Clean up for clinical-data-counts

cBioPortal · Jul 6, 2023 · a869c2a · a869c2a
1 parent 2b72870
commit a869c2a
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Showing 3 changed files with 5 additions and 9 deletions.
diff --git a/...-mybatis/src/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.java b/...-mybatis/src/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.java
@@ -13,13 +13,13 @@ public interface StudyViewMapper {
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
     List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
-                                                         boolean applyPatientIdFilters,  List<String> attributeIds, List<String> filterAttributeValues);
+                                                         boolean applyPatientIdFilters,  List<String> attributeIds, List<String> filteredAttributeValues);
 
     List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
-                                                        boolean applyPatientIdFilters, List<String> attributeIds, List<String> filterAttributeValues );
+                                                        boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues );
 
     List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
-                                                  boolean applyPatientIdFilters, List<String> attributeIds, List<String> filterAttributeValues);
+                                                  boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
 
     List<String> getClinicalAttributeNames(String tableName);
 }
diff --git a/...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml b/...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml
@@ -63,7 +63,7 @@
             </if>
             )
             AND UPPER(attribute_value) NOT IN
-            <foreach item="filteredAttributeValue" collection="filterAttributeValues" open="(" separator="," close=")">
+            <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">
                 #{filteredAttributeValue}
             </foreach>
             AND attribute_name IN
@@ -93,7 +93,7 @@
             </if>
             )
             AND UPPER(attribute_value) NOT IN
-            <foreach item="filteredAttributeValue" collection="filterAttributeValues" open="(" separator="," close=")">
+            <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">
                 #{filteredAttributeValue}
             </foreach>
             AND attribute_name IN

diff --git a/service/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java b/service/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
@@ -284,10 +284,6 @@ public List<ClinicalDataCountItem> getClinicalDataCountsFromColumnStore(StudyVie
             }).collect(Collectors.toList());
     }
 
-    private boolean isClinicalDataValueEmpty(String clinicalDataValue) {
-        return clinicalDataValue.equalsIgnoreCase("NA") || clinicalDataValue.equalsIgnoreCase("NAN") || clinicalDataValue.equalsIgnoreCase("N/A");
-    }
-
     private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter) {
         if(clinicalAttributeNameMap.isEmpty()) {
            buildClinicalAttributeNameMap();