@datagrok/helm 2.1.30 → 2.1.32

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.30",
+  "version": "2.1.32",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
@@ -15,8 +15,8 @@
     "helm/JSDraw/Pistoia.HELM-uncompressed.js"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.39.29",
-    "@datagrok-libraries/chem-meta": "^1.2.2",
+    "@datagrok-libraries/bio": "^5.40.7",
+    "@datagrok-libraries/chem-meta": "^1.2.3",
     "@datagrok-libraries/utils": "^4.1.45",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.17.0",
@@ -37,8 +37,8 @@
     "@typescript-eslint/parser": "^5.11.0",
     "eslint": "^8.18.0",
     "eslint-config-google": "^0.14.0",
-    "@datagrok/bio": "^2.11.38",
-    "@datagrok/chem": "^1.8.13"
+    "@datagrok/bio": "^2.12.11",
+    "@datagrok/chem": "^1.9.0"
   },
   "scripts": {
     "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",

package/src/cell-renderer.ts

@@ -29,7 +29,7 @@ function getSeqMonomerFromHelm(
       resSeqMonomer = {symbol: symbol, polymerType: polymerType};
   }
   if (!resSeqMonomer)
-    resSeqMonomer = {symbol: symbol};
+    throw new Error(`Monomer not found for symbol = '${symbol}' and helmPrefix = '${helmPrefix}'.`);
   return resSeqMonomer;
 }
 
@@ -162,7 +162,7 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
       const argsX = e.offsetX - gcb.x;
       const argsY = e.offsetY - gcb.y;
 
-      const helmPlacer = HelmMonomerPlacer.getOrCreate(tableCol);
+      const helmPlacer = HelmMonomerPlacer.getOrCreate(gridCell.gridColumn, tableCol);
       const editor: IEditor | null = helmPlacer.getEditor(gridCell.tableRowIndex!);
       let seqMonomer: ISeqMonomer | null;
       let missedMonomers: Set<string> = new Set<string>(); // of .size = 0
@@ -189,15 +189,10 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
 
       if (seqMonomer) {
         if (!missedMonomers.has(seqMonomer.symbol)) {
-          const monomer = helmPlacer.getMonomer(seqMonomer);
-          if (monomer) {
-            const options = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
-            const monomerSvg = grok.chem.svgMol(monomer.smiles, undefined, undefined, options);
-            ui.tooltip.show(ui.divV([
-              ui.divText(seqMonomer.symbol),
-              monomerSvg,
-            ]), e.x + 16, e.y + 16);
-          }
+          const tooltipElements: HTMLElement[] = [ui.div(seqMonomer.symbol)];
+          const monomerDiv = helmPlacer.monomerLib.getTooltip(seqMonomer.polymerType, seqMonomer.symbol);
+          tooltipElements.push(monomerDiv);
+          ui.tooltip.show(ui.divV(tooltipElements), e.x + 16, e.y + 16);
         } else {
           ui.tooltip.show(ui.divV([
             ui.divText(`Monomer '${seqMonomer.symbol}' not found.`),
@@ -244,7 +239,7 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
       const monomerList = parseHelm(seq);
       const monomers: Set<string> = new Set<string>(monomerList);
       const missedMonomers: Set<string> = findMonomers(monomerList);
-      const helmPlacer = HelmMonomerPlacer.getOrCreate(tableCol);
+      const helmPlacer = HelmMonomerPlacer.getOrCreate(gridCell.gridColumn, tableCol);
 
       if (missedMonomers.size == 0) {
         // Recreate host to avoid hanging in window.dojox.gfx.svg.Text.prototype.getTextWidth

package/src/helm-monomer-placer.ts

@@ -3,11 +3,13 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
+import {Unsubscribable} from 'rxjs';
 
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types/index';
 
 import {getParts, parseHelm} from './utils';
-import {getMonomerLib} from './package';
+
+import {_package, getMonomerLib} from './package';
 
 export const enum Temps {
   helmMonomerPlacer = 'bio-helmMonomerPlacer',
@@ -36,31 +38,60 @@ export interface IEditorPoint {
 }
 
 export interface ISeqMonomer {
+  polymerType: string
   symbol: string,
-  polymerType?: string
 }
 
 export class HelmMonomerPlacer {
-  private readonly _allPartsList: (string[] | null)[];
-  private readonly _lengthsList: (number[] | null)[];
-  private readonly _editorList: (IEditor | null)[];
-
+  private readonly grid: DG.Grid;
   public readonly monomerLib: IMonomerLib;
 
