@datagrok/bio 2.18.0 → 2.18.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.18.0",
+  "version": "2.18.2",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -44,7 +44,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.46.0",
+    "@datagrok-libraries/bio": "^5.48.1",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
     "@datagrok-libraries/ml": "^6.7.6",
@@ -69,7 +69,6 @@
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/chem": "^1.13.0",
     "@datagrok/dendrogram": "^1.2.33",
-    "@datagrok/helm": "^2.7.0",
     "@types/node": "^17.0.24",
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",

package/src/package.ts

@@ -1012,6 +1012,13 @@ export function bioSubstructureFilter(): BioSubstructureFilter {
   return new BioSubstructureFilter(_package.seqHelper, _package.logger);
 }
 
+//name: Bio Substructure Filter Test
+//description: Substructure filter for Helm package tests
+//output: object result
+export function bioSubstructureFilterTest(): BioSubstructureFilter {
+  return new BioSubstructureFilter(_package.seqHelper, _package.logger);
+}
+
 // -- Test apps --
 
 //name: webLogoLargeApp

package/src/tests/activity-cliffs-tests.ts

@@ -27,7 +27,9 @@ category('activityCliffs', async () => {
   const seqEncodingFunc = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
   const helmEncodingFunc = DG.Func.find({name: 'helmPreprocessingFunction', package: 'Bio'})[0];
   before(async () => {
-    helmHelper = await getHelmHelper(); // init Helm package
+    const helmPackInstalled = DG.Func.find({package: 'Helm', name: 'getHelmHelper'}).length;
+    if (helmPackInstalled)
+      helmHelper = await getHelmHelper(); // init Helm package
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
 
@@ -61,10 +63,13 @@ category('activityCliffs', async () => {
   });
 
   test('Helm', async () => {
-    const df = await _package.files.readCsv('samples/HELM_50.csv');
-    const _view = grok.shell.addTableView(df);
-
-    await _testActivityCliffsOpen(df, DimReductionMethods.UMAP,
-      'HELM', 'Activity', 65, 20, BitArrayMetricsNames.Tanimoto, helmEncodingFunc);
+    const helmPackInstalled = DG.Func.find({package: 'Helm', name: 'getHelmHelper'}).length;
+    if (helmPackInstalled) {
+      const df = await _package.files.readCsv('samples/HELM_50.csv');
+      const _view = grok.shell.addTableView(df);
+  
+      await _testActivityCliffsOpen(df, DimReductionMethods.UMAP,
+        'HELM', 'Activity', 65, 20, BitArrayMetricsNames.Tanimoto, helmEncodingFunc);
+    }
   });
 });

package/src/tests/renderers-test.ts

@@ -65,7 +65,7 @@ category('renderers', () => {
 
   test('scatterPlotTooltip', async () => {
     await _testScatterPlotTooltip();
-  });
+  }, {skipReason: 'GROK-17450'});
 
   async function _rendererMacromoleculeFasta() {
     const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/FASTA.csv');

package/src/tests/substructure-filters-tests.ts

@@ -20,7 +20,7 @@ import {awaitGrid, readDataframe} from './utils';
 import {
   BioSubstructureFilter, FastaBioFilter, SeparatorBioFilter, SeparatorFilterProps
 } from '../widgets/bio-substructure-filter';
-import {BioFilterProps} from '../widgets/bio-substructure-filter-types';
+import {BioFilterProps} from '@datagrok-libraries/bio/src/substructure-filter/bio-substructure-filter-types';
 import {HelmBioFilter} from '../widgets/bio-substructure-filter-helm';
 
 import {_package} from '../package-test';
@@ -62,7 +62,7 @@ category('bio-substructure-filters', async () => {
       const bf = filter.bioFilter as FastaBioFilter;
 
