feat(agora): migrate Nominated Targets (AG-1551) (#2864)

apps/agora/api/.eslintrc.json

@@ -7,12 +7,10 @@
       "rules": {}
     },
     {
-      "files": ["*.ts", "*.tsx"],
-      "rules": {}
-    },
-    {
-      "files": ["*.js", "*.jsx"],
-      "rules": {}
+      "files": ["*.ts", "*.config.ts", "webpack.config.js"],
+      "rules": {
+        "tailwindcss/no-custom-classname": "off"
+      }
     }
   ]
 }

apps/agora/api/src/api.ts

@@ -21,7 +21,7 @@ const router = express.Router();
 mongoose.connection.once('open', async () => {
   router.get('/dataversion', dataVersionRoute);
   router.get('/teams', teamsRoute);
-  router.get('/team-members/:name/image', teamMemberImageRoute);
+  router.get('/teamMembers/:name/image', teamMemberImageRoute);
 });
 
 export default router;

apps/agora/app/src/app/app.routes.ts

@@ -27,6 +27,23 @@ export const routes: Route[] = [
       description: "See what's new in Agora, from new features to our latest data updates.",
     },
   },
+  {
+    path: 'genes/nominated-targets',
+    loadChildren: () =>
+      import('@sagebionetworks/agora/nominated-targets').then((routes) => routes.routes),
+    data: {
+      title: 'Nominated Targets | Candidate genes for AD treatment or prevention',
+      description:
+        'Browse a list of genes that researchers have identified using computational analyses of high-dimensional human genomic, proteomic and metabolomic data.',
+    },
+  },
+  // {
+  //   path: 'nomination-form', component: NominationFormPageComponent,
+  //   data: {
+  //     title: 'Nominate a Target | Suggest a new AD therapeutic target',
+  //     description: 'Nominate a gene as a new candidate for AD treatment or prevention.'
+  //   }
+  // },
   {
     path: 'not-found',
     loadChildren: () => import('@sagebionetworks/agora/not-found').then((routes) => routes.routes),

apps/agora/app/src/styles.scss

@@ -1,4 +1,3 @@
 /* You can add global styles to this file, and also import other style files */
 @use 'libs/agora/styles/src/index';
-
 @use 'app-theme';

libs/agora/api-client-angular/src/lib/api/teamMember.service.ts

@@ -117,7 +117,7 @@ export class TeamMemberService {
     observe?: 'body',
     reportProgress?: boolean,
     options?: {
-      httpHeaderAccept?: 'image/jpeg' | 'application/problem+json';
+      httpHeaderAccept?: 'image/jpg' | 'image/jpeg' | 'image/png' | 'application/problem+json';
       context?: HttpContext;
     },
   ): Observable<Blob>;
@@ -126,7 +126,7 @@ export class TeamMemberService {
     observe?: 'response',
     reportProgress?: boolean,
     options?: {
-      httpHeaderAccept?: 'image/jpeg' | 'application/problem+json';
+      httpHeaderAccept?: 'image/jpg' | 'image/jpeg' | 'image/png' | 'application/problem+json';
       context?: HttpContext;
     },
   ): Observable<HttpResponse<Blob>>;
@@ -135,7 +135,7 @@ export class TeamMemberService {
     observe?: 'events',
     reportProgress?: boolean,
     options?: {
-      httpHeaderAccept?: 'image/jpeg' | 'application/problem+json';
+      httpHeaderAccept?: 'image/jpg' | 'image/jpeg' | 'image/png' | 'application/problem+json';
       context?: HttpContext;
     },
   ): Observable<HttpEvent<Blob>>;
@@ -144,7 +144,7 @@ export class TeamMemberService {
     observe: any = 'body',
     reportProgress: boolean = false,
     options?: {
-      httpHeaderAccept?: 'image/jpeg' | 'application/problem+json';
+      httpHeaderAccept?: 'image/jpg' | 'image/jpeg' | 'image/png' | 'application/problem+json';
       context?: HttpContext;
     },
   ): Observable<any> {
@@ -159,7 +159,12 @@ export class TeamMemberService {
     let localVarHttpHeaderAcceptSelected: string | undefined = options && options.httpHeaderAccept;
     if (localVarHttpHeaderAcceptSelected === undefined) {
       // to determine the Accept header
-      const httpHeaderAccepts: string[] = ['image/jpeg', 'application/problem+json'];
+      const httpHeaderAccepts: string[] = [
+        'image/jpg',
+        'image/jpeg',
+        'image/png',
+        'application/problem+json',
+      ];
       localVarHttpHeaderAcceptSelected = this.configuration.selectHeaderAccept(httpHeaderAccepts);
     }
     if (localVarHttpHeaderAcceptSelected !== undefined) {

