@datagrok/bio 2.25.13 → 2.25.15

package/files/monomer-collections/Canonical AAs.json

@@ -0,0 +1,27 @@
+{
+  "monomerSymbols": [
+    "A",
+    "C",
+    "D",
+    "E",
+    "F",
+    "G",
+    "H",
+    "I",
+    "K",
+    "L",
+    "M",
+    "N",
+    "P",
+    "Q",
+    "R",
+    "S",
+    "T",
+    "V",
+    "W",
+    "Y"
+  ],
+  "description": "Canonical amino acids collection",
+  "updatedBy": "rizhi",
+  "updatedOn": "2026-01-01T12:00:00Z"
+}

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.25.13",
+  "version": "2.25.15",
   "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": "^5.61.6",
+    "@datagrok-libraries/bio": "^5.62.0",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.9",

package/src/demo/bio03-atomic-level.ts

@@ -4,7 +4,6 @@ import * as DG from 'datagrok-api/dg';
 import {_package, PackageFunctions} from '../package';
 import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
-import {delay} from '@datagrok-libraries/test/src/test';
 import {adjustGridcolAfterRender} from '../utils/ui-utils';
 
 export async function demoToAtomicLevel(): Promise<void> {
@@ -63,7 +62,7 @@ export async function demoBio03UI(): Promise<void> {
         dlg = ui.dialog()
           .add(sketcher)
           .show();
-        await delay(3000);
+        await DG.delay(3000);
         dlg.close();
       }, {
         description: 'Display atomic level structure within a sketcher.',

package/src/substructure-search/substructure-search.ts

@@ -2,7 +2,6 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay} from '@datagrok-libraries/test/src/test';
 import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
@@ -154,7 +153,7 @@ export async function helmSubstructureSearch(
 export async function invalidateMols(col: DG.Column<string>, seqHelper: ISeqHelper, pattern: boolean): Promise<void> {
   const progressBar = DG.TaskBarProgressIndicator.create(`Invalidating molfiles for ${col.name}`);
   try {
-    await delay(10);
+    await DG.delay(10);
     const monomersDict = new Map();
     const monomericMolsCol = await getMonomericMols(col, seqHelper, pattern, monomersDict);
     col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS] = monomericMolsCol;

package/src/utils/detect-macromolecule-probe.ts

@@ -4,7 +4,6 @@ import * as DG from 'datagrok-api/dg';
 
 
 import {_package} from '../package';
-import {delay} from '@datagrok-libraries/test/src/test';
 
 type IDetectorReport = { categoriesSample: any[], rejectReason: string };
 
@@ -31,7 +30,7 @@ export async function detectMacromoleculeProbeDo(
       if ((progress - progressLast) >= 0.1) {
         progressLast = progress;
         pi.update(100 * progress, `detectMacromolecule probe ${failCount}/${i}/${probeCount} ...`);
-        await delay(0);
+        await DG.delay(0);
       }
     }
     if (failCount > 0)

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

@@ -4,9 +4,8 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay} from '@datagrok-libraries/test/src/test';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
-import {DEFAULT_FILES_LIB_PROVIDER_NAME, findProviderWithLibraryName, IMonomerLib, IMonomerSet} from '@datagrok-libraries/bio/src/types/monomer-library';
+import {DEFAULT_FILES_LIB_PROVIDER_NAME, findProviderWithLibraryName, IMonomerLib, IMonomerSet, MonomerCollection} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
@@ -20,6 +19,7 @@ import {_package} from '../../package';
 import {IMonomerLibHelper, IMonomerLibProvider} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {merge, Observable, Subject} from 'rxjs';
 import {MonomerLibFromFilesProvider} from './library-file-manager/monomers-lib-provider';
+const MONOMER_COLLECTION_STORAGE_PATH = 'System:AppData/Bio/monomer-collections/';
 
 type MonomerLibWindowType = Window & { $monomerLibHelperPromise?: Promise<MonomerLibManager> };
 declare const window: MonomerLibWindowType;
@@ -91,7 +91,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
         return true;
       })(),
       (async () => {
-        await delay(timeout);
+        await DG.delay(timeout);
         return false;
       })(),
     ]).then((res) => {
@@ -410,6 +410,39 @@ export class MonomerLibManager implements IMonomerLibHelper {
     }
   }
 
