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Draft: Genomic data counts #10293

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Draft: Genomic data counts #10293

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a789cdc
implement getting CNA types for a gene specific
qlu-cls Jul 20, 2023
fff09f4
add tests for genomic-data-counts endpoint
qlu-cls Jul 24, 2023
082f3f5
change CopyNumberDataCounterFilter to StudyViewFilter and GenomicData…
qlu-cls Jul 26, 2023
1239c3e
get DiscreteCNAProfileCaseIdentifiers with provided profileTypes
qlu-cls Jul 27, 2023
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4 changes: 4 additions & 0 deletions service/src/main/java/org/cbioportal/service/StudyViewService.java
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@@ -1,6 +1,7 @@
package org.cbioportal.service;

import org.cbioportal.model.*;
import org.cbioportal.service.exception.MolecularProfileNotFoundException;
import org.cbioportal.service.exception.StudyNotFoundException;

import java.util.List;
Expand All @@ -19,6 +20,9 @@ List<AlterationCountByGene> getStructuralVariantAlterationCountByGenes(List<Stri
List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> studyIds, List<String> sampleIds, AlterationFilter annotationFilter)
throws StudyNotFoundException;

List<GenomicDataCount> getCNAAlterationCountsByEvent(String molecularProfileId, List<Integer> entrezGeneIds,
List<Integer> alterations) throws MolecularProfileNotFoundException;

List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String> sampleIds, List<String> studyIds, List<String> stableIds, List<String> profileTypes);

}
27 changes: 27 additions & 0 deletions service/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
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Expand Up @@ -37,6 +37,9 @@ public class StudyViewServiceImpl implements StudyViewService {
@Autowired
private AlterationRepository alterationRepository;

@Autowired
private DiscreteCopyNumberService discreteCopyNumberService;

@Override
public List<GenomicDataCount> getGenomicDataCounts(List<String> studyIds, List<String> sampleIds) {
List<MolecularProfileCaseIdentifier> molecularProfileSampleIdentifiers =
Expand Down Expand Up @@ -186,6 +189,30 @@ public List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> stu
return copyNumberCountByGenes;
}

@Override
public List<GenomicDataCount> getCNAAlterationCountsByEvent(String molecularProfileId, List<Integer> entrezGeneIds,
List<Integer> alterations) throws MolecularProfileNotFoundException {

List<CopyNumberCount> copyNumberCounts = discreteCopyNumberService.fetchCopyNumberCounts(molecularProfileId, entrezGeneIds, alterations);

return copyNumberCounts
.stream()
.filter(c -> c.getNumberOfSamplesWithAlterationInGene() != null)
.map(entry -> {
int count = entry.getNumberOfSamplesWithAlterationInGene();
int alteration = entry.getAlteration();
String label = CNA.getByCode(entry.getAlteration().shortValue()).getDescription();

GenomicDataCount genomicDataCount = new GenomicDataCount();
genomicDataCount.setLabel(label);
genomicDataCount.setValue(String.valueOf(alteration));
genomicDataCount.setCount(count);

return genomicDataCount;
})
.collect(Collectors.toList());
}

@Override
public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String> sampleIds, List<String> studyIds,
List<String> stableIds, List<String> profileTypes) {
Expand Down
61 changes: 61 additions & 0 deletions service/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java
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Expand Up @@ -14,6 +14,7 @@
import org.mockito.Spy;
import org.mockito.junit.MockitoJUnitRunner;

import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
Expand Down Expand Up @@ -41,6 +42,8 @@ public class StudyViewServiceImplTest extends BaseServiceImplTest {
private SignificantCopyNumberRegionService significantCopyNumberRegionService;
@Mock
private GenericAssayService genericAssayService;
@Mock
private DiscreteCopyNumberService discreteCopyNumberService;
private AlterationFilter alterationFilter = new AlterationFilter();

@Test
Expand Down Expand Up @@ -255,6 +258,64 @@ public void getCNAAlterationCountByGenes() throws Exception {
Assert.assertEquals(1, result.size());
}

@Test
public void getCNAAlterationCountByEvent() throws Exception {

List<Integer> entrezGeneIds = new ArrayList<>();
List<Integer> alterations = new ArrayList<>();

for (int i = -2; i < 3; i++) {
entrezGeneIds.add(BaseServiceImplTest.ENTREZ_GENE_ID_1);
alterations.add(i);
}

