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Demo rfc80 density plot #10837

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merged 5 commits into from
Jun 18, 2024
Merged

Demo rfc80 density plot #10837

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c84238a
working poc
uklineale Jun 14, 2024
1e08295
refactor logic into service, so clean
uklineale Jun 17, 2024
3f0907f
refactor for parameters builder, simplify min max logic, streamline s…
uklineale Jun 18, 2024
2567fc1
remove unused services and imports
uklineale Jun 18, 2024
d369b6a
remove more unused imports
uklineale Jun 18, 2024
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12 changes: 12 additions & 0 deletions src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java
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package org.cbioportal.service;

import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.DensityPlotData;
import org.cbioportal.web.util.DensityPlotParameters;

import java.math.BigDecimal;
import java.util.List;

public interface ClinicalDataDensityPlotService {
DensityPlotData getDensityPlotData(List<ClinicalData> filteredClinicalData, DensityPlotParameters densityPlotParameters);
}
138 changes: 138 additions & 0 deletions src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java
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package org.cbioportal.service.impl;

import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.math3.stat.correlation.PearsonsCorrelation;
import org.apache.commons.math3.stat.correlation.SpearmansCorrelation;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.DensityPlotBin;
import org.cbioportal.model.DensityPlotData;
import org.cbioportal.service.ClinicalDataDensityPlotService;
import org.cbioportal.web.columnar.StudyViewColumnStoreController;
import org.cbioportal.web.util.DensityPlotParameters;
import org.springframework.stereotype.Service;

import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

@Service
public class ClinicalDataDensityPlotServiceImpl implements ClinicalDataDensityPlotService {
@Override
public DensityPlotData getDensityPlotData(List<ClinicalData> sampleClinicalData, DensityPlotParameters densityPlotParameters) {
DensityPlotData result = new DensityPlotData();
result.setBins(new ArrayList<>());

Map<String, List<ClinicalData>> clinicalDataGroupedBySampleId = sampleClinicalData.stream().
collect(Collectors.groupingBy(ClinicalData::getSampleId));

List<ClinicalData> extractedXYClinicalData = clinicalDataGroupedBySampleId.entrySet().stream()
.filter(entry -> entry.getValue().size() == 2 &&
NumberUtils.isCreatable(entry.getValue().get(0).getAttrValue()) &&
NumberUtils.isCreatable(entry.getValue().get(1).getAttrValue())
).flatMap(entry -> entry.getValue().stream())
.toList();

if (extractedXYClinicalData.isEmpty()) {
return result;
}

Map<Boolean, List<ClinicalData>> partition = extractedXYClinicalData.stream().collect(
Collectors.partitioningBy(c -> c.getAttrId().equals(densityPlotParameters.getXAxisAttributeId())));

boolean useXLogScale = densityPlotParameters.getXAxisLogScale() && ClinicalDataDensityPlotServiceImpl.isLogScalePossibleForAttribute(densityPlotParameters.getXAxisAttributeId());
boolean useYLogScale = densityPlotParameters.getYAxisLogScale() && ClinicalDataDensityPlotServiceImpl.isLogScalePossibleForAttribute(densityPlotParameters.getYAxisAttributeId());

double[] xValues = partition.get(true).stream().mapToDouble(
useXLogScale ? ClinicalDataDensityPlotServiceImpl::parseValueLog : ClinicalDataDensityPlotServiceImpl::parseValueLinear
).toArray();
double[] yValues = partition.get(false).stream().mapToDouble(
useYLogScale ? ClinicalDataDensityPlotServiceImpl::parseValueLog : ClinicalDataDensityPlotServiceImpl::parseValueLinear
).toArray();
double[] xValuesCopy = Arrays.copyOf(xValues, xValues.length);
double[] yValuesCopy = Arrays.copyOf(yValues, yValues.length); // Why copy these?
Arrays.sort(xValuesCopy);
Arrays.sort(yValuesCopy);

