@datagrok/helm 2.5.0 → 2.5.3

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

@@ -0,0 +1,85 @@
+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, expectArray, test, testEvent} from '@datagrok-libraries/utils/src/test';
+import {HelmNotSupportedError, HelmNotSupportedErrorType, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+
+import {_package} from '../package-test';
+
+type TestSrcType = { helm: string };
+type TestTgtType = { helm: string | null, map: [number, number][] };
+
+category('HelmHelper: removeGaps', () => {
+  let helmHelper: IHelmHelper;
+
+  before(async () => {
+    helmHelper = await getHelmHelper();
+  });
+
+  const tests: { [testName: string]: { src: TestSrcType, tgt: TestTgtType } } = {
+    'single-linear-start': {
+      src: {helm: 'PEPTIDE1{*.[meY].A.G.T}$$$$V2.0'},
+      tgt: {
+        helm: 'PEPTIDE1{[meY].A.G.T}$$$$V2.0',
+        map: [[1, 0], [2, 1], [3, 2], [4, 3]],
+      }
+    },
+    'single-linear-end': {
+      src: {helm: 'PEPTIDE1{[meY].A.G.T.*}$$$$V2.0'},
+      tgt: {
+        helm: 'PEPTIDE1{[meY].A.G.T}$$$$V2.0',
+        map: [[0, 0], [1, 1], [2, 2], [3, 3]],
+      }
+    },
+    'single-linear-middle': {
+      src: {helm: 'PEPTIDE1{[meY].A.*.G.T}$$$$V2.0'},
+      tgt: {
+        helm: 'PEPTIDE1{[meY].A.G.T}$$$$V2.0',
+        map: [[0, 0], [1, 1], [3, 2], [4, 3]],
+      }
+    },
+    'single-cycle-start': {
+      src: {helm: 'PEPTIDE1{*.[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,3:R3-7:R3$$$V2.0'},
+      tgt: {
+        helm: 'PEPTIDE1{[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0',
+        map: [[1, 0], [2, 1], [3, 2], [4, 3], [5, 4], [6, 5], [7, 6]],
+      }
+    },
+    'single-cycle-end': {
+      src: {helm: 'PEPTIDE1{[meY].C.R.N.P.C.T.*}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0'},
+      tgt: {
+        helm: 'PEPTIDE1{[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0',
+        map: [[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5], [6, 6]],
+      }
+    },
+    'single-cycle-middle': {
+      src: {helm: 'PEPTIDE1{[meY].C.R.N.*.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0'},
+      tgt: {
+        helm: 'PEPTIDE1{[meY].C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-6:R3$$$V2.0',
+        map: [[0, 0], [1, 1], [2, 2], [3, 3], [5, 4], [6, 5], [7, 6]],
+      }
+    },
+    'single-cycle-gap-at-connection': {
+      src: {helm: 'PEPTIDE1{[meY].*.C.R.N.P.C.T}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$V2.0'},
+      tgt: {helm: null, map: []}
+    }
+  };
+
+  for (const [testName, testData] of Object.entries(tests)) {
+    test(`${testName}`, async () => {
+      let resErr: HelmNotSupportedError | null = null;
+      try {
+        const res = helmHelper.removeGaps(testData.src.helm);
+        expect(res.resHelm, testData.tgt.helm);
+        expectArray(Array.from(res.monomerMap!.entries()), testData.tgt.map);
+      } catch (err: any) {
+        resErr = err;
+      }
+
+      expect(resErr?.type == HelmNotSupportedErrorType, testData.tgt.helm === null,
+        'HelmNotSupportedError thrown expected');
+    });
+  }
+});

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

@@ -8,7 +8,7 @@ import {after, before, category, delay, expect, test, testEvent} from '@datagrok
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
@@ -28,9 +28,7 @@ category('HelmInput', () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

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

@@ -16,7 +16,7 @@ import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {initHelmMainPackage} from './utils';
@@ -38,11 +38,7 @@ category('HelmService', () => {
       monomerLibHelper = await getMonomerLibHelper();
       userLibSettings = await getUserLibSettings();
 
