@datagrok/bio 2.25.9 → 2.25.10

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.25.9",
+  "version": "2.25.10",
   "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",
@@ -48,6 +48,7 @@
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.7",
+    "@datagrok-libraries/test": "^1.1.0",
     "@datagrok-libraries/tutorials": "^1.7.4",
     "@datagrok-libraries/utils": "^4.6.9",
     "@webgpu/types": "^0.1.40",
@@ -55,7 +56,7 @@
     "ajv-errors": "^3.0.0",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
-    "datagrok-api": "^1.25.2",
+    "datagrok-api": "^1.26.3",
     "dayjs": "^1.11.4",
     "fastest-levenshtein": "^1.0.16",
     "openchemlib": "^7.2.3",
@@ -69,18 +70,21 @@
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/chem": "^1.15.0",
     "@datagrok/dendrogram": "^1.2.33",
+    "@datagrok/eda": "^1.4.13",
+    "@datagrok/helm": "^2.13.1",
+    "@datagrok/peptides": "^1.27.4",
     "@types/node": "^17.0.24",
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",
     "@typescript-eslint/parser": "^8.8.1",
-    "datagrok-tools": "^4.14.57",
+    "datagrok-tools": "^5.1.5",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-rxjs": "^5.0.3",
     "source-map-loader": "^5.0.0",
     "ts-loader": "^9.5.1",
     "typescript": "^5.5.3",
-    "webpack": "^5.92.1",
+    "webpack": "^5.105.2",
     "webpack-bundle-analyzer": "^4.10.2",
     "webpack-cli": "^5.1.4"
   },
@@ -158,5 +162,8 @@
         }
       }
     }
+  },
+  "overrides": {
+    "datagrok-api": "$datagrok-api"
   }
 }

package/scripts/read-tree-pkl.py

@@ -1,4 +1,4 @@
-# coding: utf-8
+# This script uses UTF-8 encoding
 
 import ete3
 import numpy as np

package/src/demo/bio03-atomic-level.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 import {_package, PackageFunctions} from '../package';
 import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 import {adjustGridcolAfterRender} from '../utils/ui-utils';
 
 export async function demoToAtomicLevel(): Promise<void> {

package/src/package-test.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 {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/_first-tests';
 import './tests/Palettes-test';
@@ -49,7 +49,9 @@ export {tests};
 //input: object testContext {optional: true}
 //input: bool stressTest {optional: true}
 //output: dataframe result
-export async function test(category: string, test: string, testContext: TestContext, stressTest?: boolean): Promise<DG.DataFrame> {
+export async function test(
+  category: string, test: string, testContext: TestContext, stressTest?: boolean
+): Promise<DG.DataFrame> {
   const data = await runTests({category, test, testContext, stressTest});
   return DG.DataFrame.fromObjects(data)!;
 }

package/src/package.g.ts

@@ -8,6 +8,7 @@ export async function getMonomerLibHelper() : Promise<any> {
 }
 
 //tags: init
+//meta.role: init
 export async function initBio() : Promise<void> {
   await PackageFunctions.initBio();
 }
@@ -15,6 +16,7 @@ export async function initBio() : Promise<void> {
 //tags: tooltip
 //input: column col { semType: Macromolecule }
 //output: widget result
+//meta.role: tooltip
 export function sequenceTooltip(col: DG.Column) : any {
   return PackageFunctions.sequenceTooltip(col);
 }
@@ -50,38 +52,45 @@ export function getSeqHandler(sequence: DG.Column<any>) : any {
 //tags: panel
 //input: column seqCol { semType: Macromolecule }
 //output: widget result
+//meta.role: panel
 export function getRegionPanel(seqCol: DG.Column<any>) : any {
   return PackageFunctions.getRegionPanel(seqCol);
 }
 
 //name: Bioinformatics | Manage Monomer Libraries
-//tags: panel, exclude-actions-panel
+//tags: exclude-actions-panel
 //input: column seqColumn { semType: Macromolecule }
 //output: widget result
+//meta.exclude-actions-panel: true
+//meta.role: panel
 export async function libraryPanel(_seqColumn: DG.Column) : Promise<any> {
   return await PackageFunctions.libraryPanel(_seqColumn);
 }
 