double xAxisStartValue = densityPlotParameters.getXAxisStart() == null ? xValuesCopy[0] :
(useXLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getXAxisStart().doubleValue()) : densityPlotParameters.getXAxisStart().doubleValue());
double xAxisEndValue = densityPlotParameters.getXAxisEnd() == null ? xValuesCopy[xValuesCopy.length - 1] :
(useXLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getXAxisEnd().doubleValue()) : densityPlotParameters.getXAxisEnd().doubleValue());
double yAxisStartValue = densityPlotParameters.getYAxisStart() == null ? yValuesCopy[0] :
(useYLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getYAxisStart().doubleValue()) : densityPlotParameters.getYAxisStart().doubleValue());
double yAxisEndValue = densityPlotParameters.getYAxisEnd() == null ? yValuesCopy[yValuesCopy.length - 1] :
(useYLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getYAxisEnd().doubleValue()) : densityPlotParameters.getYAxisEnd().doubleValue());
double xAxisBinInterval = (xAxisEndValue - xAxisStartValue) / densityPlotParameters.getXAxisBinCount();
double yAxisBinInterval = (yAxisEndValue - yAxisStartValue) / densityPlotParameters.getYAxisBinCount();
List<DensityPlotBin> bins = result.getBins();
for (int i = 0; i < densityPlotParameters.getXAxisBinCount(); i++) {
for (int j = 0; j < densityPlotParameters.getYAxisBinCount(); j++) {
DensityPlotBin densityPlotBin = new DensityPlotBin();
densityPlotBin.setBinX(BigDecimal.valueOf(xAxisStartValue + (i * xAxisBinInterval)));
densityPlotBin.setBinY(BigDecimal.valueOf(yAxisStartValue + (j * yAxisBinInterval)));
densityPlotBin.setCount(0);
bins.add(densityPlotBin);
}
}

for (int i = 0; i < xValues.length; i++) {
double xValue = xValues[i];
double yValue = yValues[i];
int xBinIndex = (int) ((xValue - xAxisStartValue) / xAxisBinInterval);
int yBinIndex = (int) ((yValue - yAxisStartValue) / yAxisBinInterval);
int index = (int) (((xBinIndex - (xBinIndex == densityPlotParameters.getXAxisBinCount() ? 1 : 0)) * densityPlotParameters.getYAxisBinCount()) +
(yBinIndex - (yBinIndex == densityPlotParameters.getYAxisBinCount() ? 1 : 0)));
DensityPlotBin densityPlotBin = bins.get(index);
densityPlotBin.setCount(densityPlotBin.getCount() + 1);
BigDecimal xValueBigDecimal = BigDecimal.valueOf(xValue);
BigDecimal yValueBigDecimal = BigDecimal.valueOf(yValue);

// Set new min and max as needed
if (densityPlotBin.getMinX() == null || densityPlotBin.getMinX().compareTo(xValueBigDecimal) > 0){
densityPlotBin.setMinX(xValueBigDecimal);
}
if (densityPlotBin.getMaxX() == null || densityPlotBin.getMaxX().compareTo(xValueBigDecimal) < 0){
densityPlotBin.setMaxX(xValueBigDecimal);
}
if (densityPlotBin.getMinY() == null || densityPlotBin.getMinY().compareTo(yValueBigDecimal) > 0){
densityPlotBin.setMinY(yValueBigDecimal);
}
if (densityPlotBin.getMaxY() == null || densityPlotBin.getMaxY().compareTo(yValueBigDecimal) < 0){
densityPlotBin.setMaxY(yValueBigDecimal);
}
}

if (xValues.length > 1) {
// need at least 2 entries in each to compute correlation
result.setPearsonCorr(new PearsonsCorrelation().correlation(xValues, yValues));
result.setSpearmanCorr(new SpearmansCorrelation().correlation(xValues, yValues));
} else {
// if less than 1 entry, just set 0 correlation
result.setSpearmanCorr(0.0);
result.setPearsonCorr(0.0);
}

