From 134fd3acd4f3901a65ba4e8821e3832c9f9f60e1 Mon Sep 17 00:00:00 2001 From: tsheils Date: Fri, 12 Jan 2024 13:20:16 -0500 Subject: [PATCH 1/6] update to angular 17, prettify all files --- .gitignore | 8 + .prettierignore | 4 + apps/ramp-client/CLIENT_INSTRUCTIONS.md | 3 +- apps/ramp-client/project.json | 14 +- apps/ramp-client/server.ts | 56 +- .../ramp-client/src/app/app-routing.module.ts | 36 +- apps/ramp-client/src/app/app.component.html | 50 +- apps/ramp-client/src/app/app.component.scss | 4 +- .../ramp-client/src/app/app.component.spec.ts | 4 +- apps/ramp-client/src/app/app.component.ts | 21 +- apps/ramp-client/src/app/app.module.ts | 13 +- apps/ramp-client/src/app/app.server.module.ts | 8 +- .../src/assets/data/rFunctions.json | 16 +- apps/ramp-client/src/index.html | 82 +- apps/ramp-client/src/main.ts | 8 +- apps/ramp-client/src/styles.scss | 10 +- apps/ramp-server/.travis.yml | 5 +- apps/ramp-server/SERVER_INSTRUCTIONS.MD | 6 +- .../ramp_openapi_with_extensions.yml | 1725 ++- decorate-angular-cli.js | 2 +- .../analytes-from-pathways.component.html | 10 +- .../analytes-from-pathways.component.spec.ts | 2 +- .../analytes-from-pathways.component.ts | 58 +- ...ures-ramp-analytes-from-pathways.module.ts | 4 +- .../chemical-enrichment.component.html | 99 +- .../chemical-enrichment.component.spec.ts | 18 +- .../chemical-enrichment.component.ts | 211 +- ...eatures-ramp-chemical-enrichment.module.ts | 24 +- .../classes-from-metabolites.component.html | 8 +- ...classes-from-metabolites.component.spec.ts | 4 +- .../classes-from-metabolites.component.ts | 101 +- ...es-ramp-classes-from-metabolites.module.ts | 16 +- .../common-reaction-analytes.component.html | 5 +- ...common-reaction-analytes.component.spec.ts | 2 +- .../common-reaction-analytes.component.ts | 68 +- ...es-ramp-common-reaction-analytes.module.ts | 4 +- ...ramp-metabolites-from-ontologies.module.ts | 4 +- ...metabolites-from-ontologies.component.html | 12 +- ...abolites-from-ontologies.component.spec.ts | 2 +- .../metabolites-from-ontologies.component.ts | 103 +- .../lib/features-ramp-ontologies.module.ts | 4 +- ...ontologies-from-metabolites.component.html | 5 +- ...ologies-from-metabolites.component.spec.ts | 2 +- .../ontologies-from-metabolites.component.ts | 71 +- ...features-ramp-pathway-enrichment.module.ts | 6 +- .../pathway-enrichment.component.html | 209 +- .../pathway-enrichment.component.spec.ts | 8 +- .../pathway-enrichment.component.ts | 449 +- ...ures-ramp-pathways-from-analytes.module.ts | 6 +- .../pathways-from-analytes.component.html | 18 +- .../pathways-from-analytes.component.spec.ts | 2 +- .../pathways-from-analytes.component.ts | 75 +- ...ramp-properties-from-metabolites.module.ts | 6 +- ...properties-from-metabolites.component.html | 5 +- ...perties-from-metabolites.component.spec.ts | 2 +- .../properties-from-metabolites.component.ts | 68 +- .../src/lib/about/about.component.html | 296 +- .../src/lib/about/about.component.scss | 22 +- .../src/lib/about/about.component.spec.ts | 2 +- .../src/lib/about/about.component.ts | 68 +- .../data/ramp_openapi_with_extensions.yml | 1725 ++- .../src/lib/features-ramp-ramp-api.module.ts | 10 +- .../lib/ramp-api/ramp-api.component.spec.ts | 18 +- .../src/lib/ramp-api/ramp-api.component.ts | 26 +- .../src/lib/features-ramp-ramp-home.module.ts | 4 +- .../src/lib/home/home.component.html | 200 +- .../src/lib/home/home.component.scss | 5 +- .../src/lib/home/home.component.spec.ts | 16 +- .../ramp-home/src/lib/home/home.component.ts | 36 +- .../ramp-models/src/lib/analyte.spec.ts | 2 +- libs/models/ramp-models/src/lib/analyte.ts | 2 +- .../src/lib/chemical-enrichment.spec.ts | 22 +- .../src/lib/chemical-enrichment.ts | 16 +- libs/models/ramp-models/src/lib/classes.ts | 16 +- .../ramp-models/src/lib/entity-count.spec.ts | 2 +- .../ramp-models/src/lib/fisher-result.spec.ts | 2 +- .../ramp-models/src/lib/fisher-result.ts | 20 +- .../ramp-models/src/lib/metabolite.spec.ts | 2 +- .../ramp-models/src/lib/ontology.spec.ts | 2 +- .../ramp-models/src/lib/pathway.spec.ts | 2 +- .../ramp-models/src/lib/properties.spec.ts | 2 +- .../ramp-models/src/lib/reaction.spec.ts | 2 +- libs/models/ramp-models/src/lib/reaction.ts | 3 +- .../data-download-button.component.ts | 2 +- .../ncats-footer/ncats-footer.component.html | 73 +- .../ncats-footer/ncats-footer.component.scss | 14 +- .../ncats-footer.component.spec.ts | 17 +- .../ncats-footer/ncats-footer.component.ts | 8 +- .../lib/shared-ncats-ncats-footer.module.ts | 10 +- .../ncats-header/ncats-header.component.ts | 7 +- .../lib/input-row/input-row.component.html | 6 +- .../src/lib/input-row/input-row.component.ts | 2 +- .../src/lib/page-core/page-core.component.ts | 87 +- .../lib/query-page/query-page.component.html | 61 +- .../lib/query-page/query-page.component.ts | 9 +- libs/shared/ui/complete-dialog/project.json | 1 + .../complete-dialog.component.html | 32 +- .../complete-dialog.component.scss | 1 - .../complete-dialog.component.spec.ts | 22 +- .../complete-dialog.component.ts | 8 +- .../lib/shared-ui-complete-dialog.module.ts | 19 +- .../description/description.component.html | 10 +- .../lib/description/description.component.ts | 2 +- .../error-dialog.component.spec.ts | 10 +- .../error-dialog/error-dialog.component.ts | 1 - .../feedback-panel.component.html | 28 +- .../feedback-panel.component.spec.ts | 5 +- .../feedback-panel.component.ts | 18 +- .../lib/shared-ui-feedback-panel.module.ts | 12 +- .../filter-panel.component.spec.ts | 10 +- .../filter-panel/filter-panel.component.ts | 12 +- libs/shared/ui/header-template/project.json | 2 +- .../lib/header-template/header-animations.ts | 4 +- .../header-template.component.html | 44 +- .../header-template.component.ts | 5 +- .../header-template.theme.scss | 2 + .../highlight/src/lib/highlight.pipe.spec.ts | 2 +- .../ui/highlight/src/lib/highlight.pipe.ts | 6 +- .../src/lib/loading/loading.component.ts | 2 +- .../property-display.component.ts | 14 +- .../ncats-datatable/models/data-property.ts | 2 +- .../ncats-datatable.component.html | 7 +- .../ncats-datatable.component.ts | 26 +- .../src/lib/upset/upset.component.ts | 24 +- .../src/lib/+state/ramp-store/ramp.actions.ts | 129 +- .../src/lib/+state/ramp-store/ramp.effects.ts | 405 +- .../lib/+state/ramp-store/ramp.facade.spec.ts | 8 +- .../src/lib/+state/ramp-store/ramp.facade.ts | 4 +- .../src/lib/+state/ramp-store/ramp.models.ts | 7 +- .../src/lib/+state/ramp-store/ramp.reducer.ts | 109 +- .../+state/ramp-store/ramp.selectors.spec.ts | 4 +- .../lib/+state/ramp-store/ramp.selectors.ts | 47 +- .../ramp-store/src/lib/+state/ramp.service.ts | 312 +- libs/styles/src/styles/_utils.scss | 48 + libs/styles/src/styles/ncats-theme.scss | 25 +- nx.json | 21 +- package-lock.json | 12757 ++++++++-------- package.json | 112 +- 138 files changed, 11119 insertions(+), 9785 deletions(-) create mode 100644 libs/styles/src/styles/_utils.scss diff --git a/.gitignore b/.gitignore index ddac9acc..f099eabe 100644 --- a/.gitignore +++ b/.gitignore @@ -34,6 +34,12 @@ yarn-error.log testem.log /typings +apps/ramp-client/src/environments/environment* +apps/ramp-client/src/environments/environment.ts +apps/ramp-client/src/environments/environment-prod.ts +apps/ramp-client/src/environments/environment-prod.ts + + # System Files .DS_Store Thumbs.db @@ -42,3 +48,5 @@ Thumbs.db .Rproj.user RaMP-Client.iml + +.nx/cache diff --git a/.prettierignore b/.prettierignore