From 4e3209be5cf2d0f11f487b57b686a56a898bca2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?=
 <nicolas.diazroussel@bsc.es>
Date: Wed, 14 Sep 2022 13:47:00 +0200
Subject: [PATCH 01/13] Disable run workflow button if no report selected

---
 src/app/reports/reports.component.html | 2 +-
 src/app/reports/reports.component.ts   | 3 +++
 src/tabulator.css                      | 7 ++++---
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/app/reports/reports.component.html b/src/app/reports/reports.component.html
index 3cff460..5480afb 100644
--- a/src/app/reports/reports.component.html
+++ b/src/app/reports/reports.component.html
@@ -5,7 +5,7 @@
     </h1>
    </div> 
   <div class="w3-container">
-    <button type="button" class="btn btn-outline-primary text-nowrap"   (click)="runWorkflow()">Run Workflow</button>
+    <button type="button" class="btn btn-outline-primary text-nowrap" [disabled]="reportsWfToRun.length==0"   (click)="runWorkflow()">Run Workflow</button>
     <div *ngIf="validation_errors.length>0" class="card">
       <div class="card-header">Messages: No document will be processed until all the errors were solved.</div>
       <ul
diff --git a/src/app/reports/reports.component.ts b/src/app/reports/reports.component.ts
index bb58d2a..c901691 100644
--- a/src/app/reports/reports.component.ts
+++ b/src/app/reports/reports.component.ts
@@ -21,6 +21,7 @@ export class ReportsComponent implements OnInit {
   message = '';
   messages = [];
   validation_errors = [];
+  reportsWfToRun = [];
 
   tableData: any[] = [];
   @Input() report: Report;
@@ -139,8 +140,10 @@ export class ReportsComponent implements OnInit {
             if (data.status == 'READY') {
               if (data.runWF) {
                 cell.getElement().innerHTML = '<i class="fa-regular fa-square"> </i>';
+                documentTab.reportsWfToRun.splice(documentTab.reportsWfToRun.indexOf(data.id), 1);
               } else {
                 cell.getElement().innerHTML = '<i class="fa-solid fa-square-check"> </i>';
+                documentTab.reportsWfToRun.push(data.id);
               }
 
               data.runWF = !data.runWF;
diff --git a/src/tabulator.css b/src/tabulator.css
index 9a4af5b..4bcc05b 100644
--- a/src/tabulator.css
+++ b/src/tabulator.css
@@ -1,9 +1,10 @@
-.tabulator-cell.run-wf-checkbox {
+.tabulator-cell.run-wf-checkbox .fa-solid.fa-square-check {
+    color: green;
     cursor: pointer;
 }
 
-.tabulator-cell.run-wf-checkbox .fa-solid.fa-square-check {
-    color: green;
+.tabulator-cell.run-wf-checkbox .fa-regular.fa-square {
+    cursor: pointer;
 }
 
 .tabulator-cell.download-report-button .fa-solid.fa-file-pdf {
-- 
GitLab


From d0346354b103ffdf0ab7c65f382d4621c75438c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?=
 <nicolas.diazroussel@bsc.es>
Date: Wed, 14 Sep 2022 15:48:43 +0200
Subject: [PATCH 02/13] Add curation pencil to reports

---
 src/app/reports/reports.component.ts | 16 ++++++++++++++++
 src/tabulator.css                    | 12 +++++++++++-
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/app/reports/reports.component.ts b/src/app/reports/reports.component.ts
index c901691..82e1710 100644
--- a/src/app/reports/reports.component.ts
+++ b/src/app/reports/reports.component.ts
@@ -163,6 +163,22 @@ export class ReportsComponent implements OnInit {
         { title: 'Name', field: 'fileName', headerSort: true, headerFilter: true },
         { title: 'Upload Date', field: 'uploadDate', headerSort: true, headerFilter: true },
         { title: 'Status', field: 'status', headerSort: true, headerFilter: true },
+        {
+          title: '', width: 5, hozAlign: 'center', headerSort: false,
+          cellClick: function (e, cell) {
+            if (cell.getRow().getData().status == "COMPLETED") {
+              var data = cell.getRow().getData();
+              documentTab.openDocument(data.id);
+            }
+          },
+          formatter: function (cell, formatterParams, onRendered) {
+            if (cell.getRow().getData().status == "COMPLETED") {
+              return '<div class="start-curation"> <i class="fa fa-pencil" aria-hidden="true" title="Validate and curate findings"> </i></div>';
+            } else {
+              return '<div class="start-curation-disabled"> <i class="fa fa-pencil" aria-hidden="true" title="Validate and curate findings"> </i></div>';
+            }
+          }
+        },
         {
           title: '', width: 5, hozAlign: 'center', headerSort: false, cssClass: "download-report-button",
           cellClick: function (e, cell) {
diff --git a/src/tabulator.css b/src/tabulator.css
index 4bcc05b..f4fe546 100644
--- a/src/tabulator.css
+++ b/src/tabulator.css
@@ -1,5 +1,5 @@
 .tabulator-cell.run-wf-checkbox .fa-solid.fa-square-check {
-    color: green;
+    color: blue;
     cursor: pointer;
 }
 
@@ -85,6 +85,16 @@
     cursor: pointer;
 }
 
+.tabulator-cell .start-curation .fa.fa-pencil {
+    color: blue;
+    cursor: pointer;
+}
+
+.tabulator-cell .start-curation-disabled .fa.fa-pencil {
+    color: grey;
+    cursor: default;
+}
+
 .tabulator-cell.editable-cell {
     cursor: pointer;
     background-color: #ffcc66;
-- 
GitLab


