Add rfc80 clean arch

src/main/java/org/cbioportal/application/rest/mapper/CancerStudyMetadataMapper.java

@@ -1,7 +1,7 @@
 package org.cbioportal.application.rest.mapper;
 
 import org.cbioportal.application.rest.response.CancerStudyMetadataDTO;
-import org.cbioportal.cancerstudy.CancerStudyMetadata;
+import org.cbioportal.domain.cancerstudy.CancerStudyMetadata;
 import org.mapstruct.Mapper;
 import org.mapstruct.Mapping;
 import org.mapstruct.factory.Mappers;

src/main/java/org/cbioportal/application/rest/mapper/SampleMapper.java

@@ -0,0 +1,25 @@
+package org.cbioportal.application.rest.mapper;
+
+import org.cbioportal.application.rest.response.SampleDTO;
+import org.cbioportal.legacy.utils.Encoder;
+import org.cbioportal.domain.sample.Sample;
+import org.mapstruct.Mapper;
+import org.mapstruct.Mapping;
+import org.mapstruct.factory.Mappers;
+
+import java.util.List;
+
+@Mapper( imports = Encoder.class)
+public interface SampleMapper {
+    SampleMapper INSTANCE = Mappers.getMapper(SampleMapper.class);
+
+    @Mapping(target = "patientId", source = "patientStableId")
+    @Mapping(target = "sampleId", source = "stableId")
+    @Mapping(target = "studyId", source = "cancerStudyIdentifier")
+    @Mapping(target = "uniqueSampleKey", expression = "java( Encoder.calculateBase64(sample.stableId()," +
+            "sample.cancerStudyIdentifier()) )")
+    @Mapping(target = "uniquePatientKey", expression = "java( Encoder.calculateBase64(sample.patientStableId(), " +
+            "sample.cancerStudyIdentifier()) )")
+    SampleDTO toSampleDTO(Sample sample);
+    List<SampleDTO> toDtos(List<Sample> samples);
+}

