@datagrok/sequence-translator 1.4.4 → 1.4.6

package/files/polytool-rules/rules_example.json

@@ -25,7 +25,7 @@
   },
   {
     "type": "reaction",
-    "code": "3",
+    "code": "4",
     "monomericSubstitution": {
       "firstMonomer": "azG",
       "secondMonomer": "aG",
@@ -39,6 +39,6 @@
   },
   {
     "type": "differentFragments",
-    "code": "$4"
+    "code": "$3"
   }
 ]

package/files/samples/HELM.csv

@@ -0,0 +1,6 @@
+HELM
+"PEPTIDE1{[meI].[hHis].[Aca].N.T.[dE].[Aca].[D-Tyr_Et].[Tyr_ab-dehydroMe].[dV].E.N.[D-Orn].[D-aThr].[Phe_4Me]}$PEPTIDE1,PEPTIDE1,15:R2-1:R1$$$V2.0"
+"PEPTIDE1{R.F.C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$V2.0",
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV.Phe_ab-dehydro.N.D-Orn.D-aThr.Phe_4Me}$$$$
+"PEPTIDE1{C.A.C.A.C.A.C.A}|PEPTIDE2{C.A.C.A.C.A.C.A}|PEPTIDE3{C.A.C.A.C.A.C.A}|PEPTIDE4{C.A.C.A.C.A.C.A}$PEPTIDE1,PEPTIDE2,3:R3-8:R2|PEPTIDE3,PEPTIDE4,3:R3-8:R2|PEPTIDE1,PEPTIDE3,5:R3-5:R3$$$V2.0"
+"PEPTIDE1{C.A.C.A.C.A.C.A.C.A.C.A}|PEPTIDE2{C.A.C.A.C.A.C.A.C.A.C.A}$PEPTIDE2,PEPTIDE1,1:R1-3:R3|PEPTIDE2,PEPTIDE2,1:R3-12:R2$$$V2.0"

package/files/samples/cyclized.csv

@@ -1,8 +1,9 @@
 n,seqs
 1,R-F-C(1)-T-G-H-F-Y-G-H-F-Y-G-H-F-Y-P-C(1)-meI
-2,C(1)-T-G-H-F-Y-P-C(1)-meI
+2,C(1)-T-G-Aca-F-Y-P-C(1)-meI
 3,R-F-C(1)-T-G-H-F-Y-P-C(1)
 4,C(1)-T-G-H-F-H-P-C(1)
 5,R-F-D(2)-T-G-H-F-Y-P-NH2(2)
-6,R-F-azG(3)-T-G-H-F-Y-P-aG(3)-meI
-7,R-F-aG(3)-T-G-H-F-Y-P-azG(3)-meI
+6,D(2)-T-G-H-F-Y-P-NH2(2)
+7,R-F-azG(4)-T-G-H-F-Y-P-aG(4)-meI
+8,R-F-aG(4)-T-G-H-F-Y-P-azG(4)-meI

package/files/samples/cyclized_MSA.csv

@@ -0,0 +1,5 @@
+n,seqs
+1,R-F-C(1)-Thz-G-H-F-Y-G-P-C(1)-meI-R
+2,R-F-C(1)-T-Thz-H-F-Y-G-P-C(1)-meI-R
+3,R-F-C(1)-T-G-Thz-F-Y-G-P-C(1)-meI-R
+4,R-F-C(1)-T-G-H-Thz-Y-G-P-C(1)-meI-R

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.4.4",
+  "version": "1.4.6",
   "author": {
     "name": "Alexey Chopovsky",
     "email": "achopovsky@datagrok.ai"
@@ -22,10 +22,10 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.44.2",
+    "@datagrok-libraries/bio": "^5.45.5",
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/tutorials": "^1.4.0",
-    "@datagrok-libraries/utils": "^4.3.5",
+    "@datagrok-libraries/tutorials": "^1.4.3",
+    "@datagrok-libraries/utils": "^4.3.6",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
     "datagrok-api": "^1.21.1",
@@ -36,32 +36,32 @@
     "ts-loader": "^9.3.1",
     "typeahead-standalone": "4.14.1",
     "typescript": "^5.4.2",
-    "wu": "latest"
+    "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.11",
-    "@datagrok-libraries/js-draw-lite": "^0.0.8",
-    "@datagrok/bio": "^2.15.6",
-    "@datagrok/helm": "^2.5.3",
-    "@datagrok/chem": "^1.12.1",
+    "@datagrok-libraries/helm-web-editor": "^1.1.12",
+    "@datagrok-libraries/js-draw-lite": "^0.0.9",
+    "@datagrok/bio": "^2.16.6",
+    "@datagrok/helm": "^2.5.7",
+    "@datagrok/chem": "^1.12.4",
     "@types/jquery": "^3.5.14",
     "@types/js-yaml": "^4.0.5",
     "@types/lodash": "^4.14.202",
     "@types/node-fetch": "^2.6.2",
     "@types/object-hash": "^3.0.6",
     "@types/react": "^18.0.15",
-    "@types/wu": "latest",
+    "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^7.2.0",
     "@typescript-eslint/parser": "^7.2.0",
     "css-loader": "^6.7.3",
     "eslint": "^8.57.0",
-    "eslint-config-google": "latest",
+    "eslint-config-google": "^0.14.0",
     "style-loader": "^3.3.1",
     "ts-loader": "^9.3.1",
     "typescript": "^4.7.4",
     "typescript-eslint": "^7.2.0",
     "webpack": "^5.75.0",
-    "webpack-cli": "latest"
+    "webpack-cli": "^5.1.4"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",