-      await delay(1000); // for loading monomer libraries files
-      // Test 'helm' requires default monomer library loaded
-      await setUserLibSettingsForTests();
-      await monomerLibHelper.loadMonomerLib(true); // load default libraries
-      const libSummary = monomerLibHelper.getMonomerLib().getSummaryObj();
+      await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
 
       helmSvc = await getHelmService();
       await helmSvc.reset();

package/src/tests/helm-web-editor-tests.ts

@@ -7,7 +7,7 @@ import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {initHelmMainPackage} from './utils';
@@ -22,9 +22,8 @@ category('helm-web-editor', async () => {
     await initHelmMainPackage();
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true);
+
+    await monomerLibHelper.loadMonomerLibForTests();
 
     hh = await getHelmHelper();
   });

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

@@ -8,7 +8,7 @@ import {HelmType, IHelmDrawOptions, Mol, OrgType} from '@datagrok-libraries/bio/
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {JSDraw2Module} from '../types';
@@ -28,7 +28,7 @@ category('parseHelm', () => {
         helm: 'PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0'
       }
     },
-    'PT-cycic': {
+    'PT-cyclic': {
       src: 'PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0',
       tgt: {
         atomCount: 8, bondCount: 8,
@@ -54,10 +54,7 @@ category('parseHelm', () => {
       'get user lib settings for backup');
 
     // parseHelm is dependent on monomers RGroups available, test requires default monomer library
-    await setUserLibSettingsForTests();
-    await timeout(async () => { await libHelper.awaitLoaded(); }, 5000,
-      'await monomerLib to be loaded');
-    await libHelper.loadMonomerLib(true);
+    await libHelper.loadMonomerLibForTests();
   });
 
   after(async () => {
@@ -74,7 +71,7 @@ category('parseHelm', () => {
   for (const [testName, {src, tgt}] of Object.entries(testData)) {
     test(`woDOM-${testName}`, async () => {
       _testParseHelmWithoutDOM(src, tgt);
-    });
+    }, testName == 'RNA' ? {skipReason: 'GROK-16721'} : undefined);
   }
 });
 
@@ -103,7 +100,6 @@ function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
   io.parseHelm(plugin, src, origin, undefined);
 
   const m: Mol<HelmType> = plugin.jsd.m;
-  debugger;
   const resHelm = io.getHelm(m);
   expect(m.atoms.length, tgt.atomCount);
   expect(m.bonds.length, tgt.bondCount);

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

@@ -6,7 +6,7 @@ import {after, before, category, expect, expectObject, test, timeout} from '@dat
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {generateLongSequence} from '@datagrok-libraries/bio/src/utils/generator';
@@ -82,10 +82,7 @@ category('properties-widget', () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = getUserLibSettings();
 
-    await setUserLibSettingsForTests();
-    await timeout(async () => { await monomerLibHelper.awaitLoaded(); },
-      5000, 'MonomerLibHelper.awaitLoaded() timeout');
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/tests/renderers-tests.ts

@@ -12,7 +12,7 @@ import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {awaitGrid, initHelmMainPackage} from './utils';
@@ -32,8 +32,7 @@ category('renderers', () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/utils/get-hovered.ts

@@ -6,6 +6,9 @@ import {HelmType, PolymerType, Atom, Mol, ISeqMonomer, HelmMol, HelmAtom} from '
 
 import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
 
+import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
+import {GAP_SYMBOL, GapOriginals, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+
 import {HelmMonomerPlacer} from '../helm-monomer-placer';
 
 export function getHoveredMonomerFromEditorMol(
@@ -77,23 +80,33 @@ export function getHoveredMonomerFallback(
   }
   left = (argsX >= sumLengths[left]) ? left : left - 1; // correct left to between sumLengths
   if (left >= 0)
-    hoveredSeqMonomer = getSeqMonomerFromHelm(allParts[0], allParts[left]);
+    hoveredSeqMonomer = getSeqMonomerFromHelm(left, allParts[left], allParts[0]);
   return hoveredSeqMonomer;
 }
 
 export function getSeqMonomerFromHelmAtom(atom: HelmAtom): ISeqMonomer {
   const polymerType = helmTypeToPolymerType(atom.bio!.type);
-  return {symbol: atom.elem, polymerType: polymerType};
+  const canonicalSymbol = atom.elem === GapOriginals[NOTATION.HELM] ? GAP_SYMBOL : atom.elem;
+  return {position: parseInt(atom.bio!.continuousId as string) - 1, symbol: atom.elem, biotype: atom.bio!.type};
 }
 
