@datagrok/sequence-translator 1.10.4 → 1.10.6

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.10.4",
+  "version": "1.10.6",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -28,7 +28,7 @@
     "@datagrok-libraries/utils": "^4.6.5",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
-    "datagrok-api": "^1.25.0",
+    "datagrok-api": "^1.26.0",
     "lodash": "^4.17.21",
     "object-hash": "^3.0.0",
     "openchemlib": "6.0.1",
@@ -36,7 +36,8 @@
     "ts-loader": "^9.3.1",
     "typeahead-standalone": "4.14.1",
     "typescript": "^5.4.2",
-    "wu": "^2.1.0"
+    "wu": "^2.1.0",
+    "@datagrok-libraries/test": "^1.1.0"
   },
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.16",
@@ -54,7 +55,7 @@
     "@typescript-eslint/eslint-plugin": "^7.2.0",
     "@typescript-eslint/parser": "^7.2.0",
     "css-loader": "^6.7.3",
-    "datagrok-tools": "^4.14.55",
+    "datagrok-tools": "^5.0.0",
     "eslint": "^8.57.0",
     "eslint-config-google": "^0.14.0",
     "style-loader": "^3.3.1",
@@ -89,5 +90,8 @@
   "canView": [
     "All users"
   ],
-  "category": "Bioinformatics"
+  "category": "Bioinformatics",
+  "overrides": {
+    "datagrok-api": "$datagrok-api"
+  }
 }

package/scripts/build-monomer-lib.py

@@ -1,4 +1,3 @@
-# pylint: disable=no-member
 import os.path
 import sys
 from io import TextIOWrapper

package/src/apps/common/view/components/colored-input/input-painters.ts

@@ -24,7 +24,7 @@ export function demoPainter(input: string): HTMLSpanElement[] {
   return spans;
 }
 
-// todo: port to another place
+/* todo: port to another place */
 export function highlightInvalidSubsequence(input: string, th: ITranslationHelper): HTMLSpanElement[] {
   // validate sequence
   let cutoff = 0;

package/src/apps/structure/model/monomer-code-parser.ts

@@ -84,7 +84,7 @@ export class MonomerSequenceParser {
   }
 }
 
-// todo: to be eliminated after full helm support
+/* todo: to be eliminated after full helm support */
 function monomerHasLeftPhosphateLinker(monomerSymbol: string): boolean {
   return _package.jsonData.monomersWithPhosphate['left'].includes(monomerSymbol);
 }

package/src/apps/translator/model/conversion-utils.ts

@@ -51,7 +51,7 @@ export function getNucleotidesSequence(helmString: string, monomerLib: MonomerLi
   return nucleotides;
 }
 
-// todo: remove after refactoring as a workaround
+/* todo: remove after refactoring as a workaround */
 export function convert(
   sequence: string, sourceFormat: string, targetFormat: string, th: ITranslationHelper
 ): string | null {

package/src/demo/demo-st-ui.ts

@@ -2,7 +2,7 @@ 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/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 import {PackageFunctions} from '../package';
 import {tryCatch} from '../apps/common/model/helpers';
 

package/src/package-test.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/test/src/test';
 
 import './tests/formats-to-helm';
 import './tests/helm-to-nucleotides';

package/src/package.g.ts

@@ -4,6 +4,7 @@ import * as DG from 'datagrok-api/dg';
 //name: Oligo Toolkit
 //tags: app
 //output: view result
+//meta.role: app
 //meta.icon: img/icons/toolkit.png
 //meta.browsePath: Peptides | Oligo Toolkit
 export async function oligoToolkitApp() : Promise<any> {
@@ -11,6 +12,7 @@ export async function oligoToolkitApp() : Promise<any> {
 }
 
