From 0341455117d1bbb2f7205d7572cac1055536f67d Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Tue, 28 May 2024 12:34:56 +0200 Subject: [PATCH 01/18] :bookmark: preminor release --- package-lock.json | 4 ++-- package.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1fb5aee..d236a7c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "smarter-frontend", - "version": "0.2.2", + "version": "0.3.0-0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "smarter-frontend", - "version": "0.2.2", + "version": "0.3.0-0", "dependencies": { "@angular/animations": "^14.2.0", "@angular/cdk": "^14.2.3", diff --git a/package.json b/package.json index 3b3cae8..640cf26 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "smarter-frontend", - "version": "0.2.2", + "version": "0.3.0-0", "scripts": { "ng": "ng", "start": "ng serve", From 9e3574a0ff70847c32ffd9d5d4c8dc06ae9693dc Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Tue, 28 May 2024 12:35:47 +0200 Subject: [PATCH 02/18] :card_file_box: rename manifacturer into manufacturer --- src/app/variants/variants.model.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/app/variants/variants.model.ts b/src/app/variants/variants.model.ts index daf87c2..7a1fa9f 100644 --- a/src/app/variants/variants.model.ts +++ b/src/app/variants/variants.model.ts @@ -56,7 +56,7 @@ export interface VariantsSearch { export interface SupportedChip { _id: ObjectID; - manifacturer?: string; + manufacturer?: string; n_of_snps?: number; name: string; species: string; From e0ff9ac5031c2856d49bbabc6ba85beb601c0b18 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 7 Oct 2023 05:42:59 +0000 Subject: [PATCH 03/18] :arrow_up: Bump postcss and @angular-devkit/build-angular Bumps [postcss](https://github.com/postcss/postcss) to 8.4.31 and updates ancestor dependency [@angular-devkit/build-angular](https://github.com/angular/angular-cli). These dependencies need to be updated together. Updates `postcss` from 8.4.16 to 8.4.31 - [Release notes](https://github.com/postcss/postcss/releases) - [Changelog](https://github.com/postcss/postcss/blob/main/CHANGELOG.md) - [Commits](https://github.com/postcss/postcss/compare/8.4.16...8.4.31) Updates `@angular-devkit/build-angular` from 14.2.12 to 14.2.13 - [Release notes](https://github.com/angular/angular-cli/releases) - [Changelog](https://github.com/angular/angular-cli/blob/main/CHANGELOG.md) - [Commits](https://github.com/angular/angular-cli/compare/14.2.12...14.2.13) --- updated-dependencies: - dependency-name: postcss dependency-type: indirect - dependency-name: "@angular-devkit/build-angular" dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- package-lock.json | 306 +++++++++++++++++++++++----------------------- package.json | 2 +- 2 files changed, 156 insertions(+), 152 deletions(-) diff --git a/package-lock.json b/package-lock.json index d236a7c..b9250d1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -26,7 +26,7 @@ "zone.js": "^0.11.8" }, "devDependencies": { - "@angular-devkit/build-angular": "^14.2.10", + "@angular-devkit/build-angular": "^14.2.13", "@angular/cli": "~14.2.4", "@angular/compiler-cli": "^14.2.12", "@types/jasmine": "~4.0.0", @@ -124,15 +124,15 @@ "peer": true }, "node_modules/@angular-devkit/build-angular": { - "version": "14.2.12", - "resolved": "https://registry.npmjs.org/@angular-devkit/build-angular/-/build-angular-14.2.12.tgz", - "integrity": "sha512-ei8/FaL80Q6si/aF6FLZgtT4Kr2rudlyGMqQM4Rd2Zvt8mCh3TgM7QdLhoI11t9A0LWz6RIdROlDimMyyOEF6Q==", + "version": "14.2.13", + "resolved": "https://registry.npmjs.org/@angular-devkit/build-angular/-/build-angular-14.2.13.tgz", + "integrity": "sha512-FJZKQ3xYFvEJ807sxVy4bCVyGU2NMl3UUPNfLIdIdzwwDEP9tx/cc+c4VtVPEZZfU8jVenu8XOvL6L0vpjt3yg==", "dev": true, "dependencies": { "@ampproject/remapping": "2.2.0", - 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[Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 250 +++++++++++++++++++++++----------------------- 1 file changed, 126 insertions(+), 124 deletions(-) diff --git a/package-lock.json b/package-lock.json index b9250d1..fb28d63 100644 --- a/package-lock.json +++ b/package-lock.json @@ -854,12 +854,13 @@ "dev": true }, "node_modules/@babel/code-frame": { - "version": "7.21.4", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.21.4.tgz", - "integrity": "sha512-LYvhNKfwWSPpocw8GI7gpK2nq3HSDuEPC/uSYaALSJu9xjsalaaYFOq0Pwt5KmVqwEbZlDu81aLXwBOmD/Fv9g==", + "version": "7.22.13", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.13.tgz", + "integrity": "sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w==", "dev": true, "dependencies": { - "@babel/highlight": "^7.18.6" + "@babel/highlight": "^7.22.13", + "chalk": "^2.4.2" }, "engines": { "node": ">=6.9.0" @@ -1078,48 +1079,48 @@ } }, "node_modules/@babel/helper-environment-visitor": { - 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"@babel/helper-string-parser": "^7.21.5", - "@babel/helper-validator-identifier": "^7.19.1", + "@babel/helper-string-parser": "^7.22.5", + "@babel/helper-validator-identifier": "^7.22.20", "to-fast-properties": "^2.0.0" } }, From f1188b6b25d20a90f2569225a3be9fc296f5eb8a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 1 Dec 2023 05:30:58 +0000 Subject: [PATCH 05/18] :arrow_up: Bump @adobe/css-tools from 4.3.1 to 4.3.2 Bumps [@adobe/css-tools](https://github.com/adobe/css-tools) from 4.3.1 to 4.3.2. - [Changelog](https://github.com/adobe/css-tools/blob/main/History.md) - [Commits](https://github.com/adobe/css-tools/commits) --- updated-dependencies: - dependency-name: "@adobe/css-tools" dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index fb28d63..f8ac093 100644 --- a/package-lock.json +++ b/package-lock.json @@ -40,9 +40,9 @@ } }, "node_modules/@adobe/css-tools": { - "version": "4.3.1", - "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.3.1.tgz", - "integrity": "sha512-/62yikz7NLScCGAAST5SHdnjaDJQBDq0M2muyRTpf2VQhw6StBg2ALiu73zSJQ4fMVLA+0uBhBHAle7Wg+2kSg==", + "version": "4.3.2", + "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.3.2.tgz", + "integrity": "sha512-DA5a1C0gD/pLOvhv33YMrbf2FK3oUzwNl9oOJqE4XVjuEtt6XIakRcsd7eLiOSPkp1kTRQGICTA8cKra/vFbjw==", "dev": true }, "node_modules/@ampproject/remapping": { @@ -12681,9 +12681,9 @@ }, "dependencies": { "@adobe/css-tools": { - "version": "4.3.1", - "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.3.1.tgz", - "integrity": "sha512-/62yikz7NLScCGAAST5SHdnjaDJQBDq0M2muyRTpf2VQhw6StBg2ALiu73zSJQ4fMVLA+0uBhBHAle7Wg+2kSg==", + "version": "4.3.2", + "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.3.2.tgz", + "integrity": "sha512-DA5a1C0gD/pLOvhv33YMrbf2FK3oUzwNl9oOJqE4XVjuEtt6XIakRcsd7eLiOSPkp1kTRQGICTA8cKra/vFbjw==", "dev": true }, "@ampproject/remapping": { From 94215f57649b02a3cade81a860b4bd8684ea9dea Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 20 Jun 2024 15:26:57 +0200 Subject: [PATCH 06/18] :passport_control: remove auth guard --- src/app/app-routing.module.ts | 16 +-- src/app/app.component.ts | 12 +- src/app/app.module.ts | 10 +- src/app/auth/auth-data.model.ts | 5 - src/app/auth/auth-interceptor.service.spec.ts | 28 ---- src/app/auth/auth-interceptor.service.ts | 39 ------ src/app/auth/auth.guard.ts | 45 ------ src/app/auth/auth.service.spec.ts | 74 ---------- src/app/auth/auth.service.ts | 130 ------------------ src/app/auth/login/login.component.html | 32 ----- src/app/auth/login/login.component.scss | 5 - src/app/auth/login/login.component.spec.ts | 37 ----- src/app/auth/login/login.component.ts | 61 -------- src/app/auth/user.model.ts | 46 ------- .../navigation/header/header.component.html | 6 - src/app/navigation/header/header.component.ts | 26 +--- .../sidenav-list/sidenav-list.component.html | 10 -- .../sidenav-list/sidenav-list.component.ts | 22 +-- 18 files changed, 11 insertions(+), 593 deletions(-) delete mode 100644 src/app/auth/auth-data.model.ts delete mode 100644 src/app/auth/auth-interceptor.service.spec.ts delete mode 100644 src/app/auth/auth-interceptor.service.ts delete mode 100644 src/app/auth/auth.guard.ts delete mode 100644 src/app/auth/auth.service.spec.ts delete mode 100644 src/app/auth/auth.service.ts delete mode 100644 src/app/auth/login/login.component.html delete mode 100644 src/app/auth/login/login.component.scss delete mode 100644 src/app/auth/login/login.component.spec.ts delete mode 100644 src/app/auth/login/login.component.ts delete mode 100644 src/app/auth/user.model.ts diff --git a/src/app/app-routing.module.ts b/src/app/app-routing.module.ts index c2e0485..a9fe9ea 100644 --- a/src/app/app-routing.module.ts +++ b/src/app/app-routing.module.ts @@ -1,10 +1,8 @@ -import { Component, NgModule } from '@angular/core'; +import { NgModule } from '@angular/core'; import { RouterModule, Routes } from '@angular/router'; -import { AuthGuard } from './auth/auth.guard'; import { HomeComponent } from './home/home.component'; import { AboutComponent } from './about/about.component'; -import { LoginComponent } from './auth/login/login.component'; import { DatasetsComponent } from './datasets/datasets.component'; import { DatasetDetailComponent } from './datasets/dataset-detail/dataset-detail.component'; import { DatasetResolver } from './datasets/dataset-detail/dataset-resolver.service'; @@ -21,43 +19,35 @@ import { VariantResolver } from './variants/variant-detail/variant-resolver.serv const routes: Routes = [ { path: '', component: HomeComponent }, { path: 'about', component: AboutComponent }, - { path: 'login', component: LoginComponent }, { path: 'breeds', - component: BreedsComponent, - canActivate: [ AuthGuard ] + component: BreedsComponent }, { path: 'datasets', - component: DatasetsComponent, - canActivate: [ AuthGuard ] + component: DatasetsComponent }, { path: 'datasets/:_id', component: DatasetDetailComponent, - canActivate: [ AuthGuard ], resolve: { dataset: DatasetResolver } }, { path: 'samples', component: SamplesComponent, - canActivate: [ AuthGuard ] }, { path: 'samples/:species/:_id', component: SampleDetailComponent, - canActivate: [ AuthGuard ], resolve: { sample: SampleResolver } }, { path: 'variants', component: VariantsComponent, - canActivate: [ AuthGuard ], }, { path: 'variants/:species/:_id', component: VariantDetailComponent, - canActivate: [ AuthGuard ], resolve: { variant: VariantResolver } }, { diff --git a/src/app/app.component.ts b/src/app/app.component.ts index 55194c2..091a2f2 100644 --- a/src/app/app.component.ts +++ b/src/app/app.component.ts @@ -1,19 +1,11 @@ -import { Component, OnInit } from '@angular/core'; - -import { AuthService } from './auth/auth.service'; +import { Component } from '@angular/core'; @Component({ selector: 'app-root', templateUrl: './app.component.html', styleUrls: ['./app.component.scss'] }) -export class AppComponent implements OnInit { +export class AppComponent { title = 'SMARTER-frontend'; - constructor(private authService: AuthService) { } - - ngOnInit(): void { - // try authologin when starting application - this.authService.autoLogin(); - } } diff --git a/src/app/app.module.ts b/src/app/app.module.ts index da8b55c..c341e9b 100644 --- a/src/app/app.module.ts +++ b/src/app/app.module.ts @@ -9,11 +9,9 @@ import { AppRoutingModule } from './app-routing.module'; import { AppComponent } from './app.component'; import { MaterialModule } from './material/material.module'; import { HomeComponent } from './home/home.component'; -import { LoginComponent } from './auth/login/login.component'; import { HeaderComponent } from './navigation/header/header.component'; import { SidenavListComponent } from './navigation/sidenav-list/sidenav-list.component'; import { DatasetsComponent } from './datasets/datasets.component'; -import { AuthInterceptorService } from './auth/auth-interceptor.service'; import { NotFoundComponent } from './not-found/not-found.component'; import { ShortenPipe } from './shared/shorten.pipe'; import { BreedsComponent } from './breeds/breeds.component'; @@ -33,7 +31,6 @@ import { AboutComponent } from './about/about.component'; declarations: [ AppComponent, HomeComponent, - LoginComponent, HeaderComponent, SidenavListComponent, DatasetsComponent, @@ -62,12 +59,7 @@ import { AboutComponent } from './about/about.component'; MaterialModule ], providers: [ - { - provide: HTTP_INTERCEPTORS, - useClass: AuthInterceptorService, - // required, even if it is the only interceptor defined - multi: true - } + ], bootstrap: [AppComponent] }) diff --git a/src/app/auth/auth-data.model.ts b/src/app/auth/auth-data.model.ts deleted file mode 100644 index 6c34d22..0000000 --- a/src/app/auth/auth-data.model.ts +++ /dev/null @@ -1,5 +0,0 @@ -export interface AuthData { - username: string; - password: string; - redirectTo?: string; -} diff --git a/src/app/auth/auth-interceptor.service.spec.ts b/src/app/auth/auth-interceptor.service.spec.ts deleted file mode 100644 index e400c5f..0000000 --- a/src/app/auth/auth-interceptor.service.spec.ts +++ /dev/null @@ -1,28 +0,0 @@ -import { TestBed } from '@angular/core/testing'; -import { RouterTestingModule } from '@angular/router/testing'; -import { HttpClientTestingModule } from '@angular/common/http/testing'; - -import { MaterialModule } from '../material/material.module'; -import { AuthInterceptorService } from './auth-interceptor.service'; - -describe('AuthInterceptorService', () => { - let service: AuthInterceptorService; - - beforeEach(() => { - TestBed.configureTestingModule({ - imports: [ - HttpClientTestingModule, - RouterTestingModule, - MaterialModule, - ], - providers: [ - AuthInterceptorService - ], - }); - service = TestBed.inject(AuthInterceptorService); - }); - - it('should be created', () => { - expect(service).toBeTruthy(); - }); -}); diff --git a/src/app/auth/auth-interceptor.service.ts b/src/app/auth/auth-interceptor.service.ts deleted file mode 100644 index 8034b85..0000000 --- a/src/app/auth/auth-interceptor.service.ts +++ /dev/null @@ -1,39 +0,0 @@ -import { Injectable } from '@angular/core'; -import { HttpHandler, HttpHeaders, HttpInterceptor, HttpRequest } from '@angular/common/http'; - -import { exhaustMap, take } from 'rxjs/operators'; - -import { AuthService } from './auth.service'; - -// don't provide interceptors in root, it needs a custom configuration in -// app.module 'providers' section -@Injectable() -export class AuthInterceptorService implements HttpInterceptor { - - constructor(private authService: AuthService) {} - - intercept(req: HttpRequest, next: HttpHandler) { - // this will be executed for each request - return this.authService.user.pipe( - // take: subscribe to user subject, get N objects and then unsubscribe - take(1), - // take the results of the first subscribe and returns a new observable - exhaustMap(user => { - // during login, I don't have a token. So I need to return the unmodified request - if (!user) { - return next.handle(req); - } - - // copy the request in a new object that I can modify - const modifiedReq = req.clone({ - headers: new HttpHeaders({ - 'Authorization': 'Bearer ' + user.token - }) - }); - - // now I will add a token to each requests - return next.handle(modifiedReq); - }) - ); - } -} diff --git a/src/app/auth/auth.guard.ts b/src/app/auth/auth.guard.ts deleted file mode 100644 index fcb3be5..0000000 --- a/src/app/auth/auth.guard.ts +++ /dev/null @@ -1,45 +0,0 @@ -import { Injectable } from "@angular/core"; -import { ActivatedRouteSnapshot, CanActivate, Params, Router, RouterStateSnapshot, UrlTree } from "@angular/router"; - -import { Observable } from "rxjs"; -import { map, take } from "rxjs/operators"; - -import { AuthService } from "./auth.service"; - -@Injectable({ - providedIn: 'root' -}) -export class AuthGuard implements CanActivate { - - constructor( - private authService: AuthService, - private router: Router, - ) { } - - canActivate( - route: ActivatedRouteSnapshot, - router: RouterStateSnapshot - ): boolean | Promise | Observable { - // determine if a user is authenticated or not by watching user BehaviourSubject - return this.authService.user.pipe( - // take the latest user value and then unsusbscribe - take(1), - map(user => { - // convert a value in a true boolean, or a null/underfined value in false - const isAuth = !!user; - - if (isAuth) { - return true; - } - - // get the requested url to redirect after login - const params: Params = { - next: router.url - }; - - // if not authenticated, redirect to login page - return this.router.createUrlTree(['/login'], {queryParams: params}); - }) - ); - } -} diff --git a/src/app/auth/auth.service.spec.ts b/src/app/auth/auth.service.spec.ts deleted file mode 100644 index 2e2ff7e..0000000 --- a/src/app/auth/auth.service.spec.ts +++ /dev/null @@ -1,74 +0,0 @@ - -import { TestBed } from '@angular/core/testing'; -import { RouterTestingModule } from '@angular/router/testing'; -import { HttpClientTestingModule, HttpTestingController } from '@angular/common/http/testing'; - -import { MaterialModule } from '../material/material.module'; -import { AuthService, AuthResponseData } from './auth.service'; -import { AuthData } from './auth-data.model'; -import { environment } from 'src/environments/environment'; -import { LoginComponent } from './login/login.component'; - -describe('AuthService', () => { - let service: AuthService; - let controller: HttpTestingController; - - let authData: AuthData = { - username: 'test', - password: 'test', - redirectTo: "/" - } - let authResponse: AuthResponseData = { - token: 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJmcmVzaCI6ZmFsc2UsImlhdCI6MTY2NTY3MDMyNCwianRpIjoibWlhbyIsInR5cGUiOiJhY2Nlc3MiLCJzdWIiOiI2MGU4MThlMWYyMzBiZjQ2OWMwODNiYjUiLCJuYmYiOjE2NjU2NzAzMjQsImV4cCI6MTY2NjI3NTEyNH0.UVrnF8Ss6sNGul5-Ab59L4vZQEziRAHAkQ_egGBhAcY', - expires: new Date().toLocaleString() - } - - beforeEach(() => { - TestBed.configureTestingModule({ - imports: [ - RouterTestingModule.withRoutes([ - { path: 'login', component: LoginComponent }, - ]), - HttpClientTestingModule, - MaterialModule, - ], - }); - service = TestBed.inject(AuthService); - controller = TestBed.inject(HttpTestingController); - }); - - it('should be created', () => { - expect(service).toBeTruthy(); - }); - - it('test authentication', () => { - service.user.subscribe(user => { - if (user) { - expect(user.username).toBe('test'); - } - }) - - const expectedUrl = `${environment.backend_url}/auth/login`; - - service.login(authData); - const request = controller.expectOne(expectedUrl); - - // Answer the request so the Observable emits a value. - request.flush(authResponse); - }); - - it('test logout', () => { - // fake a login - const expectedUrl = `${environment.backend_url}/auth/login`; - service.login(authData); - const request = controller.expectOne(expectedUrl); - request.flush(authResponse); - - // do a logout - service.logout(); - - service.user.subscribe(user => { - expect(user).toBeNull(); - }); - }); -}); diff --git a/src/app/auth/auth.service.ts b/src/app/auth/auth.service.ts deleted file mode 100644 index 95b3bf3..0000000 --- a/src/app/auth/auth.service.ts +++ /dev/null @@ -1,130 +0,0 @@ -import { Injectable } from '@angular/core'; -import { Router } from '@angular/router'; -import { HttpClient, HttpErrorResponse } from '@angular/common/http'; - -import { BehaviorSubject } from 'rxjs'; - -import { environment } from '../../environments/environment'; -import { UIService } from '../shared/ui.service'; -import { AuthData } from './auth-data.model'; -import { User } from './user.model'; - -// declared here and not exported: I don't need it outside this module -export interface AuthResponseData { - token: string; - expires: string; -} - -@Injectable({ - providedIn: 'root' -}) -export class AuthService { - // A variant of Subject that requires an initial value and emits its current - // value whenever it is subscribed to. A normal Subject is optimal - // to see status changes, like when user login and logout since UI need to change - // immediately. However, I need a user to do my request, so I need this value - // even after I made the subscription (for instance, when fetching data after - // login) - user = new BehaviorSubject(null); - - // track the timer for autoLogout. If I logout manually, this need to be cleared - private tokenExpirationTimer: any; - - constructor( - private http: HttpClient, - private uiService: UIService, - private router: Router, - ) { } - - login(authData: AuthData) { - // set loading state (required to show progress spinner during queries) - this.uiService.loadingStateChanged.next(true); - - // sending the auth request - this.http.post(environment.backend_url + '/auth/login', authData) - .subscribe({ - next: (authResponseData: AuthResponseData) => { - // create a new user object - const user = new User(authData.username, authResponseData.token); - - // emit user as a currently logged user - this.user.next(user); - - // every time I emit a new user, I need to set the timer for autoLogout - // passing expiresIn (milliseconds) - this.autoLogout(user.expiresIn); - - /* we need also to save data somewhere since when I reload the page, the application - start a new instance and so all the data I have (ie, the token) is lost. I can - use localStorage which is a persistent location on the browser which can store - key->value pairs. 'userData' is the key. The value can't be a JS object, need to - be converted as a string with JSON.stringify method, which can serialize a JS object */ - localStorage.setItem('userData', JSON.stringify(user)); - - // redirect to a path or "/" - this.router.navigate([authData.redirectTo]); - }, - error: (error: HttpErrorResponse) => { - this.uiService.showSnackbar(error.message, "Dismiss"); - } - }); - - // reset loading state - this.uiService.loadingStateChanged.next(false); - } - - /* when application starts (or is reloaded), search for userData saved in localStorage - an try to setUp a user object */ - autoLogin() { - const userData: { - username: string; - _token: string; - _tokenExpirationDate: string; - // https://stackoverflow.com/a/46915314/4385116 - // JSON.parse need a string as an argument - } = JSON.parse(localStorage.getItem('userData') || '{}'); - - if (!userData._token) { - // no user data: you must sign in - return; - } - - const loadedUser = new User( - userData.username, - userData._token - ); - - // check token validity. token property is a getter method, which returns - // null if token is expired. So: - if (loadedUser.token) { - // emit loaded user with our subject - this.user.next(loadedUser); - - // set the autoLogout timer - this.autoLogout(loadedUser.expiresIn); - } - } - - autoLogout(expirationDuration: number) { - // set a timer to log out the user after a certain time. however, if I log out - // manually, this timer need to be disabled - this.tokenExpirationTimer = setTimeout(() => { - this.logout(); - }, expirationDuration) - } - - logout() { - this.user.next(null); - this.router.navigate(["/login"]); - - // if I logout, I need to clear out the localStorage from user data, since - // the token won't be valid forever - localStorage.removeItem('userData'); - - // clear the logout timer - if (this.tokenExpirationTimer) { - clearTimeout(this.tokenExpirationTimer); - this.tokenExpirationTimer = null; - } - } -} diff --git a/src/app/auth/login/login.component.html b/src/app/auth/login/login.component.html deleted file mode 100644 index c20e673..0000000 --- a/src/app/auth/login/login.component.html +++ /dev/null @@ -1,32 +0,0 @@ -