index d0b804da..928ecc22 100644 --- a/.prettierignore +++ b/.prettierignore @@ -2,3 +2,7 @@ /dist /coverage +/.angular +/.idea +/node_modules +/.nx/cache diff --git a/apps/ramp-client/CLIENT_INSTRUCTIONS.md b/apps/ramp-client/CLIENT_INSTRUCTIONS.md index b29ba662..860d69f7 100644 --- a/apps/ramp-client/CLIENT_INSTRUCTIONS.md +++ b/apps/ramp-client/CLIENT_INSTRUCTIONS.md @@ -8,5 +8,4 @@ To run the client application locally, please follow these steps: 4. Change directory (`cd`) to the `apps/ramp-client` directory of this repository 5. Type `ng s` or `nx run ramp-client:serve:development` and hit Enter -To build the application and run it in a container, just build and run the dockerfile in the client directory. - +To build the application and run it in a container, just build and run the dockerfile in the client directory. diff --git a/apps/ramp-client/project.json b/apps/ramp-client/project.json index 4c81dfe8..53cdca24 100644 --- a/apps/ramp-client/project.json +++ b/apps/ramp-client/project.json @@ -75,10 +75,10 @@ "executor": "@angular-devkit/build-angular:dev-server", "configurations": { "production": { - "browserTarget": "ramp-client:build:production" + "buildTarget": "ramp-client:build:production" }, "development": { - "browserTarget": "ramp-client:build:development" + "buildTarget": "ramp-client:build:development" } }, "defaultConfiguration": "development" @@ -86,7 +86,7 @@ "extract-i18n": { "executor": "@angular-devkit/build-angular:extract-i18n", "options": { - "browserTarget": "ramp-client:build" + "buildTarget": "ramp-client:build" } }, "lint": { @@ -150,7 +150,7 @@ } }, "serve-ssr": { - "executor": "@nguniversal/builders:ssr-dev-server", + "executor": "@angular-devkit/build-angular:ssr-dev-server", "configurations": { "development": { "browserTarget": "ramp-client:build:development", @@ -164,10 +164,10 @@ "defaultConfiguration": "development" }, "prerender": { - "executor": "@nguniversal/builders:prerender", + "executor": "@angular-devkit/build-angular:prerender", "options": { - "guessRoutes": false, - "routesFile": "./apps/ramp-client/routes.txt" + "routesFile": "./apps/ramp-client/routes.txt", + "discoverRoutes": false }, "configurations": { "production": { diff --git a/apps/ramp-client/server.ts b/apps/ramp-client/server.ts index 8ede7113..5d8928fd 100644 --- a/apps/ramp-client/server.ts +++ b/apps/ramp-client/server.ts @@ -1,7 +1,7 @@ import 'zone.js/dist/zone-node'; import { ngExpressEngine } from '@nguniversal/express-engine'; -import express from "express"; +import express from 'express'; import { join } from 'path'; import { AppServerModule } from './src/main.server'; @@ -12,29 +12,53 @@ import { InjectionToken } from '@angular/core'; // The Express app is exported so that it can be used by serverless Functions. export function app(): express.Express { const server = express(); - const distFolder = join(process.cwd(), "dist/ramp-client/browser"); - const indexHtml = existsSync(join(distFolder, "index.original.html")) ? "index.original.html" : "index"; + const distFolder = join(process.cwd(), 'dist/ramp-client/browser'); + const indexHtml = existsSync(join(distFolder, 'index.original.html')) + ? 'index.original.html' + : 'index'; // Our Universal express-engine (found @ https://github.com/angular/universal/tree/master/modules/express-engine) - server.engine("html", ngExpressEngine({ - bootstrap: AppServerModule - })); + server.engine( + 'html', + ngExpressEngine({ + bootstrap: AppServerModule, + }), + ); - server.set("view engine", "html"); - server.set("views", distFolder); + server.set('view engine', 'html'); + server.set('views', distFolder); // Example Express Rest API endpoints // server.get('/api/**', (req, res) => { }); // Serve static files from /browser - server.get("*.