From b407686a418edc394860411fb165d144b01552a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?=
 <nicolas.diazroussel@bsc.es>
Date: Wed, 14 Sep 2022 15:49:04 +0200
Subject: [PATCH 03/13] Go back when document not found

---
 src/app/document-detail/document-detail.component.ts | 6 +++++-
 src/app/services/document.service.ts                 | 5 +----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/app/document-detail/document-detail.component.ts b/src/app/document-detail/document-detail.component.ts
index bcb8d8a..0f66821 100644
--- a/src/app/document-detail/document-detail.component.ts
+++ b/src/app/document-detail/document-detail.component.ts
@@ -297,7 +297,11 @@ export class DocumentDetailComponent implements OnInit {
 
         this.tableDataPretoxSentences = data_relevant_sentences;
         this.tableDataSRDomainTemplate = srDomainFindingsGlobal;
-      });
+      },
+      err => {
+        alert("There is no annotations of this report");
+        this.goBack();
+      })
   }
 
   rowClickFindingEvidence(dataRow: any): void {
diff --git a/src/app/services/document.service.ts b/src/app/services/document.service.ts
index be6c14e..53c5d6d 100644
--- a/src/app/services/document.service.ts
+++ b/src/app/services/document.service.ts
@@ -44,10 +44,7 @@ export class DocumentService {
   /** GET document by id. Will 404 if id not found */
   getDocument(id: number): Observable<Document> {
     const url = `${this.documentsUrl}${id}`;
-    return this.http.get<Document>(url).pipe(
-      tap(_ => this.log(`fetched document id=${id}`)),
-      catchError(this.handleError<Document>(`getDocument id=${id}`))
-    );
+    return this.http.get<Document>(url);
   }
 
   /** GET document by id. Will 404 if id not found */
-- 
GitLab


From 18502321e9d2c69b970a60148af26c9d072e9eec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?=
 <nicolas.diazroussel@bsc.es>
Date: Wed, 14 Sep 2022 16:28:36 +0200
Subject: [PATCH 04/13] Relocate "run workflow" button

---
 src/app/reports/reports.component.css  |  4 ++
 src/app/reports/reports.component.html | 60 ++++++++++----------------
 2 files changed, 27 insertions(+), 37 deletions(-)

diff --git a/src/app/reports/reports.component.css b/src/app/reports/reports.component.css
index e69de29..a1d44cb 100644
--- a/src/app/reports/reports.component.css
+++ b/src/app/reports/reports.component.css
@@ -0,0 +1,4 @@
+.run-wf .btn.btn-outline-primary.text-nowrap {
+    margin-left: 50px;
+    margin-bottom: 10px;
+}
\ No newline at end of file
diff --git a/src/app/reports/reports.component.html b/src/app/reports/reports.component.html
index 5480afb..02a8d85 100644
--- a/src/app/reports/reports.component.html
+++ b/src/app/reports/reports.component.html
@@ -1,39 +1,25 @@
 <div style="text-align:center">
-    <h1>
-      <app-header></app-header>
-     <app-menu></app-menu>
-    </h1>
-   </div> 
-  <div class="w3-container">
-    <button type="button" class="btn btn-outline-primary text-nowrap" [disabled]="reportsWfToRun.length==0"   (click)="runWorkflow()">Run Workflow</button>
-    <div *ngIf="validation_errors.length>0" class="card">
-      <div class="card-header">Messages: No document will be processed until all the errors were solved.</div>
-      <ul
-        class="list-group list-group-flush"
-        *ngFor="let m of validation_errors "
-      >
-        <li class="list-group-item">
-          {{ m }}
-        </li>
-      </ul>
-    </div> 
-    
-    <div *ngIf="messages.length>0" class="card">
-      <div class="card-header">The following reports were uploaded. You can run the workflow from here or you can see your reports in the Reports panel.</div>
-      <div class="w3-container">
-          <button type="button" class="btn btn-outline-primary text-nowrap"   (click)="runWorkflow()">Run Workflow</button>
-      </div>
-          <ul class="list-group list-group-flush" *ngFor="let m of messages">
-        <li class="list-group-item">
-          {{ m.fileName }}
-        </li>
-      </ul>
-    
-    </div> 
-    <div *ngIf="message.length>0" class="card">
-      {{message}}
-    </div>
-    <div  id="my-tabular-table-reports"></div>
+  <h1>
+    <app-header></app-header>
+    <app-menu></app-menu>
+  </h1>
+</div>
+<div class="w3-container">
+  <div class="run-wf">
+    <button type="button" class="btn btn-outline-primary text-nowrap" [disabled]="reportsWfToRun.length==0"
+    (click)="runWorkflow()">Run Workflow</button>
   </div>
-  
-  
\ No newline at end of file
+  <div *ngIf="validation_errors.length>0" class="card">
+    <div class="card-header">Messages: No document will be processed until all the errors are solved.</div>
+    <ul class="list-group list-group-flush" *ngFor="let m of validation_errors ">
+      <li class="list-group-item">
+        {{ m }}
+      </li>
+    </ul>
+  </div>
+
+  <div *ngIf="message.length>0" class="card">
+    {{message}}
+  </div>
+  <div id="my-tabular-table-reports"></div>
+</div>
\ No newline at end of file
-- 
GitLab