       await testEvent(df.onRowsFiltered, () => {}, () => {
-        bf.props = new BioFilterProps(fSubStr);
+        bf.props = new BioFilterProps(fSubStr, undefined, _package.logger);
       }, 5000, 'testEvent onRowsFiltered');
       expect(filter.dataFrame!.filter.trueCount, fTrueCount);
       expect(filter.dataFrame?.filter.toBinaryString(), '10010000100000');
@@ -84,18 +84,18 @@ category('bio-substructure-filters', async () => {
       const bf = filter.bioFilter as SeparatorBioFilter;
 
       await testEvent(msa.onRowsFiltered, () => {}, () => {
-        bf.props = new SeparatorFilterProps('meI');
+        bf.props = new SeparatorFilterProps('meI', undefined, _package.logger);
       }, 5000, 'testEvent onRowsFiltered');
       expect(filter.dataFrame!.filter.trueCount, 7);
       expect(filter.dataFrame!.filter.get(2), false);
 
       await testEvent(msa.onRowsFiltered, () => {}, () => {
-        bf.props = new SeparatorFilterProps('/meI');
+        bf.props = new SeparatorFilterProps('/meI', undefined, _package.logger);
       }, 5000, 'testEvent onRowsFiltered');
       expect(filter.dataFrame!.filter.trueCount, 0);
 
       await testEvent(msa.onRowsFiltered, () => {}, () => {
-        bf.props = new SeparatorFilterProps('meI-hHis', '-');
+        bf.props = new SeparatorFilterProps('meI-hHis', '-', _package.logger);
       }, 5000, 'testEvent onRowsFiltered');
       expect(filter.dataFrame!.filter.trueCount, 7);
       expect(filter.dataFrame!.filter.get(2), false);
@@ -152,61 +152,67 @@ category('bio-substructure-filters', async () => {
   // }, {timeout: 30000});
 
   test('helm-dialog', async () => {
-    const logPrefix = 'Bio tests: substructureFilters/helm-dialog';
-    const df = await readDataframe('tests/filter_HELM.csv');
-    const view = grok.shell.addTableView(df);
-    await grok.data.detectSemanticTypes(df);
-    await df.meta.detectSemanticTypes();
-
-    _package.logger.debug(`${logPrefix}, filter attaching.`);
-    const filter = new BioSubstructureFilter(seqHelper, _package.logger);
-    filter.attach(df);
-    const dlg = ui.dialog('Test filters').add(filter.root).show(); // to waitForElementInDom
-    await filter.awaitRendered();
-    try {
-      const bf = filter.bioFilter as HelmBioFilter;
-      expect(filter.bioFilter !== null, true, 'bioFilter is not created');
-
-      // filter 1
-      _package.logger.debug(`${logPrefix}, filter 1 change awaiting...`);
-      await testEvent(df.onRowsFiltered, () => {}, () => {
-        bf.props = new BioFilterProps('PEPTIDE1{A.C}$$$$V2.0');
-      }, 20000);
-      _package.logger.debug(`${logPrefix}, filter 1 changed.`);
-      expect(filter.dataFrame!.filter.trueCount, 1);
-      expect(filter.dataFrame!.filter.toBinaryString(), '0001');
-
-      // filter 2
-      _package.logger.debug(`${logPrefix}, filter 2 change awaiting...`);
-      await testEvent(df.onRowsFiltered, () => {}, () => {
-        bf.props = new BioFilterProps('PEPTIDE1{C}$$$$V2.0');
-      }, 20000);
-      setTimeout(() => view.grid.invalidate(), 500);
-      await awaitGrid(view.grid);
-      await delay(1000);
-      _package.logger.debug(`${logPrefix}, filter 2 changed.`);
-      expect(filter.dataFrame!.filter.trueCount, 2);
-      expect(filter.dataFrame!.filter.toBinaryString(), '1001');
-    } finally {
-      dlg.close();
+    const helmPackInstalled = DG.Func.find({package: 'Helm', name: 'getHelmHelper'}).length;
+    if (helmPackInstalled) {
+      const logPrefix = 'Bio tests: substructureFilters/helm-dialog';
+      const df = await readDataframe('tests/filter_HELM.csv');
+      const view = grok.shell.addTableView(df);
+      await grok.data.detectSemanticTypes(df);
+      await df.meta.detectSemanticTypes();
+  
+      _package.logger.debug(`${logPrefix}, filter attaching.`);
+      const filter = new BioSubstructureFilter(seqHelper, _package.logger);
+      filter.attach(df);
+      const dlg = ui.dialog('Test filters').add(filter.root).show(); // to waitForElementInDom
+      await filter.awaitRendered();
+      try {
+        const bf = filter.bioFilter as HelmBioFilter;
+        expect(filter.bioFilter !== null, true, 'bioFilter is not created');
+  
+        // filter 1
+        _package.logger.debug(`${logPrefix}, filter 1 change awaiting...`);
+        await testEvent(df.onRowsFiltered, () => {}, () => {
+          bf.props = new BioFilterProps('PEPTIDE1{A.C}$$$$V2.0', undefined, _package.logger);
+        }, 20000);
+        _package.logger.debug(`${logPrefix}, filter 1 changed.`);
+        expect(filter.dataFrame!.filter.trueCount, 1);
+        expect(filter.dataFrame!.filter.toBinaryString(), '0001');
+  
+        // filter 2
+        _package.logger.debug(`${logPrefix}, filter 2 change awaiting...`);
+        await testEvent(df.onRowsFiltered, () => {}, () => {
+          bf.props = new BioFilterProps('PEPTIDE1{C}$$$$V2.0', undefined, _package.logger);
+        }, 20000);
+        setTimeout(() => view.grid.invalidate(), 500);
+        await awaitGrid(view.grid);
+        await delay(1000);
+        _package.logger.debug(`${logPrefix}, filter 2 changed.`);
+        expect(filter.dataFrame!.filter.trueCount, 2);
+        expect(filter.dataFrame!.filter.toBinaryString(), '1001');
+      } finally {
+        dlg.close();
+      }
+      await filter.awaitRendered();
+      await delay(3000); //TODO: await for grid.onLookChanged
     }
-    await filter.awaitRendered();
-    await delay(3000); //TODO: await for grid.onLookChanged
   }, {});
 
