Extending Concept Set Items with Annotations (#2403)

Co-authored-by: Hernaldo Urbina <[email protected]>
Co-authored-by: hernaldo.urbina <mailto:[email protected]>
Co-authored-by: oleg-odysseus <[email protected]>

Author: 4 people

src/main/java/org/ohdsi/webapi/conceptset/ConceptSet.java

@@ -26,6 +26,7 @@
 import javax.persistence.JoinTable;
 import javax.persistence.ManyToMany;
 import javax.persistence.Table;
+import javax.persistence.OneToOne;
 import org.hibernate.annotations.GenericGenerator;
 import org.hibernate.annotations.Parameter;
 import org.ohdsi.webapi.model.CommonEntity;

src/main/java/org/ohdsi/webapi/conceptset/annotation/ConceptSetAnnotation.java

@@ -0,0 +1,108 @@
+package org.ohdsi.webapi.conceptset.annotation;
+
+import org.hibernate.annotations.GenericGenerator;
+import org.hibernate.annotations.Parameter;
+import org.ohdsi.webapi.model.CommonEntity;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import java.io.Serializable;
+
+@Entity(name = "ConceptSetAnnotation")
+@Table(name = "concept_set_annotation")
+public class ConceptSetAnnotation implements Serializable {
+    /**
+     *
+     */
+    private static final long serialVersionUID = 1L;
+
+    @Id
+    @GenericGenerator(
+            name = "concept_set_annotation_generator",
+            strategy = "org.hibernate.id.enhanced.SequenceStyleGenerator",
+            parameters = {
+                    @Parameter(name = "sequence_name", value = "concept_set_annotation_sequence"),
+                    @Parameter(name = "increment_size", value = "1")
+            }
+    )
+    @GeneratedValue(generator = "concept_set_annotation_generator")
+    @Column(name = "concept_set_annotation_id")
+    private Integer id;
+
+    @Column(name = "concept_set_id", nullable = false)
+    private Integer conceptSetId;
+
+    @Column(name = "concept_id")
+    private Integer conceptId;
+
+    @Column(name = "annotation_details")
+    private String annotationDetails;
+
+    @Column(name = "vocabulary_version")
+    private String vocabularyVersion;
+
+    @Column(name = "concept_set_version")
+    private Integer conceptSetVersion;
+
+    @Column(name = "copied_from_concept_set_ids")
+    private String copiedFromConceptSetIds;
+
+    public Integer getId() {
+        return id;
+    }
+
+    public void setId(Integer id) {
+        this.id = id;
+    }
+
+    public Integer getConceptSetId() {
+        return conceptSetId;
+    }
+
+    public void setConceptSetId(Integer conceptSetId) {
+        this.conceptSetId = conceptSetId;
+    }
+
+    public Integer getConceptId() {
+        return conceptId;
+    }
+
+    public void setConceptId(Integer conceptId) {
+        this.conceptId = conceptId;
+    }
+
+    public String getAnnotationDetails() {
+        return annotationDetails;
+    }
+
+    public void setAnnotationDetails(String annotationDetails) {
+        this.annotationDetails = annotationDetails;
+    }
+
+    public String getVocabularyVersion() {
+        return vocabularyVersion;
+    }
+
+    public void setVocabularyVersion(String vocabularyVersion) {
+        this.vocabularyVersion = vocabularyVersion;
+    }
+
+    public Integer getConceptSetVersion() {
+        return conceptSetVersion;
+    }
+
+    public void setConceptSetVersion(Integer conceptSetVersion) {
+        this.conceptSetVersion = conceptSetVersion;
+    }
+
+    public String getCopiedFromConceptSetIds() {
+        return copiedFromConceptSetIds;
+    }
+
+    public void setCopiedFromConceptSetIds(String copiedFromConceptSetIds) {
+        this.copiedFromConceptSetIds = copiedFromConceptSetIds;
+    }
+}

src/main/java/org/ohdsi/webapi/conceptset/annotation/ConceptSetAnnotationRepository.java