List<CopyNumberCount> alterationCountByEvents = new ArrayList<>();
CopyNumberCount alterationCountByEvent1 = new CopyNumberCount();
CopyNumberCount alterationCountByEvent2 = new CopyNumberCount();
CopyNumberCount alterationCountByEvent3 = new CopyNumberCount();
CopyNumberCount alterationCountByEvent4 = new CopyNumberCount();
CopyNumberCount alterationCountByEvent5 = new CopyNumberCount();

alterationCountByEvent1.setMolecularProfileId(BaseServiceImplTest.MOLECULAR_PROFILE_ID);
alterationCountByEvent1.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_1);
alterationCountByEvent1.setAlteration(-2);
alterationCountByEvent1.setNumberOfSamples(5);
alterationCountByEvent1.setNumberOfSamplesWithAlterationInGene(1);
alterationCountByEvent2.setMolecularProfileId(BaseServiceImplTest.MOLECULAR_PROFILE_ID);
alterationCountByEvent2.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_1);
alterationCountByEvent2.setAlteration(-1);
alterationCountByEvent2.setNumberOfSamples(5);
alterationCountByEvent2.setNumberOfSamplesWithAlterationInGene(1);
alterationCountByEvent3.setMolecularProfileId(BaseServiceImplTest.MOLECULAR_PROFILE_ID);
alterationCountByEvent3.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_1);
alterationCountByEvent3.setAlteration(0);
alterationCountByEvent3.setNumberOfSamples(5);
alterationCountByEvent3.setNumberOfSamplesWithAlterationInGene(1);
alterationCountByEvent4.setMolecularProfileId(BaseServiceImplTest.MOLECULAR_PROFILE_ID);
alterationCountByEvent4.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_1);
alterationCountByEvent4.setAlteration(1);
alterationCountByEvent4.setNumberOfSamples(5);
alterationCountByEvent4.setNumberOfSamplesWithAlterationInGene(1);
alterationCountByEvent5.setMolecularProfileId(BaseServiceImplTest.MOLECULAR_PROFILE_ID);
alterationCountByEvent5.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_1);
alterationCountByEvent5.setAlteration(2);
alterationCountByEvent5.setNumberOfSamples(5);
alterationCountByEvent5.setNumberOfSamplesWithAlterationInGene(1);
alterationCountByEvents.add(alterationCountByEvent1);
alterationCountByEvents.add(alterationCountByEvent2);
alterationCountByEvents.add(alterationCountByEvent3);
alterationCountByEvents.add(alterationCountByEvent4);
alterationCountByEvents.add(alterationCountByEvent5);

Mockito.when(discreteCopyNumberService.fetchCopyNumberCounts(
eq(BaseServiceImplTest.MOLECULAR_PROFILE_ID),
eq(entrezGeneIds),
eq(alterations)
)).thenReturn(alterationCountByEvents);
List<GenomicDataCount> result = studyViewService.getCNAAlterationCountsByEvent(BaseServiceImplTest.MOLECULAR_PROFILE_ID, entrezGeneIds, alterations);
Assert.assertEquals(5, result.size());
}

@Test
public void fetchGenericAssayDataCounts() throws Exception {

Expand Down
33 changes: 26 additions & 7 deletions web/src/main/java/org/cbioportal/web/StudyViewController.java
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Expand Up @@ -11,6 +11,7 @@
import org.apache.commons.math3.stat.correlation.SpearmansCorrelation;
import org.cbioportal.model.*;
import org.cbioportal.service.*;
import org.cbioportal.service.exception.MolecularProfileNotFoundException;
import org.cbioportal.service.exception.StudyNotFoundException;
import org.cbioportal.service.util.ClinicalAttributeUtil;
import org.cbioportal.web.config.annotation.InternalApi;
Expand All @@ -27,19 +28,14 @@
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestAttribute;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import org.springframework.web.bind.annotation.*;
import springfox.documentation.annotations.ApiIgnore;

import javax.annotation.PostConstruct;
import javax.validation.Valid;
import javax.validation.constraints.Max;
import javax.validation.constraints.Min;
import javax.validation.constraints.Size;
import java.math.BigDecimal;
import java.util.*;
import java.util.function.Function;
Expand Down Expand Up @@ -845,6 +841,29 @@ public List<CaseListDataCount> fetchCaseListCounts(
.collect(Collectors.toList());