   // Generates unhandled exception accessing isFiltering before bioFilter created
   test('helm-view', async () => {
-    const logPrefix = 'Bio tests: substructureFilters/helm-view';
-    const df = await readDataframe('tests/filter_HELM.csv');
-    const col = df.getCol('HELM string');
-    await grok.data.detectSemanticTypes(df);
-    const view = grok.shell.addTableView(df);
-
-    const fg = view.getFiltersGroup();
-
-    // await awaitCheck(() => fg.filters.length == 1, 'await filters.length == 1', 1000);
-    // const filter = fg.filters.filter((f) => f.columnName == col.name)[0] as BioSubstructureFilter;
-    await awaitGrid(view.grid);
+    const helmPackInstalled = DG.Func.find({package: 'Helm', name: 'getHelmHelper'}).length;
+    if (helmPackInstalled) {
+      const logPrefix = 'Bio tests: substructureFilters/helm-view';
+      const df = await readDataframe('tests/filter_HELM.csv');
+      const col = df.getCol('HELM string');
+      await grok.data.detectSemanticTypes(df);
+      const view = grok.shell.addTableView(df);
+  
+      const fg = view.getFiltersGroup();
+  
+      // await awaitCheck(() => fg.filters.length == 1, 'await filters.length == 1', 1000);
+      // const filter = fg.filters.filter((f) => f.columnName == col.name)[0] as BioSubstructureFilter;
+      await awaitGrid(view.grid);
+    }
   });
 
   test('sync-fasta', async () => {
@@ -228,7 +234,7 @@ category('bio-substructure-filters', async () => {
       const bf2 = f2.bioFilter as FastaBioFilter;
 
       await testEvent(df.onRowsFiltered, () => {}, () => {
-        bf1.props = new BioFilterProps(fSubStr);
+        bf1.props = new BioFilterProps(fSubStr, undefined, _package.logger);
       }, 10000, 'await onRowsFiltered');
       expect(df.filter.trueCount, fTrueCount);
 