From 1cda4ef08c1c9ce621313984b0b0c3d9900fd608 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?=
 <nicolas.diazroussel@bsc.es>
Date: Wed, 14 Sep 2022 16:50:26 +0200
Subject: [PATCH 05/13] Add icon to "run workflow" column

---
 src/app/reports/reports.component.ts | 7 +++++--
 src/tabulator.css                    | 5 +++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/app/reports/reports.component.ts b/src/app/reports/reports.component.ts
index 82e1710..c11e635 100644
--- a/src/app/reports/reports.component.ts
+++ b/src/app/reports/reports.component.ts
@@ -134,7 +134,7 @@ export class ReportsComponent implements OnInit {
       paginationSizeSelector: [10, 20, 40],
       columns: [
         {
-          title: '', width: 5, hozAlign: 'center', headerSort: false, cssClass: "run-wf-checkbox",
+          title: '', width: 50, hozAlign: 'center', headerSort: false, cssClass: "run-wf-checkbox",
           cellClick: function (e, cell) {
             var data = cell.getRow().getData();
             if (data.status == 'READY') {
@@ -158,6 +158,9 @@ export class ReportsComponent implements OnInit {
                 return '<i class="fa-regular fa-square"> </i>';
               }
             }
+          },
+          titleFormatter: function() {
+            return '<div class="run-wf-col"><i class="fa-solid fa-gears"></i></div>';
           }
         },
         { title: 'Name', field: 'fileName', headerSort: true, headerFilter: true },
@@ -191,7 +194,7 @@ export class ReportsComponent implements OnInit {
         {
           title: '', width: 5, hozAlign: 'center', headerSort: false, cssClass: "delete-report-button",
           cellClick: function (e, cell) {
-            
+
             var data = cell.getRow().getData();
             documentTab.openDialog(data.id);
           }
diff --git a/src/tabulator.css b/src/tabulator.css
index f4fe546..0ae97ac 100644
--- a/src/tabulator.css
+++ b/src/tabulator.css
@@ -112,3 +112,8 @@
     border: 1px solid black;
 }
 
+.tabulator .tabulator-header .tabulator-headers .tabulator-col.run-wf-checkbox {
+    display: inline-flex;
+    align-items: center;
+    font-size: 20px;
+}
-- 
GitLab


From 24cee512a8618675bf4b3c9310d32c68b7a4e2a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?=
 <nicolas.diazroussel@bsc.es>
Date: Fri, 16 Sep 2022 15:54:56 +0200
Subject: [PATCH 06/13] Show report annotations on edition click

---
 .../document-detail.component.html            |  14 +-
 .../document-detail.component.ts              | 179 ++++++++----------
 src/app/model/report.ts                       |   4 +
 src/app/model/section.ts                      |  10 +
 .../pretoxsentences-tabulator.component.ts    |   1 -
 src/app/reports/reports.component.css         |   1 -
 src/app/reports/reports.component.html        |   2 +-
 src/app/reports/reports.component.ts          |  14 +-
 src/app/services/document.service.ts          |   6 +
 9 files changed, 113 insertions(+), 118 deletions(-)
 create mode 100644 src/app/model/section.ts

diff --git a/src/app/document-detail/document-detail.component.html b/src/app/document-detail/document-detail.component.html
index ef5ab05..d117238 100644
--- a/src/app/document-detail/document-detail.component.html
+++ b/src/app/document-detail/document-detail.component.html
@@ -10,22 +10,22 @@
   <!-- <a class="fa fa-angle-left" title='Previous Document' routerLink="" style="color:white;padding: 10px 30px;text-decoration:none;" aria-hidden="true" tooltip='Previous Document'></a>
         <a class="fa fa-angle-right" title='Next Document' routerLink="" style="color:white;padding: 10px 30px;text-decoration:none;" aria-hidden="true" tooltip='Next Document'></a> -->
   <!-- </nav> -->
-  <div *ngIf="document" class="documentName">
+  <div *ngIf="report" class="documentName">
     <div class="card">
       <div class="card-header">
         <div class="document-name">
-          <h4>{{document.name}}</h4>
+          <h4>{{report.name}}</h4>
         </div>
         <div class="send-to-srdomain-button">
-          <button type="button" class="btn btn-outline-primary text-nowrap" [disabled]="document.status != 'FINISHED'" (click)="sendToSRDomain()">Send to
+          <button type="button" class="btn btn-outline-primary text-nowrap" [disabled]="report.status != 'FINISHED'" (click)="sendToSRDomain()">Send to
             SR-Domain</button>
         </div>
         <div class="btn-group">
-          <button class="status-button" type="button" [disabled]="document.status == 'CLOSED'" [ngClass]="{'btn-warning': document.status === 'DRAFT',
-                        'btn-primary' : document.status === 'IN_PROGRESS',
-                        'btn-success' : document.status === 'FINISHED', 'btn-closed' : document.status === 'CLOSED'}" class="btn dropdown-toggle"
+          <button class="status-button" type="button" [disabled]="report.status == 'CLOSED'" [ngClass]="{'btn-warning': report.status === 'DRAFT',
+                        'btn-primary' : report.status === 'IN_PROGRESS',
+                        'btn-success' : report.status === 'FINISHED', 'btn-closed' : report.status === 'CLOSED'}" class="btn dropdown-toggle"
             data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
-            {{document.status}}
+            {{report.status}}
           </button>
           <div class="dropdown-menu">
             <a *ngFor="let status of nextStatus" class='dropdown-item btn' [ngClass]="{'bg-warning': status === 'DRAFT',
diff --git a/src/app/document-detail/document-detail.component.ts b/src/app/document-detail/document-detail.component.ts
index 0f66821..dd6e7be 100644
--- a/src/app/document-detail/document-detail.component.ts
+++ b/src/app/document-detail/document-detail.component.ts
@@ -12,6 +12,7 @@ import { environment } from './../../environments/environment';
 import { Router } from '@angular/router';
 import { CdisSendCtService } from '../services/cdis-send-ct.service';
 import { Status } from '../model/srdomainfindingstatus';
+import { Report } from '../model/report';
 
