@datagrok/bio 2.13.3 → 2.13.6

package/src/tests/scoring.ts

@@ -2,7 +2,9 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, expectFloat, before, after} from '@datagrok-libraries/utils/src/test';
+import wu from 'wu';
+
+import {category, test, expectFloat, before, after, expect} from '@datagrok-libraries/utils/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
@@ -13,6 +15,7 @@ import {
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
 category('Scoring', () => {
+  /* eslint-disable max-len */
   const sequence = 'sequence';
   const expectedSimilarity = 'expected_similarity';
   const expectedIdentity = 'expected_identity';
@@ -22,11 +25,13 @@ PEPTIDE1{Aca.Orn.gGlu.Pqa.D-His_1Bn.dH.hHis.4Abz.D-Tic.D-Dap.Y.Iva.meS.F.P.F.D-1
 PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.68,0.53
 PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.34,0.0`
   );
-  /* eslint-enable max-len */
   const seqCol: DG.Column<string> = table.getCol(sequence);
-  seqCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+  seqCol.meta.units = NOTATION.HELM;
   seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
   const reference = seqCol.get(0)!;
+  const shortReference = 'PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva}$$$$';
+  const longReference = 'PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC.I.Tyr_26diMe.P.Asu.meC}$$$$';
+  /* eslint-enable max-len */
 
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
@@ -49,15 +54,31 @@ PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[
   test('Identity', async () => {
     const scoresCol = await sequenceIdentityScoring(table, seqCol, reference);
     for (let i = 0; i < scoresCol.length; i++) {
-      expectFloat(scoresCol.get(i)!, table.get(expectedIdentity, i), 0.01,
+      const resScore = scoresCol.get(i)!;
+      const tgtScore = table.get(expectedIdentity, i);
+      expectFloat(resScore, tgtScore, 0.01,
         `Wrong identity score for sequence at position ${i}`);
     }
   });
 
+  test('Identity-shortReference', async () => {
+    const scoresCol = await sequenceIdentityScoring(table, seqCol, shortReference);
+    expect(wu.count(0).take(scoresCol.length).map((rowI) => scoresCol.get(rowI))
+      .every((v) => v != null && !isNaN(v)), true);
+  });
+
+  test('Identity-longReference', async () => {
+    const scoresCol = await sequenceIdentityScoring(table, seqCol, longReference);
+    expect(wu.count(0).take(scoresCol.length).map((rowI) => scoresCol.get(rowI))
+      .every((v) => v != null && !isNaN(v)), true);
+  });
+
   test('Similarity', async () => {
     const scoresCol = await sequenceSimilarityScoring(table, seqCol, reference);
     for (let i = 0; i < scoresCol.length; i++) {
-      expectFloat(scoresCol.get(i)!, table.get(expectedSimilarity, i), 0.01,
+      const resScore = scoresCol.get(i)!;
+      const tgtScore = table.get(expectedSimilarity, i);
+      expectFloat(resScore, tgtScore, 0.01,
         `Wrong similarity score for sequence at position ${i}`);
     }
   });

package/src/tests/seq-handler-get-region.ts

@@ -82,8 +82,8 @@ PEPTIDE1{[Cys_SEt].T.*.*}$$$$`,
       const tgtDf = DG.DataFrame.fromCsv(testData.tgtCsv);
       const tgtSeqCol = tgtDf.getCol('seq');
 
-      expect(srcSeqCol.getTag(DG.TAGS.UNITS), testData.units);
-      expect(resSeqCol.getTag(DG.TAGS.UNITS), testData.units);
+      expect(srcSeqCol.meta.units, testData.units);
+      expect(resSeqCol.meta.units, testData.units);
       expect(srcSeqCol.getTag(TAGS.alphabet), testData.alphabet);
       expect(resSeqCol.getTag(TAGS.alphabet), testData.alphabet);
       expectArray(resSeqCol.toList(), tgtSeqCol.toList());
@@ -105,8 +105,8 @@ PEPTIDE1{[Cys_SEt].T.*.*}$$$$`,
         const tgtDf = DG.DataFrame.fromCsv(testData.tgtCsv);
         const tgtSeqCol = tgtDf.getCol('seq');
 
