@datagrok/bio 2.17.4 → 2.17.6

package/files/tests/fasta_negative_words.csv

@@ -0,0 +1,6 @@
+model,mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb
+MAINTAINED,21.0,6,160,110,3.90,2.620,16.46,0,1,4,4
+WORSENED,21.0,6,160,110,3.90,2.875,17.02,0,1,4,4
+MAINTAINED,22.8,4,108,93,3.85,2.320,18.61,1,1,4,1
+IMPROVED,21.4,6,258,110,3.08,3.215,19.44,1,0,3,1
+WORSENED,18.7,8,360,175,3.15,3.440,17.02,0,0,3,2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.17.4",
+  "version": "2.17.6",
   "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/package.ts

@@ -85,7 +85,7 @@ export async function getMonomerLibHelper(): Promise<IMonomerLibHelper> {
   return await MonomerLibManager.getInstance();
 }
 
-export let hydrophobPalette: SeqPaletteCustom | null = null;
+//export let hydrophobPalette: SeqPaletteCustom | null = null;
 
 export class SeqPaletteCustom implements SeqPalette {
   private readonly _palette: { [m: string]: string };
@@ -128,39 +128,42 @@ async function initBioInt() {
     libSettings.explicit = [];
     await setUserLibSettings(libSettings);
   }
-  libHelper.awaitLoaded(Infinity).then(() => {
-    // Do not wait for monomers and sets loaded
-    return Promise.all([libHelper.loadMonomerLib(), libHelper.loadMonomerSets()]);
-  });
+  await libHelper.awaitLoaded(Infinity);
+  if (!libHelper.initialLoadCompleted)
+    await libHelper.loadMonomerLib();
+  // Do not wait for monomers and sets loaded
+  libHelper.loadMonomerSets();
   const monomerLib = libHelper.getMonomerLib();
   const monomerSets = libHelper.getMonomerSets();
   // finally log
   const t2: number = window.performance.now();
   _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
 
-  const monomers: string[] = [];
-  const logPs: number[] = [];
+  // const monomers: string[] = [];
+  // const logPs: number[] = [];
 
   const seqHelper = new SeqHelper(libHelper, rdKitModule);
   _package.completeInit(seqHelper, monomerLib, monomerSets, rdKitModule);
-  const series = monomerLib!.getMonomerMolsByPolymerType('PEPTIDE')!;
-  Object.keys(series).forEach((symbol) => {
-    monomers.push(symbol);
-    const block = series[symbol].replaceAll('#R', 'O ');
-    const mol = rdKitModule.get_mol(block);
-    const logP = JSON.parse(mol.get_descriptors()).CrippenClogP;
-    logPs.push(logP);
-    mol?.delete();
-  });
 
-  const sum = logPs.reduce((a, b) => a + b, 0);
-  const avg = (sum / logPs.length) || 0;
+  // NB! do not delete the code below. not used now but in future we might use hydrophobicity palette
+  // const series = monomerLib!.getMonomerMolsByPolymerType('PEPTIDE')!;
+  // Object.keys(series).forEach((symbol) => {
+  //   monomers.push(symbol);
+  //   const block = series[symbol].replaceAll('#R', 'O ');
+  //   const mol = rdKitModule.get_mol(block);
+  //   const logP = JSON.parse(mol.get_descriptors()).CrippenClogP;
+  //   logPs.push(logP);
+  //   mol?.delete();
+  // });
+
+  // const sum = logPs.reduce((a, b) => a + b, 0);
+  // const avg = (sum / logPs.length) || 0;
 
-  const palette: { [monomer: string]: string } = {};
-  for (let i = 0; i < monomers.length; i++)
-    palette[monomers[i]] = logPs[i] < avg ? '#4682B4' : '#DC143C';
+  // const palette: { [monomer: string]: string } = {};
+  // for (let i = 0; i < monomers.length; i++)
+  //   palette[monomers[i]] = logPs[i] < avg ? '#4682B4' : '#DC143C';
 
-  hydrophobPalette = new SeqPaletteCustom(palette);
+  // hydrophobPalette = new SeqPaletteCustom(palette);
 