src/main/java/org/cbioportal/application/rest/request/StudyViewFilterDTO.java

@@ -0,0 +1,239 @@
+package org.cbioportal.application.rest.request;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.AssertTrue;
+import jakarta.validation.constraints.Size;
+import org.cbioportal.legacy.model.AlterationFilter;
+import org.cbioportal.legacy.model.GeneFilter;
+import org.cbioportal.legacy.model.StudyViewStructuralVariantFilter;
+import org.cbioportal.legacy.web.parameter.ClinicalDataFilter;
+import org.cbioportal.legacy.web.parameter.DataFilter;
+import org.cbioportal.legacy.web.parameter.GenericAssayDataFilter;
+import org.cbioportal.legacy.web.parameter.GenomicDataFilter;
+import org.cbioportal.legacy.web.parameter.MutationDataFilter;
+import org.cbioportal.legacy.web.parameter.SampleIdentifier;
+import org.cbioportal.legacy.web.parameter.filter.AndedPatientTreatmentFilters;
+import org.cbioportal.legacy.web.parameter.filter.AndedSampleTreatmentFilters;
+
+import java.util.List;
+import java.util.Objects;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonInclude(Include.NON_NULL)
+public class StudyViewFilterDTO {
+
+    @Size(min = 1)
+    private List<SampleIdentifier> sampleIdentifiers;
+    @Size(min = 1)
+    private List<String> studyIds;
+    private List<ClinicalDataFilter> clinicalDataFilters;
+    private List<GeneFilter> geneFilters;
+    @Valid
+    private List<StudyViewStructuralVariantFilter> structuralVariantFilters;
+    private AndedSampleTreatmentFilters sampleTreatmentFilters;
+    private AndedSampleTreatmentFilters sampleTreatmentGroupFilters;
+    private AndedSampleTreatmentFilters sampleTreatmentTargetFilters;
+    private AndedPatientTreatmentFilters patientTreatmentFilters;
+    private AndedPatientTreatmentFilters patientTreatmentGroupFilters;
+    private AndedPatientTreatmentFilters patientTreatmentTargetFilters;
+	private List<List<String>> genomicProfiles;
+    private List<GenomicDataFilter> genomicDataFilters;
+    private List<GenericAssayDataFilter> genericAssayDataFilters;
+    private List<List<String>> caseLists;
+    private List<ClinicalDataFilter> customDataFilters;
+    private AlterationFilter alterationFilter;
+    private List<DataFilter> clinicalEventFilters;
+    private List<MutationDataFilter> mutationDataFilters;
+
+    @AssertTrue
+    private boolean isEitherSampleIdentifiersOrStudyIdsPresent() {
+        return sampleIdentifiers != null ^ studyIds != null;
+    }
+
+    @AssertTrue
+    private boolean isEitherValueOrRangePresentInClinicalDataIntervalFilters() {
+        return validateDataFilters(clinicalDataFilters);
+    }
+
+    @AssertTrue
+    private boolean isEitherValueOrRangePresentInGenomicDataIntervalFilters() {
+        return validateDataFilters(genomicDataFilters);
+    }
+
+    @AssertTrue
+    private boolean isEitherValueOrRangePresentInGenericAssayDataIntervalFilters() {
+        return validateDataFilters(genericAssayDataFilters);
+    }
+
+    @AssertTrue
+    private boolean isEitherValueOrRangePresentInCustomDataFilters() {
+        return validateDataFilters(customDataFilters);
+    }
+
+    private <T extends DataFilter> boolean validateDataFilters(List<T> dataFilters) {
+        long invalidCount = 0;
+
+        if (dataFilters != null) {
+            invalidCount = dataFilters.stream()
+                    .flatMap(f -> f.getValues().stream())
+                    .filter(Objects::nonNull)
+                    .filter(v -> v.getValue() != null == (v.getStart() != null || v.getEnd() != null))
+                    .count();
+        }
+
+        return invalidCount == 0;
+    }
+
+    public List<SampleIdentifier> getSampleIdentifiers() {
+        return sampleIdentifiers;
+    }
+
+    public void setSampleIdentifiers(List<SampleIdentifier> sampleIdentifiers) {
+        this.sampleIdentifiers = sampleIdentifiers;
+    }
+
+    public List<String> getStudyIds() {
+        return studyIds;
+    }
+
+    public void setStudyIds(List<String> studyIds) {
+        this.studyIds = studyIds;
+    }
+
+    public List<ClinicalDataFilter> getClinicalDataFilters() {
+        return clinicalDataFilters;
+    }
+
+    public void setClinicalDataFilters(List<ClinicalDataFilter> clinicalDataFilters) {
+        this.clinicalDataFilters = clinicalDataFilters;
+    }
+
+    public List<GeneFilter> getGeneFilters() {
+        return geneFilters;
+    }
+
+    public void setGeneFilters(List<GeneFilter> geneFilters) {
+        this.geneFilters = geneFilters;
+    }
+
+    public List<StudyViewStructuralVariantFilter> getStructuralVariantFilters() {
+        return structuralVariantFilters;
+    }
+
+    public void setStructuralVariantFilters(List<StudyViewStructuralVariantFilter> structuralVariantFilters) {
+        this.structuralVariantFilters = (structuralVariantFilters != null) ? structuralVariantFilters : List.of();
+    }
+
+    public List<List<String>> getGenomicProfiles() {
+        return genomicProfiles;
+    }
+
+    public void setGenomicProfiles(List<List<String>> genomicProfiles) {
+        this.genomicProfiles = genomicProfiles;
+    }
+
+    public List<GenomicDataFilter> getGenomicDataFilters() {
+        return genomicDataFilters;
+    }
+
+    public void setGenomicDataFilters(List<GenomicDataFilter> genomicDataFilters) {
+        this.genomicDataFilters = genomicDataFilters;
+    }
+
+    public AndedSampleTreatmentFilters getSampleTreatmentFilters() {
+        return sampleTreatmentFilters;
+    }
+
+    public void setSampleTreatmentFilters(AndedSampleTreatmentFilters sampleTreatmentFilters) {
+        this.sampleTreatmentFilters = sampleTreatmentFilters;
+    }
+
+    public AndedPatientTreatmentFilters getPatientTreatmentFilters() {
+        return patientTreatmentFilters;
+    }
+
+    public void setPatientTreatmentFilters(AndedPatientTreatmentFilters patientTreatmentFilters) {
+        this.patientTreatmentFilters = patientTreatmentFilters;
+    }
+
+    public List<List<String>> getCaseLists() {
+        return caseLists;
+    }
+
+    public void setCaseLists(List<List<String>> caseLists) {
+        this.caseLists = caseLists;
+    }
+
+	public List<GenericAssayDataFilter> getGenericAssayDataFilters() {
+		return genericAssayDataFilters;
+	}
+
+	public void setGenericAssayDataFilters(List<GenericAssayDataFilter> genericAssayDataFilters) {
+		this.genericAssayDataFilters = genericAssayDataFilters;
+	}
+
+    public List<ClinicalDataFilter> getCustomDataFilters() {
+        return customDataFilters;
+    }
+
+    public void setCustomDataFilters(List<ClinicalDataFilter> customDataFilters) {
+        this.customDataFilters = customDataFilters;
+    }
+
+    public AlterationFilter getAlterationFilter() {
+        return alterationFilter;
+    }
+
+    public void setAlterationFilter(AlterationFilter alterationFilter) {
+        this.alterationFilter = (alterationFilter != null) ? alterationFilter : new AlterationFilter();
+    }
+
+    public AndedSampleTreatmentFilters getSampleTreatmentGroupFilters() {
+        return sampleTreatmentGroupFilters;
+    }
+
+    public void setSampleTreatmentGroupFilters(AndedSampleTreatmentFilters sampleTreatmentGroupFilters) {
+        this.sampleTreatmentGroupFilters = sampleTreatmentGroupFilters;
+    }
+
+    public AndedPatientTreatmentFilters getPatientTreatmentGroupFilters() {
+        return patientTreatmentGroupFilters;
+    }
+
+    public void setPatientTreatmentGroupFilters(AndedPatientTreatmentFilters patientTreatmentGroupFilters) {
+        this.patientTreatmentGroupFilters = patientTreatmentGroupFilters;
+    }
+
+    public AndedSampleTreatmentFilters getSampleTreatmentTargetFilters() {
+        return sampleTreatmentTargetFilters;
+    }
+
+    public void setSampleTreatmentTargetFilters(AndedSampleTreatmentFilters sampleTreatmentTargetFilters) {
+        this.sampleTreatmentTargetFilters = sampleTreatmentTargetFilters;
+    }
+
+    public AndedPatientTreatmentFilters getPatientTreatmentTargetFilters() {
+        return patientTreatmentTargetFilters;
+    }
+
+    public void setPatientTreatmentTargetFilters(AndedPatientTreatmentFilters patientTreatmentTagetFilters) {
+        this.patientTreatmentTargetFilters = patientTreatmentTagetFilters;
+    }
+
+    public List<DataFilter> getClinicalEventFilters() {
+        return clinicalEventFilters;
+    }
+
+    public void setClinicalEventFilters(List<DataFilter> clinicalEventFilters) {
+        this.clinicalEventFilters = clinicalEventFilters;
+    }
+
+    public List<MutationDataFilter> getMutationDataFilters() { return mutationDataFilters; }
+
+    public void setMutationDataFilters(List<MutationDataFilter> mutationDataFilters) {
+        this.mutationDataFilters = mutationDataFilters;
+    }
+}

