Extending Concept Set Items with Annotations

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;
@@ -36,7 +37,7 @@
  *
  * @author fdefalco
  */
-@Entity(name = "ConceptSet")
+@Entity
 @Table(name="concept_set")
 public class ConceptSet extends CommonEntityExt<Integer> implements Serializable {
 

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

@@ -21,7 +21,7 @@
  * @author Anthony Sena <https://github.com/ohdsi>
  */
 
-@Entity(name = "ConceptSetGenerationInfo")
+@Entity
 @Table(name = "concept_set_generation_info")
 @IdClass(ConceptSetGenerationInfoKey.class)
 public class ConceptSetGenerationInfo implements Serializable {

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

@@ -29,7 +29,7 @@
  * @author fdefalco
  */
 
-@Entity(name = "ConceptSetItem")
+@Entity
 @Table(name="concept_set_item")
 public class ConceptSetItem implements Serializable{
 

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
+@Table(name = "concept_set_annotation")
+public class ConceptSetAnnotation extends CommonEntity<Integer> 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 String 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 String getConceptSetVersion() {
+        return conceptSetVersion;
+    }
+
+    public void setConceptSetVersion(String 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/ConceptSetAnnotationPermissionSchema.java

@@ -0,0 +1,25 @@
+package org.ohdsi.webapi.security.model;
+
+import org.springframework.stereotype.Component;
+
+import java.util.HashMap;
+import java.util.Map;
+
+@Component
+public class ConceptSetAnnotationPermissionSchema extends EntityPermissionSchema {
+
+    private static Map<String, String> writePermissions = new HashMap<String, String>() {
+        {
+            put("conceptset:annotation:%s:delete", "Delete Concept Set Annotation with ID %s");
+        }
+    };
+
+    private static Map<String, String> readPermissions = new HashMap<String, String>() {
+        {
+        }
+    };
+
+    public ConceptSetAnnotationPermissionSchema() {
+        super(EntityType.CONCEPT_SET_ANNOTATION, readPermissions, writePermissions);
+    }
+}

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

@@ -4,6 +4,7 @@
 import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
 import org.ohdsi.webapi.cohortsample.CohortSample;
 import org.ohdsi.webapi.conceptset.ConceptSet;
+import org.ohdsi.webapi.conceptset.annotation.ConceptSetAnnotation;
 import org.ohdsi.webapi.estimation.Estimation;
 import org.ohdsi.webapi.feanalysis.domain.FeAnalysisEntity;
 import org.ohdsi.webapi.ircalc.IncidenceRateAnalysis;
@@ -26,7 +27,8 @@ public enum EntityType {
     PREDICTION(PredictionAnalysis.class),
     COHORT_SAMPLE(CohortSample.class),
     TAG(Tag.class),
-    REUSABLE(Reusable.class);
+    REUSABLE(Reusable.class),
+    CONCEPT_SET_ANNOTATION(ConceptSetAnnotation.class);
 
     private final 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;