@datagrok/helm 2.5.2 → 2.5.3

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.5.2",
+  "version": "2.5.3",
   "author": {
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
@@ -16,7 +16,7 @@
     "css/helm.css"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.44.1",
+    "@datagrok-libraries/bio": "^5.44.2",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/utils": "^4.3.4",
     "cash-dom": "^8.1.1",
@@ -28,7 +28,7 @@
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.11",
     "@datagrok-libraries/js-draw-lite": "^0.0.8",
-    "@datagrok/bio": "^2.15.5",
+    "@datagrok/bio": "^2.15.6",
     "@datagrok/chem": "^1.12.1",
     "@types/node": "17.0.45",
     "@types/webpack-env": "^1.18.5",

package/src/tests/findMonomers-tests.ts

@@ -6,7 +6,7 @@ import {after, before, category, delay, expect, expectObject, test} from '@datag
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {findMonomers, parseHelm} from '../utils';
@@ -25,8 +25,7 @@ category('findMonomers', () => {
     userLibSettings = await getUserLibSettings();
 
     // Tests 'findMonomers' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries for tests
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries for tests
   });
 
   after(async () => {

package/src/tests/get-molfiles-tests.ts

@@ -5,7 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {after, before, category, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/utils/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
@@ -24,8 +24,8 @@ category('getMolfiles', () => {
     await initHelmMainPackage();
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true);
+
+    await monomerLibHelper.loadMonomerLibForTests();
   });
 
   after(async () => {

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

@@ -15,9 +15,9 @@ import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
-import {defaultMonomerLibSummary, expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
+import {expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
 
 import {rewriteLibraries} from '../utils/get-monomer';
 import {JSDraw2Module, OrgHelmModule} from '../types';
@@ -25,6 +25,7 @@ import {JSDraw2Module, OrgHelmModule} from '../types';
 import {initHelmMainPackage} from './utils';
 
 import {_package} from '../package-test';
+import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
 
 declare const org: OrgHelmModule;
 declare const JSDraw2: JSDraw2Module;
@@ -79,9 +80,7 @@ category('getMonomer', ()=>{
     [monomerLibHelper, helmHelper, userLibSettings] = await Promise.all(
       [getMonomerLibHelper(), getHelmHelper(), getUserLibSettings()]);
 
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries for tests
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries for tests
   });
 
   after(async ()=>{
@@ -106,9 +105,6 @@ category('getMonomer', ()=>{
   }, {isAggregated: true});
 
   test('monomerLib', async () =>{
-    const monomerLib = monomerLibHelper.getMonomerLib();
-    expectMonomerLib(monomerLib);
-
     const getMonomerFunc = org.helm.webeditor.Monomers.getMonomer;
     return _testAll('monomerLib', getMonomerFunc);
   }, {isAggregated: true});
@@ -138,8 +134,6 @@ category('getMonomer', ()=>{
     resDf.set('res', resI, '');
     resDf.set('tgt', resI, '');
     try {
-      const monomerLib = monomerLibHelper.getMonomerLib();
-      expectMonomerLib(monomerLib);
       resDf.set('success', resI, true);
     } catch (err) {
       const [errMsg, errStack] = errInfo(err);
@@ -172,16 +166,15 @@ category('getMonomer', ()=>{
   }
 
   test('missing', async ()=> {
+    const monomerLib = monomerLibHelper.getMonomerLib();
     /* Tests getMonomer function adding missing monomers. */
     const helmStr = 'PEPTIDE1{[mis1].R.[mis2].T.C.F}$$$$;';
 
-    expectMonomerLib(monomerLibHelper.getMonomerLib());
+    const libSummary = monomerLib.getSummaryObj();
     const editor = new JSDraw2.Editor(ui.div(), {viewonly: true});
     editor.setHelm(helmStr);
-    const withMissing = JSON.parse(JSON.stringify(
-      defaultMonomerLibSummary)) as MonomerLibSummaryType;
-    withMissing['PEPTIDE'] += 2;
-    expectMonomerLib(monomerLibHelper.getMonomerLib(), withMissing);
+    libSummary[PolymerTypes.PEPTIDE] += 2;
+    expectMonomerLib(monomerLib, libSummary);
   });
 });
 

package/src/tests/helm-helper-tests.ts

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {after, before, category, delay, expect, expectArray, test, testEvent} from '@datagrok-libraries/utils/src/test';
-import {HelmNotSupportedError, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {HelmNotSupportedError, HelmNotSupportedErrorType, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
 import {_package} from '../package-test';
@@ -69,7 +69,7 @@ category('HelmHelper: removeGaps', () => {
 
   for (const [testName, testData] of Object.entries(tests)) {
     test(`${testName}`, async () => {
-      let resErr: any = null;
+      let resErr: HelmNotSupportedError | null = null;
       try {
         const res = helmHelper.removeGaps(testData.src.helm);
         expect(res.resHelm, testData.tgt.helm);
@@ -78,17 +78,8 @@ category('HelmHelper: removeGaps', () => {
         resErr = err;
       }
 
