@datagrok/sequence-translator 1.9.9 → 1.9.11

package/src/package.ts

@@ -15,7 +15,6 @@ import {demoOligoPatternUI, demoOligoStructureUI, demoOligoTranslatorUI} from '.
 import {getExternalAppViewFactories} from './plugins/mermade';
 import {defaultErrorHandler} from './utils/err-info';
 
-//polytool specific
 import {polyToolConvert, polyToolConvertUI} from './polytool/pt-dialog';
 import {polyToolEnumerateChemUI} from './polytool/pt-dialog';
 import {polyToolEnumerateHelmUI} from './polytool/pt-enumerate-seq-dialog';
@@ -29,295 +28,368 @@ import {PolyToolTags} from './consts';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import { getPTCombineDialog } from './polytool/pt-combine-dialog';
 
-export const _package: OligoToolkitPackage = new OligoToolkitPackage({debug: true}/**/);
-
-let initSequenceTranslatorPromise: Promise<void> | null = null;
+export * from './package.g';
 
-//tags: init
-export async function init(): Promise<void> {
-  if (initSequenceTranslatorPromise === null)
-    _package.startInit(initSequenceTranslatorPromise = initSequenceTranslatorInt());
+/** Temporary polyfill */
 
-  return initSequenceTranslatorPromise;
+function getDecoratorFunc() {
+  return function(args: any) {
+    return function(
+      target: any,
+      propertyKey: string,
+      descriptor: PropertyDescriptor
+    ) { };
+  };
 }
 
-async function initSequenceTranslatorInt(): Promise<void> {
-  const [helmHelper] = await Promise.all([
-    getHelmHelper(),
-  ]);
-  _package.completeInit(helmHelper);
-}
+// Ensure decorators object exists and polyfill missing decorators
+if (!grok.decorators)
+  (grok as any).decorators = {};
 
-//name: Oligo Toolkit
-//meta.icon: img/icons/toolkit.png
-//meta.browsePath: Peptides | Oligo Toolkit
-//tags: app
-//output: view v
-export async function oligoToolkitApp(): Promise<DG.ViewBase> {
-  await _package.initLibData();
-  const externalViewFactories = await getExternalAppViewFactories(_package);
-  if (!externalViewFactories)
-    throw new Error('External app view factories not loaded');
-  const appUI = new CombinedAppUI(externalViewFactories!, _package);
-  const view = await appUI.getAppView();
-  return view;
-}
 
-//name: Oligo Translator
-//meta.icon: img/icons/translator.png
-//meta.browsePath: Peptides | Oligo Toolkit
-//tags: app
-//output: view v
-export async function oligoTranslatorApp(): Promise<DG.ViewBase> {
-  const view = await getSpecifiedAppView(APP_NAME.TRANSLATOR);
-  return view;
-}
+const decorators = [
+  'func', 'init', 'param', 'panel', 'editor', 'demo', 'app',
+  'appTreeBrowser', 'fileHandler', 'fileExporter', 'model', 'viewer', 'filter', 'cellRenderer', 'autostart',
+  'dashboard', 'folderViewer', 'semTypeDetector', 'packageSettingsEditor', 'functionAnalysis', 'converter',
+  'fileViewer', 'model', 'treeBrowser', 'polyfill'
+];
 
-//name: Oligo Pattern
-//meta.icon: img/icons/pattern.png
-//meta.browsePath: Peptides | Oligo Toolkit
-//tags: app
-//output: view v
-export async function oligoPatternApp(): Promise<DG.ViewBase> {
-  const view = await getSpecifiedAppView(APP_NAME.PATTERN);
-  return view;
-}
+decorators.forEach((decorator) => {
+  if (!(grok.decorators as any)[decorator])
+    (grok.decorators as any)[decorator] = getDecoratorFunc();
+});
 