@@ -262,7 +268,7 @@ category('bio-substructure-filters', async () => {
       const bf2 = f2.bioFilter as SeparatorBioFilter;
 
       await testEvent(df.onRowsFiltered, () => {}, () => {
-        bf1.props = new SeparatorFilterProps(fSubStr, fSepStr);
+        bf1.props = new SeparatorFilterProps(fSubStr, fSepStr, _package.logger);
       }, 10000, 'await onRowsFiltered');
       expect(df.filter.trueCount, fTrueCount);
 
@@ -276,46 +282,49 @@ category('bio-substructure-filters', async () => {
   });
 
   test('sync-helm', async () => {
-    const df = await _package.files.readCsv('tests/filter_HELM.csv');
-    await grok.data.detectSemanticTypes(df);
-    const view = grok.shell.addTableView(df);
-
-    const fSubStr: string = 'PEPTIDE1{A.C}$$$$V2.0';
-    const fTrueCount: number = 1;
-
-    const f1 = await createFilter('HELM string', df);
-    const f2 = await createFilter('HELM string', df);
-    const dlg = ui.dialog('Test filters').add(f1.root).add(f2.root).show(); // to waitForElementInDom
-    await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
-    try {
-      expect(!!f1.bioFilter, true);
-      expect(!!f2.bioFilter, true);
-      expect(f1.bioFilter!.type, 'HelmBioFilter');
-      expect(f2.bioFilter!.type, 'HelmBioFilter');
-      const bf1 = f1.bioFilter as HelmBioFilter;
-      const bf2 = f2.bioFilter as HelmBioFilter;
-
-      await testEvent(df.onRowsFiltered, () => {}, () => {
-        bf1.props = new BioFilterProps(fSubStr);
-      }, 60000, 'await onRowsFiltered'); // wait to load monomers
+    const helmPackInstalled = DG.Func.find({package: 'Helm', name: 'getHelmHelper'}).length;
+    if (helmPackInstalled) {
+      const df = await _package.files.readCsv('tests/filter_HELM.csv');
+      await grok.data.detectSemanticTypes(df);
+      const view = grok.shell.addTableView(df);
+  
+      const fSubStr: string = 'PEPTIDE1{A.C}$$$$V2.0';
+      const fTrueCount: number = 1;
+  
+      const f1 = await createFilter('HELM string', df);
+      const f2 = await createFilter('HELM string', df);
+      const dlg = ui.dialog('Test filters').add(f1.root).add(f2.root).show(); // to waitForElementInDom
+      await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
+      try {
+        expect(!!f1.bioFilter, true);
+        expect(!!f2.bioFilter, true);
+        expect(f1.bioFilter!.type, 'HelmBioFilter');
+        expect(f2.bioFilter!.type, 'HelmBioFilter');
+        const bf1 = f1.bioFilter as HelmBioFilter;
+        const bf2 = f2.bioFilter as HelmBioFilter;
+  
+        await testEvent(df.onRowsFiltered, () => {}, () => {
+          bf1.props = new BioFilterProps(fSubStr, undefined, _package.logger);
+        }, 60000, 'await onRowsFiltered'); // wait to load monomers
+        await awaitGrid(view.grid);
+        //debugger;
+  
+        _package.logger.debug('Bio tests: substructureFilters/sync-helm, before changed event');
+        await delay(f1.debounceTime * 2);
+        _package.logger.debug('Bio tests: substructureFilters/sync-helm, after changed event');
+        expect(df.filter.trueCount, fTrueCount);
+  
+        await f1.awaitRendered();
+        expect(bf2.props.substructure, fSubStr);
+      } finally {
+        f1.detach();
+        f2.detach();
+        dlg.close();
+      }
+      await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
       await awaitGrid(view.grid);
-      //debugger;
-
-      _package.logger.debug('Bio tests: substructureFilters/sync-helm, before changed event');
-      await delay(f1.debounceTime * 2);
-      _package.logger.debug('Bio tests: substructureFilters/sync-helm, after changed event');
-      expect(df.filter.trueCount, fTrueCount);
-
-      await f1.awaitRendered();
-      expect(bf2.props.substructure, fSubStr);
-    } finally {
-      f1.detach();
-      f2.detach();
-      dlg.close();
+      await delay(3000); //TODO: await for grid.onLookChanged
     }
-    await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
-    await awaitGrid(view.grid);
-    await delay(3000); //TODO: await for grid.onLookChanged
   });
 