 //tags: init
+//meta.role: init
 export async function init() : Promise<void> {
   await PackageFunctions.init();
 }
@@ -18,6 +20,7 @@ export async function init() : Promise<void> {
 //name: Oligo Translator
 //tags: app
 //output: view result
+//meta.role: app
 //meta.icon: img/icons/translator.png
 //meta.browsePath: Peptides | Oligo Toolkit
 export async function oligoTranslatorApp() : Promise<any> {
@@ -27,6 +30,7 @@ export async function oligoTranslatorApp() : Promise<any> {
 //name: Oligo Pattern
 //tags: app
 //output: view result
+//meta.role: app
 //meta.icon: img/icons/pattern.png
 //meta.browsePath: Peptides | Oligo Toolkit
 export async function oligoPatternApp() : Promise<any> {
@@ -36,6 +40,7 @@ export async function oligoPatternApp() : Promise<any> {
 //name: Oligo Structure
 //tags: app
 //output: view result
+//meta.role: app
 //meta.icon: img/icons/structure.png
 //meta.browsePath: Peptides | Oligo Toolkit
 export async function oligoStructureApp() : Promise<any> {
@@ -113,6 +118,7 @@ export async function polyToolConvertTopMenu() : Promise<void> {
 //tags: editor
 //input: funccall call 
 //output: column result
+//meta.role: editor
 export async function getPolyToolConvertEditor(call: DG.FuncCall) : Promise<any> {
   return await PackageFunctions.getPolyToolConvertEditor(call);
 }
@@ -157,6 +163,7 @@ export async function createMonomerLibraryForPolyTool(file: DG.FileInfo) : Promi
 //tags: app
 //meta.icon: img/icons/structure.png
 //meta.browsePath: Peptides | PolyTool
+//meta.role: app
 export async function ptEnumeratorHelmApp() : Promise<void> {
   await PackageFunctions.ptEnumeratorHelmApp();
 }
@@ -165,6 +172,7 @@ export async function ptEnumeratorHelmApp() : Promise<void> {
 //tags: app
 //meta.icon: img/icons/structure.png
 //meta.browsePath: Peptides | PolyTool
+//meta.role: app
 export async function ptEnumeratorChemApp() : Promise<void> {
   await PackageFunctions.ptEnumeratorChemApp();
 }

package/src/package.ts

@@ -79,7 +79,8 @@ export class PackageFunctions {
   @grok.decorators.app({
     icon: 'img/icons/toolkit.png',
     browsePath: 'Peptides | Oligo Toolkit',
-    name: 'Oligo Toolkit'
+    name: 'Oligo Toolkit',
+    tags: ['app']
   })
   static async oligoToolkitApp(): Promise<DG.ViewBase> {
     await _package.initLibData();
@@ -92,7 +93,7 @@ export class PackageFunctions {
   }
 
 
-  @grok.decorators.init()
+  @grok.decorators.init({tags: ['init']})
   static async init(): Promise<void> {
     if (initSequenceTranslatorPromise === null)
       _package.startInit(initSequenceTranslatorPromise = initSequenceTranslatorInt());
@@ -103,7 +104,8 @@ export class PackageFunctions {
   @grok.decorators.app({
     icon: 'img/icons/translator.png',
     browsePath: 'Peptides | Oligo Toolkit',
-    name: 'Oligo Translator'
+    name: 'Oligo Translator',
+    tags: ['app']
   })
   static async oligoTranslatorApp(): Promise<DG.ViewBase> {
     const view = await getSpecifiedAppView(APP_NAME.TRANSLATOR);
@@ -114,7 +116,8 @@ export class PackageFunctions {
   @grok.decorators.app({
     icon: 'img/icons/pattern.png',
     browsePath: 'Peptides | Oligo Toolkit',
-    name: 'Oligo Pattern'
+    name: 'Oligo Pattern',
+    tags: ['app']
   })
   static async oligoPatternApp(): Promise<DG.ViewBase> {
     const view = await getSpecifiedAppView(APP_NAME.PATTERN);
@@ -125,7 +128,8 @@ export class PackageFunctions {
   @grok.decorators.app({
     icon: 'img/icons/structure.png',
     browsePath: 'Peptides | Oligo Toolkit',
-    name: 'Oligo Structure'
+    name: 'Oligo Structure',
+    tags: ['app']
   })
   static async oligoStructureApp(): Promise<DG.ViewBase> {
     const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
@@ -229,7 +233,7 @@ export class PackageFunctions {
     await polyToolConvertUI();
   }
 
-  @grok.decorators.editor()
+  @grok.decorators.editor({tags: ['editor']})
   static async getPolyToolConvertEditor(
     call: DG.FuncCall): Promise<DG.Column<string> | null> {
     const funcEditor = await PolyToolConvertFuncEditor.create(call);
@@ -296,10 +300,11 @@ export class PackageFunctions {
   @grok.decorators.func({
     meta: {
       icon: 'img/icons/structure.png',
-      browsePath: 'Peptides | PolyTool'
+      browsePath: 'Peptides | PolyTool',
+      role: 'app'
     },
-    tags: ['app'],
-    name: 'HELM Enumerator'
+    name: 'HELM Enumerator',
+    tags: ['app']
   })
   static async ptEnumeratorHelmApp(): Promise<void> {
     await polyToolEnumerateHelmUI();
@@ -309,10 +314,11 @@ export class PackageFunctions {
   @grok.decorators.func({
     meta: {
       icon: 'img/icons/structure.png',
-      browsePath: 'Peptides | PolyTool'
+      browsePath: 'Peptides | PolyTool',
+      role: 'app'
     },
-    tags: ['app'],
-    name: 'Chem Enumerator'
+    name: 'Chem Enumerator',
+    tags: ['app']
   })
   static async ptEnumeratorChemApp(): Promise<void> {
     polyToolEnumerateChemUI();

package/src/polytool/conversion/pt-synthetic.ts

@@ -70,19 +70,27 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
   for (let i = 0; i < rule.firstMonomers.length; i++) {
     const monomer = mLib.getMonomer('PEPTIDE', rule.firstMonomers[i]);
 
