Remove components that irrelevant to GSoC

package.json

@@ -20,11 +20,11 @@
     "@ng-bootstrap/ng-bootstrap": "1.0.0",
     "@ng-select/ng-select": "^1.4.1",
     "@swimlane/ngx-datatable": "^11.3.2",
+    "core-js": "2.4.1",
     "angular": "^1.7.8",
     "@sentry/browser": "^4.6.5",
     "angular-datatables": "^5.0.0",
     "bootstrap": "^4.3.1",
-    "core-js": "2.4.1",
     "datatables.net": "^1.10.16",
     "datatables.net-dt": "^1.10.16",
     "file-saver": "^1.3.8",

src/main/webapp/app/app.module.ts

@@ -42,7 +42,6 @@ import {
     PageRibbonComponent,
     ErrorComponent
 } from './layouts';
-import { EmailService } from './service/email.service';
 import { ConverterComponent } from './converter/converter.component';
 import { ConnectionService } from './service/connection.service';
 import { DrugComponent } from './drug/drug.component';
@@ -108,7 +107,6 @@ export class SentryErrorHandler implements ErrorHandler {
         UserRouteAccessService,
         TrialService,
         ConnectionService,
-        EmailService,
         MetaService,
         UserRouteAccessService,
         {

src/main/webapp/app/genomic/genomic.component.ts

@@ -92,19 +92,7 @@ export class GenomicComponent implements OnInit {
         });
     }
     validateGenomicExample() {
-        if (this.genomicInput.hugo_symbol && this.genomicInput.annotated_variant && this.genomicInput.matching_examples) {
-            const variantsTobeValidated = 'hugoSymbol=' + this.genomicInput.hugo_symbol + '&variant=' +
-                this.genomicInput.annotated_variant + '&examples=' + this.genomicInput.matching_examples;
-            this.connectionService.validateGenomicExample(variantsTobeValidated).subscribe((result) => {
-                if (result[this.genomicInput.matching_examples] === true) {
-                    this.validationMessage['example'] = 'Valid';
-                    this.exampleValidation = true;
-                } else {
-                    this.validationMessage['example'] = 'Invalid';
-                    this.exampleValidation = false;
-                }
-            });
-        }
+        // TODO: generate new logics to validate genomic variant format
     }
     getMessageStyle(type) {
         const result = (type === 'gene' ? this.geneValidation : this.exampleValidation);

src/main/webapp/app/layouts/footer/footer.component.html

@@ -3,18 +3,17 @@
         <div class="row footer-row-2">
             <div class="col-md-4 col-lg-4 col-sm-12 col-xs-12">
                 <div class="">
-                    <a href="mailto:team@oncokb.org" target="_top">Contact us</a>
                     <a href="https://twitter.com/OncoKB" target="_blank">Twitter</a>
                     <a href="swagger-ui/index.html">API</a>
                 </div>
             </div>
             <div class="col-md-4 col-lg-4 col-sm-12 col-xs-12 mskcc-footer-logo0-wrapper">
-                <a class="logo" href="http://mskcc.org" title="Memorial Sloan Kettering Cancer Center">
+                <a class="logo" href="https://www.mskcc.org" title="Memorial Sloan Kettering Cancer Center">
                     <span><img src="../../../content/images/MSKLogo_fff.png" class="mskcc-footer-logo"></span>
                 </a>
             </div>
             <div class="col-md-4 col-lg-4 col-sm-12 col-xs-12 mskcc">
-                <span>© 2018 Memorial Sloan Kettering Cancer Center</span>
+                <span>© 2023 Memorial Sloan Kettering Cancer Center</span>
             </div>
         </div>
     </div>

src/main/webapp/app/layouts/navbar/navbar.component.html

@@ -10,12 +10,6 @@
             <li class="nav-item">
                 <a class="nav-link" routerLink="trials" routerLinkActive="active">Trials</a>
             </li>
-            <li class="nav-item" *ngIf="!oncokb">
-                <a class="nav-link" routerLink="data" routerLinkActive="active">Data</a>
-            </li>
-            <li class="nav-item" *ngIf="oncokb">
-                <a class="nav-link" routerLink="meta" routerLinkActive="active">Meta</a>
-            </li>
         </ul>
     </div>
     <div class="navbar-collapse collapse" id="navbarResponsive" [ngbCollapse]="isNavbarCollapsed" [ngSwitch]="isAuthenticated()">

