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Feature/add clinical data counts endpoint #10262

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merged 12 commits into from
Jul 10, 2023
Merged

Feature/add clinical data counts endpoint #10262

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e2821be
Update StudyView Mapper to utilize CategorizedClinicalDataFilter
haynescd Jun 29, 2023
e696f22
Add Categorical Filtering for SampleClinicalData
haynescd Jun 30, 2023
dbf4358
Update Studyview Filter to abstract common clinicalDataFilter
haynescd Jul 5, 2023
bdf7f94
Fix bug with null ClinicalDataFilter
haynescd Jul 5, 2023
f397d02
Update test
haynescd Jul 5, 2023
24ee286
Add clinical-data-counts api endpoint
haynescd Jul 6, 2023
2b72870
Add test for clinicalDataCount fn
haynescd Jul 6, 2023
a869c2a
Clean up for clinical-data-counts
haynescd Jul 6, 2023
34425b0
Add parallelStream for getClinicalDataCounts
haynescd Jul 6, 2023
9178c29
Fix multiple gene filter (#10256)
alisman Jul 6, 2023
4fa24f1
remove duplicate code
haynescd Jul 7, 2023
2aa3101
Update mutated-genes api to use filtered samples from ch
haynescd Jul 10, 2023
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18 changes: 16 additions & 2 deletions ...istence/persistence-api/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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@@ -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);
}
15 changes: 15 additions & 0 deletions ...tence-api/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataSource.java
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@@ -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;
}
}
16 changes: 16 additions & 0 deletions ...istence-api/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java
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@@ -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;
}
}
17 changes: 15 additions & 2 deletions ...-mybatis/src/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.java
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@@ -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);
}
44 changes: 40 additions & 4 deletions ...c/main/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMyBatisRepository.java
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@@ -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;
Expand All @@ -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();
}
}
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