@datagrok/hit-triage 1.9.1 → 1.10.0

package/src/package.g.ts

@@ -20,6 +20,7 @@ export async function peptiHitAppTreeBrowser(treeNode: any) : Promise<void> {
 }
 
 //name: Hit Triage
+//tags: app
 //output: view result
 //meta.role: app
 //meta.browsePath: Chem
@@ -28,6 +29,7 @@ export async function hitTriageApp() : Promise<any> {
 }
 
 //name: Hit Design
+//tags: app
 //output: view result
 //meta.role: app
 //meta.icon: images/icons/hit-design-icon.png
@@ -37,6 +39,7 @@ export async function hitDesignApp() : Promise<any> {
 }
 
 //name: PeptiHit
+//tags: app
 //output: view result
 //meta.role: app
 //meta.icon: images/icons/pepti-hit-icon.png
@@ -45,6 +48,22 @@ export async function peptiHitApp() : Promise<any> {
   return await PackageFunctions.peptiHitApp();
 }
 
+//input: dynamic treeNode 
+//meta.app: PepTriage
+export async function pepTriageAppTreeBrowser(treeNode: any) : Promise<void> {
+  await PackageFunctions.pepTriageAppTreeBrowser(treeNode);
+}
+
+//name: PepTriage
+//tags: app
+//output: view result
+//meta.role: app
+//meta.icon: images/icons/hit-triage-icon.png
+//meta.browsePath: Peptides
+export async function pepTriageApp() : Promise<any> {
+  return await PackageFunctions.pepTriageApp();
+}
+
 //name: Demo Molecules 100
 //output: dataframe result
 //meta.role: hitTriageDataSource
@@ -67,6 +86,14 @@ export async function demoFileIngest2(numberOfMolecules: number) : Promise<any>
   return await PackageFunctions.demoFileIngest2(numberOfMolecules);
 }
 
+//name: Demo Peptide Sequences
+//input: double peptideCount 
+//output: dataframe result
+//meta.role: pepTriageDataSource
+export async function demoPeptideSequences(peptideCount: number) : Promise<any> {
+  return await PackageFunctions.demoPeptideSequences(peptideCount);
+}
+
 //name: Demo File Submit
 //input: dataframe df { description: Dataframe }
 //input: string molecules { description: Molecules column name }
@@ -98,6 +125,7 @@ export function gasteigerCellRenderer() : any {
 }
 
 //name: Hit Triage package settings editor
+//tags: packageSettingsEditor
 //input: object propList 
 //output: widget result
 //meta.role: packageSettingsEditor

package/src/package.ts

@@ -9,6 +9,7 @@ import {GasteigerPngRenderer} from './pngRenderers';
 import {loadCampaigns, timeoutOneTimeEventListener} from './app/utils';
 import {AppName, CampaignsType} from './app';
 import {PeptiHitApp} from './app/pepti-hit-app';
+import {PepTriageApp} from './app/pep-triage-app';
 import {CampaignJsonName, PeptiHitHelmColName} from './app/consts';
 import {htPackageSettingsEditorWidget} from './packageSettingsEditor';
 import {deobfuscateSmiles, registerAllCampaignMols} from './app/utils/molreg';
@@ -152,6 +153,7 @@ export class PackageFunctions {
   @grok.decorators.app({
     browsePath: 'Chem',
     name: 'Hit Triage',
+    tags: ['app'],
   })
   static async hitTriageApp(): Promise<DG.ViewBase> {
     const c = grok.functions.getCurrentCall();
@@ -163,6 +165,7 @@ export class PackageFunctions {
     icon: 'images/icons/hit-design-icon.png',
     browsePath: 'Chem',
     name: 'Hit Design',
+    tags: ['app'],
   })
   static async hitDesignApp(): Promise<DG.ViewBase> {
     const c = grok.functions.getCurrentCall();
@@ -174,6 +177,7 @@ export class PackageFunctions {
     icon: 'images/icons/pepti-hit-icon.png',
     browsePath: 'Peptides',
     name: 'PeptiHit',
+    tags: ['app'],
   })
   static async peptiHitApp(): Promise<DG.ViewBase> {
     const c = grok.functions.getCurrentCall();
@@ -182,6 +186,25 @@ export class PackageFunctions {
   }
 
