Merge pull request #76 from EBISPOT/29-03-22-release

29 03 22 release

.gitignore

@@ -45,3 +45,7 @@ testem.log
 # System Files
 .DS_Store
 Thumbs.db
+!/src/environments/environment.ts
+
+tailwind.config.js
+src/environments/environment.ts

.gitlab-ci.yml

@@ -1,13 +1,13 @@
-image: docker:latest
+image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/docker:latest
 services:
   - docker:dind
 
 stages:
-  - sandbox-build
+  - sandbox-build-migration
   - prod-build
   - docker-build
   - docker-build-release
-  - deploy-sandbox
+  - deploy-sandbox-migration
   - deploy-production
   - deploy-fallback
 
@@ -17,23 +17,27 @@ variables:
   CI_REGISTRY_IMAGE: ebispot/gwas-curation-ui
   CURATION_UI_SERVICE_NAME: gwas-curation-ui
 
-sandbox-build:
-  image: node:14.15.5
-  stage: sandbox-build
+
+
+
+sandbox-build-migration:
+  image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/node:14.15.5
+  stage: sandbox-build-migration
   script:
     - npm -v
     - node -v
     - rm -rf node_modules
     - npm install
-    - CI=false npm run build -- --base-href=/gwas/depo-curation/ --configuration sandbox
+    - CI=false npm run build -- --base-href=/gwas/depo-curation/ --configuration sandbox-migration
   artifacts:
     paths:
       - dist/gwas-curation-ui/*
   only:
     - develop
 
+
 prod-build:
-  image: node:14.15.5
+  image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/node:14.15.5
   stage: prod-build
   script:
     - npm -v
@@ -47,6 +51,7 @@ prod-build:
   except:
     - tags
     - develop
+    - curation-477-sandbox-migration
 
 docker-build:
   stage: docker-build
@@ -74,23 +79,24 @@ docker-build-release:
   only:
     - tags
 
-deploy-sandbox:
-  image: dtzar/helm-kubectl:2.13.1
-  stage: deploy-sandbox
+
+deploy-sandbox-migration:
+  image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/dtzar/helm-kubectl:2.13.1
+  stage: deploy-sandbox-migration
   script:
     - echo "Deploy to sandbox server"
     - mkdir -p /root/.kube
-    - echo ${SANBOX_KUBECONF} | base64 -d > /root/.kube/config
+    - echo ${PLIVE_KUBECONFIG} | base64 -d > /root/.kube/config
     - helm init --stable-repo-url https://charts.helm.sh/stable
-    - helm delete --purge gwas-curation-ui || true
-    - helm install --name gwas-curation-ui --set k8Namespace=gwas,image.repository=$CI_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA ./k8chart/ --wait
+    - helm delete --purge gwas-curation-ui-dev || true
+    - helm install --name gwas-curation-ui-dev --set k8Namespace=gwas-dev,service.name=gwas-curation-ui-dev,ingress.name=curation-ui-ingress-dev,image.repository=$CI_REGISTRY_IMAGE,image.tag=$CI_COMMIT_SHA ./k8chart/ --wait
   environment:
-    name: sandbox
+    name: sandbox-migration
   only:
     - develop
 
 deploy-fallback:
-  image: dtzar/helm-kubectl:2.13.1
+  image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/dtzar/helm-kubectl:2.13.1
   stage: deploy-fallback
   script:
     - echo "Deploy to Production fallback server"
@@ -105,7 +111,7 @@ deploy-fallback:
     - tags
 
 deploy-production:
-  image: dtzar/helm-kubectl:2.13.1
+  image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/dtzar/helm-kubectl:2.13.1
   stage: deploy-production
   script:
     - echo "Deploy to Production server"

angular.json

@@ -83,6 +83,32 @@
                   "maximumError": "10kb"
                 }
               ]
+            },"sandbox-migration": {
+              "fileReplacements": [
+                {
+                  "replace": "src/environments/environment.ts",
+                  "with": "src/environments/environment.sandbox-migration.ts"
+                }
+              ],
+              "optimization": true,
+              "outputHashing": "all",
+              "sourceMap": false,
+              "namedChunks": false,
+              "extractLicenses": true,
+              "vendorChunk": false,
+              "buildOptimizer": true,
+              "budgets": [
+                {
+                  "type": "initial",
+                  "maximumWarning": "2mb",
+                  "maximumError": "5mb"
+                },
+                {
+                  "type": "anyComponentStyle",
+                  "maximumWarning": "6kb",
+                  "maximumError": "10kb"
+                }
+              ]
             },
             "local-sandbox": {
               "fileReplacements": [

