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Harmonize identifiers.
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@Mailaender
Mailaender committed Feb 15, 2024
1 parent 982f452 commit ea4f5a9
Showing 1 changed file with 61 additions and 50 deletions.
111 changes: 61 additions & 50 deletions ....supplier.animl/src/net/openchrom/wsd/converter/supplier/animl/io/ChromatogramWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@
import javax.xml.datatype.DatatypeConfigurationException;
import javax.xml.datatype.DatatypeFactory;

import org.apache.commons.io.FilenameUtils;
import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IScan;
Expand Down Expand Up @@ -51,6 +50,7 @@
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SIUnitType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SampleSetType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SampleType;
import net.openchrom.xxd.converter.supplier.animl.model.astm.core.SeriesSetType;
Expand All @@ -77,7 +77,7 @@ public void writeChromatogram(File file, IChromatogramWSD chromatogram, IProgres
AnIMLType anIML = new AnIMLType();
anIML.setVersion("0.90");
anIML.setSampleSet(createSampleSet(chromatogram));
anIML.setExperimentStepSet(createExperimentStep(chromatogram));
anIML.setExperimentStepSet(createSingleWavelengthExperimentStep(chromatogram));
anIML.setAuditTrailEntrySet(createAuditTrail(chromatogram));
marshaller.marshal(anIML, file);
} catch(JAXBException e) {
Expand All @@ -91,28 +91,25 @@ private SampleSetType createSampleSet(IChromatogramWSD chromatogram) {

SampleSetType sampleSet = new SampleSetType();
SampleType sample = new SampleType();
sample.setId("OPENCHROM_WSD_EXPORT");
sample.setName(chromatogram.getSampleName());
sample.setBarcode(chromatogram.getBarcode());
sample.setComment(chromatogram.getMiscInfo());
sample.setSampleID(FilenameUtils.removeExtension(chromatogram.getFile().getName()));
sample.setSampleID(chromatogram.getSampleName());
sampleSet.getSample().add(sample);
return sampleSet;
}

private ExperimentStepSetType createExperimentStep(IChromatogramWSD chromatogram) {
private ExperimentStepSetType createSingleWavelengthExperimentStep(IChromatogramWSD chromatogram) {

