@datagrok/peptides 1.27.3 → 1.27.4

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.27.3",
+  "version": "1.27.4",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -25,7 +25,8 @@
     "file-loader": "^6.2.0",
     "rxjs": "^6.5.5",
     "uuid": "^10.0.0",
-    "wu": "^2.1.0"
+    "wu": "^2.1.0",
+    "@datagrok-libraries/test": "^1.1.0"
   },
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.16",
@@ -40,7 +41,7 @@
     "@typescript-eslint/eslint-plugin": "^8.8.1",
     "@typescript-eslint/parser": "^8.8.1",
     "css-loader": "^7.1.2",
-    "datagrok-tools": "^4.14.65",
+    "datagrok-tools": "^5.0.0",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "style-loader": "^4.0.0",
@@ -80,5 +81,8 @@
   "canView": [
     "All users"
   ],
-  "category": "Bioinformatics"
+  "category": "Bioinformatics",
+  "overrides": {
+    "datagrok-api": "$datagrok-api"
+  }
 }

package/src/demo/fasta.ts

@@ -7,7 +7,7 @@ import * as C from '../utils/constants';
 import {scaleActivity} from '../utils/misc';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {PeptidesModel} from '../model';
-import {awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {awaitCheck, delay} from '@datagrok-libraries/test/src/test';
 import {MCLSettings} from '../utils/types';
 
 export async function macromoleculeSarFastaDemoUI(): Promise<void> {

package/src/package-test.ts

@@ -1,5 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import {runTests, TestContext, tests, initAutoTests as initTests } from '@datagrok-libraries/utils/src/test';
+import {runTests, TestContext, tests, initAutoTests as initTests } from '@datagrok-libraries/test/src/test';
 
 import './tests/core';
 import './tests/benchmarks';

package/src/package.g.ts

@@ -2,6 +2,7 @@ import {PackageFunctions} from './package';
 import * as DG from 'datagrok-api/dg';
 
 //tags: init
+//meta.role: init
 export async function initPeptides() : Promise<void> {
   await PackageFunctions.initPeptides();
 }
@@ -23,9 +24,10 @@ export async function testInitFunctionPeptides(v: any) : Promise<void> {
 }
 
 //name: Peptides
-//tags: panel, widgets
+//tags: widgets, panel
 //input: column col { semType: Macromolecule }
 //output: widget result
+//meta.role: widgets,panel
 export function peptidesPanel(col: DG.Column) : any {
   return PackageFunctions.peptidesPanel(col);
 }
@@ -35,6 +37,7 @@ export function peptidesPanel(col: DG.Column) : any {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/peptide-sar-viewer.svg
+//meta.role: viewer
 export function monomerPosition() : any {
   return PackageFunctions.monomerPosition();
 }
@@ -44,6 +47,7 @@ export function monomerPosition() : any {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/peptide-sar-vertical-viewer.svg
+//meta.role: viewer
 export function mostPotentResidues() : any {
   return PackageFunctions.mostPotentResidues();
 }
@@ -53,6 +57,7 @@ export function mostPotentResidues() : any {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/sequence-statistics-viewer.svg
+//meta.role: viewer
 export function mutationCliffs() : any {
   return PackageFunctions.mutationCliffs();
 }
@@ -61,6 +66,7 @@ export function mutationCliffs() : any {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/logo-summary-viewer.svg
+//meta.role: viewer
 export function logoSummaryTable() : any {
   return PackageFunctions.logoSummaryTable();
 }
@@ -69,6 +75,7 @@ export function logoSummaryTable() : any {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/sequence-statistics-viewer.svg
+//meta.role: viewer
 export function sequencePositionStatistics() : any {
   return PackageFunctions.sequencePositionStatistics();
 }
@@ -76,14 +83,16 @@ export function sequencePositionStatistics() : any {
 //name: Active peptide selection
 //tags: viewer
 //output: viewer result
+//meta.role: viewer
 export function clusterMaxActivity() : any {
   return PackageFunctions.clusterMaxActivity();
 }
 
 //name: Manual Alignment
-//tags: panel, widgets
+//tags: widgets, panel
 //input: string _monomer { semType: Monomer }
 //output: widget result
+//meta.role: widgets,panel
 export function manualAlignment(_monomer: string) : any {
   return PackageFunctions.manualAlignment(_monomer);
 }
@@ -101,6 +110,7 @@ export async function macromoleculeSarFastaDemo() : Promise<void> {
 //output: grid_cell_renderer result
 //meta.cellType: lst-pie-chart
 //meta.gridChart: true
+//meta.role: cellRenderer
 export function lstPiechartCellRenderer() : any {
   return PackageFunctions.lstPiechartCellRenderer();
 }

package/src/package.ts

@@ -79,7 +79,7 @@ async function openDemoData(chosenFile: string): Promise<void> {
 
 
 export class PackageFunctions {
-  @grok.decorators.init()
+  @grok.decorators.init({tags: ['init']})
   static async initPeptides(): Promise<void> {
     try {
       monomerWorks ??= new MonomerWorks(await grok.functions.call('Bio:getBioLib'));
@@ -159,8 +159,9 @@ export class PackageFunctions {
 