-
- - - Please enter a valid user name - Invalid or missing user name - - - - - Please enter your password - Missing password - - - -
-
diff --git a/src/app/auth/login/login.component.scss b/src/app/auth/login/login.component.scss deleted file mode 100644 index c219af1..0000000 --- a/src/app/auth/login/login.component.scss +++ /dev/null @@ -1,5 +0,0 @@ - -mat-form-field { - margin-top: 2rem; - width: 300px; -} diff --git a/src/app/auth/login/login.component.spec.ts b/src/app/auth/login/login.component.spec.ts deleted file mode 100644 index cfa1c0b..0000000 --- a/src/app/auth/login/login.component.spec.ts +++ /dev/null @@ -1,37 +0,0 @@ -import { ReactiveFormsModule } from '@angular/forms'; -import { ComponentFixture, TestBed } from '@angular/core/testing'; -import { RouterTestingModule } from '@angular/router/testing'; -import { BrowserAnimationsModule } from '@angular/platform-browser/animations'; -import { HttpClientTestingModule } from '@angular/common/http/testing'; - -import { MaterialModule } from '../../material/material.module'; -import { LoginComponent } from './login.component'; - -describe('LoginComponent', () => { - let component: LoginComponent; - let fixture: ComponentFixture; - - beforeEach(async () => { - await TestBed.configureTestingModule({ - imports: [ - RouterTestingModule.withRoutes([]), - BrowserAnimationsModule, - HttpClientTestingModule, - ReactiveFormsModule, - MaterialModule, - ], - declarations: [ LoginComponent ] - }) - .compileComponents(); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(LoginComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/src/app/auth/login/login.component.ts b/src/app/auth/login/login.component.ts deleted file mode 100644 index f7d60a0..0000000 --- a/src/app/auth/login/login.component.ts +++ /dev/null @@ -1,61 +0,0 @@ -import { Component, OnDestroy, OnInit } from '@angular/core'; -import { FormControl, FormGroup, Validators } from '@angular/forms'; -import { ActivatedRoute } from '@angular/router'; -import { Subscription } from 'rxjs'; - -import { UIService } from '../../shared/ui.service'; -import { AuthService } from '../auth.service'; - -@Component({ - selector: 'app-login', - templateUrl: './login.component.html', - styleUrls: ['./login.component.scss'] -}) -export class LoginComponent implements OnInit, OnDestroy { - // https://www.typescriptlang.org/docs/handbook/release-notes/typescript-2-7.html#definite-assignment-assertions - // tell TS that this property will be used as this, even if I don't assign a value here or in constructor - loginForm!: FormGroup; - isLoading = false; - private loadingSubscription!: Subscription; - redirectTo!: string; - hide = true; - - constructor( - private route: ActivatedRoute, - private authService: AuthService, - private uiService: UIService - ) { } - - ngOnInit(): void { - // partially inspired from https://jasonwatmore.com/post/2016/12/08/angular-2-redirect-to-previous-url-after-login-with-auth-guard - // get return url from route parameters or default to '/' - this.redirectTo = this.route.snapshot.queryParams['next'] || '/'; - - // subscribe to see when request are performed by the server - this.loadingSubscription = this.uiService.loadingStateChanged.subscribe(isLoading => { - this.isLoading = isLoading; - }); - - this.loginForm = new FormGroup({ - // same ways to define validators - username: new FormControl('', {validators: [Validators.required]}), - password: new FormControl('', [Validators.required]) - }); - } - - onSubmit(): void { - this.authService.login({ - // this is reactive approach - username: this.loginForm.value.username, - password: this.loginForm.value.password, - redirectTo: this.redirectTo - }); - } - - ngOnDestroy() { - if (this.loadingSubscription) { - this.loadingSubscription.unsubscribe(); - } - } - -} diff --git a/src/app/auth/user.model.ts b/src/app/auth/user.model.ts deleted file mode 100644 index 318d0d7..0000000 --- a/src/app/auth/user.model.ts +++ /dev/null @@ -1,46 +0,0 @@ - -import jwt_decode, { JwtPayload } from 'jwt-decode' - -export class User { - private _tokenExpirationDate: Date; - private decoded: JwtPayload; - - // constructor enable the new keyword to create an object - constructor( - public username: string, - /* _ and private: I don't want to access the token from outside, if I need the - Token, I will call a method that will also check the validity before returning - a token string */ - private _token: string - ) { - // determining expiration time from token - // https://github.com/auth0/jwt-decode/issues/82#issuecomment-782941154 - this.decoded = jwt_decode(_token); - this._tokenExpirationDate = new Date(Number(this.decoded.exp) * 1000); - } - - // getter: is like a function but is accessed as a property (ex user.token) - // code will be executed when accessing this property. Assign a value to - // token will throw and error: we need a setter method to set this property - get token() { - // if i don't have an expiration date or this is less that current time (new Date()) - if (!this._tokenExpirationDate || new Date() > this._tokenExpirationDate) { - // the token is expired, return null even if I have a token - return null - } - - // return value of a private string - return this._token; - } - - get expiresIn() { - const now = new Date().getTime(); - const expiresIn = this._tokenExpirationDate.getTime() - now; - - if (expiresIn < 0) { - return 0; - } else { - return expiresIn; - } - } -} diff --git a/src/app/navigation/header/header.component.html b/src/app/navigation/header/header.component.html index b751c4c..a6feb7c 100644 --- a/src/app/navigation/header/header.component.html +++ b/src/app/navigation/header/header.component.html @@ -26,12 +26,6 @@
  • Variants
    • -
  • - Login -
    • -
  • - Logout -
    • diff --git a/src/app/navigation/header/header.component.ts b/src/app/navigation/header/header.component.ts index 28d669c..b671866 100644 --- a/src/app/navigation/header/header.component.ts +++ b/src/app/navigation/header/header.component.ts @@ -1,42 +1,22 @@ -import { Component, EventEmitter, OnDestroy, OnInit, Output } from '@angular/core'; +import { Component, EventEmitter, Output } from '@angular/core'; import { Subscription } from 'rxjs'; -import { AuthService } from '../../auth/auth.service'; - @Component({ selector: 'app-header', templateUrl: './header.component.html', styleUrls: ['./header.component.scss'] }) -export class HeaderComponent implements OnInit, OnDestroy { - // listed to sidenav frout outside +export class HeaderComponent { + // listed to sidenav from outside @Output() sidenavToggle = new EventEmitter(); // mind authentication isAuthenticated = false; authSubscription!: Subscription; - constructor(private authService: AuthService) { } - - ngOnInit(): void { - this.authSubscription = this.authService.user.subscribe(user => { - // if I have a user, I'm authenticated - this.isAuthenticated = !user ? false : true; - }); - } - onToggleSidenav() { this.sidenavToggle.emit(); } - onLogout() { - this.authService.logout(); - } - - ngOnDestroy() { - if (this.authSubscription) { - this.authSubscription.unsubscribe(); - } - } } diff --git a/src/app/navigation/sidenav-list/sidenav-list.component.html b/src/app/navigation/sidenav-list/sidenav-list.component.html index 39e7ad0..a7e2ccb 100644 --- a/src/app/navigation/sidenav-list/sidenav-list.component.html +++ b/src/app/navigation/sidenav-list/sidenav-list.component.html @@ -23,14 +23,4 @@ list Variants - - face - Login - - - - diff --git a/src/app/navigation/sidenav-list/sidenav-list.component.ts b/src/app/navigation/sidenav-list/sidenav-list.component.ts index 0e2773d..81e477d 100644 --- a/src/app/navigation/sidenav-list/sidenav-list.component.ts +++ b/src/app/navigation/sidenav-list/sidenav-list.component.ts @@ -1,30 +1,19 @@ -import { Component, EventEmitter, OnDestroy, OnInit, Output } from '@angular/core'; +import { Component, EventEmitter, Output } from '@angular/core'; import { Subscription } from 'rxjs'; -import { AuthService } from '../../auth/auth.service'; - @Component({ selector: 'app-sidenav-list', templateUrl: './sidenav-list.component.html', styleUrls: ['./sidenav-list.component.scss'] }) -export class SidenavListComponent implements OnInit, OnDestroy { +export class SidenavListComponent { @Output() closeSidenav = new EventEmitter(); // mind authentication isAuthenticated = false; authSubscription!: Subscription; - constructor(private authService: AuthService) { } - - ngOnInit(): void { - this.authSubscription = this.authService.user.subscribe(user => { - // if I have a user, I'm authenticated - this.isAuthenticated = !user ? false : true; - }); - } - onClose() { this.closeSidenav.emit(); } @@ -32,13 +21,6 @@ export class SidenavListComponent implements OnInit, OnDestroy { onLogout() { // required to close the sidebar this.onClose(); - this.authService.logout(); - } - - ngOnDestroy() { - if (this.authSubscription) { - this.authSubscription.unsubscribe(); - } } } From 4daf9e47f4be0806f2aa17759d5420990ea4c6c5 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 20 Jun 2024 16:34:20 +0200 Subject: [PATCH 07/18] :sparkles: deal with date objects --- src/app/shared/shared.model.ts | 12 ++++++++++++ .../variant-detail/variant-detail.component.html | 1 + src/app/variants/variants.model.ts | 4 ++-- src/app/variants/variants.service.ts | 13 ++++++++++++- 4 files changed, 27 insertions(+), 3 deletions(-) diff --git a/src/app/shared/shared.model.ts b/src/app/shared/shared.model.ts index a4043b7..db62d66 100644 --- a/src/app/shared/shared.model.ts +++ b/src/app/shared/shared.model.ts @@ -5,6 +5,18 @@ export interface ObjectID { $oid: string; } +export class ObjectDate { + $date: Date; + + constructor(value: string | Date) { + if (value instanceof Date) { + this.$date = value; + } else { + this.$date = new Date(value); + } + } +} + // https://dev.to/ankittanna/how-to-create-a-type-for-complex-json-object-in-typescript-d81 export type JSONValue = | string diff --git a/src/app/variants/variant-detail/variant-detail.component.html b/src/app/variants/variant-detail/variant-detail.component.html index 4ca3d54..1fbec0b 100644 --- a/src/app/variants/variant-detail/variant-detail.component.html +++ b/src/app/variants/variant-detail/variant-detail.component.html @@ -48,6 +48,7 @@

