@datagrok/helm 2.2.0 → 2.2.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.2.0",
+  "version": "2.2.1",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
@@ -15,30 +15,30 @@
     "helm/JSDraw/Pistoia.HELM.js"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.41.0",
+    "@datagrok-libraries/bio": "^5.41.2",
     "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/utils": "^4.2.2",
     "cash-dom": "^8.1.1",
-    "datagrok-api": "^1.17.0",
+    "datagrok-api": "^1.17.4",
     "dayjs": "^1.10.6",
     "rxjs": "^6.5.5",
     "wu": "latest"
   },
   "devDependencies": {
+    "@datagrok/bio": "^2.12.18",
+    "@datagrok/chem": "^1.9.2",
     "@types/node": "17.0.45",
     "@types/wu": "latest",
+    "@typescript-eslint/eslint-plugin": "^5.11.0",
+    "@typescript-eslint/parser": "^5.11.0",
+    "eslint": "^8.18.0",
+    "eslint-config-google": "^0.14.0",
     "path": "^0.12.7",
     "source-map-loader": "^4.0.1",
     "ts-loader": "^9.2.6",
     "typescript": "^4.8.4",
     "webpack": "^5.76.3",
-    "webpack-cli": "^4.9.1",
-    "@typescript-eslint/eslint-plugin": "^5.11.0",
-    "@typescript-eslint/parser": "^5.11.0",
-    "eslint": "^8.18.0",
-    "eslint-config-google": "^0.14.0",
-    "@datagrok/bio": "^2.12.17",
-    "@datagrok/chem": "^1.9.2"
+    "webpack-cli": "^4.9.1"
   },
   "scripts": {
     "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",

package/src/cell-renderer.ts

@@ -7,13 +7,13 @@ import wu from 'wu';
 
 import {printLeftOrCentered} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
+import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 import {findMonomers, parseHelm, removeGapsFromHelm} from './utils';
 import {HelmMonomerPlacer, ISeqMonomer} from './helm-monomer-placer';
 import {getHoveredMonomerFallback, getHoveredMonomerFromEditorMol} from './utils/get-hovered';
-import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
-// import {_package} from './package'; // NullError: method not found: '_package' on null
+import {getMonomerLib} from './package';
 
 const enum tempTAGS {
   helmSumMaxLengthWords = 'helm-sum-maxLengthWords',
@@ -73,7 +73,9 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
       if (seqMonomer) {
         if (!missedMonomers.has(seqMonomer.symbol)) {
           const tooltipElements: HTMLElement[] = [ui.div(seqMonomer.symbol)];
-          const monomerDiv = helmPlacer.monomerLib.getTooltip(seqMonomer.polymerType, seqMonomer.symbol);
+          const monomerLib = getMonomerLib();
+          const monomerDiv = monomerLib ? monomerLib.getTooltip(seqMonomer.polymerType, seqMonomer.symbol) :
+            ui.divText('Monomer library is not available.');
           tooltipElements.push(monomerDiv);
           ui.tooltip.show(ui.divV(tooltipElements), e.x + 16, e.y + 16);
         } else {

package/src/constants.ts

@@ -12,17 +12,6 @@ export const jsonSdfMonomerLibDict = {
   'symbol': 'MonomerCode'
 };
 
-export type WebEditorMonomer = {
-  /** symbol */ id: string,
-  /** name */ n: string,
-  /** natural analog */ na?: string,
-  /** polymer type */type: string,
-  /** monomer type */ mt: string,
-  /** molfile */ m: string,
-  /** substituents */ at: { [group: string]: string },
-  /** number of substituents */ rs: number
-};
-
 export const SMILES = 'smiles';
 export const RGROUPS = 'rgroups';
 export const MONOMER_SYMBOL = 'symbol';

package/src/helm-monomer-placer.ts

@@ -8,19 +8,18 @@ import wu from 'wu';
 
