[ATL-58] Implemented copying of annotations along with ConceptSet

Author: oleg-odysseus

src/main/java/org/ohdsi/webapi/service/ConceptSetService.java

@@ -47,6 +47,7 @@
 import org.ohdsi.webapi.service.dto.ConceptSetDTO;
 import org.ohdsi.webapi.service.dto.ConceptSetAnnotationDTO;
 import org.ohdsi.webapi.service.dto.AnnotationDTO;
+import org.ohdsi.webapi.service.dto.CopyAnnotationsRequest;
 import org.ohdsi.webapi.shiro.Entities.UserEntity;
 import org.ohdsi.webapi.shiro.Entities.UserRepository;
 import org.ohdsi.webapi.shiro.management.Security;
@@ -916,6 +917,32 @@ public boolean saveConceptSetAnnotation(@PathParam("id") final int id, ConceptSe
         return true;
     }
 
+    private ConceptSetAnnotation copyAnnotation(ConceptSetAnnotation sourceConceptSetAnnotation, int targetConceptSetId){
+        ConceptSetAnnotation targetConceptSetAnnotation = new ConceptSetAnnotation();
+        targetConceptSetAnnotation.setConceptSetId(targetConceptSetId);
+        targetConceptSetAnnotation.setConceptSetVersion(sourceConceptSetAnnotation.getConceptSetVersion());
+        targetConceptSetAnnotation.setAnnotationDetails(sourceConceptSetAnnotation.getAnnotationDetails());
+        targetConceptSetAnnotation.setConceptId(sourceConceptSetAnnotation.getConceptId());
+        targetConceptSetAnnotation.setVocabularyVersion(sourceConceptSetAnnotation.getVocabularyVersion());
+        targetConceptSetAnnotation.setCreatedBy(sourceConceptSetAnnotation.getCreatedBy());
+        targetConceptSetAnnotation.setCreatedDate(sourceConceptSetAnnotation.getCreatedDate());
+        targetConceptSetAnnotation.setModifiedBy(sourceConceptSetAnnotation.getModifiedBy());
+        targetConceptSetAnnotation.setModifiedDate(sourceConceptSetAnnotation.getModifiedDate());
+        return targetConceptSetAnnotation;
+    }
+
+    @POST
+    @Path("/copy-annotations")
+    @Produces(MediaType.APPLICATION_JSON)
+    @Transactional
+    public void copyAnnotations(CopyAnnotationsRequest copyAnnotationsRequest ) {
+        List<ConceptSetAnnotation> sourceAnnotations = getConceptSetAnnotationRepository().findByConceptSetId(copyAnnotationsRequest.getSourceConceptSetId());
+        List<ConceptSetAnnotation> copiedAnnotations= sourceAnnotations.stream()
+                .map(sourceAnnotation -> copyAnnotation(sourceAnnotation, copyAnnotationsRequest.getTargetConceptSetId()))
+                .collect(Collectors.toList());
+        getConceptSetAnnotationRepository().save(copiedAnnotations);
+    }
+
     @GET
     @Path("/{id}/annotation")
     @Produces(MediaType.APPLICATION_JSON)

src/main/java/org/ohdsi/webapi/service/dto/CopyAnnotationsRequest.java

@@ -0,0 +1,23 @@
+package org.ohdsi.webapi.service.dto;
+
+public class CopyAnnotationsRequest {
+
+    private int sourceConceptSetId;
+    private int targetConceptSetId;
+
+    public int getSourceConceptSetId() {
+        return sourceConceptSetId;
+    }
+
+    public int getTargetConceptSetId() {
+        return targetConceptSetId;
+    }
+
+    public void setSourceConceptSetId(int sourceConceptSetId) {
+        this.sourceConceptSetId = sourceConceptSetId;
+    }
+
+    public void setTargetConceptSetId(int targetConceptSetId) {
+        this.targetConceptSetId = targetConceptSetId;
+    }
+}

src/main/resources/db/migration/postgresql/V2.14.0.202407301000__copy_annotations_permission.sql

@@ -0,0 +1,20 @@
+
+INSERT INTO ${ohdsiSchema}.sec_permission(id, value, description) VALUES
+    (nextval('${ohdsiSchema}.sec_permission_id_seq'), 'conceptset:copy-annotations', 'Copy Concept Set Annotations');
+
+INSERT INTO ${ohdsiSchema}.sec_role_permission(id, role_id, permission_id)
+SELECT nextval('${ohdsiSchema}.sec_role_permission_sequence'), sr.id, sp.id
+FROM ${ohdsiSchema}.sec_permission SP, ${ohdsiSchema}.sec_role sr
+WHERE sp.value IN (
+    'conceptset:copy-annotations'
+    ) AND sr.name IN ('admin');
+
+INSERT INTO ${ohdsiSchema}.sec_role_permission(id, role_id, permission_id)
+SELECT nextval('${ohdsiSchema}.sec_role_permission_sequence'), sr.id, sp.id
+FROM ${ohdsiSchema}.sec_permission SP, ${ohdsiSchema}.sec_role sr
+WHERE sp.value IN (
+    'conceptset:copy-annotations'
+    ) AND sr.name IN ('Atlas users');
+
+UPDATE ${ohdsiSchema}.sec_permission SET value='conceptset:annotation:*:delete'
+WHERE value='conceptset:annotation:%s:delete';