    id: {{ variant._id.$oid }}

    Chrom: {{ location.chrom }} Position: {{ location.position }} + Date: {{ location.date.$date | date:'longDate':'en-US' }} Illumina: {{ location.illumina }} Illumina TOP: {{ location.illumina_top }} Illumina Forward: {{ location.illumina_forward }} diff --git a/src/app/variants/variants.model.ts b/src/app/variants/variants.model.ts index 7a1fa9f..73f98f8 100644 --- a/src/app/variants/variants.model.ts +++ b/src/app/variants/variants.model.ts @@ -1,5 +1,5 @@ -import { JSONObject, ObjectID } from "../shared/shared.model"; +import { JSONObject, ObjectID, ObjectDate } from "../shared/shared.model"; export interface Location { ss_id?: string; @@ -14,7 +14,7 @@ export interface Location { affymetrix_ab?: string; strand?: string; imported_from: string; - date?: JSONObject; + date?: ObjectDate; } export interface Probeset { diff --git a/src/app/variants/variants.service.ts b/src/app/variants/variants.service.ts index 458989c..e1c44d4 100644 --- a/src/app/variants/variants.service.ts +++ b/src/app/variants/variants.service.ts @@ -1,3 +1,4 @@ +import { map } from 'rxjs/operators'; import { HttpClient, HttpParams } from '@angular/common/http'; import { Injectable } from '@angular/core'; import { SortDirection } from '@angular/material/sort'; @@ -5,6 +6,7 @@ import { environment } from 'src/environments/environment'; import { SupportedChip, SupportedChipsAPI, Variant, VariantsAPI, VariantsSearch } from './variants.model'; import { Observable, Subject, forkJoin } from 'rxjs'; +import { ObjectDate } from '../shared/shared.model'; @Injectable({ providedIn: 'root' @@ -69,7 +71,16 @@ export class VariantsService { getVariant(_id: string, species: string) { const url = environment.backend_url + '/variants/' + species + "/" + _id; - return this.http.get(url); + return this.http.get(url).pipe( + map((variant: Variant) => { + variant.locations.forEach((location) => { + if (location.date) { + location.date = new ObjectDate(location.date.$date); + } + }); + return variant; + }) + ); } getSupportedChips(species: string,): void { From 823499eb9f91e10038ad9fe8e2eca0b4aa521b4e Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 20 Jun 2024 16:57:15 +0200 Subject: [PATCH 08/18] :white_check_mark: fix variant details tests --- .../variants/variant-detail/variant-detail.component.spec.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/app/variants/variant-detail/variant-detail.component.spec.ts b/src/app/variants/variant-detail/variant-detail.component.spec.ts index 6414b0e..cb5a5f1 100644 --- a/src/app/variants/variant-detail/variant-detail.component.spec.ts +++ b/src/app/variants/variant-detail/variant-detail.component.spec.ts @@ -21,7 +21,7 @@ const variant: Variant = { { "chrom": "15", "date": { - "$date": "2009-01-07T00:00:00Z" + "$date": new Date("2009-01-07T00:00:00Z") }, "illumina": "A/G", "illumina_strand": "TOP", @@ -47,7 +47,7 @@ const variant: Variant = { { "chrom": "15", "date": { - "$date": "2017-03-13T00:00:00Z" + "$date": new Date("2017-03-13T00:00:00Z") }, "illumina": "A/G", "illumina_strand": "TOP", From 6578629c6bb1976dded094a825c76543a23cfe81 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 21 Jun 2024 11:41:41 +0200 Subject: [PATCH 09/18] :white_check_mark: improve samples service coverage --- src/app/samples/countries-example.json | 32 +++++++++++++++++++++++++ src/app/samples/samples.model.ts | 4 ++-- src/app/samples/samples.service.spec.ts | 14 +++++++---- 3 files changed, 43 insertions(+), 7 deletions(-) create mode 100644 src/app/samples/countries-example.json diff --git a/src/app/samples/countries-example.json b/src/app/samples/countries-example.json new file mode 100644 index 0000000..8abb726 --- /dev/null +++ b/src/app/samples/countries-example.json @@ -0,0 +1,32 @@ +{ + "items": [ + { + "_id": { + "$oid": "665679be2c1c55629d917d14" + }, + "alpha_2": "AL", + "alpha_3": "ALB", + "name": "Albania", + "numeric": 8, + "official_name": "Republic of Albania", + "species": ["Sheep"] + }, + { + "_id": { + "$oid": "665679be2c1c55629d917d15" + }, + "alpha_2": "DZ", + "alpha_3": "DZA", + "name": "Algeria", + "numeric": 12, + "official_name": "People's Democratic Republic of Algeria", + "species": ["Sheep"] + } + ], + "next": "/smarter-api/countries?species=Sheep&size=2&page=2", + "page": 1, + "pages": 1, + "prev": null, + "size": 2, + "total": 2 +} diff --git a/src/app/samples/samples.model.ts b/src/app/samples/samples.model.ts index e54fa6c..06b4791 100644 --- a/src/app/samples/samples.model.ts +++ b/src/app/samples/samples.model.ts @@ -55,10 +55,10 @@ export interface Country { export interface CountriesAPI { items: Country[]; - next?: string; + next?: string | null; page: number; pages: number; - prev?: string; + prev?: string | null; size: number; total: number; } diff --git a/src/app/samples/samples.service.spec.ts b/src/app/samples/samples.service.spec.ts index 872cacb..7173743 100644 --- a/src/app/samples/samples.service.spec.ts +++ b/src/app/samples/samples.service.spec.ts @@ -4,11 +4,13 @@ import { SortDirection } from '@angular/material/sort'; import { environment } from '../../environments/environment'; import { SamplesService } from './samples.service'; -import { SamplesSearch } from './samples.model'; +import { CountriesAPI, SamplesSearch } from './samples.model'; +import countriesData from './countries-example.json'; describe('SamplesService', () => { let service: SamplesService; let controller: HttpTestingController; + let mockCountries: CountriesAPI = countriesData; beforeEach(() => { TestBed.configureTestingModule({ @@ -23,15 +25,15 @@ describe('SamplesService', () => { }); it('Test for searching samples', () => { - const pageIndex = 0; - const pageSize = 10; - const sortActive = ''; + const pageIndex = 1; + const pageSize = 2; + const sortActive = 'sample_id'; const sortDirection: SortDirection = "desc"; const samplesSearch: SamplesSearch = { breed: "Merino" }; - const expectedUrl = `${environment.backend_url}/samples/${service.selectedSpecie.toLowerCase()}?size=${pageSize}&breed=Merino`; + const expectedUrl = `${environment.backend_url}/samples/${service.selectedSpecie.toLowerCase()}?page=2&size=2&sort=sample_id&order=desc&breed=Merino`; service.getSamples(sortActive, sortDirection, pageIndex, pageSize, samplesSearch).subscribe( (samples) => {}); @@ -55,6 +57,8 @@ describe('SamplesService', () => { service.getCountries(); const request = controller.expectOne(expectedUrl); + request.flush(mockCountries); + expect(service.countries.length).toBe(mockCountries.total) controller.verify(); }); From 03475ab900a1769ce7f6a142cb770e67f01f3a74 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 21 Jun 2024 12:08:14 +0200 Subject: [PATCH 10/18] :white_check_mark: improve samples service coverage test for getBreeds() method --- src/app/breeds/breeds-example.json | 131 ++++++++++++++++++++++++ src/app/breeds/breeds.model.ts | 4 +- src/app/samples/samples.service.spec.ts | 5 + 3 files changed, 138 insertions(+), 2 deletions(-) create mode 100644 src/app/breeds/breeds-example.json diff --git a/src/app/breeds/breeds-example.json b/src/app/breeds/breeds-example.json new file mode 100644 index 0000000..bc1d3e1 --- /dev/null +++ b/src/app/breeds/breeds-example.json @@ -0,0 +1,131 @@ +{ + "items": [ + { + "_id": { + "$oid": "66544d35719e7ca41a58d257" + }, + "aliases": [ + { + "dataset_id": { + "$oid": "604f75a61a08c53cebd09b67" + }, + "fid": "TEXEL_UY" + }, + { + "dataset_id": { + "$oid": "638a3fc844981838fd398504" + }, + "fid": "TEX" + }, + { + "dataset_id": { + "$oid": "638a3fc844981838fd398505" + }, + "fid": "TEX" + }, + { + "dataset_id": { + "$oid": "638a3fc944981838fd398506" + }, + "fid": "TEX" + }, + { + "dataset_id": { + "$oid": "638a3fca44981838fd398507" + }, + "fid": "TEX" + }, + { + "dataset_id": { + "$oid": "638a3fcb44981838fd398508" + }, + "fid": "TEX" + }, + { + "dataset_id": { + "$oid": "638a3fcc44981838fd398509" + }, + "fid": "TEX" + }, + { + "country": "Netherlands", + "dataset_id": { + "$oid": "604f75a61a08c53cebd09b58" + }, + "fid": "TEX" + }, + { + "country": "Netherlands", + "dataset_id": { + "$oid": "632addae76fa33fed2d2cc6d" + }, + "fid": "TEX" + }, + { + "country": "Unknown", + "dataset_id": { + "$oid": "632c869f0b8c366746d6e8b7" + }, + "fid": "TEX" + } + ], + "code": "TEX", + "n_individuals": 686, + "name": "Texel", + "species": "Sheep" + }, + { + "_id": { + "$oid": "66544d36655c76b775dbebd1" + }, + "aliases": [ + { + "dataset_id": { + "$oid": "604f74db1a08c53cebd09ae1" + }, + "fid": "0" + }, + { + "dataset_id": { + "$oid": "614ece6d6ac707ecf33bd641" + }, + "fid": "FRI" + }, + { + "dataset_id": { + "$oid": "614ece766ac707ecf33bd642" + }, + "fid": "FRI" + }, + { + "dataset_id": { + "$oid": "618d4568d65f4170c18fb2a4" + }, + "fid": "0" + }, + { + "dataset_id": { + "$oid": "6197b5a58aaeeb2699e4c925" + }, + "fid": "FRI" + }, + { + "dataset_id": { + "$oid": "621d081f020817ce8440ca9b" + }, + "fid": "FRZ" + } + ], + "code": "FRZ", + "n_individuals": 688, + "name": "Frizarta", + "species": "Sheep" + } + ], + "next": "/smarter-api/breeds?species=Sheep&size=2&page=2", + "page": 1, + "pages": 1, + "prev": null, + "size": 2, + "total": 2 +} diff --git a/src/app/breeds/breeds.model.ts b/src/app/breeds/breeds.model.ts index 9c570ed..7943ac6 100644 --- a/src/app/breeds/breeds.model.ts +++ b/src/app/breeds/breeds.model.ts @@ -10,10 +10,10 @@ export interface Breed { export interface BreedsAPI { items: Breed[]; - next?: string; + next?: string | null; page: number; pages: number; - prev?: string; + prev?: string | null; size: number; total: number; } diff --git a/src/app/samples/samples.service.spec.ts b/src/app/samples/samples.service.spec.ts index 7173743..a0a0678 100644 --- a/src/app/samples/samples.service.spec.ts +++ b/src/app/samples/samples.service.spec.ts @@ -6,11 +6,14 @@ import { environment } from '../../environments/environment'; import { SamplesService } from './samples.service'; import { CountriesAPI, SamplesSearch } from './samples.model'; import countriesData from './countries-example.json'; +import breedsData from '../breeds/breeds-example.json'; +import { BreedsAPI } from '../breeds/breeds.model'; describe('SamplesService', () => { let service: SamplesService; let