package/src/apps/common/model/oligo-toolkit-package.ts

@@ -16,8 +16,16 @@ import {MonomerLibWrapper} from './monomer-lib/lib-wrapper';
 import {FormatConverter} from '../../translator/model/format-converter';
 import {FormatDetector} from './parsing-validation/format-detector';
 import {highlightInvalidSubsequence} from '../view/components/colored-input/input-painters';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 export class OligoToolkitPackage extends DG.Package implements ITranslationHelper {
+  private _seqHelper: ISeqHelper;
+  public get seqHelper(): ISeqHelper {
+    if (!this._seqHelper)
+      throw new Error('Package SequenceTranslator .seqHelper is not initialized');
+    return this._seqHelper;
+  }
+
   private _monomerLib?: IMonomerLib;
   get monomerLib(): IMonomerLib {
     if (!this._monomerLib)
@@ -39,17 +47,28 @@ export class OligoToolkitPackage extends DG.Package implements ITranslationHelpe
     return this._monomerLibWrapper;
   }
 
+  private _initPromise: Promise<void>;
+  public get initPromise(): Promise<void> { return this._initPromise; }
+
   constructor(opts: { debug: boolean } = {debug: false}) {
     super();
     // @ts-ignore
     super._logger = new LoggerWrapper(super.logger, opts.debug);
   }
 
-  private initPromise?: Promise<void>;
+  startInit(initPromise: Promise<void>): void {
+    this._initPromise = initPromise;
+  }
+
+  completeInit(seqHelper: ISeqHelper): void {
+    this._seqHelper = seqHelper;
+  }
+
+  private initLibDataPromise?: Promise<void>;
 
   async initLibData(): Promise<void> {
-    if (!this.initPromise) {
-      this.initPromise = (async () => {
+    if (!this.initLibDataPromise) {
+      this.initLibDataPromise = (async () => {
         const packageSettings = await this.getSettings();
         let monomersPath: string = packageSettings['MonomersPath'];
         if (!monomersPath || !(await grok.dapi.files.exists(monomersPath))) {
@@ -64,7 +83,7 @@ export class OligoToolkitPackage extends DG.Package implements ITranslationHelpe
         this._monomerLibWrapper = new MonomerLibWrapper(this.monomerLib, this.jsonData);
       })();
     }
-    return this.initPromise;
+    return this.initLibDataPromise;
   }
 
   async getTranslationHelper(): Promise<ITranslationHelper> {

package/src/apps/common/view/components/molecule-img.ts

@@ -17,8 +17,8 @@ export class MoleculeImage {
     this.molblock = molblok;
   }
 
-  private _validMolBlock: string;
-  get molblock(): string { return this._validMolBlock; }
+  private _validMolBlock!: string;
+  get molblock(): string { return this._validMolBlock!; }
 
   set molblock(value: string) {
     if (value === '') {

package/src/apps/pattern/model/data-manager.ts

@@ -33,7 +33,7 @@ export class DataManager {
     instance.currentUserName = await instance.fetchCurrentUserName();
     instance.currentUserId = await instance.fetchCurrentUserId();
 
-    const patternRecords = await instance.fetchPatterns();
+    const patternRecords = instance.fetchPatterns();
     await instance.initializePatternMaps(patternRecords);
 
     return instance;
@@ -81,7 +81,7 @@ export class DataManager {
     if (hash === null || hash === '')
       return null;
     try {
-      const patternConfig = await grok.dapi.userDataStorage.getValue(STORAGE_NAME, hash, false);
+      const patternConfig = grok.userSettings.getValue(STORAGE_NAME, hash, false) ?? 'null';
       const config = JSON.parse(patternConfig) as PatternConfigRecord;
       return config;
     } catch {
@@ -181,7 +181,7 @@ export class DataManager {
         [D.MODIFY]: timestamp,
       };
       const record = JSON.stringify(recordObj);
-      await grok.dapi.userDataStorage.postValue(STORAGE_NAME, hash, record, false);
+      grok.userSettings.add(STORAGE_NAME, hash, record, false);
       this.currentUserPatternNameToHash.set(patternName, hash);
 
