Add mzML HPLC-DAD read/write support.

eclipse · Sep 11, 2024 · 9e7cfb4 · 9e7cfb4
1 parent 14a3b60
commit 9e7cfb4
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Showing 185 changed files with 3,064 additions and 1,115 deletions.
diff --git a/chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml b/chemclipse/features/org.eclipse.chemclipse.msd.converter.supplier.mzml.feature/feature.xml
@@ -26,16 +26,22 @@
 
    <plugin
          id="org.eclipse.chemclipse.msd.converter.supplier.mzml"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
+         version="0.0.0"/>
 
    <plugin
          id="org.eclipse.chemclipse.msd.converter.supplier.mzml.ui"
-         download-size="0"
-         install-size="0"
-         version="0.0.0"
-         unpack="false"/>
+         version="0.0.0"/>
+
+   <plugin
+         id="org.eclipse.chemclipse.wsd.converter.supplier.mzml"
+         version="0.0.0"/>
+
+   <plugin
+         id="org.eclipse.chemclipse.xxd.converter.supplier.mzml"
+         version="0.0.0"/>
+
+   <plugin
+         id="org.eclipse.chemclipse.wsd.converter.supplier.mzml.ui"
+         version="0.0.0"/>
 
 </feature>
diff --git a/...clipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF b/...clipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml.ui/META-INF/MANIFEST.MF
@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Automatic-Module-Name: org.eclipse.chemclipse.msd.converter.supplier.mzml.ui
 Bundle-ManifestVersion: 2
-Bundle-Name: mzML UI
+Bundle-Name: mzML MSD UI
 Bundle-SymbolicName: org.eclipse.chemclipse.msd.converter.supplier.mzml.ui;singleton:=true
 Bundle-Version: 0.9.0.qualifier
 Bundle-Activator: org.eclipse.chemclipse.msd.converter.supplier.mzml.ui.Activator

diff --git a/...src/org/eclipse/chemclipse/msd/converter/supplier/mzml/ui/preferences/PreferencePage.java b/...src/org/eclipse/chemclipse/msd/converter/supplier/mzml/ui/preferences/PreferencePage.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021 Lablicate GmbH.
+ * Copyright (c) 2021, 2024 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -29,13 +29,15 @@ public PreferencePage() {
 		setDescription("mzML Converter");
 	}
 
+	@Override
 	public void createFieldEditors() {
 
 		addField(new SpacerFieldEditor(getFieldEditorParent()));
 		addField(new ComboFieldEditor(PreferenceSupplier.P_CHROMATOGRAM_VERSION_SAVE, "Save (*.mzML) as version:", PreferenceSupplier.getChromatogramVersions(), getFieldEditorParent()));
 		addField(new BooleanFieldEditor(PreferenceSupplier.P_CHROMATOGRAM_SAVE_COMPRESSION, "Compress values", getFieldEditorParent()));
 	}
 