-function getSeqMonomerFromHelm(
-  helmPrefix: string, symbol: string
-): ISeqMonomer {
+/** Linear
+ * @deprecated
+ */
+function getSeqMonomerFromHelm(pos: number, symbol: string, helmPrefix: string): ISeqMonomer {
   let resSeqMonomer: ISeqMonomer | undefined = undefined;
   const polymerTypeList: PolymerType[] = ['RNA', 'PEPTIDE', 'CHEM', 'BLOB', 'G'];
   for (const polymerType of polymerTypeList) {
-    if (helmPrefix.startsWith(polymerType))
-      resSeqMonomer = {symbol: symbol, polymerType: polymerType};
+    if (helmPrefix.startsWith(polymerType)) {
+      let helmType: HelmType = HelmTypes.AA;
+      if (polymerType == 'RNA')
+        helmType = HelmTypes.NUCLEOTIDE;
+      else if (polymerType == 'PEPTIDE')
+        helmType = HelmTypes.AA;
+      else if (polymerType == 'CHEM')
+        helmType = HelmTypes.CHEM;
+      resSeqMonomer = {position: pos, symbol: symbol, biotype: helmType};
+    }
   }
   if (!resSeqMonomer)
     throw new Error(`Monomer not found for symbol = '${symbol}' and helmPrefix = '${helmPrefix}'.`);

package/src/utils/get-monomer.ts

@@ -5,14 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {Atom, HelmType, IWebEditorMonomer, GetMonomerResType} from '@datagrok-libraries/bio/src/helm/types';
-import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
-import {
-  HELM_REQUIRED_FIELD as REQ
-} from '@datagrok-libraries/bio/src/utils/const';
-import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 
-import {AmbiguousWebEditorMonomer, GapWebEditorMonomer, getRS, MissingWebEditorMonomer} from './get-monomer-dummy';
-import {LibraryWebEditorMonomer} from './get-monomer-of-library';
 import {OrgHelmModule, ScilModule} from '../types';
 import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
 
@@ -21,10 +14,6 @@ import {_package} from '../package';
 declare const org: OrgHelmModule;
 declare const scil: ScilModule;
 
-const monomerRe = /[\w()]+/;
-//** Do not mess with monomer symbol with parenthesis enclosed in square brackets */
-const ambMonomerRe = RegExp(String.raw`\(${monomerRe}(,${monomerRe})+\)`);
-
 type GetMonomerOverridingFunc = (
   a: Atom<HelmType> | HelmType, name: string | undefined, monomerLib: IMonomerLib,
   originalGetMonomer: (a: Atom<HelmType> | HelmType, name: string) => GetMonomerResType) => GetMonomerResType;
@@ -52,69 +41,6 @@ export function getMonomerOverrideAndLogAlert(
   }
 }
 