   _package.logger.debug(`${logPrefix}, end`);
 }
@@ -961,19 +964,36 @@ export async function manageMonomersView() {
   await monomerManager.getViewRoot();
 }
 
-//name: Manage Monomers
+//name: Monomers
 //tags: app
-//meta.browsePath: Peptides | Monomers
-export async function manageMonomersApp() {
-  const monomerManager = await MonomerManager.getInstance();
-  await monomerManager.getViewRoot();
-}
+//meta.browsePath: Peptides
+//meta.icon: files/icons/monomers.png
+//output: view v
+export async function manageLibrariesApp(): Promise<DG.View> {
+  return await showManageLibrariesView(false);
+}
+
+//name: Monomer Manager Tree Browser
+//input: dynamic treeNode
+//input: view browseView
+export async function manageLibrariesAppTreeBrowser(treeNode: DG.TreeViewGroup, browseView: DG.BrowseView) {
+  const libraries = (await (await MonomerLibManager.getInstance()).getFileManager()).getValidLibraryPaths();
+  libraries.forEach((libName) => {
+    const libNode = treeNode.item(libName);
+    // eslint-disable-next-line rxjs/no-ignored-subscription, rxjs/no-async-subscribe
+    libNode.onSelected.subscribe(async () => {
+      const monomerManager = await MonomerManager.getNewInstance();
+      browseView.preview = await monomerManager.getViewRoot(libName, false);
+    });
 
-//name: Manage Libraries
-//tags: app
-//meta.browsePath: Peptides | Monomers
-export async function manageLibrariesApp(): Promise<void> {
-  await showManageLibrariesView();
+    libNode.root.addEventListener('dblclick', async (e) => {
+      e.preventDefault();
+      e.stopImmediatePropagation();
+      const monomerManager = await MonomerManager.getInstance();
+      await monomerManager.getViewRoot(libName, true);
+      monomerManager.resetCurrentRowFollowing();
+    });
+  });
 }
 
 //name: saveAsFasta

package/src/tests/detectors-tests.ts

@@ -1,3 +1,5 @@
+/* eslint-disable max-lines */
+/* eslint-disable max-lines-per-function */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
@@ -271,6 +273,7 @@ MWRSWY-CKHPMWRSWY-CKHP`;
     testSpgi = 'testSpgi',
     testSpgi100 = 'testSpgi100',
     testUrl = 'testUrl',
+    fastaNegativeWords = 'fasta_negative_words'
   }
 
   const samples: { [key: string]: string } = {
@@ -295,6 +298,7 @@ MWRSWY-CKHPMWRSWY-CKHP`;
     [Samples.testSpgi100]: 'System:AppData/Bio/tests/testSpgi100.csv',
     [Samples.testSpgi]: 'System:AppData/Bio/tests/SPGI-derived.csv',
     [Samples.testUrl]: 'System:AppData/Bio/tests/testUrl.csv',
+    [Samples.fastaNegativeWords]: 'System:AppData/Bio/tests/fasta_negative_words.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -505,6 +509,10 @@ MWRSWY-CKHPMWRSWY-CKHP`;
   test('samplesTestUrl', async () => {
     await _testDf(readSamples(Samples.testUrl), {} /* no positive */, seqHelper);
   });
+
+  test('samplesFastaNegativeWords', async () => {
+    await _testDf(readSamples(Samples.fastaNegativeWords), {} /* no positive */, seqHelper);
+  });
 });
 
 export async function _testNegList(list: string[]): Promise<void> {

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

@@ -30,7 +30,8 @@ declare const window: MonomerLibWindowType;
 export class MonomerLibManager implements IMonomerLibHelper {
   private readonly _monomerLib = new MonomerLib({}, 'MAIN');
   private readonly _monomerSets = new MonomerSet('MAIN', []);
-
+  private _initialLoadCompleted: boolean = false;
+  public get initialLoadCompleted(): boolean { return this._initialLoadCompleted; }
   private _eventManager: MonomerLibFileEventManager;
 
   public get eventManager(): IMonomerLibFileEventManager { return this._eventManager; }
@@ -85,7 +86,8 @@ export class MonomerLibManager implements IMonomerLibHelper {
     return this._monomerSets;
   }
 