 //brat
 declare var head: any;
@@ -54,6 +55,8 @@ export class DocumentDetailComponent implements OnInit {
 
   @ViewChild('documentText', { static: false }) myDiv: ElementRef;
 
+  @Input() report: Report;
+
   @Input() document: Document;
 
   addFindingEnabled: boolean;
@@ -202,112 +205,86 @@ export class DocumentDetailComponent implements OnInit {
     this.cdiscSendCTService.findStudyDomainList();
   }
 
-  getEvidence() {
-    const id = +this.route.snapshot.paramMap.get('id');
-    this.documentService.getEvidence(id)
-      .subscribe(text => {
-        this.docData = text;
-        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);
-        });
-      });
-  }
-
-  save(): void {
-    this.documentService.updateDocument(this.document)
-      .subscribe(() => this.goBack());
-  }
-
   getDocument(): void {
-    const id = +this.route.snapshot.paramMap.get('id');
-    this.documentService.getDocument(id)
-      .subscribe(document => {
-        this.document = document;
-        this.setNextStatus(this.document.status);
+    const id = this.route.snapshot.paramMap.get('id');
+    this.documentService.getReport(id)
+      .subscribe(report => {
+        this.report = report;
+        this.setNextStatus(this.report.status);
         var data_relevant_sentences = [];
         var srDomainFindingsGlobal = [];
-        document.relevantSentences.forEach(annotation => {
-          var findings = [];
-          annotation.findings.forEach(find => {
-            var srDomainFindings = [];
-            find.srDomainFindings.forEach(srDomainFinding => {
-              const currentFinding = ({
-                studyid: srDomainFinding.studyid,
-                domain: srDomainFinding.domain,
-                srseq: srDomainFinding.srseq,
-                srrisk: srDomainFinding.srrisk,
-
-                spgrpcd: srDomainFinding.spgrpcd,
-                srgrpnam: srDomainFinding.srgrpnam,
-                srgrpdos: srDomainFinding.srgrpdos,
-                srsex: srDomainFinding.srsex,
-
-                srstdy: srDomainFinding.srstdy,
-                srstphse: srDomainFinding.srstphse,
-                srobstdy: srDomainFinding.srobstdy,
-                srendy: srDomainFinding.srendy,
-
-                srenphse: srDomainFinding.srenphse,
-                srobendy: srDomainFinding.srobendy,
-                srdomain: srDomainFinding.srdomain,
-                srspec: srDomainFinding.srspec,
-
-                srtstcd: srDomainFinding.srtstcd,
-                srfndg: srDomainFinding.srfndg,
-                srores: srDomainFinding.srores,
-                srobsv: srDomainFinding.srobsv,
-
-                srobsq: srDomainFinding.srobsq,
-                srsev: srDomainFinding.srsev,
-                srpcnt: srDomainFinding.srpcnt,
-                srsigf: srDomainFinding.srsigf,
-
-                srtrtef: srDomainFinding.srpcnt,
-                srcomnt: srDomainFinding.srsigf,
-
-                export: srDomainFinding.export,
-                srDomainId: srDomainFinding.srDomainId,
-                findingId: srDomainFinding.findingId,
-                status: srDomainFinding.status
+        report.sections.forEach(section => {
+          section.annotations.relevantSentences.forEach(annotation => {
+            var findings = [];
+            annotation.findings.forEach(find => {
+              var srDomainFindings = [];
+              find.srDomainFindings.forEach(srDomainFinding => {
+                const currentFinding = ({
+                  studyid: srDomainFinding.studyid,
+                  domain: srDomainFinding.domain,
+                  srseq: srDomainFinding.srseq,
+                  srrisk: srDomainFinding.srrisk,
+
+                  spgrpcd: srDomainFinding.spgrpcd,
+                  srgrpnam: srDomainFinding.srgrpnam,
+                  srgrpdos: srDomainFinding.srgrpdos,
+                  srsex: srDomainFinding.srsex,
+
+                  srstdy: srDomainFinding.srstdy,
+                  srstphse: srDomainFinding.srstphse,
+                  srobstdy: srDomainFinding.srobstdy,
+                  srendy: srDomainFinding.srendy,
+
+                  srenphse: srDomainFinding.srenphse,
+                  srobendy: srDomainFinding.srobendy,
+                  srdomain: srDomainFinding.srdomain,
+                  srspec: srDomainFinding.srspec,
+
+                  srtstcd: srDomainFinding.srtstcd,
+                  srfndg: srDomainFinding.srfndg,
+                  srores: srDomainFinding.srores,
+                  srobsv: srDomainFinding.srobsv,
+
+                  srobsq: srDomainFinding.srobsq,
+                  srsev: srDomainFinding.srsev,
+                  srpcnt: srDomainFinding.srpcnt,
+                  srsigf: srDomainFinding.srsigf,
+
+                  srtrtef: srDomainFinding.srpcnt,
+                  srcomnt: srDomainFinding.srsigf,
+
+                  export: srDomainFinding.export,
+                  srDomainId: srDomainFinding.srDomainId,
+                  findingId: srDomainFinding.findingId,
+                  status: srDomainFinding.status,
+                  section: section.name,
+                  documentId: section.annotations.documentId
+                });
+
+                findings.push(currentFinding);
+                srDomainFindings.push(currentFinding);
               });
 