controller: HttpTestingController; let mockCountries: CountriesAPI = countriesData; + let mockBreeds: BreedsAPI = breedsData; beforeEach(() => { TestBed.configureTestingModule({ @@ -67,6 +70,8 @@ describe('SamplesService', () => { service.getBreeds(); const request = controller.expectOne(expectedUrl); + request.flush(mockBreeds); + expect(service.breeds.length).toBe(mockBreeds.total); controller.verify(); }) }); From e1da260fa6d5d13a6dba7fc84deed241736cc3f9 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 21 Jun 2024 15:03:50 +0200 Subject: [PATCH 11/18] :white_check_mark: write tests for shared components --- src/app/shared/overlay.service.spec.ts | 60 +++++++++++++++++ .../progress-spinner.component.spec.ts | 67 ++++++++++++++++--- .../progress-spinner.component.ts | 5 ++ src/app/shared/shared.model.spec.ts | 21 ++++++ src/app/shared/shared.model.ts | 9 ++- src/app/shared/ui.service.spec.ts | 35 ++++++++++ 6 files changed, 186 insertions(+), 11 deletions(-) create mode 100644 src/app/shared/overlay.service.spec.ts create mode 100644 src/app/shared/shared.model.spec.ts create mode 100644 src/app/shared/ui.service.spec.ts diff --git a/src/app/shared/overlay.service.spec.ts b/src/app/shared/overlay.service.spec.ts new file mode 100644 index 0000000..1e8cab4 --- /dev/null +++ b/src/app/shared/overlay.service.spec.ts @@ -0,0 +1,60 @@ +import { TestBed, ComponentFixture } from '@angular/core/testing'; +import { Overlay } from '@angular/cdk/overlay'; +import { OverlayService } from './overlay.service'; +import { Component, ViewChild, TemplateRef, ViewContainerRef } from '@angular/core'; + +// A fake component with ViewContainerRef +@Component({ + template: ` +
    + + ` +}) +class TestComponent { + @ViewChild('testContainer', { read: ViewContainerRef }) vcRef!: ViewContainerRef; + @ViewChild('testTemplate') templateRef!: TemplateRef; +} + +describe('OverlayService', () => { + let component: TestComponent; + let fixture: ComponentFixture; + let service: OverlayService; + let overlay: Overlay; + + beforeEach(() => { + TestBed.configureTestingModule({ + declarations: [TestComponent], + providers: [OverlayService, Overlay] + }).compileComponents(); + + fixture = TestBed.createComponent(TestComponent); + component = fixture.componentInstance; + service = TestBed.inject(OverlayService); + overlay = TestBed.inject(Overlay); + fixture.detectChanges(); + }); + + it('should be created', () => { + expect(service).toBeTruthy(); + }); + + it('should create an overlay', () => { + const spy = spyOn(overlay, 'create').and.callThrough(); + service.createOverlay({}); + expect(spy).toHaveBeenCalled(); + }); + + it('should attach a template portal', () => { + const overlayRef = service.createOverlay({}); + const spy = spyOn(overlayRef, 'attach').and.callThrough(); + const templateRef = component.templateRef; + const vcRef = component.vcRef; + service.attachTemplatePortal(overlayRef, templateRef, vcRef); + expect(spy).toHaveBeenCalled(); + }); + + it('should position globally center', () => { + const positionStrategy = service.positionGloballyCenter(); + expect(positionStrategy).toBeTruthy(); + }); +}); diff --git a/src/app/shared/progress-spinner/progress-spinner.component.spec.ts b/src/app/shared/progress-spinner/progress-spinner.component.spec.ts index 54a5e19..88eab8b 100644 --- a/src/app/shared/progress-spinner/progress-spinner.component.spec.ts +++ b/src/app/shared/progress-spinner/progress-spinner.component.spec.ts @@ -1,25 +1,74 @@ import { ComponentFixture, TestBed } from '@angular/core/testing'; -import { Overlay } from '@angular/cdk/overlay'; - +import { Overlay, OverlayRef, PositionStrategy } from '@angular/cdk/overlay'; import { ProgressSpinnerComponent } from './progress-spinner.component'; +import { OverlayService } from '../overlay.service'; describe('ProgressSpinnerComponent', () => { let component: ProgressSpinnerComponent; let fixture: ComponentFixture; + let overlayService: OverlayService; + let overlayRefSpy: jasmine.SpyObj; + let positionStrategySpy: jasmine.SpyObj; + + beforeEach(() => { + overlayRefSpy = jasmine.createSpyObj( + 'OverlayRef', + ['hasAttached', 'detach'] + ); + positionStrategySpy = jasmine.createSpyObj('PositionStrategy', ['global', 'centerHorizontally', 'centerVertically']); - beforeEach(async () => { - await TestBed.configureTestingModule({ - declarations: [ ProgressSpinnerComponent ], - providers: [ Overlay ], - }) - .compileComponents(); + TestBed.configureTestingModule({ + declarations: [ProgressSpinnerComponent], + providers: [ + { + provide: Overlay, + useValue: { + create: () => overlayRefSpy, + position: () => positionStrategySpy + } + }, + OverlayService + ] + }); fixture = TestBed.createComponent(ProgressSpinnerComponent); component = fixture.componentInstance; - fixture.detectChanges(); + overlayService = TestBed.inject(OverlayService); + + // add a custom overlayRef to the component for testing purposes + component.setOverlayRefForTesting(overlayRefSpy); }); it('should create', () => { expect(component).toBeTruthy(); }); + + it('should attach the template portal when displayProgressSpinner is true', () => { + component.displayProgressSpinner = true; + overlayRefSpy.hasAttached.and.returnValue(false); + const attachSpy = spyOn(overlayService, 'attachTemplatePortal'); + + component.ngDoCheck(); + + expect(attachSpy).toHaveBeenCalled(); + }); + + it('should detach the template portal when displayProgressSpinner is false', () => { + component.displayProgressSpinner = false; + overlayRefSpy.hasAttached.and.returnValue(true); + + component.ngDoCheck(); + + expect(overlayRefSpy.detach).toHaveBeenCalled(); + }); + + it('should create overlay on init', () => { + const createSpy = spyOn(overlayService, 'createOverlay'); + const positionSpy = spyOn(overlayService, 'positionGloballyCenter'); + + component.ngOnInit(); + + expect(createSpy).toHaveBeenCalled(); + expect(positionSpy).toHaveBeenCalled(); + }); }); diff --git a/src/app/shared/progress-spinner/progress-spinner.component.ts b/src/app/shared/progress-spinner/progress-spinner.component.ts index 0d2dd90..9930855 100644 --- a/src/app/shared/progress-spinner/progress-spinner.component.ts +++ b/src/app/shared/progress-spinner/progress-spinner.component.ts @@ -29,6 +29,11 @@ export class ProgressSpinnerComponent { private vcRef: ViewContainerRef, private overlayService: OverlayService) { } + // For testing purposes + public setOverlayRefForTesting(overlayRef: OverlayRef): void { + this.overlayRef = overlayRef; + } + ngOnInit() { // Config for Overlay Service this.progressSpinnerOverlayConfig = { diff --git a/src/app/shared/shared.model.spec.ts b/src/app/shared/shared.model.spec.ts new file mode 100644 index 0000000..fa92705 --- /dev/null +++ b/src/app/shared/shared.model.spec.ts @@ -0,0 +1,21 @@ +import { ObjectDate } from './shared.model'; + +describe('ObjectDate', () => { + it('should create an instance with a Date object', () => { + const date = new Date(); + const objectDate = new ObjectDate(date); + expect(objectDate.$date).toEqual(date); + }); + + it('should create an instance with a string', () => { + const dateString = '2022-01-01T00:00:00Z'; + const objectDate = new ObjectDate(dateString); + expect(objectDate.$date).toEqual(new Date(dateString)); + }); + + it('should copy the original date for for invalid date string', () => { + const invalidDateString = 'invalid-date'; + const objectDate = new ObjectDate(invalidDateString); + expect(objectDate.$date).toEqual(invalidDateString); + }); +}); diff --git a/src/app/shared/shared.model.ts b/src/app/shared/shared.model.ts index db62d66..67fdba8 100644 --- a/src/app/shared/shared.model.ts +++ b/src/app/shared/shared.model.ts @@ -6,13 +6,18 @@ export interface ObjectID { } export class ObjectDate { - $date: Date; + $date: Date | string; constructor(value: string | Date) { if (value instanceof Date) { this.$date = value; } else { - this.$date = new Date(value); + const date = new Date(value); + if (isNaN(date.getTime())) { + this.$date = value; // Store the original string + } else { + this.$date = date; + } } } } diff --git a/src/app/shared/ui.service.spec.ts b/src/app/shared/ui.service.spec.ts new file mode 100644 index 0000000..1023ac0 --- /dev/null +++ b/src/app/shared/ui.service.spec.ts @@ -0,0 +1,35 @@ +import { TestBed } from '@angular/core/testing'; +import { MatSnackBar, MatSnackBarModule } from '@angular/material/snack-bar'; +import { NoopAnimationsModule } from '@angular/platform-browser/animations'; +import { UIService } from './ui.service'; + +describe('UIService', () => { + let service: UIService; + let snackBar: MatSnackBar; + + beforeEach(() => { + TestBed.configureTestingModule({ + imports: [MatSnackBarModule, NoopAnimationsModule], + providers: [UIService] + }); + + service = TestBed.inject(UIService); + snackBar = TestBed.inject(MatSnackBar); + }); + + it('should be created', () => { + expect(service).toBeTruthy(); + }); + + it('should show a snackbar', () => { + const spy = spyOn(snackBar, 'open').and.callThrough(); + service.showSnackbar('Test message', 'Test action', 3000); + expect(spy).toHaveBeenCalledWith('Test message', 'Test action', { duration: 3000 }); + }); + + it('should show a snackbar with default duration when no duration is provided', () => { + const spy = spyOn(snackBar, 'open').and.callThrough(); + service.showSnackbar('Test message', 'Test action'); + expect(spy).toHaveBeenCalledWith('Test message', 'Test action', { duration: 5000 }); + }); +}); From eb2e43e8b39e0f52b508751b16b5ab588ed5d4da Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 21 Jun 2024 15:27:49 +0200 Subject: [PATCH 12/18] :white_check_mark: increase navigation components coverage --- .../navigation/header/header.component.spec.ts | 16 ++++++++++++++++ .../sidenav-list/sidenav-list.component.spec.ts | 17 +++++++++++++++++ 2 files changed, 33 insertions(+) diff --git a/src/app/navigation/header/header.component.spec.ts b/src/app/navigation/header/header.component.spec.ts index 0fec6ad..d7748bd 100644 --- a/src/app/navigation/header/header.component.spec.ts +++ b/src/app/navigation/header/header.component.spec.ts @@ -2,6 +2,7 @@ import { ComponentFixture, TestBed } from '@angular/core/testing'; import { RouterTestingModule } from '@angular/router/testing'; import { BrowserAnimationsModule } from '@angular/platform-browser/animations'; import { HttpClientTestingModule } from '@angular/common/http/testing'; +import { By } from '@angular/platform-browser'; import { MaterialModule } from '../../material/material.module'; import { HeaderComponent } from './header.component'; @@ -32,4 +33,19 @@ describe('HeaderComponent', () => { it('should create', () => { expect(component).toBeTruthy(); }); + + it('should call onToggleSidenav when the menu button is clicked', () => { + spyOn(component, 'onToggleSidenav'); + const button = fixture.debugElement.query(By.css('button[mat-icon-button]')).nativeElement; + button.click(); + expect(component.onToggleSidenav).toHaveBeenCalled(); + }); + + it('should emit sidenavToggle event when onToggleSidenav is called', () => { + spyOn(component.sidenavToggle, 'emit'); + + component.onToggleSidenav(); + + expect(component.sidenavToggle.emit).toHaveBeenCalled(); + }); }); diff --git a/src/app/navigation/sidenav-list/sidenav-list.component.spec.ts b/src/app/navigation/sidenav-list/sidenav-list.component.spec.ts index 3010d17..8058175 100644 --- a/src/app/navigation/sidenav-list/sidenav-list.component.spec.ts +++ b/src/app/navigation/sidenav-list/sidenav-list.component.spec.ts @@ -32,4 +32,21 @@ describe('SidenavListComponent', () => { it('should create', () => { expect(component).toBeTruthy(); }); + + it('should emit closeSidenav event when onClose is called', () => { + spyOn(component.closeSidenav, 'emit'); + + component.onClose(); + + expect(component.closeSidenav.emit).toHaveBeenCalled(); + }); + + it('should call onClose when onLogout is called', () => { + spyOn(component, 'onClose'); + + component.onLogout(); + + expect(component.onClose).toHaveBeenCalled(); + }); + }); From 605438c15229239dda2989adbf83f496dc208c26 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 21 Jun 2024 16:11:55 +0200 Subject: [PATCH 13/18] :white_check_mark: improved datasets coverage --- src/app/datasets/datasets.component.spec.ts | 62 ++++++++++++++++++++- src/app/datasets/datasets.service.spec.ts | 8 +-- 2 files changed, 64 insertions(+), 6 deletions(-) diff --git a/src/app/datasets/datasets.component.spec.ts b/src/app/datasets/datasets.component.spec.ts index 8a773a1..e112134 100644 --- a/src/app/datasets/datasets.component.spec.ts +++ b/src/app/datasets/datasets.component.spec.ts @@ -1,25 +1,50 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; +import { ComponentFixture, TestBed, fakeAsync, tick } from '@angular/core/testing'; import { BrowserAnimationsModule } from '@angular/platform-browser/animations'; import { HttpClientTestingModule } from '@angular/common/http/testing'; import { CUSTOM_ELEMENTS_SCHEMA } from '@angular/core'; import { RouterTestingModule } from '@angular/router/testing'; +import { ActivatedRoute, Router } from '@angular/router'; +import { Observable } from 'rxjs/internal/Observable'; +import { of } from 'rxjs/internal/observable/of'; +import { map } from 'rxjs/operators'; import { MaterialModule } from '../material/material.module'; import { DatasetsComponent } from './datasets.component'; +import { DatasetsService } from './datasets.service'; describe('DatasetsComponent', () => { let component: DatasetsComponent; let fixture: ComponentFixture; + let datasetsService: DatasetsService; + let router: Router; + + // Creates an observable that will be used for testing ActivatedRoute params + const paramsMock = new Observable((observer) => { + observer.next({ + page: 1, + size: 5, + sort: 'name', + order: 'desc', + search: null + }); + observer.complete(); + }); beforeEach(async () => { await TestBed.configureTestingModule({ imports: [ BrowserAnimationsModule, HttpClientTestingModule, - RouterTestingModule, + RouterTestingModule.withRoutes( + [{path: 'datasets', component: DatasetsComponent}] + ), MaterialModule, ], declarations: [ DatasetsComponent ], + providers: [ + { provide: DatasetsService, useValue: { getDatasets: () => of([]) } }, + { provide: ActivatedRoute, useValue: { queryParams: paramsMock }} + ], // https://testing-angular.com/testing-components-with-children/#unit-test schemas: [ CUSTOM_ELEMENTS_SCHEMA ], }) @@ -27,12 +52,45 @@ describe('DatasetsComponent', () => { }); beforeEach(() => { + router = jasmine.createSpyObj('Router', ['navigate']); fixture = TestBed.createComponent(DatasetsComponent); component = fixture.componentInstance; + datasetsService = TestBed.inject(DatasetsService); fixture.detectChanges(); }); it('should create', () => { expect(component).toBeTruthy(); }); + + it('should have the correct columns', () => { + expect(component.displayedColumns).toEqual(['file', 'species', 'breed', 'country', 'type']); + }); + + it('should call getDatasets on init', fakeAsync(() => { + spyOn(datasetsService, 'getDatasets').and.callThrough(); + component.ngAfterViewInit(); + tick(1); + expect(datasetsService.getDatasets).toHaveBeenCalled(); + })); + + it('should update searchValue and navigate to /datasets with query params', () => { + const event = { target: { value: 'test' } }; + const queryParams = component.getQueryParams(); + + of(event).pipe( + map((event: any) => { + component.searchValue = event.target.value; + router.navigate( + ["/datasets"], + { + queryParams: queryParams + } + ) + }) + ).subscribe(); + + expect(component.searchValue).toBe('test'); + expect(router.navigate).toHaveBeenCalledWith(['/datasets'], { queryParams: queryParams }); + }); }); diff --git a/src/app/datasets/datasets.service.spec.ts b/src/app/datasets/datasets.service.spec.ts index de66d65..6891122 100644 --- a/src/app/datasets/datasets.service.spec.ts +++ b/src/app/datasets/datasets.service.spec.ts @@ -22,13 +22,13 @@ describe('DatasetsService', () => { }); it('Test for searching datasets', () => { - const pageIndex = 0; - const pageSize = 10; - const sortActive = ''; + const pageIndex = 1; + const pageSize = 2; + const sortActive = 'file'; const sortDirection: SortDirection = "desc"; const searchValue = 'adaptmap'; - const expectedUrl = `${environment.backend_url}/datasets?size=${pageSize}&search=${searchValue}`; + const expectedUrl = `${environment.backend_url}/datasets?page=${pageSize}&size=${pageSize}&sort=${sortActive}&order=${sortDirection}&search=${searchValue}`; service.getDatasets(sortActive, sortDirection, pageIndex, pageSize, searchValue).subscribe( (datasets) => {}); From b986129c337acbe3f72ddfb61dc6e87c1f138394 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Fri, 21 Jun 2024 16:59:29 +0200 Subject: [PATCH 14/18] :white_check_mark: improve dataset-detail coverage --- .../dataset-detail.component.spec.ts | 40 +++++++++++++++---- 1 file changed, 33 insertions(+), 7 deletions(-) diff --git a/src/app/datasets/dataset-detail/dataset-detail.component.spec.ts b/src/app/datasets/dataset-detail/dataset-detail.component.spec.ts index d4c935e..60d2d80 100644 --- a/src/app/datasets/dataset-detail/dataset-detail.component.spec.ts +++ b/src/app/datasets/dataset-detail/dataset-detail.component.spec.ts @@ -1,12 +1,15 @@ import { ComponentFixture, TestBed } from '@angular/core/testing'; +import { SpyLocation } from '@angular/common/testing'; import { RouterTestingModule } from '@angular/router/testing'; import { HttpClientTestingModule } from '@angular/common/http/testing'; import { of } from 'rxjs'; -import { ActivatedRoute } from '@angular/router'; +import { ActivatedRoute, Router } from '@angular/router'; +import { Location } from '@angular/common'; import { CUSTOM_ELEMENTS_SCHEMA } from '@angular/core'; import { DatasetDetailComponent } from './dataset-detail.component'; import { Dataset } from '../datasets.model'; +import { SamplesComponent } from 'src/app/samples/samples.component'; const dataset: Dataset = { "_id": { @@ -38,11 +41,17 @@ const route = { data: of({ dataset: dataset }) }; describe('DatasetDetailComponent', () => { let component: DatasetDetailComponent; let fixture: ComponentFixture; + let location: SpyLocation; + let mockRouter = { + navigate: jasmine.createSpy('navigate') // Create a spy for the navigate method + }; beforeEach(async () => { await TestBed.configureTestingModule({ imports: [ - RouterTestingModule, + RouterTestingModule.withRoutes( + [{path: 'samples', component: SamplesComponent}] + ), HttpClientTestingModule, ], declarations: [ DatasetDetailComponent ], @@ -50,12 +59,15 @@ describe('DatasetDetailComponent', () => { schemas: [ CUSTOM_ELEMENTS_SCHEMA ], providers: [ { provide: ActivatedRoute, useValue: route }, + { provide: Location, useClass: SpyLocation }, + { provide: Router, useValue: mockRouter }, ] }) .compileComponents(); fixture = TestBed.createComponent(DatasetDetailComponent); component = fixture.componentInstance; + location = TestBed.inject(Location); fixture.detectChanges(); }); @@ -63,10 +75,24 @@ describe('DatasetDetailComponent', () => { expect(component).toBeTruthy(); }); - describe('ngOnInit', () => { - it('should get dataset data', () => { - component.ngOnInit(); - expect(component.dataset).toEqual(dataset); - }); + it('should get dataset data', () => { + component.ngOnInit(); + expect(component.dataset).toEqual(dataset); }); + + // https://codeutility.org/unit-testing-angular-6-location-go-back-stack-overflow/ + it('should go back to previous page on back button click', () => { + spyOn(location, 'back'); + component.goBack(); + expect(location.back).toHaveBeenCalled(); + }); + + it('should navigate to /samples with query params when getSamples is called', () => { + component.getSamples(); + expect(mockRouter.navigate).toHaveBeenCalledWith( + ['/samples'], + { queryParams: { dataset: component.dataset._id.$oid, species: component.dataset.species } } + ); + }); + }); From e12ce9c2cedfe787f64bc3dd958d6fdaf0f6f28f Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 24 Jun 2024 11:35:38 +0200 Subject: [PATCH 15/18] :memo: work on about page --- src/app/about/about.component.html | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/src/app/about/about.component.html b/src/app/about/about.component.html index 1b4b053..b4a4461 100644 --- a/src/app/about/about.component.html +++ b/src/app/about/about.component.html @@ -6,7 +6,8 @@