libs/agora/api-description/build/openapi.yaml

@@ -72,12 +72,17 @@ paths:
             type: string
       responses:
         '200':
+          description: Success
           content:
+            image/jpg:
+              schema:
+                $ref: '#/components/schemas/TeamImage'
             image/jpeg:
               schema:
-                type: string
-                format: binary
-          description: Success
+                $ref: '#/components/schemas/TeamImage'
+            image/png:
+              schema:
+                $ref: '#/components/schemas/TeamImage'
         '400':
           $ref: '#/components/responses/BadRequest'
         '500':
@@ -163,6 +168,9 @@ components:
           type: array
           items:
             $ref: '#/components/schemas/Team'
+    TeamImage:
+      type: string
+      format: binary
   responses:
     BadRequest:
       description: Invalid request

libs/agora/api-description/src/components/schemas/TeamImage.yaml

@@ -0,0 +1,2 @@
+type: string
+format: binary

libs/agora/api-description/src/paths/teamMembers/@{name}/image.yaml

@@ -12,12 +12,17 @@ get:
         type: string
   responses:
     '200':
+      description: Success
       content:
+        image/jpg:
+          schema:
+            $ref: ../../../components/schemas/TeamImage.yaml
         image/jpeg:
           schema:
-            type: string
-            format: binary
-      description: Success
+            $ref: ../../../components/schemas/TeamImage.yaml
+        image/png:
+          schema:
+            $ref: ../../../components/schemas/TeamImage.yaml
     '400':
       $ref: ../../../components/responses/BadRequest.yaml
     '500':

libs/agora/genes/.eslintrc.json

@@ -0,0 +1,46 @@
+{
+  "extends": ["../../../.eslintrc.json"],
+  "ignorePatterns": ["!**/*"],
+  "env": {
+    "jest": true
+  },
+  "overrides": [
+    {
+      "files": ["*.ts"],
+      "extends": [
+        "plugin:@nx/angular",
+        "plugin:@angular-eslint/template/process-inline-templates",
+        "plugin:jest/recommended"
+      ],
+      "rules": {
+        "@angular-eslint/directive-selector": [
+          "error",
+          {
+            "type": "attribute",
+            "prefix": "agora",
+            "style": "camelCase"
+          }
+        ],
+        "@angular-eslint/component-selector": [
+          "error",
+          {
+            "type": "element",
+            "prefix": "agora",
+            "style": "kebab-case"
+          }
+        ]
+      }
+    },
+    {
+      "files": ["*.html"],
+      "extends": ["plugin:@nx/angular-template"],
+      "rules": {}
+    },
+    {
+      "files": ["*.ts", "jest.config.ts"],
+      "rules": {
+        "tailwindcss/no-custom-classname": "off"
+      }
+    }
+  ]
+}

libs/agora/genes/README.md

@@ -0,0 +1,7 @@
+# agora-genes
+
+This library was generated with [Nx](https://nx.dev).
+
+## Running unit tests
+
+Run `nx test agora-genes` to execute the unit tests.

libs/agora/genes/jest.config.ts

@@ -0,0 +1,23 @@
+/* eslint-disable */
+export default {
+  displayName: 'agora-genes',
+  preset: '../../../jest.preset.js',
+  setupFilesAfterEnv: ['<rootDir>/src/test-setup.ts'],
+  globals: {},
+  coverageDirectory: '../../../coverage/libs/agora/genes',
+  transform: {
+    '^.+\\.(ts|mjs|js|html)$': [
+      'jest-preset-angular',
+      {
+        tsconfig: '<rootDir>/tsconfig.spec.json',
+        stringifyContentPathRegex: '\\.(html|svg)$',
+      },
+    ],
+  },
+  transformIgnorePatterns: ['node_modules/(?!.*\\.mjs$)'],
+  snapshotSerializers: [
+    'jest-preset-angular/build/serializers/no-ng-attributes',
+    'jest-preset-angular/build/serializers/ng-snapshot',
+    'jest-preset-angular/build/serializers/html-comment',
+  ],
+};

libs/agora/genes/project.json

@@ -0,0 +1,27 @@
+{
+  "name": "agora-genes",
+  "$schema": "../../../node_modules/nx/schemas/project-schema.json",
+  "projectType": "library",
+  "sourceRoot": "libs/agora/genes/src",
+  "prefix": "agora",
+  "targets": {
+    "test": {
+      "executor": "@nx/jest:jest",
+      "outputs": ["{workspaceRoot}/coverage/libs/agora/genes"],
+      "options": {
+        "jestConfig": "libs/agora/genes/jest.config.ts"
+      }
+    },
+    "lint": {
+      "executor": "@nx/eslint:lint"
+    },
+    "lint-fix": {
+      "executor": "@nx/eslint:lint",
+      "options": {
+        "fix": true
+      }
+    }
+  },
+  "tags": ["type:feature", "scope:agora", "language:typescript"],
+  "implicitDependencies": []
+}

libs/agora/genes/src/index.ts

@@ -0,0 +1,2 @@
+export * from './lib/components/gene-search/gene-search.component';
+export * from './lib/components/gene-table/gene-table.component';