-              findings.push(currentFinding);
-              srDomainFindings.push(currentFinding);
+              srDomainFindingsGlobal = srDomainFindingsGlobal.concat(srDomainFindings);
             });
 
-            srDomainFindingsGlobal = srDomainFindingsGlobal.concat(srDomainFindings);
+            data_relevant_sentences.push({
+              id: annotation.id,
+              text: annotation.text,
+              findings: findings
+            });
           });
 
-          data_relevant_sentences.push({
-            id: annotation.id,
-            text: annotation.text,
-            findings: findings
-          });
+          if (section.annotations.srdomainfindings) {
+            section.annotations.srdomainfindings.forEach(newFinding => {
+              srDomainFindingsGlobal.push(newFinding);
+            });
+          }
         });
 
-        if (this.document.srdomainfindings) {
-          this.document.srdomainfindings.forEach(newFinding => {
-            srDomainFindingsGlobal.push(newFinding);
-          });
-        }
-
         this.tableDataPretoxSentences = data_relevant_sentences;
         this.tableDataSRDomainTemplate = srDomainFindingsGlobal;
-      },
-      err => {
-        alert("There is no annotations of this report");
-        this.goBack();
-      })
-  }
-
-  rowClickFindingEvidence(dataRow: any): void {
-    const finding = new Finding();
-    finding.findingId = dataRow.id;
-    this.findingSelected(finding);
+      });
   }
 
   rowClickSentenceEvidence(dataRow: any): void {
@@ -319,11 +296,11 @@ export class DocumentDetailComponent implements OnInit {
   rowClickSRDomainTemplateEvidence(dataRow: any): void {
     const finding = new Finding();
     finding.findingId = dataRow.findingId;
-    this.findingSelected(finding);
+    this.findingSelected(dataRow.documentId, finding);
   }
 
-  findingSelected(finding): void {
-    this.documentService.findingSelected(this.document.documentId, finding)
+  findingSelected(documentId, finding): void {
+    this.documentService.findingSelected(documentId, finding)
       .subscribe(text => {
         var loading = document.getElementById('loadingDiv');
         loading.addEventListener("load", this.loaded);
@@ -505,14 +482,8 @@ export class DocumentDetailComponent implements OnInit {
   onActivate(componentReference) {
     componentReference.activation(this);
 
-    if (componentReference.rowClickEventFinding != undefined) {
-      componentReference.rowClickEventFinding.subscribe((data) => {
-        this.rowClickFindingEvidence(data);
-      })
-    }
-
     if (componentReference.rowClickEvent != undefined) {
-      this.getSentencesEvidence();
+      //this.getSentencesEvidence();
       componentReference.rowClickEvent.subscribe((data) => {
         this.rowClickSentenceEvidence(data);
       })
@@ -531,7 +502,7 @@ export class DocumentDetailComponent implements OnInit {
     }
 
     if (componentReference.srFindingType != undefined) {
-      this.getAllEvidence();
+      //this.getAllEvidence();
     }
 
     if (componentReference.rowClickEventSRDomainTemplateEvidence != undefined) {
diff --git a/src/app/model/report.ts b/src/app/model/report.ts
index 4399418..bf18dd0 100644
--- a/src/app/model/report.ts
+++ b/src/app/model/report.ts
@@ -1,3 +1,5 @@
+import { Section } from "./section";
+
 export class Report {
     id:number;
 	uploadDate:string;
@@ -7,4 +9,6 @@ export class Report {
 	gridFSId:number; 
     status:string; 
     runWF:boolean=false;
+	hasSections:boolean;
+	sections:Section[];
 }
diff --git a/src/app/model/section.ts b/src/app/model/section.ts
new file mode 100644
index 0000000..d4c877a
--- /dev/null
+++ b/src/app/model/section.ts
@@ -0,0 +1,10 @@
+import {Document} from './document';
+
+export class Section {
+    id:number;
+	name:string;
+	text:string;
+	processDate:string;
+	fileName:string;
+    annotations:Document;
+}
diff --git a/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts b/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts
index 5e053ba..e14909b 100644
--- a/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts
+++ b/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts
@@ -24,7 +24,6 @@ export class PretoxsentencesTabulatorComponent implements OnInit {
   // list properties you want to set per implementation here...
 