-  /** Object containing symbols for each type of polymer where duplicate monomers are found in different libs (based on symbol as key) */
+  /** Object containing symbols for each type of polymer where duplicate monomers
+   * are found in different libs (based on symbol as key) */
   get duplicateMonomers() {
     return this._monomerLib.duplicateMonomers;
   }
@@ -107,6 +109,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
       this._fileManagerPromise = (async () => {
         const fileManager: MonomerLibFileManager =
           await MonomerLibFileManager.create(this, this._eventManager, this.logger);
+        await fileManager.initializedPromise;
         return fileManager;
       })();
     }
@@ -158,6 +161,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
               });
           })),]);
         this._monomerLib.updateLibs(libs, reload);
+        this._initialLoadCompleted = true;
       } catch (err: any) {
         // WARNING: This function is not allowed to throw any exception,
         // because it will prevent further handling monomer library settings

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

@@ -28,6 +28,7 @@ import {_package} from '../../../package';
  * All files **must** be aligned to the HELM standard before adding. */
 export class MonomerLibFileManager implements IMonomerLibFileManager {
   public filesPromise: Promise<void> = Promise.resolve();
+  public initializedPromise: Promise<void> = Promise.resolve();
 
   private constructor(
     private readonly fileValidator: MonomerLibFileValidator,
@@ -35,8 +36,19 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
     public readonly eventManager: MonomerLibFileEventManager,
     private readonly logger: ILogger,
   ) {
+    // these both are behavioral subjects, i.e. they emit their value when subscribed.
+    // initial creation/request from bio package on awaiting files promise makes no sense,
+    // until the subscription fires first time
+    let resolveFilesPromise: () => void;
+    let initialized = false;
+    this.initializedPromise =
+      Promise.race([DG.delay(1000), new Promise<void>((resolve) => resolveFilesPromise = resolve)]);
     const _libSub = this.eventManager.updateValidLibraryFileListRequested$.subscribe(() => {
       this.updateValidLibList().then(() => {});
+      if (!initialized) {
+        initialized = true;
+        resolveFilesPromise();
+      }
     });
     const _setSub = this.eventManager.updateValidSetFileListRequested$.subscribe(() => {
       this.updateValidSetList().then(() => {});
@@ -181,7 +193,7 @@ export class MonomerLibFileManager implements IMonomerLibFileManager {
 
       if (this.libListHasChanged(validLibPathList)) {
         this.eventManager.changeValidLibPathList(validLibPathList);
-        this.libHelper.loadMonomerLib(true);
+        await this.libHelper.loadMonomerLib(true);
       }
       // console.log(`files after validation:`, this.libraryEventManager.getValidFilesPathList());
 

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

@@ -24,8 +24,8 @@ export async function showManageLibrariesDialog(): Promise<void> {
   await DialogWrapper.showDialog();
 }
 
-export async function showManageLibrariesView() {
-  await LibManagerView.showView();
+export async function showManageLibrariesView(addView = true) {
+  return await LibManagerView.showView(addView);
 }
 
 export async function getMonomerLibraryManagerLink(): Promise<DG.Widget> {
@@ -68,8 +68,9 @@ class MonomerLibraryManagerWidget {
   private async createWidget() {
     const content = await this.getWidgetContent();
     const monomerLibHelper = await getMonomerLibHelper();
+    // eslint-disable-next-line rxjs/no-ignored-subscription
     monomerLibHelper.eventManager.addLibraryFileRequested$.subscribe(
-      async () => await this.promptToAddLibraryFiles()
+      () => this.promptToAddLibraryFiles()
     );
     return new DG.Widget(content);
   }
@@ -109,11 +110,13 @@ class LibraryControlsManager {
     private fileManager: IMonomerLibFileManager,
     private readonly userLibSettings: UserLibSettings,
   ) {
+    // eslint-disable-next-line rxjs/no-ignored-subscription
     this.fileManager.eventManager.updateUIControlsRequested$.subscribe(() => {
       this.updateControlsForm();
     });
-    this.fileManager.eventManager.librarySelectionRequested$.subscribe(async ([fileName, isSelected]) => {
-      await this.updateLibrarySelectionStatus(isSelected, fileName);
+    // eslint-disable-next-line rxjs/no-ignored-subscription
+    this.fileManager.eventManager.librarySelectionRequested$.subscribe(([fileName, isSelected]) => {
+      this.updateLibrarySelectionStatus(isSelected, fileName);
     });
   }
 
@@ -222,6 +225,7 @@ class DialogWrapper {
   static async showDialog(): Promise<void> {
     if (!DialogWrapper._instance) {
       DialogWrapper._instance = new DialogWrapper();
+      // eslint-disable-next-line rxjs/no-ignored-subscription
       DialogWrapper._instance.closeDialogSubject$.subscribe(
         () => { DialogWrapper._instance.dialog = undefined; }
       );
@@ -251,7 +255,10 @@ class DialogWrapper {
       'Upload new HELM monomer library'
     );
     dialog.add(widget);
-    dialog.onClose.subscribe(() => this.closeDialogSubject$.next());
+    const sub = dialog.onClose.subscribe(() => {
+      this.closeDialogSubject$.next();
+      sub.unsubscribe();
+    });
     return dialog;
   }
 }
@@ -259,10 +266,11 @@ class DialogWrapper {
 class LibManagerView {
   private constructor() {};
   private static _instance: LibManagerView;
+  static viewName = 'Manage Monomer Libraries';
   private _view: DG.View;
   private _duplicateManager: DuplicateMonomerManager;
   private libManager: MonomerLibManager;
-  private async getView() {
+  private async getView(addView = true) {
     const eventManager = MonomerLibFileEventManager.getInstance();
     const widget = (await MonomerLibraryManagerWidget.getInstance()).widget;
     const addButton = ui.bigButton('Add',
@@ -275,7 +283,10 @@ class LibManagerView {
         this._duplicateManager.root],
       {style: {width: '100%', height: '100%'}},
       true);
-    this._view = grok.shell.newView('Manage Monomer Libraries', [v]);
+    this._view = DG.View.fromRoot(v);
+    this._view.name = LibManagerView.viewName;
+    if (addView)
+      grok.shell.addView(this._view);
 
     ui.tools.waitForElementInDom(v).then(() => {
       setTimeout(() => {
@@ -300,24 +311,32 @@ class LibManagerView {
         }
       }));
     });
+    return this._view;
     //grok.shell.dockManager.dock(this._duplicateManager.root, DG.DOCK_TYPE.RIGHT, null, '', 0.4);
   }
 
-  static async showView() {
+  static async showView(addView = true) {
     if (!LibManagerView._instance)
       LibManagerView._instance = new LibManagerView();
     if (!LibManagerView._instance._duplicateManager)
       LibManagerView._instance._duplicateManager = await DuplicateMonomerManager.getInstance();
     if (!LibManagerView._instance.libManager)
       LibManagerView._instance.libManager = await MonomerLibManager.getInstance();
-    if (LibManagerView._instance._view &&
+    if (addView && LibManagerView._instance._view &&
         Array.from(grok.shell.views).find((v) => v.id && v.id === LibManagerView._instance._view.id)) {
       grok.shell.v = LibManagerView._instance._view;
       await LibManagerView._instance._duplicateManager.refresh();
-      return;
+      return LibManagerView._instance._view;
     }
-    LibManagerView._instance.getView();
+    // something can conflict with browse view, so need to make sure that we close all existing views
+    LibManagerView.closeExistingViews();
+    return LibManagerView._instance.getView(addView);
   }
+
+  private static closeExistingViews() {
+    Array.from(grok.shell.views).filter((v) => v.name === LibManagerView.viewName).forEach((v) => v.close());
+  }
+
   async mergeSelectedLibs() {
     const libraryExistsError = 'Library with this name already exists';
     const libManager = await MonomerLibManager.getInstance();

