@datagrok/helm 2.13.0 → 2.13.2

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.13.0",
+  "version": "2.13.2",
   "author": {
     "name": "Maria Dolotova",
     "email": "mdolotova@datagrok.ai"
@@ -16,7 +16,7 @@
     "css/helm.css"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.61.0",
+    "@datagrok-libraries/bio": "^5.63.4",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/helm-web-editor": "^1.1.16",
     "@datagrok-libraries/utils": "^4.6.9",
@@ -25,18 +25,19 @@
     "dayjs": "^1.10.6",
     "lru-cache": "^10.4.3",
     "rxjs": "^6.5.5",
-    "wu": "^2.1.0"
+    "wu": "^2.1.0",
+    "@datagrok-libraries/test": "^1.1.0"
   },
   "devDependencies": {
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
-    "@datagrok/bio": "^2.24.0",
-    "@datagrok/chem": "^1.13.0",
+    "@datagrok/bio": "^2.25.1",
+    "@datagrok/chem": "^1.17.0",
     "@types/node": "17.0.45",
     "@types/webpack-env": "^1.18.5",
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^7.16.0",
     "@typescript-eslint/parser": "^7.16.0",
-    "datagrok-tools": "^4.14.65",
+    "datagrok-tools": "^5.0.0",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-deprecation": "^3.0.0",
@@ -79,5 +80,8 @@
     "url": "https://github.com/datagrok-ai/public.git",
     "directory": "packages/Helm"
   },
-  "category": "Bioinformatics"
+  "category": "Bioinformatics",
+  "overrides": {
+    "datagrok-api": "$datagrok-api"
+  }
 }

package/src/package-test.ts

@@ -5,7 +5,7 @@ import * as grok from 'datagrok-api/grok';
 // import {JSDraw2ModuleType} from '@datagrok/js-draw-lite/src/types/jsdraw2';
 // import {HelmType, OrgHelmModuleType} from '@datagrok/helm-web-editor/src/types/org-helm';
 
-import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext, initAutoTests as initTests} from '@datagrok-libraries/test/src/test';
 
 import './tests/_first-tests';
 import './tests/helm-tests';

package/src/package-utils.ts

@@ -5,7 +5,8 @@ import * as DG from 'datagrok-api/dg';
 
 import {Unsubscribable} from 'rxjs';
 
-import {delay, timeout} from '@datagrok-libraries/utils/src/test';
+import {timeout} from '@datagrok-libraries/utils/src/test';
+
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {
@@ -152,7 +153,7 @@ export async function initHelmLoadAndPatchDojo(): Promise<void> {
             `Loading Helm Web Editor ${dojoProgress}/${dojoTargetList.length}`);
           _package.logger.debug(`${logPrefix}, dojo loading ... ` +
             `${dojoNotReadyList.map((m) => `'${m}'`).join(',')} ...`);
-          await delay(100);
+          await DG.delay(100);
         }
         _package.logger.debug(`${logPrefix}, dojo ready all modules`);
       }, 60000, 'timeout dojox.gfx.svg');

package/src/package.g.ts

@@ -1,7 +1,7 @@
 import {PackageFunctions} from './package';
 import * as DG from 'datagrok-api/dg';
 
-//tags: init
+//meta.role: init
 export async function initHelm() : Promise<void> {
   await PackageFunctions.initHelm();
 }
@@ -12,18 +12,18 @@ export async function getHelmService() : Promise<any> {
   return await PackageFunctions.getHelmService();
 }
 
-//tags: cellRenderer
 //output: grid_cell_renderer result
 //meta.columnTags: quality=Macromolecule, units=helm
 //meta.cellType: helm
+//meta.role: cellRenderer
 export function helmCellRenderer() : any {
   return PackageFunctions.helmCellRenderer();
 }
 
 //description: Macromolecule
-//tags: cellEditor
 //input: grid_cell cell 
 //meta.columnTags: quality=Macromolecule, units=helm
+//meta.role: cellEditor
 export function editMoleculeCell(cell: any) : void {
   PackageFunctions.editMoleculeCell(cell);
 }
@@ -37,9 +37,10 @@ export function openEditor(mol: DG.SemanticValue) : void {
 }
 
 //name: Properties
-//tags: panel, bio, helm, widgets
 //input: semantic_value sequence { semType: Macromolecule }
 //output: widget result
+//meta.role: widgets,panel
+//meta.domain: bio
 export function propertiesWidget(sequence: DG.SemanticValue) : any {
   return PackageFunctions.propertiesWidget(sequence);
 }
@@ -50,12 +51,12 @@ export function getMolfiles(col: DG.Column<any>) : any {
   return PackageFunctions.getMolfiles(col);
 }
 
-//tags: valueEditor
 //input: string name { optional: true }
 //input: object options { optional: true }
 //output: object result
 //meta.propertyType: string
 //meta.semType: Macromolecule
+//meta.role: valueEditor
 export function helmInput(name: string, options: any) : any {
   return PackageFunctions.helmInput(name, options);
 }

package/src/package.ts

@@ -26,6 +26,37 @@ import type {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
 export * from './package.g';
 export const _package = new HelmPackage(/*{debug: true}/**/);
 
