Rebase with feature branch

gblaih · Aug 20, 2024 · de09473 · de09473
1 parent a7a2b5e
commit de09473
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Showing 4 changed files with 5 additions and 8 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -14,7 +14,6 @@
 import org.cbioportal.model.SampleTreatment;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.CustomSampleIdentifier;
-import org.cbioportal.web.parameter.SampleIdentifier;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -17,7 +17,7 @@
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.ClinicalDataType;
-import org.cbioportal.web.parameter.SampleIdentifier;
+import org.cbioportal.web.parameter.CustomSampleIdentifier;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -18,7 +18,6 @@
 import org.cbioportal.service.treatment.TreatmentCountReportService;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.CustomSampleIdentifier;
-import org.cbioportal.web.parameter.SampleIdentifier;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.cbioportal.web.columnar.util.CustomDataFilterUtil;
@@ -27,7 +26,6 @@
 import org.springframework.stereotype.Service;
 
 import java.util.ArrayList;
-import java.math.BigDecimal;
 import java.util.List;
 import java.util.stream.Collectors;
 import java.util.Map;

diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java
@@ -45,7 +45,7 @@ public void getMolecularProfileCounts() {
         studyViewFilter.setGenomicProfiles(profileGroups);
 
         var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, List.of());
 
         var size = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations"))
             .findFirst().get().getCount().intValue();
@@ -64,7 +64,7 @@ public void getMolecularProfileCountsMultipleStudies() {
         studyViewFilter.setGenomicProfiles(profileGroups);
 
         var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, List.of());
 
         var size = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations"))
             .findFirst().get().getCount().intValue();
@@ -83,7 +83,7 @@ public void getMolecularProfileCountsMultipleProfilesUnion() {
         studyViewFilter.setGenomicProfiles(profileGroups);
 
         var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, List.of() );
 
         var sizeMutations = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations"))
             .findFirst().get().getCount().intValue();
@@ -107,7 +107,7 @@ public void getMolecularProfileCountsMultipleProfilesIntersect() {
         studyViewFilter.setGenomicProfiles(profileGroups);
 
         var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, List.of());
 
         var sizeMutations = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations"))
             .findFirst().get().getCount().intValue();