   // two seq columns
@@ -360,36 +369,36 @@ category('bio-substructure-filters', async () => {
     const seq2Bf = seq2Filter.bioFilter as FastaBioFilter;
 
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq1Bf.props = new BioFilterProps(fSeq1SubStr);
+      seq1Bf.props = new BioFilterProps(fSeq1SubStr, undefined, _package.logger);
     }, 1000);
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq2Bf.props = new BioFilterProps('');
+      seq2Bf.props = new BioFilterProps('', undefined, _package.logger);
     }, 1000, 'testEvent onRowsFiltered on seq1');
     expect(df.filter.trueCount, fSeq1Trues.filter((v) => v === 1).length);
     expect(df.filter.toBinaryString(), fSeq1Trues.map((v) => v.toString()).join(''));
 
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq1Bf.props = new BioFilterProps('');
+      seq1Bf.props = new BioFilterProps('', undefined, _package.logger);
     }, 1000);
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq2Bf.props = new BioFilterProps(fSeq2SubStr);
+      seq2Bf.props = new BioFilterProps(fSeq2SubStr, undefined, _package.logger);
     }, 1000, 'testEvent onRowsFiltered on seq2');
     expect(df.filter.trueCount, fSeq2Trues.filter((v) => v === 1).length);
     expect(df.filter.toBinaryString(), fSeq2Trues.map((v) => v.toString()).join(''));
 
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq1Bf.props = new BioFilterProps('');
+      seq1Bf.props = new BioFilterProps('', undefined, _package.logger);
     }, 1000);
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq2Bf.props = new BioFilterProps('');
+      seq2Bf.props = new BioFilterProps('', undefined, _package.logger);
     }, 1000, 'testEvent onRowsFiltered on neither');
     expect(df.filter.trueCount, df.rowCount);
 
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq1Bf.props = new BioFilterProps(fSeq1SubStr);
+      seq1Bf.props = new BioFilterProps(fSeq1SubStr, undefined, _package.logger);
     }, 5000);
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seq2Bf.props = new BioFilterProps(fSeq2SubStr);
+      seq2Bf.props = new BioFilterProps(fSeq2SubStr, undefined, _package.logger);
     }, 5000, 'testEvent onRowsFiltered on both');
     const bothTrues: number[] = wu.count(0).take(df.rowCount)
       .map((rowI) => fSeq1Trues[rowI] * fSeq2Trues[rowI]).toArray();
@@ -421,7 +430,7 @@ category('bio-substructure-filters', async () => {
     const seqFilter = fg.filters[0] as BioSubstructureFilter;
     const seqBf = seqFilter.bioFilter as FastaBioFilter;
     await testEvent(df.onRowsFiltered, () => {}, () => {
-      seqBf.props = new BioFilterProps(fSubStr);
+      seqBf.props = new BioFilterProps(fSubStr, undefined, _package.logger);
     }, 1000, 'testEvent onRowsFiltered');
     expect(df.filter.trueCount, fTrueCount);
     expect(seqBf.props.substructure, fSubStr);

