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Fixed a crash in mzData reader due to missing fields #1894

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merged 2 commits into from
Oct 10, 2024
Merged

Fixed a crash in mzData reader due to missing fields #1894

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ce65b51
Fix a crash when there is no processing method.
Mailaender Oct 9, 2024
6409498
Add support for time in minutes.
Mailaender Oct 9, 2024
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10 changes: 7 additions & 3 deletions ...se/chemclipse/msd/converter/supplier/mzdata/internal/io/ChromatogramReaderVersion104.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v104.model.MzData;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v104.model.MzData.SpectrumList.Spectrum;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v104.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v104.model.ParamType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v104.model.PersonType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.io.AbstractChromatogramReader;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.model.IVendorChromatogram;
Expand Down Expand Up @@ -82,9 +83,12 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
chromatogram.setInstrument(mzData.getDescription().getInstrument().getInstrumentName());
DataProcessingType dataProcessing = mzData.getDescription().getDataProcessing();
Software software = dataProcessing.getSoftware();
for(Object object : dataProcessing.getProcessingMethod().getCvParamOrUserParam()) {
if(object instanceof CvParamType cvParamType) {
chromatogram.getEditHistory().add(new EditInformation(cvParamType.getName(), software.getName() + " " + software.getVersion()));
ParamType processingMethod = dataProcessing.getProcessingMethod();
if(processingMethod != null) {
for(Object object : processingMethod.getCvParamOrUserParam()) {
if(object instanceof CvParamType cvParamType) {
chromatogram.getEditHistory().add(new EditInformation(cvParamType.getName(), software.getName() + " " + software.getVersion()));
}
}
}
for(Spectrum spectrum : mzData.getSpectrumList().getSpectrum()) {
Expand Down
15 changes: 11 additions & 4 deletions ...se/chemclipse/msd/converter/supplier/mzdata/internal/io/ChromatogramReaderVersion105.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
import javax.xml.parsers.ParserConfigurationException;

import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IChromatogramOverview;
import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.AdminType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.CvParamType;
Expand All @@ -28,6 +29,7 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.MzData;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.MzData.SpectrumList.Spectrum;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.ParamType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.PersonType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.io.AbstractChromatogramReader;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.model.IVendorChromatogram;
Expand Down Expand Up @@ -83,9 +85,12 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
chromatogram.setInstrument(mzData.getDescription().getInstrument().getInstrumentName());
DataProcessingType dataProcessing = mzData.getDescription().getDataProcessing();
Software software = dataProcessing.getSoftware();
for(Object object : dataProcessing.getProcessingMethod().getCvParamOrUserParam()) {
if(object instanceof CvParamType cvParamType) {
chromatogram.getEditHistory().add(new EditInformation(cvParamType.getName(), software.getName() + " " + software.getVersion()));
ParamType processingMethod = dataProcessing.getProcessingMethod();
if(processingMethod != null) {
for(Object object : processingMethod.getCvParamOrUserParam()) {
if(object instanceof CvParamType cvParamType) {
chromatogram.getEditHistory().add(new EditInformation(cvParamType.getName(), software.getName() + " " + software.getVersion()));
}
}
}
for(Spectrum spectrum : mzData.getSpectrumList().getSpectrum()) {
Expand All @@ -98,7 +103,9 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
for(Object object : params) {
if(object instanceof CvParamType cvParamType) {
if(cvParamType.getName().equals("TimeInSeconds")) {
retentionTime = Math.round(Float.parseFloat(cvParamType.getValue()) * 1000); // milliseconds
retentionTime = (int)Math.round(Double.parseDouble(cvParamType.getValue()) * IChromatogramOverview.SECOND_CORRELATION_FACTOR);
} else if(cvParamType.getName().equals("TimeInMinutes")) {
retentionTime = (int)Math.round(Double.parseDouble(cvParamType.getValue()) * IChromatogramOverview.MINUTE_CORRELATION_FACTOR);
}
}
}
Expand Down
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