}

@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
@RequestMapping(value = "/genomic-data-counts/fetch", method = RequestMethod.POST,
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consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
@ApiOperation("Fetch genomic data counts by CopyNumberCountFilter")
public ResponseEntity<List<GenomicDataCount>> fetchGenomicDataCounts(
@ApiIgnore // prevent reference to this attribute in the swagger-ui interface
@RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
@ApiParam(required = true, value = "List of copy number count identifiers")
@RequestBody CopyNumberCountFilter copyNumberCountFilter
) throws MolecularProfileNotFoundException {
String molecularProfileId = copyNumberCountFilter.getMolecularProfileId();
int entrezGeneId = copyNumberCountFilter.getEntrezGeneId();

List<Integer> entrezGeneIds = new ArrayList<>();
List<Integer> alterations = DiscreteCopyNumberEventType.ALL.getAlterationTypes();
for (int i = 0; i < alterations.size(); i++) entrezGeneIds.add(entrezGeneId);

return new ResponseEntity<>(
studyViewService.getCNAAlterationCountsByEvent(molecularProfileId, entrezGeneIds, alterations),
HttpStatus.OK
);
}

@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
@RequestMapping(value = "/genomic-data-bin-counts/fetch", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
Expand Down
20 changes: 20 additions & 0 deletions web/src/main/java/org/cbioportal/web/parameter/CopyNumberCountFilter.java
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@@ -0,0 +1,20 @@
package org.cbioportal.web.parameter;

public class CopyNumberCountFilter {

private String molecularProfileId;
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should support multi profile, use profileType instead of molecularProfileId

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Do you mean List?

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Looks like you are not using this class anymore. could you remove it?


private Integer entrezGeneId;
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public String getMolecularProfileId() {return molecularProfileId; }

public void setMolecularProfileId(String molecularProfileId) {this.molecularProfileId = molecularProfileId; }

public Integer getEntrezGeneId() {
return entrezGeneId;
}

public void setEntrezGeneId(Integer entrezGeneId) {
this.entrezGeneId = entrezGeneId;
}
}
3 changes: 2 additions & 1 deletion web/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java
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Expand Up @@ -75,6 +75,7 @@ public class InvolvedCancerStudyExtractorInterceptor extends HandlerInterceptorA
public static final String STUDY_VIEW_CLINICAL_DATA_BIN_COUNTS_PATH = "/clinical-data-bin-counts/fetch";
public static final String STUDY_VIEW_CUSTOM_DATA_BIN_COUNTS_PATH = "/custom-data-bin-counts/fetch";
public static final String STUDY_VIEW_GENOMICL_DATA_BIN_COUNTS_PATH = "/genomic-data-bin-counts/fetch";
public static final String STUDY_VIEW_GENOMICL_DATA_COUNTS_PATH = "/genomic-data-counts/fetch";
public static final String STUDY_VIEW_GENERIC_ASSAY_DATA_BIN_COUNTS_PATH = "/generic-assay-data-bin-counts/fetch";
public static final String STUDY_VIEW_GENERIC_ASSAY_DATA_COUNTS_PATH = "/generic-assay-data-counts/fetch";
public static final String STUDY_VIEW_CLINICAL_DATA_COUNTS_PATH = "/clinical-data-counts/fetch";
Expand Down Expand Up @@ -137,7 +138,7 @@ public class InvolvedCancerStudyExtractorInterceptor extends HandlerInterceptorA
} else if (Arrays.asList(STUDY_VIEW_CLINICAL_DATA_COUNTS_PATH, STUDY_VIEW_CUSTOM_DATA_COUNTS_PATH)
.contains(requestPathInfo)) {
return extractAttributesFromClinicalDataCountFilter(request);
} else if (Arrays.asList(STUDY_VIEW_CLINICAL_DATA_DENSITY_PATH, STUDY_VIEW_CLINICAL_DATA_VIOLIN_PATH, STUDY_VIEW_CNA_GENES,
} else if (Arrays.asList(STUDY_VIEW_CLINICAL_DATA_DENSITY_PATH, STUDY_VIEW_CLINICAL_DATA_VIOLIN_PATH, STUDY_VIEW_CNA_GENES,
STUDY_VIEW_FILTERED_SAMPLES, STUDY_VIEW_MUTATED_GENES, STUDY_VIEW_STRUCTURAL_VARIANT_GENES,
STUDY_VIEW_STRUCTURAL_VARIANT_COUNTS, STUDY_VIEW_SAMPLE_COUNTS, STUDY_VIEW_SAMPLE_LIST_COUNTS_PATH, STUDY_VIEW_CLINICAL_TABLE_DATA_FETCH_PATH,
TREATMENTS_PATIENT_PATH, TREATMENTS_SAMPLE_PATH, STUDY_VIEW_PROFILE_SAMPLE_COUNTS_PATH, CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH
Expand Down
38 changes: 38 additions & 0 deletions web/src/test/java/org/cbioportal/web/StudyViewControllerTest.java
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Expand Up @@ -62,6 +62,9 @@ public class StudyViewControllerTest {
private static final String TEST_GENERIC_ASSAY_DATA_VALUE_2 = "value2";
private static final String TEST_CLINICAL_EVENT_TYPE = "STATUS";
private static final Integer TEST_CLINICAL_EVENT_TYPE_COUNT = 513;
private static final String TEST_CNA_ALTERATION_NAME = "test_cna_event_type";
private static final String TEST_CNA_ALTERATION_VALUE = "2";
private static final String TEST_MOLECULAR_PROFILE_ID = "test_molecular_profile_id";

