@datagrok/helm 2.3.3 → 2.4.1

package/src/package-utils.ts

@@ -5,6 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {Unsubscribable} from 'rxjs';
 
 import {delay, timeout} from '@datagrok-libraries/utils/src/test';
+import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {
   DojoType, DojoxType, HweWindow, IOrgHelmWebEditor, Monomers
@@ -13,7 +14,6 @@ import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service'
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
 import {HelmHelper} from './helm-helper';
 import {HelmService} from './utils/helm-service';
@@ -30,8 +30,8 @@ declare const org: OrgHelmModule;
 type DojoConfigWindowType = {
   dojoConfig: {
     packages?: (string | { name: string, location: string })[],
-    deps?: string[], callback: Function, has?: any, parseOnLoad?: boolean, async?: boolean | string
-  };
+    deps?: string[], callback: Function, has?: any, parseOnLoad?: boolean, async?: boolean | string, locale?: string,
+  },
 };
 type HelmWindowType = {
   $helmService?: HelmServiceBase,
@@ -51,100 +51,85 @@ export async function initHelmLoadAndPatchDojo(): Promise<void> {
   /** get the text width in pixels */
   const pi = DG.TaskBarProgressIndicator.create('Loading Helm Web Editor ...');
   try {
-    await delay(2000);
     const requireBackup = window.require;
 
-    await timeout(async () => {
-
-      await new Promise<void>((resolve, reject) => {
-        window.dojoConfig = {
-          deps: [
-            // 'dojo/dom', 'dojo/window', 'dojo/io/script', 'dojo/io/iframe',
-            // 'dojox/storage/LocalStorageProvider',
-            // 'dijit/layout/ContentPane',
-          ],
-          // packages: [
-          //   'dojo.ready', 'dojo.window', 'dojo.io.script', 'dojo.io.iframe', 'dojo.dom',
-          //   'dojox.gfx', 'dojox.gfx.shape',
-          // ],
-          callback: () => { resolve(); },
-          // has: {
-          //   "dojo-firebug": true,
-          //   "dojo-debug-messages": true,
-          // },
-          parseOnLoad: true,
-          async: false
-        };
-        // Load dojo without package/sources section for the settings dojoConfig to take effect+
-        DG.Utils.loadJsCss([
-          // 'https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js.uncompressed.js',
-          `${_package.webRoot}/vendor/dojo-1.10.10/dojo/dojo.js.uncompressed.js`,
-        ]).then(() => {});
-      });
-
-      const dojoRequire = window.require;
-      const cmp = dojoRequire == requireBackup;
-      try {
+    // dojo.window','dojo.io.script','dojo.io.iframe','dojo.dom','dojox.gfx','dojox.gfx.svg','dojox.gfx.shape','dojox.charting'
+    const dojoTargetList: { name: string, checker: () => boolean }[] = [
+      {name: 'dojo.window', checker: () => !!dojo?.window},
+      {name: 'dojo.ready', checker: () => !!dojo?.ready},
+      {name: 'dojo.io.script', checker: () => !!dojo?.io?.script},
+      {name: 'dojo.io.iframe', checker: () => !!dojo?.io?.iframe},
+      // {name: 'dojo.dom', checker: () => !!dojo?.dom},
+      {name: 'dojox.gfx', checker: () => !!dojox?.gfx},
+      {name: 'dojox.gfx.svg', checker: () => !!dojox?.gfx?.svg},
+      {name: 'dojox.gfx.createSurface', checker: () => !!dojox?.gfx?.createSurface},
+      {name: 'dojox.gfx.shape', checker: () => !!dojox?.gfx?.shape},
+      {name: 'dojox.storage.Provider', checker: () => !!dojox?.storage?.Provider},
+      {name: 'dojox.storage.LocalStorageProvider', checker: () => !!dojox?.storage?.LocalStorageProvider},
+      // {name: 'dojox.charting', checker: () => !!dojox.charting},
+      // {name: 'dojox.charting.themes.Claro', checker: () => !!dojox.charting?.themes?.Claro},
+      // {name: 'dojox.charting.themes.Wetland', checker: () => !!dojox.charting?.themes?.Wetland},
+      // {name: 'dojox.charting.plot2d.Base', checker: () => !!dojox.charting?.plot2d?.Base},
+      // {name: 'dojox.charting.Series', checker: () => !!dojox?.charting?.Series},
+      // {name: 'dojox.charting.Chart2D', checker: () => !!dojox?.charting?.Chart2D},
+    ];
+    /** Gets list ofd modules not ready yet */
+    const getDojoNotReadyList = (): string[] => {
+      return dojoTargetList.filter((dt) => !dt.checker()).map((dt) => dt.name);
+    };
+
+    try {
+      await timeout(async () => {
+
         await new Promise<void>((resolve, reject) => {
-          dojoRequire(['dojo/window', 'dojo/dom', 'dojo/io/script', 'dojo/io/iframe',
-              'dojox/gfx', 'dojox/gfx/svg', 'dojox/gfx/shape',
-              'dijit/_base', 'dijit/Tooltip', 'dijit/form/_FormValueWidget',
-              'dijit/form/DropDownButton', 'dijit/layout/AccordionContainer', 'dijit/form/ComboButton',
-              'dijit/layout/StackController', 'dijit/layout/StackContainer',
-            ],
-            (...args: any[]) => {
-              resolve();
-            });
+          window.dojoConfig = {
+            callback: () => { resolve(); },
+            parseOnLoad: true,
+            async: false,
+            locale: 'en-us', // to limit dijit/nls file set
+          };
+          // Load dojo without package/sources section for the settings dojoConfig to take effect
+          DG.Utils.loadJsCss([
+            // 'https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js.uncompressed.js',
+            `${_package.webRoot}/vendor/dojo-1.10.10/dojo/dojo.js.uncompressed.js`,
+          ]).then(() => {});
         });
-      } finally {
-        window.require = function(...args: any[]) {
-          _package.logger.debug(`${logPrefix}, window.require( ${JSON.stringify(args)} )`);
-          dojoRequire(...args);
-        };
-      }
 
