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Merge branch 'refs/heads/demo-rfc80-poc' into demo-rfc80-poc-mutation…
…_type_count # Conflicts: # src/main/java/org/cbioportal/persistence/StudyViewRepository.java # src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java # src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java # src/main/java/org/cbioportal/service/StudyViewColumnarService.java # src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java # src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java # src/main/resources/db-scripts/clickhouse/clickhouse.sql # src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| package org.cbioportal.model; | ||
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| import java.io.Serializable; | ||
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| public record PatientTreatment (String treatment, int count) implements Serializable { | ||
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| } |
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11
src/main/java/org/cbioportal/model/PatientTreatmentReport.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| package org.cbioportal.model; | ||
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| import java.io.Serializable; | ||
| import java.util.Collections; | ||
| import java.util.List; | ||
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| public record PatientTreatmentReport (int totalPatients, int totalSamples, List<PatientTreatment> patientTreatments) implements Serializable { | ||
| public PatientTreatmentReport(int totalPatients, int totalSamples) { | ||
| this(totalPatients, totalSamples, Collections.emptyList()); | ||
| } | ||
| } |
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78 changes: 78 additions & 0 deletions
78
src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,78 @@ | ||
| package org.cbioportal.persistence.helper; | ||
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| import org.cbioportal.model.ClinicalAttribute; | ||
| import org.cbioportal.persistence.enums.ClinicalAttributeDataSource; | ||
| import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; | ||
| import org.cbioportal.web.parameter.StudyViewFilter; | ||
| import org.springframework.lang.NonNull; | ||
| import org.springframework.lang.Nullable; | ||
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| import java.util.EnumMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Objects; | ||
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| public class StudyViewFilterHelper { | ||
| public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter, @Nullable EnumMap<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap) { | ||
| if (Objects.isNull(studyViewFilter)) { | ||
| studyViewFilter = new StudyViewFilter(); | ||
| } | ||
| if (Objects.isNull(clinicalAttributesMap)) { | ||
| clinicalAttributesMap = new EnumMap<>(ClinicalAttributeDataSource.class); | ||
| } | ||
| return new StudyViewFilterHelper(studyViewFilter, clinicalAttributesMap); | ||
| } | ||
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| private final StudyViewFilter studyViewFilter; | ||
| private final CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter; | ||
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| private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, @NonNull Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap ) { | ||
| this.studyViewFilter = studyViewFilter; | ||
| this.categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter, clinicalAttributesMap); | ||
| } | ||
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| private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter, Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap) { | ||
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| if (studyViewFilter.getClinicalDataFilters() == null || clinicalAttributesMap.isEmpty()) { | ||
| return CategorizedClinicalDataCountFilter.getBuilder().build(); | ||
| } | ||
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| List<String> patientCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT) | ||
| .stream().filter(ca -> ca.getDatatype().equals("STRING")) | ||
| .map(ClinicalAttribute::getAttrId) | ||
| .toList(); | ||
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| List<String> patientNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT) | ||
| .stream().filter(ca -> ca.getDatatype().equals("NUMBER")) | ||
| .map(ClinicalAttribute::getAttrId) | ||
| .toList(); | ||
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| List<String> sampleCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE) | ||
| .stream().filter(ca -> ca.getDatatype().equals("STRING")) | ||
| .map(ClinicalAttribute::getAttrId) | ||
| .toList(); | ||
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| List<String> sampleNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE) | ||
| .stream().filter(ca -> ca.getDatatype().equals("NUMBER")) | ||
| .map(ClinicalAttribute::getAttrId) | ||
| .toList(); | ||
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| return CategorizedClinicalDataCountFilter.getBuilder() | ||
| .setPatientCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters() | ||
| .stream().filter(clinicalDataFilter -> patientCategoricalAttributes.contains(clinicalDataFilter.getAttributeId())) | ||
| .toList()) | ||
| .setPatientNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream() | ||
| .filter(clinicalDataFilter -> patientNumericalAttributes.contains(clinicalDataFilter.getAttributeId())) | ||
| .toList()) | ||
| .setSampleCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream() | ||
| .filter(clinicalDataFilter -> sampleCategoricalAttributes.contains(clinicalDataFilter.getAttributeId())) | ||
| .toList()) | ||
| .setSampleNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream() | ||
| .filter(clinicalDataFilter -> sampleNumericalAttributes.contains(clinicalDataFilter.getAttributeId())) | ||
| .toList()) | ||
| .build(); | ||
| } | ||
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| } |
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