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types/index';
 import {CellRendererBackBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
+import {IEditorMol} from '@datagrok-libraries/bio/src/types/helm-web-editor';
 
 import {getParts, parseHelm} from './utils';
 
 import {_package, getMonomerLib} from './package';
 
 export interface ISeqMonomer {
-  polymerType: string
-  symbol: string,
+  polymerType: org.helm.PolymerType;
+  symbol: string;
 }
 
 export class HelmMonomerPlacer extends CellRendererBackBase<string> {
-  public readonly monomerLib: IMonomerLib;
-
   private _allPartsList: (string[] | null)[];
   private _lengthsList: (number[] | null)[];
   private _editorMolList: (JSDraw2.IEditorMol | null)[];
@@ -34,8 +33,6 @@ export class HelmMonomerPlacer extends CellRendererBackBase<string> {
     tableCol: DG.Column<string>
   ) {
     super(gridCol, tableCol, _package.logger);
-    this.monomerLib = getMonomerLib();
-    this.subs.push(this.monomerLib.onChanged.subscribe(this.monomerLibOnChanged.bind(this)));
   }
 
   protected override reset(): void {
@@ -80,19 +77,6 @@ export class HelmMonomerPlacer extends CellRendererBackBase<string> {
     return [allParts, lengths];
   }
 
-  getMonomer(monomer: ISeqMonomer): Monomer | null {
-    let res: Monomer | null = null;
-    if (monomer.polymerType)
-      res = this.monomerLib.getMonomer(monomer.polymerType, monomer.symbol);
-    else {
-      for (const polymerType of this.monomerLib.getPolymerTypes()) {
-        res = this.monomerLib.getMonomer(polymerType, monomer.symbol);
-        if (res) break;
-      }
-    }
-    return res;
-  }
-
   // -- Handle events --
 
   private monomerLibOnChanged(_value: any): void {

package/src/package-test.ts

@@ -1,15 +1,17 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
+import '@datagrok-libraries/bio/src/types/helm';
 import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
 
 import './tests/helm-tests.ts';
 import './tests/findMonomers-tests';
 import './tests/helm-service-tests';
 import './tests/renderers-tests';
-import './tests/get-molfiles';
+import './tests/get-molfiles-tests';
 import './tests/properties-widget-tests';
 import './tests/get-all-parts-tests';
+import './tests/get-monomer-tests';
 
 export const _package = new DG.Package();
 export {tests};
@@ -21,6 +23,7 @@ export {tests};
 //input: object testContext {optional: true}
 //output: dataframe result
 export async function test(category: string, test: string, testContext: TestContext): Promise<DG.DataFrame> {
-  const data = await runTests({category, test, testContext});
+  // verbose: true - for tests returning dataframe
+  const data = await runTests({category, test, testContext, verbose: true});
   return DG.DataFrame.fromObjects(data)!;
 }

package/src/package-utils.ts

@@ -2,8 +2,19 @@ import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
+import * as org from 'org';
+import * as scil from 'scil';
+import * as JSDraw2 from 'JSDraw2';
+import Atom = JSDraw2.Atom;
+
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
+import {IMonomerLib, HelmType} from '@datagrok-libraries/bio/src/types';
+import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
+
 import {HelmService} from './utils/helm-service';
+import {GetMonomerFunc, GetMonomerResType, getWebEditorMonomer} from './utils/get-monomer';
+
 