+  private _allPartsList: (string[] | null)[];
+  private _lengthsList: (number[] | null)[];
+  private _editorList: (IEditor | null)[];
+
   public monomerCharWidth: number = 7;
   public leftPadding: number = 5;
   public monomerTextSizeMap: { [p: string]: TextMetrics } = {};
 
-  constructor(public readonly col: DG.Column<string>) {
-    this.col.dataFrame.onDataChanged.subscribe();
+  private subs: Unsubscribable[] = [];
+
+  protected constructor(
+    public readonly gridCol: DG.GridColumn,
+    public readonly col: DG.Column<string>
+  ) {
+    this.grid = this.gridCol.grid;
+    this.reset();
+    if (this.grid) {
+      this.subs.push(this.col.dataFrame.onDataChanged.subscribe(() => {
+        try {
+          this.reset();
+        } catch (err: any) {
+          console.error(err);
+        }
+      }));
+      this.subs.push(grok.events.onViewRemoved.subscribe((view: DG.View) => {
+        try {
+          if (this.gridCol.grid.view?.id === view.id) this.destroy();
+        } catch (err: any) {
+          console.error(err);
+        }
+      }));
+    }
     this.monomerLib = getMonomerLib();
-    this.monomerLib.onChanged.subscribe(this.monomerLibOnChanged.bind(this));
+    this.subs.push(this.monomerLib.onChanged.subscribe(this.monomerLibOnChanged.bind(this)));
+  }
 
+  private reset(): void {
     this._allPartsList = new Array<string[] | null>(this.col.length).fill(null);
     this._lengthsList = new Array<number[] | null>(this.col.length).fill(null);
     this._editorList = new Array<IEditor | null>(this.col.length).fill(null);
   }
 
+  private destroy(): void {
+    for (const sub of this.subs) sub.unsubscribe();
+  }
+
   /** Skips cell for the fallback rendering */
   public skipCell(rowIdx: number): void {
     this._allPartsList[rowIdx] = [];
@@ -80,8 +111,10 @@ export class HelmMonomerPlacer {
 
   private getCellMonomerLengthsForSeq(rowIdx: number): [string[], number[]] {
     let allParts: string[] | null = this._allPartsList![rowIdx];
-    if (allParts === null)
-      allParts = this._allPartsList![rowIdx] = this.getAllParts(rowIdx);
+    if (allParts === null) {
+      const seq = this.col.get(rowIdx);
+      allParts = this._allPartsList![rowIdx] = getAllParts(seq);
+    }
 
     let lengths: number[] | null = this._lengthsList![rowIdx];
     if (lengths === null) {
@@ -95,12 +128,6 @@ export class HelmMonomerPlacer {
     return [allParts, lengths];
   }
 
-  getAllParts(rowIdx: number): string[] {
-    const seq: string | null = this.col.get(rowIdx);
-    const monomerList: string[] = seq ? parseHelm(seq) : [];
-    return seq ? getParts(monomerList, seq) : [];
-  }
-
   getMonomer(monomer: ISeqMonomer): Monomer | null {
     let res: Monomer | null = null;
     if (monomer.polymerType)
@@ -117,15 +144,14 @@ export class HelmMonomerPlacer {
   // -- Handle events --
 
   private monomerLibOnChanged(_value: any): void {
-    this._lengthsList.fill(null);
-    this._allPartsList.fill(null);
-    this._editorList.fill(null);
-    // TODO: Invalidate all grids of this.col.dataFrame
+    this.reset();
+    if (this.grid) this.grid.invalidate();
   }
 
