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Refactor sort/search/pagination for ClinicalData table endpoint
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@pvannierop @alisman
pvannierop authored and alisman committed Jan 30, 2024
1 parent 3cfca1e commit bff1453
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Showing 38 changed files with 792 additions and 443 deletions.
33 changes: 0 additions & 33 deletions src/main/java/org/cbioportal/model/ClinicalDataCollection.java
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This file was deleted.

19 changes: 19 additions & 0 deletions src/main/java/org/cbioportal/model/SampleClinicalDataCollection.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
package org.cbioportal.model;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

public class SampleClinicalDataCollection {

private Map<String, List<ClinicalData>> byUniqueSampleKey = new HashMap<>();

public Map<String, List<ClinicalData>> getByUniqueSampleKey() {
return byUniqueSampleKey;
}

public void setByUniqueSampleKey(Map<String, List<ClinicalData>> byUniqueSampleKey) {
this.byUniqueSampleKey = byUniqueSampleKey;
}

}
18 changes: 9 additions & 9 deletions src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,14 +47,6 @@ BaseMeta fetchMetaClinicalDataInStudy(String studyId, List<String> ids, List<Str
List<ClinicalData> fetchClinicalData(List<String> studyIds, List<String> ids, List<String> attributeIds,
String clinicalDataType, String projection);

List<ClinicalData> fetchSampleClinicalTable(List<String> studyIds, List<String> ids,
Integer pageSize, Integer pageNumber, String searchTerm,
String sortBy, String direction);

@Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
Integer fetchSampleClinicalTableCount(List<String> studyIds, List<String> ids, String searchTerm,
String sortBy, String direction);

@Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
BaseMeta fetchMetaClinicalData(List<String> studyIds, List<String> ids, List<String> attributeIds,
String clinicalDataType);
Expand All @@ -65,5 +57,13 @@ List<ClinicalDataCount> fetchClinicalDataCounts(List<String> studyIds, List<Stri

@Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
List<ClinicalData> getPatientClinicalDataDetailedToSample(List<String> studyIds, List<String> patientIds,
List<String> attributeIds);
List<String> attributeIds);

List<Integer> getVisibleSampleInternalIdsForClinicalTable(List<String> studyIds, List<String> sampleIds,
Integer pageSize, Integer pageNumber, String searchTerm,
String sortBy, String direction);

List<ClinicalData> getSampleClinicalDataBySampleInternalIds(List<Integer> visibleSampleInternalIds);

List<ClinicalData> getPatientClinicalDataBySampleInternalIds(List<Integer> visibleSampleInternalIds);
}
6 changes: 3 additions & 3 deletions src/main/java/org/cbioportal/persistence/mybatis/CancerTypeMyBatisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import org.cbioportal.model.meta.BaseMeta;
import org.cbioportal.persistence.CancerTypeRepository;
import org.cbioportal.persistence.PersistenceConstants;
import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

Expand All @@ -16,14 +16,14 @@ public class CancerTypeMyBatisRepository implements CancerTypeRepository {
@Autowired
private CancerTypeMapper cancerTypeMapper;
@Autowired
private OffsetCalculator offsetCalculator;
private PaginationCalculator paginationCalculator;

@Override
public List<TypeOfCancer> getAllCancerTypes(String projection, Integer pageSize, Integer pageNumber, String sortBy,
String direction) {

return cancerTypeMapper.getAllCancerTypes(projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
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8 changes: 4 additions & 4 deletions src/main/java/org/cbioportal/persistence/mybatis/ClinicalAttributeMyBatisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import org.cbioportal.model.meta.BaseMeta;
import org.cbioportal.persistence.ClinicalAttributeRepository;
import org.cbioportal.persistence.PersistenceConstants;
import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