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

@@ -51,9 +51,14 @@ export const MONOMER_DF_COLUMNS = {
 
 
 export class MonomerManager implements IMonomerManager {
-  private adjustColWidths() {
+  private adjustTable() {
+    if (this.tv?.dataFrame) {
+      grok.data.detectSemanticTypes(this.tv.dataFrame);
+      this.tv.dataFrame.meta.detectSemanticTypes();
+    }
     setTimeout(() => {
       if (this.tv?.grid) {
+        this.tv!.grid.props.allowEdit = false;
         this.tv!.grid.col(MONOMER_DF_COLUMN_NAMES.NAME)!.width = 100;
         this.tv!.grid.col(MONOMER_DF_COLUMN_NAMES.SYMBOL)!.width = 70;
       }
@@ -75,7 +80,7 @@ export class MonomerManager implements IMonomerManager {
       const df = await this.getMonomersDf(this.libInput.value!);
       if (this.tv?.dataFrame) {
         this.tv.dataFrame = df;
-        this.adjustColWidths();
+        this.adjustTable();
         if (scrollToRowSymbol != undefined) {
           setTimeout(() => {
             const col = df.col(MONOMER_DF_COLUMN_NAMES.SYMBOL)!;
@@ -99,6 +104,13 @@ export class MonomerManager implements IMonomerManager {
     return this.instance;
   }
 
+  public static async getNewInstance(): Promise<MonomerManager> {
+    const monManager = await MonomerLibManager.getInstance();
+    await monManager.awaitLoaded();
+    await monManager.loadLibrariesPromise;
+    return new MonomerManager(monManager);
+  }
+
   async createNewMonomerLib(libName: string, _monomers: Monomer[]): Promise<void> {
     this.tv?.grid && ui.setUpdateIndicator(this.tv.grid.root, true);
     try {
@@ -168,11 +180,11 @@ export class MonomerManager implements IMonomerManager {
     return this._newMonomerForm;
   }
 
-  private async getMonomersTableView(fileName?: string): Promise<DG.TableView> {
+  private async getMonomersTableView(fileName?: string, addView = true): Promise<DG.TableView> {
     const df = await this.getMonomersDf(fileName);
-    this.tv = DG.TableView.create(df, true);
-    //const f = tv.filters();
-    this.adjustColWidths();
+    this.tv = DG.TableView.create(df, addView);
+
+    this.adjustTable();
     this.tv.subs.push(
       grok.events.onContextMenu.subscribe(({args}) => {
         if (!args || !args.menu || !args.context || args.context.type !== DG.VIEWER.GRID || !args.context.tableView ||
@@ -205,21 +217,28 @@ export class MonomerManager implements IMonomerManager {
     return this.tv;
   }
 
+  private static closeAllMonomerManagers() {
+    Array.from(grok.shell.tableViews ?? []).filter((v) => v.name === MonomerManager.VIEW_NAME).forEach((v) => v.close());
+  }
+
   private findActiveManagerView() {
     if (!this.tv)
       return null;
     const tv = Array.from(grok.shell.tableViews ?? []).find((tv) => tv.id === this.tv!.id);
     if (tv)
       grok.shell.v = tv;
+    else
+      MonomerManager.closeAllMonomerManagers();
+
     return tv ?? null;
   }
 
   private _skipLibInputOnchange: boolean = false;
 
-  async getViewRoot(libName?: string) {
+  async getViewRoot(libName?: string, addView = true) {
     const availableMonLibs = (await this.monomerLibManamger.getFileManager()).getValidLibraryPaths();
     this._newMonomerForm.molSketcher.resize();
-    if ((this.tv = this.findActiveManagerView()) && (libName ?? this.libInput.value)) {
+    if (addView && (this.tv = this.findActiveManagerView()) && (libName ?? this.libInput.value)) {
       // get monomer library list
       try {
         this._skipLibInputOnchange = true;
@@ -233,12 +252,12 @@ export class MonomerManager implements IMonomerManager {
       }
       const df = await this.getMonomersDf(libName);
       this.tv.dataFrame = df;
-      this.adjustColWidths();
+      this.adjustTable();
       return this.tv;
     }
 
     libName ??= availableMonLibs[0];
-    this.tv = await this.getMonomersTableView(libName);
+    this.tv = await this.getMonomersTableView(libName, addView);
 