 type HelmWindowType = Window & {
   $helmService?: HelmServiceBase,
@@ -15,3 +26,125 @@ export function _getHelmService(): HelmServiceBase {
   if (!res) res = window.$helmService = new HelmService();
   return res;
 }
+
+export function initHelmPatchDojo(): void {
+  // patch window.dojox.gfx.svg.Text.prototype.getTextWidth hangs
+  /** get the text width in pixels */
+  // @ts-ignore
+  window.dojox.gfx.svg.Text.prototype.getTextWidth = function() {
+    const rawNode = this.rawNode;
+    const oldParent = rawNode.parentNode;
+    const _measurementNode = rawNode.cloneNode(true);
+    _measurementNode.style.visibility = 'hidden';
+
+    // solution to the "orphan issue" in FF
+    let _width = 0;
+    const _text = _measurementNode.firstChild.nodeValue;
+    oldParent.appendChild(_measurementNode);
+
+    // solution to the "orphan issue" in Opera
+    // (nodeValue == "" hangs firefox)
+    if (_text != '') {
+      let watchdogCounter = 100;
+      while (!_width && --watchdogCounter > 0) { // <-- hangs
+        //Yang: work around svgweb bug 417 -- http://code.google.com/p/svgweb/issues/detail?id=417
+        if (_measurementNode.getBBox)
+          _width = parseInt(_measurementNode.getBBox().width);
+        else
+          _width = 68;
+      }
+    }
+    oldParent.removeChild(_measurementNode);
+    return _width;
+  };
+}
+
+export const helmJsonReplacer = (key: string, value: any): any => {
+  switch (key) {
+  case '_parent': {
+    return `${value.toString()}`;
+  }
+  default:
+    return value;
+  }
+};
+
+export class HelmPackage extends DG.Package {
+  public getMonomerOriginal: GetMonomerFunc;
+  public alertOriginal: (s: string) => void;
+
+  /** Patches Pistoia Monomers.getMonomer method to utilize DG Bio monomer Lib */
+  public initHelmPatchPistoia(monomerLib: IMonomerLib, logger: ILogger): void {
+    const logPrefix: string = 'Helm: initHelmPatchPistoia()';
+    const monomers = org.helm.webeditor.Monomers;
+
+    this.getMonomerOriginal = monomers.getMonomer.bind(monomers);
+    this.logger.debug(`${logPrefix}, this.getMonomerOriginal stored`);
+
+    this.alertOriginal = scil.Utils.alert;
+
+    org.helm.webeditor.Monomers.getMonomer = (
+      a: Atom<HelmType> | HelmType, name: string
+    ): GetMonomerResType => {
+      const logPrefixInt = `${logPrefix}, org.helm.webeditor.Monomers.getMonomer()`;
+      try {
+        // logger.debug(`${logPrefixInt}, a: ${JSON.stringify(a, helmJsonReplacer)}, name: '${name}'`);
+
+        // Creates monomers in lib
+        const dgWem = getWebEditorMonomer(monomerLib, a, name);
+
+        // // Returns null for gap
+        // const oWem = this.getMonomerOriginal(a, name);
+        // if (!oWem)
+        //   logger.warning(`${logPrefixInt}, getMonomerOriginal( a: ${a}, name: ${name}) returns null`);
+        return dgWem; //dgWem;
+      } catch (err) {
+        const [errMsg, errStack] = errInfo(err);
+        logger.error(`${logPrefixInt}, Error: ${errMsg}`, undefined, errStack);
+        throw err;
+      }
+    };
+    scil.Utils.alert = (s: string): void => {
+      logger.warning(`${logPrefix}, scil.Utils.alert() s = 's'.`);
+    };
+
+    // @ts-ignore, intercept with proxy to observe access and usage
+    org.helm.webeditor.Monomers = new class {
+      constructor(base: org.helm.IMonomers) {
+        return new Proxy(base, {
+          get(target: any, p: string | symbol, _receiver: any): any {
+            return target[p];
+          },
+          set(target: any, p: string | symbol, newValue: any, _receiver: any): boolean {
+            if (p != 'sugars' && p != 'linkers' && p != 'bases' && p != 'aas') {
+              const k = 11;
+            }
+            target[p] = newValue;
+            return true;
+          },
+          apply(target: any, thisArg: any, argArray: any[]): any {
+            return target[thisArg](...argArray);
+          },
+        });
+      }
+    }(org.helm.webeditor.Monomers) as org.helm.IMonomers;
+
+    // @ts-ignore, intercept with proxy to observe access and usage
+    org.helm.webeditor = new class {
+      constructor(base: org.helm.IOrgHelmWebEditor) {
+        return new Proxy(base, {
+          get(target: any, p: string | symbol, _receiver: any): any {
+            return target[p];
+          },
+          set(target: any, p: string | symbol, newValue: any, _receiver: any): boolean {
+            target[p] = newValue;
+            return true;
+          },
+          apply(target: any, thisArg: any, argArray: any[]): any {
+            return target[thisArg](...argArray);
+          },
+        });
+      }
+    }(org.helm.webeditor) as org.helm.IOrgHelmWebEditor;
+  }
+}

package/src/package.ts

@@ -6,9 +6,9 @@ import * as DG from 'datagrok-api/dg';
 // import '@datagrok-libraries/bio/src/types/dojo';
 // import * as dojo from 'DOJO';
 import '@datagrok-libraries/bio/src/types/helm';
+import '@datagrok-libraries/bio/src/types/jsdraw2';
 import * as scil from 'scil';
 import * as org from 'org';
-import '@datagrok-libraries/bio/src/types/jsdraw2';
 import * as JSDraw2 from 'JSDraw2';
 
 import $ from 'cash-dom';
@@ -20,50 +20,15 @@ import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 
-import {findMonomers, parseHelm} from './utils';
 import {HelmCellRenderer} from './cell-renderer';
 import {HelmHelper} from './helm-helper';
 import {getPropertiesWidget} from './widgets/properties-widget';
 import {HelmGridCellRenderer, HelmGridCellRendererBack} from './utils/helm-grid-cell-renderer';
-import {_getHelmService} from './package-utils';
-
-import {WebEditorMonomer, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
+import {_getHelmService, HelmPackage, initHelmPatchDojo} from './package-utils';
 
 let monomerLib: IMonomerLib | null = null;
 