ExperimentStepSetType experimentStepSet = new ExperimentStepSetType();
//
ExperimentStepType chromatographyStep = new ExperimentStepType();
chromatographyStep.setName("Chromatography");
chromatographyStep.setExperimentStepID("CHROMATOGRAPHY");
chromatographyStep.setTechnique(createChromatographyTechnique());
experimentStepSet.getExperimentStep().add(chromatographyStep);
//
ExperimentStepType singleWavelengthStep = new ExperimentStepType();
singleWavelengthStep.setName("Single Wavelength");
singleWavelengthStep.setExperimentStepID("SINGLE_WAVELENGTH");
singleWavelengthStep.setName(chromatogram.getDataName());
singleWavelengthStep.getResult().add(createSignal(chromatogram));
singleWavelengthStep.setMethod(createMethod(chromatogram));
singleWavelengthStep.setSourceDataLocation(chromatogram.getFile().getAbsolutePath());
Expand All @@ -121,7 +118,6 @@ private ExperimentStepSetType createExperimentStep(IChromatogramWSD chromatogram
//
ExperimentStepType multiWavelengthsStep = new ExperimentStepType();
multiWavelengthsStep.setName("Multi Wavelength");
multiWavelengthsStep.setExperimentStepID("MULTI_WAVELENGTH");
multiWavelengthsStep.setResult(createSpectra(chromatogram));
multiWavelengthsStep.setMethod(createMethod(chromatogram));
multiWavelengthsStep.setSourceDataLocation(chromatogram.getFile().getAbsolutePath());
Expand All @@ -130,7 +126,6 @@ private ExperimentStepSetType createExperimentStep(IChromatogramWSD chromatogram
//
ExperimentStepType peakStep = new ExperimentStepType();
peakStep.setName("Peaks");
peakStep.setExperimentStepID("PEAKS");
peakStep.getResult().add(Common.createPeaks(chromatogram));
peakStep.setTechnique(createPeakTableTechnique());
experimentStepSet.getExperimentStep().add(peakStep);
Expand All @@ -143,27 +138,23 @@ private List<ResultType> createSpectra(IChromatogramWSD chromatogram) {
for(IScan scan : chromatogram.getScans()) {
IScanWSD scanWSD = (IScanWSD)scan;
SeriesSetType seriesSet = new SeriesSetType();
seriesSet.setId("WAVELENGTH_SPECTRUM");
seriesSet.setName("Spectrum");
seriesSet.setLength(scanWSD.getNumberOfScanSignals());
//
SeriesType wavelengthSeries = new SeriesType();
wavelengthSeries.setSeriesID("SPECTRUM");
wavelengthSeries.setName("Spectrum");
UnitType wavelengthUnit = new UnitType();
wavelengthUnit.setLabel("Wavelength");
wavelengthUnit.setQuantity("nm");
wavelengthUnit.setLabel("nm");
wavelengthUnit.setQuantity("Wavelength");
wavelengthSeries.setUnit(wavelengthUnit);
wavelengthSeries.setDependency(DependencyType.DEPENDENT);
wavelengthSeries.setSeriesType(ParameterTypeType.FLOAT_32);
wavelengthSeries.setPlotScale(PlotScaleType.LINEAR);
//
SeriesType intensitySeries = new SeriesType();
intensitySeries.setSeriesID("INTENSITY");
intensitySeries.setName("Intensity");
UnitType intensityUnit = new UnitType();
intensityUnit.setLabel("Absorbance");
intensityUnit.setQuantity("AU");
intensityUnit.setLabel("mAU");
intensitySeries.setUnit(intensityUnit);
intensitySeries.setDependency(DependencyType.DEPENDENT);
intensitySeries.setSeriesType(ParameterTypeType.FLOAT_32);
Expand Down Expand Up @@ -198,6 +189,7 @@ private List<ResultType> createSpectra(IChromatogramWSD chromatogram) {
seriesSet.getSeries().add(wavelengthSeries);
seriesSet.getSeries().add(intensitySeries);
ResultType result = new ResultType();
result.setName("Spectrum");
result.setSeriesSet(seriesSet);
results.add(result);
}
Expand All @@ -207,27 +199,10 @@ private List<ResultType> createSpectra(IChromatogramWSD chromatogram) {
private ResultType createSignal(IChromatogramWSD chromatogram) {

SeriesSetType seriesSet = new SeriesSetType();
seriesSet.setId("UV_VIS");
seriesSet.setName("UV/Vis Trace");
seriesSet.setName("Intensity");
seriesSet.setLength(chromatogram.getNumberOfScans());
//
SeriesType retentionTimeSeries = new SeriesType();
retentionTimeSeries.setSeriesID("RETENTION_TIME");
retentionTimeSeries.setName("Retention Time");
UnitType retentionTimeUnit = new UnitType();
retentionTimeUnit.setLabel("Time");
retentionTimeUnit.setQuantity("ms");
retentionTimeSeries.setUnit(retentionTimeUnit);
retentionTimeSeries.setDependency(DependencyType.INDEPENDENT);
retentionTimeSeries.setSeriesType(ParameterTypeType.INT_32);
//
SeriesType intensitySeries = new SeriesType();
UnitType intensityUnit = new UnitType();
intensityUnit.setLabel("Intensity");
intensityUnit.setQuantity("arbitrary");
intensitySeries.setUnit(intensityUnit);
intensitySeries.setDependency(DependencyType.DEPENDENT);
intensitySeries.setSeriesType(ParameterTypeType.FLOAT_32);
SeriesType retentionTimeSeries = describeRetentionTime();
SeriesType intensitySeries = describeIntensities();
//
int scans = chromatogram.getNumberOfScans();
if(PreferenceSupplier.getChromatogramSaveEncoded()) {
Expand Down Expand Up @@ -260,10 +235,52 @@ private ResultType createSignal(IChromatogramWSD chromatogram) {
}
seriesSet.getSeries().add(retentionTimeSeries);
seriesSet.getSeries().add(intensitySeries);
ResultType result = new ResultType();
result.getCategory().add(annotateWavelength(chromatogram));
result.setSeriesSet(seriesSet);
result.setName("Trace");
return result;
}

