Merge pull request #192 from OmicsDI/dev

Dev

Author: glmanhtu

angular-cli.json

@@ -10,7 +10,7 @@
       "assets": [
         "css","img","static","intl",
         "assets", ".well-known",
-        "favicon.ico"
+        "favicon.ico","test"
       ],
       "index": "index.html",
       "main": "main.ts",

karma.conf.js

@@ -2,43 +2,36 @@
 // https://karma-runner.github.io/0.13/config/configuration-file.html
 
 module.exports = function (config) {
-  config.set({
-    basePath: '',
-    frameworks: ['jasmine', '@angular/cli'],
-    plugins: [
-      require('karma-jasmine'),
-      require('karma-chrome-launcher'),
-      require('karma-jasmine-html-reporter'),
-      require('karma-coverage-istanbul-reporter'),
-      require('@angular/cli/plugins/karma')
-    ],
-    client:{
-      clearContext: false // leave Jasmine Spec Runner output visible in browser
-    },
-    files: [
-      { pattern: './src/test.ts', watched: false }
-    ],
-    preprocessors: {
-      './src/test.ts': ['@angular/cli']
-    },
-    mime: {
-      'text/x-typescript': ['ts','tsx']
-    },
-    coverageIstanbulReporter: {
-      reports: [ 'html', 'lcovonly' ],
-      fixWebpackSourcePaths: true
-    },
-    angularCli: {
-      environment: 'dev'
-    },
-    reporters: config.angularCli && config.angularCli.codeCoverage
-      ? ['progress', 'coverage-istanbul']
-      : ['progress', 'kjhtml'],
-    port: 9876,
-    colors: true,
-    logLevel: config.LOG_INFO,
-    autoWatch: true,
-    browsers: ['ChromeHeadless'],
-    singleRun: false
-  });
+    config.set({
+        basePath: '',
+        // browserNoActivityTimeout: 4000000,
+        frameworks: ['jasmine', '@angular/cli'],
+        plugins: [
+            require('karma-jasmine'),
+            require('karma-chrome-launcher'),
+            require('karma-jasmine-html-reporter'),
+            require('karma-coverage-istanbul-reporter'),
+            require('@angular/cli/plugins/karma')
+        ],
+        client:{
+            clearContext: false // leave Jasmine Spec Runner output visible in browser
+        },
+        coverageIstanbulReporter: {
+            reports: [ 'html', 'lcovonly' ],
+            fixWebpackSourcePaths: true
+        },
+        angularCli: {
+            environment: 'dev'
+        },
+        preprocessors: {
+            './src/test.ts': ['@angular/cli']
+        },
+        reporters: ['progress', 'kjhtml'],
+        port: 9876,
+        colors: true,
+        logLevel: config.LOG_INFO,
+        autoWatch: true,
+        browsers: ['ChromeHeadless'],
+        singleRun: false
+    });
 };

package.json

@@ -9,7 +9,8 @@
     "test": "ng test",
     "pree2e": "webdriver-manager update --standalone false --gecko false",
     "e2e": "ng e2e --no-webdriver-update --port=4200",
-    "build": "ng build"
+    "build": "ng build",
+    "release": "ng build --prod"
   },
   "private": true,
   "dependencies": {

pom.xml

@@ -73,18 +73,18 @@
               <goal>install-node-and-npm</goal>
             </goals>
             <configuration>
-              <nodeVersion>v6.10.0</nodeVersion>
-              <npmVersion>3.10.10</npmVersion>
+              <nodeVersion>v10.6.0</nodeVersion>
+              <npmVersion>6.1.0</npmVersion>
             </configuration>
           </execution>
           <execution>
-            <id>npm run build</id>
+            <id>npm run release</id>
             <goals>
               <goal>npm</goal>
             </goals>
             <phase>generate-resources</phase>
             <configuration>
-              <arguments>run build -- --environment=${angular.environment} --base-href=${angular.base.href}</arguments>
+              <arguments>run release -- --environment=${angular.environment} --base-href=${angular.base.href}</arguments>
             </configuration>
           </execution>
         </executions>

src/app/model/DataSetDetail.ts

@@ -2,6 +2,7 @@ import {Protocol} from './Protocol';
 import {Organism} from './Organism';
 import {Dates} from './Dates';
 import {SimilarDataset} from './SimilarDataset';
+import {DataSet} from 'model/DataSet';
 