-export const _package = new DG.Package();
-
-function initHelmPatchDojo(): void {
-  // patch window.dojox.gfx.svg.Text.prototype.getTextWidth hangs
-  /** get the text width in pixels */
-  // @ts-ignore
-  window.dojox.gfx.svg.Text.prototype.getTextWidth = function() {
-    const rawNode = this.rawNode;
-    const oldParent = rawNode.parentNode;
-    const _measurementNode = rawNode.cloneNode(true);
-    _measurementNode.style.visibility = 'hidden';
-
-    // solution to the "orphan issue" in FF
-    let _width = 0;
-    const _text = _measurementNode.firstChild.nodeValue;
-    oldParent.appendChild(_measurementNode);
-
-    // solution to the "orphan issue" in Opera
-    // (nodeValue == "" hangs firefox)
-    if (_text != '') {
-      let watchdogCounter = 100;
-      while (!_width && --watchdogCounter > 0) { // <-- hangs
-        //Yang: work around svgweb bug 417 -- http://code.google.com/p/svgweb/issues/detail?id=417
-        if (_measurementNode.getBBox)
-          _width = parseInt(_measurementNode.getBBox().width);
-        else
-          _width = 68;
-      }
-    }
-    oldParent.removeChild(_measurementNode);
-    return _width;
-  };
-}
+export const _package = new HelmPackage();
 
 //tags: init
 export async function initHelm(): Promise<void> {
@@ -71,31 +36,42 @@ export async function initHelm(): Promise<void> {
   _package.logger.debug(`${logPrefix}, start`);
   org.helm.webeditor.kCaseSensitive = true; // GROK-13880
 
-  return Promise.all([
+  await Promise.all([
     new Promise((resolve, reject) => {
       // @ts-ignore
       dojo.ready(function() { resolve(null); });
     }).then(() => {
       initHelmPatchDojo();
     }),
-    grok.functions.call('Bio:getBioLib'),
+    (async () => {
+      const libHelper = await getMonomerLibHelper();
+      return libHelper.getBioLib();
+    })()
   ])
     .then(([_, lib]: [unknown, IMonomerLib]) => {
       _package.logger.debug(`${logPrefix}, then(), lib loaded`);
       monomerLib = lib;
       rewriteLibraries(); // initHelm()
+      _package.initHelmPatchPistoia(monomerLib, _package.logger);
+
       monomerLib.onChanged.subscribe((_) => {
         try {
+          const libSummary = monomerLib!.getSummary();
+          const isLibEmpty = Object.keys(libSummary).length == 0;
+          const libSummaryLog = isLibEmpty ? 'empty' : Object.entries(libSummary)
+            .map(([pt, count]) => `${pt}: ${count}`)
+            .join(', ');
           const logPrefixInt = `${logPrefix} monomerLib.onChanged()`;
-          _package.logger.debug(`${logPrefixInt}, start, org,helm.webeditor.Monomers updating`);
-          rewriteLibraries(); // initHelm()
+          _package.logger.debug(`${logPrefixInt}, start, lib: { ${libSummaryLog} }`);
 
-          const libSummary: string = monomerLib!.getSummary()
-            .replaceAll('\n', '<br />\n')
-            .replaceAll(',', ' ');
-          const libMsg: string = `Monomer lib updated:<br /> ${libSummary}'`;
+          const libSummaryHtml = isLibEmpty ? 'empty' : Object.entries(libSummary)
+            .map(([pt, count]) => `${pt} ${count}`)
+            .join('<br />');
+          const libMsg: string = `Monomer lib updated:<br /> ${libSummaryHtml}`;
           grok.shell.info(libMsg);
 