-        expect(srcSeqCol.getTag(DG.TAGS.UNITS), testData.units);
-        expect(resSeqCol.getTag(DG.TAGS.UNITS), testData.units);
+        expect(srcSeqCol.meta.units, testData.units);
+        expect(resSeqCol.meta.units, testData.units);
         expect(srcSeqCol.getTag(TAGS.alphabet), testData.alphabet);
         expect(resSeqCol.getTag(TAGS.alphabet), testData.alphabet);
         expectArray(resSeqCol.toList(), tgtSeqCol.toList());

package/src/tests/sequence-space-test.ts

@@ -21,7 +21,7 @@ category('sequenceSpace', async () => {
     await _testSequenceSpaceReturnsResult(testFastaDf, DimReductionMethods.UMAP, 'sequence');
     //grok.shell.closeTable(testFastaDf);
     //testFastaTableView.close();
-  });
+  }, {benchmark: true});
 
   test('sequenceSpaceWithEmptyRows', async () => {
     testHelmWithEmptyRows = await readDataframe('tests/100_3_clustests_empty_vals.csv');

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

@@ -5,15 +5,16 @@ import * as DG from 'datagrok-api/dg';
 import $ from 'cash-dom';
 import wu from 'wu';
 
-
 import {after, before, category, test, expect, delay, testEvent, awaitCheck} from '@datagrok-libraries/utils/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
 import {awaitGrid, readDataframe} from './utils';
+
 import {
   BioSubstructureFilter, FastaBioFilter, SeparatorBioFilter, SeparatorFilterProps
 } from '../widgets/bio-substructure-filter';
@@ -24,11 +25,13 @@ import {_package} from '../package-test';
 
 
 category('bio-substructure-filters', async () => {
+  let helmHelper: IHelmHelper;
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
   let userLibSettings: UserLibSettings;
 
   before(async () => {
+    helmHelper = await getHelmHelper(); // init Helm package
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
 

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

@@ -205,7 +205,7 @@ PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.Thr_PO3H2.Aca.Tyr
     const srcDf = DG.DataFrame.fromCsv(srcCsv);
     const seqCol = srcDf.getCol('seq');
     seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+    seqCol.meta.units = NOTATION.FASTA;
     seqCol.setTag(bioTAGS.alphabet, ALPHABET.PT);
     const sh = SeqHandler.forColumn(seqCol);
     const resCol = (await _testToAtomicLevel(srcDf, 'seq', monomerLibHelper))!;

package/src/utils/cell-renderer.ts

@@ -154,7 +154,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const msaGapLength = 8;
 
     // Cell renderer settings
-    let maxLengthOfMonomer: number = (_package.properties ? _package.properties.MaxMonomerLength : 4) ?? 50;
+    let maxLengthOfMonomer: number = (_package.properties ? _package.properties.maxMonomerLength : 4) ?? 50;
     if (mmcrTAGS.maxMonomerLength in tableCol.tags) {
       const v = parseInt(tableCol.getTag(mmcrTAGS.maxMonomerLength));
       maxLengthOfMonomer = !isNaN(v) && v ? v : 50;
@@ -209,7 +209,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       g.textBaseline = 'top';
 
       //TODO: can this be replaced/merged with splitSequence?
-      const units = tableCol.getTag(DG.TAGS.UNITS);
+      const units = tableCol.meta.units;
       const aligned: string = tableCol.getTag(bioTAGS.aligned);
 
       const palette = getPaletteByType(paletteType);
@@ -298,7 +298,7 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
     const tableCol = gridCell.tableColumn as DG.Column<string>;
     const s: string = cell.value ?? '';
     const separator = tableCol.tags[bioTAGS.separator];
-    const units: string = tableCol.tags[DG.TAGS.UNITS];
+    const units: string = tableCol.meta.units!;
     w = getUpdatedWidth(grid, g, x, w, dpr);
     //TODO: can this be replaced/merged with splitSequence?
     const [s1, s2] = s.split('#');
@@ -345,7 +345,7 @@ export function drawMoleculeDifferenceOnCanvas(
   g.textBaseline = 'top';
 