// filter out empty bins
result.setBins(result.getBins().stream().filter((bin)->(bin.getCount() > 0)).collect(Collectors.toList()));
return result;
}


private static boolean isLogScalePossibleForAttribute(String clinicalAttributeId) {
return clinicalAttributeId.equals("MUTATION_COUNT");
}

private static double logScale(double val) {
return Math.log(1+val);
}

private static double parseValueLog(ClinicalData c) {
return ClinicalDataDensityPlotServiceImpl.logScale(Double.parseDouble(c.getAttrValue()));
}

private static double parseValueLinear(ClinicalData c) {
return Double.parseDouble(c.getAttrValue());
}
}
116 changes: 114 additions & 2 deletions src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
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package org.cbioportal.web.columnar;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import jakarta.validation.Valid;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.math3.stat.correlation.PearsonsCorrelation;
import org.apache.commons.math3.stat.correlation.SpearmansCorrelation;
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.AlterationFilter;
import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataBin;
import org.cbioportal.model.ClinicalDataCountItem;
import org.cbioportal.model.DensityPlotBin;
import org.cbioportal.model.DensityPlotData;
import org.cbioportal.model.Patient;
import org.cbioportal.model.Sample;
import org.cbioportal.persistence.mybatisclickhouse.StudyViewMapper;
import org.cbioportal.service.ClinicalAttributeService;
import org.cbioportal.service.ClinicalDataDensityPlotService;
import org.cbioportal.service.StudyViewColumnarService;
import org.cbioportal.service.StudyViewService;
import org.cbioportal.service.exception.StudyNotFoundException;
import org.cbioportal.service.impl.ClinicalAttributeServiceImpl;
import org.cbioportal.service.impl.PatientServiceImpl;
import org.cbioportal.service.impl.SampleServiceImpl;
import org.cbioportal.service.util.ClinicalAttributeUtil;
import org.cbioportal.web.StudyViewController;
import org.cbioportal.web.columnar.util.NewStudyViewFilterUtil;
import org.cbioportal.web.config.annotation.InternalApi;
import org.cbioportal.web.parameter.ClinicalDataBinCountFilter;
import org.cbioportal.web.parameter.ClinicalDataCountFilter;
import org.cbioportal.web.parameter.ClinicalDataFilter;
import org.cbioportal.web.parameter.DataBinMethod;
import org.cbioportal.web.parameter.Projection;
import org.cbioportal.web.parameter.StudyViewFilter;
import org.cbioportal.web.util.ClinicalDataBinUtil;
import org.cbioportal.web.util.ClinicalDataFetcher;
import org.cbioportal.web.util.DensityPlotParameters;
import org.cbioportal.web.util.StudyViewFilterApplier;
import org.cbioportal.web.util.StudyViewFilterUtil;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
Expand All @@ -29,9 +58,12 @@
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

@InternalApi
Expand All @@ -41,16 +73,39 @@
public class StudyViewColumnStoreController {

private final StudyViewColumnarService studyViewColumnarService;
private final StudyViewService studyViewService;
private final ClinicalDataBinner clinicalDataBinner;
private final StudyViewService studyViewService;
@Autowired
private final ClinicalAttributeService clinicalAttributeService;
@Autowired
private ClinicalAttributeUtil clinicalAttributeUtil;
@Autowired
private PatientServiceImpl patientService;
@Autowired
private StudyViewFilterApplier studyViewFilterApplier;
@Autowired
private StudyViewFilterUtil studyViewFilterUtil;
@Autowired
private SampleServiceImpl sampleService;
@Autowired
private ClinicalDataFetcher clinicalDataFetcher;
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@Autowired
private ClinicalDataDensityPlotService clinicalDataDensityPlotService;
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@Autowired
public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnarService, StudyViewService studyViewService, ClinicalDataBinner clinicalDataBinner) {
public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnarService, StudyViewService studyViewService,
ClinicalDataBinner clinicalDataBinner, ClinicalAttributeService clinicalAttributeService,
ClinicalDataDensityPlotService clinicalDataDensityPlotService
) {
this.studyViewColumnarService = studyViewColumnarService;
this.studyViewService = studyViewService;
this.clinicalDataBinner = clinicalDataBinner;
this.clinicalAttributeService = clinicalAttributeService;
this.clinicalDataDensityPlotService = clinicalDataDensityPlotService;
}