-//name: Oligo Structure
-//meta.icon: img/icons/structure.png
-//meta.browsePath: Peptides | Oligo Toolkit
-//tags: app
-//output: view v
-export async function oligoStructureApp(): Promise<DG.ViewBase> {
-  const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
-  return view;
-}
+/** End temporary polyfill */
 
-//name: getTranslationHelper
-//output: object result
-export async function getTranslationHelper(): Promise<ITranslationHelper> {
-  await _package.initLibData();
-  return _package;
-}
-
-//name: getCodeToWeightsMap
-//output: object result
-export function getCodeToWeightsMap(): { [key: string]: number } {
-  const monomerLibWrapper = _package.monomerLibWrapper;
-  const map = monomerLibWrapper.getCodesToWeightsMap();
-  return Object.fromEntries(map);
-}
-
-//name: validateSequence
-//input: string sequence
-//output: bool result
-export function validateSequence(sequence: string): boolean {
-  const validator = _package.createSequenceValidator(sequence);
-  const format = _package.createFormatDetector(sequence).getFormat();
-  return (format === null) ? false : validator.isValidSequence(format!);
-}
-
-//name: validateSequence
-//input: string sequence
-//input: bool invert
-//output: string result
-export function getMolfileFromGcrsSequence(sequence: string, invert: boolean): string {
-  return (new SequenceToMolfileConverter(sequence, invert, 'GCRS')).convert();
-}
-
-//name: linkStrands
-//input: object strands
-//output: string result
-export function linkStrands(strands: { senseStrands: string[], antiStrands: string[] }): string {
-  return linkStrandsV3000(strands, true);
-}
-
-//name: demoOligoTranslator
-//meta.demoPath: Bioinformatics | Oligo Toolkit | Translator
-//description: Translate oligonucleotide sequences across various formats accepted by different synthesizers
-//meta.path: /apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Translate
-//meta.demoSkip: GROK-14320
-export async function demoTranslateSequence(): Promise<void> {
-  await demoOligoTranslatorUI();
-}
+export const _package: OligoToolkitPackage = new OligoToolkitPackage({debug: true}/**/);
 
-//name: demoOligoPattern
-//meta.demoPath: Bioinformatics | Oligo Toolkit | Pattern
-//description: Design a modification pattern for an oligonucleotide sequence
-//meta.path:%20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex
-export async function demoOligoPattern(): Promise<void> {
-  await demoOligoPatternUI();
-}
+let initSequenceTranslatorPromise: Promise<void> | null = null;
 
-//name: demoOligoStructure
-//meta.demoPath: Bioinformatics | Oligo Toolkit | Structure
-//description: Visualize duplex and save SDF
-//meta.path:%20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex
-export async function demoOligoStructure(): Promise<void> {
-  await demoOligoStructureUI();
+async function initSequenceTranslatorInt(): Promise<void> {
+  const [helmHelper] = await Promise.all([
+    getHelmHelper(),
+  ]);
+  _package.completeInit(helmHelper);
 }
 
