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Commit 231e8b6e authored by jcorvi's avatar jcorvi
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Merge branch 'develop' into 'master' 

"Merge branch 'draft_version' into 'develop'"

See merge request !15
parents c2ba3bf0 b0c4d3f4
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src/app/app-routing.module.ts
View file @ 231e8b6e
......@@ -20,7 +20,7 @@ const routes: Routes = [
{ path: 'find/:id', component: DocumentDetailComponent,
children: [
{ path: '', redirectTo: 'third', pathMatch: 'full' },
{ path: '', redirectTo: 'first', pathMatch: 'full' },
{ path: 'first', component: PretoxsentencesTabulatorComponent },
{ path: 'second',component: FindingTabulatorComponent },
{ path: 'third',component: SrdomaintemplateTabulatorComponent },
......
src/app/app.module.ts
View file @ 231e8b6e
......@@ -24,6 +24,10 @@ import {BrowserAnimationsModule} from '@angular/platform-browser/animations';
import { SrdomainLevelComponent } from './srdomain-level/srdomain-level.component';
import { LogoutComponent } from './logout/logout.component';
import { HistoryTrackingComponent } from './history-tracking/history-tracking.component';
import {MatProgressSpinnerModule, MatProgressBarModule} from '@angular/material'
@NgModule({
declarations: [
AppComponent,
......@@ -50,7 +54,10 @@ import { HistoryTrackingComponent } from './history-tracking/history-tracking.co
HttpModule,
MatTabsModule,
BrowserAnimationsModule,
MatToolbarModule
MatToolbarModule,
MatProgressSpinnerModule,
MatProgressBarModule
],
providers: [LoginService, CookieService, {
provide: HTTP_INTERCEPTORS,
......
src/app/document-detail/document-detail.component.css
View file @ 231e8b6e
.loader{
position: absolute;
top:0px;
right:0px;
width:100%;
height:100%;
background-color:#eceaea;
background-image:url('loader.gif');
background-size: 100px;
background-repeat:no-repeat;
background-position:center;
z-index:10000000;
opacity: 0.4;
filter: alpha(opacity=40);
}
.FixedHeightContainer
{
}
.brat_div
{
overflow:auto;
}
\ No newline at end of file
src/app/document-detail/document-detail.component.html
View file @ 231e8b6e
......@@ -56,11 +56,10 @@
</div>
</div>
<div id="data2" class="w3-container">
<div id="data1" data-ng-init="clear()">
</div>
</div>
<div id="commentpopup"></div>
<!-- <mat-spinner></mat-spinner>
<div id="loadingDiv8" class="loader"></div> -->
<!-- <nav class="navbar navbar-light bg-light">
......@@ -89,14 +88,17 @@
<a href="#data2" style="text-decoration:none;cursor: pointer;" data-toggle="collapse">
<i class="fa fa-angle-down" style="color:black;padding: 10px 30px; font-size: 3rem;" title="Minimize Evidence"></i>
</a>
<a (click)="clear()" style="text-decoration:none;cursor: pointer;">
<!-- <a (click)="clear()" style="text-decoration:none;cursor: pointer;">
<i class="fa fa-eraser" style="color:black;padding: 10px 30px; font-size: 2rem;" title="Clear Evidence"></i>
</a>
</a> -->
<!-- <a title="Export Findings" (click)="exportDocument" download="download.json">
<i class="fa fa-file-export" style="color:black;padding: 10px 30px; font-size: 2rem;"></i>
</a> -->
<a (click)="getAllEvidence()" style="text-decoration:none;cursor: pointer;">
<i class="fa fa-eye" style="color:black;padding: 10px 30px; font-size: 2rem;" title="Show All Evidence"> </i>
</a>
<a (click)="findDocumentText()" style="text-decoration:none;cursor: pointer;">
<i class="fa fa-file-text" style="color:black;padding: 10px 30px; font-size: 2rem;" title="Show Plain Text"> </i>
</a>
<a (click)="exportDocument()" style="text-decoration:none;cursor: pointer;">
<i class="fa fa-download" style="color:black;padding: 10px 30px; font-size: 2rem;" title="Export Findings"> </i>
......@@ -104,7 +106,12 @@
<a routerLink="./tracking" style="text-decoration:none;cursor: pointer;">
<i class="fa fa-history" style="color:black;padding: 10px 30px; font-size: 2rem;" title="History changes"> </i>