k8chart/templates/gwas-curation-ui-ingress.yaml

@@ -1,8 +1,8 @@
 apiVersion: extensions/v1beta1
 kind: Ingress
 metadata:
-  name: curation-ui-ingress
-  namespace: gwas
+  name: {{.Values.ingress.name}}
+  namespace: {{.Values.k8Namespace}}
   annotations:
     nginx.ingress.kubernetes.io/rewrite-target: /gwas/depo-curation/$2
     nginx.ingress.kubernetes.io/ssl-redirect: "false"

k8chart/values.yaml

@@ -20,6 +20,7 @@ service:
   port: 80
 
 ingress:
+  name: curation-ui-ingress
   enabled: false
   annotations: {}
     # kubernetes.io/ingress.class: nginx

src/app/app-routing.module.ts

@@ -6,6 +6,14 @@ const routes: Routes = [
     path: 'submissions',
     loadChildren: () => import('./feature/submission/submission.module').then(m => m.SubmissionModule)
   },
+  {
+    path: 'reported-traits',
+    loadChildren: () => import('./feature/reported-trait/reported-trait.module').then(m => m.ReportedTraitModule)
+  },
+  {
+    path: 'efo-traits',
+    loadChildren: () => import('./feature/efo-trait/efo-trait.module').then(m => m.EfoTraitModule)
+  },
   {
     path: 'login',
     loadChildren: () => import('./feature/authentication/authentication.module').then(m => m.AuthenticationModule)

src/app/app.component.html

@@ -1,7 +1,7 @@
 <div style="min-height: 70vh">
-  <app-header></app-header>
+  <app-header *ngIf="routePath !== 'login'"></app-header>
   <div>
     <router-outlet></router-outlet>
   </div>
 </div>
-<app-footer></app-footer>
+<!--<app-footer></app-footer>-->

src/app/app.component.ts

@@ -1,9 +1,19 @@
 import { Component } from '@angular/core';
+import {ActivationEnd, Router} from "@angular/router";
 
 @Component({
   selector: 'app-root',
   templateUrl: 'app.component.html',
   styleUrls: ['app.component.css']
 })
 export class AppComponent {
+
+  routePath: string;
+  constructor(private router: Router) {
+    router.events.subscribe((val) => {
+      if (val instanceof ActivationEnd) {
+        this.routePath = val.snapshot.routeConfig.path;
+      }
+    });
+  }
 }

src/app/core/components/header/header.component.html

@@ -1,6 +1,6 @@
 <nav class="bg-gray-800 mat-elevation-z9 sticky w-full" style="z-index: 200; top: -1px">
   <div class="max-w-7xl mx-auto px-2 sm:px-4 lg:px-6">
-    <div class="relative flex items-center justify-between h-16">
+    <div class="relative flex items-center justify-between" style="height: 3.3rem;">
       <div class="absolute inset-y-0 left-0 flex items-center sm:hidden">
         <!-- Mobile menu button-->
         <button (click)="showMenu()" mat-icon-button type="button" class="rounded-md text-gray-400 hover:text-white hover:bg-gray-700">
@@ -16,6 +16,8 @@
         <div class="hidden sm:block sm:ml-6">
           <div class="flex flex-wrap space-x-4">
             <a routerLink="submissions" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">Submissions</a>
+            <a routerLink="reported-traits" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">Reported traits</a>
+            <a routerLink="efo-traits" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white px-2 py-2 rounded-md text-sm font-medium">EFO traits</a>
           </div>
         </div>
       </div>
@@ -40,9 +42,12 @@
   <div class="sm:hidden" id="mobile-menu" *ngIf="menuOpen">
     <div class="px-2 pt-2 pb-3 space-y-1">
       <a routerLink="submissions" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white block px-3 py-2 rounded-md text-base font-medium">Submissions</a>
+      <a routerLink="reported-traits" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white block px-3 py-2 rounded-md text-base font-medium">Reported traits</a>
+      <a routerLink="efo-traits" mat-button class="text-gray-300 hover:bg-gray-700 hover:text-white block px-3 py-2 rounded-md text-base font-medium">EFO traits</a>
     </div>
   </div>
 </nav>
-<mat-toolbar color="accent" class="mb-3">
-  {{pathName}}
-</mat-toolbar>
+
+<!--<mat-toolbar color="primary" class="mb-3">-->
+<!--  {{pathName}}-->
+<!--</mat-toolbar>-->