*", express.static(distFolder, { - maxAge: "1y" - })); + server.get( + '*.*', + express.static(distFolder, { + maxAge: '1y', + }), + ); // All regular routes use the Universal engine - server.get("*", ( - req: { baseUrl: any; }, res: { render: (arg0: string, arg1: { req: any; providers: { provide: InjectionToken; useValue: any; }[]; }) => void; }) => { - res.render(indexHtml, { req, providers: [{ provide: APP_BASE_HREF, useValue: req.baseUrl }] }); - }); + server.get( + '*', + ( + req: { baseUrl: any }, + res: { + render: ( + arg0: string, + arg1: { + req: any; + providers: { provide: InjectionToken; useValue: any }[]; + }, + ) => void; + }, + ) => { + res.render(indexHtml, { + req, + providers: [{ provide: APP_BASE_HREF, useValue: req.baseUrl }], + }); + }, + ); return server; } @@ -54,7 +78,7 @@ function run(): void { // The below code is to ensure that the server is run only when not requiring the bundle. declare const __non_webpack_require__: NodeRequire; const mainModule = __non_webpack_require__.main; -const moduleFilename = mainModule && mainModule.filename || ''; +const moduleFilename = (mainModule && mainModule.filename) || ''; if (moduleFilename === __filename || moduleFilename.includes('iisnode')) { run(); } diff --git a/apps/ramp-client/src/app/app-routing.module.ts b/apps/ramp-client/src/app/app-routing.module.ts index d815abfa..c163e972 100644 --- a/apps/ramp-client/src/app/app-routing.module.ts +++ b/apps/ramp-client/src/app/app-routing.module.ts @@ -10,7 +10,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/ramp-home').then( - (m) => m.FeaturesRampRampHomeModule + (m) => m.FeaturesRampRampHomeModule, ), }, { @@ -19,7 +19,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/ramp-home').then( - (m) => m.FeaturesRampRampHomeModule + (m) => m.FeaturesRampRampHomeModule, ), }, { @@ -28,7 +28,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/ramp-about').then( - (m) => m.FeaturesRampRampAboutModule + (m) => m.FeaturesRampRampAboutModule, ), }, { @@ -37,7 +37,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/ramp-api').then( - (m) => m.FeaturesRampRampApiModule + (m) => m.FeaturesRampRampApiModule, ), }, { @@ -46,7 +46,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/ontologies-from-metabolites').then( - (m) => m.FeaturesRampOntologiesModule + (m) => m.FeaturesRampOntologiesModule, ), data: { ...rFunctions['ontologies-from-analytes'], @@ -58,7 +58,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/metabolites-from-ontologies').then( - (m) => m.FeaturesRampMetabolitesFromOntologiesModule + (m) => m.FeaturesRampMetabolitesFromOntologiesModule, ), data: { ...rFunctions['metabolites-from-ontologies'], @@ -70,7 +70,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/analytes-from-pathways').then( - (m) => m.FeaturesRampAnalytesFromPathwaysModule + (m) => m.FeaturesRampAnalytesFromPathwaysModule, ), data: { ...rFunctions['analytes-from-pathways'], @@ -82,7 +82,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/pathways-from-analytes').then( - (m) => m.FeaturesRampPathwaysFromAnalytesModule + (m) => m.FeaturesRampPathwaysFromAnalytesModule, ), data: { ...rFunctions['pathways-from-analytes'], @@ -94,7 +94,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/common-reaction-analytes').then( - (m) => m.FeaturesRampCommonReactionAnalytesModule + (m) => m.FeaturesRampCommonReactionAnalytesModule, ), data: { ...rFunctions['common-reaction-analytes'], @@ -106,7 +106,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/classes-from-metabolites').then( - (m) => m.FeaturesRampClassesFromMetabolitesModule + (m) => m.FeaturesRampClassesFromMetabolitesModule, ), data: { ...rFunctions['classes-from-metabolites'], @@ -118,7 +118,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/properties-from-metabolites').then( - (m) => m.FeaturesRampPropertiesFromMetabolitesModule + (m) => m.FeaturesRampPropertiesFromMetabolitesModule, ), data: { ...rFunctions['properties-from-metabolites'], @@ -131,7 +131,7 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/chemical-enrichment').then( - (m) => m.FeaturesRampChemicalEnrichmentModule + (m) => m.FeaturesRampChemicalEnrichmentModule, ), data: { ...rFunctions['chemical-enrichment'], @@ -143,18 +143,20 @@ const routes: Routes = [ runGuardsAndResolvers: 'paramsOrQueryParamsChange', loadChildren: () => import('@ramp/features/ramp/pathway-enrichment').then( - (m) => m.FeaturesRampPathwayEnrichmentModule + (m) => m.FeaturesRampPathwayEnrichmentModule, ), data: { ...rFunctions['pathway-enrichment'], }, - } + }, ]; @NgModule({ - imports: [RouterModule.forRoot(routes, { - initialNavigation: 'enabledBlocking' -})], + imports: [ + RouterModule.forRoot(routes, { + initialNavigation: 'enabledBlocking', + }), + ], exports: [RouterModule], }) export class AppRoutingModule {} diff --git a/apps/ramp-client/src/app/app.component.html b/apps/ramp-client/src/app/app.component.html index a191a2ca..e6ed7067 100644 --- a/apps/ramp-client/src/app/app.component.html +++ b/apps/ramp-client/src/app/app.component.html @@ -1,26 +1,26 @@ -
-
- -
-
-
- - -
-
- +
+
+ +
+
+
+

This is a test

+ + +
+
+
diff --git a/apps/ramp-client/src/app/app.component.scss b/apps/ramp-client/src/app/app.component.scss index 119cafd4..ba086041 100644 --- a/apps/ramp-client/src/app/app.component.scss +++ b/apps/ramp-client/src/app/app.component.scss @@ -1,7 +1,5 @@ @use '@angular/material' as mat; -@import 'libs/styles/src/styles/ncats-theme'; - - +@import 'ncats-theme'; .toolbar-template { background-color: mat.get-color-from-palette($app-accent); diff --git a/apps/ramp-client/src/app/app.component.spec.ts b/apps/ramp-client/src/app/app.component.spec.ts index 2b74248d..595b4739 100644 --- a/apps/ramp-client/src/app/app.component.spec.ts +++ b/apps/ramp-client/src/app/app.component.spec.ts @@ -5,7 +5,7 @@ import { RouterTestingModule } from '@angular/router/testing'; import { EffectsModule } from '@ngrx/effects'; import { StoreModule } from '@ngrx/store'; import { FeaturesRampRampHeaderModule } from '@ramp/features/ramp/ramp-header'; -import { SharedNcatsNcatsFooterModule } from "@ramp/shared/ncats/ncats-footer"; +import { SharedNcatsNcatsFooterModule } from '@ramp/shared/ncats/ncats-footer'; import { SharedUiLoadingSpinnerModule } from '@ramp/shared/ui/loading-spinner'; import { RampFacade, StoresRampStoreModule } from '@ramp/stores/ramp-store'; import { environment } from '../environments/environment'; @@ -31,7 +31,7 @@ describe('AppComponent', () => { strictActionImmutability: true, strictStateImmutability: true, }, - } + }, ), EffectsModule.forRoot([]), ], diff --git a/apps/ramp-client/src/app/app.component.ts b/apps/ramp-client/src/app/app.component.ts index 700b1215..f779449a 100644 --- a/apps/ramp-client/src/app/app.component.ts +++ b/apps/ramp-client/src/app/app.component.ts @@ -3,12 +3,12 @@ import { ChangeDetectorRef, Component, OnInit, - ViewEncapsulation -} from "@angular/core"; + ViewEncapsulation, +} from '@angular/core'; import { MatDialog } from '@angular/material/dialog'; import { LinkTemplateProperty } from '@ramp/shared/ui/header-template'; import { RampFacade } from '@ramp/stores/ramp-store'; - +import { environment } from '../environments/environment'; @Component({ selector: 'ramp-root', @@ -20,6 +20,7 @@ import { RampFacade } from '@ramp/stores/ramp-store'; export class AppComponent implements OnInit { title = 