-//name: translateOligonucleotideSequence
-//input: string sequence
-//input: string sourceFormat
-//input: string targetFormat
-//output: string result
-export async function translateOligonucleotideSequence(
-  sequence: string, sourceFormat: string, targetFormat: string
-): Promise<string> {
-  await _package.initLibData();
-  return _package.createFormatConverter(sequence, sourceFormat).convertTo(targetFormat);
+export class PackageFunctions{
+  @grok.decorators.app({
+    icon: 'img/icons/toolkit.png',
+    browsePath: 'Peptides | Oligo Toolkit',
+    name: 'Oligo Toolkit'
+  })
+  static async oligoToolkitApp(): Promise<DG.ViewBase> {
+  
+    await _package.initLibData();
+    const externalViewFactories = await getExternalAppViewFactories(_package);
+    if (!externalViewFactories)
+      throw new Error('External app view factories not loaded');
+    const appUI = new CombinedAppUI(externalViewFactories!, _package);
+    const view = await appUI.getAppView();
+    return view;
+  }
+
+    
+  @grok.decorators.init()
+  static async init(): Promise<void> {
+  
+    if (initSequenceTranslatorPromise === null)
+      _package.startInit(initSequenceTranslatorPromise = initSequenceTranslatorInt());
+
+    return initSequenceTranslatorPromise;
+  }
+
+  @grok.decorators.app({
+    icon: 'img/icons/translator.png',
+    browsePath: 'Peptides | Oligo Toolkit',
+    name: 'Oligo Translator'
+  })
+  static async oligoTranslatorApp(): Promise<DG.ViewBase> {
+  
+    const view = await getSpecifiedAppView(APP_NAME.TRANSLATOR);
+    return view;
+  }
+
+
+  @grok.decorators.app({
+    icon: 'img/icons/pattern.png',
+    browsePath: 'Peptides | Oligo Toolkit',
+    name: 'Oligo Pattern'
+  })
+  static async oligoPatternApp(): Promise<DG.ViewBase> {
+  
+    const view = await getSpecifiedAppView(APP_NAME.PATTERN);
+    return view;
+  }
+
+
+  @grok.decorators.app({
+    icon: 'img/icons/structure.png',
+    browsePath: 'Peptides | Oligo Toolkit',
+    name: 'Oligo Structure'
+  })
+  static async oligoStructureApp(): Promise<DG.ViewBase> {
+  
+    const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
+    return view;
+  }
+
+
+  @grok.decorators.func({outputs: [{type: 'object', name: 'result'}]})
+  static async getTranslationHelper(): Promise<ITranslationHelper> {
+  
+    await _package.initLibData();
+    return _package;
+  }
+
+
+  @grok.decorators.func({outputs: [{type: 'object', name: 'result'}]})
+  static getCodeToWeightsMap(): Record<string, number> {
+  
+    const monomerLibWrapper = _package.monomerLibWrapper;
+    const map = monomerLibWrapper.getCodesToWeightsMap();
+    return Object.fromEntries(map);
+  }
+
+
+  @grok.decorators.func()
+  static validateSequence(
+    sequence: string): boolean {
+  
+    const validator = _package.createSequenceValidator(sequence);
+    const format = _package.createFormatDetector(sequence).getFormat();
+    return (format === null) ? false : validator.isValidSequence(format!);
+  }
+
+
+  @grok.decorators.func({
+    name: 'validateSequence'
+  })
+  static getMolfileFromGcrsSequence(
+    sequence: string,