</a>
<div id="data2">
<div id="loadingDiv"></div>
<div id="data1" data-ng-init="clear()">
</div>
</div>
<div id="commentpopup"></div>
<!-- <a mat-tab-link md-align-tabs="right" style="padding-left: 650px;"
routerLink="./tracking"
routerLinkActive #rla="routerLinkActive"
......@@ -174,6 +181,9 @@
<app-srdomaintemplate-tabulator [tableData]=tableDataSRDomainTemplate (rowClickEventSRDomainTemplateEvidence)="rowClickSRDomainTemplateEvidence($event)" (rowClickExportSRDomainEvent)="setExportSRDomain($event)"></app-srdomaintemplate-tabulator>
</div> -->
</div>
<!-- <div>
<app-pretoxsentences-tabulator [columnNames]=columnNamesPretoxSentences [tableData]=tableDataPretoxSentences (rowClickEventFinding)="rowClick($event)" (rowClickEvent)="rowClickSentence($event)" (rowClickAcceptFindingEvent)="acceptFinding($event)" (rowClickRejectFindingEvent)="rejectFinding($event)" (rowClickExportFindingEvent)="setExportFinding($event)">></app-pretoxsentences-tabulator>
</div> -->
......
src/app/document-detail/document-detail.component.ts
View file @ 231e8b6e
......@@ -8,12 +8,14 @@ import { Finding } from '../finding';
import { Annotation } from '../annotation';
import { environment } from './../../environments/environment';
import {MatToolbarModule} from '@angular/material/toolbar';
import { Router } from '@angular/router';
//brat
declare var head: any;
declare var Util: any;
declare var Visualizer: any;
var displaySpanComment = function (evt, target, spanId, spanType, mods, spanText, commentText, commentType, normalizations) {
var left = evt.clientX + "px";
......@@ -159,36 +161,92 @@ export class DocumentDetailComponent implements OnInit {
this.navLinks = [
{
label: 'Sentence Level',
label: 'Relevant Sentences',
link: './first',
index: 0
}, {
}, /*{
label: 'Findings Level',
link: './second',
index: 1
}, {
label: 'SR-Domain Level',
}, */{
label: 'Findings',
link: './third',
index: 2
index: 1
}
];
this.nextStatus = ['DRAFT', 'IN_PROGRESS', 'FINISHED'];
;
}
loadBratVisualizer():void{
const bratLocation = environment.bratUrl;
//const bratLocation = 'http://10.32.6.2:8001';
head.js(
// External libraries
bratLocation + '/client/lib/jquery.min.js',
bratLocation + '/client/lib/jquery.svg.min.js',
bratLocation + '/client/lib/jquery.svgdom.min.js',
// brat helper modules
bratLocation + '/client/src/configuration.js',
bratLocation + '/client/src/util.js',
bratLocation + '/client/src/annotation_log.js',
bratLocation + '/client/lib/webfont.js',
// brat modules
bratLocation + '/client/src/dispatcher.js',
bratLocation + '/client/src/url_monitor.js',
bratLocation + '/client/src/visualizer.js'
);
}
// ngOnInit() {
// this.getDocument();
// }
loaded(): void {
alert('loaded');
var loading = document.getElementById('loadingDiv');
loading.style.display='none';
}
ngOnInit(): void {
this.router.events.subscribe((res) => {
this.activeLinkIndex = this.navLinks.indexOf(this.navLinks.find(tab => tab.link === '.' + this.router.url));
});
this.getDocument();
//this.getEvidence();
}
getEvidence() {
//alert('getAllEvidence');
const id = +this.route.snapshot.paramMap.get('id');
//this.documentService.getAllEvidence(this.document.documentId)
this.documentService.getEvidence(id)
.subscribe(text => {
this.docData = text;
//console.log(this.docData);
// console.log(JSON.parse(this.docData));
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
//document.getElementById('loadingDiv').className = 'loader';
var j = JSON.parse(this.docData);
//this.loadBratVisualizer();
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
//dispatcher.on('displaySpanComment', displaySpanComment);
//dispatcher.on('hideComment', hideComment);
// setTimeout(() => {
// document.getElementById('loadingDiv').className = '';
// }, 4000);
});
});
}
save(): void {
this.documentService.updateDocument(this.document)
