Feature/add clinical data counts endpoint (cBioPortal#10262)

Migrate mutated-genes and clinical-data-counts to clickhouse-ish implementations --------- Co-authored-by: haynescd <haynescd@chop.edu>
pughlab · Nov 8, 2023 · f0f6a8a · f0f6a8a
1 parent 7aefa76
commit f0f6a8a
Show file tree

Hide file tree

Showing 12 changed files with 643 additions and 78 deletions.
diff --git a/...istence/persistence-api/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/...istence/persistence-api/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -1,13 +1,27 @@
 package org.cbioportal.persistence;
 
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.Sample;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
+import org.cbioportal.webparam.CategorizedClinicalDataCountFilter;
 import org.cbioportal.webparam.StudyViewFilter;
 
 import java.util.List;
 
 public interface StudyViewRepository {
-    List<Sample> getFilteredSamplesFromColumnstore(StudyViewFilter studyViewFilter);
+    List<Sample> getFilteredSamplesFromColumnstore(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
+
+    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+
+    List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+
+    List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);
+
+    List<String> getClinicalDataAttributeNames(ClinicalAttributeDataSource clinicalAttributeDataSource, ClinicalAttributeDataType dataType);
 
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
 }
diff --git a/...tence-api/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataSource.java b/...tence-api/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataSource.java
@@ -0,0 +1,15 @@
+package org.cbioportal.persistence.enums;
+
+public enum ClinicalAttributeDataSource {
+    PATIENT("PATIENT"),SAMPLE("SAMPLE");
+
+    private final String value;
+
+    ClinicalAttributeDataSource(String value) {
+        this.value = value;
+    }
+
+    public String getValue() {
+        return this.value;
+    }
+}
diff --git a/...istence-api/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java b/...istence-api/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java
@@ -0,0 +1,16 @@
+package org.cbioportal.persistence.enums;
+
+public enum ClinicalAttributeDataType {
+    CATEGORICAL("CATEGORICAL"),
+    NUMERIC("NUMERIC");
+
+    private final String value;
+
+    ClinicalAttributeDataType(String value) {
+        this.value = value;
+    }
+
+    public String getValue() {
+        return this.value;
+    }
+}
diff --git a/...-mybatis/src/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.java b/...-mybatis/src/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.java
@@ -1,12 +1,25 @@
 package org.cbioportal.persistence.mybatiscolumnstore;
 
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.Sample;
+import org.cbioportal.webparam.CategorizedClinicalDataCountFilter;
 import org.cbioportal.webparam.StudyViewFilter;
 
 import java.util.List;
 
 public interface StudyViewMapper {
-    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter);
-    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
+    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+
+    List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                         boolean applyPatientIdFilters,  List<String> attributeIds, List<String> filteredAttributeValues);
+
+    List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                        boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues );
+
+    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
+                                                  boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
+
+    List<String> getClinicalAttributeNames(String tableName);
 }
diff --git a/...c/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMyBatisRepository.java b/...c/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMyBatisRepository.java
@@ -1,8 +1,13 @@
 package org.cbioportal.persistence.mybatiscolumnstore;
 
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.StudyViewRepository;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
+import org.cbioportal.webparam.CategorizedClinicalDataCountFilter;
 import org.cbioportal.webparam.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
@@ -12,16 +17,47 @@
 @Repository
 public class StudyViewMyBatisRepository implements StudyViewRepository {
 
+    private final List<String> FILTERED_CLINICAL_ATTR_VALUES = List.of("NA", "NAN", "N/A");
     @Autowired
     private StudyViewMapper studyViewMapper;
 
     @Override
-    public List<Sample> getFilteredSamplesFromColumnstore(StudyViewFilter studyViewFilter) {
-        return studyViewMapper.getFilteredSamples(studyViewFilter);
+    public List<Sample> getFilteredSamplesFromColumnstore(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+
+        return studyViewMapper.getFilteredSamples(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
     }
 
     @Override
-    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter) {
-        return studyViewMapper.getMutatedGenes(studyViewFilter);
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+        return studyViewMapper.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
+    }
+
+    @Override
+    public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes) {
+        return studyViewMapper.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+            filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES );
+    }
+
+    @Override
+    public List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes) {
+        return studyViewMapper.getSampleClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+           filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES );
+    }
+
+    @Override
+    public List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes) {
+        return studyViewMapper.getPatientClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+            filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES);
+    }
+
+    @Override
+    public List<String> getClinicalDataAttributeNames(ClinicalAttributeDataSource clinicalAttributeDataSource, ClinicalAttributeDataType dataType) {
+        String tableName = clinicalAttributeDataSource.getValue().toLowerCase() + "_clinical_attribute_" + dataType.getValue().toLowerCase();
+        return studyViewMapper.getClinicalAttributeNames(tableName);
+    }
+
+    private boolean shouldApplyPatientIdFilters(CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
+        return categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
+            || categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters().isEmpty();
     }
 }