src/main/webapp/app/service/connection.service.ts

@@ -19,33 +19,21 @@ export class ConnectionService {
                     return 'http://oncotree.mskcc.org/api/mainTypes?version=' + MainUtil.oncotreeVersion;
                 case 'SubType':
                     return 'http://oncotree.mskcc.org/api/tumorTypes/search';
-                case 'OncoKBVariant':
-                    return 'http://oncokb.org/api/v1/variants';
                 case 'GeneValidation':
                     return 'http://mygene.info/v3/query?species=human&q=symbol:';
                 case 'ClinicalTrials':
                     return 'https://clinicaltrialsapi.cancer.gov/v1/clinical-trial/';
-                case 'MskTrials':
-                    return 'https://discover.mskcc.org:443/api/trials/';
-                case 'ExampleValidation':
-                    return 'http://oncokb.org/api/v1/utils/match/variant?';
             }
         } else {
             switch (type) {
                 case 'MainType':
                     return SERVER_API_URL + 'proxy/http/oncotree.mskcc.org/api/mainTypes?version=' + MainUtil.oncotreeVersion;
                 case 'SubType':
                     return SERVER_API_URL + 'proxy/http/oncotree.mskcc.org/api/tumorTypes/search';
-                case 'OncoKBVariant':
-                    return SERVER_API_URL + 'proxy/http/oncokb.org/api/v1/variants';
                 case 'GeneValidation':
                     return SERVER_API_URL + 'proxy/http/mygene.info/v3/query?species=human&q=symbol:';
                 case 'ClinicalTrials':
                     return SERVER_API_URL + 'proxy/https/clinicaltrialsapi.cancer.gov/v1/clinical-trial/';
-                case 'MskTrials':
-                    return SERVER_API_URL + 'proxy/https/discover.mskcc.org:443/api/trials/';
-                case 'ExampleValidation':
-                    return SERVER_API_URL + 'proxy/http/oncokb.org/api/v1/utils/match/variant?';
             }
         }
     }
@@ -54,18 +42,10 @@ export class ConnectionService {
         return this.http.get(this.getAPIUrl('GeneValidation') + hugoSymbol);
     }
 
-    validateGenomicExample(variantsTobeValidated: string) {
-        return this.http.get(this.getAPIUrl('ExampleValidation') + variantsTobeValidated);
-    }
-
     importTrials(tempTrial: string) {
         return this.http.get(this.getAPIUrl('ClinicalTrials') + tempTrial);
     }
 
-    getTrialByProtocolNo(protocolNo: string) {
-        return this.http.get(this.getAPIUrl('MskTrials') + protocolNo);
-    }
-
     getMainType() {
         return this.http.get(this.getAPIUrl('MainType'));
     }
@@ -74,10 +54,6 @@ export class ConnectionService {
         return this.http.post(this.getAPIUrl('SubType'), query);
     }
 
-    getOncoKBVariant(): Observable<Array<any>> {
-        return this.http.get<Array<any>>(this.getAPIUrl('OncoKBVariant'));
-    }
-
     getDrugs(query: string) {
         return this.http.get(this.getAPIUrl('Drugs') + `?name=${query}`);
     }

src/main/webapp/app/service/trial.service.ts

@@ -6,7 +6,6 @@ import { Clinical } from '../clinical/clinical.model';
 import { MovingPath } from '../panel/movingPath.model';
 import { Arm } from '../arm/arm.model';
 import * as _ from 'lodash';
-import { EmailService } from './email.service';
 import { ConnectionService } from './connection.service';
 import { HttpErrorResponse } from '@angular/common/http';
 import { of } from 'rxjs/observable/of';
@@ -83,7 +82,7 @@ export class TrialService {
     nctIdChosen = '';
     errorList: Array<object> = [];
 