.subscribe(() => this.goBack());
......@@ -201,26 +259,26 @@ export class DocumentDetailComponent implements OnInit {
.subscribe(document => {
this.document = document;
this.setNextStatus(this.document.status);
var data = [];
//var data = [];
var data_relevant_sentences = [];
document.findings.forEach(find => {
data.push({
id : find.findingId,
finding: find.finding != null ? find.finding.value : '',
study_testcd: find.study_testcd != null ? find.study_testcd.value : '',
manifestation_finding: find.manifestation_finding != null ? find.manifestation_finding.value : '',
study_domain: find.study_domain != null ? find.study_domain.value : '',
specimen: find.specimen != null ? find.specimen.value : '',
sex: find.sex != null ? find.sex.value : '',
dose: find.dose != null ? find.dose.value : '',
group: find.group != null ? find.group.value : '',
is_trf: find.is_treatment_related != null ? find.is_treatment_related.value : ''
});
});
// document.findings.forEach(find => {
// data.push({
// id : find.findingId,
// finding: find.finding != null ? find.finding.value : '',
// study_testcd: find.study_testcd != null ? find.study_testcd.value : '',
// manifestation_finding: find.manifestation_finding != null ? find.manifestation_finding.value : '',
// study_domain: find.study_domain != null ? find.study_domain.value : '',
// specimen: find.specimen != null ? find.specimen.value : '',
// sex: find.sex != null ? find.sex.value : '',
// dose: find.dose != null ? find.dose.value : '',
// group: find.group != null ? find.group.value : '',
// is_trf: find.is_treatment_related != null ? find.is_treatment_related.value : ''
// });
// });
//alert(data);
//alert(JSON.stringify(data));
this.tableData = data;
//this.tableData = data;
//this.clear();
//alert(JSON.stringify(document.findings));
//var j = JSON.parse('{ text:' + document.text + '}');
......@@ -338,39 +396,138 @@ export class DocumentDetailComponent implements OnInit {
findingSelected(finding): void {
this.documentService.findingSelected(this.document.documentId, finding)
.subscribe(text => {
this.docData = text;
console.log(this.docData);
var loading = document.getElementById('loadingDiv');
//loading.style.display='block';
loading.addEventListener("load", this.loaded);
this.docData = text;
//console.log(this.docData);
// console.log(JSON.parse(this.docData));
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
//document.getElementById('loadingDiv').className = 'loader';
var j = JSON.parse(this.docData);
//this.loadBratVisualizer();
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
dispatcher.on('displaySpanComment', displaySpanComment);
dispatcher.on('hideComment', hideComment);
//dispatcher.on('displaySpanComment', displaySpanComment);
//dispatcher.on('hideComment', hideComment);
// setTimeout(() => {
// document.getElementById('loadingDiv').className = '';
// }, 4000);
});
});
}
pretoxSentenceSelected(pretoxSentence): void {
this.documentService.pretoxSentenceSelected(this.document.documentId, pretoxSentence)
.subscribe(text => {
this.docData = text;
console.log(this.docData);
//console.log(this.docData);
// console.log(JSON.parse(this.docData));
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
//document.getElementById('loadingDiv').className = 'loader';
var j = JSON.parse(this.docData);
//this.loadBratVisualizer();
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
//dispatcher.post('resetData');
//dispatcher.post('collectionChanged');
//dispatcher.post('triggerRender');
dispatcher.on('displaySpanComment', displaySpanComment);
dispatcher.on('hideComment', hideComment);
// setTimeout(() => {
// document.getElementById('loadingDiv').className = '';
// }, 4000);
});
});
}
findDocumentText(): void {
this.documentService.findDocumentText(this.document.documentId)
.subscribe(text => {
this.docData = text;
//console.log(this.docData);