 /**
  * Created by user on 3/25/2017.
@@ -35,6 +36,35 @@ export class DataSetDetail {
     related_omics = 'related_omics';
     secondary_accession: string[];
     repositories: string[];
+    score = 0;
+    visitCount = 0;
+    claimable = false;
+    citationsCount = 0;
+    connectionsCount = 0;
+    reanalysisCount = 0;
+    viewsCount = 0;
+
+    public static toDataset(datasetDetails: DataSetDetail): DataSet {
+        const dataset = new DataSet();
+        dataset.id = datasetDetails.id;
+        dataset.source = datasetDetails.source;
+        dataset.title = datasetDetails.name;
+        dataset.description = datasetDetails.description;
+        dataset.keywords = datasetDetails.keywords;
+        dataset.organisms = datasetDetails.organisms;
+        dataset.tissues = datasetDetails.tissues;
+        dataset.diseases = datasetDetails.diseases;
+        dataset.omicsType = datasetDetails.omics_type;
+        dataset.publicationDate = datasetDetails.publicationDate;
+        dataset.score = datasetDetails.score;
+        dataset.visitCount = datasetDetails.visitCount;
+        dataset.claimable = datasetDetails.claimable;
+        dataset.citationsCount = datasetDetails.citationsCount;
+        dataset.connectionsCount = datasetDetails.connectionsCount;
+        dataset.reanalysisCount = datasetDetails.reanalysisCount;
+        dataset.viewsCount = datasetDetails.viewsCount;
+        return dataset;
+    }
 
     constructor() {
         this.omics_type = [];
@@ -47,7 +77,6 @@ export class DataSetDetail {
         return (this.omics_type.indexOf(omics) !== -1);
     }
 
-
 }
 
 

src/app/modules/commonplace/components/unauthorized/unauthorized.component.ts

@@ -8,17 +8,21 @@ import {Router} from '@angular/router';
 })
 export class UnauthorizedComponent implements OnInit {
 
-    returnTime: number;
+    returnTime = 3;
     constructor(private router: Router) {
     }
 
     ngOnInit() {
-        this.returnTime = 3;
-        const interval = setInterval( () => {
-            this.returnTime = this.returnTime - 1;
-            if ( this.returnTime < 0) {
-                this.router.navigate(['home']);
-            }
+        this.sleep(this.returnTime);
+    }
+
+    private sleep(second: number) {
+        if (second === 0) {
+            this.router.navigate(['home']);
+        }
+        setTimeout(() => {
+            this.returnTime -= 1;
+            this.sleep(this.returnTime);
         }, 1000);
     }
 }

src/app/modules/dashboard/components/selected/selected.component.html

@@ -59,7 +59,7 @@
                 class="repeated-item ng-scope"
                 style="min-width:400px;">
 
-                <app-datasetwidget [d]="d" (buttonClicked)="this.remove(d.source,d.id)"
+                <app-datasetwidget [d]="toDataset(d)" (buttonClicked)="this.remove(d.source,d.id)"
                                                    [allowSelect]="false"></app-datasetwidget>
 
 

src/app/modules/dashboard/components/selected/selected.component.ts

@@ -18,8 +18,8 @@ import {DialogService} from '@shared/services/dialog.service';
 export class DashboardSelectedComponent implements OnInit {
 
     dataSets: DataSetDetail[];
-
     p: 0;
+    toDataset = DataSetDetail.toDataset;
 
     constructor(public selectedService: SelectedService
         , private dataSetService: DataSetService

src/app/modules/database/components/database/database.component.ts

@@ -64,6 +64,10 @@ export class DatabaseComponent implements OnInit {
         console.log(this.domainStats);
         for (const d of this.domainStats) {
 
+            if (domain === 'Omics-ENA' && d.domain.name === 'ENA' ) {
+                return d.domain.value;
+            }
+
             if (d.domain.name === domain) {
                 return d.domain.value;
             }