 
   @grok.decorators.panel({
-    tags: ['widgets'],
     name: 'Peptides',
+    meta: {role: 'widgets'},
+    tags: ['widgets', 'panel'],
   })
   static peptidesPanel(
     @grok.decorators.param({'options': {'semType': 'Macromolecule'}}) col: DG.Column): DG.Widget {
@@ -172,9 +173,9 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    meta: {icon: 'files/icons/peptide-sar-viewer.svg'},
-    tags: ['viewer'],
+    meta: {icon: 'files/icons/peptide-sar-viewer.svg', role: 'viewer'},
     name: 'Sequence Variability Map',
+    tags: ['viewer'],
     description: 'Peptides Sequence Variability Map Viewer',
     outputs: [{type: 'viewer', name: 'result'}],
   })
@@ -184,9 +185,9 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    meta: {icon: 'files/icons/peptide-sar-vertical-viewer.svg'},
-    tags: ['viewer'],
+    meta: {icon: 'files/icons/peptide-sar-vertical-viewer.svg', role: 'viewer'},
     name: 'Most Potent Residues',
+    tags: ['viewer'],
     description: 'Peptides Most Potent Residues Viewer',
     outputs: [{type: 'viewer', name: 'result'}],
   })
@@ -195,10 +196,10 @@ export class PackageFunctions {
   }
 
   @grok.decorators.func({
-    meta: {icon: 'files/icons/sequence-statistics-viewer.svg'},
-    tags: ['viewer'],
+    meta: {icon: 'files/icons/sequence-statistics-viewer.svg', role: 'viewer'},
     name: 'Sequence Mutation Cliffs',
     description: 'Mutation Cliffs Line Chart',
+    tags: ['viewer'],
     outputs: [{type: 'viewer', name: 'result'}],
   })
   static mutationCliffs(): DG.Viewer {
@@ -207,9 +208,9 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    meta: {icon: 'files/icons/logo-summary-viewer.svg'},
-    tags: ['viewer'],
+    meta: {icon: 'files/icons/logo-summary-viewer.svg', role: 'viewer'},
     name: 'Logo Summary Table',
+    tags: ['viewer'],
     outputs: [{type: 'viewer', name: 'result'}],
   })
   static logoSummaryTable(): DG.Viewer {
@@ -218,10 +219,10 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    meta: {icon: 'files/icons/sequence-statistics-viewer.svg'},
-    tags: ['viewer'],
+    meta: {icon: 'files/icons/sequence-statistics-viewer.svg', role: 'viewer'},
     name: 'Sequence Position Statistics',
     outputs: [{type: 'viewer', name: 'result'}],
+    tags: ['viewer'],
   })
   static sequencePositionStatistics(): DG.Viewer {
     return new SequencePositionStatsViewer();
@@ -229,9 +230,10 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    tags: ['viewer'],
     name: 'Active peptide selection',
     outputs: [{type: 'viewer', name: 'result'}],
+    meta: {role: 'viewer'},
+    tags: ['viewer'],
   })
   static clusterMaxActivity(): DG.Viewer {
     return new ClusterMaxActivityViewer();
@@ -239,8 +241,9 @@ export class PackageFunctions {
 
 
   @grok.decorators.panel({
-    tags: ['widgets'],
     name: 'Manual Alignment',
+    meta: {role: 'widgets'},
+    tags: ['widgets', 'panel'],
   })
   static manualAlignment(
     @grok.decorators.param({'options': {'semType': 'Monomer'}}) _monomer: string): DG.Widget {
@@ -273,6 +276,7 @@ export class PackageFunctions {
     meta: {
       cellType: 'lst-pie-chart',
       gridChart: 'true',
+      role: 'cellRenderer',
     },
     tags: ['cellRenderer'],
     name: 'LST Pie Chart',

package/src/tests/benchmarks.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, test} from '@datagrok-libraries/test/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 import {_package} from '../package-test';

package/src/tests/core.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {awaitCheck, before, category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
+import {awaitCheck, before, category, delay, expect, test} from '@datagrok-libraries/test/src/test';
 
 import {_package} from '../package-test';
 import {startAnalysis} from '../widgets/peptides';

package/src/tests/misc.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/test/src/test';
 
 import {findMutations, MutationCliffsOptions} from '../utils/algorithms';
 import * as type from '../utils/types';

package/src/tests/model.ts

@@ -10,7 +10,7 @@ import {
   expect,
   expectFloat,
   test,
-} from '@datagrok-libraries/utils/src/test';
+} from '@datagrok-libraries/test/src/test';
 import {
   _package,
 } from '../package-test';

package/src/tests/table-view.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {after, awaitCheck, before, category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, awaitCheck, before, category, delay, expect, test} from '@datagrok-libraries/test/src/test';
 import {_package} from '../package-test';
 import {PeptidesModel, VIEWER_TYPE} from '../model';
 import {startAnalysis} from '../widgets/peptides';

package/src/tests/viewers.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test, testViewer} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test, testViewer} from '@datagrok-libraries/test/src/test';
 import {PeptidesModel, VIEWER_TYPE} from '../model';
 import {_package} from '../package-test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';

package/src/tests/widgets.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, delay, expect, test} from '@datagrok-libraries/test/src/test';
 import {_package} from '../package-test';
 import {PeptidesModel, VIEWER_TYPE} from '../model';
 import {scaleActivity} from '../utils/misc';

package/src/utils/misc.ts

@@ -106,7 +106,7 @@ export type DistributionLabelMap = { [key in SPLIT_CATEGORY]?: string };
  * @param labelMap - Mapping object for distribution labels.
  * @return - Panel with distribution plot and statistics.
  */
-// @ts-ignore TODO: fix after api update
+/* @ts-ignore TODO: fix after api update */
 export function getDistributionPanel(hist: DG.Viewer<DG.IHistogramSettings>, statsMap: StringDictionary,
   labelMap: DistributionLabelMap = {}): HTMLDivElement {
   const splitCol = hist.dataFrame.getCol(C.COLUMNS_NAMES.SPLIT_COL);