-/** Inputs logic */
-export function getMonomerHandleArgs(
-  a: Atom<HelmType> | HelmType, name?: string
-): [/** biotype */ HelmType, /** elem */ string] {
-  if (!a)
-    throw new Error(`Argument 'a' of type Atom or HelmType is mandatory.`);
-  let biotype: HelmType;
-  let elem: string;
-  if ((a as Atom<HelmType>).T === 'ATOM') {
-    biotype = (a as Atom<HelmType>).biotype()!;
-    elem = (a as Atom<HelmType>).elem;
-  } else {
-    biotype = a as HelmType;
-    elem = org.helm.webeditor.IO.trimBracket(name!);
-  }
-  return [biotype, elem];
-}
-
-
-/** Substitutes {@link org.helm.webeditor.Monomers.getMonomer()} */
-export function getWebEditorMonomer(
-  monomerLib: IMonomerLib,
-  a: Atom<HelmType> | HelmType, argName?: string,
-): IWebEditorMonomer | null {
-  const [biotype, elem] = getMonomerHandleArgs(a, argName);
-  const pt = helmTypeToPolymerType(biotype);
-
-  /** Get or create {@link Monomer} object (in case it is missing in monomer library current config) */
-  let m: Monomer | null = monomerLib.getMonomer(pt, elem);
-  if (m && biotype == HelmTypes.LINKER && m[REQ.RGROUPS].length != 2) {
-    // Web Editor expects null
-    return null;
-  }
-  if (m && biotype == HelmTypes.SUGAR && m[REQ.RGROUPS].length != 3) {
-    // Web Editor expects null
-    return null;
-  }
-  if (!m /* && biotype != HelmTypes.LINKER*/)
-    m = monomerLib.addMissingMonomer(pt, elem);
-
-  /** Get or create {@link org,helm.WebEditorMonomer} */
-  let resWem: IWebEditorMonomer | null = m.wem ?? null;
-  if (!resWem) {
-    if (elem === '*')
-      resWem = m.wem = new GapWebEditorMonomer(biotype, elem);
-    else if (
-      (biotype === 'HELM_NUCLETIDE' && elem === 'N') ||
-      (biotype === 'HELM_AA' && elem === 'X') ||
-      (biotype === 'HELM_CHEM' && false) || // TODO: Ambiguous monomer for CHEM
-      ambMonomerRe.test(elem) // e.g. (A,R,_)
-    )
-      resWem = m.wem = new AmbiguousWebEditorMonomer(biotype, elem);
-    else if (!m.lib)
-      resWem = m.wem = new MissingWebEditorMonomer(biotype, elem);
-
-
-    if (!resWem)
-      resWem = m.wem = LibraryWebEditorMonomer.fromMonomer(biotype, m);
-  }
-
-  return resWem;
-}
-
 /** Fills org.helm.webeditor.Monomers dictionary for WebEditor */
 export function rewriteLibraries(monomerLib: IMonomerLib): void {
   org.helm.webeditor.Monomers.clear();
@@ -145,7 +71,7 @@ export function rewriteLibraries(monomerLib: IMonomerLib): void {
       } else if (monomer[SMILES] != null) {
         // @ts-ignore
         webEditorMonomer.rs = Object.keys(getRS(monomer[SMILES].toString())).length;
-        webEditorMonomer.at = getRS(monomer[SMILES].toString());
+        webEditorMonomer.at = monomerLib.getRS(monomer[SMILES].toString());
       } else
         isBroken = true;
 

package/src/utils/helm-grid-cell-renderer.ts

@@ -12,8 +12,9 @@ import {HelmAux, HelmProps} from '@datagrok-libraries/bio/src/viewers/helm-servi
 import {_getHelmService} from '../package-utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
-import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
+import {getGridCellColTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {execMonomerHoverLinks} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
 
 import {getHoveredMonomerFromEditorMol, getSeqMonomerFromHelmAtom} from './get-hovered';
 
@@ -129,16 +130,23 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
     }
     const hoveredAtom = getHoveredMonomerFromEditorMol(argsX, argsY, editorMol, gridCell.bounds.height);
 
+    let seqMonomer: ISeqMonomer | null = null;
     if (hoveredAtom) {
-      const seqMonomer = getSeqMonomerFromHelmAtom(hoveredAtom);
+      seqMonomer = getSeqMonomerFromHelmAtom(hoveredAtom);
       const monomerLib = _package.monomerLib;
-      const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.polymerType, seqMonomer.symbol) :
+      const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
         ui.divText('Monomer library is not available');
       ui.tooltip.show(tooltipEl, e.x + 16, e.y + 16);
     } else {
       // Tooltip for missing monomers
       ui.tooltip.hide();
     }
+
+    execMonomerHoverLinks(gridCell, seqMonomer);
+  }
+
+  onMouseLeave(gridCell: DG.GridCell, e: MouseEvent): void {
+    execMonomerHoverLinks(gridCell, null);
   }
 
   public override render(g: CanvasRenderingContext2D,
@@ -161,10 +169,10 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
 
   static getOrCreate(gridCell: DG.GridCell): HelmGridCellRendererBack {
     const [gridCol, tableCol, temp] =
-      getGridCellRendererBack<string, HelmGridCellRendererBack>(gridCell);
+      getGridCellColTemp<string, HelmGridCellRendererBack>(gridCell);
 
