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Fix reading mzML instrument #2655

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Merged
eselmeister merged 2 commits into from
Jan 23, 2026
Merged

Fix reading mzML instrument #2655

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b74561c
Don't export deleted packages.
Mailaender Jan 23, 2026
6b2714a
Read the (referenced) instrument of all vendors.
Mailaender Jan 23, 2026
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3 changes: 1 addition & 2 deletions chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF
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Expand Up @@ -24,8 +24,7 @@ Bundle-ActivationPolicy: lazy
Import-Package: jakarta.xml.bind,
jakarta.xml.bind.annotation,
jakarta.xml.bind.annotation.adapters
Export-Package: org.eclipse.chemclipse.msd.converter.supplier.mzml,
org.eclipse.chemclipse.msd.converter.supplier.mzml.converter,
Export-Package: org.eclipse.chemclipse.msd.converter.supplier.mzml.converter,
org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io,
org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model,
org.eclipse.chemclipse.msd.converter.supplier.mzml.io,
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28 changes: 25 additions & 3 deletions ...ier.mzml/src/org/eclipse/chemclipse/xxd/converter/supplier/mzml/io/MetadataReader110.java
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Expand Up @@ -12,6 +12,8 @@
*******************************************************************************/
package org.eclipse.chemclipse.xxd.converter.supplier.mzml.io;

import java.util.List;

import org.eclipse.chemclipse.model.core.IChromatogram;
import org.eclipse.chemclipse.support.history.EditInformation;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.CVParamType;
Expand All @@ -20,6 +22,7 @@
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.MzMLType;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ParamGroupType;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ProcessingMethodType;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ReferenceableParamGroupRefType;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SampleListType;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SampleType;
import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SoftwareType;
Expand All @@ -37,6 +40,7 @@ public static IChromatogram readMetadata(MzMLType mzML, IChromatogram chromatogr
}
}
}

SampleListType sampleList = mzML.getSampleList();
if(sampleList != null) {
for(SampleType sample : sampleList.getSample()) {
Expand All @@ -47,13 +51,19 @@ public static IChromatogram readMetadata(MzMLType mzML, IChromatogram chromatogr
}
}
}

for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) {
for(CVParamType cvParam : instrument.getCvParam()) {
if(cvParam.getAccession().equals("MS:1000554")) {
chromatogram.setInstrument(cvParam.getName());

List<ReferenceableParamGroupRefType> referenceableParamGroupRef = instrument.getReferenceableParamGroupRef();
if(referenceableParamGroupRef != null) {
for(ReferenceableParamGroupRefType referenceableParamGroupRefType : referenceableParamGroupRef) {
readInstrument(referenceableParamGroupRefType.getRef().getCvParam(), chromatogram);
}
}

readInstrument(instrument.getCvParam(), chromatogram);
}

for(DataProcessingType dataProcessing : mzML.getDataProcessingList().getDataProcessing()) {
for(ProcessingMethodType processingMethod : dataProcessing.getProcessingMethod()) {
SoftwareType software = (SoftwareType)processingMethod.getSoftwareRef();
Expand All @@ -64,6 +74,18 @@ public static IChromatogram readMetadata(MzMLType mzML, IChromatogram chromatogr
}
}
}

return chromatogram;
}

private static void readInstrument(List<CVParamType> cvParams, IChromatogram chromatogram) {

for(CVParamType cvParam : cvParams) {
if(cvParam.getAccession().equals("MS:1000529") && cvParam.getName().equals("instrument serial number")) {
continue;
} else {
chromatogram.setInstrument(cvParam.getName());
}
}
}
}
3 changes: 1 addition & 2 deletions ...onverter/supplier/mzml/converter/ChromatogramImportConverterTinyProteoWizard10_ITest.java
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Expand Up @@ -15,7 +15,6 @@
import static org.junit.jupiter.api.Assertions.assertEquals;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.TestPathHelper;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram;
Expand All @@ -36,7 +35,7 @@ public class ChromatogramImportConverterTinyProteoWizard10_ITest {
private IVendorChromatogram chromatogram;

