@datagrok/bio 2.11.34 → 2.11.36

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.34",
+  "version": "2.11.36",
   "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/analysis/sequence-diversity-viewer.ts

@@ -40,7 +40,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
         this.tags.forEach((tag) => resCol.setTag(tag, this.moleculeColumn!.getTag(tag)));
         const resDf = DG.DataFrame.fromColumns([resCol]);
         resDf.onCurrentRowChanged.subscribe(
-          (_) => { this.dataFrame.currentRowIdx = this.renderMolIds![resDf.currentRowIdx]; });
+          (_: any) => { this.dataFrame.currentRowIdx = this.renderMolIds![resDf.currentRowIdx]; });
         updateDivInnerHTML(this.root, resDf.plot.grid().root);
         this.computeCompleted.next(true);
       }
@@ -61,7 +61,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
 
   private async computeByMM() {
     const encodedSequences =
-        (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
+      (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
     const distanceMatrixService = new DistanceMatrixService(true, false);
     const distanceMatrixData = await distanceMatrixService.calc(encodedSequences, MmDistanceFunctionsNames.LEVENSHTEIN);
     distanceMatrixService.terminate();

package/src/analysis/sequence-similarity-viewer.ts

@@ -60,7 +60,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
         this.molCol.semType = DG.SEMTYPE.MACROMOLECULE;
         this.tags.forEach((tag) => this.molCol!.setTag(tag, this.moleculeColumn!.getTag(tag)));
         const resDf = DG.DataFrame.fromColumns([this.idxs!, this.molCol!, this.scores!]);
-        resDf.onCurrentRowChanged.subscribe((_) => {
+        resDf.onCurrentRowChanged.subscribe((_: any) => {
           this.dataFrame.currentRowIdx = resDf.col('indexes')!.get(resDf.currentRowIdx);
           setTimeout(() => { this.createPropertyPanel(resDf); }, 1000);
           this.gridSelect = true;

package/src/package.ts

@@ -60,6 +60,7 @@ import {getCompositionAnalysisWidget} from './widgets/composition-analysis-widge
 import {MacromoleculeColumnWidget} from './utils/macromolecule-column-widget';
 import {addCopyMenuUI} from './utils/context-menu';
 import {getPolyToolDialog} from './utils/poly-tool/ui';
+import {PolyToolCsvLibHandler} from './utils/poly-tool/csv-to-json-monomer-lib-converter';
 import {_setPeptideColumn} from './utils/poly-tool/utils';
 import {getRegionDo} from './utils/get-region';
 import {GetRegionApp} from './apps/get-region-app';
@@ -1018,6 +1019,17 @@ export async function polyToolColumnChoice(df: DG.DataFrame, macroMolecule: DG.C
   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: SDF to JSON Library
 //input: dataframe table
 export async function sdfToJsonLib(table: DG.DataFrame) {

package/src/tests/monomer-libraries-tests.ts

@@ -53,14 +53,18 @@ category('monomerLibraries', () => {
     const libSettings = await getUserLibSettings();
     const libFileEventManager = MonomerLibFileEventManager.getInstance();
     const libFileManager = await MonomerLibFileManager.getInstance(libFileEventManager);
-    const libFnList = libFileManager.getValidLibraryPaths();
+
+    let libFnList = libFileManager.getValidLibraryPaths();
+    if (libFnList.length === 0)
+      libFnList = await libFileManager.getValidLibraryPathsAsynchronously();
+
     libSettings.exclude = libFnList;
     libSettings.explicit = [];
     await setUserLibSettings(libSettings);
 
     await monomerLibHelper.loadLibraries(true);
     const currentMonomerLib = monomerLibHelper.getBioLib();
-    expect(currentMonomerLib.getPolymerTypes().length === 0, true);
-    const monomerOfTypesList = currentMonomerLib.getMonomerMolsByPolymerType('PEPTIDE');
-  }, {skipReason: '#2690'});
+    const polymerTypes = currentMonomerLib.getPolymerTypes();
+    expect(polymerTypes.length === 0, true);
+  });
 });

package/src/tests/similarity-diversity-tests.ts

@@ -28,7 +28,7 @@ async function _testSimilaritySearchViewer() {
   const viewer: SequenceSimilarityViewer = (await moleculesView.dataFrame.plot
     .fromType('Sequence Similarity Search')) as SequenceSimilarityViewer;
   let computeCompleted: boolean = false;
-  viewer.computeCompleted.subscribe((value) => {
+  viewer.computeCompleted.subscribe((value: any) => {
     if (value) computeCompleted = true;
   });
   moleculesView.dockManager.dock(viewer, DG.DOCK_TYPE.RIGHT, null, 'Similarity');
@@ -78,7 +78,7 @@ async function _testDiversitySearchViewer() {
   const viewer: SequenceDiversityViewer = (await moleculesView.dataFrame.plot
     .fromType('Sequence Diversity Search')) as SequenceDiversityViewer;
   let computeCompleted: boolean = false;
-  viewer.computeCompleted.subscribe((value) => {
+  viewer.computeCompleted.subscribe((value: boolean) => {
     if (value) computeCompleted = true;
   });
   moleculesView.dockManager.dock(viewer, DG.DOCK_TYPE.DOWN, null, 'Diversity');

package/src/utils/convert.ts

@@ -102,7 +102,7 @@ export function convert(col?: DG.Column): void {
       })
       .show({x: 350, y: 100});
 