+  async listMonomerCollections(): Promise<string[]> {
+    // these are provider less functions. coleections will be in files storage in txt format
+    const collections = (await grok.dapi.files.list(MONOMER_COLLECTION_STORAGE_PATH))
+      .filter((file) => file.extension === 'json' || file.name.endsWith('.json'));
+    return collections.map((file) => file.name);
+  }
+
+  async deleteMonomerCollection(collectionName: string): Promise<void> {
+    if (!collectionName.endsWith('.json'))
+      collectionName += '.json';
+    if (await grok.dapi.files.exists(MONOMER_COLLECTION_STORAGE_PATH + collectionName))
+      await grok.dapi.files.delete(MONOMER_COLLECTION_STORAGE_PATH + collectionName);
+  }
+
+  async readMonomerCollection(collectionName: string): Promise<MonomerCollection> {
+    if (!collectionName.endsWith('.json'))
+      collectionName += '.json';
+    const file = await grok.dapi.files.readAsText(MONOMER_COLLECTION_STORAGE_PATH + collectionName);
+    return JSON.parse(file) as MonomerCollection;
+  }
+
+  async addOrUpdateMonomerCollection(collectionName: string, monomerSymbols: string[], desc?: string): Promise<void> {
+    if (!collectionName.endsWith('.json'))
+      collectionName += '.json';
+    const content = JSON.stringify({
+      description: desc,
+      monomerSymbols: monomerSymbols,
+      updatedBy: DG.User.current().login,
+      updatedOn: new Date().toISOString(),
+    } satisfies MonomerCollection, null, 2);
+    await grok.dapi.files.writeAsText(MONOMER_COLLECTION_STORAGE_PATH + collectionName, content);
+  }
+
   // -- Instance singleton --
   public static async getInstance(): Promise<MonomerLibManager> {
     let res = window.$monomerLibHelperPromise;

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

@@ -255,6 +255,58 @@ export class MonomerManager implements IMonomerManager {
     }
   }
 
+  async createNewMonomersCollectionDialog(monomerSymbols: string[]) {
+    const existingCollections = (await this.monomerLibManamger.listMonomerCollections()).map((name) => name.toLowerCase());
+    const nameInput = ui.input.string('Collection Name', {tooltipText: 'Name of the monomer collection, should be unique', placeholder: 'Enter collection name', nullable: false});
+    const descriptionInput = ui.input.string('Description', {tooltipText: 'Description of the monomer collection', placeholder: 'Enter collection description', nullable: true});
+    const d = ui.dialog('Create New Monomer Collection')
+      .add(nameInput)
+      .add(descriptionInput)
+      .addButton('Add', async () => {
+        if (!nameInput.value || !nameInput.value.trim()) {
+          grok.shell.warning('Collection name cannot be empty');
+          return;
+        }
+        const saveAction = async (symbols: string[]) => {
+          await this.monomerLibManamger.addOrUpdateMonomerCollection(nameInput.value!, symbols, descriptionInput.value ?? undefined);
+          grok.shell.info(`Collection ${nameInput.value} saved successfully`);
+        };
+        if (existingCollections.includes(nameInput.value!.toLowerCase()) || existingCollections.includes(nameInput.value!.toLowerCase() + '.json')) {
+          const confD = ui.dialog('Collection already exists')
+            .add(ui.divText(`A collection with the name ${nameInput.value} already exists. Do you want to merge or overwrite it?`));
+          confD.addButton('Merge', async () => {
+            const existingCollection = await this.monomerLibManamger.readMonomerCollection(nameInput.value!);
+            const mergedSymbols = Array.from(new Set([...(existingCollection.monomerSymbols ?? []), ...monomerSymbols]));
+            try {
+              await saveAction(mergedSymbols);
+            } catch (e) {
+              grok.shell.error('Error merging monomer collection');
+              console.error(e);
+            }
+            confD.close();
+          });
+          confD.addButton('Overwrite', async () => {
+            try {
+              await saveAction(monomerSymbols);
+            } catch (e) {
+              grok.shell.error('Error overwriting monomer collection');
+              console.error(e);
+            }
+            confD.close();
+          });
+          confD.show();
+        } else {
+          try {
+            await saveAction(monomerSymbols);
+          } catch (e) {
+            grok.shell.error('Error creating monomer collection');
+            console.error(e);
+          }
+        }
+        d.close();
+      }).show();
+  }
+
   async createNewLibDialog(monomers?: Monomer[]) {
     const monomerLibs = await this.monomerLibManamger.getAvaliableLibraryNames();
     const libNameInput = ui.input.string('Library Name', {
@@ -321,26 +373,36 @@ export class MonomerManager implements IMonomerManager {
           args.context.tableView.id !== (this.tv!.id ?? '') || !args.item || !args.item.isTableCell || (args.item.tableRowIndex ?? -1) < 0)
           return;
         const rowIdx = args.item.tableRowIndex;
-        args.menu.item('Edit Monomer', async () => {
+        const menu = args.menu as DG.Menu;
+        menu.item('Edit Monomer', async () => {
           await this.editMonomer(this.tv!.dataFrame.rows.get(rowIdx));
         });
 