-      //await delay(50);
-
-      // dojo.window','dojo.io.script','dojo.io.iframe','dojo.dom','dojox.gfx','dojox.gfx.svg','dojox.gfx.shape','dojox.charting'
-      const dojoTargetList: { name: string, module: string | null, checker: () => boolean }[] = [
-        {name: 'dojo.window', module: null, checker: () => !!dojo?.window},
-        {name: 'dojo.ready', module: null, checker: () => !!dojo?.ready},
-        {name: 'dojo.io.script', module: null, checker: () => !!dojo?.io?.script},
-        {name: 'dojo.io.iframe', module: null, checker: () => !!dojo?.io?.iframe},
-        // //{name: 'dojo.request.script', module: 'dojo.request.script', checker: () => !!dojo?.request?.iframe},
-        // {name: 'dojo.dom', module: 'dojo.dom', checker: () => !!dojo?.dom},
-        // {name: 'dojox.gfx', module: 'dojox.gfx', checker: () => !!dojox?.gfx},
-        // {name: 'dojox.gfx.svg', module: 'dojox.gfx.svg', checker: () => !!dojox?.gfx?.svg},
-        {name: 'dojox.gfx.createSurface', module: null, checker: () => !!dojox?.gfx?.createSurface},
-        // {name: 'dojox.gfx.shape', module: 'dojox.gfx.shape', checker: () => !!dojox?.gfx?.shape},
-        // {name: 'dojox.charting.themes.Claro', module: 'dojox.charting.themes.Claro', checker: () => !!dojox.charting?.themes?.Claro},
-        // {name: 'dojox.charting.themes.Wetland', module: 'dojox.charting.themes.Wetland', checker: () => !!dojox.charting?.themes?.Wetland},
-        // {name: 'dojox.charting.plot2d.Base', module: 'dojox.charting.plot2d.Base', checker: () => !!dojox.charting?.plot2d?.Base},
-        // {name: 'dojox.charting.Series', module: 'dojox.charting.Series', checker: () => !!dojox?.charting?.Series},
-        // {name: 'dojox.charting.Chart2D', module: 'dojox.charting.Chart2D', checker: () => !!dojox?.charting?.Chart2D},
-        // //{module: 'dojox.charting', checker: () => !!dojox.charting},
-        // // {module: 'dojox.storage.Provider', checker: () => !!dojox?.storage?.Provider},
-        // // {module: 'dojox.storage.LocalStorageProvider', checker: () => !!dojox?.storage?.LocalStorageProvider},
-      ];
-      for (const dojoTarget of dojoTargetList) {
-        try { if (dojoTarget.module) dojo.require(dojoTarget.module); } catch (err: any) {
-          _package.logger.error(err.message);
+        const dojoRequire = window.require;
+        const cmp = dojoRequire == requireBackup;
+        try {
+          await new Promise<void>((resolve, reject) => {
+            dojoRequire(['dojo/window', 'dojo/dom', 'dojo/io/script', 'dojo/io/iframe',
+                'dojox/gfx', 'dojox/gfx/svg', 'dojox/gfx/shape',
+                'dojox/storage/Provider', 'dojox/storage/LocalStorageProvider',
+                'dijit/_base', 'dijit/Tooltip', 'dijit/form/_FormValueWidget',
+                'dijit/form/DropDownButton', 'dijit/layout/AccordionContainer', 'dijit/form/ComboButton',
+                'dijit/layout/StackController', 'dijit/layout/StackContainer',
+              ],
+              (...args: any[]) => { resolve(); });
+          });
+        } finally {
+          // TODO: Check interference with NGL
+          window.require = function(...args: any[]) {
+            _package.logger.debug(`${logPrefix}, window.require( ${JSON.stringify(args)} )`);
+            dojoRequire(...args);
+          };
         }
-      }
-      /** Gets list ofd modules not ready yet */
-      const getDojoNotReadyList = (): string[] => {
-        return dojoTargetList.filter((dt) => !dt.checker()).map((dt) => dt.name);
-      };
-      /** List of dojo modules not ready yet */ let dojoNotReadyList: string[];
-      while ((dojoNotReadyList = getDojoNotReadyList()).length > 0) {
-        const dojoProgress = dojoTargetList.length - dojoNotReadyList.length;
-        pi.update(Math.round(100 * dojoProgress / dojoTargetList.length),
-          `Loading Helm Web Editor ${dojoProgress}/${dojoTargetList.length}`);
-        _package.logger.debug(`${logPrefix}, dojo loading ... ${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
-        await delay(100);
-      }
-      _package.logger.debug(`${logPrefix}, dojo ready all modules`);
-    }, 60000, 'timeout dojox.gfx.svg');
+
+        /** List of dojo modules not ready yet */ let dojoNotReadyList: string[];
+        while ((dojoNotReadyList = getDojoNotReadyList()).length > 0) {
+          const dojoProgress = dojoTargetList.length - dojoNotReadyList.length;
+          pi.update(Math.round(100 * dojoProgress / dojoTargetList.length),
+            `Loading Helm Web Editor ${dojoProgress}/${dojoTargetList.length}`);
+          _package.logger.debug(`${logPrefix}, dojo loading ... ${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
+          await delay(100);
+        }
+        _package.logger.debug(`${logPrefix}, dojo ready all modules`);
+      }, 60000, 'timeout dojox.gfx.svg');
+    } catch (err: any) {
+      const dojoNotReadyList = getDojoNotReadyList();
+      _package.logger.error(`${logPrefix}, dojo not ready ${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
+    }
 