@@ -0,0 +1,20 @@
+package org.ohdsi.webapi.conceptset.annotation;
+
+import java.util.List;
+import java.util.Optional;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+
+public interface ConceptSetAnnotationRepository extends JpaRepository<ConceptSetAnnotation, Integer> {
+    
+    @Query("DELETE FROM ConceptSetAnnotation cc WHERE cc.conceptSetId = :conceptSetId and cc.conceptId in :conceptId")
+    void deleteAnnotationByConceptSetIdAndInConceptId(int conceptSetId, List<Integer> conceptId);
+
+    void deleteAnnotationByConceptSetIdAndConceptId(int conceptSetId, int conceptId);
+
+    List<ConceptSetAnnotation> findByConceptSetId(int conceptSetId);
+    ConceptSetAnnotation findById(int id);
+    void deleteById(int id);
+    Optional<ConceptSetAnnotation> findConceptSetAnnotationByConceptIdAndConceptId(int conceptSetId, int conceptId);
+}

src/main/java/org/ohdsi/webapi/security/model/ConceptSetPermissionSchema.java

@@ -11,17 +11,21 @@ public class ConceptSetPermissionSchema extends EntityPermissionSchema {
     private static Map<String, String> writePermissions = new HashMap<String, String>() {{
         put("conceptset:%s:put", "Update Concept Set with ID = %s");
         put("conceptset:%s:items:put", "Update Items of Concept Set with ID = %s");
+        put("conceptset:*:annotation:put", "Create Concept Set Annotation");
+        put("conceptset:%s:annotation:*:delete", "Delete Annotations of Concept Set with ID = %s");
+        put("conceptset:*:annotation:*:delete", "Delete Annotations of any Concept Set");
         put("conceptset:%s:delete", "Delete Concept Set with ID = %s");
     }};
 
     private static Map<String, String> readPermissions = new HashMap<String, String>() {{
         put("conceptset:%s:get", "view conceptset  definition with id %s");
         put("conceptset:%s:expression:get", "Resolve concept set %s expression");
+        put("conceptset:%s:annotation:get", "Resolve concept set annotations");
+        put("conceptset:*:annotation:get", "Resolve concept set annotations");
         put("conceptset:%s:version:*:expression:get", "Get expression for concept set %s items for default source");
     }};
 
     public ConceptSetPermissionSchema() {
-
         super(EntityType.CONCEPT_SET, readPermissions, writePermissions);
     }
 }

src/main/java/org/ohdsi/webapi/security/model/EntityType.java

@@ -27,7 +27,6 @@ public enum EntityType {
     COHORT_SAMPLE(CohortSample.class),
     TAG(Tag.class),
     REUSABLE(Reusable.class);
-
     private final Class<? extends CommonEntity> entityClass;
 
     EntityType(Class<? extends CommonEntity> entityClass) {

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

@@ -20,6 +20,7 @@
 import org.ohdsi.webapi.conceptset.ConceptSetComparison;
 import org.ohdsi.webapi.conceptset.ConceptSetItemRepository;
 import org.ohdsi.webapi.conceptset.ConceptSetRepository;
+import org.ohdsi.webapi.conceptset.annotation.ConceptSetAnnotationRepository;
 import org.ohdsi.webapi.exception.BadRequestAtlasException;
 import org.ohdsi.webapi.ircalc.IncidenceRateAnalysis;
 import org.ohdsi.webapi.model.CommonEntity;
@@ -106,6 +107,9 @@ public abstract class AbstractDaoService extends AbstractAdminService {
   @Autowired
   private ConceptSetItemRepository conceptSetItemRepository;
 
+  @Autowired
+  private ConceptSetAnnotationRepository conceptSetAnnotationRepository;
+
   @Autowired
   protected Security security;
 
@@ -120,6 +124,9 @@ public abstract class AbstractDaoService extends AbstractAdminService {
   public ConceptSetItemRepository getConceptSetItemRepository() {
     return conceptSetItemRepository;
   }
+  public ConceptSetAnnotationRepository getConceptSetAnnotationRepository() {
+    return conceptSetAnnotationRepository;
+  }
 
   @Autowired 
   private ConceptSetRepository conceptSetRepository;