+/** Temporary polyfill */
+
+function getDecoratorFunc() {
+  return function(args: any) {
+    return function(
+      target: any,
+      propertyKey: string,
+      descriptor: PropertyDescriptor
+    ) { };
+  };
+}
+
+// Ensure decorators object exists and polyfill missing decorators
+if (!grok.decorators)
+  (grok as any).decorators = {};
+
+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'
+];
+
+decorators.forEach((decorator) => {
+  if (!(grok.decorators as any)[decorator])
+    (grok.decorators as any)[decorator] = getDecoratorFunc();
+});
+
+/** End temporary polyfill */
+
+
 /*
   Loading modules:
   Through Helm/package.json/sources section
@@ -111,10 +142,10 @@ export class PackageFunctions {
   }
 
   @grok.decorators.func({
-    'tags': ['cellRenderer'],
     'meta': {
       'columnTags': 'quality=Macromolecule, units=helm',
-      'cellType': 'helm'
+      'cellType': 'helm',
+      'role': 'cellRenderer'
     },
     'outputs': [{name: 'result', type: 'grid_cell_renderer'}]
   })
@@ -127,8 +158,10 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    'meta': {'columnTags': 'quality=Macromolecule, units=helm'},
-    'tags': ['cellEditor'],
+    'meta': {
+      'columnTags': 'quality=Macromolecule, units=helm',
+      'role': 'cellEditor'
+    },
     'description': 'Macromolecule'
   })
   static editMoleculeCell(
@@ -162,12 +195,8 @@ export class PackageFunctions {
 
 
   @grok.decorators.panel({
-    'tags': [
-      'bio',
-      'helm',
-      'widgets'
-    ],
-    'name': 'Properties'
+    'name': 'Properties',
+    'meta': {role: 'widgets', domain: 'bio'},
   })
   static propertiesWidget(
     @grok.decorators.param({'options': {'semType': 'Macromolecule'}}) sequence: DG.SemanticValue): DG.Widget {
@@ -187,9 +216,9 @@ export class PackageFunctions {
   @grok.decorators.func({
     'meta': {
       'propertyType': 'string',
-      'semType': 'Macromolecule'
+      'semType': 'Macromolecule',
+      'role': 'valueEditor'
     },
-    'tags': ['valueEditor'],
     'outputs': [{'type': 'object', 'name': 'result'}]
   })
   static helmInput(

package/src/tests/_first-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test} from '@datagrok-libraries/utils/src/test';
+import {category, test} from '@datagrok-libraries/test/src/test';
 
 category('_first', () => {
   /** The first test of the package to evaluate problems with imports. */

package/src/tests/findMonomers-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, expectObject, test} from '@datagrok-libraries/test/src/test';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {

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

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
   getUserLibSettings, setUserLibSettings,

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

@@ -6,7 +6,7 @@ import wu from 'wu';
 
 import {
   after, before, category, delay, expect, test, expectArray, testEvent, expectFloat, timeout
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper, getMonomerHandleArgs} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {Atom, HelmType, IJsAtom, GetMonomerFunc, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';

package/src/tests/helm-activity-cliffs.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {after, awaitCheck, before, category, test} from '@datagrok-libraries/utils/src/test';
+import {after, awaitCheck, before, category, test} from '@datagrok-libraries/test/src/test';
 
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
@@ -11,7 +11,7 @@ import {
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {expect} from '@datagrok-libraries/utils/src/test';
+import {expect} from '@datagrok-libraries/test/src/test';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';

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';
 
 /* eslint-disable max-len */
-import {after, before, category, delay, expect, expectArray, test, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, expectArray, test, testEvent} from '@datagrok-libraries/test/src/test';
 import {HelmNotSupportedError, HelmNotSupportedErrorType, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';

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

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 
-import {after, before, category, delay, expect, test, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, testEvent} from '@datagrok-libraries/test/src/test';
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {

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

@@ -6,7 +6,7 @@ import {Subject} from 'rxjs';
 
 import {
   category, expect, test, awaitCheck, delay, testEvent, before, after
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
   getHelmService, HelmServiceBase, HelmAux, HelmProps

package/src/tests/helm-substructure-filter.ts

@@ -4,7 +4,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, test, expect, delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, test, expect, delay, testEvent} from '@datagrok-libraries/test/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings

package/src/tests/helm-tests.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 
 import {parseHelm} from '../utils';
 import {initHelmMainPackage} from './utils';

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

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/test/src/test';
 import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/parse-helm-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, test, expectArray, timeout} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/test/src/test';
 import {HelmMol, HelmType, IHelmBio, IHelmEditorOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

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

@@ -2,7 +2,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {after, before, category, expect, expectObject, test, timeout} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, expectObject, test, timeout} from '@datagrok-libraries/test/src/test';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {
   getUserLibSettings, setUserLibSettings

package/src/tests/renderers-tests.ts

@@ -7,7 +7,7 @@ import {fromEvent} from 'rxjs';
 
 import {
   after, before, category, test, expect, awaitCheck, delay, testEvent
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/tests/to-atomic-level-ui-non-linear.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, test} from '@datagrok-libraries/test/src/test';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';

package/src/tests/utils.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {delay, testEvent} from '@datagrok-libraries/test/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {_package} from '../package-test';