     // remove project save button and download from ribbons
     let ribbons = this.tv.getRibbonPanels();
@@ -300,7 +319,7 @@ export class MonomerManager implements IMonomerManager {
         if (this._skipLibInputOnchange) return;
         const df = await this.getMonomersDf(this.libInput.value!);
           this.tv!.dataFrame = df;
-          this.adjustColWidths();
+          this.adjustTable();
       } catch (e) {
         console.error(e);
       }
@@ -308,7 +327,9 @@ export class MonomerManager implements IMonomerManager {
     this.libInput.addOptions(ui.icons.add(() => { this.createNewLibDialog(); }, 'Create new monomer library...'));
     const monForm = this._newMonomerForm.form;
     monForm.prepend(this.libInput.root);
-    this.tv.dockManager.dock(monForm, DG.DOCK_TYPE.LEFT, null, undefined, 0.4);
+    ui.tools.waitForElementInDom(this.tv.root).then(() => {
+      this.tv!.dockManager.dock(monForm, DG.DOCK_TYPE.LEFT, null, undefined, 0.4);
+    });
     return this.tv;
   }
 
@@ -403,6 +424,10 @@ export class MonomerManager implements IMonomerManager {
       this.tv?.grid && ui.setUpdateIndicator(this.tv.grid.root, false);
     }
   }
+
+  public resetCurrentRowFollowing() {
+    this._newMonomerForm.molChanged = false;
+  }
 }
 
 // some monomers might be in form of cap groups in place of r-groups (with supplied rgroups info), this function will convert them to r-groups
@@ -474,7 +499,7 @@ function getCaseInvariantValue<T>(obj: { [key: string]: T }, key: string): T | u
 
 // some r groups for some monomers can lack smiles, or something else :D this function will try to fix that
 function resolveRGroupInfo(rgps: RGroup[]): RGroup[] {
-  return rgps.map((rg) => {
+  return (rgps.map((rg) => {
     const cp = assignObjectCaseInvariant(RGROUP_FIELDS, rg);
     const smi = getCaseInvariantValue(cp, HELM_RGROUP_FIELDS.CAP_GROUP_SMILES_UPPERCASE);
     const altId = getCaseInvariantValue(cp, HELM_RGROUP_FIELDS.ALTERNATE_ID);
@@ -498,7 +523,7 @@ function resolveRGroupInfo(rgps: RGroup[]): RGroup[] {
         cp[HELM_RGROUP_FIELDS.ALTERNATE_ID] = `${label}-${capName}`;
     }
     return cp;
-  }) as RGroup[];
+  }) as RGroup[]).sort((a, b) => a.label?.localeCompare(b.label ?? '') ?? 0);
 }
 
 
@@ -522,6 +547,7 @@ class MonomerForm implements INewMonomerForm {
   rgroupsGridRoot: HTMLElement;
   private _molChanged: boolean = false;
   get molChanged() { return this._molChanged; }
+  set molChanged(v: boolean) { this._molChanged = v; }
   private saveValidationResult?: string | null = null;
   private triggerMolChange: boolean = true; // makes sure that change is not triggered by copying the molecule from grid
   inputsTabControl: DG.TabControl;
@@ -607,7 +633,7 @@ class MonomerForm implements INewMonomerForm {
           } as unknown as RGroup;
         });
         // if (this.rgroupsGrid.items.length !== rGroupItems.length)
-        this.rgroupsGrid.items = rGroupItems.sort((a, b) => a.label.localeCompare(b.label));
+        this.rgroupsGrid.items = rGroupItems.sort((a, b) => a.label?.localeCompare(b.label ?? '') ?? 0);
         this.rgroupsGrid.render();
         this.rgroupsGridRoot.style.display = 'flex';
         const mostSimilar = await mostSimilarNaturalAnalog(capSmiles(smiles, rGroupItems), this.polymerTypeInput.value ?? '');