From dd085edbfd4ec886dfcdb18f5ca90e76ae7e6d96 Mon Sep 17 00:00:00 2001 From: Gaofei Zhao <15748980+dippindots@users.noreply.github.com> Date: Tue, 6 Aug 2024 03:29:37 -0400 Subject: [PATCH 1/4] Genomic and Generic Assay bin counts endpoints --- .../persistence/StudyViewRepository.java | 7 + .../helper/StudyViewFilterHelper.java | 59 +++- .../mybatisclickhouse/StudyViewMapper.java | 6 + .../StudyViewMyBatisRepository.java | 34 +- .../service/StudyViewColumnarService.java | 4 + .../impl/StudyViewColumnarServiceImpl.java | 24 ++ .../web/columnar/BasicDataBinner.java | 306 ++++++++++++++++++ .../StudyViewColumnStoreController.java | 47 +++ .../CategorizedClinicalDataCountFilter.java | 100 +++++- .../web/util/StudyViewFilterApplier.java | 4 +- .../db-scripts/clickhouse/clickhouse.sql | 108 ++++++- .../StudyViewFilterMapper.xml | 171 +++++++++- .../mybatisclickhouse/StudyViewMapper.xml | 63 ++++ .../MolecularProfileCountTest.java | 8 +- .../StudyViewCaseListSamplesCountsTest.java | 8 +- .../StudyViewMapperClinicalDataCountTest.java | 18 +- .../StudyViewMapperTest.java | 32 +- src/test/resources/clickhouse_cgds.sql | 3 +- 18 files changed, 950 insertions(+), 52 deletions(-) create mode 100644 src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java index b5c7748ffe9..3b60e17fcd4 100644 --- a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java +++ b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java @@ -9,6 +9,7 @@ import org.cbioportal.model.CopyNumberCountByGene; import org.cbioportal.model.GenomicDataCountItem; import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.MolecularProfile; import org.cbioportal.model.PatientTreatment; import org.cbioportal.model.Sample; import org.cbioportal.model.SampleTreatment; @@ -67,4 +68,10 @@ public interface StudyViewRepository { Map getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter); List getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters); + + List getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List filteredAttributes); + + List getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List filteredAttributes); + + List getGenericAssayProfiles(); } diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java index a5d16a6de94..1c6c2a6c127 100644 --- a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java +++ b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java @@ -1,5 +1,8 @@ package org.cbioportal.persistence.helper; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.persistence.enums.ClinicalAttributeDataSource; +import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; import org.cbioportal.web.parameter.ClinicalDataFilter; import org.cbioportal.web.parameter.CustomSampleIdentifier; import org.cbioportal.web.parameter.StudyViewFilter; @@ -7,28 +10,38 @@ import org.springframework.lang.Nullable; import java.util.ArrayList; +import java.util.HashMap; import java.util.List; +import java.util.Map; import java.util.Objects; +import java.util.stream.Collectors; public final class StudyViewFilterHelper { public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter, - @Nullable List customDataSamples) { + @Nullable Map> genericAssayProfilesMap, + @Nullable List customDataSamples) { if (Objects.isNull(studyViewFilter)) { studyViewFilter = new StudyViewFilter(); } + if (Objects.isNull(genericAssayProfilesMap)) { + genericAssayProfilesMap = new HashMap<>(); + } if (Objects.isNull(customDataSamples)) { customDataSamples = new ArrayList<>(); } - return new StudyViewFilterHelper(studyViewFilter, customDataSamples); + return new StudyViewFilterHelper(studyViewFilter, genericAssayProfilesMap, customDataSamples); } private final StudyViewFilter studyViewFilter; private final List customDataSamples; + private final CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter; + private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, - @NonNull List customDataSamples) { + @NonNull Map> genericAssayProfilesMap, + @NonNull List customDataSamples) { this.studyViewFilter = studyViewFilter; - + this.categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter, genericAssayProfilesMap); this.customDataSamples = customDataSamples; } @@ -39,6 +52,44 @@ public StudyViewFilter studyViewFilter() { public List customDataSamples() { return this.customDataSamples; } + + private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter, Map> genericAssayProfilesMap) { + if ((studyViewFilter.getGenericAssayDataFilters() == null || genericAssayProfilesMap.isEmpty()) && + studyViewFilter.getGenomicDataFilters() == null) + { + return CategorizedClinicalDataCountFilter.getBuilder().build(); + } + + CategorizedClinicalDataCountFilter.Builder builder = CategorizedClinicalDataCountFilter.getBuilder(); + + if (studyViewFilter.getGenomicDataFilters() != null) { + builder.setSampleNumericalGenomicDataFilters(studyViewFilter.getGenomicDataFilters().stream() + .filter(genomicDataFilter -> !genomicDataFilter.getProfileType().equals("cna") && !genomicDataFilter.getProfileType().equals("gistic")) + .collect(Collectors.toList())); + builder.setSampleCategoricalGenomicDataFilters(studyViewFilter.getGenomicDataFilters().stream() + .filter(genomicDataFilter -> genomicDataFilter.getProfileType().equals("cna") || genomicDataFilter.getProfileType().equals("gistic")) + .collect(Collectors.toList())); + } + if (studyViewFilter.getGenericAssayDataFilters() != null) { + // TODO: Support patient level profiles and data filtering + List sampleCategoricalProfileTypes = genericAssayProfilesMap.get(ClinicalAttributeDataSource.SAMPLE) + .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY")) + .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", "")) + .toList(); + + List sampleNumericalProfileTypes = genericAssayProfilesMap.get(ClinicalAttributeDataSource.SAMPLE) + .stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE")) + .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", "")) + .toList(); + builder.setSampleNumericalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream() + .filter(genericAssayDataFilter -> sampleNumericalProfileTypes.contains(genericAssayDataFilter.getProfileType())) + .collect(Collectors.toList())); + builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream() + .filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType())) + .collect(Collectors.toList())); + } + return builder.build(); + } public boolean isCategoricalClinicalDataFilter(ClinicalDataFilter clinicalDataFilter) { var filterValue = clinicalDataFilter.getValues().getFirst(); diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java index 6dabd46d0df..5bc659e5c5a 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java +++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java @@ -12,6 +12,7 @@ import org.cbioportal.model.GenomicDataCount; import org.cbioportal.model.GenomicDataCountItem; import org.cbioportal.model.PatientTreatment; +import org.cbioportal.model.MolecularProfile; import org.cbioportal.model.Sample; import org.cbioportal.model.SampleTreatment; import org.cbioportal.persistence.helper.AlterationFilterHelper; @@ -65,4 +66,9 @@ public interface StudyViewMapper { Map getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter); List getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List genomicDataFilters); + + List getGenomicDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List attributeIds); + List getGenericAssayDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List attributeIds); + + List getGenericAssayProfiles(); } diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java index d522b2f3b9b..68272c46bb5 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java +++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java @@ -9,6 +9,7 @@ import org.cbioportal.model.GenomicDataCountItem; import org.cbioportal.model.GenomicDataCount; import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.MolecularProfile; import org.cbioportal.model.PatientTreatment; import org.cbioportal.model.Sample; import org.cbioportal.model.SampleTreatment; @@ -17,8 +18,10 @@ import org.cbioportal.persistence.enums.ClinicalAttributeDataSource; import org.cbioportal.persistence.helper.AlterationFilterHelper; import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; import org.cbioportal.web.parameter.ClinicalDataType; import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; @@ -34,6 +37,7 @@ public class StudyViewMyBatisRepository implements StudyViewRepository { private Map> clinicalAttributesMap = new HashMap<>(); + private Map> genericAssayProfilesMap = new HashMap<>(); private static final List FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList(); @@ -101,7 +105,7 @@ public List getMolecularProfileSampleCounts(StudyViewFilterCon } public StudyViewFilterHelper createStudyViewFilterHelper(StudyViewFilterContext studyViewFilterContext) { - return StudyViewFilterHelper.build(studyViewFilterContext.studyViewFilter(), studyViewFilterContext.customDataFilterSamples()); + return StudyViewFilterHelper.build(studyViewFilterContext.studyViewFilter() , getGenericAssayProfilesMap(), studyViewFilterContext.customDataFilterSamples()); } @Override @@ -109,6 +113,11 @@ public List getClinicalAttributes() { return mapper.getClinicalAttributes(); } + @Override + public List getGenericAssayProfiles() { + return mapper.getGenericAssayProfiles(); + } + @Override public Map getClinicalAttributeDatatypeMap() { if (clinicalAttributesMap.isEmpty()) { @@ -199,12 +208,28 @@ public List getSampleTreatments(StudyViewFilterContext studyVie public int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext) { return mapper.getTotalSampleTreatmentCounts(createStudyViewFilterHelper(studyViewFilterContext)); } + + @Override + public List getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List attributeIds) { + return mapper.getGenomicDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), attributeIds); + } + + @Override + public List getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List attributeIds) { + return mapper.getGenericAssayDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), attributeIds); + } private void buildClinicalAttributeNameMap() { clinicalAttributesMap = this.getClinicalAttributes() .stream() .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute() ? ClinicalAttributeDataSource.PATIENT : ClinicalAttributeDataSource.SAMPLE)); } + + private void buildGenericAssayProfilesMap() { + genericAssayProfilesMap = this.getGenericAssayProfiles() + .stream() + .collect(Collectors.groupingBy(ca -> ca.getPatientLevel() ? ClinicalAttributeDataSource.PATIENT : ClinicalAttributeDataSource.SAMPLE)); + } private Map> getClinicalAttributeNameMap() { if (clinicalAttributesMap.isEmpty()) { @@ -212,6 +237,13 @@ private Map> getClinicalAtt } return clinicalAttributesMap; } + + private Map> getGenericAssayProfilesMap() { + if (genericAssayProfilesMap.isEmpty()) { + buildGenericAssayProfilesMap(); + } + return genericAssayProfilesMap; + } @Override public List getCNACounts(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters) { diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java index 369f33aab41..4a631a67204 100644 --- a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java +++ b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java @@ -45,6 +45,10 @@ public interface StudyViewColumnarService { List getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters); List getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters); + + List getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List filteredAttributes); + + List getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List filteredAttributes); List getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters); } diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java index c3ebffa4a4f..5c7c1756ed8 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java +++ b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java @@ -81,6 +81,30 @@ public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewF return treatmentCountReportService.getSampleTreatmentReport(createContext(studyViewFilter)); } + @Override + public List getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List filteredAttributes) { + return studyViewRepository.getGenomicDataBinCounts(createContext(studyViewFilter), filteredAttributes) + .stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId)) + .entrySet().parallelStream().map(e -> { + ClinicalDataCountItem item = new ClinicalDataCountItem(); + item.setAttributeId(e.getKey()); + item.setCounts(e.getValue()); + return item; + }).collect(Collectors.toList()); + } + + @Override + public List getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List filteredAttributes) { + return studyViewRepository.getGenericAssayDataBinCounts(createContext(studyViewFilter), filteredAttributes) + .stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId)) + .entrySet().parallelStream().map(e -> { + ClinicalDataCountItem item = new ClinicalDataCountItem(); + item.setAttributeId(e.getKey()); + item.setCounts(e.getValue()); + return item; + }).collect(Collectors.toList()); + } + public List getCnaGenes(StudyViewFilter studyViewFilter) { return alterationCountService.getCnaGenes(createContext(studyViewFilter)); } diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java new file mode 100644 index 00000000000..f47beb9f9b6 --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java @@ -0,0 +1,306 @@ +package org.cbioportal.web.columnar; + +import org.cbioportal.model.*; +import org.cbioportal.service.StudyViewColumnarService; +import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.web.parameter.*; +import org.cbioportal.web.util.DataBinner; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.stream.Collectors; + +import static java.util.Collections.emptyList; + +@Component +public class BasicDataBinner { + private final StudyViewColumnarService studyViewColumnarService; + private final DataBinner dataBinner; + + @Autowired + public BasicDataBinner( + StudyViewColumnarService studyViewColumnarService, + DataBinner dataBinner + ) { + this.studyViewColumnarService = studyViewColumnarService; + this.dataBinner = dataBinner; + } + + // convert from counts to clinical data + private List convertCountsToData(List clinicalDataCounts) + { + return clinicalDataCounts + .stream() + .map(NewClinicalDataBinUtil::generateClinicalDataFromClinicalDataCount) + .flatMap(Collection::stream) + .toList(); + } + + @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()") + public List getDataBins( + DataBinMethod dataBinMethod, + T dataBinCountFilter, + boolean shouldRemoveSelfFromFilter) { + // get data bin filters based on the type of the filter + // either Genomic data or Generic Assay data or clinical data + List dataBinFilters = fetchDataBinFilters(dataBinCountFilter); + StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); + + if (shouldRemoveSelfFromFilter && dataBinFilters.size() == 1) { + removeSelfFromFilter(dataBinFilters.get(0), studyViewFilter); + } + + List uniqueKeys = dataBinFilters.stream().map(this::getDataBinFilterUniqueKey).collect(Collectors.toList()); + + // a new StudyView filter to partially filter by study and sample ids only + // we need this additional partial filter because we always need to know the bins generated for the initial state + // which allows us to keep the number of bins and bin ranges consistent even if there are additional data filters. + // we only want to update the counts for each bin, we don't want to regenerate the bins for the filtered data. + // NOTE: partial filter is only needed when dataBinMethod == DataBinMethod.STATIC but that's always the case + // for the frontend implementation. we can't really use dataBinMethod == DataBinMethod.DYNAMIC because of the + // complication it brings to the frontend visualization and filtering + StudyViewFilter partialFilter = new StudyViewFilter(); + partialFilter.setStudyIds(studyViewFilter.getStudyIds()); + partialFilter.setSampleIdentifiers(studyViewFilter.getSampleIdentifiers()); + + // we need to fetch data for the partial filter in order to generate the bins for initial state + // we use the filtered data to calculate the counts for each bin, we do not regenerate bins for the filtered data + List unfilteredClinicalDataCounts; + List filteredClinicalDataCounts; + Map attributeDatatypeMap; + switch (dataBinCountFilter) { + // TODO: first case is to support clinical data, but clinical data is not using this now. We should update controller to use this method later + case ClinicalDataBinCountFilter clinicalDataBinCountFilter -> { + unfilteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(partialFilter, uniqueKeys); + filteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, uniqueKeys); + attributeDatatypeMap = studyViewColumnarService.getClinicalAttributeDatatypeMap(); + } + case GenomicDataBinCountFilter genomicDataBinCountFilter -> { + unfilteredClinicalDataCounts = studyViewColumnarService.getGenomicDataBinCounts(partialFilter, uniqueKeys); + filteredClinicalDataCounts = studyViewColumnarService.getGenomicDataBinCounts(studyViewFilter, uniqueKeys); + attributeDatatypeMap = Collections.emptyMap(); + } + case GenericAssayDataBinCountFilter genericAssayDataBinCountFilter -> { + unfilteredClinicalDataCounts = studyViewColumnarService.getGenericAssayDataBinCounts(partialFilter, uniqueKeys); + filteredClinicalDataCounts = studyViewColumnarService.getGenericAssayDataBinCounts(studyViewFilter, uniqueKeys); + attributeDatatypeMap = Collections.emptyMap(); + } + default -> { + unfilteredClinicalDataCounts = Collections.emptyList(); + filteredClinicalDataCounts = Collections.emptyList(); + attributeDatatypeMap = Collections.emptyMap(); + } + } + + // TODO ignoring conflictingPatientAttributeIds for now + List unfilteredClinicalData = convertCountsToData( + unfilteredClinicalDataCounts.stream().flatMap(c -> c.getCounts().stream()).toList() + ); + List filteredClinicalData = convertCountsToData( + filteredClinicalDataCounts.stream().flatMap(c -> c.getCounts().stream()).toList() + ); + + Map> unfilteredClinicalDataByAttributeId = + unfilteredClinicalData.stream().collect(Collectors.groupingBy(Binnable::getAttrId)); + + Map> filteredClinicalDataByAttributeId = + filteredClinicalData.stream().collect(Collectors.groupingBy(Binnable::getAttrId)); + + // Define result variables + List resultDataBins = Collections.emptyList(); + + // TODO: need to update attributeDatatypeMap to include patient level data for Generic Assay Profiles + if (dataBinMethod == DataBinMethod.STATIC) { + if (!unfilteredClinicalData.isEmpty()) { + resultDataBins = calculateStaticDataBins( + dataBinner, + dataBinFilters, + attributeDatatypeMap, + unfilteredClinicalDataByAttributeId, + filteredClinicalDataByAttributeId + ); + } + } + // TODO: need to update attributeDatatypeMap to include patient level data for Generic Assay Profiles + else { // dataBinMethod == DataBinMethod.DYNAMIC + // TODO we should consider removing dynamic binning support + // we never use dynamic binning in the frontend because number of bins and the bin ranges can change + // each time there is a new filter which makes the frontend implementation complicated + if (!filteredClinicalData.isEmpty()) { + resultDataBins = calculateDynamicDataBins( + dataBinner, + dataBinFilters, + attributeDatatypeMap, + filteredClinicalDataByAttributeId + ); + } + } + + return resultDataBins; + } + + private void removeSelfFromFilter(S dataBinFilter, StudyViewFilter studyViewFilter) { + if (studyViewFilter != null) { + if (dataBinFilter instanceof ClinicalDataBinFilter clinicalDataBinFilter && + studyViewFilter.getClinicalDataFilters() != null) { + studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId())); + } else if (dataBinFilter instanceof GenomicDataBinFilter genomicDataBinFilter && + studyViewFilter.getGenomicDataFilters() != null) { + studyViewFilter.getGenomicDataFilters().removeIf(f -> + f.getHugoGeneSymbol().equals(genomicDataBinFilter.getHugoGeneSymbol()) + && f.getProfileType().equals(genomicDataBinFilter.getProfileType()) + ); + } else if (dataBinFilter instanceof GenericAssayDataBinFilter genericAssayDataBinFilter && + studyViewFilter.getGenericAssayDataFilters() != null) { + studyViewFilter.getGenericAssayDataFilters().removeIf(f -> + f.getStableId().equals(genericAssayDataBinFilter.getStableId()) + && f.getProfileType().equals(genericAssayDataBinFilter.getProfileType()) + ); + } + } + } + + private List fetchDataBinFilters(T dataBinCountFilter) { + if (dataBinCountFilter instanceof ClinicalDataBinCountFilter) { + return (List) ((ClinicalDataBinCountFilter) dataBinCountFilter).getAttributes(); + } else if (dataBinCountFilter instanceof GenomicDataBinCountFilter) { + return (List) ((GenomicDataBinCountFilter) dataBinCountFilter).getGenomicDataBinFilters(); + } else if (dataBinCountFilter instanceof GenericAssayDataBinCountFilter) { + return (List) ((GenericAssayDataBinCountFilter) dataBinCountFilter).getGenericAssayDataBinFilters(); + } + return new ArrayList<>(); + } + + private String getDataBinFilterUniqueKey(S dataBinFilter) { + if (dataBinFilter instanceof ClinicalDataBinFilter clinicalDataBinFilter) { + return clinicalDataBinFilter.getAttributeId(); + } else if (dataBinFilter instanceof GenomicDataBinFilter genomicDataBinFilter) { + return genomicDataBinFilter.getHugoGeneSymbol() + genomicDataBinFilter.getProfileType(); + } else if (dataBinFilter instanceof GenericAssayDataBinFilter genericAssayDataBinFilter) { + return genericAssayDataBinFilter.getStableId() + genericAssayDataBinFilter.getProfileType(); + } + return null; + } + + private List calculateStaticDataBins( + DataBinner dataBinner, + List dataBinFilters, + Map attributeDatatypeMap, + Map> unfilteredClinicalDataByAttributeId, + Map> filteredClinicalDataByAttributeId + ) { + List result = new ArrayList<>(); + + for (T dataBinFilter : dataBinFilters) { + // if there is data for requested attribute + // TODO: consider if this is correct to passing in a empty map + if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) { + List dataBins = dataBinner + .calculateClinicalDataBins( + dataBinFilter, + filteredClinicalDataByAttributeId.getOrDefault(getDataBinFilterUniqueKey(dataBinFilter), emptyList()), + unfilteredClinicalDataByAttributeId.getOrDefault(getDataBinFilterUniqueKey(dataBinFilter), emptyList()) + ) + .stream() + .map(dataBin -> (U) transform(dataBinFilter, dataBin)) + .toList(); + + result.addAll(dataBins); + } + } + + return result; + } + + private List calculateDynamicDataBins( + DataBinner dataBinner, + List dataBinFilters, + Map attributeDatatypeMap, + Map> filteredClinicalDataByAttributeId + ) { + List result = new ArrayList<>(); + + for (T dataBinFilter : dataBinFilters) { + // if there is data for requested attribute + // TODO: consider if this is correct to passing in a empty map + if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) { + List dataBins = dataBinner + .calculateDataBins( + dataBinFilter, + filteredClinicalDataByAttributeId.getOrDefault(getDataBinFilterUniqueKey(dataBinFilter), emptyList()) + ) + .stream() + .map(dataBin -> (U) transform(dataBinFilter, dataBin)) + .toList(); + result.addAll(dataBins); + } + } + + return result; + } + + private T transform(S dataBinFilter, DataBin dataBin) { + if (dataBinFilter instanceof ClinicalDataBinFilter clinicalDataBinFilter) { + return (T) dataBinToClinicalDataBin(clinicalDataBinFilter, dataBin); + } else if (dataBinFilter instanceof GenomicDataBinFilter genomicDataBinFilter) { + return (T) dataBintoGenomicDataBin(genomicDataBinFilter, dataBin); + } else if (dataBinFilter instanceof GenericAssayDataBinFilter genericAssayDataBinFilter) { + return (T) dataBintoGenericAssayDataBin(genericAssayDataBinFilter, dataBin); + } + return null; + } + + private ClinicalDataBin dataBinToClinicalDataBin(ClinicalDataBinFilter attribute, DataBin dataBin) { + ClinicalDataBin clinicalDataBin = new ClinicalDataBin(); + clinicalDataBin.setAttributeId(attribute.getAttributeId()); + clinicalDataBin.setCount(dataBin.getCount()); + if (dataBin.getEnd() != null) { + clinicalDataBin.setEnd(dataBin.getEnd()); + } + if (dataBin.getSpecialValue() != null) { + clinicalDataBin.setSpecialValue(dataBin.getSpecialValue()); + } + if (dataBin.getStart() != null) { + clinicalDataBin.setStart(dataBin.getStart()); + } + return clinicalDataBin; + } + + private GenomicDataBin dataBintoGenomicDataBin(GenomicDataBinFilter genomicDataBinFilter, DataBin dataBin) { + GenomicDataBin genomicDataBin = new GenomicDataBin(); + genomicDataBin.setCount(dataBin.getCount()); + genomicDataBin.setHugoGeneSymbol(genomicDataBinFilter.getHugoGeneSymbol()); + genomicDataBin.setProfileType(genomicDataBinFilter.getProfileType()); + if (dataBin.getSpecialValue() != null) { + genomicDataBin.setSpecialValue(dataBin.getSpecialValue()); + } + if (dataBin.getStart() != null) { + genomicDataBin.setStart(dataBin.getStart()); + } + if (dataBin.getEnd() != null) { + genomicDataBin.setEnd(dataBin.getEnd()); + } + return genomicDataBin; + } + + private GenericAssayDataBin dataBintoGenericAssayDataBin(GenericAssayDataBinFilter genericAssayDataBinFilter, + DataBin dataBin) { + GenericAssayDataBin genericAssayDataBin = new GenericAssayDataBin(); + genericAssayDataBin.setCount(dataBin.getCount()); + genericAssayDataBin.setStableId(genericAssayDataBinFilter.getStableId()); + genericAssayDataBin.setProfileType(genericAssayDataBinFilter.getProfileType()); + if (dataBin.getSpecialValue() != null) { + genericAssayDataBin.setSpecialValue(dataBin.getSpecialValue()); + } + if (dataBin.getStart() != null) { + genericAssayDataBin.setStart(dataBin.getStart()); + } + if (dataBin.getEnd() != null) { + genericAssayDataBin.setEnd(dataBin.getEnd()); + } + return genericAssayDataBin; + } + +} diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java index ffeff0ad7b3..fc55e05481b 100644 --- a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java +++ b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java @@ -19,6 +19,8 @@ import org.cbioportal.model.ClinicalViolinPlotData; import org.cbioportal.model.CopyNumberCountByGene; import org.cbioportal.model.DensityPlotData; +import org.cbioportal.model.GenericAssayDataBin; +import org.cbioportal.model.GenomicDataBin; import org.cbioportal.model.GenomicDataCount; import org.cbioportal.model.PatientTreatmentReport; import org.cbioportal.model.Sample; @@ -34,6 +36,8 @@ import org.cbioportal.web.parameter.ClinicalDataCountFilter; import org.cbioportal.web.parameter.ClinicalDataFilter; import org.cbioportal.web.parameter.DataBinMethod; +import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.web.parameter.GenomicDataBinCountFilter; import org.cbioportal.web.parameter.GenomicDataCountFilter; import org.cbioportal.web.parameter.GenomicDataFilter; import org.cbioportal.web.parameter.MutationOption; @@ -70,6 +74,8 @@ public class StudyViewColumnStoreController { private final StudyViewColumnarService studyViewColumnarService; private final ClinicalDataBinner clinicalDataBinner; + + private final BasicDataBinner basicDataBinner; private final ClinicalDataDensityPlotService clinicalDataDensityPlotService; private final ViolinPlotService violinPlotService; @@ -79,11 +85,13 @@ public class StudyViewColumnStoreController { @Autowired public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnarService, ClinicalDataBinner clinicalDataBinner, + BasicDataBinner basicDataBinner, ClinicalDataDensityPlotService clinicalDataDensityPlotService, ViolinPlotService violinPlotService ) { this.studyViewColumnarService = studyViewColumnarService; this.clinicalDataBinner = clinicalDataBinner; + this.basicDataBinner = basicDataBinner; this.clinicalDataDensityPlotService = clinicalDataDensityPlotService; this.violinPlotService = violinPlotService; } @@ -524,4 +532,43 @@ public ResponseEntity fetchSampleTreatmentCounts( // // return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK); // } + + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostMapping(value = "/column-store/genomic-data-bin-counts/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenomicDataBin.class)))) + public ResponseEntity> fetchGenomicDataBinCounts( + @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod, + @RequestBody(required = false) GenomicDataBinCountFilter genomicDataBinCountFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedGenomicDataBinCountFilter") GenomicDataBinCountFilter interceptedGenomicDataBinCountFilter + ) { + List genomicDataBins = basicDataBinner.getDataBins( + dataBinMethod, + interceptedGenomicDataBinCountFilter, + true + ); + return new ResponseEntity<>(genomicDataBins, HttpStatus.OK); + } + + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @PostMapping(value = "/column-store/generic-assay-data-bin-counts/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenericAssayDataBin.class)))) + public ResponseEntity> fetchGenericAssayDataBinCounts( + @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod, + @RequestBody(required = false) GenericAssayDataBinCountFilter genericAssayDataBinCountFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedGenericAssayDataBinCountFilter") GenericAssayDataBinCountFilter interceptedGenericAssayDataBinCountFilter + ) { + List genericAssayDataBins = basicDataBinner.getDataBins( + dataBinMethod, + interceptedGenericAssayDataBinCountFilter, + true + ); + return new ResponseEntity<>(genericAssayDataBins, HttpStatus.OK); + } + } diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java b/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java index 734d9bb53e7..a1e59701d80 100644 --- a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java +++ b/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java @@ -11,11 +11,29 @@ public static Builder getBuilder() { private final List sampleCategoricalClinicalDataFilters; private final List patientNumericalClinicalDataFilters; private final List patientCategoricalClinicalDataFilters; + + private final List sampleNumericalGenomicDataFilters; + private final List sampleCategoricalGenomicDataFilters; + private final List patientNumericalGenomicDataFilters; + private final List patientCategoricalGenomicDataFilters; + + private final List sampleNumericalGenericAssayDataFilters; + private final List sampleCategoricalGenericAssayDataFilters; + private final List patientNumericalGenericAssayDataFilters; + private final List patientCategoricalGenericAssayDataFilters; private CategorizedClinicalDataCountFilter(Builder builder) { this.sampleCategoricalClinicalDataFilters = builder.sampleCategoricalClinicalDataFilters; this.sampleNumericalClinicalDataFilters = builder.sampleNumericalClinicalDataFilters; this.patientCategoricalClinicalDataFilters = builder.patientCategoricalClinicalDataFilters; this.patientNumericalClinicalDataFilters = builder.patientNumericalClinicalDataFilters; + this.sampleCategoricalGenomicDataFilters = builder.sampleCategoricalGenomicDataFilters; + this.sampleNumericalGenomicDataFilters = builder.sampleNumericalGenomicDataFilters; + this.patientCategoricalGenomicDataFilters = builder.patientCategoricalGenomicDataFilters; + this.patientNumericalGenomicDataFilters = builder.patientNumericalGenomicDataFilters; + this.sampleCategoricalGenericAssayDataFilters = builder.sampleCategoricalGenericAssayDataFilters; + this.sampleNumericalGenericAssayDataFilters = builder.sampleNumericalGenericAssayDataFilters; + this.patientCategoricalGenericAssayDataFilters = builder.patientCategoricalGenericAssayDataFilters; + this.patientNumericalGenericAssayDataFilters = builder.patientNumericalGenericAssayDataFilters; } public List getSampleNumericalClinicalDataFilters() { @@ -34,15 +52,55 @@ public List getPatientCategoricalClinicalDataFilters() { return patientCategoricalClinicalDataFilters; } + public List getSampleNumericalGenomicDataFilters() { + return sampleNumericalGenomicDataFilters; + } + + public List getSampleCategoricalGenomicDataFilters() { + return sampleCategoricalGenomicDataFilters; + } + + public List getPatientNumericalGenomicDataFilters() { + return patientNumericalGenomicDataFilters; + } + + public List getPatientCategoricalGenomicDataFilters() { + return patientCategoricalGenomicDataFilters; + } + + public List getSampleNumericalGenericAssayDataFilters() { + return sampleNumericalGenericAssayDataFilters; + } + + public List getSampleCategoricalGenericAssayDataFilters() { + return sampleCategoricalGenericAssayDataFilters; + } + + public List getPatientNumericalGenericAssayDataFilters() { + return patientNumericalGenericAssayDataFilters; + } + + public List getPatientCategoricalGenericAssayDataFilters() { + return patientCategoricalGenericAssayDataFilters; + } + public static class Builder { private List sampleNumericalClinicalDataFilters; private List sampleCategoricalClinicalDataFilters; private List patientNumericalClinicalDataFilters; private List patientCategoricalClinicalDataFilters; + private List sampleNumericalGenomicDataFilters; + private List sampleCategoricalGenomicDataFilters; + private List patientNumericalGenomicDataFilters; + private List patientCategoricalGenomicDataFilters; + private List sampleNumericalGenericAssayDataFilters; + private List sampleCategoricalGenericAssayDataFilters; + private List patientNumericalGenericAssayDataFilters; + private List patientCategoricalGenericAssayDataFilters; private Builder(){ - + } public Builder setSampleCategoricalClinicalDataFilters(List sampleCategoricalClinicalDataFilters) { this.sampleCategoricalClinicalDataFilters = sampleCategoricalClinicalDataFilters; @@ -63,6 +121,46 @@ public Builder setPatientNumericalClinicalDataFilters(List p this.patientNumericalClinicalDataFilters = patientNumericalClinicalDataFilters; return this; } + + public Builder setSampleCategoricalGenomicDataFilters(List sampleCategoricalGenomicDataFilters) { + this.sampleCategoricalGenomicDataFilters = sampleCategoricalGenomicDataFilters; + return this; + } + + public Builder setSampleNumericalGenomicDataFilters(List sampleNumericalGenomicDataFilters) { + this.sampleNumericalGenomicDataFilters = sampleNumericalGenomicDataFilters; + return this; + } + + public Builder setPatientCategoricalGenomicDataFilters(List patientCategoricalGenomicDataFilters) { + this.patientCategoricalGenomicDataFilters = patientCategoricalGenomicDataFilters; + return this; + } + + public Builder setPatientNumericalGenomicDataFilters(List patientNumericalGenomicDataFilters) { + this.patientNumericalGenomicDataFilters = patientNumericalGenomicDataFilters; + return this; + } + + public Builder setSampleCategoricalGenericAssayDataFilters(List sampleCategoricalGenericAssayDataFilters) { + this.sampleCategoricalGenericAssayDataFilters = sampleCategoricalGenericAssayDataFilters; + return this; + } + + public Builder setSampleNumericalGenericAssayDataFilters(List sampleNumericalGenericAssayDataFilters) { + this.sampleNumericalGenericAssayDataFilters = sampleNumericalGenericAssayDataFilters; + return this; + } + + public Builder setPatientCategoricalGenericAssayDataFilters(List patientCategoricalGenericAssayDataFilters) { + this.patientCategoricalGenericAssayDataFilters = patientCategoricalGenericAssayDataFilters; + return this; + } + + public Builder setPatientNumericalGenericAssayDataFilters(List patientNumericalGenericAssayDataFilters) { + this.patientNumericalGenericAssayDataFilters = patientNumericalGenericAssayDataFilters; + return this; + } public CategorizedClinicalDataCountFilter build() { return new CategorizedClinicalDataCountFilter(this); diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java index 0fb4e83dc2c..16e5483d6dd 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java +++ b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java @@ -723,7 +723,6 @@ public List getUniqkeyKeys(List studyIds, List caseIds) public List getDataBins( DataBinMethod dataBinMethod, T dataBinCountFilter) { List dataBinFilters = fetchDataBinFilters(dataBinCountFilter); - StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); if (dataBinFilters.size() == 1) { @@ -733,6 +732,7 @@ public resultDataBins; List filteredSampleIds = new ArrayList<>(); List filteredStudyIds = new ArrayList<>(); + List filteredData = fetchData(dataBinCountFilter, studyViewFilter, filteredSampleIds, filteredStudyIds); @@ -740,7 +740,7 @@ public > filteredClinicalDataByAttributeId = filteredData.stream() .collect(Collectors.groupingBy(Binnable::getAttrId)); - + if (dataBinMethod == DataBinMethod.STATIC) { StudyViewFilter filter = studyViewFilter == null ? null : new StudyViewFilter(); diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql index 9e89e8506f9..ffb18b1979d 100644 --- a/src/main/resources/db-scripts/clickhouse/clickhouse.sql +++ b/src/main/resources/db-scripts/clickhouse/clickhouse.sql @@ -323,10 +323,116 @@ FROM WHERE alteration_value != 'NA') AS subquery JOIN sample_derived sd ON sd.internal_id = subquery.sample_id; +CREATE TABLE IF NOT EXISTS genetic_alteration_numerical_derived +( + sample_unique_id String, + cancer_study_identifier LowCardinality(String), + hugo_gene_symbol String, + profile_type LowCardinality(String), + alteration_value String + ) + ENGINE = MergeTree() + ORDER BY (profile_type, cancer_study_identifier, hugo_gene_symbol, sample_unique_id ); + +INSERT INTO TABLE genetic_alteration_numerical_derived +SELECT + sample_unique_id, + cancer_study_identifier, + hugo_gene_symbol, + profile_type, + alteration_value +FROM + (SELECT + sample_id, + hugo_gene_symbol, + profile_type, + alteration_value + FROM + (SELECT + g.hugo_gene_symbol AS hugo_gene_symbol, + replaceOne(stable_id, concat(cs.cancer_study_identifier, '_'), '') as profile_type, -- Compute profile_type + arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(trim(trailing ',' from ga.values)))) AS alteration_value, + arrayMap(x -> (x = '' ? NULL : toInt32(x)), splitByString(',', assumeNotNull(trim(trailing ',' from gps.ordered_sample_list)))) AS sample_id + FROM + genetic_profile gp + JOIN cancer_study cs ON cs.cancer_study_id = gp.cancer_study_id + JOIN genetic_profile_samples gps ON gp.genetic_profile_id = gps.genetic_profile_id + JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id + JOIN gene g ON ga.genetic_entity_id = g.genetic_entity_id + WHERE + gp.genetic_alteration_type != 'COPY_NUMBER_ALTERATION') + ARRAY JOIN alteration_value, sample_id + ) AS subquery + JOIN sample_derived sd ON sd.internal_id = subquery.sample_id; + +CREATE TABLE IF NOT EXISTS generic_assay_data_derived +( + sample_unique_id String, + genetic_entity_id String, + value String, + generic_assay_type String, + profile_stable_id String, + entity_stable_id String, + datatype String, + patient_level NUMERIC, + profile_type String +) + ENGINE = MergeTree() + ORDER BY (profile_type, entity_stable_id, sample_unique_id); + +INSERT INTO TABLE generic_assay_data_derived +SELECT + sd.sample_unique_id as sample_unique_id, + genetic_entity_id, + value, + generic_assay_type, + profile_stable_id, + entity_stable_id, + datatype, + patient_level, + replaceOne(profile_stable_id, concat(cs.cancer_study_identifier, '_'), '') as profile_type +FROM + (SELECT + sample_id, + genetic_entity_id, + value, + cancer_study_id, + generic_assay_type, + genetic_profile_id, + profile_stable_id, + entity_stable_id, + patient_level, + datatype + FROM + (SELECT + sample_id as sample_unique_id, + gp.cancer_study_id AS cancer_study_id, + ga.genetic_entity_id as genetic_entity_id, + gp.genetic_profile_id as genetic_profile_id, + gp.generic_assay_type as generic_assay_type, + gp.stable_id as profile_stable_id, + ge.stable_id as entity_stable_id, + gp.datatype as datatype, + gp.patient_level as patient_level, + arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(trim(trailing ',' from ga.values)))) AS value, + arrayMap(x -> (x = '' ? NULL : toInt64(x)), splitByString(',', assumeNotNull(trim(trailing ',' from gps.ordered_sample_list)))) AS sample_id + FROM genetic_profile gp + JOIN genetic_profile_samples gps ON gp.genetic_profile_id = gps.genetic_profile_id + JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id + JOIN genetic_entity ge on ga.genetic_entity_id = ge.id + WHERE + gp.generic_assay_type IS NOT NULL + ) + ARRAY JOIN value, sample_id) AS subquery + JOIN cancer_study cs ON cs.cancer_study_id = subquery.cancer_study_id + JOIN sample_derived sd ON sd.internal_id = subquery.sample_id; + OPTIMIZE TABLE sample_to_gene_panel_derived; OPTIMIZE TABLE gene_panel_to_gene_derived; OPTIMIZE TABLE sample_derived; OPTIMIZE TABLE genomic_event_derived; OPTIMIZE TABLE clinical_data_derived; OPTIMIZE TABLE clinical_event_derived; -OPTIMIZE TABLE genetic_alteration_cna_derived; \ No newline at end of file +OPTIMIZE TABLE genetic_alteration_cna_derived; +OPTIMIZE TABLE genetic_alteration_numerical_derived; +OPTIMIZE TABLE generic_assay_data_derived; diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index ca289ebc4b5..ac638ce1444 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -131,18 +131,46 @@ - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -157,7 +185,7 @@ - + @@ -361,6 +389,131 @@ + + SELECT ${unique_id} + FROM ${table_name} + WHERE hugo_gene_symbol = '${genomicDataFilter.hugoGeneSymbol}' AND + profile_type='${genomicDataFilter.profileType}' + + + + AND + + + + + + AND match(alteration_value, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$') + + + AND match(alteration_value, '^<?=?[-+]?[0-9]*[.,]?[0-9]+$') + + + AND match(alteration_value, '^[-+]?[0-9]*[.,]?[0-9]+$') + + + + + AND abs( + minus( + + + , + ${dataFilterValue.start} + ) + ) < exp(-11) + + + + AND + + + > ${dataFilterValue.start} + + + AND + + + <= ${dataFilterValue.end} + + + + + + + + + + + SELECT ${unique_id} + FROM ${table_name} + WHERE entity_stable_id = '${genericAssayDataFilter.stableId}' AND + profile_type='${genericAssayDataFilter.profileType}' + + + + AND + + + + + + AND match(value, '^>?=?[-+]?[0-9]*[.,]?[0-9]+$') + + + AND match(value, '^<?=?[-+]?[0-9]*[.,]?[0-9]+$') + + + AND match(value, '^[-+]?[0-9]*[.,]?[0-9]+$') + + + + + AND abs( + minus( + + + , + ${dataFilterValue.start} + ) + ) < exp(-11) + + + + AND + + + > ${dataFilterValue.start} + + + AND + + + <= ${dataFilterValue.end} + + + + + + + + + + SELECT ${unique_id} + FROM ${table_name} + WHERE entity_stable_id = '${genericAssayDataFilter.stableId}' AND + profile_type='${genericAssayDataFilter.profileType}' + + + AND ( + + + + ) = '${dataFilterValue.value}' + + + + diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml index 2da2eff0f0b..a4f56674922 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml @@ -551,6 +551,69 @@ GROUP BY treatments.treatment; + + + + + + - - - + + - - - + + - - + + - - - + + - @@ -503,11 +499,11 @@ FROM ${table_name} WHERE entity_stable_id = '${genericAssayDataFilter.stableId}' AND profile_type='${genericAssayDataFilter.profileType}' - + AND ( - + ) = '${dataFilterValue.value}' diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml index a4f56674922..ddd65175da7 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml @@ -553,11 +553,11 @@ SELECT - concat(entity_stable_id, profile_type) as attributeId, + concat(entity_stable_id, profile_type) AS attributeId, - as value, - count(value) as count + AS value, + count(value) AS count FROM generic_assay_data_derived diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java index 425a37f4d47..ae16aedb97f 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java @@ -1,6 +1,8 @@ package org.cbioportal.persistence.mybatisclickhouse; +import org.cbioportal.model.ClinicalAttribute; import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.persistence.enums.DataSource; import org.cbioportal.persistence.helper.StudyViewFilterHelper; import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; import org.cbioportal.web.parameter.ClinicalDataFilter; @@ -18,7 +20,9 @@ import java.math.BigDecimal; import java.util.Collections; +import java.util.HashMap; import java.util.List; +import java.util.Map; import static org.junit.Assert.assertEquals; @@ -181,7 +185,7 @@ public void getMutationCountsFilteredByAge() { studyViewFilter.setClinicalDataFilters(List.of(filter)); var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts( - StudyViewFilterHelper.build(studyViewFilter, null, null), + StudyViewFilterHelper.build(studyViewFilter, null, null), List.of("mutation_count"), Collections.emptyList() ); @@ -203,7 +207,7 @@ public void getMutationCountsFilteredByAgeWithOpenStartValues() { studyViewFilter.setClinicalDataFilters(List.of(filter)); var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts( - StudyViewFilterHelper.build(studyViewFilter, null, null), + StudyViewFilterHelper.build(studyViewFilter, null, null), List.of("mutation_count"), Collections.emptyList() ); From 002e51530960dde9f0c22405a06d57d693ebff03 Mon Sep 17 00:00:00 2001 From: Gaofei Zhao <15748980+dippindots@users.noreply.github.com> Date: Wed, 11 Sep 2024 10:33:31 -0400 Subject: [PATCH 3/4] add api tests in backend and skip NA mismatch tests --- .../specs/generic-assay-data-bin-counts.json | 126 +++++++++++++++ .../specs/genomic-data-bin-counts.json | 150 ++++++++++++++++++ 2 files changed, 276 insertions(+) create mode 100644 test/api-e2e/specs/generic-assay-data-bin-counts.json create mode 100644 test/api-e2e/specs/genomic-data-bin-counts.json diff --git a/test/api-e2e/specs/generic-assay-data-bin-counts.json b/test/api-e2e/specs/generic-assay-data-bin-counts.json new file mode 100644 index 00000000000..a296fee7b28 --- /dev/null +++ b/test/api-e2e/specs/generic-assay-data-bin-counts.json @@ -0,0 +1,126 @@ +[ + { + "name":"two_tcga_one_numerical_generic_assay_chart_no_filter", + "note":"two tcga studies without any filters, this can be used to verify the endpoint itself, e.g. NA counts validation", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterString": "", + "tests":[ + {"hash":384235647,"filterString":"","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genericAssayDataBinFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","disableLogScale":false}],"studyViewFilter":{"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenericAssayDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_generic_assay_chart_filter_higher_end", + "note":"two tcga studies with one numerical generic assay data chart filter from middle to higher end", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText": "ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65", + "tests":[ + {"hash":518256268,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":544912293,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1813843242,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":2142367180,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1196124544,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1038360983,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1640929326,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-739871817,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genericAssayDataBinFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","disableLogScale":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenericAssayDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-6047940,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1763270972,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):> 0.65","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.65,"end":0.7},{"start":0.7,"end":0.75},{"start":0.75,"end":0.8},{"start":0.8,"end":0.85},{"start":0.85,"end":0.9},{"start":0.9}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75},{\"start\":0.75,\"end\":0.8},{\"start\":0.8,\"end\":0.85},{\"start\":0.85,\"end\":0.9},{\"start\":0.9}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_generic_assay_chart_filter_lower_end", + "note":"two tcga studies with one numerical generic assay data chart filter from middle to lower end", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText": "ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45", + "tests":[ + {"hash":19097513,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genericAssayDataBinFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","disableLogScale":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenericAssayDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":33672580,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-359049970,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-77983304,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-171346021,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-877967529,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1707804262,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-63687826,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-697236490,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1444086658,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge):≤ 0.45","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"end":0.25},{"start":0.25,"end":0.3},{"start":0.3,"end":0.35},{"start":0.35,"end":0.4},{"start":0.4,"end":0.45}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"end\":0.25},{\"start\":0.25,\"end\":0.3},{\"start\":0.3,\"end\":0.35},{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_generic_assay_chart_filter_in_middle", + "note":"two tcga studies with one numerical generic assay data chart filter in the middle", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75", + "tests":[ + {"hash":40003668,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":966795425,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1308637388,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1584071516,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1212290320,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1344755530,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1695551179,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-587763972,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1471859358,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1714083403,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genericAssayDataBinFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","disableLogScale":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenericAssayDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_two_numerical_generic_assay_chart_filters", + "note":"two tcga studies with two numerical generic assay data chart filters", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07", + "tests":[ + {"hash":392475908,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":497155497,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":578993847,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genericAssayDataBinFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","disableLogScale":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenericAssayDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1252830588,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1600325568,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1066250134,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-569730587,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1661933492,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1137996270,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1948966133,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genericAssayDataBinFilters":[{"stableId":"AFR","profileType":"genetic_ancestry","disableLogScale":false}],"studyViewFilter":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/generic-assay-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenericAssayDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-617008116,"filterString":"ATP2A1 (cg00000292): Methylation (HM27 and HM450 merge): < x ≤ 0.350.75AFR: Genetic Ancestry: < x ≤ 0.020.07","data":{"genericAssayDataFilters":[{"stableId":"cg00000292","profileType":"methylation_hm27_hm450_merge","values":[{"start":0.35,"end":0.4},{"start":0.4,"end":0.45},{"start":0.45,"end":0.5},{"start":0.5,"end":0.55},{"start":0.55,"end":0.6},{"start":0.6,"end":0.65},{"start":0.65,"end":0.7},{"start":0.7,"end":0.75}]},{"stableId":"AFR","profileType":"genetic_ancestry","values":[{"start":0.02,"end":0.025},{"start":0.025,"end":0.03},{"start":0.03,"end":0.035},{"start":0.035,"end":0.04},{"start":0.04,"end":0.045},{"start":0.045,"end":0.05},{"start":0.05,"end":0.055},{"start":0.055,"end":0.06},{"start":0.06,"end":0.065},{"start":0.065,"end":0.07}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genericAssayDataFilters\":[{\"stableId\":\"cg00000292\",\"profileType\":\"methylation_hm27_hm450_merge\",\"values\":[{\"start\":0.35,\"end\":0.4},{\"start\":0.4,\"end\":0.45},{\"start\":0.45,\"end\":0.5},{\"start\":0.5,\"end\":0.55},{\"start\":0.55,\"end\":0.6},{\"start\":0.6,\"end\":0.65},{\"start\":0.65,\"end\":0.7},{\"start\":0.7,\"end\":0.75}]},{\"stableId\":\"AFR\",\"profileType\":\"genetic_ancestry\",\"values\":[{\"start\":0.02,\"end\":0.025},{\"start\":0.025,\"end\":0.03},{\"start\":0.03,\"end\":0.035},{\"start\":0.035,\"end\":0.04},{\"start\":0.04,\"end\":0.045},{\"start\":0.045,\"end\":0.05},{\"start\":0.05,\"end\":0.055},{\"start\":0.055,\"end\":0.06},{\"start\":0.06,\"end\":0.065},{\"start\":0.065,\"end\":0.07}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + } +] \ No newline at end of file diff --git a/test/api-e2e/specs/genomic-data-bin-counts.json b/test/api-e2e/specs/genomic-data-bin-counts.json new file mode 100644 index 00000000000..9cca5e7058b --- /dev/null +++ b/test/api-e2e/specs/genomic-data-bin-counts.json @@ -0,0 +1,150 @@ +[ + { + "name":"two_tcga_one_numerical_genomic_chart_no_filter", + "note":"two tcga studies without any filters, this can be used to verify the endpoint itself, e.g. NA counts validation", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterString": "", + "tests":[ + {"hash":-1058303076,"filterString":"","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genomicDataBinFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","disableLogScale":false}],"studyViewFilter":{"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/genomic-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenomicDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_genomic_chart_filter_higher_end", + "note":"two tcga studies with one numerical genomic data chart filter from middle to higher end", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText": "TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000", + "tests":[ + {"hash":517957775,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1084072374,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1879535509,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1994780762,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genomicDataBinFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","disableLogScale":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/genomic-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenomicDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1852594951,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-826852934,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-684418853,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1580730653,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-950159475,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-792416931,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 100010000","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":1000,"end":3162},{"start":3162,"end":10000}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":1000,\"end\":3162},{\"start\":3162,\"end\":10000}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_genomic_chart_filter_lower_end", + "note":"two tcga studies with one numerical genomic data chart filter from middle to lower end", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText": "TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316", + "tests":[ + {"hash":950614605,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1629744591,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1929531989,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1955799069,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1990053959,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-2099315334,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-627706762,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-2054238693,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-6354525,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1537996902,"filterString":"TP53: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2): < x ≤ 31316","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genomicDataBinFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","disableLogScale":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna","values":[{"start":31,"end":100},{"start":100,"end":316}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/genomic-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenomicDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna\",\"values\":[{\"start\":31,\"end\":100},{\"start\":100,\"end\":316}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_genomic_chart_filter_only_negative_values_selected", + "note":"two tcga studies with one numerical genomic data chart filter contains only negative values", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25", + "tests":[ + {"hash":710206650,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1118484004,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1168645812,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1567017101,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":2087302238,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1009889640,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1234322951,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1113995100,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-2049879636,"filterString":"TP53: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -2.5-1.25","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-2.5,"end":-2.25},{"start":-2.25,"end":-2},{"start":-2,"end":-1.75},{"start":-1.75,"end":-1.5},{"start":-1.5,"end":-1.25}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-2.5,\"end\":-2.25},{\"start\":-2.25,\"end\":-2},{\"start\":-2,\"end\":-1.75},{\"start\":-1.75,\"end\":-1.5},{\"start\":-1.5,\"end\":-1.25}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_one_numerical_genomic_chart_filter_in_middle", + "note":"two tcga studies with one numerical genomic data chart filter in the middle", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75", + "tests":[ + {"hash":368283586,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":455445948,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":592309141,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1962607958,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1997503577,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genomicDataBinFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","disableLogScale":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/genomic-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenomicDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1976140656,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1207606015,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"RACE"},{"attributeId":"SEX"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"ETHNICITY"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1254418276,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1568011476,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1904973132,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","data":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1944771519,"filterString":"TP53: Protein expression z-scores (RPPA): < x ≤ -1.250.75","skip": "NA counts mismatch, we should enable this after NA counts is correctly calculated","data":{"genomicDataBinFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna","disableLogScale":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"TP53","profileType":"rppa_Zscores","values":[{"start":-1.25,"end":-1},{"start":-1,"end":-0.75},{"start":-0.75,"end":-0.5},{"start":-0.5,"end":-0.25},{"start":-0.25,"end":0},{"start":0,"end":0.25},{"start":0.25,"end":0.5},{"start":0.5,"end":0.75}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/genomic-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"GenomicDataBinCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa_Zscores\",\"values\":[{\"start\":-1.25,\"end\":-1},{\"start\":-1,\"end\":-0.75},{\"start\":-0.75,\"end\":-0.5},{\"start\":-0.5,\"end\":-0.25},{\"start\":-0.25,\"end\":0},{\"start\":0,\"end\":0.25},{\"start\":0.25,\"end\":0.5},{\"start\":0.5,\"end\":0.75}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name":"two_tcga_two_numerical_genomic_chart_filters", + "note":"two tcga studies with two numerical genomic data chart filters", + "studies":["blca_tcga_pan_can_atlas_2018", "coadread_tcga_pan_can_atlas_2018"], + "filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2", + "tests":[ + {"hash":388930409,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"attributes":[{"attributeId":"OS_STATUS"},{"attributeId":"DFS_STATUS"},{"attributeId":"DSS_STATUS"},{"attributeId":"PFS_STATUS"},{"attributeId":"SUBTYPE"},{"attributeId":"PATH_M_STAGE"},{"attributeId":"TUMOR_TYPE"},{"attributeId":"PATH_T_STAGE"},{"attributeId":"SEX"},{"attributeId":"ETHNICITY"},{"attributeId":"AJCC_STAGING_EDITION"},{"attributeId":"RACE"},{"attributeId":"CANCER_TYPE_DETAILED"},{"attributeId":"OS_STATUS"},{"attributeId":"CANCER_TYPE"}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-counts/fetch?","label":"ClinicalDataCounts","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":514826369,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/molecular-profile-sample-counts/fetch?","label":"MolecularProfileSample","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":908457008,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/clinical-data-density-plot/fetch?xAxisAttributeId=FRACTION_GENOME_ALTERED&xAxisBinCount=44&xAxisStart=0&xAxisEnd=1&yAxisAttributeId=MUTATION_COUNT&yAxisBinCount=38&yAxisStart=0&xAxisLogScale=false&yAxisLogScale=false&","label":"ClinicalDataDensity","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1126057128,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/sample-lists-counts/fetch?","label":"CaseList","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":1274481956,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/filtered-samples/fetch?","label":"FilteredSamples","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-341016470,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"attributes":[{"attributeId":"MUTATION_COUNT","disableLogScale":false,"showNA":false},{"attributeId":"FRACTION_GENOME_ALTERED","disableLogScale":false,"showNA":false},{"attributeId":"AGE","disableLogScale":false,"showNA":false},{"attributeId":"MSI_SCORE_MANTIS","disableLogScale":false,"showNA":false,"customBins":[0.4,0.6]},{"attributeId":"MSI_SENSOR_SCORE","disableLogScale":false,"showNA":false,"customBins":[4,10]},{"attributeId":"ANEUPLOIDY_SCORE","disableLogScale":false,"showNA":false},{"attributeId":"DAYS_TO_BIRTH","disableLogScale":false,"showNA":false}],"studyViewFilter":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}},"url":"/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&","label":"ClinicalDataBin","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-1818300242,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-2057215208,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/mutated-genes/fetch?","label":"MutatedGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}, + + {"hash":-2043897696,"filterString":"EGFR: mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM): < x ≤ -12TP53: Protein expression (RPPA): < x ≤ -2.2-0.2","data":{"genomicDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"rna_seq_v2_mrna_median_Zscores","values":[{"start":-1,"end":-0.5},{"start":-0.5,"end":0},{"start":0,"end":0.5},{"start":0.5,"end":1},{"start":1,"end":1.5},{"start":1.5,"end":2}]},{"hugoGeneSymbol":"TP53","profileType":"rppa","values":[{"start":-2.2,"end":-2},{"start":-2,"end":-1.8},{"start":-1.8,"end":-1.6},{"start":-1.6,"end":-1.4},{"start":-1.4,"end":-1.2},{"start":-1.2,"end":-1},{"start":-1,"end":-0.8},{"start":-0.8,"end":-0.6},{"start":-0.6,"end":-0.4},{"start":-0.4,"end":-0.2}]}],"studyIds":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/cna-genes/fetch?","label":"CNAGenes","studies":["blca_tcga_pan_can_atlas_2018","coadread_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=blca_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018#filterJson={\"genomicDataFilters\":[{\"hugoGeneSymbol\":\"EGFR\",\"profileType\":\"rna_seq_v2_mrna_median_Zscores\",\"values\":[{\"start\":-1,\"end\":-0.5},{\"start\":-0.5,\"end\":0},{\"start\":0,\"end\":0.5},{\"start\":0.5,\"end\":1},{\"start\":1,\"end\":1.5},{\"start\":1.5,\"end\":2}]},{\"hugoGeneSymbol\":\"TP53\",\"profileType\":\"rppa\",\"values\":[{\"start\":-2.2,\"end\":-2},{\"start\":-2,\"end\":-1.8},{\"start\":-1.8,\"end\":-1.6},{\"start\":-1.6,\"end\":-1.4},{\"start\":-1.4,\"end\":-1.2},{\"start\":-1.2,\"end\":-1},{\"start\":-1,\"end\":-0.8},{\"start\":-0.8,\"end\":-0.6},{\"start\":-0.6,\"end\":-0.4},{\"start\":-0.4,\"end\":-0.2}]}],\"studyIds\":[\"blca_tcga_pan_can_atlas_2018\",\"coadread_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + } +] \ No newline at end of file From 8c0f82bb2dd3208aff295c90e2c145139d1f1612 Mon Sep 17 00:00:00 2001 From: Gaofei Zhao <15748980+dippindots@users.noreply.github.com> Date: Wed, 11 Sep 2024 14:08:44 -0400 Subject: [PATCH 4/4] Address sonorcloud issues --- .../helper/StudyViewFilterHelper.java | 4 ++-- .../StudyViewMyBatisRepository.java | 14 +++----------- .../web/columnar/BasicDataBinner.java | 18 ++++-------------- .../StudyViewMapperClinicalDataCountTest.java | 4 ---- 4 files changed, 9 insertions(+), 31 deletions(-) diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java index dbc3e53de1c..c94600c57d8 100644 --- a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java +++ b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java @@ -11,7 +11,7 @@ import org.springframework.lang.Nullable; import java.util.ArrayList; -import java.util.HashMap; +import java.util.EnumMap; import java.util.List; import java.util.Map; import java.util.Objects; @@ -24,7 +24,7 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil studyViewFilter = new StudyViewFilter(); } if (Objects.isNull(genericAssayProfilesMap)) { - genericAssayProfilesMap = new HashMap<>(); + genericAssayProfilesMap = new EnumMap<>(DataSource.class); } if (Objects.isNull(customDataSamples)) { customDataSamples = new ArrayList<>(); diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java index c73877f45d1..41687281c5d 100644 --- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java +++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java @@ -37,8 +37,7 @@ public class StudyViewMyBatisRepository implements StudyViewRepository { private Map> clinicalAttributesMap = new EnumMap<>(DataSource.class); private Map> genericAssayProfilesMap = new EnumMap<>(DataSource.class); - - + private static final List FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList(); private final StudyViewMapper mapper; @@ -217,11 +216,11 @@ public List getGenomicDataBinCounts(StudyViewFilterContext st public List getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List attributeIds) { return mapper.getGenericAssayDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), attributeIds); } - + private void buildClinicalAttributeNameMap() { clinicalAttributesMap = this.getClinicalAttributes() .stream() - .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute() ? DataSource.PATIENT : DataSource.SAMPLE)); + .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE)); } private void buildGenericAssayProfilesMap() { @@ -229,13 +228,6 @@ private void buildGenericAssayProfilesMap() { .stream() .collect(Collectors.groupingBy(ca -> ca.getPatientLevel().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE)); } - - private Map> getClinicalAttributeNameMap() { - if (clinicalAttributesMap.isEmpty()) { - buildClinicalAttributeNameMap(); - } - return clinicalAttributesMap; - } private Map> getGenericAssayProfilesMap() { if (genericAssayProfilesMap.isEmpty()) { diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java index 495b815be8a..d6978e35a5e 100644 --- a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java +++ b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java @@ -152,28 +152,20 @@ public void removeSelfFromFilter(S dataBinFilter, StudyViewFilter studyViewFilter) { switch (dataBinFilter) { - case ClinicalDataBinFilter clinicalDataBinFilter -> { - if (studyViewFilter.getClinicalDataFilters() != null) { + case ClinicalDataBinFilter clinicalDataBinFilter when studyViewFilter.getClinicalDataFilters() != null -> studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId())); - } - } - case GenomicDataBinFilter genomicDataBinFilter -> { - if (studyViewFilter.getGenomicDataFilters() != null) { + case GenomicDataBinFilter genomicDataBinFilter when studyViewFilter.getGenomicDataFilters() != null -> studyViewFilter.getGenomicDataFilters().removeIf(f -> f.getHugoGeneSymbol().equals(genomicDataBinFilter.getHugoGeneSymbol()) && f.getProfileType().equals(genomicDataBinFilter.getProfileType()) ); - } - } - case GenericAssayDataBinFilter genericAssayDataBinFilter -> { - if (studyViewFilter.getGenericAssayDataFilters() != null) { + case GenericAssayDataBinFilter genericAssayDataBinFilter when studyViewFilter.getGenericAssayDataFilters() != null -> studyViewFilter.getGenericAssayDataFilters().removeIf(f -> f.getStableId().equals(genericAssayDataBinFilter.getStableId()) && f.getProfileType().equals(genericAssayDataBinFilter.getProfileType()) ); - } - } default -> { + // Do not remove any filters } } } @@ -223,7 +215,6 @@ private List calculateStaticData for (T dataBinFilter : dataBinFilters) { // if there is data for requested attribute - // TODO: consider if this is correct to passing in a empty map if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) { List dataBins = dataBinner .calculateClinicalDataBins( @@ -252,7 +243,6 @@ private List calculateDynamicDat for (T dataBinFilter : dataBinFilters) { // if there is data for requested attribute - // TODO: consider if this is correct to passing in a empty map if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) { List dataBins = dataBinner .calculateDataBins( diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java index ae16aedb97f..8013aa5f6a2 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java @@ -1,8 +1,6 @@ package org.cbioportal.persistence.mybatisclickhouse; -import org.cbioportal.model.ClinicalAttribute; import org.cbioportal.model.ClinicalDataCount; -import org.cbioportal.persistence.enums.DataSource; import org.cbioportal.persistence.helper.StudyViewFilterHelper; import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; import org.cbioportal.web.parameter.ClinicalDataFilter; @@ -20,9 +18,7 @@ import java.math.BigDecimal; import java.util.Collections; -import java.util.HashMap; import java.util.List; -import java.util.Map; import static org.junit.Assert.assertEquals;