Expand All @@ -18,14 +18,14 @@ public class ClinicalAttributeMyBatisRepository implements ClinicalAttributeRepo
@Autowired
private ClinicalAttributeMapper clinicalAttributeMapper;
@Autowired
private OffsetCalculator offsetCalculator;
private PaginationCalculator paginationCalculator;

@Override
public List<ClinicalAttribute> getAllClinicalAttributes(String projection, Integer pageSize, Integer pageNumber,
String sortBy, String direction) {

return clinicalAttributeMapper.getClinicalAttributes(null, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
Expand All @@ -47,7 +47,7 @@ public List<ClinicalAttribute> getAllClinicalAttributesInStudy(String studyId, S
String direction) {

return clinicalAttributeMapper.getClinicalAttributes(Arrays.asList(studyId), projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
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12 changes: 11 additions & 1 deletion src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@ List<ClinicalData> getPatientClinicalData(List<String> studyIds, List<String> pa

List<ClinicalData> getSampleClinicalTable(List<String> studyIds, List<String> sampleIds, String projection,
Integer limit, Integer offset, String searchTerm,
String sortBy, String direction);
String sortByAttrId, Boolean sortAttrIsNumber, Boolean sortIsPatientAttr,
String direction);

Integer getSampleClinicalTableCount(List<String> studyIds, List<String> sampleIds, String projection,
String searchTerm, String sortBy, String direction);
Expand All @@ -36,4 +37,13 @@ List<ClinicalDataCount> fetchPatientClinicalDataCounts(List<String> studyIds, Li
List<ClinicalData> getPatientClinicalDataDetailedToSample(List<String> studyIds, List<String> patientIds,
List<String> attributeIds, String projection, Integer limit,
Integer offset, String sortBy, String direction);

List<Integer> getVisibleSampleInternalIdsForClinicalTable(List<String> studyIds, List<String> sampleIds,
String projection, Integer limit, Integer offset,
String searchTerm, String sortAttrId, Boolean sortAttrIsNumber,
Boolean sortIsPatientAttr, String direction);

List<ClinicalData> getSampleClinicalDataBySampleInternalIds(List<Integer> sampleInternalIds);

List<ClinicalData> getPatientClinicalDataBySampleInternalIds(List<Integer> sampleInternalIds);
}
74 changes: 51 additions & 23 deletions src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java
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Original file line number Diff line number Diff line change
@@ -1,20 +1,22 @@
package org.cbioportal.persistence.mybatis;

import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.Patient;
import org.cbioportal.model.meta.BaseMeta;
import org.cbioportal.persistence.ClinicalDataRepository;
import org.cbioportal.persistence.ClinicalAttributeRepository;
import org.cbioportal.persistence.PatientRepository;
import org.cbioportal.persistence.PersistenceConstants;
import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;
import org.springframework.util.Assert;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;

@Repository
public class ClinicalDataMyBatisRepository implements ClinicalDataRepository {
Expand All @@ -24,7 +26,9 @@ public class ClinicalDataMyBatisRepository implements ClinicalDataRepository {
@Autowired
private PatientRepository patientRepository;
@Autowired
private OffsetCalculator offsetCalculator;
private PaginationCalculator paginationCalculator;
@Autowired
private ClinicalAttributeRepository clinicalAttributeRepository;

@Override
public List<ClinicalData> getAllClinicalDataOfSampleInStudy(String studyId, String sampleId,
Expand All @@ -34,7 +38,7 @@ public List<ClinicalData> getAllClinicalDataOfSampleInStudy(String studyId, Stri

return clinicalDataMapper.getSampleClinicalData(Arrays.asList(studyId), Arrays.asList(sampleId),
attributeId != null ? Arrays.asList(attributeId) : null, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
Expand All @@ -51,7 +55,7 @@ public List<ClinicalData> getAllClinicalDataOfPatientInStudy(String studyId, Str