 //tags: editor
 //input: funccall call 
+//meta.role: editor
 export function GetRegionEditor(call: DG.FuncCall) : void {
   PackageFunctions.GetRegionEditor(call);
 }
 
 //tags: editor
 //input: funccall call 
+//meta.role: editor
 export function SplitToMonomersEditor(call: DG.FuncCall) : void {
   PackageFunctions.SplitToMonomersEditor(call);
 }
 
 //tags: editor
 //input: funccall call 
+//meta.role: editor
 export function SequenceSpaceEditor(call: DG.FuncCall) : void {
   PackageFunctions.SequenceSpaceEditor(call);
 }
 
 //tags: editor
 //input: funccall call 
+//meta.role: editor
 export function SeqActivityCliffsEditor(call: DG.FuncCall) : void {
   PackageFunctions.SeqActivityCliffsEditor(call);
 }
@@ -90,6 +99,7 @@ export function SeqActivityCliffsEditor(call: DG.FuncCall) : void {
 //output: grid_cell_renderer result
 //meta.cellType: sequence
 //meta.columnTags: quality=Macromolecule, units=custom
+//meta.role: cellRenderer
 export function customSequenceCellRenderer() : any {
   return PackageFunctions.customSequenceCellRenderer();
 }
@@ -98,6 +108,7 @@ export function customSequenceCellRenderer() : any {
 //output: grid_cell_renderer result
 //meta.cellType: sequence
 //meta.columnTags: quality=Macromolecule, units=fasta
+//meta.role: cellRenderer
 export function fastaSequenceCellRenderer() : any {
   return PackageFunctions.fastaSequenceCellRenderer();
 }
@@ -106,6 +117,7 @@ export function fastaSequenceCellRenderer() : any {
 //output: grid_cell_renderer result
 //meta.cellType: sequence
 //meta.columnTags: quality=Macromolecule, units=separator
+//meta.role: cellRenderer
 export function separatorSequenceCellRenderer() : any {
   return PackageFunctions.separatorSequenceCellRenderer();
 }
@@ -114,6 +126,7 @@ export function separatorSequenceCellRenderer() : any {
 //output: grid_cell_renderer result
 //meta.cellType: sequence
 //meta.columnTags: quality=Macromolecule, units=biln
+//meta.role: cellRenderer
 export function bilnSequenceCellRenderer() : any {
   return PackageFunctions.bilnSequenceCellRenderer();
 }
@@ -123,6 +136,7 @@ export function bilnSequenceCellRenderer() : any {
 //input: object stats 
 //input: string separator { nullable: true; optional: true }
 //output: bool result
+//meta.role: notationRefiner
 export function refineNotationProviderForBiln(col: DG.Column<any>, stats: any, separator: any) : boolean {
   return PackageFunctions.refineNotationProviderForBiln(col, stats, separator);
 }
@@ -131,14 +145,17 @@ export function refineNotationProviderForBiln(col: DG.Column<any>, stats: any, s
 //tags: panel
 //input: column molColumn { semType: Macromolecule }
 //output: widget result
+//meta.role: panel
 export function macroMolColumnPropertyPanel(molColumn: DG.Column) : any {
   return PackageFunctions.macroMolColumnPropertyPanel(molColumn);
 }
 
 //name: Composition analysis
-//tags: panel, bio, widgets
+//tags: bio, widgets, panel
 //input: semantic_value sequence { semType: Macromolecule }
 //output: widget result
+//meta.role: widgets,panel
+//meta.domain: bio
 export function compositionAnalysisWidget(sequence: DG.SemanticValue) : any {
   return PackageFunctions.compositionAnalysisWidget(sequence);
 }
@@ -148,6 +165,7 @@ export function compositionAnalysisWidget(sequence: DG.SemanticValue) : any {
 //output: grid_cell_renderer result
 //meta.cellType: MacromoleculeDifference
 //meta.columnTags: quality=MacromoleculeDifference
+//meta.role: cellRenderer
 export function macromoleculeDifferenceCellRenderer() : any {
   return PackageFunctions.macromoleculeDifferenceCellRenderer();
 }
@@ -164,18 +182,20 @@ export function sequenceAlignment(alignType: string, alignTable: string, gap: nu
 
