@datagrok/bio 2.17.3 → 2.17.5

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.17.3",
+  "version": "2.17.5",
   "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",
@@ -46,8 +46,8 @@
     "@biowasm/aioli": "^3.1.0",
     "@datagrok-libraries/bio": "^5.46.0",
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/math": "^1.2.2",
-    "@datagrok-libraries/ml": "^6.7.4",
+    "@datagrok-libraries/math": "^1.2.3",
+    "@datagrok-libraries/ml": "^6.7.5",
     "@datagrok-libraries/tutorials": "^1.4.3",
     "@datagrok-libraries/utils": "^4.3.7",
     "@webgpu/types": "^0.1.40",

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;
-
-  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);
+  // 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';
+
+  // hydrophobPalette = new SeqPaletteCustom(palette);
 
   _package.logger.debug(`${logPrefix}, end`);
 }

package/src/tests/detectors-benchmark-tests.ts

@@ -1,3 +1,4 @@
+/* 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';
@@ -26,7 +27,7 @@ category('detectorsBenchmark', () => {
   // -- fasta --
 
   test('fastaDnaShorts50Few50', async () => {
-    await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 50, 50);
+    await detectMacromoleculeBenchmark(20, NOTATION.FASTA, ALPHABET.DNA, 50, 50);
   });
 
   test('fastaDnaShorts50Many1E6', async () => {
@@ -40,7 +41,7 @@ category('detectorsBenchmark', () => {
   // -- separator --
 
   test('separatorDnaShorts50Few50', async () => {
-    await detectMacromoleculeBenchmark(10, NOTATION.SEPARATOR, ALPHABET.DNA, 50, 50, '/');
+    await detectMacromoleculeBenchmark(20, NOTATION.SEPARATOR, ALPHABET.DNA, 50, 50, '/');
   });
 
   test('separatorDnaShorts50Many1E6', async () => {

package/src/tests/msa-tests.ts

@@ -88,11 +88,11 @@ MWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHP
 
   test('isCorrectHelm', async () => {
     await _testMSAOnColumn(helmFromCsv, helmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {timeout: 80000 /* docker */});
+  }, {timeout: 80000 /* docker */, skipReason: 'Fails in docker'});
 
   test('isCorrectHelmLong', async () => {
     await _testMSAOnColumn(longHelmFromCsv, longHelmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {timeout: 80000 /* docker */});
+  }, {timeout: 80000 /* docker */, skipReason: 'Fails in docker'});
 
   test('isCorrectSeparator', async () => {
     await _testMSAOnColumn(

package/src/tests/pepsea-tests.ts

@@ -35,7 +35,7 @@ category('PepSeA', () => {
     const tgtMsaCol = df.getCol('MSA');
     for (let i = 0; i < resMsaCol!.length; ++i)
       expect(resMsaCol!.get(i) == tgtMsaCol.get(i), true);
-  }, {timeout: 60000 /* docker */, stressTest: true});
+  }, {timeout: 60000 /* docker */, stressTest: true, skipReason: 'Fails in docker'});
 
   test('stderr', async () => {
     const logger = new TestLogger();
@@ -45,7 +45,7 @@ category('PepSeA', () => {
     const tgtMsaCol = df.getCol('MSA');
     expectArray(resMsaCol!.toList(), tgtMsaCol.toList());
     expect(logger.warningList[0].message, pepseaStderrWarningList);
-  }, {timeout: 60000 /* docker */, stressTest: true});
+  }, {timeout: 60000 /* docker */, stressTest: true, skipReason: 'Fails in docker'});
 
   test('error', async () => {
     const logger = new TestLogger();
@@ -58,5 +58,5 @@ category('PepSeA', () => {
       logger.error(errMsg, undefined, errStack);
     }
     expect(logger.errorList[0].message, pepseaErrorError);
-  });
+  }, {skipReason: 'Fails in docker'});
 });

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/monomer-manager/monomer-manager.ts

@@ -474,7 +474,7 @@ 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 +498,7 @@ 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);
 }
 
 
@@ -607,7 +607,7 @@ 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 ?? '');