     _package.logger.debug(`${logPrefix}, patch window.dojox.gfx.svg.Text.prototype.getTextWidth`);
     // @ts-ignore
@@ -192,9 +177,9 @@ export const helmJsonReplacer = (key: string, value: any): any => {
 };
 
 export class HelmPackage extends DG.Package {
-  public alertOriginal: (s: string) => void;
+  public alertOriginal: ((s: string) => void) | null = null;
   public readonly helmHelper: HelmHelper;
-  public libHelper: IMonomerLibHelper;
+  public libHelper!: IMonomerLibHelper;
 
   constructor(opts: { debug: boolean } = {debug: false}) {
     super();
@@ -204,13 +189,9 @@ export class HelmPackage extends DG.Package {
     this.helmHelper = new HelmHelper(this.logger);
   }
 
-  setLibHelper(libHelper: IMonomerLibHelper) {
-    this.libHelper = libHelper;
-  }
-
   // -- Init --
   /** Loads Dojo and HelmWebEditor, waits for init, patches */
-  async initHelm(): Promise<void> {
+  async initHELMWebEditor(): Promise<void> {
     const logPrefix: string = 'Helm: Package.initDojo()';
 
     _package.logger.debug(`${logPrefix}, dependence loading …`);
@@ -235,12 +216,6 @@ export class HelmPackage extends DG.Package {
     _package.logger.debug(`${logPrefix}, dependence loaded, ET: ${(t2 - t1)} ms`);
   }
 
