Merge pull request #131 from TheJacksonLaboratory/develop

release 1.0.8

build.gradle

@@ -10,7 +10,7 @@ plugins {
 }
 
 group = 'org.monarchinitiative.poet'
-version = '1.0.6'
+version = '1.0.8'
 sourceCompatibility = '11'
 
 configurations {

src/main/java/org/monarchinitiative/poet/model/entities/AnnotationSource.java

@@ -8,6 +8,10 @@
 import java.util.Objects;
 
 @Entity
+@Table(
+        uniqueConstraints=
+        @UniqueConstraint(columnNames={"publication_id", "disease_id"})
+)
 public class AnnotationSource {
 
     @Id

src/main/java/org/monarchinitiative/poet/model/entities/TreatmentAnnotation.java

@@ -134,4 +134,11 @@ public String getExtensionId() {
     public String getExtensionLabel() {
         return extensionLabel;
     }
+
+    public String getExportPhenotypeId() {
+        if (hpoId.equals("HP:0000118")){
+            return super.getAnnotationSource().getDisease().getExportDiseaseId();
+        }
+        return hpoId;
+    }
 }

src/main/java/org/monarchinitiative/poet/service/ExportService.java

@@ -93,9 +93,10 @@ public void exportMAXOAnnotations(PrintWriter writer, CSVFormat format, boolean
 
                 annotationService.getLastUpdatedForAnnotation(annotation);
                 annotationService.getCreatedDateForAnnotation(annotation);
+                String hpoId = annotation.getHpoId();
                 csvPrinter.printRecord(annotation.getAnnotationSource().getDisease().getExportDiseaseId(),
                         annotation.getAnnotationSource().getDisease().getDiseaseName(), reference,
-                        annotation.getMaxoId(), annotation.getMaxoName(), annotation.getHpoId(), annotation.getRelation(),
+                        annotation.getMaxoId(), annotation.getMaxoName(), annotation.getExportPhenotypeId(), annotation.getRelation(),
                         annotation.getEvidence(), annotation.getExtensionId(), annotation.getExtensionLabel(),
                         annotation.getComment(), "", annotation.getOwner().getExportName(), annotation.getExportLastUpdatedDate(), annotation.getCreatedDate()
                 );

src/main/poet/package.json

@@ -1,6 +1,6 @@
 {
   "name": "poet",
-  "version": "1.0.6",
+  "version": "1.0.8",
   "scripts": {
     "ng": "ng",
     "start": "ng serve",

src/main/poet/src/app/portal/portal-curate/dialog-source/dialog-source.component.html

@@ -1,15 +1,9 @@
-<h2 mat-dialog-title>Source Selection</h2>
 <mat-dialog-content class="mat-typography">
   <!-- Find disease or publication, then find all annotation sources for it. -->
   <div class="existing-curation" *ngIf="!newPublication">
     <div *ngIf="selectedDisease">
+      <button class="new-btn" mat-stroked-button (click)="selectPublication('new')">New Publication</button>
       <mat-selection-list #publications (selectionChange)="selectPublication(publications.selectedOptions.selected[0].value)" multiple="false">
-        <mat-list-option class="selection-wrapper" value="new">
-          <mat-icon matListIcon>add_box</mat-icon>
-          <div class="selection-text">
-            <strong>Add New Publication for {{selectedDisease.diseaseName}}</strong>
-          </div>
-        </mat-list-option>
         <mat-list-option class="selection-wrapper"
                          *ngFor="let publication of annotatedPublications$ | async"
                          [value]="publication">

src/main/poet/src/app/portal/portal-curate/dialog-source/dialog-source.component.scss

@@ -61,3 +61,7 @@
   margin: 0 auto;
   text-align: center;
 }
+
+.new-btn {
+  margin-left: 1rem;
+}

src/main/poet/src/app/portal/portal-curate/dialog-source/dialog-source.component.ts

@@ -3,7 +3,7 @@ import { ErrorStateMatcher } from '@angular/material/core';
 import { UntypedFormControl, FormGroupDirective, NgForm, Validators } from '@angular/forms';
 import { MAT_DIALOG_DATA, MatDialogRef } from '@angular/material/dialog';
 import { CurationService } from '../../../shared/services/curation/curation.service';
-import { debounceTime, distinctUntilChanged } from 'rxjs/operators';
+import { debounceTime, distinctUntilChanged, filter, map } from 'rxjs/operators';
 import { PubmedService } from '../../../shared/services/external/pubmed.service';
 import { StateService } from '../../../shared/services/state/state.service';
 import { Publication } from '../../../shared/models/models';
@@ -105,17 +105,28 @@ export class DialogSourceComponent implements OnInit {
         firstAuthor: this.selectedPublication.sortfirstauthor
       }
     };
-    this.curationService.savePublication(source).subscribe(() => {
-      this.annotatedPublications$ = this.curationService.getDiseasePublications(this.selectedDisease.diseaseId);
-      this.newPublication = false;
-      this.selectedPublication = source.publication;
-      this.closeDialog();
-    }, error => {
-      const message = this.getErrorMessage(error);
-      this._snackBar.open(message, 'Close', {
-        duration: 5000,
-      });
-    });
+
+    this.annotatedPublications$.pipe(
+      map(items =>
+      items.filter(item => item.publicationId == source.publication.publicationId)
+      )).subscribe((existing) => {
+        if(existing && existing.length > 0){
+          this.newPublication = false;
+          this.selectPublication(existing[0]);
+        } else {
+          this.curationService.savePublication(source).subscribe(() => {
+            this.annotatedPublications$ = this.curationService.getDiseasePublications(this.selectedDisease.diseaseId);
+            this.newPublication = false;
+            this.selectedPublication = source.publication;
+            this.closeDialog();
+          }, error => {
+            const message = this.getErrorMessage(error);
+            this._snackBar.open(message, 'Close', {
+              duration: 5000,
+            });
+          });
+        }
+    })
   }
 
   getErrorMessage(error: any) {