private List<SampleIdentifier> filteredSampleIdentifiers = new ArrayList<>();
private List<ClinicalData> clinicalData = new ArrayList<>();
Expand Down Expand Up @@ -506,6 +509,41 @@ public void fetchSampleCounts() throws Exception {
.andExpect(MockMvcResultMatchers.jsonPath("$[1].count").value(2));
}


@Test
public void fetchGenomicDataCounts() throws Exception {
List<GenomicDataCount> genomicDataCounts = new ArrayList<>();
GenomicDataCount genomicDataCount1 = new GenomicDataCount();
genomicDataCount1.setLabel(TEST_CNA_ALTERATION_NAME);
genomicDataCount1.setValue(TEST_CNA_ALTERATION_VALUE);
genomicDataCount1.setCount(1);
genomicDataCounts.add(genomicDataCount1);

List<Integer> entrezGeneIds = new ArrayList<>();
List<Integer> alterations = DiscreteCopyNumberEventType.ALL.getAlterationTypes();
for (int i = 0; i < alterations.size(); i++) entrezGeneIds.add(TEST_ENTREZ_GENE_ID_1);

when(studyViewService.getCNAAlterationCountsByEvent(
eq(TEST_MOLECULAR_PROFILE_ID),
eq(entrezGeneIds),
eq(alterations)))
.thenReturn(genomicDataCounts);

CopyNumberCountFilter copyNumberCountFilter = new CopyNumberCountFilter();
copyNumberCountFilter.setEntrezGeneId(TEST_ENTREZ_GENE_ID_1);
copyNumberCountFilter.setMolecularProfileId(TEST_MOLECULAR_PROFILE_ID);

mockMvc.perform(MockMvcRequestBuilders.post("/genomic-data-counts/fetch")
.accept(MediaType.APPLICATION_JSON)
.contentType(MediaType.APPLICATION_JSON)
.content(objectMapper.writeValueAsString(copyNumberCountFilter)))
.andExpect(MockMvcResultMatchers.status().isOk())
.andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
.andExpect(MockMvcResultMatchers.jsonPath("$[0].label").value(TEST_CNA_ALTERATION_NAME))
.andExpect(MockMvcResultMatchers.jsonPath("$[0].value").value(TEST_CNA_ALTERATION_VALUE))
.andExpect(MockMvcResultMatchers.jsonPath("$[0].count").value(1));
}

@Ignore("Skip StudyViewControllerTest.fetchClinicalDataDensityPlot due to assertion errors")
@Test
public void fetchClinicalDataDensityPlot() throws Exception {
Expand Down
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