-  async getMonomerLib(): Promise<IMonomerLib> {
-    const libHelper = await getMonomerLibHelper();
-    _package.setLibHelper(libHelper);
-    return libHelper.getBioLib();
-  }
-
   public initHelmPatchScilAlert(): void {
     const logPrefix: string = 'Helm: initHelmPatchScilAlert()';
     this.alertOriginal = scil.Utils.alert;
@@ -256,7 +231,7 @@ export class HelmPackage extends DG.Package {
 
     this.logger.debug(`${logPrefix}, this.getMonomerOriginal stored`);
 
-    this.helmHelper.overrideGetMonomer(this.helmHelper.buildGetMonomerFromLib(this.monomerLib));
+    this.helmHelper.overrideMonomersFuncs(this.helmHelper.buildMonomersFuncsFromLib(this.monomerLib));
 
     // @ts-ignore, intercept with proxy to observe access and usage
     org.helm.webeditor.Monomers = new class {
@@ -300,21 +275,21 @@ export class HelmPackage extends DG.Package {
 
   // -- MonomerLib --
 
-  private _monomerLib: IMonomerLib;
   public get monomerLib(): IMonomerLib {
-    if (!this._monomerLib)
-      throw new Error(`Helm: _package._monomerLib is not initialized yet`);
-    return this._monomerLib;
+    if (!this.libHelper)
+      throw new Error(`Helm: _package.libHelper is not initialized yet`);
+    return this.libHelper.getMonomerLib();
   }
 
-  private _monomerLibSub: Unsubscribable;
+  private _monomerLibSub?: Unsubscribable;
+
+  /** Requires both Bio & HELMWebEditor initialized */
+  initMonomerLib(libHelper: IMonomerLibHelper): void {
+    this.libHelper = libHelper;
 
-  initMonomerLib(lib: IMonomerLib) {
-    if (!!this._monomerLib)
-      throw new Error(`Helm: _package._monomerLib is initialized already`);
-    this._monomerLib = lib;
-    rewriteLibraries(this._monomerLib); // initHelm()
-    this._monomerLibSub = this._monomerLib.onChanged
+    const lib = this.monomerLib;
+    rewriteLibraries(lib); // initHelm()
+    this._monomerLibSub = lib.onChanged
       .subscribe(this.monomerLibOnChangedHandler.bind(this));
 
     this.initHelmPatchPistoia();
@@ -337,7 +312,7 @@ export class HelmPackage extends DG.Package {
       grok.shell.info(libMsg);
 
       _package.logger.debug(`${logPrefix}, org,helm.webeditor.Monomers updating ...`);
-      rewriteLibraries(this._monomerLib); // initHelm() monomerLib.onChanged()
+      rewriteLibraries(this.monomerLib); // initHelm() monomerLib.onChanged()
       _package.logger.debug(`${logPrefix}, end, org.helm.webeditor.Monomers completed`);
     } catch (err: any) {
       const errMsg = errorToConsole(err);

package/src/package.ts

@@ -4,6 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
+import {Unsubscribable} from 'rxjs';
 
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
@@ -11,8 +12,8 @@ import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
-import {App, HelmMol, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
-import {IHelmHelper, IInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {App, Editor, HelmMol, HelmType, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmInputBase, IHelmHelper, IHelmInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
@@ -25,12 +26,9 @@ import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
 import {getRS} from './utils/get-monomer-dummy';
 
 // Do not import anything than types from @datagrok/helm-web-editor/src/types
-import {buildWebEditorApp} from './helm-web-editor';
-import {JSDraw2HelmModule, OrgHelmModule, ScilModule} from './types';
+import type {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
 
-export const _package = new HelmPackage({debug: true}/**/);
-
-let monomerLib: IMonomerLib | null = null;
+export const _package = new HelmPackage({debug: true});
 
 /*
   Loading modules:
@@ -42,7 +40,7 @@ let monomerLib: IMonomerLib | null = null;
 
 declare const window: Window & HweWindow;
 declare const scil: ScilModule;
-declare const JSDraw2: JSDraw2HelmModule;
+declare const JSDraw2: JSDraw2Module;
 declare const org: OrgHelmModule;
 