src/app/core/models/efoTrait.ts

@@ -0,0 +1,10 @@
+import { Provenance } from './provenance';
+
+export interface EfoTrait {
+  efoTraitId: string;
+  trait: string;
+  shortForm: string;
+  uri: string;
+  created: Provenance;
+  edited: Provenance;
+}

src/app/core/models/reportedTrait.ts

@@ -0,0 +1,7 @@
+import { Provenance } from './provenance';
+
+export interface ReportedTrait {
+  diseaseTraitId: string;
+  trait: string;
+  created: Provenance;
+}

src/app/core/models/rest/api-responses/efoTraitsListApiResponse.ts

@@ -0,0 +1,9 @@
+import { EfoTrait } from '../../efoTrait';
+import { ApiResponse } from './apiResponse';
+
+export interface EfoTraitsListApiResponse extends ApiResponse {
+
+  _embedded: {
+    efoTraits: EfoTrait[];
+  };
+}

src/app/core/models/rest/api-responses/reportedTraitsListApiResponse.ts

@@ -0,0 +1,8 @@
+import { ApiResponse } from './apiResponse';
+import { ReportedTrait } from '../../reportedTrait';
+
+export interface ReportedTraitsListApiResponse extends ApiResponse {
+  _embedded: {
+    diseaseTraits: ReportedTrait[];
+  };
+}

src/app/core/api-responses/submissionListApiResponse.ts → src/app/core/models/rest/api-responses/submissionListApiResponse.ts

@@ -1,5 +1,5 @@
-import { ApiResponse } from '../models/apiResponse';
-import { Submission } from '../models/submission';
+import { ApiResponse } from './apiResponse';
+import { Submission } from '../../submission';
 
 export interface SubmissionListApiResponse extends ApiResponse {
   _embedded: {

src/app/core/models/rest/api-responses/traitUploadApiResponse.ts

@@ -0,0 +1,6 @@
+// TODO delete
+export interface TraitUploadApiResponse {
+  trait: string;
+  uploadComment: string;
+  links: string[];
+}

src/app/core/models/study.ts

@@ -0,0 +1,33 @@
+import { ReportedTrait } from './reportedTrait';
+import { EfoTrait } from './efoTrait';
+
+export interface Study {
+  studyId: string;
+  study_tag: string;
+  study_accession: string;
+  genotyping_technology: string;
+  array_manufacturer: string;
+  array_information: string;
+  imputation: boolean;
+  variant_count: number;
+  sample_description: string;
+  statistical_model: string;
+  study_description: string;
+  trait: string;
+  efo_trait: string;
+  background_trait: string;
+  background_efo_trait: string;
+  checksum: string;
+  summary_statistics_file: string;
+  raw_sumstats_file: string;
+  summary_statistics_assembly: string;
+  readme_file: string;
+  cohort: string;
+  cohort_id: string;
+  // associations: Association[];
+  // samples: Sample[];
+  // notes: Note[];
+  agreedToCc0: boolean;
+  diseaseTrait: ReportedTrait;
+  efoTraits: EfoTrait[];
+}

src/app/core/services/curation-http.service.ts

@@ -13,7 +13,7 @@ export class CurationHttpService {
   }
 
   private static formatErrors(error: any) {
-    return throwError(error.error);
+    return throwError(error);
   }
 
   get(path: string, params: HttpParams = new HttpParams()): Observable<any> {
@@ -24,15 +24,15 @@ export class CurationHttpService {
   put(path: string, body: any = {}, params: HttpParams = new HttpParams()): Observable<any> {
     return this.http.put(
       `${environment.CURATION_API_URL}${path}`,
-      JSON.stringify(body),
+      body,
       {params}
     ).pipe(catchError(CurationHttpService.formatErrors));
   }
 
   post(path: string, body: any = {}): Observable<any> {
     return this.http.post(
       `${environment.CURATION_API_URL}${path}`,
-      JSON.stringify(body)
+      body
     ).pipe(catchError(CurationHttpService.formatErrors));
   }
 

src/app/core/services/efo-trait.service.spec.ts

@@ -0,0 +1,16 @@
+import { TestBed } from '@angular/core/testing';
+
+import { EfoTraitService } from './efo-trait.service';
+
+describe('EfoTraitService', () => {
+  let service: EfoTraitService;
+
+  beforeEach(() => {
+    TestBed.configureTestingModule({});
+    service = TestBed.inject(EfoTraitService);
+  });
+
+  it('should be created', () => {
+    expect(service).toBeTruthy();
+  });
+});