-    if (monomer) {
-      const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
-      monomers[counter] = sMolBlock;
-      monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    if (monomer && monomer.molfile) {
+      try {
+        const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
+        monomers[counter] = sMolBlock;
+        monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+      } catch (e: any) {
+        console.error(e);
+      }
     }
     counter++;
   }
   for (let i = 0; i < rule.secondMonomers.length; i++) {
     const monomer = mLib.getMonomer('PEPTIDE', rule.secondMonomers[i]);
-    if (monomer) {
-      const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
-      monomers[counter] = sMolBlock;
-      monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    if (monomer && monomer.molfile) {
+      try {
+        const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
+        monomers[counter] = sMolBlock;
+        monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+      } catch (e: any) {
+        console.error(e);
+      }
     }
     counter++;
   }

package/src/polytool/pt-enumerate-seq-dialog.ts

@@ -19,6 +19,7 @@ import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {InputColumnBase} from '@datagrok-libraries/bio/src/types/input';
 import {SeqValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqTemps} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 import {PolyToolEnumeratorParams, PolyToolEnumeratorType, PolyToolEnumeratorTypes} from './types';
 import {getLibrariesList, LIB_PATH} from './utils';
@@ -32,11 +33,13 @@ import {RuleInputs, RULES_PATH, RULES_STORAGE_NAME} from './conversion/pt-rules'
 import {Chain} from './conversion/pt-chain';
 import {polyToolConvert} from './pt-dialog';
 
-import {_package, PackageFunctions} from '../package';
+import {_package, applyNotationProviderForCyclized, PackageFunctions} from '../package';
 import {buildMonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 
 import {PolymerTypes} from '@datagrok-libraries/js-draw-lite/src/types/org';
+import { CyclizedNotationProvider } from '../utils/cyclized';
+import { INotationProvider } from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 
 type PolyToolEnumerateInputs = {
   macromolecule: HelmInputBase;
@@ -161,9 +164,22 @@ async function getPolyToolEnumerateDialog(
     const getValue = (cell?: DG.Cell): [SeqValueBase, PolyToolDataRole] => {
       let resSeqValue: SeqValueBase;
       let resDataRole: PolyToolDataRole;
+      let resHelm: string | null = null;
       if (cell && cell.rowIndex >= 0 && cell?.column.semType == DG.SEMTYPE.MACROMOLECULE) {
         const sh = seqHelper.getSeqHandler(cell.column);
         resSeqValue = sh.getValue(cell.rowIndex);
+        // if (cell.column.temp?.[SeqTemps.notationProvider])
+        if (cell.column.temp?.[SeqTemps.notationProvider] && !(cell.column.temp[SeqTemps.notationProvider] instanceof CyclizedNotationProvider)) {
+          const notationProvider = cell.column.temp[SeqTemps.notationProvider] as INotationProvider;
+          resHelm = notationProvider.getHelm(resSeqValue.value, {});
+          // create temp helm column to apply notation provider for cyclized sequences
+          let seqCol: DG.Column;
+          DG.DataFrame.fromColumns([seqCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [resHelm])]);
+          seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+          seqCol.meta.units = NOTATION.HELM;
+          const sh = seqHelper.getSeqHandler(seqCol);
+          resSeqValue = sh.getValue(0);
+        }
         resDataRole = (resSeqValue.tags[PolyToolTags.dataRole] as PolyToolDataRole.template) ?? PolyToolDataRole.macromolecule;
       } else {
         const seqCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [PT_HELM_EXAMPLE]);
@@ -200,8 +216,13 @@ async function getPolyToolEnumerateDialog(
                 if (aa.T === 'ATOM') {
                   try {
                     if (!seqValue.isDna() && !seqValue.isRna()) {
-                      const canonicalSymbol = seqValue.getSplitted().getCanonical(aa.bio!.continuousId - 1);
-                      return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
+                      if (cell?.column?.temp?.[SeqTemps.notationProvider] instanceof CyclizedNotationProvider) {
+                        const canonicalSymbol = seqValue.getSplitted().getCanonical(aa.bio!.continuousId - 1);
+                        return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
+                      } else {
+                        const canonicalSymbol = aa.elem;
+                        return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
+                      }
                     } else {
                       const canonicalSymbol = seqValue.getSplittedWithSugarsAndPhosphates().getCanonical(aa.bio!.continuousId - 1);
                       return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
@@ -475,7 +496,7 @@ async function getPolyToolEnumerateDialog(
       const cell = grok.shell.tv.dataFrame.currentCell;
       if (cell.column.semType !== DG.SEMTYPE.MACROMOLECULE) return;
 