   let palette: SeqPalette = UnknownSeqPalettes.Color;
-  if (units != 'HELM')
+  if (units !== 'HELM')
     palette = getPaletteByType(units.substring(units.length - 2));
 
   const vShift = 7;

package/src/utils/context-menu.ts

@@ -17,7 +17,7 @@ export function addCopyMenuUI(cell: DG.Cell, menu: DG.Menu): void {
       const srcCol = cell.column;
       const srcRowIdx = cell.rowIndex;
       const srcSh = SeqHandler.forColumn(srcCol);
-      const separator = tgtNotation === NOTATION.SEPARATOR ? _package.properties.DefaultSeparator : undefined;
+      const separator = tgtNotation === NOTATION.SEPARATOR ? _package.properties.defaultSeparator : undefined;
       const joiner = srcSh.getJoiner({notation: tgtNotation as NOTATION, separator});
       const srcSS = srcSh.getSplitted(srcRowIdx);
       const tgtSeq = joiner(srcSS);

package/src/utils/convert.ts

@@ -52,7 +52,8 @@ export function convert(col?: DG.Column): void {
       separatorInput.value = '/'; // helm monomers can have - in the name like D-aThr;
     dialogHeader.textContent = 'Current notation: ' + currentNotation;
     filteredNotations = notations.filter((e) => e !== currentNotation);
-    targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations, toggleSeparator);
+    targetNotationInput = ui.input.choice('Convert to', {value: filteredNotations[0], items: filteredNotations,
+      onValueChanged: toggleSeparator});
     toggleSeparator();
     convertDialog?.clear();
     convertDialog?.add(ui.div([
@@ -63,12 +64,13 @@ export function convert(col?: DG.Column): void {
     ]));
   };
 
-  const targetColumnInput = ui.columnInput('Column', grok.shell.t, srcCol, toggleColumn);
+  const targetColumnInput = ui.input.column('Column', {table: grok.shell.t, value: srcCol,
+    onValueChanged: (input) => toggleColumn(input.value)});
 
   const separatorArray = ['-', '.', '/'];
   let filteredNotations = notations.filter((e) => e !== currentNotation);
 
-  const separatorInput = ui.choiceInput('Separator', separatorArray[0], separatorArray);
+  const separatorInput = ui.input.choice('Separator', {value: separatorArray[0], items: separatorArray});
 
   // hide the separator input for non-SEPARATOR target notations
   const toggleSeparator = () => {
@@ -77,7 +79,8 @@ export function convert(col?: DG.Column): void {
     else
       $(separatorInput.root).show();
   };
-  let targetNotationInput = ui.choiceInput('Convert to', filteredNotations[0], filteredNotations, toggleSeparator);
+  let targetNotationInput = ui.input.choice('Convert to', {value: filteredNotations[0], items: filteredNotations,
+    onValueChanged: toggleSeparator});
 
   // set correct visibility on init
   toggleSeparator();

package/src/utils/get-region-func-editor.ts

@@ -37,25 +37,20 @@ export class GetRegionFuncEditor {
   ) {
     const getDesc = (paramName: string) => this.call.inputParams[paramName].property.description;
 
-    this.inputs.table = ui.tableInput('Table',
-      this.call.inputParams['table'].value ?? grok.shell.tv.dataFrame, undefined,
-      () => {});
+    this.inputs.table = ui.input.table('Table', {value: this.call.inputParams['table'].value ?? grok.shell.tv.dataFrame});
 