+    invert: boolean): string {
+  
+    return (new SequenceToMolfileConverter(sequence, invert, 'GCRS')).convert();
+  }
+
+
+  @grok.decorators.func()
+  static linkStrands(
+    @grok.decorators.param({type:'object'})  strands: { senseStrands: string[], antiStrands: string[] }): string {
+    return linkStrandsV3000(strands, true);
+  }
+
+
+  @grok.decorators.func({
+    meta: {
+      demoPath: 'Bioinformatics | Oligo Toolkit | Translator',
+      path: '/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Translate',
+      demoSkip: 'GROK-14320'
+    },
+    name: 'demoOligoTranslator',
+    description: 'Translate oligonucleotide sequences across various formats accepted by different synthesizers'
+  })
+  static async demoTranslateSequence(): Promise<void> {
+    await demoOligoTranslatorUI();
+  }
+
+
+  @grok.decorators.func({
+    meta: {
+      demoPath: 'Bioinformatics | Oligo Toolkit | Pattern',
+      path: '%20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex'
+    },
+    description: 'Design a modification pattern for an oligonucleotide sequence'
+  })
+  static async demoOligoPattern(): Promise<void> {
+  
+    await demoOligoPatternUI();
+  }
+
+
+  @grok.decorators.func({
+    meta: {
+      demoPath: 'Bioinformatics | Oligo Toolkit | Structure',
+      path: '%20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex'
+    },
+    description: 'Visualize duplex and save SDF'
+  })
+  static async demoOligoStructure(): Promise<void> {
+  
+    await demoOligoStructureUI();
+  }
+
+
+  @grok.decorators.func()
+  static async translateOligonucleotideSequence(
+    sequence: string, sourceFormat: string, targetFormat: string
+  ): Promise<string> {
+  
+    await _package.initLibData();
+    return _package.createFormatConverter(sequence, sourceFormat).convertTo(targetFormat);
+  }
+
+  @grok.decorators.func({
+    'top-menu': 'Bio | PolyTool | Convert...',
+    name: 'polyToolConvert',
+    description: 'Perform cyclization of polymers'
+  })
+  static async polyToolConvertTopMenu(): Promise<void> {
+  
+    await polyToolConvertUI();
+  }
+
+  @grok.decorators.editor()
+  static async getPolyToolConvertEditor(
+    call: DG.FuncCall): Promise<DG.Column<string> | null> {
+  
+    const funcEditor = await PolyToolConvertFuncEditor.create(call);
+    return await funcEditor.showDialog();
+  }
+
+
+  @grok.decorators.func({
+    editor: 'SequenceTranslator:getPolyToolConvertEditor', 
+  })
+  static async polyToolConvert2(
+    table: DG.DataFrame,
+    @grok.decorators.param({options: { caption: 'Sequence'}}) seqCol: DG.Column, 
+    @grok.decorators.param({options: { initialValue: 'true'}}) generateHelm: boolean, 
+    @grok.decorators.param({options: { initialValue: 'true'}}) chiralityEngine: boolean, 
+    @grok.decorators.param({type: 'object'}) rules: string[]
+  ): Promise<DG.Column<string>> {
+  
+    const ptConvertRes = await polyToolConvert(seqCol, generateHelm, false, chiralityEngine, false, rules);
+    return ptConvertRes[0];
+  }
+
+
+
+  @grok.decorators.func({
+    'top-menu': 'Bio | PolyTool | Enumerate HELM...',
+    name: 'polyToolEnumerateHelm',