+          _package.logger.debug(`${logPrefixInt}, org,helm.webeditor.Monomers updating ...`);
+          rewriteLibraries(); // initHelm()
           _package.logger.debug(`${logPrefixInt}, end, org.helm.webeditor.Monomers completed`);
         } catch (err: any) {
           const errMsg = errorToConsole(err);
@@ -111,10 +87,11 @@ export async function initHelm(): Promise<void> {
       errRes.stack = err.stack;
       throw errRes;
     });
+  _package.logger.debug(`${logPrefix}, end`);
 }
 
-export function getMonomerLib(): IMonomerLib {
-  return monomerLib!;
+export function getMonomerLib(): IMonomerLib | null {
+  return monomerLib;
 }
 
 /** Fills org.helm.webeditor.Monomers dictionary for WebEditor */
@@ -125,7 +102,7 @@ function rewriteLibraries() {
     monomerSymbols.forEach((monomerSymbol) => {
       let isBroken = false;
       const monomer: Monomer = monomerLib!.getMonomer(polymerType, monomerSymbol)!;
-      const webEditorMonomer: WebEditorMonomer = {
+      const webEditorMonomer: org.helm.WebEditorMonomer = {
         id: monomerSymbol,
         m: monomer.molfile,
         n: monomer.name,
@@ -137,6 +114,7 @@ function rewriteLibraries() {
       };
 
       if (monomer.rgroups.length > 0) {
+        // @ts-ignore
         webEditorMonomer.rs = monomer.rgroups.length;
         const at: { [prop: string]: any } = {};
         monomer.rgroups.forEach((it) => {
@@ -144,6 +122,7 @@ function rewriteLibraries() {
         });
         webEditorMonomer.at = at;
       } else if (monomer[SMILES] != null) {
+        // @ts-ignore
         webEditorMonomer.rs = Object.keys(getRS(monomer[SMILES].toString())).length;
         webEditorMonomer.at = getRS(monomer[SMILES].toString());
       } else
@@ -177,19 +156,7 @@ export function helmCellRenderer(): HelmCellRenderer {
 }
 
 function checkMonomersAndOpenWebEditor(cell: DG.Cell, value?: string, units?: string) {
-  const cellValue: string = !!cell && units === undefined ? cell.value : value;
-  const monomerList: string[] = parseHelm(cellValue);
-  const missedMonomerSet = findMonomers(monomerList);
-  if (missedMonomerSet.size === 0)
-    webEditor(cell, value, units);
-  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 ${Array.from(missedMonomerSet).map((m) => `'${m}'`).join(', ')} are not found. <br/>` +
-      `Please specify the monomer library to use. <br/>` +
-      `<a href="https://datagrok.ai/help/datagrok/solutions/domains/bio/#manage-monomer-libraries" target="_blank">Learn more</a>`);
-  }
+  openWebEditor(cell, value, units);
 }
 
 //tags: cellEditor
@@ -224,7 +191,7 @@ export function propertiesWidget(sequence: DG.SemanticValue): DG.Widget {
   return getPropertiesWidget(sequence);
 }
 
-function webEditor(cell: DG.Cell, value?: string, units?: string) {
+function openWebEditor(cell: DG.Cell, value?: string, units?: string) {
   const view = ui.div();
   // const df = grok.shell.tv.grid.dataFrame;
   // const col = df.columns.bySemType('Macromolecule')!;
@@ -273,30 +240,6 @@ function webEditor(cell: DG.Cell, value?: string, units?: string) {
     }).show({modal: true, fullScreen: true});
 }
 
-function getRS(smiles: string) {
-  const newS = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
-  const res: { [name: string]: string } = {};
-  let el = '';
-  let digit;
-  if (!!newS) {
-    for (let i = 0; i < newS.length; i++) {
-      if (newS[i] != null) {
-        if (/\d/.test(newS[i])) {
-          digit = newS[i][newS[i].length - 1];
-          newS[i] = newS[i].replace(/[0-9]/g, '');
-          for (let j = 0; j < newS[i].length; j++) {
-            if (newS[i][j] != ':')
-              el += newS[i][j];
-          }
-          res['R' + digit] = el;
-          el = '';
-        }
-      }
-    }
-  }
-  return res;
-}
-
 //name: getMolfiles
 //input: column col {semType: Macromolecule}
 //output: column res
@@ -329,6 +272,9 @@ export async function getHelmHelper(): Promise<IHelmHelper> {
 
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {CellRendererBackAsyncBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
+import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
+import {getRS} from './utils/dummy-monomer';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 //name: measureCellRenderer
 export async function measureCellRenderer(): Promise<void> {