     const seqColValue = this.call.inputParams['sequence'].value ??
       this.inputs.table.value!.columns.bySemType(DG.SEMTYPE.MACROMOLECULE);
-    const seqColOptions = {filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE};
-    this.inputs.sequence = ui.columnInput('Sequence', grok.shell.tv.dataFrame, seqColValue,
-      this.sequenceInputChanged.bind(this), seqColOptions);
-    this.inputs.start = ui.choiceInput(
-      'Start', undefined, [], this.startInputChanged.bind(this)) as unknown as DG.InputBase<string>;
-    this.inputs.end = ui.choiceInput(
-      'End', undefined, [], this.endInputChanged.bind(this)) as unknown as DG.InputBase<string>;
-
-    this.inputs.region = ui.choiceInput<SeqRegion>('Region', null as unknown as SeqRegion, [],
-      this.regionInputChanged.bind(this)) as DG.InputBase<SeqRegion>;
-
-    this.inputs.name = ui.stringInput('Column name', this.getDefaultName(),
-      this.nameInputChanged.bind(this), {clearIcon: true});
+    this.inputs.sequence = ui.input.column('Sequence', {table: grok.shell.tv.dataFrame, value: seqColValue,
+      onValueChanged: this.sequenceInputChanged.bind(this), filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE});
+    this.inputs.start = ui.input.choice('Start', {onValueChanged: this.startInputChanged.bind(this)}) as unknown as DG.InputBase<string>;
+    this.inputs.end = ui.input.choice('End', {onValueChanged: this.endInputChanged.bind(this)}) as unknown as DG.InputBase<string>;
+
+    this.inputs.region = ui.input.choice<SeqRegion>('Region', {value: null as unknown as SeqRegion, items: [],
+      onValueChanged: this.regionInputChanged.bind(this)}) as DG.InputBase<SeqRegion>;
+
+    this.inputs.name = ui.input.string('Column name', {value: this.getDefaultName(),
+      onValueChanged: this.nameInputChanged.bind(this), clearIcon: true});
     this.inputs.name.onInput(this.nameInputInput.bind(this)); // To catch clear event
 
     // tooltips

package/src/utils/get-region.ts

@@ -8,11 +8,11 @@ import {TaskBarProgressIndicator} from 'datagrok-api/dg';
 export function getRegionUI(col: DG.Column<string>): void {
   const sh = SeqHandler.forColumn(col);
 
-  const nameInput = ui.stringInput('Name', '');
-  const startPositionInput = ui.choiceInput('Start Position', sh.posList[0], sh.posList,
-    () => { /* TODO: update name placeholder with getDefaultName() */ });
-  const endPositionInput = ui.choiceInput('End Position', sh.posList[sh.posList.length], sh.posList,
-    () => { /* TODO: update name placeholder with getDefaultName() */ });
+  const nameInput = ui.input.string('Name', {value: ''});
+  const startPositionInput = ui.input.choice('Start Position', {value: sh.posList[0], items: sh.posList,
+    onValueChanged: () => { /* TODO: update name placeholder with getDefaultName() */ }});
+  const endPositionInput = ui.input.choice('End Position', {value: sh.posList[sh.posList.length], items: sh.posList,
+    onValueChanged: () => { /* TODO: update name placeholder with getDefaultName() */ }});
 
   const getDefaultName = (): string => {
     return `${col.name}:${startPositionInput.value}-${endPositionInput.value}`;

package/src/utils/macromolecule-column-widget.ts

@@ -25,7 +25,7 @@ export class MacromoleculeColumnWidget extends DG.Widget {
 
   async init(): Promise<void> {
     const sh = SeqHandler.forColumn(this.seqCol);
-    const pkgTooltipWebLogo = _package.properties.TooltipWebLogo;
+    const pkgTooltipWebLogo = _package.properties.tooltipWebLogo;
     const colTooltipWebLogo = this.seqCol.getTag(wlTAGS.tooltipWebLogo);
 
     if (pkgTooltipWebLogo !== false && !['false', 'off', 'disable', 'disabled'].includes(colTooltipWebLogo)) {

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

@@ -4,6 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {delay} from '@datagrok-libraries/utils/src/test';
+import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {
   getUserLibSettings, setUserLibSettings, LIB_PATH
@@ -49,7 +50,9 @@ export class MonomerLibManager implements IMonomerLibHelper {
   }
 
   /** Protect constructor to prevent multiple instantiation. */
-  protected constructor() {}
+  protected constructor(
+    private readonly logger: ILogger,
+  ) {}
 