+	@Override
 	public void init(IWorkbench workbench) {
 
 	}

diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/META-INF/MANIFEST.MF
@@ -15,14 +15,16 @@ Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.chemclipse.converter;bundle-version="0.8.0",
  org.eclipse.chemclipse.model;bundle-version="0.8.0",
  org.eclipse.chemclipse.support;bundle-version="0.8.0",
- org.apache.commons.commons-codec;bundle-version="1.15.0",
- org.eclipse.chemclipse.xxd.converter.supplier.mzml,
- org.apache.commons.lang3;bundle-version="3.13.0"
+ org.eclipse.chemclipse.xxd.converter.supplier.mzml;bundle-version="0.9.0",
+ org.apache.commons.lang3
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 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.converter.io,
- org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter,
- org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.v110.model
+Export-Package: org.eclipse.chemclipse.msd.converter.supplier.mzml,
+ 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,
+ org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences
diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/plugin.xml b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/plugin.xml
@@ -7,11 +7,11 @@
             description="Reads mzML Chromatograms"
             exportConverter="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.ChromatogramExportConverter"
             fileExtension=".mzML"
-            filterName="mzML Chromatogram (*.mzML)"
+            filterName="MSD Chromatogram (*.mzML)"
             id="org.eclipse.chemclipse.msd.converter.supplier.mzml"
             importContentMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.ChromatogramFileContentMatcher"
             importConverter="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.ChromatogramImportConverter"
-            importMagicNumberMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MagicNumberMatcher"
+            importMagicNumberMatcher="org.eclipse.chemclipse.xxd.converter.supplier.mzml.converter.MagicNumberMatcher"
             isExportable="true"
             isImportable="true">
       </ChromatogramSupplier>
@@ -26,7 +26,7 @@
             id="org.eclipse.chemclipse.msd.converter.supplier.mzml.ms"
             importContentMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MassSpectrumFileContentMatcher"
             importConverter="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MassSpectrumImportConverter"
-            importMagicNumberMatcher="org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.MagicNumberMatcher"
+            importMagicNumberMatcher="org.eclipse.chemclipse.xxd.converter.supplier.mzml.converter.MagicNumberMatcher"
             isExportable="false"
             isImportable="true">
       </MassSpectrumSupplier>

diff --git a/...er.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/PathResolver.java b/...er.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/PathResolver.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2018 Lablicate GmbH.
+ * Copyright (c) 2013, 2024 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -25,7 +25,7 @@ public class PathResolver {
 	/**
 	 * Returns a absolute path of the specified Folder. For example
 	 * TESTDATA_IMPORT_EMPTY as an absolute Path:
-	 * $PluginPath$/testData/files/EMPTY.D/DATA.MS
+	 * $PluginPath$/testData/files/data.mzML
 	 * 
 	 * @param string
 	 * @return String absolutePath
@@ -36,7 +36,7 @@ public static String getAbsolutePath(String string) {
 		IPath path = new Path(string);
 		URL url = FileLocator.find(bundle, path, null);
 		try {
-			return FileLocator.resolve(url).getPath().toString();
+			return FileLocator.resolve(url).getPath();
 		} catch(IOException e) {
 			e.printStackTrace();
 		}

diff --git a/...eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramExportConverter.java b/...eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramExportConverter.java
@@ -23,7 +23,6 @@
 import org.eclipse.chemclipse.model.core.IPeak;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io.ChromatogramWriter;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.SpecificationValidator;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -38,7 +37,6 @@ public class ChromatogramExportConverter extends AbstractChromatogramExportConve
 	@Override
 	public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> chromatogram, IProgressMonitor monitor) {
 
-		file = SpecificationValidator.validateSpecification(file);
 		IProcessingInfo<File> processingInfo = super.validate(file);
 		if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramMSD chromatogramMSD) {
 			monitor.subTask(EXPORT_CHROMATOGRAM);

diff --git a/...ipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramFileContentMatcher.java b/...ipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramFileContentMatcher.java
@@ -36,6 +36,7 @@ public boolean checkFileFormat(File file) {
 			XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(new FileInputStream(file));
 			boolean hasChromatogramList = false;
 			boolean hasRootElement = false;
+			boolean hasMS = false;
 			while(xmlStreamReader.hasNext()) {
 				int eventType = xmlStreamReader.next();
 				if(eventType == XMLStreamConstants.START_ELEMENT) {
@@ -44,8 +45,24 @@ public boolean checkFileFormat(File file) {
 						hasRootElement = true;
 					} else if(elementName.equals("chromatogramList")) {
 						hasChromatogramList = true;
+					} else if(elementName.equals("fileContent")) {
+						while(xmlStreamReader.hasNext()) {
+							int innerEventType = xmlStreamReader.next();
+							if(innerEventType == XMLStreamConstants.START_ELEMENT && xmlStreamReader.getLocalName().equals("cvParam")) {
+								String accession = xmlStreamReader.getAttributeValue(null, "accession");
+								String paramName = xmlStreamReader.getAttributeValue(null, "name");
+								if(accession.equals("MS:1000579") && paramName.equals("MS1 spectrum") || //
+										accession.equals("MS:1000580") && paramName.equals("MSn spectrum")) {
+									hasMS = true;
+									break;
+								}
+							}
+							if(innerEventType == XMLStreamConstants.END_ELEMENT && xmlStreamReader.getLocalName().equals("fileContent")) {
+								break;
+							}
+						}
 					}
-					if(hasRootElement && hasChromatogramList) {
+					if(hasRootElement && hasChromatogramList && hasMS) {
 						isValidFormat = true;
 						break;
 					}