+    description: 'Perform cyclization of polymers'
+  })
+  static async polyToolEnumerateHelmTopMenu(): Promise<void> {
+  
+    await polyToolEnumerateHelmUI(grok.shell.tv?.dataFrame.currentCell);
+  }
+
+
+  @grok.decorators.func({
+    'top-menu': 'Bio | PolyTool | Enumerate Chem...',
+    name: 'polyToolEnumerateChem',
+    description: 'Perform cyclization of polymers'
+  })
+  static async polyToolEnumerateChemTopMenu(): Promise<void> {
+  
+    polyToolEnumerateChemUI();
+  }
+
+
+  @grok.decorators.func()
+  static async polyToolColumnChoice(
+    @grok.decorators.param({options: {description: 'Input data table'}}) df: DG.DataFrame,
+    macroMolecule: DG.Column): Promise<void> {
+  
+    _setPeptideColumn(macroMolecule);
+    await grok.data.detectSemanticTypes(df);
+  }
+
+
+  @grok.decorators.func()
+  static async createMonomerLibraryForPolyTool(
+    file: DG.FileInfo) {
+  
+    const fileContent = await file.readAsString();
+    const libHandler = new PolyToolCsvLibHandler(file.fileName, fileContent);
+    const libObject = await libHandler.getJson();
+    const jsonFileName = file.fileName.replace(/\.csv$/, '.json');
+    const jsonFileContent = JSON.stringify(libObject, null, 2);
+    DG.Utils.download(jsonFileName, jsonFileContent);
+  }
+
+
+  @grok.decorators.func({
+    meta: {
+      icon: 'img/icons/structure.png',
+      browsePath: 'Peptides | PolyTool'
+    },
+    tags: ['app'],
+    name: 'HELM Enumerator'
+  })
+  static async ptEnumeratorHelmApp(): Promise<void> {
+  
+    await polyToolEnumerateHelmUI();
+  }
+
+
+  @grok.decorators.func({
+    meta: {
+      icon: 'img/icons/structure.png',
+      browsePath: 'Peptides | PolyTool'
+    },
+    tags: ['app'],
+    name: 'Chem Enumerator'
+  })
+  static async ptEnumeratorChemApp(): Promise<void> {
+  
+    polyToolEnumerateChemUI();
+  }
+
+
+
+  @grok.decorators.func({
+    name: 'Polytool Helm Enumerator dialog'
+  })
+  static async getPtHelmEnumeratorDialog(
+    @grok.decorators.param({type:'object',options:{nullable:true}})  cell?: DG.Cell) {
+  
+    return polyToolEnumerateHelmUI(cell);
+  }
+
+
+  @grok.decorators.func({
+    name: 'Polytool Chem Enumerator dialog'
+  })
+  static async getPtChemEnumeratorDialog(
+    @grok.decorators.param({type:'object',options:{nullable:true}})  cell?: DG.Cell) {
+  
+    return polyToolEnumerateChemUI(cell);
+  }
+
+
+  @grok.decorators.func({
+    name: 'Combine Sequences',
+    'top-menu': 'Bio | PolyTool | Combine Sequences...'
+  })
+  static async getPolyToolCombineDialog() {
+  
+    getPTCombineDialog();
+  }
+
+
+
+  @grok.decorators.func({
+    name: 'applyNotationProviderForHarmonizedSequence'
+  })
+  static applyNotationProviderForCyclized(
+    @grok.decorators.param({type:'column'}) col: DG.Column<string>,
+    separator: string) {
+  
+    col.setTag('aligned', 'SEQ');
+    col.setTag('alphabet', 'UN');
+    col.setTag('.alphabetIsMultichar', 'true');
+    col.meta.units = NOTATION.CUSTOM;
+    col.tags[PolyToolTags.dataRole] = 'template';
+    col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator, _package.helmHelper);
+  }
 }
 