       eventBus.selectAuthor(this.getCurrentUserAuthorshipCategory());
@@ -212,14 +212,14 @@ export class DataManager {
     newRecordObj[R.DATE] = {
       [D.MODIFY]: timestamp,
     };
-    const oldPattern = await grok.dapi.userDataStorage.getValue(STORAGE_NAME, oldHash, false);
+    const oldPattern = grok.userSettings.getValue(STORAGE_NAME, oldHash, false) ?? 'null';
     const oldPatternsRecord = JSON.parse(oldPattern) as PatternConfigRecord;
     if (oldPatternsRecord[R.DATE] !== undefined && oldPatternsRecord[R.DATE][D.CREATE] != undefined)
       newRecordObj[R.DATE][D.CREATE] = oldPatternsRecord[R.DATE][D.CREATE];
 
     const newRecord = JSON.stringify(newRecordObj);
-    await grok.dapi.userDataStorage.postValue(STORAGE_NAME, newHash, newRecord, false);
-    await grok.dapi.userDataStorage.remove(STORAGE_NAME, oldHash, false);
+    grok.userSettings.add(STORAGE_NAME, newHash, newRecord, false);
+    grok.userSettings.delete(STORAGE_NAME, oldHash, false);
 
     this.currentUserPatternNameToHash.set(patternName, newHash);
     eventBus.requestPatternLoad(newHash);
@@ -237,7 +237,7 @@ export class DataManager {
     }
     if (hash === undefined)
       throw new Error(`Pattern with name ${patternName} not found`);
-    await grok.dapi.userDataStorage.remove(STORAGE_NAME, hash, false);
+    grok.userSettings.delete(STORAGE_NAME, hash, false);
     this.currentUserPatternNameToHash.delete(patternName);
     eventBus.updatePatternList();
 
@@ -264,8 +264,8 @@ export class DataManager {
     return (await grok.dapi.users.current()).id;
   }
 
-  private async fetchPatterns() {
-    const patternsRecord = await grok.dapi.userDataStorage.get(STORAGE_NAME, false) as RawPatternRecords;
+  private fetchPatterns(): RawPatternRecords {
+    const patternsRecord = (grok.userSettings.get(STORAGE_NAME, false) ?? {}) as RawPatternRecords;
     return patternsRecord;
   }
 

package/src/apps/translator/view/ui.ts

@@ -3,9 +3,10 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 
+import $ from 'cash-dom';
 import {Subject, BehaviorSubject, Observable} from 'rxjs';
 
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 import {DEFAULT_FORMATS} from '../../common/model/const';
@@ -22,7 +23,6 @@ import {ITranslationHelper} from '../../../types';
 
 import {NUCLEOTIDES_FORMAT, SEQUENCE_COPIED_MSG, SEQ_TOOLTIP_MSG} from './const';
 import './style.css';
-import $ from 'cash-dom';
 import {_package} from '../../../package';
 
 const enum REQUIRED_COLUMN_LABEL {
@@ -34,9 +34,10 @@ const REQUIRED_COLUMN_LABELS = [REQUIRED_COLUMN_LABEL.SEQUENCE];
 class TranslatorAppLayout {
   private eventBus: EventBus;
   private inputFormats = Object.keys(_package.jsonData.codesToHelmDict).concat(DEFAULT_FORMATS.HELM);
+  private readonly seqHelper: ISeqHelper = _package.seqHelper;
 
   constructor(
-    private readonly th: ITranslationHelper
+    private readonly th: ITranslationHelper,
   ) {
     this.moleculeImgDiv = ui.div([]);
     this.moleculeImgDiv.className = 'mol-host';
@@ -171,9 +172,9 @@ class TranslatorAppLayout {
       translatedColumn.semType = DG.SEMTYPE.MACROMOLECULE;
       const units = outputFormat == NUCLEOTIDES_FORMAT ? NOTATION.FASTA : NOTATION.HELM;
       translatedColumn.meta.units = units;
-      const seqHandler = SeqHandler.forColumn(translatedColumn as DG.Column<string>);
-      const setUnits = outputFormat == NUCLEOTIDES_FORMAT ? SeqHandler.setUnitsToFastaColumn :
-        SeqHandler.setUnitsToHelmColumn;
+      const seqHandler = this.seqHelper.getSeqHandler(translatedColumn as DG.Column<string>);
+      const setUnits = outputFormat == NUCLEOTIDES_FORMAT ? this.seqHelper.setUnitsToFastaColumn :
+        this.seqHelper.setUnitsToHelmColumn;
       setUnits(seqHandler);
     }
 