 //tags: init
@@ -51,13 +49,13 @@ export async function initHelm(): Promise<void> {
   _package.logger.debug(`${logPrefix}, start`);
 
   try {
-    const [_, lib]: [void, IMonomerLib] = await Promise.all([
-      _package.initHelm(),
-      _package.getMonomerLib(),
+    const [_, libHelper] = await Promise.all([
+      _package.initHELMWebEditor(),
+      getMonomerLibHelper(),
     ]);
 
-    _package.logger.debug(`${logPrefix}, then(), lib loaded`);
-    _package.initMonomerLib(lib);
+    _package.logger.debug(`${logPrefix}, lib loaded`);
+    _package.initMonomerLib(libHelper);
   } catch (err: any) {
     const [errMsg, errStack] = errInfo(err);
     // const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Exception \'undefined\'';
@@ -132,14 +130,7 @@ function openWebEditor(cell: DG.Cell, value?: string, units?: string) {
   const col = cell.column as DG.Column<string>;
   const sh = SeqHandler.forColumn(col);
   const rowIdx = cell.rowIndex;
-  let app: App;
-  setTimeout(async () => {
-    app = await buildWebEditorApp(view);
-    if (!!cell && units === undefined)
-      app.canvas!.helm!.setSequence(cell.value, 'HELM');
-    else
-      app.canvas!.helm!.setSequence(value!, 'HELM');
-  }, 20);
+  const app: App = _package.helmHelper.createWebEditorApp(view, !!cell && units === undefined ? cell.value : value!);
   const dlg = ui.dialog({showHeader: false, showFooter: true});
   dlg.add(view)
     .onOK(() => {
@@ -191,7 +182,7 @@ export function getMolfiles(col: DG.Column): DG.Column {
 //input: string name =undefined {optional: true}
 //input: object options =undefined {optional: true}
 //output: object result
-export function helmInput(name: string, options: IInputInitOptions<HelmMol>): DG.InputBase<HelmMol> {
+export function helmInput(name: string, options: IHelmInputInitOptions): HelmInputBase {
   // TODO: Annotate for semType = 'Macromolecule' AND units = 'helm'
   return _package.helmHelper.createHelmInput(name, options);
 }

package/src/tests/findMonomers-tests.ts

@@ -26,12 +26,12 @@ category('findMonomers', () => {
 
     // Tests 'findMonomers' requires default monomer library loaded
     await setUserLibSettingsForTests();
-    await monomerLibHelper.loadLibraries(true); // load default libraries for tests
+    await monomerLibHelper.loadMonomerLib(true); // load default libraries for tests
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   const tests: { [testName: string]: { test: string, tgt: Set<string> } } = {
@@ -53,7 +53,7 @@ category('findMonomers', () => {
   }
 
   function _testFindMonomers(testHelmValue: string, tgtMissedSet: Set<string>): void {
-    const monomerLib = monomerLibHelper.getBioLib();
+    const monomerLib = monomerLibHelper.getMonomerLib();
     const monomerSymbolList: string[] = parseHelm(testHelmValue);
     const resMissedSet: Set<string> = findMonomers(monomerSymbolList, monomerLib);
     expectObject(resMissedSet, tgtMissedSet);

package/src/tests/get-molfiles-tests.ts

@@ -25,12 +25,12 @@ category('getMolfiles', () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
     await setUserLibSettingsForTests();
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   const csv = `Helm, atoms, bonds

package/src/tests/get-monomer-tests.ts

@@ -20,13 +20,17 @@ import {
 import {defaultMonomerLibSummary, expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
 
 import {getMonomerHandleArgs, rewriteLibraries} from '../utils/get-monomer';
-import {JSDraw2HelmModule, OrgHelmModule} from '../types';
+import {JSDraw2Module, OrgHelmModule} from '../types';
+
+import {HelmHelper} from '../helm-helper';
+import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
+import {getRS} from '../utils/get-monomer-dummy';
 import {initHelmMainPackage} from './utils';
 
 import {_package} from '../package-test';
 
 declare const org: OrgHelmModule;
-declare const JSDraw2: JSDraw2HelmModule;
+declare const JSDraw2: JSDraw2Module;
 
 type TestDataType = { args: { a: any, name?: string }, tgt: any };
 