   /** Singleton monomer library
    * @return {MonomerLibManager} MonomerLibHelper instance
@@ -64,7 +67,8 @@ export class MonomerLibManager implements IMonomerLibHelper {
   async getFileManager(): Promise<MonomerLibFileManager> {
     if (this._fileManagerPromise === undefined) {
       this._fileManagerPromise = (async () => {
-        const fileManager: MonomerLibFileManager = await MonomerLibFileManager.create(this, this._eventManager);
+        const fileManager: MonomerLibFileManager =
+          await MonomerLibFileManager.create(this, this._eventManager, this.logger);
         return fileManager;
       })();
     }
@@ -82,6 +86,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
       // WARNING: This function is not allowed to throw any exception,
       // because it will prevent further handling monomer library settings
       // through blocking this.loadLibrariesPromise
+      const pi = DG.TaskBarProgressIndicator.create('Loading monomers ...');
       try {
         const [libFileNameList, settings]: [string[], UserLibSettings] = await Promise.all([
           (await this.getFileManager()).getValidLibraryPaths(),
@@ -95,14 +100,19 @@ export class MonomerLibManager implements IMonomerLibHelper {
           return isFileIncluded && isExplicit;
         });
 
+        let completedLibCount: number = 0;
         const libs: IMonomerLib[] = await Promise.all(filteredLibFnList
           .map((libFileName) => {
             //TODO handle whether files are in place
-            return this.readLibrary(LIB_PATH, libFileName).catch((err: any) => {
-              const errMsg: string = `Loading monomers from '${libFileName}' error: ` +
-                `${err instanceof Error ? err.message : err.toString()}`;
-              return new MonomerLib({}, libFileName, errMsg);
-            });
+            return this.readLibrary(LIB_PATH, libFileName)
+              .catch((err: any) => {
+                const errMsg: string = `Loading monomers from '${libFileName}' error: ` +
+                  `${err instanceof Error ? err.message : err.toString()}`;
+                return new MonomerLib({}, libFileName, errMsg);
+              }).finally(() => {
+                pi.update(Math.round(100 * (++completedLibCount) / filteredLibFnList.length),
+                  `Loading monomer libs ${completedLibCount}/${filteredLibFnList.length}`);
+              });
           }));
         this._monomerLib.updateLibs(libs, reload);
       } catch (err: any) {
@@ -112,6 +122,8 @@ export class MonomerLibManager implements IMonomerLibHelper {
 
         const errStack = err instanceof Error ? err.stack : undefined;
         _package.logger.error(errMsg, undefined, errStack);
+      } finally {
+        pi.close();
       }
     });
   }
@@ -149,7 +161,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
     let res = window.$monomerLibHelperPromise;
     if (res === undefined) {
       res = window.$monomerLibHelperPromise = (async () => {
-        const instance = new MonomerLibManager();
+        const instance = new MonomerLibManager(_package.logger);
         instance._eventManager = MonomerLibFileEventManager.getInstance();
         return instance;
       })();

package/src/utils/monomer-lib/library-file-manager/file-manager.ts

@@ -6,6 +6,7 @@ import * as DG from 'datagrok-api/dg';
 import {JSONSchemaType} from 'ajv';
 
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {LIB_PATH} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {
   HELM_REQUIRED_FIELD as REQ,
@@ -31,6 +32,7 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
     private readonly fileValidator: MonomerLibFileValidator,
     private readonly libHelper: IMonomerLibHelper,
     public readonly eventManager: MonomerLibFileEventManager,
+    private readonly logger: ILogger,
   ) {
     this.eventManager.updateValidLibraryFileListRequested$.subscribe(async () => {
       await this.updateValidLibraryList();
@@ -46,19 +48,20 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
 
   /** For internal use only, get {@link IMonomerLibHelper.getFileManager} */
   public static async create(
-    libHelper: IMonomerLibHelper, eventManager: MonomerLibFileEventManager
+    libHelper: IMonomerLibHelper, eventManager: MonomerLibFileEventManager, logger: ILogger,
   ): Promise<MonomerLibFileManager> {
     const helmSchemaRaw = await grok.dapi.files.readAsText(HELM_JSON_SCHEMA_PATH);
     const helmSchema = JSON.parse(helmSchemaRaw) as JSONSchemaType<any>;
 
     const fileValidator = new MonomerLibFileValidator(helmSchema);
-    return new MonomerLibFileManager(fileValidator, libHelper, eventManager);
+    return new MonomerLibFileManager(fileValidator, libHelper, eventManager, logger);
   }
 