-    convertDialogSubs.push(convertDialog.onClose.subscribe((_value) => {
+    convertDialogSubs.push(convertDialog.onClose.subscribe((_: any) => {
       convertDialogSubs.forEach((s) => { s.unsubscribe(); });
       convertDialogSubs = [];
       convertDialog = null;

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

@@ -56,9 +56,14 @@ export class MonomerLibManager implements IMonomerLibHelper {
           getLibFileNameList(),
           getUserLibSettings(),
         ]);
-        const filteredLibFnList = libFileNameList
-          .filter((libFileName) => !settings.exclude.includes(libFileName))
-          .filter((libFileName) => settings.explicit.length > 0 ? settings.explicit.includes(libFileName) : true);
+
+        const filteredLibFnList = libFileNameList.filter((libFileName) => {
+          const isFileIncluded = !settings.exclude.includes(libFileName);
+          const isExplicit = settings.explicit.length === 0 || settings.explicit.includes(libFileName);
+
+          return isFileIncluded && isExplicit;
+        });
+
         const libs: IMonomerLib[] = await Promise.all(filteredLibFnList
           .map((libFileName) => {
             //TODO handle whether files are in place

package/src/utils/monomer-lib/library-file-manager/custom-monomer-lib-handlers.ts

@@ -4,7 +4,6 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {createJsonMonomerLibFromSdf} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {PolyToolMonomerLibHandler} from '../../poly-tool/monomer-lib-handler';
 
 interface CustomMonomerLibHandler {
   getHelmLibContent(): Promise<string>;
@@ -40,41 +39,3 @@ export class SdfMonomerLibHandler implements CustomMonomerLibHandler {
       throw new Error(`File ${this.fileName} is not an SDF file`);
   }
 }
-
-
-/** Handler of custom monomer libs for PolyTool  */
-export class PolyToolCsvLibHandler implements CustomMonomerLibHandler {
-  constructor(private fileName: string, private fileContent: string) {
-    this.validateFileType();
-    const df = DG.DataFrame.fromCsv(this.fileContent);
-    const json = this.toJson(df);
-    this.polyToolMonomerLib = new PolyToolMonomerLibHandler(json);
-    this.validateContent();
-  }
-
-  private polyToolMonomerLib: PolyToolMonomerLibHandler;
-
-  async getHelmLibContent(): Promise<string> {
-    const rawLibData = this.polyToolMonomerLib.getJsonMonomerLib();
-    return JSON.stringify(rawLibData);
-  }
-
-  private toJson(df: DG.DataFrame): any[] {
-    return Array.from({length: df.rowCount}, (_, idx) =>
-      df.columns.names().reduce((entry: { [key: string]: any }, colName) => {
-        entry[colName] = df.get(colName, idx);
-        return entry;
-      }, {})
-    );
-  }
-
-  private validateFileType(): void {
-    if (!this.fileName.endsWith('.csv'))
-      throw new Error(`File ${this.fileName} is not an CSV file`);
-  }
-
-  private validateContent(): void {
-    if (!this.polyToolMonomerLib.isValid())
-      throw new Error('Invalid format of CSV monomer lib');
-  }
-}

package/src/utils/monomer-lib/library-file-manager/event-manager.ts

@@ -1,5 +1,5 @@
 import * as rxjs from 'rxjs';
-import {debounceTime, tap} from 'rxjs/operators';
+import {debounceTime, tap, skip} from 'rxjs/operators';
 
 export class MonomerLibFileEventManager {
   // WARNING: this must be a singleton because it manages the unique state
@@ -22,6 +22,18 @@ export class MonomerLibFileEventManager {
     return this._libraryFilesUpdateSubject$.getValue();
   }
 
+  // TODO: remove after adding init from user data storage
+  // WARNING: a temporary solution
+  async getValidLibraryPathsAsynchronously(): Promise<string[]> {
+    return new Promise((resolve) => {
+      this._libraryFilesUpdateSubject$.pipe(
+        skip(1)
+      ).subscribe((fileNames) => {
+        resolve(fileNames);
+      });
+    });
+  }
+
   changeValidFilesPathList(newList: string[]): void {
     this._libraryFilesUpdateSubject$.next(newList);
   }