@@ -89,34 +93,33 @@ category('getMonomer', ()=>{
       'set user lib settings for tests');
     await timeout(async ()=> { await monomerLibHelper.awaitLoaded(); }, 5000,
       'await monomerLib to be loaded');
-    await timeout(async () => { await monomerLibHelper.loadLibraries(true); }, 5000,
+    await timeout(async () => { await monomerLibHelper.loadMonomerLib(true); }, 5000,
       'reload monomerLib with settings for tests'); // load default libraries for tests
   });
 
   after(async ()=>{
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   test('original', async () =>{
-    const monomerLib = libHelper.getBioLib();
+    const monomerLib = libHelper.getMonomerLib();
     rewriteLibraries(monomerLib);
 
-    // const overriddenGetMonomer = helmHelper.revertOriginalGetMonomer();
+    // const overriddenMonomersFuncs = helmHelper.revertOriginalMonomersFuncs();
     // try {
-    const helmHelper: IHelmHelper = await getHelmHelper();
-    expect(helmHelper != null, true);
-    // @ts-ignore
-    const getMonomerFunc = helmHelper.originalGetMonomer!;
+      const helmHelper: IHelmHelper = await getHelmHelper();
+      expect(helmHelper != null, true);
+      const getMonomerFunc: GetMonomerFunc = helmHelper.originalMonomersFuncs!.getMonomer!;
 
-    return _testAll('original', getMonomerFunc);
+      return _testAll('original', getMonomerFunc);
     // } finally {
-    //   helmHelper.overrideGetMonomer(overriddenGetMonomer);
+    //   helmHelper.overrideMonomersFuncs(overriddenMonomersFuncs);
     // }
   }, {isAggregated: true});
 
   test('monomerLib', async () =>{
-    const monomerLib = monomerLibHelper.getBioLib();
+    const monomerLib = monomerLibHelper.getMonomerLib();
     expectMonomerLib(monomerLib);
 
     const getMonomerFunc = org.helm.webeditor.Monomers.getMonomer;
@@ -148,7 +151,7 @@ category('getMonomer', ()=>{
     resDf.set('res', resI, '');
     resDf.set('tgt', resI, '');
     try {
-      const monomerLib = monomerLibHelper.getBioLib();
+      const monomerLib = monomerLibHelper.getMonomerLib();
       expectMonomerLib(monomerLib);
       resDf.set('success', resI, true);
     } catch (err) {
@@ -185,13 +188,13 @@ category('getMonomer', ()=>{
     /* Tests getMonomer function adding missing monomers. */
     const helmStr = 'PEPTIDE1{[mis1].R.[mis2].T.C.F}$$$$;';
 
-    expectMonomerLib(monomerLibHelper.getBioLib());
+    expectMonomerLib(monomerLibHelper.getMonomerLib());
     const editor = new JSDraw2.Editor(ui.div(), {viewonly: true});
     editor.setHelm(helmStr);
     const withMissing = JSON.parse(JSON.stringify(
       defaultMonomerLibSummary)) as MonomerLibSummaryType;
     withMissing['PEPTIDE'] += 2;
-    expectMonomerLib(monomerLibHelper.getBioLib(), withMissing);
+    expectMonomerLib(monomerLibHelper.getMonomerLib(), withMissing);
   });
 });
 

package/src/tests/helm-input-tests.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 
-import {after, before, category, delay, expect, test, timeout} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, testEvent} from '@datagrok-libraries/utils/src/test';
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
@@ -30,12 +30,12 @@ category('HelmInput', () => {
     // Test 'helm' requires default monomer library loaded
     await setUserLibSettingsForTests();
     await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadLibraries(true); // load default libraries
+    await monomerLibHelper.loadMonomerLib(true); // load default libraries
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
   });
 
   test('inDialog', async () => {
@@ -47,7 +47,7 @@ category('HelmInput', () => {
       .show();
     await delay(500);
 