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
//document.getElementById('loadingDiv').className = 'loader';
var j = JSON.parse(this.docData);
//this.loadBratVisualizer();
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
//dispatcher.on('displaySpanComment', displaySpanComment);
//dispatcher.on('hideComment', hideComment);
// setTimeout(() => {
// document.getElementById('loadingDiv').className = '';
// }, 4000);
});
});
}
getAllEvidence() {
//alert('getAllEvidence');
const id = +this.route.snapshot.paramMap.get('id');
//this.documentService.getAllEvidence(this.document.documentId)
this.documentService.getAllEvidence(id)
.subscribe(text => {
this.docData = text;
//console.log(this.docData);
// console.log(JSON.parse(this.docData));
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
//document.getElementById('loadingDiv').className = 'loader';
var j = JSON.parse(this.docData);
//this.loadBratVisualizer();
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
//dispatcher.on('displaySpanComment', displaySpanComment);
//dispatcher.on('hideComment', hideComment);
// setTimeout(() => {
// document.getElementById('loadingDiv').className = '';
// }, 4000);
});
});
}
getSentencesEvidence() {
//alert('getSentencesEvidence');
const id = +this.route.snapshot.paramMap.get('id');
//this.documentService.getAllEvidence(this.document.documentId)
this.documentService.getSentencesEvidence(id)
.subscribe(text => {
this.docData = text;
//console.log(this.docData);
// console.log(JSON.parse(this.docData));
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
document.getElementById('loadingDiv').className = 'loader';
var j = JSON.parse(this.docData);
this.loadBratVisualizer();
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
dispatcher.on('displaySpanComment', displaySpanComment);
dispatcher.on('hideComment', hideComment);
document.getElementById('data2').className = 'FixedHeightContainer';
document.getElementById('data1').className = 'brat_div';
setTimeout(() => {
document.getElementById('loadingDiv').className = '';
}, 4000);
});
});
}
setExportSRDomain(data) {
const id = +this.route.snapshot.paramMap.get('id');
//alert(data);
......@@ -390,6 +547,15 @@ export class DocumentDetailComponent implements OnInit {
//alert(text);
});
}
setSRFindingValidation(data) {
const id = +this.route.snapshot.paramMap.get('id');
//alert(data.status);
this.documentService.setSRFindingValidation(id, data.srDomainId, data.status)
.subscribe(text => {
//alert(text);
});
}
setNextStatus(status){
if(status=='DRAFT'){
......@@ -422,48 +588,48 @@ export class DocumentDetailComponent implements OnInit {
exportDocument() {
const id = +this.route.snapshot.paramMap.get('id');
this.documentService.exportDocument(id);
this.documentService.exportDocument(id, this.document.name);
}
getAllEvidence() {
const id = +this.route.snapshot.paramMap.get('id');
this.documentService.getAllEvidence(this.document.documentId)
.subscribe(text => {
this.docData = text;
console.log(this.docData);
// console.log(JSON.parse(this.docData));
document.getElementById('data2').className = 'collapse show';
document.getElementById('data1').innerHTML = '';
document.getElementById('data1').className = '';
var j = JSON.parse(this.docData);
head.ready( function() {
const dispatcher = Util.embed('data1' , DocumentDetailComponent.collData, j, DocumentDetailComponent.webFontURLs);
dispatcher.on('displaySpanComment', displaySpanComment);
dispatcher.on('hideComment', hideComment);
});
});
}
onActivate(componentReference) {
console.log(componentReference)
componentReference.activation(this.document);
// if(componentReference.constructor.name=='PretoxsentencesTabulatorComponent'){
// this.getSentencesEvidence();
// }else if(componentReference.constructor.name=='SrdomaintemplateTabulatorComponent'){
// this.getAllEvidence();
// }else if(componentReference.constructor.name=='FindingTabulatorComponent'){