libs/agora/genes/src/lib/components/gene-search/gene-search.component.html

@@ -0,0 +1 @@
+<p>gene-search works!</p>

libs/agora/genes/src/lib/components/gene-search/gene-search.component.spec.ts

@@ -0,0 +1,21 @@
+import { ComponentFixture, TestBed } from '@angular/core/testing';
+import { GeneSearchComponent } from './gene-search.component';
+
+describe('GeneSearchComponent', () => {
+  let component: GeneSearchComponent;
+  let fixture: ComponentFixture<GeneSearchComponent>;
+
+  beforeEach(async () => {
+    await TestBed.configureTestingModule({
+      imports: [GeneSearchComponent],
+    }).compileComponents();
+
+    fixture = TestBed.createComponent(GeneSearchComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should create', () => {
+    expect(component).toBeTruthy();
+  });
+});

libs/agora/genes/src/lib/components/gene-search/gene-search.component.ts

@@ -0,0 +1,11 @@
+import { Component } from '@angular/core';
+import { CommonModule } from '@angular/common';
+
+@Component({
+  selector: 'agora-gene-search',
+  standalone: true,
+  imports: [CommonModule],
+  templateUrl: './gene-search.component.html',
+  styleUrl: './gene-search.component.scss',
+})
+export class GeneSearchComponent {}

libs/agora/genes/src/lib/components/gene-table/gene-table.component.html

@@ -0,0 +1 @@
+<p>gene table works!</p>

libs/agora/genes/src/lib/components/gene-table/gene-table.component.spec.ts

@@ -0,0 +1,21 @@
+import { ComponentFixture, TestBed } from '@angular/core/testing';
+import { GeneTableComponent } from './gene-table.component';
+
+describe('GeneSearchComponent', () => {
+  let component: GeneTableComponent;
+  let fixture: ComponentFixture<GeneTableComponent>;
+
+  beforeEach(async () => {
+    await TestBed.configureTestingModule({
+      imports: [GeneTableComponent],
+    }).compileComponents();
+
+    fixture = TestBed.createComponent(GeneTableComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should create', () => {
+    expect(component).toBeTruthy();
+  });
+});

libs/agora/genes/src/lib/components/gene-table/gene-table.component.ts

@@ -0,0 +1,24 @@
+import { Component, inject, OnInit } from '@angular/core';
+import { CommonModule } from '@angular/common';
+import { RouterModule } from '@angular/router';
+import { Dataversion, DataversionService } from '@sagebionetworks/agora/api-client-angular';
+import { Observable } from 'rxjs';
+import { SafeUrl } from '@angular/platform-browser';
+import { PathSanitizer } from '@sagebionetworks/agora/util';
+import { ConfigService } from '@sagebionetworks/agora/config';
+// import { NavigationLink } from '../../models/navigation-link';
+
+@Component({
+  selector: 'agora-gene-table',
+  standalone: true,
+  imports: [CommonModule, RouterModule],
+  templateUrl: './gene-table.component.html',
+  styleUrls: ['./gene-table.component.scss'],
+})
+export class GeneTableComponent {
+  // configService = inject(ConfigService);
+  // dataVersionService = inject(DataversionService);
+  // sanitizer = inject(PathSanitizer);
+  // footerLogoPath!: SafeUrl;
+  // dataVersion$!: Observable<Dataversion>;
+}

libs/agora/genes/src/test-setup.ts

@@ -0,0 +1 @@
+import 'jest-preset-angular/setup-jest';

libs/agora/genes/tsconfig.json

@@ -0,0 +1,28 @@
+{
+  "extends": "../../../tsconfig.base.json",
+  "files": [],
+  "include": [],
+  "references": [
+    {
+      "path": "./tsconfig.lib.json"
+    },
+    {
+      "path": "./tsconfig.spec.json"
+    }
+  ],
+  "compilerOptions": {
+    "forceConsistentCasingInFileNames": true,
+    "strict": true,
+    "noImplicitOverride": true,
+    "noPropertyAccessFromIndexSignature": true,
+    "noImplicitReturns": true,
+    "noFallthroughCasesInSwitch": true,
+    "target": "es2020",
+    "esModuleInterop": true
+  },
+  "angularCompilerOptions": {
+    "strictInjectionParameters": true,
+    "strictInputAccessModifiers": true,
+    "strictTemplates": true
+  }
+}

libs/agora/genes/tsconfig.lib.json

@@ -0,0 +1,12 @@
+{
+  "extends": "./tsconfig.json",
+  "compilerOptions": {
+    "outDir": "../../../dist/out-tsc",
+    "declaration": true,
+    "declarationMap": true,
+    "inlineSources": true,
+    "types": []
+  },
+  "exclude": ["src/test-setup.ts", "**/*.spec.ts", "**/*.test.ts", "jest.config.ts"],
+  "include": ["**/*.ts"]
+}