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* working poc * refactor logic into service, so clean * refactor for parameters builder, simplify min max logic, streamline service call * remove unused services and imports * remove more unused imports
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src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java
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| package org.cbioportal.service; | ||
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| import org.cbioportal.model.ClinicalData; | ||
| import org.cbioportal.model.DensityPlotData; | ||
| import org.cbioportal.web.util.DensityPlotParameters; | ||
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| import java.math.BigDecimal; | ||
| import java.util.List; | ||
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| public interface ClinicalDataDensityPlotService { | ||
| DensityPlotData getDensityPlotData(List<ClinicalData> filteredClinicalData, DensityPlotParameters densityPlotParameters); | ||
| } |
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src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java
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| package org.cbioportal.service.impl; | ||
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| 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; | ||
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| 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; | ||
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| @Service | ||
| public class ClinicalDataDensityPlotServiceImpl implements ClinicalDataDensityPlotService { | ||
| @Override | ||
| public DensityPlotData getDensityPlotData(List<ClinicalData> sampleClinicalData, DensityPlotParameters densityPlotParameters) { | ||
| DensityPlotData result = new DensityPlotData(); | ||
| result.setBins(new ArrayList<>()); | ||
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| Map<String, List<ClinicalData>> clinicalDataGroupedBySampleId = sampleClinicalData.stream(). | ||
| collect(Collectors.groupingBy(ClinicalData::getSampleId)); | ||
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| 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(); | ||
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| if (extractedXYClinicalData.isEmpty()) { | ||
| return result; | ||
| } | ||
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| Map<Boolean, List<ClinicalData>> partition = extractedXYClinicalData.stream().collect( | ||
| Collectors.partitioningBy(c -> c.getAttrId().equals(densityPlotParameters.getXAxisAttributeId()))); | ||
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| boolean useXLogScale = densityPlotParameters.getXAxisLogScale() && ClinicalDataDensityPlotServiceImpl.isLogScalePossibleForAttribute(densityPlotParameters.getXAxisAttributeId()); | ||
| boolean useYLogScale = densityPlotParameters.getYAxisLogScale() && ClinicalDataDensityPlotServiceImpl.isLogScalePossibleForAttribute(densityPlotParameters.getYAxisAttributeId()); | ||
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| 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); | ||
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| 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); | ||
| } | ||
| } | ||
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| 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); | ||
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| // 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); | ||
| } | ||
| } | ||
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| 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); | ||
| } | ||
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| // filter out empty bins | ||
| result.setBins(result.getBins().stream().filter((bin)->(bin.getCount() > 0)).collect(Collectors.toList())); | ||
| return result; | ||
| } | ||
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| private static boolean isLogScalePossibleForAttribute(String clinicalAttributeId) { | ||
| return clinicalAttributeId.equals("MUTATION_COUNT"); | ||
| } | ||
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| private static double logScale(double val) { | ||
| return Math.log(1+val); | ||
| } | ||
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| private static double parseValueLog(ClinicalData c) { | ||
| return ClinicalDataDensityPlotServiceImpl.logScale(Double.parseDouble(c.getAttrValue())); | ||
| } | ||