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

@@ -28,20 +28,22 @@ export class MonomerLibFileManager {
     });
   }
 
-  private static instance: MonomerLibFileManager | undefined;
+  private static instancePromise: Promise<MonomerLibFileManager> | undefined;
 
   static async getInstance(
     libraryEventManager: MonomerLibFileEventManager,
   ): Promise<MonomerLibFileManager> {
-    if (MonomerLibFileManager.instance === undefined) {
-      const helmSchemaRaw = await grok.dapi.files.readAsText(HELM_JSON_SCHEMA_PATH);
-      const helmSchema = JSON.parse(helmSchemaRaw) as JSONSchemaType<any>;
-
-      const fileValidator = new MonomerLibFileValidator(helmSchema);
-      MonomerLibFileManager.instance = new MonomerLibFileManager(fileValidator, libraryEventManager);
+    if (!MonomerLibFileManager.instancePromise) {
+      MonomerLibFileManager.instancePromise = (async () => {
+        const helmSchemaRaw = await grok.dapi.files.readAsText(HELM_JSON_SCHEMA_PATH);
+        const helmSchema = JSON.parse(helmSchemaRaw) as JSONSchemaType<any>;
+
+        const fileValidator = new MonomerLibFileValidator(helmSchema);
+        return new MonomerLibFileManager(fileValidator, libraryEventManager);
+      })();
     }
 
-    return MonomerLibFileManager.instance;
+    return MonomerLibFileManager.instancePromise;
   }
 
   /** Add standard .json monomer library  */
@@ -103,6 +105,13 @@ export class MonomerLibFileManager {
     return this.libraryEventManager.getValidFilesPathList();
   }
 
+  // TODO: remove after adding init from user data storage
+  // WARNING: a temporary solution
+  async getValidLibraryPathsAsynchronously(): Promise<string[]> {
+    return await this.libraryEventManager.getValidLibraryPathsAsynchronously();
+  }
+
+
   private async libraryFileExists(fileName: string): Promise<boolean> {
     return await grok.dapi.files.exists(LIB_PATH + `${fileName}`);
   }
@@ -142,7 +151,7 @@ export class MonomerLibFileManager {
       `, consider fixing or removing them: ${invalidFiles.join(', ')}`;
 
       console.warn(message);
-      grok.shell.warning(message);
+      // grok.shell.warning(message);
     }
   }
 

package/src/utils/monomer-lib/library-file-manager/file-validator.ts

@@ -41,7 +41,7 @@ export class MonomerLibFileValidator {
       isValid = this.validateMonomerSchema(monomer);
       if (!isValid) {
         console.warn(
-          `Bio: Monomer Library File Validator:\nfile${fileName}\n monomer violating JSON schema:`,
+          `Bio: Monomer Library File Validator:\nfile ${fileName}\n monomer violating JSON schema:`,
           monomer,
           '\nError reason: ',
           this.validateMonomerSchema.errors,

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -208,7 +208,12 @@ class DialogWrapper {
   private async getDialog(): Promise<DG.Dialog> {
     const eventManager = MonomerLibFileEventManager.getInstance();
     const widget = await MonomerLibraryManagerWidget.getContent(eventManager);
-    const dialog = ui.dialog('Manage monomer libraries');
+    const dialog = ui.dialog(
+      {
+        title: 'Manage monomer libraries',
+        helpUrl: '/help/datagrok/solutions/domains/bio/bio.md#manage-monomer-libraries'
+      }
+    );
     $(dialog.root).css('width', '350px');
     dialog.clear();
     dialog.addButton(

package/src/utils/poly-tool/csv-to-json-monomer-lib-converter.ts

@@ -0,0 +1,40 @@
+import * as DG from 'datagrok-api/dg';
+
+import {PolyToolMonomerLibHandler} from './monomer-lib-handler';
+
+/** Handler of custom monomer libs for PolyTool  */
+export class PolyToolCsvLibHandler {
+  constructor(private fileName: string, private fileContent: string) {
+    this.validateFileType();
+    const df = DG.DataFrame.fromCsv(this.fileContent);
+    const json = this.toJson(df);
+    this.polyToolMonomerLib = new PolyToolMonomerLibHandler(json);
+    this.validateContent();
+  }
+
+  private polyToolMonomerLib: PolyToolMonomerLibHandler;
+
+  async getJson(): Promise<any> {
+    const rawLibData = this.polyToolMonomerLib.getJsonMonomerLib();
+    return rawLibData;
+  }
+
+  private toJson(df: DG.DataFrame): any[] {
+    return Array.from({length: df.rowCount}, (_, idx) =>
+      df.columns.names().reduce((entry: { [key: string]: any }, colName) => {
+        entry[colName] = df.get(colName, idx);
+        return entry;
+      }, {})
+    );
+  }
+
+  private validateFileType(): void {
+    if (!this.fileName.endsWith('.csv'))
+      throw new Error(`File ${this.fileName} is not an CSV file`);
+  }
+
+  private validateContent(): void {
+    if (!this.polyToolMonomerLib.isValid())
+      throw new Error('Invalid format of CSV monomer lib');
+  }
+}