src/main/java/org/cbioportal/application/rest/response/CancerStudyMetadataDTO.java

@@ -1,7 +1,7 @@
 package org.cbioportal.application.rest.response;
 
 import io.swagger.v3.oas.annotations.media.Schema;
-import org.cbioportal.cancerstudy.TypeOfCancer;
+import org.cbioportal.domain.cancerstudy.TypeOfCancer;
 
 @Schema(name = "CancerStudyMetadata", description = "Represents a cancer study")
 public record CancerStudyMetadataDTO(String cancerStudyIdentifier, String typeOfCancerId,

src/main/java/org/cbioportal/application/rest/response/SampleDTO.java

@@ -0,0 +1,7 @@
+package org.cbioportal.application.rest.response;
+
+import org.cbioportal.domain.sample.SampleType;
+
+public record SampleDTO(String sampleId, SampleType sampleType, String patientId, String studyId, Boolean sequenced,
+                        Boolean copyNumberSegmentPresent, String uniqueSampleKey, String uniquePatientKey) {
+}

src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnStoreStudyController.java

@@ -4,7 +4,7 @@
 import io.swagger.v3.oas.annotations.Parameter;
 import org.cbioportal.application.rest.mapper.CancerStudyMetadataMapper;
 import org.cbioportal.application.rest.response.CancerStudyMetadataDTO;
-import org.cbioportal.cancerstudy.usecase.GetCancerStudyMetadataUseCase;
+import org.cbioportal.domain.cancerstudy.usecase.GetCancerStudyMetadataUseCase;
 import org.cbioportal.legacy.web.parameter.Direction;
 import org.cbioportal.legacy.web.parameter.sort.StudySortBy;
 import org.cbioportal.shared.SortAndSearchCriteria;