Move ClinicalCategoricalFilter to repository (#10847)

* use clinical_data_derived instead of sample_clinical_attribute_numeric_mv and patient_clinical_attribute_numeric_mv * use clinical_attribute_meta instead of sample_clinical_attribute_numeric_mv and patient_clinical_attribute_numeric_mv * remove unused clinical data count methods and SQL * fix numericalClinicalDataCountFilter * Move CategoricalClinicalAttributeFilter to repository * remove unused columns * Add override to methods --------- Co-authored-by: haynescd <[email protected]>
cBioPortal · Jun 24, 2024 · a484e2e · a484e2e
1 parent 110236b
commit a484e2e
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Showing 8 changed files with 146 additions and 189 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -1,51 +1,44 @@
 package org.cbioportal.persistence;
 
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.Sample;
-import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
-import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
-import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
 public interface StudyViewRepository {
-    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter);
 
-    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
 
-    List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
-    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter);
+    List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter);
 
-    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
 
-    List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+    List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 
-    List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
-
-    List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
-
-
-    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    List<ClinicalAttribute> getClinicalAttributes();
 
-    List<String> getClinicalDataAttributeNames(ClinicalAttributeDataSource clinicalAttributeDataSource, ClinicalAttributeDataType dataType);
+    List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter);
 
-    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType);
 
-    int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+    int getFilteredSamplesCount(StudyViewFilter studyViewFilter);
 
-    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+    Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, String alterationType);
 
-    int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
+    int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -3,6 +3,7 @@
 import org.apache.ibatis.annotations.MapKey;
 import org.cbioportal.model.AlterationCountByGene;
 import org.cbioportal.model.CaseListDataCount;
+import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
@@ -42,7 +43,7 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
 
     List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
-    List<String> getClinicalAttributeNames(String tableName);
+    List<ClinicalAttribute> getClinicalAttributes();
 
     List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);