    About the SMARTER database

    The SMARTER project site is a place where WP4 partners of the Smarter project - can browse and access their data. + can browse and access their data. Now this dataset is open and available + to the community.

    The SMARTER project

    @@ -40,7 +41,7 @@

    The SMARTER project

    - Data are made available to the community using three different instruments: + Data are made available to the community using four different instruments:

      @@ -53,7 +54,7 @@

      The SMARTER project

      manual pages.
    • - The SMARTER-backend, + The SMARTER-backend, which is a REST API service developed on top of the SMARTER-database which provide methods to interact and access with SMARTER data using web resources. By using SMARTER-backend, you can develop softwares or scripts which get @@ -70,13 +71,24 @@

      The SMARTER project

      (this site), which is a web interface to browse SMARTER-database data relying on SMARTER-backend.
      • +
    • + The SMARTER FTP site which collects + the genotype files of the animals described in the SMARTER-database. +

    Those instrument can be used to collect metadata and other samples information: genotypes are available for both Goat and Sheep species as a whole PLINK binary file for each - of the supported assemblies. Users are required to identify their samples of interest and then - subset the genotype files according their needs. Additional filtering steps + of the supported assemblies. You can download the genotype files from the + FTP site for the available assemblies. + Users are required to identify their samples of interest using the + SMARTER-frontend, + the SMARTER-backend or + smarterapi R package + (they are three different ways to access the same data, the first one is a web interface, + the second one is a REST API service and the third one is an R package to interact with the API service). + Then, users can subset the genotype files according their needs. Additional filtering steps on the selected genotypes can be done to get rid of missing samples or variants.

    From 2c4d1df3fb3327ff648a4df6a1ea4386d2888fad Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 24 Jun 2024 12:16:43 +0200 Subject: [PATCH 16/18] :memo: update about page --- src/app/about/about.component.html | 139 +++++++++++++++-------------- 1 file changed, 70 insertions(+), 69 deletions(-) diff --git a/src/app/about/about.component.html b/src/app/about/about.component.html index b4a4461..628b417 100644 --- a/src/app/about/about.component.html +++ b/src/app/about/about.component.html @@ -1,36 +1,37 @@ -

    About the SMARTER database

    +

    About the SMARTER Database

    +

    The SMARTER project site is a place where WP4 partners of the - Smarter project - can browse and access their data. Now this dataset is open and available + SMARTER project + can browse and access their data. This dataset is now open and available to the community.

    -

    The SMARTER project

    +

    The SMARTER Project

    - Small ruminant populations play a fundamental role for the livelihood and + Small ruminant populations play a fundamental role in the livelihood and socio-economic well-being of human settlements, especially in marginal areas of Europe. Under-utilized sheep and goat breeds may be highly valuable in - increasing the profitability of small ruminant farming in such marginal areas. - These breeds are valuable because they have peculiar and often atypical - genetic make-up which make them a potentially extraordinary resource to - be exploited for adaptation to (harsh) environments, resilience to farming + increasing the profitability of small ruminant farming in these marginal areas. + These breeds are valuable because they have unique and often atypical + genetic make-ups, making them potentially extraordinary resources for + adaptation to harsh environments, resilience to farming conditions, resistance to biotic and abiotic stressors, and the production - of quality of products of animal origin. + of high-quality animal products.