return clinicalDataMapper.getPatientClinicalData(Arrays.asList(studyId), Arrays.asList(patientId),
attributeId != null ? Arrays.asList(attributeId) : null, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
Expand All @@ -69,11 +73,11 @@ public List<ClinicalData> getAllClinicalDataInStudy(String studyId, String attri
if (clinicalDataType.equals(PersistenceConstants.SAMPLE_CLINICAL_DATA_TYPE)) {
return clinicalDataMapper.getSampleClinicalData(Arrays.asList(studyId), null,
attributeId != null ? Arrays.asList(attributeId) : null, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
} else {
return clinicalDataMapper.getPatientClinicalData(Arrays.asList(studyId), null,
attributeId != null ? Arrays.asList(attributeId) : null, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}
}

Expand Down Expand Up @@ -137,23 +141,35 @@ public List<ClinicalData> fetchClinicalData(List<String> studyIds, List<String>
}
}

@Override
public List<ClinicalData> fetchSampleClinicalTable(List<String> studyIds, List<String> ids,
Integer pageSize, Integer pageNumber, String searchTerm,
String sortBy, String direction) {
if (ids.isEmpty()) {
public List<Integer> getVisibleSampleInternalIdsForClinicalTable(List<String> studyIds, List<String> sampleIds,
Integer pageSize, Integer pageNumber, String searchTerm,
String sortAttrId, String direction) {
if (sampleIds.isEmpty()) {
return new ArrayList<>();
}
int offset = offsetCalculator.calculate(pageSize, pageNumber);
return clinicalDataMapper.getSampleClinicalTable(studyIds, ids,"SUMMARY", pageSize,
offset, searchTerm, sortBy, direction);
Integer offset = paginationCalculator.offset(pageSize, pageNumber);
Boolean sortAttrIsNumber = null;
Boolean sortIsPatientAttr = null;
if (sortAttrId != null && ! sortAttrId.isEmpty()) {
ClinicalAttribute clinicalAttributeMeta = getClinicalAttributeMeta(studyIds, sortAttrId);
sortAttrIsNumber = clinicalAttributeMeta.getDatatype().equals("NUMBER");
sortIsPatientAttr = clinicalAttributeMeta.getPatientAttribute();
}
return clinicalDataMapper.getVisibleSampleInternalIdsForClinicalTable(studyIds, sampleIds,"SUMMARY", pageSize,
offset, searchTerm, sortAttrId, sortAttrIsNumber, sortIsPatientAttr, direction);
}

@Override
public Integer fetchSampleClinicalTableCount(List<String> studyIds, List<String> sampleIds,
String searchTerm, String sortBy, String direction) {
return clinicalDataMapper.getSampleClinicalTableCount(studyIds, sampleIds,"SUMMARY",
searchTerm, sortBy, direction);

private ClinicalAttribute getClinicalAttributeMeta(List<String> studyIds, String attrId) {
Assert.notNull(studyIds, "Arguments may not be null");
Assert.notNull(attrId, "Arguments may not be null");
Stream<String> uniqueStudyIds = studyIds.stream().distinct();
Optional<ClinicalAttribute> clinicalAttributeMeta = uniqueStudyIds
.map(studyId -> clinicalAttributeRepository.getClinicalAttribute(studyId, attrId))
.filter(Objects::nonNull)
.findFirst();
Assert.isTrue(clinicalAttributeMeta.isPresent(), "Clinical Attribute " + attrId +
" was not found in studies " + studyIds.stream().collect(Collectors.joining(", ")) );
return clinicalAttributeMeta.get();
}

@Override
Expand Down Expand Up @@ -195,4 +211,16 @@ public List<ClinicalData> getPatientClinicalDataDetailedToSample(List<String> st
return clinicalDataMapper.getPatientClinicalDataDetailedToSample(studyIds, patientIds, attributeIds, "SUMMARY",
0, 0, null, null);
}

@Override
public List<ClinicalData> getSampleClinicalDataBySampleInternalIds(List<Integer> sampleInternalIds) {
return sampleInternalIds == null || sampleInternalIds.isEmpty() ?
new ArrayList<>() : clinicalDataMapper.getSampleClinicalDataBySampleInternalIds(sampleInternalIds);
}

@Override
public List<ClinicalData> getPatientClinicalDataBySampleInternalIds(List<Integer> sampleInternalIds) {
return sampleInternalIds == null || sampleInternalIds.isEmpty() ?
new ArrayList<>() : clinicalDataMapper.getPatientClinicalDataBySampleInternalIds(sampleInternalIds);
}
}
8 changes: 4 additions & 4 deletions src/main/java/org/cbioportal/persistence/mybatis/ClinicalEventMyBatisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import org.cbioportal.model.ClinicalEventData;
import org.cbioportal.model.meta.BaseMeta;
import org.cbioportal.persistence.ClinicalEventRepository;
import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

Expand All @@ -21,14 +21,14 @@ public class ClinicalEventMyBatisRepository implements ClinicalEventRepository {
@Autowired
private ClinicalEventMapper clinicalEventMapper;
@Autowired
private OffsetCalculator offsetCalculator;
private PaginationCalculator paginationCalculator;

@Override
public List<ClinicalEvent> getAllClinicalEventsOfPatientInStudy(String studyId, String patientId, String projection,
Integer pageSize, Integer pageNumber, String sortBy,
String direction) {
return clinicalEventMapper.getPatientClinicalEvent(studyId, patientId, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
Expand All @@ -47,7 +47,7 @@ public List<ClinicalEventData> getDataOfClinicalEvents(List<Integer> clinicalEve
public List<ClinicalEvent> getAllClinicalEventsInStudy(String studyId, String projection, Integer pageSize,
Integer pageNumber, String sortBy, String direction) {
return clinicalEventMapper.getStudyClinicalEvent(studyId, projection, pageSize,
offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/org/cbioportal/persistence/mybatis/CopyNumberSegmentMyBatisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import org.cbioportal.model.CopyNumberSeg;
import org.cbioportal.model.meta.BaseMeta;
import org.cbioportal.persistence.CopyNumberSegmentRepository;
import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

Expand All @@ -16,7 +16,7 @@ public class CopyNumberSegmentMyBatisRepository implements CopyNumberSegmentRepo
@Autowired
private CopyNumberSegmentMapper copyNumberSegmentMapper;
@Autowired
private OffsetCalculator offsetCalculator;
private PaginationCalculator paginationCalculator;


@Override
Expand All @@ -26,7 +26,7 @@ public List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(String studyId,
String direction) {

return copyNumberSegmentMapper.getCopyNumberSegments(Arrays.asList(studyId), Arrays.asList(sampleId), chromosome,
projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber), sortBy, direction);
projection, pageSize, paginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
}

@Override
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/org/cbioportal/persistence/mybatis/GeneMyBatisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import org.cbioportal.model.meta.BaseMeta;
import org.cbioportal.persistence.GeneRepository;
import org.cbioportal.persistence.PersistenceConstants;
import org.cbioportal.persistence.mybatis.util.OffsetCalculator;
import org.cbioportal.persistence.mybatis.util.PaginationCalculator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

Expand All @@ -17,13 +17,13 @@ public class GeneMyBatisRepository implements GeneRepository {
@Autowired
private GeneMapper geneMapper;
@Autowired
private OffsetCalculator offsetCalculator;
private PaginationCalculator paginationCalculator;

@Override
public List<Gene> getAllGenes(String keyword, String alias, String projection, Integer pageSize, Integer pageNumber, String sortBy,
String direction) {

return geneMapper.getGenes(keyword, alias, projection, pageSize, offsetCalculator.calculate(pageSize, pageNumber),
return geneMapper.getGenes(keyword, alias, projection, pageSize, paginationCalculator.offset(pageSize, pageNumber),
sortBy, direction);
}

Expand Down

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