src/app/modules/dataset/components/dataset/dataset.component.html

@@ -39,7 +39,7 @@ <h3>Dataset Information</h3>
                     <div>
                         <h4>
                             <app-annotated-text [text]="d.name"
-                                                        [sections]="title_sections"></app-annotated-text>
+                                                        [sections]="title_sections" ></app-annotated-text>
                         </h4>
                         <p id="ontology_highlight_box" (click)="enrich_click()" class="hotword" style="">
                             <i class="fa fa-pencil-square-o" aria-hidden="true">Ontology highlight</i>
@@ -50,7 +50,7 @@ <h4>
                         <div>
                             <p class="align-justify"><b>ABSTRACT</b>:
                                 <app-annotated-text [text]="d.description"
-                                                            [sections]="abstract_sections"></app-annotated-text>
+                                                            [sections]="abstract_sections" id="abstract"></app-annotated-text>
                             </p>
                         </div>
                     </div>
@@ -69,25 +69,25 @@ <h4>
                         <!--</span>-->
                     <!--</p>-->
                     <div *ngIf="d.similars">
-                        <p class="align-justify" *ngIf="reanalysis_of(d)">
+                        <p class="align-justify" *ngIf="reanalysis_of(d)" id="reanalisys_of">
                             <b>REANALYSIS of:</b> <span *ngFor="let s of reanalysis_of(d)"><a
                                 [routerLink]="['/dataset',getSourceByDatabaseName(s.database),s.accession]">{{s.accession}}</a></span>
                             <span *ngIf="reanalysisoverflow(d)">(first 100 items shown)</span>
                         </p>
-                        <p class="align-justify" *ngIf="null!=reanalised_by(d)">
+                        <p class="align-justify" *ngIf="null!=reanalised_by(d)" id="reanalisys_by">
                             <b>REANALYZED by:</b> <span href="#" *ngFor="let s of reanalised_by(d)"><a
                                 [routerLink]="['/dataset',getSourceByDatabaseName(s.database),s.accession]">{{s.accession}}</a> </span>
                             <span *ngIf="reanalysisoverflow(d)">(first 100 items shown)</span>
                         </p>
-                        <p class="align-justify" *ngIf="null!=related_omics(d)">
+                        <p class="align-justify" *ngIf="null!=related_omics(d)" id="relate_omics">
                             <b>OTHER RELATED OMICS DATASETS IN:</b> <span href="#" *ngFor="let s of related_omics(d)"><a
                                 [routerLink]="['/dataset',getSourceByDatabaseName(s.database),s.accession]">{{s.accession}}</a> </span>
                         </p>
                     </div>
-                    <p class="align-justify" *ngIf="null!=d.instruments">
+                    <p class="align-justify" *ngIf="null!=d.instruments" id="instruments">
                         <b>INSTRUMENT(S):</b>{{d.instruments}}
                     </p>
-                    <p class="align-justify" *ngIf="null!=d.organisms">
+                    <p class="align-justify" *ngIf="null!=d.organisms"  id="organisms">
                         <b>ORGANISM(S):</b>
                         <span *ngFor="let o of d.organisms">
                 <a class="biological" [routerLink]="['/search']"
@@ -96,14 +96,14 @@ <h4>
                 </a>&nbsp;
               </span>
                     </p>
-                    <p class="align-justify ng-hide" *ngIf="null!=d.tissues"><b>TISSUE(S):</b>
+                    <p class="align-justify ng-hide" *ngIf="null!=d.tissues" id="tissues"><b>TISSUE(S):</b>
                         {{d.tissues}}
                     </p>
-                    <p class="align-justify ng-hide" *ngIf="null!=d.diseases && d.diseases.length > 0">
+                    <p class="align-justify ng-hide" *ngIf="null!=d.diseases && d.diseases.length > 0"  id="diseases">
                         <b>DISEASE(S):</b>
                         {{d.diseases}}
                     </p>
-                    <p class="align-justify" *ngIf="null!=d.submitter">
+                    <p class="align-justify" *ngIf="null!=d.submitter"  id="submitter">
                         <b>SUBMITTER:</b>
                         <span *ngFor="let o of d.submitter; let i = index;">
                 <span *ngIf="d.submitterMail && d.submitterMail[i]">
@@ -124,13 +124,13 @@ <h4>
                     </p>
                     <p class="align-justify">
                         <b>PROVIDER:</b>
-                        <a [href]="d.full_dataset_link">{{d.id}}</a> |
+                        <a [href]="d.full_dataset_link" id="id">{{d.id}}</a> |
                         <a [href]="this.getDatabaseUrl(d.source)"> <span class="ng-binding">{{this.getDatabaseTitle(d.source)}}</span>
                         </a>
-                        <span>| {{d.publicationDate}} </span>
+                        <span id="publicationDate">| {{d.publicationDate}} </span>
                     </p>
 
-                    <p class="align-justify" *ngIf="d.secondary_accession">
+                    <p class="align-justify" *ngIf="d.secondary_accession"  id="secondary_accession">
                         <b>SECONDARY ACCESSION(S):</b>&nbsp;
 
                         <span *ngFor="let o of d.secondary_accession;">