   /** Add standard .json monomer library  */
   async addLibraryFile(fileContent: string, fileName: string): Promise<void> {
     try {
-      if (await this.libraryFileExists(fileName)) {
+      const alreadyFileExists = await grok.dapi.files.exists(LIB_PATH + `${fileName}`);
+      if (alreadyFileExists) {
         grok.shell.error(`File ${fileName} already exists`);
         return;
       }
@@ -122,21 +125,17 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
     return await this.eventManager.getValidLibraryPathsAsynchronously();
   }
 
-  private async libraryFileExists(fileName: string): Promise<boolean> {
-    return await grok.dapi.files.exists(LIB_PATH + `${fileName}`);
-  }
-
   private async updateValidLibraryList(): Promise<void> {
     const logPrefix: string = `${this.toLog()}.updateValidLibraryList()`;
-    _package.logger.debug(`${logPrefix}, start`);
-    return this.filesPromise = this.filesPromise.then(async () => {
-      _package.logger.debug(`${logPrefix}, IN`);
+    this.logger.debug(`${logPrefix}, start`);
+    this.filesPromise = this.filesPromise.then(async () => {
+      this.logger.debug(`${logPrefix}, IN`);
       const invalidFiles = [] as string[];
       // console.log(`files before validation:`, this.libraryEventManager.getValidFilesPathList());
       const filePaths = await this.getFilePathsAtDefaultLocation();
 
       if (!this.fileListHasChanged(filePaths)) {
-        _package.logger.debug(`${logPrefix}, end, not changed`);
+        this.logger.debug(`${logPrefix}, end, not changed`);
         return;
       }
 
@@ -160,18 +159,19 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
       // console.log(`files after validation:`, this.libraryEventManager.getValidFilesPathList());
 
       if (validLibraryPaths.some((el) => !el.endsWith('.json')))
-        _package.logger.warning(`Wrong validation: ${validLibraryPaths}`);
+        this.logger.warning(`Wrong validation: ${validLibraryPaths}`);
 
       if (invalidFiles.length > 0) {
         const message = `Invalid monomer library files in ${LIB_PATH}` +
           `, consider fixing or removing them: ${invalidFiles.join(', ')}`;
 
-        _package.logger.warning(message);
+        this.logger.warning(message);
         // grok.shell.warning(message);
       }
-      _package.logger.debug(`${logPrefix}, OUT`);
+      this.logger.debug(`${logPrefix}, OUT`);
     });
-    _package.logger.debug(`${logPrefix}, end`);
+    this.logger.debug(`${logPrefix}, end`);
+    return this.filesPromise;
   }
 
   private fileListHasChanged(newList: string[]): boolean {
@@ -191,21 +191,25 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
 
   /** Get relative paths for files in LIB_PATH  */
   private async getFilePathsAtDefaultLocation(): Promise<string[]> {
+    const logPrefix = `${this.toLog()}.getFilePathsAtDefaultLocation()`;
+    this.logger.debug(`${logPrefix}, start`);
     const list = await grok.dapi.files.list(LIB_PATH);
     const paths = list.map((fileInfo) => {
       return fileInfo.fullPath;
     });
 
-    // console.log(`retreived paths:`, paths);
-
-    // WARNING: an extra sanity check,
-    // caused by unexpected behavior of grok.dapi.files.list() when it returns non-existent paths
+    const checkForUi = false;
     const existingPaths = [] as string[];
-    for (const path of paths) {
-      const exists = await grok.dapi.files.exists(path);
-      if (exists)
-        existingPaths.push(path);
-    }
+    if (checkForUi) {
+      // WARNING: an extra sanity check,
+      // caused by unexpected behavior of grok.dapi.files.list() when it returns non-existent paths
+      for (const path of paths) {
+        const exists = await grok.dapi.files.exists(path);
+        if (exists)
+          existingPaths.push(path);
+      }
+    } else
+      existingPaths.push(...paths);
 
     return existingPaths.map((path) => {
       // Get relative path (to LIB_PATH)

