Delete concept sets per OHDSI/Atlas#87

OHDSI · Sep 16, 2016 · 7857c9c · 7857c9c
1 parent 9d833a0
commit 7857c9c
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Showing 3 changed files with 70 additions and 3 deletions.
diff --git a/src/main/java/org/ohdsi/webapi/evidence/NegativeControlRepository.java b/src/main/java/org/ohdsi/webapi/evidence/NegativeControlRepository.java
@@ -6,6 +6,7 @@
 package org.ohdsi.webapi.evidence;
 
 import java.util.Collection;
+import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
@@ -17,4 +18,8 @@
 public interface NegativeControlRepository extends CrudRepository<NegativeControlRecord, Integer> {
   @Query("SELECT n FROM NegativeControlRecord n WHERE n.sourceId = :sourceId AND n.conceptSetId = :conceptSetId")
   Collection<NegativeControlRecord> findAllBySourceIdAndConceptId(@Param("sourceId") int sourceId, @Param("conceptSetId") int conceptSetId);
+
+  @Modifying
+  @Query("DELETE FROM NegativeControlRecord n WHERE n.conceptSetId = :conceptSetId")
+  void deleteAllByConceptSetId(@Param("conceptSetId") int conceptSetId);
 }
diff --git a/src/main/java/org/ohdsi/webapi/service/ConceptSetService.java b/src/main/java/org/ohdsi/webapi/service/ConceptSetService.java
@@ -48,10 +48,12 @@
 import org.ohdsi.webapi.conceptset.ConceptSetGenerationInfoRepository;
 import org.ohdsi.webapi.conceptset.ConceptSetItem;
 import org.ohdsi.webapi.conceptset.ExportUtil;
+import org.ohdsi.webapi.evidence.NegativeControlRepository;
 import org.ohdsi.webapi.source.SourceInfo;
 import org.ohdsi.webapi.vocabulary.Concept;
 import org.ohdsi.webapi.vocabulary.ConceptSetExpression;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.EmptyResultDataAccessException;
 import org.springframework.stereotype.Component;
 
 /**
@@ -62,9 +64,11 @@
 @Component
 public class ConceptSetService extends AbstractDaoService {
 
-  @Autowired
-  private ConceptSetGenerationInfoRepository conceptSetGenerationInfoRepository;
-
+    @Autowired
+    private ConceptSetGenerationInfoRepository conceptSetGenerationInfoRepository;
+
+    @Autowired
+    private NegativeControlRepository negativeControlRepository;
 
     @Autowired
     private VocabularyService vocabService;
@@ -243,4 +247,53 @@ private ConceptSetExport getConceptSetForExport(int conceptSetId, SourceInfo voc
   public Collection<ConceptSetGenerationInfo> getConceptSetGenerationInfo(@PathParam("id") final int id) {
       return this.conceptSetGenerationInfoRepository.findAllByConceptSetId(id);
   }
+
+  @POST
+  @Transactional(rollbackOn = Exception.class, dontRollbackOn = EmptyResultDataAccessException.class)
+  @Path("{id}/delete")
+  public void deleteConceptSet(@PathParam("id") final int id) throws Exception {
+      // Remove the concept set
+      try {
+        getConceptSetRepository().delete(id);
+      } catch (EmptyResultDataAccessException e) {
+          // Ignore - there may be no data
+          log.debug(e.getMessage());
+      }
+      catch (Exception e) {
+          throw e;
+      }
+
+      // Remove the concept set items
+      try {
+        getConceptSetItemRepository().deleteByConceptSetId(id);
+      } catch (EmptyResultDataAccessException e) {
+          // Ignore - there may be no data
+          log.debug(e.getMessage());
+      }
+      catch (Exception e) {
+          throw e;
+      }
+
+      // Remove any generation info
+      try {
+        this.conceptSetGenerationInfoRepository.deleteByConceptSetId(id);
+      } catch (EmptyResultDataAccessException e) {
+          // Ignore - there may be no data
+          log.debug(e.getMessage());
+      }
+      catch (Exception e) {
+          throw e;
+      }
+
+      // Remove any evidence
+      try {
+        this.negativeControlRepository.deleteAllByConceptSetId(id);
+      } catch (EmptyResultDataAccessException e) {
+          // Ignore - there may be no data
+          log.debug(e.getMessage());
+      }
+      catch (Exception e) {
+          throw e;
+      }
+  }
 }
diff --git a/src/main/java/org/ohdsi/webapi/service/VocabularyService.java b/src/main/java/org/ohdsi/webapi/service/VocabularyService.java
@@ -658,13 +658,16 @@ public ConceptSetOptimizationResult optimizeConceptSet(@PathParam("sourceKey") S
     Hashtable<String, ConceptSetExpression.ConceptSetItem> allConceptSetItems = new Hashtable<String, ConceptSetExpression.ConceptSetItem>();
     ArrayList<String> includedConcepts = new ArrayList<String>();
     ArrayList<String> descendantConcepts = new ArrayList<String>();
+    ArrayList<String> allOtherConcepts = new ArrayList<String>();
     for(ConceptSetExpression.ConceptSetItem item : conceptSetExpression.items) {
         allConceptSetItems.put(item.concept.conceptId.toString(), item);
         if (!item.isExcluded) {
             includedConcepts.add(item.concept.conceptId.toString());
             if (item.includeDescendants) {
                 descendantConcepts.add(item.concept.conceptId.toString());
             }
+        } else {
+            allOtherConcepts.add(item.concept.conceptId.toString());
         }
     }
 
@@ -696,6 +699,12 @@ public ConceptSetOptimizationResult optimizeConceptSet(@PathParam("sourceKey") S
             removedExpressionItems.add(csi);
         }
     }
+    // Re-add back the other concepts that are not considered
+    // as part of the optimizatin process
+    for(String conceptId : allOtherConcepts) {
+        ConceptSetExpression.ConceptSetItem csi = allConceptSetItems.get(conceptId);
+        optimzedExpressionItems.add(csi);
+    }
     returnVal.optimizedConceptSet.items = optimzedExpressionItems.toArray(new ConceptSetExpression.ConceptSetItem[optimzedExpressionItems.size()]);
     returnVal.removedConceptSet.items = removedExpressionItems.toArray(new ConceptSetExpression.ConceptSetItem[removedExpressionItems.size()]);