@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
@PostMapping(value = "/column-store/filtered-samples/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
Expand Down Expand Up @@ -118,4 +173,61 @@ public ResponseEntity<List<ClinicalDataBin>> fetchClinicalDataBinCounts(
);
return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK);
}

@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
@RequestMapping(value = "/column-store/clinical-data-density-plot/fetch", method = RequestMethod.POST,
consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
@Operation(description = "Fetch clinical data density plot bins by study view filter")
@ApiResponse(responseCode = "200", description = "OK",
content = @Content(schema = @Schema(implementation = DensityPlotData.class)))
@Validated
public ResponseEntity<DensityPlotData> fetchClinicalDataDensityPlot(
@Parameter(required = true, description = "Clinical Attribute ID of the X axis")
@RequestParam String xAxisAttributeId,
@Parameter(description = "Number of the bins in X axis")
@RequestParam(defaultValue = "50") Integer xAxisBinCount,
@Parameter(description = "Starting point of the X axis, if different than smallest value")
@RequestParam(required = false) BigDecimal xAxisStart,
@Parameter(description = "Starting point of the X axis, if different than largest value")
@RequestParam(required = false) BigDecimal xAxisEnd,
@Parameter(required = true, description = "Clinical Attribute ID of the Y axis")
@RequestParam String yAxisAttributeId,
@Parameter(description = "Number of the bins in Y axis")
@RequestParam(defaultValue = "50") Integer yAxisBinCount,
@Parameter(description = "Starting point of the Y axis, if different than smallest value")
@RequestParam(required = false) BigDecimal yAxisStart,
@Parameter(description = "Starting point of the Y axis, if different than largest value")
@RequestParam(required = false) BigDecimal yAxisEnd,
@Parameter(description="Use log scale for X axis")
@RequestParam(required = false, defaultValue = "false") Boolean xAxisLogScale,
@Schema(defaultValue = "false")
@Parameter(description="Use log scale for Y axis")
@RequestParam(required = false, defaultValue = "false") Boolean yAxisLogScale,
@Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
@RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
@Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
@Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter,
@Parameter(required = true, description = "Study view filter")
@RequestBody(required = false) StudyViewFilter studyViewFilter) {

List<String> xyAttributeId = new ArrayList<>(Arrays.asList(xAxisAttributeId, yAxisAttributeId));
DensityPlotParameters densityPlotParameters =
new DensityPlotParameters.Builder()
.xAxisAttributeId(xAxisAttributeId)
.yAxisAttributeId(yAxisAttributeId)
.xAxisBinCount(xAxisBinCount)
.yAxisBinCount(yAxisBinCount)
.xAxisStart(xAxisStart)
.yAxisStart(yAxisStart)
.xAxisEnd(xAxisEnd)
.yAxisEnd(yAxisEnd)
.xAxisLogScale(xAxisLogScale)
.yAxisLogScale(yAxisLogScale)
.build();

List<ClinicalData> sampleClinicalDataList = studyViewColumnarService.getSampleClinicalData(interceptedStudyViewFilter, xyAttributeId);
DensityPlotData result = clinicalDataDensityPlotService.getDensityPlotData(sampleClinicalDataList, densityPlotParameters);

return new ResponseEntity<>(result, HttpStatus.OK);
}
}
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