-      if (testData.tgt.helm === null) { // err expected, for debug on GitHub CI
-        expect(resErr != null, true, 'Error expected');
-        const isErrorInstance = resErr instanceof HelmNotSupportedError;
-        const errCtorName = resErr.constructor.name;
-        const isErrorCtor = errCtorName === 'HelmNotSupportedError';
-        _package.logger.debug(`Check error object. ` +
-          `isErrorInstance: ${isErrorInstance}, isErrorCtor: ${isErrorCtor}, errCtorName: ${errCtorName}`);
-      }
-
-      expect((resErr instanceof HelmNotSupportedError) || resErr?.constructor.name === 'HelmNotSupportedError',
-        testData.tgt.helm === null, 'HelmNotSupportedError thrown expected');
-    }, testData.tgt.helm == null ? {skipReason: 'GitHub CI does not support testing exceptions'} : undefined);
+      expect(resErr?.type == HelmNotSupportedErrorType, testData.tgt.helm === null,
+        'HelmNotSupportedError thrown expected');
+    });
   }
 });

package/src/tests/helm-input-tests.ts

@@ -8,7 +8,7 @@ import {after, before, category, delay, expect, test, testEvent} from '@datagrok
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
@@ -28,9 +28,7 @@ category('HelmInput', () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/tests/helm-service-tests.ts

@@ -16,7 +16,7 @@ import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {initHelmMainPackage} from './utils';
@@ -38,11 +38,7 @@ category('HelmService', () => {
       monomerLibHelper = await getMonomerLibHelper();
       userLibSettings = await getUserLibSettings();
 
-      await delay(1000); // for loading monomer libraries files
-      // Test 'helm' requires default monomer library loaded
-      await setUserLibSettingsForTests();
-      await monomerLibHelper.loadMonomerLib(true); // load default libraries
-      const libSummary = monomerLibHelper.getMonomerLib().getSummaryObj();
+      await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
 
       helmSvc = await getHelmService();
       await helmSvc.reset();

package/src/tests/helm-web-editor-tests.ts

@@ -7,7 +7,7 @@ import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {initHelmMainPackage} from './utils';
@@ -22,9 +22,8 @@ category('helm-web-editor', async () => {
     await initHelmMainPackage();
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true);
+
+    await monomerLibHelper.loadMonomerLibForTests();
 
     hh = await getHelmHelper();
   });

package/src/tests/parse-helm-tests.ts

@@ -8,7 +8,7 @@ import {HelmType, IHelmDrawOptions, Mol, OrgType} from '@datagrok-libraries/bio/
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {JSDraw2Module} from '../types';
@@ -54,9 +54,7 @@ category('parseHelm', () => {
       'get user lib settings for backup');
 
     // parseHelm is dependent on monomers RGroups available, test requires default monomer library
-    await setUserLibSettingsForTests();
-    await libHelper.awaitLoaded();
-    await libHelper.loadMonomerLib(true);
+    await libHelper.loadMonomerLibForTests();
   });
 
   after(async () => {

package/src/tests/properties-widget-tests.ts

@@ -6,7 +6,7 @@ import {after, before, category, expect, expectObject, test, timeout} from '@dat
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {generateLongSequence} from '@datagrok-libraries/bio/src/utils/generator';
@@ -82,10 +82,7 @@ category('properties-widget', () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = getUserLibSettings();
 
-    await setUserLibSettingsForTests();
-    await timeout(async () => { await monomerLibHelper.awaitLoaded(); },
-      5000, 'MonomerLibHelper.awaitLoaded() timeout');
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/tests/renderers-tests.ts

@@ -12,7 +12,7 @@ import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {awaitGrid, initHelmMainPackage} from './utils';
@@ -32,8 +32,7 @@ category('renderers', () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {