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Move ClinicalCategoricalFilter to repository (#10847)
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* 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

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Co-authored-by: haynescd <[email protected]>
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@onursumer @haynescd
2 people authored and haynescd committed Nov 24, 2024
1 parent 3dd1e2a commit a7af899
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Showing 8 changed files with 146 additions and 189 deletions.
37 changes: 15 additions & 22 deletions src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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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);
}
3 changes: 2 additions & 1 deletion src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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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;
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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);

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