-        args.menu.item('Fix all monomers', () => {
+        menu.item('Fix all monomers', () => {
           this.fixAllMonomers();
         });
         if (this.tv!.dataFrame.selection.trueCount > 0) {
-          args.menu.item('Remove Selected Monomers', async () => {
+          const group = menu.group('Selected Monomers');
+          group.item('Remove', async () => {
             const monomers = await Promise.all(Array.from(this.tv!.dataFrame.selection.getSelectedIndexes())
               .map((r) => monomerFromDfRow(this.tv!.dataFrame.rows.get(r))));
             this._newMonomerForm.removeMonomers(monomers, this.libInput.value!);
           });
-          args.menu.item('Selection To New Library', async () => {
+          group.item('Create Library', async () => {
             const monomers = await Promise.all(Array.from(this.tv!.dataFrame.selection.getSelectedIndexes())
               .map((r) => monomerFromDfRow(this.tv!.dataFrame.rows.get(r))));
             this.createNewLibDialog(monomers);
           });
+          group.item('Create Collection', async () => {
+            const monomerSymbols = Array.from(this.tv!.dataFrame.selection.getSelectedIndexes())
+              .map((r) => this.tv!.dataFrame.col(MONOMER_DF_COLUMN_NAMES.SYMBOL)!.get(r) as string)
+              .filter((s): s is string => !!s && s.trim().length > 0);
+            if (monomerSymbols.length === 0)
+              return grok.shell.warning('No valid monomer symbols found in selection');
+            this.createNewMonomersCollectionDialog(monomerSymbols);
+          });
         } else {
-          args.menu.item('Remove Monomer', async () => {
+          menu.item('Remove Monomer', async () => {
             const monomer = await monomerFromDfRow(this.tv!.dataFrame.rows.get(rowIdx));
             this._newMonomerForm.removeMonomers([monomer], this.libInput.value!);
           });

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

@@ -6,7 +6,6 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {ColumnInputOptions} from '@datagrok-libraries/utils/src/type-declarations';
-import {delay} from '@datagrok-libraries/test/src/test';
 import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
@@ -82,7 +81,7 @@ export async function multipleSequenceAlignmentUI(
         table: table, value: seqCol, onValueChanged: async (value: DG.Column<any>) => {
           if (!value || value.semType !== DG.SEMTYPE.MACROMOLECULE) {
             okBtn.disabled = true;
-            await delay(0); // to
+            await DG.delay(0); // to
             colInput.value = prevSeqCol as DG.Column<string>;
             return;
           }

