        if (this.seqCol && !this.cp) {
-          this.msgHost!.innerText = `Unknown palette (column semType: '${this.seqCol.semType}').`;
-          this.msgHost!.style.display = '';
-        } else {
-          this.msgHost!.style.display = 'none';
-        }
+    if (this.msgHost) {
+      if (this.seqCol && !this.cp) {
+        this.msgHost!.innerText = `Unknown palette (column semType: '${this.seqCol.semType}').`;
+        this.msgHost!.style.display = '';
+      } else {
+        this.msgHost!.style.display = 'none';
       }
+    }
 
-      if (!this.seqCol || !this.dataFrame || !this.cp || this.host == null || this.slider == null)
-        return;
+    if (!this.seqCol || !this.dataFrame || !this.cp || this.host == null || this.slider == null)
+      return;
 
-      const dpr: number = window.devicePixelRatio;
-      /** 0 is for no position labels */
-      const positionLabelsHeight = this.showPositionLabels ? POSITION_LABELS_HEIGHT : 0;
-      if (recalcLevel >= WlRenderLevel.Freqs) calculateFreqsInt();
-      this.calcLayout(dpr); // after _skipEmptyPositions
-      if (this.positions.length === 0 || this.startPosition === -1 || this.endPosition === -1) return;
-      if (recalcLevel >= WlRenderLevel.Layout) calculateLayoutInt(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);
-      }
+    const dpr: number = window.devicePixelRatio;
+    /** 0 is for no position labels */
+    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);
 
-      _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.renderInt( recalcLevel=${recalcLevel} ), end`);
-    };
+    const g = this.canvas.getContext('2d');
+    if (!g) return;
 
-    this.renderLevelRequested = Math.max(this.renderLevelRequested, recalcLevel);
-    return new Promise<void>((resolve, reject) => {
-      window.setTimeout(() => {
-        try {
-          if (this.renderLevelRequested > WlRenderLevel.None) {
-            try {
-              renderInt(this.renderLevelRequested);
-            } finally {
-              this.renderLevelRequested = WlRenderLevel.None;
-            }
-          }
-        } catch (err: any) {
-          reject(err);
-        }
-      }, 0 /* next event cycle */);
-    });
+    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 = `${positionFontSize.toFixed(1)}px Roboto, Roboto Local, sans-serif`;
+    const posNameMaxWidth = Math.max(...this.positions.map((pos) => g.measureText(pos.name).width));
+    const hScale = posNameMaxWidth < (this._positionWidth * dpr - 2) ? 1 :
+      (this._positionWidth * dpr - 2) / posNameMaxWidth;
+
+    if (positionLabelsHeight > 0) {
+      renderPositionLabels(g, dpr, hScale, this._positionWidthWithMargin, this._positionWidth,
+        this.positions, this.slider.min, this.slider.max);
+    }
+    //#endregion Plot positionNames
+    const fontStyle = '16px Roboto, Roboto Local, sans-serif';
+    // Hacks to scale uppercase characters to target rectangle
+    const uppercaseLetterAscent = 0.25;
+    const uppercaseLetterHeight = 12.2;
+    for (let jPos = Math.floor(this.slider.min); jPos <= Math.floor(this.slider.max); jPos++) {
+      this.positions[jPos].render(g, (m) => { return this.unitsHandler!.isGap(m); },
+        fontStyle, uppercaseLetterAscent, uppercaseLetterHeight,
+        /* this._positionWidthWithMargin, firstVisiblePosIdx,*/ this.cp);
+    }
+
+    _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.render.renderInt( recalcLevel=${renderLevel} ), end`);
+  }
+
+  private renderRequestOnDebounce(renderLevel: WlRenderLevel): void {
+    this.requestedRenderLevel = WlRenderLevel.None;
+    this.renderInt(renderLevel)
+      .catch((err: any) => {
+        const [errMsg, errStack] = errInfo(err);
+        _package.logger.error(errMsg, undefined, errStack);
+      });
   }
 
   private _lastWidth: number;
@@ -1062,7 +1068,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
       };
       _package.logger.debug(
         `Bio: WebLogoViewer<${this.viewerId}>.sliderOnValuesChanged( ${JSON.stringify(val)} ), start`);
-      this.render(WlRenderLevel.Layout, 'sliderOnValuesChanged').then(() => {});
+      this.render(WlRenderLevel.Layout, 'sliderOnValuesChanged');
     } catch (err: any) {
       const errMsg = errorToConsole(err);
       _package.logger.error(`Bio: WebLogoViewer<${this.viewerId}>.sliderOnValuesChanged() error:\n` + errMsg);
@@ -1075,7 +1081,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     try {
       this.updatePositions();
       if (this.filterSource === FilterSources.Filtered)
-        this.render(WlRenderLevel.Freqs, 'dataFrameFilterOnChanged').then(() => {});
+        this.render(WlRenderLevel.Freqs, 'dataFrameFilterOnChanged');
     } catch (err: any) {
       const errMsg = errorToConsole(err);
       _package.logger.error(`Bio: WebLogoViewer<${this.viewerId}>.dataFrameFilterOnChanged() error:\n` + errMsg);
@@ -1087,7 +1093,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
     _package.logger.debug(`Bio: WebLogoViewer<${this.viewerId}>.dataFrameSelectionOnChanged()`);
     try {
       if (this.filterSource === FilterSources.Selected)
-        this.render(WlRenderLevel.Freqs, 'dataFrameSelectionOnChanged').then(() => {});
+        this.render(WlRenderLevel.Freqs, 'dataFrameSelectionOnChanged');
     } catch (err: any) {
       const errMsg = errorToConsole(err);
       _package.logger.error(`Bio: WebLogoViewer<${this.viewerId}>.dataFrameSelectionOnChanged() error:\n` + errMsg);