package/src/utils/monomer-lib/library-file-manager/file-validator.ts

@@ -14,7 +14,8 @@ export class MonomerLibFileValidator {
   constructor(
     private helmMonomerSchema: JSONSchemaType<any>
   ) {
-    const ajv = new Ajv2020({allErrors: true, strictTuples: false});
+    // HELMMonomerSchema.json / #/properties/id uses a union type (string added by Maria Dolotova)
+    const ajv = new Ajv2020({allErrors: true, strictTuples: false, allowUnionTypes: true});
     addErrors(ajv);
     this.validateMonomerSchema = ajv.compile(this.helmMonomerSchema);
   }

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -139,12 +139,9 @@ class LibraryControlsManager {
     const logPrefix = `${this.toLog()}.createLibInput()`;
     _package.logger.debug(`${logPrefix}, libFileName = '${libFileName}', start`);
     const isMonomerLibrarySelected = !this.userLibSettings.exclude.includes(libFileName);
-    const libInput = ui.boolInput(
-      libFileName,
-      isMonomerLibrarySelected,
-      (isSelected: boolean) => {
-        this.fileManager.eventManager.updateLibrarySelectionStatus(libFileName, isSelected);
-      });
+    const libInput = ui.input.bool(libFileName, {value: isMonomerLibrarySelected, onValueChanged: (input) => {
+      this.fileManager.eventManager.updateLibrarySelectionStatus(libFileName, input.value);
+    }});
     ui.tooltip.bind(libInput.root, `Include monomers from ${libFileName}`);
     const deleteIcon = ui.iconFA('trash-alt', () => this.promptForLibraryDeletion(libFileName));
     ui.tooltip.bind(deleteIcon, `Delete ${libFileName}`);

package/src/utils/multiple-sequence-alignment-ui.ts

@@ -38,18 +38,18 @@ export async function multipleSequenceAlignmentUI(
     }
 
     // UI for PepSea alignment
-    const methodInput = ui.choiceInput('Method', options.pepsea.method, pepseaMethods);
+    const methodInput = ui.input.choice('Method', {value: options.pepsea.method, items: pepseaMethods});
     methodInput.setTooltip('Alignment method');
 
     // UI for Kalign alignment
-    const terminalGapInput = ui.floatInput('Terminal gap', options?.kalign?.terminalGap ?? null);
+    const terminalGapInput = ui.input.float('Terminal gap', {value: options?.kalign?.terminalGap});
     terminalGapInput.setTooltip('Penalty for opening a gap at the beginning or end of the sequence');
     const kalignVersionDiv = ui.p(`Kalign version: ${kalignVersion}`, 'kalign-version');
 
     // shared UI
-    const gapOpenInput = ui.floatInput('Gap open', options.pepsea.gapOpen);
+    const gapOpenInput = ui.input.float('Gap open', {value: options.pepsea.gapOpen});
     gapOpenInput.setTooltip('Gap opening penalty at group-to-group alignment');
-    const gapExtendInput = ui.floatInput('Gap extend', options.pepsea.gapExtend);
+    const gapExtendInput = ui.input.float('Gap extend', {value: options.pepsea.gapExtend});
     gapExtendInput.setTooltip('Gap extension penalty to skip the alignment');
 
     const msaParamsDiv = ui.inputs([gapOpenInput, gapExtendInput, terminalGapInput]);
@@ -69,25 +69,24 @@ export async function multipleSequenceAlignmentUI(
     let performAlignment: (() => Promise<DG.Column<string> | null>) | undefined;
 