package/src/utils/seq-helper/seq-handler.ts

@@ -50,9 +50,19 @@ export class SeqHandler implements ISeqHandler {
     if (col.type !== DG.TYPE.STRING)
       throw new Error(`Unexpected column type '${col.type}', must be '${DG.TYPE.STRING}'.`);
     this._column = col;
-    const units: string | null = this._column.meta.units;
-    if (!units)
-      throw new Error('Units are not specified in column');
+    let units: string | null = this._column.meta.units;
+    if (!units) {
+      // it may be from layout that the macromolecule semtype is set but every other tag is missing, so we manually run detectors
+      if (!this._column.temp['seqHandlerDetectorRun']) {
+        this._column.temp['seqHandlerDetectorRun'] = true;
+        const detectorFunc = DG.Func.find({name: 'detectMacromolecule', meta: {role: 'semTypeDetector'}})[0];
+        if (detectorFunc)
+          detectorFunc.applySync({col: this._column});
+        units = this._column.meta.units;
+      }
+      if (!units)
+        throw new Error('Units are not specified in column');
+    }
     this._units = units!;
 
     this._notation = this.getNotation();
@@ -182,7 +192,7 @@ export class SeqHandler implements ISeqHandler {
 
       let aligned = uh.column.getTag(TAGS.aligned);
       if (aligned == null) {
-        aligned = uh.stats.sameLength ? ALIGNMENT.SEQ_MSA : ALIGNMENT.SEQ;
+        aligned = uh.stats.sameLength || uh.column.categories.slice(0, 5).filter((a) => !!a).every((a) => a.length > 100) ? ALIGNMENT.SEQ_MSA : ALIGNMENT.SEQ;
         uh.column.setTag(TAGS.aligned, aligned);
       }
 

package/src/utils/split-to-monomers.ts

@@ -2,7 +2,6 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay} from '@datagrok-libraries/test/src/test';
 import {checkInputColumnUI} from './check-input-column';
 import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
 import * as C from './constants';
@@ -17,7 +16,7 @@ export async function splitToMonomersUI(
 ): Promise<DG.DataFrame> {
   // Delay is required for initial function dialog to close before starting invalidating of molfiles.
   // Otherwise, dialog is freezing
-  await delay(10);
+  await DG.delay(10);
   if (!checkInputColumnUI(seqCol, 'Sequence space')) return table;
 
   const seqHelper = _package.seqHelper;

package/src/viewers/vd-regions-viewer.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {fromEvent, Observable, Subject, Unsubscribable} from 'rxjs';
 
-import {testEvent} from '@datagrok-libraries/test/src/test';
+import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {
   IVdRegionsViewer,
   VdRegion, VdRegionType,

package/src/viewers/web-logo-viewer.ts

@@ -22,7 +22,7 @@ import {
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {intToHtmlA} from '@datagrok-libraries/utils/src/color';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {testEvent} from '@datagrok-libraries/test/src/test';
+import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';
 import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';

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

@@ -9,7 +9,6 @@ import {App, IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {delay} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {updateDivInnerHTML} from '../utils/ui-utils';
@@ -141,7 +140,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
     const logPrefix = `${this.viewerToLog()}.substructureSearch( column = <${column.name}> )`;
     _package.logger.debug(`${logPrefix}, start`);
     try {
-      await delay(10);
+      await DG.delay(10);
       const res = await helmSubstructureSearch(this.props.substructure, column, this.seqHelper);
       return res;
     } finally {
@@ -163,7 +162,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
   // async awaitRendered(timeout: number = 10000): Promise<void> {
   //   const callLog = `awaitRendered( ${timeout} )`;
   //   const logPrefix = `${this.viewerToLog()}.${callLog}`;
-  //   await delay(0);
+  //   await DG.delay(0);
   //   await testEvent(this.onRendered, () => {
   //     this.logger.debug(`${logPrefix}, ` + '_onRendered event caught');
   //   }, () => {

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

@@ -14,7 +14,7 @@ import wu from 'wu';
 import {Observable, Subject, Unsubscribable} from 'rxjs';
 
 import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {delay, testEvent} from '@datagrok-libraries/test/src/test';
+import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {IRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';
@@ -269,7 +269,7 @@ export class BioSubstructureFilter extends DG.Filter implements IRenderer {
   async awaitRendered(timeout: number = 10000): Promise<void> {
     const callLog = `awaitRendered( ${timeout} )`;
     const logPrefix = `${this.filterToLog()}.${callLog}`;
-    await delay(10);
+    await DG.delay(10);
     await testEvent(this.onRendered, () => {
       this.logger.debug(`${logPrefix}, ` + '_onRendered event caught');
     }, () => {