@@ -462,8 +463,7 @@ class ColumnInputsManager {
     const input = ui.input.choice(`${columnLabel}`, {
       value: selectedColumnName, items: columnNames,
       onValueChanged: (value) => this.selectColumnIfTableNotNull(selectedTable, value, columnLabel)
-    }
-    );
+    });
 
     return input;
   }

package/src/consts.ts

@@ -0,0 +1,12 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+export const enum PolyToolTags {
+  dataRole = 'polytool-data-role',
+}
+
+export const enum PolyToolDataRole {
+  template = 'template',
+  macromolecule = 'macromolecule',
+}

package/src/global.d.ts

@@ -0,0 +1,13 @@
+import * as grokNamespace from 'datagrok-api/grok';
+import * as uiNamespace from 'datagrok-api/ui';
+import * as DGNamespace from 'datagrok-api/dg';
+import * as rxjsNamespace from 'rxjs';
+import $Namespace from 'cash-dom';
+
+declare global {
+    const grok: typeof grokNamespace;
+    const ui: typeof uiNamespace;
+    const DG: typeof DGNamespace;
+    const rjxs: typeof rxjsNamespace;
+    const $: typeof $Namespace;
+}

package/src/package-test.ts

@@ -8,10 +8,13 @@ import './tests/formats-to-helm';
 import './tests/helm-to-nucleotides';
 import './tests/formats-support';
 import './tests/files-tests';
+import './tests/polytool-detectors-custom-notation-test';
 import './tests/polytool-convert-tests';
 import './tests/polytool-unrule-tests';
 import './tests/polytool-enumerate-tests';
 import './tests/polytool-enumerate-breadth-tests';
+import './tests/polytool-chain-parse-notation-tests';
+import './tests/polytool-chain-from-notation-tests';
 import './tests/toAtomicLevel-tests';
 
 import {OligoToolkitTestPackage} from './tests/utils';

package/src/package.ts

@@ -2,16 +2,15 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {MonomerLibWrapper} from './apps/common/model/monomer-lib/lib-wrapper';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {SeqTemps} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+
 import {OligoToolkitPackage} from './apps/common/model/oligo-toolkit-package';
-import {FormatDetector} from './apps/common/model/parsing-validation/format-detector';
-import {SequenceValidator} from './apps/common/model/parsing-validation/sequence-validator';
 import {APP_NAME} from './apps/common/view/const';
 import {getSpecifiedAppUI} from './apps/common/view/utils';
 import {CombinedAppUI} from './apps/common/view/combined-app-ui';
 import {linkStrandsV3000} from './apps/structure/model/mol-transformations';
 import {SequenceToMolfileConverter} from './apps/structure/model/sequence-to-molfile';
-import {FormatConverter} from './apps/translator/model/format-converter';
 import {demoOligoPatternUI, demoOligoStructureUI, demoOligoTranslatorUI} from './demo/demo-st-ui';
 import {getExternalAppViewFactories} from './plugins/mermade';
 import {defaultErrorHandler} from './utils/err-info';
@@ -25,10 +24,29 @@ import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converte
 import {ITranslationHelper} from './types';
 import {addContextMenuUI} from './utils/context-menu';
 import {PolyToolConvertFuncEditor} from './polytool/pt-convert-editor';
-import {polyToolUnruleUI} from './polytool/pt-unrule';
+import {CyclizedNotationProvider} from './utils/cyclized';
+import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {PolyToolTags} from './consts';
 
 export const _package: OligoToolkitPackage = new OligoToolkitPackage({debug: true}/**/);
 
+let initSequenceTranslatorPromise: Promise<void> | null = null;
+
+//tags: init
+export async function init(): Promise<void> {
+  if (initSequenceTranslatorPromise === null) {
+    _package.startInit(initSequenceTranslatorPromise = initSequenceTranslatorInt());
+  }
+  return initSequenceTranslatorPromise;
+}
+
+async function initSequenceTranslatorInt(): Promise<void> {
+  const [seqHelper] = await Promise.all([
+    getSeqHelper(),
+  ]);
+  _package.completeInit(seqHelper);
+}
+
 //name: Oligo Toolkit
 //meta.icon: img/icons/toolkit.png
 //meta.browsePath: Oligo
@@ -277,3 +295,12 @@ export async function ptEnumeratorHelmApp(): Promise<void> {
 export async function ptEnumeratorChemApp(): Promise<void> {
   polyToolEnumerateChemUI();
 }
+
+//name: applyNotationProviderForHarmonizedSequence
+//input: column col
+//input: string separator
+export function applyNotationProviderForCyclized(col: DG.Column<string>, separator: string) {
+  col.meta.units = NOTATION.CUSTOM;
+  col.tags[PolyToolTags.dataRole] = 'template';
+  col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator, _package.seqHelper);
+}