// this.getAllEvidence();
// }
//Below will subscribe to the searchItem emitter
if(componentReference.rowClickEventFinding!=undefined){
componentReference.rowClickEventFinding.subscribe((data) => {
//alert('rowClickEventFinding');
this.rowClickFindingEvidence(data);
})
}
}
//Below will subscribe to the searchItem emitter
if(componentReference.rowClickEvent!=undefined){
//alert('sentence activation');
this.getSentencesEvidence();
componentReference.rowClickEvent.subscribe((data) => {
//alert('rowClickEvent');
this.rowClickSentenceEvidence(data);
})
}
//Below will subscribe to the searchItem emitter
if(componentReference.rowClickSRFindingValidationEvent!=undefined){
componentReference.rowClickSRFindingValidationEvent.subscribe((data) => {
//alert('rowClickFindingValidationEvent');
this.setSRFindingValidation(data);
})
}
//Below will subscribe to the searchItem emitter
if(componentReference.rowClickFindingValidationEvent!=undefined){
......@@ -473,8 +639,14 @@ export class DocumentDetailComponent implements OnInit {
})
}
if(componentReference.srFindingType!=undefined){
this.getAllEvidence();
}
//Below will subscribe to the searchItem emitter
if(componentReference.rowClickEventSRDomainTemplateEvidence!=undefined){
//alert('sr-domain activation');
//this.getAllEvidence();
componentReference.rowClickEventSRDomainTemplateEvidence.subscribe((data) => {
//alert('rowClickSRDomainTemplateEvidence');
this.rowClickSRDomainTemplateEvidence(data);
......
src/app/document.service.ts
View file @ 231e8b6e
......@@ -48,15 +48,17 @@ export class DocumentService {
}
/** GET document by id. Will 404 if id not found */
exportDocument(id: number): any {
exportDocument(id: number, name: string): any {
const url = `${this.documentsUrl}export/${id}`;
return this.http.get(url, {
responseType: 'blob',
observe: 'response'
})
.pipe(map(res => {
console.log(res.headers.get('content-disposition'));
return {
filename: id+'.txt',
data: res
filename: name + '.csv',
data: res.body
};
}))
.subscribe(res => {
......@@ -82,6 +84,15 @@ export class DocumentService {
);
}
/** set validation of finding */
setSRFindingValidation(id: number, srfindingId: number, finding_validation: string): Observable<string> {
const url = `${this.documentsUrl}${id}/srFindingValidation/${srfindingId}/${finding_validation}`;
return this.http.get(url , {responseType: 'text'}).pipe(
tap(_ => this.log(`finding_validation id=${srfindingId}`)),
catchError(this.handleError<string>(`finding_validation id=${srfindingId}`))
);
}
/** set export finding */
setExportSRDomain(id: number, findingId: number, export_finding: string): Observable<string> {
const url = `${this.documentsUrl}${id}/setExportSRDomain/${findingId}/${export_finding}`;
......@@ -117,6 +128,17 @@ export class DocumentService {
catchError(this.handleError<string>(`getFinding id=${finding.findingId}`))
);
}
/** GET Snipped of the full text with no annotations */
findDocumentText(id: number): Observable<string> {
const url = `${this.documentsUrl}${id}/text/`;
return this.http.get(url , {responseType: 'text'}).pipe(
tap(_ => this.log(`fetched text id=${id}`)),
catchError(this.handleError<string>(`getText id=${id}`))
);
}
/** GET Snipped of findings selected just in case is needed, is not complete only the calls againt rest api is done*/
findingsSelected(id: number, finding: Finding): Observable<string> {
......@@ -130,13 +152,30 @@ export class DocumentService {
/** GET Snipped of all finding evidence */
getAllEvidence(id: number): Observable<string> {
const url = `${this.documentsUrl}${id}/evidence/all`;
const url = `${this.documentsUrl}${id}/evidence/findings`;
return this.http.get(url , {responseType: 'text'}).pipe(
tap(_ => this.log(`fetched all evidence id=${id}`)),
catchError(this.handleError<string>(`getFindings id=${id}`))
);
}
/** GET Snipped of all finding evidence */