   @Output() rowClickEvent = new EventEmitter();
-  @Output() rowClickEventFinding = new EventEmitter();
   @Output() rowClickExportSRDomainEvent = new EventEmitter();
   @Output() rowClickSRFindingValidationEvent = new EventEmitter();
   @Output() rowClickEventSRDomainTemplateEvidence = new EventEmitter();
diff --git a/src/app/reports/reports.component.css b/src/app/reports/reports.component.css
index a1d44cb..3a55c77 100644
--- a/src/app/reports/reports.component.css
+++ b/src/app/reports/reports.component.css
@@ -1,4 +1,3 @@
 .run-wf .btn.btn-outline-primary.text-nowrap {
-    margin-left: 50px;
     margin-bottom: 10px;
 }
\ No newline at end of file
diff --git a/src/app/reports/reports.component.html b/src/app/reports/reports.component.html
index 02a8d85..8c6d8ea 100644
--- a/src/app/reports/reports.component.html
+++ b/src/app/reports/reports.component.html
@@ -7,7 +7,7 @@
 <div class="w3-container">
   <div class="run-wf">
     <button type="button" class="btn btn-outline-primary text-nowrap" [disabled]="reportsWfToRun.length==0"
-    (click)="runWorkflow()">Run Workflow</button>
+    (click)="runWorkflow()">Run Workflow(s)</button>
   </div>
   <div *ngIf="validation_errors.length>0" class="card">
     <div class="card-header">Messages: No document will be processed until all the errors are solved.</div>
diff --git a/src/app/reports/reports.component.ts b/src/app/reports/reports.component.ts
index c11e635..3a74da6 100644
--- a/src/app/reports/reports.component.ts
+++ b/src/app/reports/reports.component.ts
@@ -55,7 +55,9 @@ export class ReportsComponent implements OnInit {
             fileName: report.fileName,
             uploadDate: report.uploadDate,
             status: report.status,
-            gridfsId: report.gridFSId
+            gridfsId: report.gridFSId,
+            hasSections: report.hasSections,
+            sections: report.sections
           });
         });
 
@@ -105,8 +107,12 @@ export class ReportsComponent implements OnInit {
 
   }
 
-  openDocument(documentId) {
-    this.router.navigate(['/find/' + documentId]);
+  openAnnotations(data) {
+    if (data.hasSections) {
+      this.router.navigate(['/find/' + data.id]);
+    } else {
+      alert("There is no sections in this report");
+    }
   }
 
   openLegacyReport(gridFSId) {
@@ -171,7 +177,7 @@ export class ReportsComponent implements OnInit {
           cellClick: function (e, cell) {
             if (cell.getRow().getData().status == "COMPLETED") {
               var data = cell.getRow().getData();
-              documentTab.openDocument(data.id);
+              documentTab.openAnnotations(data);
             }
           },
           formatter: function (cell, formatterParams, onRendered) {
diff --git a/src/app/services/document.service.ts b/src/app/services/document.service.ts
index 53c5d6d..4d74a2f 100644
--- a/src/app/services/document.service.ts
+++ b/src/app/services/document.service.ts
@@ -41,6 +41,12 @@ export class DocumentService {
     );
   }
 
+  /** GET report by id. Will 404 if id not found */
+  getReport(id: string): Observable<Report> {
+    const url = `${this.reportsUrl}${id}`;
+    return this.http.get<Report>(url);
+  }
+
   /** GET document by id. Will 404 if id not found */
   getDocument(id: number): Observable<Document> {
     const url = `${this.documentsUrl}${id}`;
-- 
GitLab


From febebf84f318188f6f2a36c7c9ce531549cd1bdc Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 11:24:17 +0200
Subject: [PATCH 07/13] status standardization

---
 src/app/reports/reports.component.ts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/app/reports/reports.component.ts b/src/app/reports/reports.component.ts
index bb58d2a..7fc6c4d 100644
--- a/src/app/reports/reports.component.ts
+++ b/src/app/reports/reports.component.ts
@@ -136,7 +136,7 @@ export class ReportsComponent implements OnInit {
           title: '', width: 5, hozAlign: 'center', headerSort: false, cssClass: "run-wf-checkbox",
           cellClick: function (e, cell) {
             var data = cell.getRow().getData();
-            if (data.status == 'READY') {
+            if (data.status == 'WORKFLOW_READY') {
               if (data.runWF) {
                 cell.getElement().innerHTML = '<i class="fa-regular fa-square"> </i>';
               } else {
@@ -148,7 +148,7 @@ export class ReportsComponent implements OnInit {
           },
           formatter: function (cell, formatterParams, onRendered) {
             var data = cell.getRow().getData();
-            if (data.status == 'READY') {
+            if (data.status == 'WORKFLOW_READY') {
               if (data.runWF) {
                 return '<i class="fa-solid fa-square-check"> </i>';
               } else {
@@ -172,7 +172,7 @@ export class ReportsComponent implements OnInit {
         {
           title: '', width: 5, hozAlign: 'center', headerSort: false, cssClass: "delete-report-button",
           cellClick: function (e, cell) {
-            
+
             var data = cell.getRow().getData();
             documentTab.openDialog(data.id);
           }
-- 
GitLab


From b568369058e05d243bf4652d0c828e4fadadb136 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 11:35:56 +0200
Subject: [PATCH 08/13] status standardization change

---
 src/app/reports/reports.component.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/app/reports/reports.component.ts b/src/app/reports/reports.component.ts
index 8629010..d4e028e 100644
--- a/src/app/reports/reports.component.ts
+++ b/src/app/reports/reports.component.ts
@@ -175,13 +175,13 @@ export class ReportsComponent implements OnInit {
         {
           title: '', width: 5, hozAlign: 'center', headerSort: false,
           cellClick: function (e, cell) {
-            if (cell.getRow().getData().status == "COMPLETED") {
+            if (cell.getRow().getData().status == "WORKFLOW_COMPLETED") {
               var data = cell.getRow().getData();
               documentTab.openAnnotations(data);
             }
           },
           formatter: function (cell, formatterParams, onRendered) {
-            if (cell.getRow().getData().status == "COMPLETED") {
+            if (cell.getRow().getData().status == "WORKFLOW_COMPLETED") {
               return '<div class="start-curation"> <i class="fa fa-pencil" aria-hidden="true" title="Validate and curate findings"> </i></div>';
             } else {
               return '<div class="start-curation-disabled"> <i class="fa fa-pencil" aria-hidden="true" title="Validate and curate findings"> </i></div>';
-- 
GitLab