'ramp-client'; loading = true; + showBanner = false; links: LinkTemplateProperty[] = [ { link: 'Biological Pathways', @@ -31,7 +32,7 @@ export class AppComponent implements OnInit { { link: 'analytes-from-pathways', label: 'Analytes from Input Pathways', - } + }, ], }, { @@ -65,9 +66,10 @@ export class AppComponent implements OnInit { children: [ { link: 'common-reaction-analytes', - label: 'Retrieve Analytes involved in Same Reactions as input Analytes\n', - } - ] + label: + 'Retrieve Analytes involved in Same Reactions as input Analytes\n', + }, + ], }, { link: 'Enrichment Analyses', @@ -96,13 +98,14 @@ export class AppComponent implements OnInit { constructor( public dialog: MatDialog, private changeRef: ChangeDetectorRef, - protected rampFacade: RampFacade + protected rampFacade: RampFacade, ) {} ngOnInit() { + this.showBanner = !environment.production; this.rampFacade.error$.subscribe((error) => { if (error) { - // console.log(error); + // console.log(error); /* this.dialog.open(ErrorDialogComponent, { data: { error: error, diff --git a/apps/ramp-client/src/app/app.module.ts b/apps/ramp-client/src/app/app.module.ts index 29ca6d83..872b055f 100644 --- a/apps/ramp-client/src/app/app.module.ts +++ b/apps/ramp-client/src/app/app.module.ts @@ -4,7 +4,7 @@ import { APP_INITIALIZER, NgModule } from '@angular/core'; import { EffectsModule } from '@ngrx/effects'; import { StoreModule } from '@ngrx/store'; import { StoreDevtoolsModule } from '@ngrx/store-devtools'; -import { SharedNcatsNcatsFooterModule } from "@ramp/shared/ncats/ncats-footer"; +import { SharedNcatsNcatsFooterModule } from '@ramp/shared/ncats/ncats-footer'; import { SharedUiLoadingSpinnerModule } from '@ramp/shared/ui/loading-spinner'; import { AppRoutingModule } from './app-routing.module'; import { AppComponent } from './app.component'; @@ -50,16 +50,17 @@ export function rampInit(rampFacade: RampFacade) { metaReducers: !environment.production ? [] : [], runtimeChecks: { strictActionImmutability: true, - strictStateImmutability: true - } - } + strictStateImmutability: true, + }, + }, ), EffectsModule.forRoot([]), StoreDevtoolsModule.instrument({ maxAge: 25, - logOnly: !environment.production + logOnly: !environment.production, + connectInZone: true, }), - SharedNcatsNcatsFooterModule + SharedNcatsNcatsFooterModule, ], providers: [ RampFacade, diff --git a/apps/ramp-client/src/app/app.server.module.ts b/apps/ramp-client/src/app/app.server.module.ts index ab0a4d73..97e7c28f 100644 --- a/apps/ramp-client/src/app/app.server.module.ts +++ b/apps/ramp-client/src/app/app.server.module.ts @@ -1,16 +1,12 @@ import { NgModule } from '@angular/core'; -import { FlexLayoutServerModule } from "@angular/flex-layout/server"; +import { FlexLayoutServerModule } from '@angular/flex-layout/server'; import { ServerModule } from '@angular/platform-server'; import { AppModule } from './app.module'; import { AppComponent } from './app.component'; @NgModule({ - imports: [ - AppModule, - ServerModule, - FlexLayoutServerModule - ], + imports: [AppModule, ServerModule, FlexLayoutServerModule], bootstrap: [AppComponent], }) export class AppServerModule {} diff --git a/apps/ramp-client/src/assets/data/rFunctions.json b/apps/ramp-client/src/assets/data/rFunctions.json index 45ea63ff..5d39066e 100644 --- a/apps/ramp-client/src/assets/data/rFunctions.json +++ b/apps/ramp-client/src/assets/data/rFunctions.json @@ -6,7 +6,7 @@ "examples": "ensembl:ENSG00000135679, hmdb:HMDB0000064, hmdb:HMDB0000148, ensembl:ENSG00000141510", "description": "Enter a list of metabolites. IDs should be prepended by ID source (e.g. kegg:C00412). See below for supported sources." }, - "metabolites-from-ontologies" : { + "metabolites-from-ontologies": { "title": "Retrieve