package/src/tests/to-atomic-level-ui-tests.ts

@@ -88,12 +88,17 @@ category('toAtomicLevel-ui', () => {
       await _testToAtomicLevelFunc(seqCol, false, testData.tgt);
     });
   }
-  for (const [testName, testData] of Object.entries(tests)) {
-    test(`${testName}-nonlinear`, async () => {
-      const seqCol = await getSeqCol(testData);
-      await _testToAtomicLevelFunc(seqCol, true, testData.tgt);
-    });
-  }
+
+  //test non-linear cases only if helm package is installed
+  const helmPackInstalled = DG.Func.find({package: 'Helm', name: 'getHelmHelper'}).length;
+  if (helmPackInstalled) {
+    for (const [testName, testData] of Object.entries(tests)) {
+      test(`${testName}-nonlinear`, async () => {
+        const seqCol = await getSeqCol(testData);
+        await _testToAtomicLevelFunc(seqCol, true, testData.tgt);
+      });
+    }
+  } 
 
   async function _testToAtomicLevelFunc(
     seqCol: DG.Column<string>, nonlinear: boolean, tgt: TestDataTargetType,

package/src/utils/monomer-cell-renderer.ts

@@ -15,8 +15,6 @@ const Tags = new class {
   tooltipHandlerTemp = 'tooltip-handler.Monomer';
 }();
 
-const svgMolOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
-
 export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase {
   constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column) {
     super(gridCol, tableCol);

package/src/utils/monomer-lib/monomer-lib-base.ts

@@ -25,6 +25,12 @@ const monomerRe = /[\w()]+/;
 //** Do not mess with monomer symbol with parenthesis enclosed in square brackets */
 const ambMonomerRe = RegExp(String.raw`\(${monomerRe}(,${monomerRe})+\)`);
 
+const drawMoleculeCall = (s: string) => {
+  const canvas = ui.canvas(250, 250);
+  grok.chem.canvasMol(0, 0, 250, 250, canvas, s);
+  return canvas;
+};
+
 export type MonomerLibDataType = { [polymerType: string]: { [monomerSymbol: string]: Monomer } };
 
 const whiteColorV = new Vector([255.0, 255.0, 255.0]);
@@ -189,10 +195,10 @@ export class MonomerLibBase implements IMonomerLibBase {
       const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
       let structureEl: HTMLElement;
       if (monomer.molfile)
-        structureEl = grok.chem.svgMol(monomer.molfile, undefined, undefined, chemOptions);
+        structureEl = drawMoleculeCall(monomer.molfile);
       else if (monomer.smiles) {
         structureEl = ui.divV([
-          grok.chem.svgMol(monomer.smiles, undefined, undefined, chemOptions),
+          drawMoleculeCall(monomer.smiles),
           ui.divText('from smiles', {style: {fontSize: 'smaller'}}),
         ]);
       } else {
@@ -271,13 +277,12 @@ export class MonomerLibBase implements IMonomerLibBase {
       }
 
       const naSymbol: string | undefined = monomer[OPT.NATURAL_ANALOG];
-      if (!res && naSymbol) {
+      if (!res && naSymbol)
         return this.getMonomerColors(biotype, naSymbol);
-      }
     }
 
     if (!res)
-      res = {textColor: "#202020", lineColor: "#202020", backgroundColor: "#A0A0A0"};
+      res = {textColor: '#202020', lineColor: '#202020', backgroundColor: '#A0A0A0'};
 
     return {
       textcolor: res.text ?? res.textColor,

package/src/widgets/bio-substructure-filter-helm.ts

@@ -14,12 +14,13 @@ import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {helmSubstructureSearch} from '../substructure-search/substructure-search';
-import {BioFilterBase, BioFilterProps} from './bio-substructure-filter-types';
+import {BioFilterBase, BioFilterProps}
+  from '@datagrok-libraries/bio/src/substructure-filter/bio-substructure-filter-types';
 
 import {_package} from '../package';
 
 export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements IRenderer */ {
-  readonly emptyProps = new BioFilterProps('');
+  readonly emptyProps = new BioFilterProps('', undefined, _package.logger);
 