@BeforeAll
public void setUp() throws IOException {
public void setUp() {

File importFile = new File(TestPathHelper.TESTFILE_IMPORT_TINY_PWIZ_1_0);
ChromatogramImportConverter converter = new ChromatogramImportConverter();
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3 changes: 1 addition & 2 deletions ...nverter/supplier/mzml/converter/ChromatogramImportConverterTinyProteoWizard110_ITest.java
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Expand Up @@ -15,7 +15,6 @@
import static org.junit.jupiter.api.Assertions.assertEquals;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.TestPathHelper;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram;
Expand All @@ -36,7 +35,7 @@ public class ChromatogramImportConverterTinyProteoWizard110_ITest {
private IVendorChromatogram chromatogram;

@BeforeAll
public void setUp() throws IOException {
public void setUp() {

File importFile = new File(TestPathHelper.TESTFILE_IMPORT_TINY_PWIZ_1_1);
ChromatogramImportConverter converter = new ChromatogramImportConverter();
Expand Down
3 changes: 1 addition & 2 deletions ...e/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportExport110_ITest.java
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Expand Up @@ -17,7 +17,6 @@
import static org.junit.jupiter.api.Assertions.assertNotNull;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.TestPathHelper;
Expand All @@ -38,7 +37,7 @@ public class ChromatogramImportExport110_ITest {
private File fileExport;

@BeforeAll
public void setUp() throws IOException {
public void setUp() {

/*
* Import
Expand Down
3 changes: 1 addition & 2 deletions ...hemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter110_ITest.java
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Expand Up @@ -15,7 +15,6 @@
import static org.junit.jupiter.api.Assertions.assertEquals;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.TestPathHelper;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorMassSpectra;
Expand All @@ -36,7 +35,7 @@ public class MassSpectrumImportConverter110_ITest {
private IVendorMassSpectra massSpectra;

@BeforeAll
public void setUp() throws IOException {
public void setUp() {

File importFile = new File(TestPathHelper.TESTFILE_IMPORT_TINY1_1_1);
MassSpectrumImportConverter converter = new MassSpectrumImportConverter();
Expand Down
3 changes: 1 addition & 2 deletions ...msd/converter/supplier/mzml/converter/MassSpectrumImportConverterCentroided110_ITest.java
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Expand Up @@ -15,7 +15,6 @@
import static org.junit.jupiter.api.Assertions.assertEquals;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.TestPathHelper;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorMassSpectra;
Expand All @@ -36,7 +35,7 @@ public class MassSpectrumImportConverterCentroided110_ITest {
private IVendorMassSpectra massSpectra;

@BeforeAll
public void setUp() throws IOException {
public void setUp() {

File importFile = new File(TestPathHelper.TESTFILE_IMPORT_TINY1_CENTROIDED_1_1);
MassSpectrumImportConverter converter = new MassSpectrumImportConverter();
Expand Down
3 changes: 1 addition & 2 deletions ...msd/converter/supplier/mzml/converter/MassSpectrumImportConverterCompressed110_ITest.java
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Expand Up @@ -15,7 +15,6 @@
import static org.junit.jupiter.api.Assertions.assertEquals;

import java.io.File;
import java.io.IOException;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.TestPathHelper;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorMassSpectra;
Expand All @@ -36,7 +35,7 @@ public class MassSpectrumImportConverterCompressed110_ITest {
private IVendorMassSpectra massSpectra;

@BeforeAll
public void setUp() throws IOException {
public void setUp() {

File importFile = new File(TestPathHelper.TESTFILE_IMPORT_TINY1_COMPRESSED_1_1);
MassSpectrumImportConverter converter = new MassSpectrumImportConverter();
Expand Down