@datagrok/bio 2.25.13 → 2.25.14

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.25.13",
+  "version": "2.25.14",
   "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",

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

@@ -4,7 +4,6 @@ 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 {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 {
@@ -91,7 +90,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
         return true;
       })(),
       (async () => {
-        await delay(timeout);
+        await DG.delay(timeout);
         return false;
       })(),
     ]).then((res) => {

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');
     }, () => {