 //name: WebLogo
 //description: WebLogo
-//tags: panel, viewer
+//tags: viewer, panel
 //output: viewer result
 //meta.icon: files/icons/weblogo-viewer.svg
+//meta.role: viewer,panel
 export function webLogoViewer() {
   return PackageFunctions.webLogoViewer();
 }
 
 //name: VdRegions
 //description: V-Domain regions viewer
-//tags: panel, viewer
+//tags: viewer
 //output: viewer result
 //meta.icon: files/icons/vdregions-viewer.svg
+//meta.role: viewer,panel
 export function vdRegionsViewer() {
   return PackageFunctions.vdRegionsViewer();
 }
@@ -186,7 +206,7 @@ export function vdRegionsViewer() {
 //input: string end { optional: true }
 //input: string name { optional: true; description: Name of the column to be created }
 //output: column result
-export function getRegion(sequence: DG.Column<any>, start: any, end: any, name: any) : any {
+export function getRegion(sequence: DG.Column<any>, start?: string, end?: string, name?: string) : any {
   return PackageFunctions.getRegion(sequence, start, end, name);
 }
 
@@ -199,7 +219,7 @@ export function getRegion(sequence: DG.Column<any>, start: any, end: any, name:
 //input: string name { optional: true; description: Region column name }
 //top-menu: Bio | Calculate | Get Region...
 //editor: Bio:GetRegionEditor
-export async function getRegionTopMenu(table: DG.DataFrame, sequence: DG.Column, start: any, end: any, name: any) : Promise<void> {
+export async function getRegionTopMenu(table: DG.DataFrame, sequence: DG.Column, start?: string, end?: string, name?: string) : Promise<void> {
   await PackageFunctions.getRegionTopMenu(table, sequence, start, end, name);
 }
 
@@ -231,6 +251,7 @@ export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<a
 //meta.supportedSemTypes: Macromolecule
 //meta.supportedTypes: string
 //meta.supportedDistanceFunctions: Hamming,Levenshtein,Monomer chemical distance,Needlemann-Wunsch
+//meta.role: dim-red-preprocessing-function
 export async function macromoleculePreprocessingFunction(col: DG.Column, metric: any, gapOpen: number, gapExtend: number, fingerprintType: string) : Promise<any> {
   return await PackageFunctions.macromoleculePreprocessingFunction(col, metric, gapOpen, gapExtend, fingerprintType);
 }
@@ -300,9 +321,11 @@ export async function toAtomicLevelAction(seqCol: DG.Column) : Promise<void> {
 }
 
 //name: Molecular Structure
-//tags: panel, bio, widgets
+//tags: bio, widgets, panel
 //input: semantic_value sequence { semType: Macromolecule }
 //output: widget result
+//meta.role: widgets,panel
+//meta.domain: bio
 export async function toAtomicLevelPanel(sequence: DG.SemanticValue) : Promise<any> {
   return await PackageFunctions.toAtomicLevelPanel(sequence);
 }
@@ -316,16 +339,20 @@ export async function toAtomicLevelSingleSeq(sequence: string) : Promise<string>
 }
 
 //name: Molecular 3D Structure
-//tags: panel, bio, widgets
+//tags: bio, widgets, panel
 //input: semantic_value sequence { semType: Macromolecule }
 //output: widget result
+//meta.role: widgets,panel
+//meta.domain: bio
 export async function sequence3dStructureWidget(sequence: DG.SemanticValue) : Promise<any> {
   return await PackageFunctions.sequence3dStructureWidget(sequence);
 }
 