-  public static getOrCreate(col: DG.Column<string>): HelmMonomerPlacer {
-    if (!(Temps.helmMonomerPlacer in col.temp)) col.temp[Temps.helmMonomerPlacer] = new HelmMonomerPlacer(col);
-    return col.temp[Temps.helmMonomerPlacer];
+  public static getOrCreate(gridCol: DG.GridColumn, col: DG.Column<string>): HelmMonomerPlacer {
+    let res: HelmMonomerPlacer = gridCol.temp[Temps.helmMonomerPlacer];
+    if (!res) res = gridCol.temp[Temps.helmMonomerPlacer] = new HelmMonomerPlacer(gridCol, col);
+    return res;
   }
 
   public setEditor(tableRowIndex: number, editor: IEditor) {
@@ -136,3 +162,8 @@ export class HelmMonomerPlacer {
     return this._editorList![tableRowIndex];
   }
 }
+
+export function getAllParts(seq: string | null): string[] {
+  const monomerList: string[] = seq ? parseHelm(seq) : [];
+  return seq ? getParts(monomerList, seq) : [];
+}

package/src/package-test.ts

@@ -8,6 +8,7 @@ import './tests/findMonomers-tests';
 import './tests/renderers-tests';
 import './tests/get-molfiles';
 import './tests/properties-widget-tests';
+import './tests/get-all-parts-tests';
 
 export const _package = new DG.Package();
 export {tests};

package/src/package.ts

@@ -7,7 +7,7 @@ import $ from 'cash-dom';
 
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {GapSymbols, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
@@ -156,17 +156,17 @@ export function helmCellRenderer(): HelmCellRenderer {
   return new HelmCellRenderer();
 }
 
-function checkMonomersAndOpenWebEditor(cell?: DG.Cell, value?: string, units?: string) {
+function checkMonomersAndOpenWebEditor(cell: DG.Cell, value?: string, units?: string) {
   const cellValue: string = !!cell && units === undefined ? cell.value : value;
   const monomerList: string[] = parseHelm(cellValue);
-  const monomers = findMonomers(monomerList);
-  if (monomers.size === 0)
+  const missedMonomerSet = findMonomers(monomerList);
+  if (missedMonomerSet.size === 0)
     webEditor(cell, value, units);
-  else if (monomers.size === 1 && monomers.has(GapSymbols[NOTATION.HELM]))
-    grok.shell.warning(`WebEditor doesn't support Helm with gaps '${GapSymbols[NOTATION.HELM]}'.`);
+  else if (missedMonomerSet.size === 1 && missedMonomerSet.has(GapOriginals[NOTATION.HELM]))
+    grok.shell.warning(`WebEditor doesn't support Helm with gaps '${GapOriginals[NOTATION.HELM]}'.`);
   else {
     grok.shell.warning(
-      `Monomers ${Array.from(monomers).map((m) => `'${m}'`).join(', ')} are absent! <br/>` +
+      `Monomers ${Array.from(missedMonomerSet).map((m) => `'${m}'`).join(', ')} are absent! <br/>` +
       `Please, upload the monomer library! <br/>` +
       `<a href="https://datagrok.ai/help/domains/bio/macromolecules" target="_blank">Learn more</a>`);
   }
@@ -187,11 +187,11 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 export function openEditor(mol: string): void {
   const df = grok.shell.tv.grid.dataFrame;
   const col = df.columns.bySemType('Macromolecule')!;
-  const colUh = UnitsHandler.getOrCreate(col);
+  const colSh = SeqHandler.forColumn(col);
   const colUnits = col.getTag(DG.TAGS.UNITS);
   if (colUnits === NOTATION.HELM)
     checkMonomersAndOpenWebEditor(df.currentCell, undefined, undefined);
-  const convert = colUh.getConverter(NOTATION.HELM);
+  const convert = colSh.getConverter(NOTATION.HELM);
   const helmMol = convert(mol);
   checkMonomersAndOpenWebEditor(df.currentCell, helmMol, col.getTag(DG.TAGS.UNITS));
 }
@@ -204,11 +204,13 @@ export function propertiesWidget(sequence: DG.SemanticValue): DG.Widget {
   return getPropertiesWidget(sequence);
 }
 