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| private static double parseValueLinear(ClinicalData c) { | ||
| return Double.parseDouble(c.getAttrValue()); | ||
| } | ||
| } |
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118 changes: 118 additions & 0 deletions
118
src/main/java/org/cbioportal/web/util/DensityPlotParameters.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,118 @@ | ||
| package org.cbioportal.web.util; | ||
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| import java.math.BigDecimal; | ||
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| public class DensityPlotParameters { | ||
| private final Integer xAxisBinCount; | ||
| private final Integer yAxisBinCount; | ||
| private final BigDecimal xAxisStart; | ||
| private final BigDecimal xAxisEnd; | ||
| private final BigDecimal yAxisStart; | ||
| private final BigDecimal yAxisEnd; | ||
| private final Boolean xAxisLogScale; | ||
| private final Boolean yAxisLogScale; | ||
| private final String xAxisAttributeId; | ||
| private final String yAxisAttributeId; | ||
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| DensityPlotParameters(Builder builder) { | ||
| this.xAxisBinCount = builder.xAxisBinCount; | ||
| this.yAxisBinCount = builder.yAxisBinCount; | ||
| this.xAxisStart = builder.xAxisStart; | ||
| this.xAxisEnd = builder.xAxisEnd; | ||
| this.yAxisStart = builder.yAxisStart; | ||
| this.yAxisEnd = builder.yAxisEnd; | ||
| this.xAxisAttributeId = builder.xAxisAttributeId; | ||
| this.yAxisAttributeId = builder.yAxisAttributeId; | ||
| this.xAxisLogScale = builder.xAxisLogScale; | ||
| this.yAxisLogScale = builder.yAxisLogScale; | ||
| } | ||
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| public Integer getXAxisBinCount() { | ||
| return xAxisBinCount; | ||
| } | ||
| public Integer getYAxisBinCount() { | ||
| return yAxisBinCount; | ||
| } | ||
| public BigDecimal getXAxisStart() { | ||
| return xAxisStart; | ||
| } | ||
| public BigDecimal getXAxisEnd() { | ||
| return xAxisEnd; | ||
| } | ||
| public BigDecimal getYAxisStart() { | ||
| return yAxisStart; | ||
| } | ||
| public BigDecimal getYAxisEnd() { | ||
| return yAxisEnd; | ||
| } | ||
| public Boolean getXAxisLogScale() { | ||
| return xAxisLogScale; | ||
| } | ||
| public Boolean getYAxisLogScale() { | ||
| return yAxisLogScale; | ||
| } | ||
| public String getXAxisAttributeId() { | ||
| return xAxisAttributeId; | ||
| } | ||
| public String getYAxisAttributeId() { | ||
| return yAxisAttributeId; | ||
| } | ||
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| public static class Builder { | ||
| private Integer xAxisBinCount; | ||
| private Integer yAxisBinCount; | ||
| private BigDecimal xAxisStart; | ||
| private BigDecimal xAxisEnd; | ||
| private BigDecimal yAxisStart; | ||
| private BigDecimal yAxisEnd; | ||
| private Boolean xAxisLogScale; | ||
| private Boolean yAxisLogScale; | ||
| private String xAxisAttributeId; | ||
| private String yAxisAttributeId; | ||
|
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| public Builder xAxisBinCount(Integer xAxisBinCount) { | ||
| this.xAxisBinCount = xAxisBinCount; | ||
| return this; | ||
| } | ||
| public Builder yAxisBinCount(Integer yAxisBinCount) { | ||
| this.yAxisBinCount = yAxisBinCount; | ||
| return this; | ||
| } | ||
| public Builder xAxisStart(BigDecimal xAxisStart) { | ||
| this.xAxisStart = xAxisStart; | ||
| return this; | ||
| } | ||
| public Builder xAxisEnd(BigDecimal xAxisEnd) { | ||
| this.xAxisEnd = xAxisEnd; | ||
| return this; | ||
| } | ||
| public Builder yAxisStart(BigDecimal yAxisStart) { | ||
| this.yAxisStart = yAxisStart; | ||
| return this; | ||
| } | ||
| public Builder yAxisEnd(BigDecimal yAxisEnd) { | ||
| this.yAxisEnd = yAxisEnd; | ||
| return this; | ||
| } | ||
| public Builder xAxisLogScale(Boolean xAxisLogScale) { | ||
| this.xAxisLogScale = xAxisLogScale; | ||
| return this; | ||
| } | ||
| public Builder yAxisLogScale(Boolean yAxisLogScale) { | ||
| this.yAxisLogScale = yAxisLogScale; | ||
| return this; | ||
| } | ||
| public Builder xAxisAttributeId(String xAxisAttributeId) { | ||
| this.xAxisAttributeId = xAxisAttributeId; | ||
| return this; | ||
| } | ||
| public Builder yAxisAttributeId(String yAxisAttributeId) { | ||
| this.yAxisAttributeId = yAxisAttributeId; | ||
| return this; | ||
| } | ||
| public DensityPlotParameters build() { | ||
| return new DensityPlotParameters(this); | ||
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| } | ||
| } | ||
| } |