-      [seqValue, dataRole] = getValue();
+      [seqValue, dataRole] = getValue(cell);
       fillForCurrentCell(seqValue, dataRole, cell);
     }));
 
@@ -554,9 +575,9 @@ async function getPolyToolEnumerateDialog(
     const exec = async (): Promise<void> => {
       try {
         const srcHelm = inputs.macromolecule.stringValue;
-        const helmSelections: number[] = wu.enumerate<HelmAtom>(inputs.macromolecule.molValue.atoms)
+        const helmSelections = wu.enumerate<HelmAtom>(inputs.macromolecule.molValue.atoms)
           .filter(([a, aI]) => a.highlighted)
-          .map(([a, aI]) => aI).toArray();
+          .map(([a, aI]) => a).toArray();
         if (inputs.enumeratorType.value === PolyToolEnumeratorTypes.Library) {
           if (helmSelections.length === 0) {
             grok.shell.warning('PolyTool: position for enumeration was not selected');
@@ -595,7 +616,8 @@ async function getPolyToolEnumerateDialog(
               grok.shell.warning(`Monomer Library '${monLibName}' was not found`);
               return;
             }
-            const peptideMonomers = monLib.getMonomerSymbolsByType(PolymerTypes.PEPTIDE);
+            const polymerType = helmTypeToPolymerType(helmSelections[0].biotype() ?? 'HELM_AA');
+            const peptideMonomers = monLib.getMonomerSymbolsByType(polymerType);
             placeHoldersValue[0].monomers = peptideMonomers;
             enumerationType = PolyToolEnumeratorTypes.Single;
           }

package/src/tests/files-tests.ts

@@ -2,7 +2,7 @@ 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, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 
 import {getHelm} from './utils';

package/src/tests/formats-support.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {DEFAULT_FORMATS} from '../apps/common/model/const';
 import {getTranslatedSequences} from '../apps/translator/model/conversion-utils';
 import {ITranslationHelper} from '../types';

package/src/tests/formats-to-helm.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {getFormat, getHelm} from './utils';
 import {ITranslationHelper} from '../types';
 

package/src/tests/helm-to-nucleotides.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {getNucleotidesSequence} from '../apps/translator/model/conversion-utils';
 import {ITranslationHelper} from '../types';
 

package/src/tests/polytool-chain-from-notation-tests.ts

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 import {Chain} from '../polytool/conversion/pt-chain';
 import {getRules} from '../polytool/conversion/pt-rules';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';

package/src/tests/polytool-chain-parse-notation-tests.ts

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 import {Chain} from '../polytool/conversion/pt-chain';
 import {getInnerIdx, getOuterIdx} from '../polytool/conversion/pt-misc';
 import {getRules} from '../polytool/conversion/pt-rules';

package/src/tests/polytool-convert-tests.ts

@@ -4,7 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {before, after, category, expect, test, expectArray, testEvent, expectObject}
-  from '@datagrok-libraries/utils/src/test';
+  from '@datagrok-libraries/test/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {

package/src/tests/polytool-detectors-custom-notation-test.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, expect, before} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, before} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper, getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {ALIGNMENT, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {_testNeg, _testPos, DetectorTestData, DfReaderFunc, PosCol} from './utils/detect-macromolecule-utils';

package/src/tests/polytool-enumerate-breadth-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/polytool-enumerate-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/polytool-unrule-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 
 import {doPolyToolUnrule} from '../polytool/pt-unrule';
 import {getRules} from '../polytool/conversion/pt-rules';

package/src/tests/toAtomicLevel-tests.ts

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/test/src/test';
 import {Monomer, MonomerLibData} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';

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

@@ -3,7 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {ALIGNMENT, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {delay, expect} from '@datagrok-libraries/utils/src/test';
+import {delay, expect} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 export type DetectorTestData = { [testName: string]: { csv: string, neg?: string[], pos?: { [colName: string]: PosCol } } };