    - In this particular context, WP4 aims to address knowledge gaps concerning + In this context, WP4 aims to address knowledge gaps concerning genetic diversity in goats and sheep. Its objective is to identify genetic factors that contribute to their ability to adapt to climate conditions and, more broadly, to withstand environmental disturbances. - Available datasets relevant to the genomic characterization - were identified and furthermore comprehensive data on hardy and under-utilized + Available datasets relevant to genomic characterization + were identified, and comprehensive data on hardy and under-utilized breeds were collected, including genotypes, phenotypes, and environmental measurements associated with rearing conditions. To ensure consistency, the recording of this data was standardized: genotypes @@ -44,86 +45,86 @@

    The SMARTER project

    Data are made available to the community using four different instruments:

    -
      -
    • - The SMARTER-database, - which is a collection of tools and scripts to collect, standardize and provide - to the community a collection of genotype data and metadata information - in hardy goat and sheep populations by combining new with already existing datasets. - This project is better explained and documented in its - manual pages. -
      • -
    • - The SMARTER-backend, - which is a REST API service developed on top of the SMARTER-database - which provide methods to interact and access with SMARTER data using web resources. - By using SMARTER-backend, you can develop softwares or scripts which get - access to SMARTER data through web, without have a local instance - of the SMARTER-database. An example of this is the - smarterapi R package, - which allow to collect SMARTER data using the SMARTER-backend. More - information can be found in the - SMARTER-backend documentation - and smarterapi manual pages. -
      • -
    • - The SMARTER-frontend - (this site), which is a web interface to browse SMARTER-database - data relying on SMARTER-backend. -
      • -
    • - The SMARTER FTP site which collects - the genotype files of the animals described in the SMARTER-database. -
      • -
    +
      +
    • + The SMARTER database, + which is a collection of tools and scripts to collect, standardize, and provide + a collection of genotype data and metadata information + on hardy goat and sheep populations by combining new and existing datasets. + This project is better explained and documented in its + manual pages. +
      • +
    • + The SMARTER backend, + which is a REST API service developed on top of the SMARTER database + providing methods to interact with and access SMARTER data using web resources. + By using the SMARTER backend, you can develop software or scripts that access + SMARTER data via the web without needing a local instance + of the SMARTER database. An example of this is the + smarterapi R package, + which allows the collection of SMARTER data using the SMARTER backend. More + information can be found in the + SMARTER backend documentation + and smarterapi manual pages. +
      • +
    • + The SMARTER frontend + (this site), which is a web interface to browse SMARTER database + data relying on the SMARTER backend. +
      • +
    • + The SMARTER FTP site, which collects + the genotype files of the animals described in the SMARTER database. +
      • +
    -

    - Those instrument can be used to collect metadata and other samples information: genotypes - are available for both Goat and Sheep species as a whole PLINK binary file for each - of the supported assemblies. You can download the genotype files from the - FTP site for the available assemblies. - Users are required to identify their samples of interest using the - SMARTER-frontend, - the SMARTER-backend or - smarterapi R package - (they are three different ways to access the same data, the first one is a web interface, - the second one is a REST API service and the third one is an R package to interact with the API service). - Then, users can subset the genotype files according their needs. Additional filtering steps - on the selected genotypes can be done to get rid of missing samples or variants. -

    +

    + These instruments can be used to collect metadata and other sample information. Genotypes + are available for both Goat and Sheep species as whole PLINK binary files for each + of the supported assemblies. You can download the genotype files from the + FTP site for the available assemblies. + Users are required to identify their samples of interest using the + SMARTER frontend, + the SMARTER backend, or the + smarterapi R package. + These are three different ways to access the same data: the first one is a web interface, + the second one is a REST API service, and the third one is an R package to interact with the API service. + Users can then subset the genotype files according to their needs. Additional filtering steps + on the selected genotypes can be done to remove missing samples or variants. +

    -

    About this site

    +

    About This Site

    - You can browse WP4 SMARTER using the different tabs. Data like samples, variants - and breed can be browsed by species (Goat, Sheep): you will find - a button on the top of the page which will select the data you can browse. - Data like datasets are available in the same page for both species. Here's + You can browse WP4 SMARTER data using the different tabs. Data like samples, variants, + and breeds can be browsed by species (Goat, Sheep). You will find + a button on the top of the page to select the data you want to browse. + Data like datasets are available on the same page for both species. Here's a list of the site sections:

    • - Breeds: navigate data by breeds, you can + Breeds: navigate data by breeds. You can search for a specific breed or get general information about how many samples belong to the same breed. You can follow the links to retrieve all samples of a particular breed.
    • - Datasets: navigate data by datasets, browse + Datasets: navigate data by datasets. Browse data relying on the files submitted by the partners or by file content. For - a genotypes dataset you can follow the links a retrieve all samples + a genotypes dataset, you can follow the links to retrieve all samples belonging to the same dataset.
    • Samples: navigate samples by species. - You can filter out samples by filling the form fields. + You can filter samples by filling out the form fields.
    • Variants: navigate the variants used to normalize the genotype files and collect information about their positions and genotype codings. You can browse variants by species and - by assembly versions, and filter out variants by filling the form fields. + by assembly versions, and filter variants by filling out the form fields.
    From 905fc7d30c49ef032e6a8e5f1eb10c8e2d5d07ac Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 24 Jun 2024 12:17:51 +0200 Subject: [PATCH 17/18] :lipstick: rename free-text style into small-padding --- src/app/breeds/breeds.component.html | 2 +- src/app/datasets/datasets.component.html | 2 +- src/app/samples/samples.component.html | 2 +- src/app/variants/variants.component.html | 2 +- src/styles.scss | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/app/breeds/breeds.component.html b/src/app/breeds/breeds.component.html index f70b54a..c6948e5 100644 --- a/src/app/breeds/breeds.component.html +++ b/src/app/breeds/breeds.component.html @@ -1,5 +1,5 @@ -

    +

    Searching {{ speciesControl.value }} breeds

    diff --git a/src/app/datasets/datasets.component.html b/src/app/datasets/datasets.component.html index 21d62e5..786dbb9 100644 --- a/src/app/datasets/datasets.component.html +++ b/src/app/datasets/datasets.component.html @@ -1,5 +1,5 @@ -

    +

    Searching datasets

    diff --git a/src/app/samples/samples.component.html b/src/app/samples/samples.component.html index 70712d6..0abe8ce 100644 --- a/src/app/samples/samples.component.html +++ b/src/app/samples/samples.component.html @@ -1,5 +1,5 @@ -

    +

    Searching {{ speciesControl.value }} samples

    diff --git a/src/app/variants/variants.component.html b/src/app/variants/variants.component.html index ef08881..4f0cf0b 100644 --- a/src/app/variants/variants.component.html +++ b/src/app/variants/variants.component.html @@ -1,4 +1,4 @@ -

    +

    Searching {{ speciesControl.value }} SNPs in {{ selectedAssembly }} assembly

    diff --git a/src/styles.scss b/src/styles.scss index 07993b9..a3db279 100644 --- a/src/styles.scss +++ b/src/styles.scss @@ -46,7 +46,7 @@ html, body { height: 100%; } body { margin: 0; font-family: Roboto, "Helvetica Neue", sans-serif; } -.free-text { +.small-padding { padding-left: 15px; } From 26147d043b566f891cf6f15f031190721ccbffa1 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 24 Jun 2024 14:53:50 +0200 Subject: [PATCH 18/18] :lipstick: work on home page --- src/app/home/home.component.html | 7 ++++++- src/app/home/home.component.scss | 12 ++++++++++++ src/app/home/home.component.spec.ts | 2 +- src/styles.scss | 24 ++++++++++++------------ 4 files changed, 31 insertions(+), 14 deletions(-) diff --git a/src/app/home/home.component.html b/src/app/home/home.component.html index 4f62461..b27d740 100644 --- a/src/app/home/home.component.html +++ b/src/app/home/home.component.html @@ -1,6 +1,11 @@
    SMAll Ruminants breeding for Efficiency and Resilience -

    Welcome to the SMARTER database

    +

    Welcome to the SMARTER Database

    +

    + The SMARTER database is a collection of data from small ruminant research projects.
    + The data is open and available to the community. See our + about page for more information. +

    diff --git a/src/app/home/home.component.scss b/src/app/home/home.component.scss index 7c9fabe..85a6d03 100644 --- a/src/app/home/home.component.scss +++ b/src/app/home/home.component.scss @@ -8,3 +8,15 @@ width: 85%; height: auto; } + +h1 { + text-align: center; + font-size: 2.5rem; + margin: 1rem; +} + +p { + text-align: center; + margin: 1rem; + padding-top: 1rem; +} diff --git a/src/app/home/home.component.spec.ts b/src/app/home/home.component.spec.ts index bb6a041..3e142f7 100644 --- a/src/app/home/home.component.spec.ts +++ b/src/app/home/home.component.spec.ts @@ -27,6 +27,6 @@ describe('HomeComponent', () => { const fixture = TestBed.createComponent(HomeComponent); fixture.detectChanges(); const compiled = fixture.nativeElement; - expect(compiled.querySelector('h1').textContent).toContain('Welcome to the SMARTER database'); + expect(compiled.querySelector('h1').textContent).toContain('Welcome to the SMARTER Database'); }); }); diff --git a/src/styles.scss b/src/styles.scss index a3db279..47a734e 100644 --- a/src/styles.scss +++ b/src/styles.scss @@ -10,6 +10,18 @@ $my-accent: mat.define-palette(mat.$orange-palette, A200, A100, A400); // The "warn" palette is optional and defaults to red if not specified. $my-warn: mat.define-palette(mat.$red-palette); +// define the light theme +$my-theme: mat.define-light-theme(( + color: ( + primary: $my-primary, + accent: $my-accent, + warn: $my-warn, + ) +)); + +// includes styles for all components in the library +@include mat.all-component-themes($my-theme); + // A mixin to deal with mat-row hover // https://github.com/angular/components/issues/8204 @mixin mat-table-hover($is-dark) { @@ -27,18 +39,6 @@ $my-warn: mat.define-palette(mat.$red-palette); } } -// define the light theme -$my-theme: mat.define-light-theme(( - color: ( - primary: $my-primary, - accent: $my-accent, - warn: $my-warn, - ) -)); - -// includes styles for all components in the library -@include mat.all-component-themes($my-theme); - // include custom mixins @include mat-table-hover(false);