     let prevSeqCol = seqCol;
-    const colInput = ui.columnInput(
-      'Sequence', table, seqCol,
-      async (valueCol: DG.Column) => {
-        if (!valueCol || valueCol.semType !== DG.SEMTYPE.MACROMOLECULE) {
+    const colInput = ui.input.column(
+      'Sequence', {table: table, value: seqCol, onValueChanged: async (input: DG.InputBase<DG.Column<string>>): Promise<void> => {
+        if (!input.value || input.value.semType !== DG.SEMTYPE.MACROMOLECULE) {
           okBtn.disabled = true;
           await delay(0); // to
           colInput.value = prevSeqCol as DG.Column<string>;
           return;
         }
-        prevSeqCol = valueCol;
+        prevSeqCol = input.value;
         okBtn.disabled = false;
         performAlignment = await onColInputChange(
           colInput.value, table, pepseaInputRootStyles, kalignInputRootStyles,
           methodInput, clustersColInput, gapOpenInput, gapExtendInput, terminalGapInput,
         );
-      }, {filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE} as ColumnInputOptions
+      }, filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE} as ColumnInputOptions
     ) as DG.InputBase<DG.Column<string>>;
     colInput.setTooltip('Sequences column to use for alignment');
-    const clustersColInput = ui.columnInput('Clusters', table, options.clustersCol);
+    const clustersColInput = ui.input.column('Clusters', {table: table, value: options.clustersCol!});
     clustersColInput.nullable = true;
 
     const dlg = ui.dialog('MSA')

package/src/utils/multiple-sequence-alignment.ts

@@ -103,13 +103,13 @@ export async function runKalign(srcCol: DG.Column<string>, isAligned: boolean =
   }
 
   // units
-  const srcUnits = srcCol.getTag(DG.TAGS.UNITS);
+  const srcUnits = srcCol.meta.units;
   //aligned
   const tgtAligned = ALIGNMENT.SEQ_MSA;
   //alphabet
   const srcAlphabet = srcCol.getTag(bioTAGS.alphabet);
 
-  tgtCol.setTag(DG.TAGS.UNITS, srcUnits);
+  tgtCol.meta.units = srcUnits;
   tgtCol.setTag(bioTAGS.aligned, tgtAligned);
   tgtCol.setTag(bioTAGS.alphabet, srcAlphabet);
   tgtCol.semType = DG.SEMTYPE.MACROMOLECULE;

package/src/utils/pepsea.ts

@@ -91,7 +91,7 @@ export async function runPepsea(srcCol: DG.Column<string>, unUsedName: string,
   }
 
   const alignedSequencesCol: DG.Column<string> = DG.Column.fromStrings(unUsedName, alignedSequences);
-  alignedSequencesCol.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+  alignedSequencesCol.meta.units = NOTATION.SEPARATOR;
   alignedSequencesCol.setTag(bioTAGS.separator, C.PEPSEA.SEPARATOR);
   alignedSequencesCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
   alignedSequencesCol.setTag(bioTAGS.alphabet, ALPHABET.UN);

package/src/utils/save-as-fasta.ts

@@ -20,8 +20,8 @@ export function saveAsFastaUI() {
     .find((gcol: DG.GridColumn) => gcol.name.toLowerCase().indexOf('id') !== -1);
   const idDefaultValue = defaultIdGCol ? [defaultIdGCol.name] : [];
 
-  const idGColListInput = ui.multiChoiceInput('Seq id columns', idDefaultValue,
-    idGColList.map((gcol: DG.GridColumn) => gcol.name));
+  const idGColListInput = ui.input.multiChoice('Seq id columns', {value: idDefaultValue,
+    items: idGColList.map((gcol: DG.GridColumn) => gcol.name)});
 
   const seqGColList: DG.GridColumn[] = wu.count(0).take(grid.columns.length)/* range rom 0 to grid.columns.length */
     .map((colI: number) => grid.columns.byIndex(colI)!)
@@ -35,10 +35,10 @@ export function saveAsFastaUI() {
     }).toArray();
 
   const seqDefaultValue = seqGColList.length > 0 ? seqGColList[0].name : [];
-  const seqColInput = ui.choiceInput('Seq column', seqDefaultValue,
-    seqGColList.map((gCol: DG.GridColumn) => gCol.name));
+  const seqColInput = ui.input.choice('Seq column', {value: seqDefaultValue,
+    items: seqGColList.map((gCol: DG.GridColumn) => gCol.name)});
 
-  const lineWidthInput = ui.intInput('FASTA line width', FASTA_LINE_WIDTH);
+  const lineWidthInput = ui.input.int('FASTA line width', {value: FASTA_LINE_WIDTH});
 
   ui.dialog({title: 'Save as FASTA'})
     .add(ui.inputs([