private SeriesType describeRetentionTime() {

SeriesType retentionTimeSeries = new SeriesType();
retentionTimeSeries.setName("Time");
UnitType retentionTimeUnit = new UnitType();
retentionTimeUnit.setLabel("ms");
retentionTimeUnit.setQuantity("Time");
retentionTimeUnit.getSIUnit().add(createMilisecond());
retentionTimeSeries.setUnit(retentionTimeUnit);
retentionTimeSeries.setDependency(DependencyType.INDEPENDENT);
retentionTimeSeries.setSeriesType(ParameterTypeType.INT_32);
return retentionTimeSeries;
}

private SeriesType describeIntensities() {

SeriesType intensitySeries = new SeriesType();
intensitySeries.setName("Absorbance");
UnitType intensityUnit = new UnitType();
intensityUnit.setLabel("mAU");
intensitySeries.setUnit(intensityUnit);
intensitySeries.setDependency(DependencyType.DEPENDENT);
intensitySeries.setSeriesType(ParameterTypeType.FLOAT_32);
return intensitySeries;
}

private SIUnitType createMilisecond() {

SIUnitType si = new SIUnitType();
si.setExponent(-3d);
si.setValue("s");
return si;
}

private CategoryType annotateWavelength(IChromatogramWSD chromatogram) {

CategoryType category = new CategoryType();
category.setName("Acquisition Wavelength");
category.setName("Extraction Parameters");
ParameterType lowerBounds = new ParameterType();
ResultType result = new ResultType();
IScanWSD firstScan = chromatogram.getSupplierScan(1);
List<IScanSignalWSD> signals = firstScan.getScanSignals();
double[] wavelengths = signals.stream().mapToDouble(s -> s.getWavelength()).toArray();
Expand All @@ -273,10 +290,8 @@ private ResultType createSignal(IChromatogramWSD chromatogram) {
ParameterType upperBounds = new ParameterType();
upperBounds.getD().add(Doubles.max(wavelengths));
upperBounds.setName("Upper Bound");
result.getCategory().add(category);
result.setSeriesSet(seriesSet);
result.setName("UV/VIS");
return result;
category.getParameter().add(upperBounds);
return category;
}

private MethodType createMethod(IChromatogramWSD chromatogram) {
Expand All @@ -292,7 +307,6 @@ private MethodType createMethod(IChromatogramWSD chromatogram) {
private TechniqueType createChromatographyTechnique() {

TechniqueType technique = new TechniqueType();
technique.setId("CHROMATOGRAPHY");
technique.setName("Chromatography");
technique.setUri("https://github.com/AnIML/techniques/blob/6e30b1e593e6df661a44ae2a9892b6198def0641/chromatography.atdd");
return technique;
Expand All @@ -301,26 +315,23 @@ private TechniqueType createChromatographyTechnique() {
private TechniqueType createUltraVioletDetectorTechnique() {

TechniqueType technique = new TechniqueType();
technique.setId("UV_VIS");
technique.setName("UV/Vis Trace Detector");
technique.setName("UV Trace");
technique.setUri("https://github.com/AnIML/techniques/blob/995bef06f90afba00a618239f40c6e591a1c0845/uv-vis-trace.atdd");
return technique;
}

private TechniqueType createDiodeArrayDetectorTechnique() {

TechniqueType technique = new TechniqueType();
technique.setId("DAD");
technique.setName("UV/Vis");
technique.setName("Spectrum");
technique.setUri("https://raw.githubusercontent.com/AnIML/techniques/995bef06f90afba00a618239f40c6e591a1c0845/uv-vis.atdd");
return technique;
}

private TechniqueType createPeakTableTechnique() {

TechniqueType technique = new TechniqueType();
technique.setId("CHROMATOGRAPHY_PEAK_TABLE");
technique.setName("Chromatography Peak Table");
technique.setName("Peak Table");
technique.setUri("https://github.com/AnIML/techniques/blob/d749979fc21322b97c61e2efd6efe60cfa5a29be/chromatography-peak-table.atdd");
return technique;
}
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