-    const mol = helmInput.value;
+    const mol = helmInput.molValue;
     expect(mol.atoms.length, 4);
     expect(mol.bonds.length, 3);
   });
@@ -61,26 +61,37 @@ async function _testTooltipOnHelmInput(): Promise<void> {
   const helmValue = 'PEPTIDE1{[meY].A.G.T}$$$$';
   const helmInput = (await ui.input.helmAsync('Macromolecule')) as HelmInput;
   helmInput.stringValue = helmValue;
+  // Show dialog to the right of the TestManager test tree
+  // to prevent interfering mousemove position for tooltip.
+  const tmBcr = grok.shell.v ? grok.shell.v.root.getBoundingClientRect() : null;
   const dlg = ui.dialog('Helm Input Test')
     .add(helmInput)
-    .show();
-  const dialogInputEl = $(dlg.root)
-    .find('div.d4-dialog-contents > div.ui-input-helm > div.ui-input-editor').get(0);
-  expect(helmInput.getInput(), dialogInputEl);
+    .show({...(tmBcr ? {x: tmBcr.right + 20, y: tmBcr.top + 20} : {})});
+  try {
+    const dialogInputEl = $(dlg.root)
+      .find('div.d4-dialog-contents > div.ui-input-helm > div.ui-input-editor').get(0);
+    expect(helmInput.getInput(), dialogInputEl);
 
-  const mon = {i: 0, elem: 'meY'};
-  const a = helmInput.value.atoms[mon.i];
-  const iEl = helmInput.getInput();
-  const iBcr = iEl.getBoundingClientRect();
-  const ev = new MouseEvent('mousemove', {
-    cancelable: true, bubbles: true, view: window, button: 0,
-    clientX: iBcr.left + a.p.x, clientY: iBcr.top + a.p.y
-  });
-  iEl.dispatchEvent(ev);
-  await delay(200);
-
-  const tooltipEl = $(document).find('body > div.d4-tooltip').get(0) as HTMLElement;
-  const elemDiv = $(tooltipEl).find('div > div.d4-flex-row.ui-div > div:nth-child(1)').get(0);
-  expect(tooltipEl.style.display != 'none', true);
-  expect(elemDiv?.innerText, mon.elem);
+    const mon = {i: 0, elem: 'meY'};
+    const a = helmInput.molValue.atoms[mon.i];
+    const iEl = helmInput.getInput();
+    const iBcr = iEl.getBoundingClientRect();
+    const ev = new MouseEvent('mousemove', {
+      cancelable: true, bubbles: true, view: window, button: 0,
+      clientX: iBcr.left + a.p.x, clientY: iBcr.top + a.p.y
+    });
+    await testEvent(ui.tooltip.onTooltipShown, () => { /* tooltip shown*/ },
+      () => {
+        iEl.dispatchEvent(ev);
+        // do not await after event dispatch before test tooltip content
+        // await leads to tooltip changed (with TestManager tree node tooltip)
+      }, 100, 'timeout await ui.tooltip.onTooltipShown');
+    const tooltipEl = $(document).find('body > div.d4-tooltip').get(0) as HTMLElement;
+    const elemDiv = $(tooltipEl).find('div > div.d4-flex-row.ui-div > div:nth-child(1)').get(0);
+    expect(tooltipEl.style.display != 'none', true);
+    expect(elemDiv?.innerText, mon.elem);
+  } finally {
+    await delay(50);
+    ui.tooltip.hide();
+  }
 }

package/src/tests/helm-service-tests.ts

@@ -41,8 +41,8 @@ category('HelmService', () => {
       await delay(1000); // for loading monomer libraries files
       // Test 'helm' requires default monomer library loaded
       await setUserLibSettingsForTests();
-      await monomerLibHelper.loadLibraries(true); // load default libraries
-      const libSummary = monomerLibHelper.getBioLib().getSummary();
+      await monomerLibHelper.loadMonomerLib(true); // load default libraries
+      const libSummary = monomerLibHelper.getMonomerLib().getSummaryObj();
 
       helmSvc = await getHelmService();
       await helmSvc.reset();
@@ -60,7 +60,7 @@ category('HelmService', () => {
     await helmSvc.reset();
 
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
     _package.logger.debug(`${logPrefix}, end`);
   });
 

package/src/tests/helm-tests.ts

@@ -4,7 +4,6 @@ import * as DG from 'datagrok-api/dg';
 
 import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
 
-//import {findMonomers, helmToFasta, helmToPeptide, helmToRNA, initHelm} from '../package';
 import {parseHelm} from '../utils';
 import {initHelmMainPackage} from './utils';
 
@@ -74,7 +73,7 @@ category('Helm', () => {
   ];
 
   const complexTestNames = [
-    'comples-monomer', 'complex-monomer+side-chain', 'complex-monomer+side-chain-RNA',
+    'complex-monomer', 'complex-monomer+side-chain', 'complex-monomer+side-chain-RNA',
     'complex-side-chain', 'complex+side-chain+linker'
   ];