+//name: getSpecifiedAppView
 async function getSpecifiedAppView(appName: string): Promise<DG.ViewBase> {
   await _package.initLibData();
   const appUI = getSpecifiedAppUI(appName, _package);
   const view = await appUI.getAppView();
   return view;
-}
-
-//top-menu: Bio | PolyTool | Convert...
-//name: polyToolConvert
-//description: Perform cyclization of polymers
-export async function polyToolConvertTopMenu(): Promise<void> {
-  await polyToolConvertUI();
-}
-
-// //top-menu: Bio | PolyTool | Unrule...
-// //name: polyToolUnrule
-// //description: Perform uncyclization of polymers by rules
-// export async function polyToolUnruleTopMenu(): Promise<void> {
-//   await polyToolUnruleUI();
-// }
-
-//name: getPolyToolConvertEditor
-//tags: editor
-//input: funccall call
-//output: column resCol
-export async function getPolyToolConvertEditor(call: DG.FuncCall): Promise<DG.Column<string> | null> {
-  const funcEditor = await PolyToolConvertFuncEditor.create(call);
-  return await funcEditor.showDialog();
-}
-
-//name: polyToolConvert2
-//input: dataframe table
-//input: column seqCol { caption: Sequence }
-//input: bool generateHelm = true
-//input: bool chiralityEngine = true
-//input: object rules
-//output: column resCol
-//editor: SequenceTranslator:getPolyToolConvertEditor
-export async function polyToolConvert2(table: DG.DataFrame,
-  seqCol: DG.Column, generateHelm: boolean, chiralityEngine: boolean, rules: string[]
-): Promise<DG.Column<string>> {
-  const ptConvertRes = await polyToolConvert(seqCol, generateHelm, false, chiralityEngine, false, rules);
-  return ptConvertRes[0];
-}
-
-
-//top-menu: Bio | PolyTool | Enumerate HELM...
-//name: polyToolEnumerateHelm
-//description: Perform cyclization of polymers
-export async function polyToolEnumerateHelmTopMenu(): Promise<void> {
-  await polyToolEnumerateHelmUI(grok.shell.tv?.dataFrame.currentCell);
-}
-
-//top-menu: Bio | PolyTool | Enumerate Chem...
-//name: polyToolEnumerateChem
-//description: Perform cyclization of polymers
-export async function polyToolEnumerateChemTopMenu(): Promise<void> {
-  polyToolEnumerateChemUI();
-}
-
-//name: polyToolColumnChoice
-//input: dataframe df [Input data table]
-//input: column macroMolecule
-export async function polyToolColumnChoice(df: DG.DataFrame, macroMolecule: DG.Column): Promise<void> {
-  _setPeptideColumn(macroMolecule);
-  await grok.data.detectSemanticTypes(df);
-}
-
-//name: createMonomerLibraryForPolyTool
-//input: file file
-export async function createMonomerLibraryForPolyTool(file: DG.FileInfo) {
-  const fileContent = await file.readAsString();
-  const libHandler = new PolyToolCsvLibHandler(file.fileName, fileContent);
-  const libObject = await libHandler.getJson();
-  const jsonFileName = file.fileName.replace(/\.csv$/, '.json');
-  const jsonFileContent = JSON.stringify(libObject, null, 2);
-  DG.Utils.download(jsonFileName, jsonFileContent);
-}
-
-// //name: PolyTool Converter
-// //meta.icon: img/icons/structure.png
-// //meta.browsePath: PolyTool
-// //tags: app
-// export async function ptConverterApp(): Promise<void> {
-//   const view = grok.shell.v as DG.TableView;
-//   const table = view.dataFrame;
-//   const colNames = table.columns.names();
-//   let covertableName = '';
-
-//   for (let i = 0; i < colNames.length; i++) {
-//     const col = table.columns.byName(colNames[i]);
-//     if (col.semType === DG.SEMTYPE.MACROMOLECULE && col.meta.units === NOTATION.SEPARATOR) {
-//       covertableName = colNames[i];
-//       break;
-//     }
-//   }
-
-//   if (covertableName === '')
-//     grok.shell.error('To run the app open a view with convertable separator notation for macromolecules');
-//   else {
-//     const dialog = await getPolyToolConversionDialog();
-//     dialog.show();
-//   }
-// }
-
-//name: HELM Enumerator
-//meta.icon: img/icons/structure.png
-//meta.browsePath: Peptides | PolyTool
-//tags: app
-export async function ptEnumeratorHelmApp(): Promise<void> {
-  await polyToolEnumerateHelmUI();
-}
-
-//name: Chem Enumerator
-//meta.icon: img/icons/structure.png
-//meta.browsePath: Peptides | PolyTool
-//tags: app
-export async function ptEnumeratorChemApp(): Promise<void> {
-  polyToolEnumerateChemUI();
-}
-
-
-//name: Polytool Helm Enumerator dialog
-//input: object cell {nullable: true}
-export async function getPtHelmEnumeratorDialog(cell?: DG.Cell) {
-  return polyToolEnumerateHelmUI(cell);
-}
-
-//name: Polytool Chem Enumerator dialog
-//input: object cell {nullable: true}
-export async function getPtChemEnumeratorDialog(cell?: DG.Cell) {
-  return polyToolEnumerateChemUI(cell);
-}
-
-//name: Combine Sequences
-//top-menu: Bio | PolyTool | Combine Sequences...
-export async function getPolyToolCombineDialog() {
-  getPTCombineDialog();
-}
-
-
-//name: applyNotationProviderForHarmonizedSequence
-//input: column col
-//input: string separator
-export function applyNotationProviderForCyclized(col: DG.Column<string>, separator: string) {
-  col.setTag('aligned', 'SEQ');
-  col.setTag('alphabet', 'UN');
-  col.setTag('.alphabetIsMultichar', 'true');
-  col.meta.units = NOTATION.CUSTOM;
-  col.tags[PolyToolTags.dataRole] = 'template';
-  col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator, _package.helmHelper);
-}
+}