   helmEditor: IHelmWebEditor;
   _filterPanel = ui.div('', {style: {cursor: 'pointer'}});
@@ -68,7 +69,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
             try {
               const webEditorValue = webEditorApp!.canvas!.getHelm(true)
                 .replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
-              this.props = new BioFilterProps(webEditorValue);
+              this.props = new BioFilterProps(webEditorValue, undefined, _package.logger);
             } catch (err: any) {
               this.logger.error(err);
             } finally {

package/src/widgets/bio-substructure-filter.ts

@@ -23,8 +23,9 @@ import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {helmSubstructureSearch, linearSubstructureSearch} from '../substructure-search/substructure-search';
 import {updateDivInnerHTML} from '../utils/ui-utils';
-import {BioFilterBase, BioFilterProps, IBioFilter, IFilterProps} from './bio-substructure-filter-types';
+import {BioFilterBase, BioFilterProps, IBioFilter, IFilterProps} from '@datagrok-libraries/bio/src/substructure-filter/bio-substructure-filter-types';
 import {HelmBioFilter} from './bio-substructure-filter-helm';
+import { _package } from '../package';
 
 const FILTER_SYNC_EVENT: string = 'bio-substructure-filter';
 
@@ -42,8 +43,9 @@ export class SeparatorFilterProps extends BioFilterProps {
   constructor(
     substructure: string,
     public readonly separator?: string,
+    logger?: DG.PackageLogger
   ) {
-    super(substructure, false);
+    super(substructure, false, logger);
     this.readOnly = true;
   }
 }
@@ -276,7 +278,7 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
 }
 
 export class FastaBioFilter extends BioFilterBase<BioFilterProps> {
-  readonly emptyProps = new BioFilterProps('');
+  readonly emptyProps = new BioFilterProps('', undefined, _package.logger);
 
   readonly substructureInput: DG.InputBase<string>;
 
@@ -288,7 +290,7 @@ export class FastaBioFilter extends BioFilterBase<BioFilterProps> {
     this.substructureInput = ui.input.string('', {
       value: '', onValueChanged: (value) => {
         window.setTimeout(() => {
-          this.props = new BioFilterProps(value);
+          this.props = new BioFilterProps(value, undefined, _package.logger);
           if (!this._propsChanging) this.onChanged.next();
         }, 0 /* next event cycle */);
       }, placeholder: 'Substructure'
@@ -318,7 +320,7 @@ export class FastaBioFilter extends BioFilterBase<BioFilterProps> {
 }
 
 export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
-  readonly emptyProps = new SeparatorFilterProps('', undefined);
+  readonly emptyProps = new SeparatorFilterProps('', undefined, _package.logger);
 
   readonly substructureInput: DG.InputBase<string>;
   readonly separatorInput: DG.InputBase<string>;
@@ -331,14 +333,14 @@ export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
 
     this.substructureInput = ui.input.string('', {
       value: '', onValueChanged: (value) => {
-        this.props = new SeparatorFilterProps(value, this.props.separator);
+        this.props = new SeparatorFilterProps(value, this.props.separator, _package.logger);
         if (!this._propsChanging) this.onChanged.next();
       }, placeholder: 'Substructure'
     });
     this.separatorInput = ui.input.string('', {
       value: this.colSeparator = colSeparator, onValueChanged: (value) => {
         const separator: string | undefined = !!value ? value : undefined;
-        this.props = new SeparatorFilterProps(this.props.substructure, separator);
+        this.props = new SeparatorFilterProps(this.props.substructure, separator, _package.logger);
         if (!this._propsChanging) this.onChanged.next();
       }, placeholder: 'Separator'
     });
@@ -361,7 +363,7 @@ export class SeparatorBioFilter extends BioFilterBase<SeparatorFilterProps> {
   get isFiltering(): boolean { return this.props.substructure !== ''; };
 
   resetFilter(): void {
-    this.props = new SeparatorFilterProps('');
+    this.props = new SeparatorFilterProps('', undefined, _package.logger);
   }
 
   get filterPanel() {