-    let res: HelmGridCellRendererBack = temp['rendererBack'];
-    if (!res) res = temp['rendererBack'] = new HelmGridCellRendererBack(gridCol, tableCol);
+    let res: HelmGridCellRendererBack = temp.rendererBack;
+    if (!res) res = temp.rendererBack = new HelmGridCellRendererBack(gridCol, tableCol);
     return res;
   }
 }
@@ -191,6 +199,19 @@ export class HelmGridCellRenderer extends DG.GridCellRenderer {
     }
   }
 
+  override onMouseLeave(gridCell: DG.GridCell, e: MouseEvent) {
+    const logPrefix = `Helm: HelmGridCellRenderer.onMouseLeave()`;
+    try {
+      HelmGridCellRendererBack.getOrCreate(gridCell).onMouseLeave(gridCell, e);
+    } catch (err: any) {
+      const [errMsg, errStack] = errInfo(err);
+      _package.logger.error(errMsg, undefined, errStack);
+    } finally {
+      e.preventDefault();
+      e.stopPropagation();
+    }
+  }
+
   override render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number,
     gridCell: DG.GridCell, cellStyle: DG.GridCellStyle

package/src/widgets/helm-input.ts

@@ -5,7 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import $ from 'cash-dom';
 import {fromEvent, Observable, Unsubscribable} from 'rxjs';
 
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
 import {HelmInputBase, IHelmHelper, IHelmInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmAtom, HelmMol, HelmString, IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
 
@@ -72,7 +72,7 @@ export class HelmInput extends HelmInputBase {
 
   protected constructor(
     private readonly helmHelper: IHelmHelper,
-    private readonly monomerLib: IMonomerLib,
+    private readonly monomerLib: IMonomerLibBase,
     name?: string,
     public readonly options?: IHelmInputInitOptions,
     private readonly logger = _package.logger,
@@ -135,7 +135,7 @@ export class HelmInput extends HelmInputBase {
   }
 
   /** Inspired by {@link DG.MarkdownInput}, {@link ui._create} */
-  static create(helmHelper: IHelmHelper, monomerLib: IMonomerLib,
+  static create(helmHelper: IHelmHelper, monomerLib: IMonomerLibBase,
     name?: string, options?: IHelmInputInitOptions
   ): HelmInput {
     const input = new HelmInput(helmHelper, monomerLib, name, options);
@@ -183,7 +183,7 @@ export class HelmInput extends HelmInputBase {
     if (hoveredAtom) {
       const seqMonomer = getSeqMonomerFromHelmAtom(hoveredAtom);
       const monomerLib = _package.monomerLib;
-      const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.polymerType, seqMonomer.symbol) :
+      const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
         ui.divText('Monomer library is not available');
       this.showTooltip(tooltipEl, hoveredAtom);
       event.preventDefault();

package/vendor/dojo-1.10.10/dijit/_base.js.uncompressed.js

@@ -0,0 +1,27 @@
+define("dijit/_base", [
+	"./main",
+	"./a11y",	// used to be in dijit/_base/manager
+	"./WidgetSet",	// used to be in dijit/_base/manager
+	"./_base/focus",
+	"./_base/manager",
+	"./_base/place",
+	"./_base/popup",
+	"./_base/scroll",
+	"./_base/sniff",
+	"./_base/typematic",
+	"./_base/wai",
+	"./_base/window"
+], function(dijit){
+
+	// module:
+	//		dijit/_base
+
+	/*=====
+	return {
+		// summary:
+		//		Includes all the modules in dijit/_base
+	};
+	=====*/
+
+	return dijit._base;
+});