-function webEditor(cell?: DG.Cell, value?: string, units?: string) {
+function webEditor(cell: DG.Cell, value?: string, units?: string) {
   const view = ui.div();
-  const df = grok.shell.tv.grid.dataFrame;
-  const col = df.columns.bySemType('Macromolecule')!;
-  const uh = UnitsHandler.getOrCreate(col);
+  // const df = grok.shell.tv.grid.dataFrame;
+  // const col = df.columns.bySemType('Macromolecule')!;
+  const col = cell.column;
+  const sh = SeqHandler.forColumn(col);
+  const rowIdx = cell.rowIndex;
   // @ts-ignore
   org.helm.webeditor.MolViewer.molscale = 0.8;
   // @ts-ignore
@@ -244,13 +246,13 @@ function webEditor(cell?: DG.Cell, value?: string, units?: string) {
   ui.dialog({showHeader: false, showFooter: true})
     .add(view)
     .onOK(() => {
-      const helmValue = app.canvas.getHelm(true).replace(/<\/span>/g, '')
+      const helmValue: string = app.canvas.getHelm(true).replace(/<\/span>/g, '')
         .replace(/<span style='background:#bbf;'>/g, '');
       if (!!cell) {
         if (units === undefined)
           cell.value = helmValue;
         else {
-          const convertedRes = uh.convertHelmToFastaSeparator(helmValue, units!);
+          const convertedRes = sh.convertHelmToFastaSeparator(helmValue, units!, sh.separator);
           cell.value = convertedRes;
         }
       }

package/src/tests/get-all-parts-tests.ts

@@ -0,0 +1,34 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+
+import {getAllParts} from '../helm-monomer-placer';
+
+category('getAllParts', () => {
+  /** All parts of Helm string are required for fallback rendering. */
+
+  const tests: { [testName: string]: { tgt: string[]; seq: string } } = {
+    'peptideSimpleSingleChar': {
+      seq: 'PEPTIDE1{L.V.A}$$$$',
+      tgt: ['PEPTIDE1{', 'L', '.', 'V', '.', 'A', '}$$$$'],
+    },
+    'peptideSimpleMultiChar': {
+      seq: 'PEPTIDE1{[Ac].V.A}$$$$',
+      /* doubt joining square brackets to separator or notation is correct */
+      tgt: ['PEPTIDE1{[', 'Ac', '].', 'V', '.', 'A', '}$$$$'],
+    }
+  };
+
+  for (const [testName, testData] of Object.entries(tests)) {
+    test(`${testName}`, async () => {
+      await _testAllParts(testData.seq, testData.tgt);
+    });
+  }
+});
+
+async function _testAllParts(seq: string | null, tgt: string[]): Promise<void> {
+  const res: string[] = getAllParts(seq);
+  expectArray(res, tgt);
+}

package/src/tests/properties-widget-tests.ts

@@ -2,9 +2,11 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {category, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {getPropertiesDict} from '../widgets/properties-widget';
 
@@ -60,6 +62,22 @@ const TestsData: {
 };
 
 category('properties-widget', () => {
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: any = null;
+
+  before(async () => {
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = getUserLibSettings();
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true); // load default libraries
+  });
+
+  after(async () => {
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+  });
+
   for (const [testName, testData] of Object.entries(TestsData)) {
     test(testName, async () => {
       testPropertiesDict(testData.seq, testData.units, testData.separator, testData.alphabet, testData.res);
@@ -75,7 +93,7 @@ function testPropertiesDict(
   col.setTag(DG.TAGS.UNITS, units);
   if (separator) col.setTag(bioTAGS.separator, separator);
   if (alphabet) col.setTag(bioTAGS.alphabet, alphabet);
-  const uh = UnitsHandler.getOrCreate(col);
+  const uh = SeqHandler.forColumn(col);
   const actPropDict = getPropertiesDict(seq, uh);
   expectObject(actPropDict, expPropDict);
 }

package/src/widgets/properties-widget.ts

@@ -4,13 +4,13 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 import {removeGapsFromHelm} from '../utils';
 
-export function getPropertiesDict(seq: string, uh: UnitsHandler): {} {
-  const helmString = uh.isHelm() ? seq : uh.getConverter(NOTATION.HELM)(seq);
+export function getPropertiesDict(seq: string, sh: SeqHandler): {} {
+  const helmString = sh.isHelm() ? seq : sh.getConverter(NOTATION.HELM)(seq);
   // Remove gap symbols for compatibility with WebEditor
   const helmString2 = removeGapsFromHelm(helmString);
 
@@ -36,8 +36,8 @@ export function getPropertiesDict(seq: string, uh: UnitsHandler): {} {
 
 
 export function getPropertiesWidget(value: DG.SemanticValue): DG.Widget {
-  const uh = UnitsHandler.getOrCreate(value.cell.column);
-  const propDict = getPropertiesDict(value.value, uh);
+  const sh = SeqHandler.forColumn(value.cell.column);
+  const propDict = getPropertiesDict(value.value, sh);
   return new DG.Widget(
     ui.tableFromMap(propDict)
   );