From a6459aa4762bb0173db75fae1f3dd7704c61ee36 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 14:46:19 +0200
Subject: [PATCH 09/13] report textual evidence

---
 src/app/document-detail/document-detail.component.ts | 11 ++++++-----
 .../pretoxsentences-tabulator.component.ts           | 12 ++++++------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/app/document-detail/document-detail.component.ts b/src/app/document-detail/document-detail.component.ts
index dd6e7be..73c6084 100644
--- a/src/app/document-detail/document-detail.component.ts
+++ b/src/app/document-detail/document-detail.component.ts
@@ -271,7 +271,8 @@ export class DocumentDetailComponent implements OnInit {
             data_relevant_sentences.push({
               id: annotation.id,
               text: annotation.text,
-              findings: findings
+              findings: findings,
+              documentId: section.annotations.documentId
             });
           });
 
@@ -290,7 +291,7 @@ export class DocumentDetailComponent implements OnInit {
   rowClickSentenceEvidence(dataRow: any): void {
     const annotation = new Annotation();
     annotation.id = dataRow.id;
-    this.pretoxSentenceSelected(annotation);
+    this.pretoxSentenceSelected(dataRow.documentId, annotation);
   }
 
   rowClickSRDomainTemplateEvidence(dataRow: any): void {
@@ -320,8 +321,8 @@ export class DocumentDetailComponent implements OnInit {
       });
   }
 
-  pretoxSentenceSelected(pretoxSentence): void {
-    this.documentService.pretoxSentenceSelected(this.document.documentId, pretoxSentence)
+  pretoxSentenceSelected(documentId, pretoxSentence): void {
+    this.documentService.pretoxSentenceSelected(documentId, pretoxSentence)
       .subscribe(text => {
         this.docData = text;
         document.getElementById('data2').className = 'collapse show';
@@ -344,7 +345,7 @@ export class DocumentDetailComponent implements OnInit {
   }
 
   findDocumentText(): void {
-    this.documentService.findDocumentText(this.document.documentId)
+    this.documentService.findDocumentText(this.report.id)
       .subscribe(text => {
         this.docData = text;
         document.getElementById('data2').className = 'collapse show';
diff --git a/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts b/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts
index e14909b..9670b67 100644
--- a/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts
+++ b/src/app/pretoxsentences-tabulator/pretoxsentences-tabulator.component.ts
@@ -42,7 +42,7 @@ export class PretoxsentencesTabulatorComponent implements OnInit {
   activation(parentComponent){
     this.document = parentComponent.document;
     this.sentence_data = parentComponent.tableDataPretoxSentences;
-  } 
+  }
 
   ngOnChanges(changes: SimpleChanges): void {
     this.drawTable(this);
@@ -93,17 +93,17 @@ export class PretoxsentencesTabulatorComponent implements OnInit {
         },
         {
           title: '', width: 5, field: 'id',
-          cellClick: function (e, cell) {
+          /*cellClick: function (e, cell) {
             cell.getRow().getElement().style.border = "1px solid black";
             pretoxSentencesTab.rowClickEvent.emit(cell.getData());
-          }
+          }*/
         },
         {
           title: 'Toxicological relevant phrase', field: 'text', headerSort: false,
-          cellClick: function (e, cell) {
+          /*cellClick: function (e, cell) {
             cell.getRow().getElement().style.border = "1px solid black";
-            pretoxSentencesTab.rowClickEvent.emit(cell.getData());
-          }
+           pretoxSentencesTab.rowClickEvent.emit(cell.getData());
+          }*/
         }],
       rowFormatter: function (row) {
         //create and style holder elements
-- 
GitLab


From 2ac0c1dba5eea8a3bc7bec3200b292e8fd313592 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 15:54:51 +0200
Subject: [PATCH 10/13] plain text, finding and sentence textual evidence

---
 src/app/services/document.service.ts | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/app/services/document.service.ts b/src/app/services/document.service.ts
index 4d74a2f..7ff7647 100644
--- a/src/app/services/document.service.ts
+++ b/src/app/services/document.service.ts
@@ -185,7 +185,7 @@ export class DocumentService {
 
   /** GET Snipped of finding selected */
   findingSelected(id: number, finding: Finding): Observable<string> {
-    const url = `${this.documentsUrl}${id}/evidence/finding/${finding.findingId}`;
+    const url = `${this.reportsUrl}${id}/evidence/finding/${finding.findingId}`;
     return this.http.get(url, { responseType: 'text' }).pipe(
       tap(_ => this.log(`fetched finding id=${finding.findingId}`)),
       catchError(this.handleError<string>(`getFinding id=${finding.findingId}`))
@@ -194,7 +194,7 @@ export class DocumentService {
 
   /** GET Snipped of the full text with no annotations */
   findDocumentText(id: number): Observable<string> {
-    const url = `${this.documentsUrl}${id}/text/`;
+    const url = `${this.reportsUrl}${id}/text/`;
     return this.http.get(url, { responseType: 'text' }).pipe(
       tap(_ => this.log(`fetched text id=${id}`)),
       catchError(this.handleError<string>(`getText id=${id}`))
@@ -203,7 +203,7 @@ export class DocumentService {
 