-    constructor(public connectionService: ConnectionService, public db: AngularFireDatabase, private emailService: EmailService) {
+    constructor(public connectionService: ConnectionService, public db: AngularFireDatabase) {
         this.nctIdChosenObs.subscribe((message) => this.nctIdChosen = message);
         this.trialsRef = db.object('Trials');
         this.additionalRef = db.object('Additional');
@@ -129,22 +128,6 @@ export class TrialService {
         }, (error: HttpErrorResponse) => {
             this.getErrorResponse(error, 'main type');
         });
-        // prepare oncokb variant list
-        this.connectionService.getOncoKBVariant().subscribe((res) => {
-           const allAnnotatedVariants = res;
-           for (const item of  allAnnotatedVariants) {
-                if (item['gene']['hugoSymbol']) {
-                    if (this.annotated_variants[item['gene']['hugoSymbol']]) {
-                        this.annotated_variants[item['gene']['hugoSymbol']].push(item['alteration']);
-                    } else {
-                        this.annotated_variants[item['gene']['hugoSymbol']] = [item['alteration']];
-                    }
-                }
-           }
-           for (const key of _.keys(this.annotated_variants)) {
-                this.annotated_variants[key].sort();
-           }
-        });
     }
     fetchTrials() {
         this.trialsRef.snapshotChanges().subscribe((action) => {
@@ -274,19 +257,11 @@ export class TrialService {
         });
     }
     saveErrors(info: string, content: object, error: object) {
-        if (info.includes('failed') && info.includes('database')) {
-            this.emailService.sendEmail({
-                sendTo: MainUtil.devEmail,
-                subject: info,
-                content: 'Content: \n' + JSON.stringify(content) + '\n\n Error: \n' + JSON.stringify(error)
-            });
-        } else {
-            this.errorList.push({
-                'info': info,
-                'content': content,
-                'error': error
-            });
-        }
+        this.errorList.push({
+            'info': info,
+            'content': content,
+            'error': error
+        });
     }
     getNodeDisplayContent(key: string, node: object) {
         let result = '';
@@ -306,11 +281,6 @@ export class TrialService {
         } else if (error.status === 503) {
             alert('Sorry, required data source is unavailable now.');
         } else {
-            this.emailService.sendEmail({
-                sendTo: MainUtil.devEmail,
-                subject: 'Matchminer Curate http request failed.',
-                content: 'Error: \n' + JSON.stringify(error)
-            });
             alert('Sorry, unexpected error happens. Our development team has been notified.');
         }
     }

src/main/webapp/app/trial/trial.component.html

@@ -1,6 +1,6 @@
 <div class="container trial-container">
     <div class="input-group">
-        <input type="text" class="form-control" [(ngModel)]="trialsToImport" placeholder="Enter trial in the format: NCT02057133 or 14-085"
+        <input type="text" class="form-control" [(ngModel)]="trialsToImport" placeholder="Enter trial in the format: NCT02057133"
             size="100">
         <span class="input-group-btn">
             <button class="btn btn-primary" [disabled]="!trialsToImport" (click)="importTrials()">Import New Trials</button>

src/main/webapp/app/trial/trial.component.ts

@@ -128,27 +128,6 @@ export class TrialComponent implements OnInit, AfterViewInit {
                     }
                 }
                 this.importTrialsFromNct(nctId);
-            } else if ( tempTrial.match( /^\d+-\d+$/g ) && this.oncokb) {
-                this.connectionService.getTrialByProtocolNo( tempTrial ).subscribe( ( res ) => {
-                    nctId = res['tds_data']['nct_id'];
-                    if ( this.trialListIds.includes( nctId ) ) {
-                        if (!this.isRedownloadTrial(tempTrial + '/' + nctId)) {
-                            return;
-                        }
-                    }
-                    const mskInfo = {
-                        protocol_no: res['msk_id'],
-                        principal_investigator: {
-                            full_name: res['tds_data']['primary_investigator']['full_name'],
-                            credentials: res['tds_data']['primary_investigator']['credentials'],
-                            email: res['tds_data']['primary_investigator']['email'],
-                            url: res['tds_data']['primary_investigator']['msk_url']
-                        }
-                    };
-                    this.importTrialsFromNct(nctId, mskInfo);
-                }, ( error ) => {
-                    this.messages.push( tempTrial + ' not found' );
-                });
             } else {
                 this.messages.push( tempTrial + ' is invalid trial format' );
                 continue;