 
+  @grok.decorators.treeBrowser({meta: {app: 'PepTriage'}})
+  static async pepTriageAppTreeBrowser(treeNode: DG.TreeViewGroup) {
+    await hitAppTB(treeNode, 'PepTriage');
+  }
+
+
+  @grok.decorators.app({
+    icon: 'images/icons/hit-triage-icon.png',
+    browsePath: 'Peptides',
+    name: 'PepTriage',
+    tags: ['app'],
+  })
+  static async pepTriageApp(): Promise<DG.ViewBase> {
+    const c = grok.functions.getCurrentCall();
+    await grok.functions.call('Bio:initBio', {});
+    return new PepTriageApp(c).multiView;
+  }
+
+
   @grok.decorators.func({
     name: 'Demo Molecules 100',
     meta: {role: 'hitTriageDataSource'},
@@ -217,6 +240,48 @@ export class PackageFunctions {
   }
 
 
+  @grok.decorators.func({
+    name: 'Demo Peptide Sequences',
+    meta: {role: 'pepTriageDataSource'},
+  })
+  static async demoPeptideSequences(peptideCount: number): Promise<DG.DataFrame> {
+    const sequences = [
+      'PEPTIDE1{A.G.L.V.K}$$$$V2.0',
+      'PEPTIDE1{G.A.V.L.I.P}$$$$V2.0',
+      'PEPTIDE1{F.W.Y.H.K.R}$$$$V2.0',
+      'PEPTIDE1{D.E.N.Q.S.T}$$$$V2.0',
+      'PEPTIDE1{A.R.N.D.C.E}$$$$V2.0',
+      'PEPTIDE1{G.H.I.L.K.M}$$$$V2.0',
+      'PEPTIDE1{F.P.S.T.W.Y}$$$$V2.0',
+      'PEPTIDE1{V.A.G.L.I}$$$$V2.0',
+      'PEPTIDE1{K.R.H.D.E}$$$$V2.0',
+      'PEPTIDE1{N.Q.S.T.C.M}$$$$V2.0',
+      'PEPTIDE1{A.V.L.I.P.F}$$$$V2.0',
+      'PEPTIDE1{W.Y.G.A.R}$$$$V2.0',
+      'PEPTIDE1{K.H.D.E.N.Q}$$$$V2.0',
+      'PEPTIDE1{S.T.C.M.F.W}$$$$V2.0',
+      'PEPTIDE1{Y.A.G.V.L.I}$$$$V2.0',
+      'PEPTIDE1{P.K.R.H.D}$$$$V2.0',
+      'PEPTIDE1{E.N.Q.S.T.C}$$$$V2.0',
+      'PEPTIDE1{M.F.W.Y.A.G}$$$$V2.0',
+      'PEPTIDE1{V.L.I.P.K.R}$$$$V2.0',
+      'PEPTIDE1{H.D.E.N.Q.S}$$$$V2.0',
+    ];
+    const extendedSequences = [];
+    for (let i = 0; i < peptideCount; i++)
+      extendedSequences.push(sequences[i % sequences.length]);
+
+
+    const col = DG.Column.fromStrings('Helm', extendedSequences);
+    col.semType = DG.SEMTYPE.MACROMOLECULE;
+    col.setTag('units', 'helm');
+    col.setTag('.alphabetIsMultichar', 'true');
+    const df = DG.DataFrame.fromColumns([col]);
+    df.name = 'Demo Peptide Sequences';
+    return df;
+  }
+
+
   @grok.decorators.func({
     name: 'Demo File Submit',
     meta: {role: 'hitTriageSubmitFunction'},
@@ -285,6 +350,7 @@ export class PackageFunctions {
   @grok.decorators.func({
     name: 'Hit Triage package settings editor',
     meta: {role: 'packageSettingsEditor'},
+    tags: ['packageSettingsEditor'],
   })
   static async htPackageSettingEditor(
     @grok.decorators.param({'name': 'propList', 'type': 'object'}) properties: DG.Property[]) : Promise<DG.Widget> {