 //name: MSA
 //description: Performs multiple sequence alignment
-//tags: panel, bio
+//tags: bio, panel
+//meta.domain: bio
+//meta.role: panel
 //top-menu: Bio | Analyze | MSA...
 export function multipleSequenceAlignmentDialog() : void {
   PackageFunctions.multipleSequenceAlignmentDialog();
@@ -333,11 +360,11 @@ export function multipleSequenceAlignmentDialog() : void {
 
 //name: Multiple Sequence Alignment
 //description: Multiple sequence alignment
-//tags: bio
 //input: column sequenceCol { semType: Macromolecule }
 //input: column clustersCol 
 //input: object options { optional: true }
 //output: column result
+//meta.domain: bio
 export async function alignSequences(sequenceCol: any, clustersCol: any, options?: any) : Promise<any> {
   return await PackageFunctions.alignSequences(sequenceCol, clustersCol, options);
 }
@@ -352,18 +379,20 @@ export async function compositionAnalysis() {
 }
 
 //description: Opens FASTA file
-//tags: file-handler
+//tags: fileHandler
 //input: string fileContent 
 //output: list<dataframe> result
+//meta.role: fileHandler
 //meta.ext: fasta, fna, ffn, faa, frn, fa, fst
 export function importFasta(fileContent: string) : any {
   return PackageFunctions.importFasta(fileContent);
 }
 
 //description: Opens Bam file
-//tags: file-handler
+//tags: fileHandler
 //input: string fileContent 
 //output: list<dataframe> result
+//meta.role: fileHandler
 //meta.ext: bam, bai
 export function importBam(fileContent: string) : any {
   return PackageFunctions.importBam(fileContent);
@@ -385,6 +414,7 @@ export function convertColumnAction(col: DG.Column) : void {
 //output: grid_cell_renderer result
 //meta.cellType: Monomer
 //meta.columnTags: quality=Monomer
+//meta.role: cellRenderer
 export function monomerCellRenderer() : any {
   return PackageFunctions.monomerCellRenderer();
 }
@@ -416,6 +446,7 @@ export function getHelmMonomers(sequence: DG.Column<any>) : string[] {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/sequence-similarity-viewer.svg
+//meta.role: viewer
 export function similaritySearchViewer() : any {
   return PackageFunctions.similaritySearchViewer();
 }
@@ -432,6 +463,7 @@ export function similaritySearchTopMenu() {
 //tags: viewer
 //output: viewer result
 //meta.icon: files/icons/sequence-diversity-viewer.svg
+//meta.role: viewer
 export function diversitySearchViewer() : any {
   return PackageFunctions.diversitySearchViewer();
 }
@@ -447,6 +479,7 @@ export function diversitySearchTopMenu() {
 //name: SearchSubsequenceEditor
 //tags: editor
 //input: funccall call 
+//meta.role: editor
 export function searchSubsequenceEditor(call: DG.FuncCall) : void {
   PackageFunctions.searchSubsequenceEditor(call);
 }
@@ -502,6 +535,7 @@ export async function manageMonomersView() : Promise<void> {
 //name: Manage Monomer Libraries
 //tags: app
 //output: view result
+//meta.role: app
 //meta.browsePath: Peptides
 //meta.icon: files/icons/monomers.png
 export async function manageMonomerLibrariesView() : Promise<any> {
@@ -511,12 +545,13 @@ export async function manageMonomerLibrariesView() : Promise<any> {
 //name: Monomer Manager Tree Browser
 //input: dynamic treeNode 
 //meta.role: appTreeBrowser
+//meta.app: Manage Monomer Libraries
 export async function manageMonomerLibrariesViewTreeBrowser(treeNode: any) : Promise<void> {
   await PackageFunctions.manageMonomerLibrariesViewTreeBrowser(treeNode);
 }
 
 //description: As FASTA...
-//tags: fileExporter
+//meta.role: fileExporter
 export function saveAsFasta() : void {
   PackageFunctions.saveAsFasta();
 }
@@ -526,6 +561,7 @@ export function saveAsFasta() : void {
 //tags: filter
 //output: filter result
 //meta.semType: Macromolecule
+//meta.role: filter
 export function bioSubstructureFilter() : any {
   return PackageFunctions.bioSubstructureFilter();
 }