Analytes (Metabolites) from Ontologies", "input": "ontology", "supportedIdTypes": [], @@ -27,9 +27,9 @@ "examples": "ensembl:ENSG00000135679, hmdb:HMDB0000064, hmdb:HMDB0000148, ensembl:ENSG00000141510", "description": "Retrieve pathway(s) for a given analyte(s). IDs should be prepended by ID source (e.g. hmdb:HMDB0000122). See below for supported sources." }, - "analyteid-types" : { + "analyteid-types": { "title": "Retrieve Analyte ID types", - "function": "idtypes <- RaMP::getPrefixesFromAnalytes(\"metabolite\"); RaMP::getPrefixesFromAnalytes(\"gene\"))", + "function": "idtypes <- RaMP::getPrefixesFromAnalytes(\"metabolite\"); RaMP::getPrefixesFromAnalytes(\"gene\"))", "description": "Retrieve analyte ID types to be used as prefixes for other RaMP function calls." }, "common-reaction-analytes": { @@ -48,8 +48,8 @@ }, "properties-from-metabolites": { "title": "Retrieve Chemical Properties from Input Metabolites", - "input": "metabolites", - "function": "analytes <- RaMP::getChemicalProperties(mets=\"###REPLACE###\")", + "input": "metabolites", + "function": "analytes <- RaMP::getChemicalProperties(mets=\"###REPLACE###\")", "supportedIdTypes": ["Metabolites"], "examples": "hmdb:HMDB0000056, hmdb:HMDB0000439, hmdb:HMDB0000479, hmdb:HMDB0000532, hmdb:HMDB0001015, hmdb:HMDB0001138, hmdb:HMDB0029159, hmdb:HMDB0029412, hmdb:HMDB0034365, hmdb:HMDB0035227, hmdb:HMDB0007973, hmdb:HMDB0008057, hmdb:HMDB0011211", "description": "Retrieve chemical properties (smiles, inchi_key, inchi_key_prefix, inchi, mw, monoisotop_mass, formula, common_name) from input metabolites. IDs should be prepended by ID source (e.g. hmdb:HMDB0000122). See below for supported sources." @@ -58,14 +58,14 @@ "title": "Perform Chemical Class Enrichment", "input": "metabolites", "supportedIdTypes": ["Metabolites"], - "function": "analytes <- RaMP::chemicalClassEnrichment(mets=\"###REPLACE###\")", + "function": "analytes <- RaMP::chemicalClassEnrichment(mets=\"###REPLACE###\")", "examples": "hmdb:HMDB0000056, hmdb:HMDB0000439, hmdb:HMDB0000479, hmdb:HMDB0000532, hmdb:HMDB0001015, hmdb:HMDB0001138, hmdb:HMDB0029159, hmdb:HMDB0029412, hmdb:HMDB0034365, hmdb:HMDB0035227, hmdb:HMDB0007973, hmdb:HMDB0008057, hmdb:HMDB0011211, hmdb:HMDB0001085, hmdb:HMDB0002122, hmdb:HMDB0002685, hmdb:HMDB0004241, hmdb:HMDB0005079, hmdb:HMDB0006245", "description": "Perform chemical class enrichment on ClassyFire and LIPIDMAPS classes. IDs should be prepended by ID source (e.g. hmdb:HMDB0000122). See below for supported sources." }, "pathway-enrichment": { "title": "Perform Pathway Enrichment", - "input": "analytes", - "function": "analytes <- RaMP::runCombinedFisherTest(analytes=\"###REPLACE###\")", + "input": "analytes", + "function": "analytes <- RaMP::runCombinedFisherTest(analytes=\"###REPLACE###\")", "supportedIdTypes": ["Metabolites", "Genes/Proteins"], "examples": "hmdb:HMDB0000033, hmdb:HMDB0000052, hmdb:HMDB0000094, hmdb:HMDB0000161, hmdb:HMDB0000168, hmdb:HMDB0000191, hmdb:HMDB0000201, chemspider:10026, hmdb:HMDB0006059, Chemspider:6405,CAS:5657-19-2,hmdb:HMDB0002511, chemspider:20171375, CAS:133-32-4, CAS:5746-90-7, CAS:477251-67-5, hmdb:HMDB0000695, chebi:15934, CAS:838-07-3, hmdb:HMDBP00789, hmdb:HMDBP00283, hmdb:HMDBP00284,hmdb:HMDBP00850", "description": "Perform Pathway Enrichment. IDs should be prepended by ID source (e.g. hmdb:HMDB0000122). Input analyte IDs can be a mix of genes/proteins or metabolites. See below for supported sources." diff --git a/apps/ramp-client/src/index.html b/apps/ramp-client/src/index.html index 0215810e..f84887d8 100644 --- a/apps/ramp-client/src/index.html +++ b/apps/ramp-client/src/index.html @@ -1,4 +1,4 @@ - + @@ -7,10 +7,15 @@ - +