   /** Get SRDomain format and send to srdomain api */
   sendToSRDomain(id: number): any {
-    //call to get srdomain 
+    //call to get srdomain
     const url_2 = `${this.documentsUrl}srdomain/${id}`;
     this.http.get<SRDomainDocument>(url_2).subscribe({
       next: doc => {
@@ -269,8 +269,7 @@ export class DocumentService {
   }
 
   pretoxSentenceSelected(id: number, pretoxSentence: Annotation): Observable<string> {
-    const url = `${this.documentsUrl}${id}/evidence/sentence/${pretoxSentence.id}`;
-    //const url = `${this.documentsUrl}/${id}/sentence/1`;
+    const url = `${this.reportsUrl}${id}/evidence/sentence/${pretoxSentence.id}`;
     return this.http.get(url, { responseType: 'text' }).pipe(
       tap(_ => this.log(`fetched pretox sentence id=${pretoxSentence.id}`)),
       catchError(this.handleError<string>(`getPretoxSentence id=${pretoxSentence.id}`))
-- 
GitLab


From d3ecdbdebc1e7767f42abf421e77806658ce0a0f Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 16:29:50 +0200
Subject: [PATCH 11/13] all findings evidence

---
 src/app/services/document.service.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/app/services/document.service.ts b/src/app/services/document.service.ts
index 7ff7647..6a4c4c0 100644
--- a/src/app/services/document.service.ts
+++ b/src/app/services/document.service.ts
@@ -243,7 +243,7 @@ export class DocumentService {
 
   /** GET Snipped of all finding evidence */
   getAllEvidence(id: number): Observable<string> {
-    const url = `${this.documentsUrl}${id}/evidence/findings`;
+    const url = `${this.reportsUrl}${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}`))
-- 
GitLab


From 2b611c7e5d6c395ce1acb68176ee20a0dac358d8 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 16:29:50 +0200
Subject: [PATCH 12/13] all findings evidence

---
 src/app/document-detail/document-detail.component.ts | 3 ++-
 src/app/services/document.service.ts                 | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/app/document-detail/document-detail.component.ts b/src/app/document-detail/document-detail.component.ts
index 73c6084..bf11544 100644
--- a/src/app/document-detail/document-detail.component.ts
+++ b/src/app/document-detail/document-detail.component.ts
@@ -365,7 +365,8 @@ export class DocumentDetailComponent implements OnInit {
   }
 
   getAllEvidence() {
-    const id = +this.route.snapshot.paramMap.get('id');
+    //const id = +this.route.snapshot.paramMap.get('id');
+    const id = this.report.id;
     this.documentService.getAllEvidence(id)
       .subscribe(text => {
         this.docData = text;
diff --git a/src/app/services/document.service.ts b/src/app/services/document.service.ts
index 7ff7647..6a4c4c0 100644
--- a/src/app/services/document.service.ts
+++ b/src/app/services/document.service.ts
@@ -243,7 +243,7 @@ export class DocumentService {
 
   /** GET Snipped of all finding evidence */
   getAllEvidence(id: number): Observable<string> {
-    const url = `${this.documentsUrl}${id}/evidence/findings`;
+    const url = `${this.reportsUrl}${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}`))
-- 
GitLab


From 52afa116de4e8c434f8da0dd5cf2e1437ccd4959 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 21 Sep 2022 16:44:09 +0200
Subject: [PATCH 13/13] get sentences evidence

---
 src/app/document-detail/document-detail.component.ts | 7 ++++---
 src/app/services/document.service.ts                 | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/app/document-detail/document-detail.component.ts b/src/app/document-detail/document-detail.component.ts
index bf11544..051405c 100644
--- a/src/app/document-detail/document-detail.component.ts
+++ b/src/app/document-detail/document-detail.component.ts
@@ -386,7 +386,8 @@ export class DocumentDetailComponent implements OnInit {
   }
 
   getSentencesEvidence() {
-    const id = +this.route.snapshot.paramMap.get('id');
+    //const id = +this.route.snapshot.paramMap.get('id');
+    const id = this.report.id;
     this.documentService.getSentencesEvidence(id)
       .subscribe(text => {
         this.docData = text;
@@ -485,7 +486,7 @@ export class DocumentDetailComponent implements OnInit {
     componentReference.activation(this);
 
     if (componentReference.rowClickEvent != undefined) {
-      //this.getSentencesEvidence();
+      this.getSentencesEvidence();
       componentReference.rowClickEvent.subscribe((data) => {
         this.rowClickSentenceEvidence(data);
       })
@@ -504,7 +505,7 @@ export class DocumentDetailComponent implements OnInit {
     }
 
     if (componentReference.srFindingType != undefined) {
-      //this.getAllEvidence();
+      this.getAllEvidence();
     }
 
     if (componentReference.rowClickEventSRDomainTemplateEvidence != undefined) {
diff --git a/src/app/services/document.service.ts b/src/app/services/document.service.ts
index 6a4c4c0..ee7ede3 100644
--- a/src/app/services/document.service.ts
+++ b/src/app/services/document.service.ts
@@ -261,7 +261,7 @@ export class DocumentService {
 
   /** GET Snipped of sentences evidence */
   getSentencesEvidence(id: number): Observable<string> {
-    const url = `${this.documentsUrl}${id}/evidence/sentences`;
+    const url = `${this.reportsUrl}${id}/evidence/sentences`;
     return this.http.get(url, { responseType: 'text' }).pipe(
       tap(_ => this.log(`fetched all sentences evidence id=${id}`)),
       catchError(this.handleError<string>(`getSentencesEvidence id=${id}`))
-- 
GitLab