diff --git a/...eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverter.java b/...eclipse/chemclipse/msd/converter/supplier/mzml/converter/ChromatogramImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2023 Lablicate GmbH.
+ * Copyright (c) 2013, 2024 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -20,7 +20,6 @@
 import org.eclipse.chemclipse.model.core.IChromatogramOverview;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io.ChromatogramReader;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.SpecificationValidator;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -41,7 +40,6 @@ public IProcessingInfo<IChromatogramMSD> convert(File file, IProgressMonitor mon
 			/*
 			 * Read the chromatogram.
 			 */
-			file = SpecificationValidator.validateSpecification(file);
 			IChromatogramMSDReader reader = new ChromatogramReader();
 			monitor.subTask(IMPORT_CHROMATOGRAM);
 			try {
@@ -64,7 +62,6 @@ public IProcessingInfo<IChromatogramOverview> convertOverview(File file, IProgre
 
 		IProcessingInfo<IChromatogramOverview> processingInfo = super.validate(file);
 		if(!processingInfo.hasErrorMessages()) {
-			file = SpecificationValidator.validateSpecification(file);
 			IChromatogramMSDReader reader = new ChromatogramReader();
 			monitor.subTask(IMPORT_CHROMATOGRAM_OVERVIEW);
 			try {

diff --git a/...eclipse/chemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter.java b/...eclipse/chemclipse/msd/converter/supplier/mzml/converter/MassSpectrumImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021, 2022 Lablicate GmbH.
+ * Copyright (c) 2021, 2024 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -17,14 +17,15 @@
 
 import org.eclipse.chemclipse.converter.exceptions.FileIsEmptyException;
 import org.eclipse.chemclipse.converter.exceptions.FileIsNotReadableException;
+import org.eclipse.chemclipse.converter.l10n.ConverterMessages;
 import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
 import org.eclipse.chemclipse.msd.converter.massspectrum.AbstractMassSpectrumImportConverter;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.io.MassSpectrumReader;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.SpecificationValidator;
 import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.osgi.util.NLS;
 
 public class MassSpectrumImportConverter extends AbstractMassSpectrumImportConverter {
 
@@ -37,26 +38,25 @@ public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor monitor
 		IProcessingInfo<IMassSpectra> processingInfo = super.validate(file);
 		if(!processingInfo.hasErrorMessages()) {
 			try {
-				file = SpecificationValidator.validateSpecification(file);
 				IMassSpectraReader massSpectraReader = new MassSpectrumReader();
 				IMassSpectra massSpectra = massSpectraReader.read(file, monitor);
 				if(massSpectra != null && !massSpectra.isEmpty()) {
 					processingInfo.setProcessingResult(massSpectra);
 				} else {
-					processingInfo.addErrorMessage(DESCRIPTION, "No mass spectra are stored." + file.getAbsolutePath());
+					processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.noMassSpectraStored, file.getAbsolutePath()));
 				}
 			} catch(FileNotFoundException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(DESCRIPTION, "The file couldn't be found: " + file.getAbsolutePath());
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath()));
 			} catch(FileIsNotReadableException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(DESCRIPTION, "The file is not readable: " + file.getAbsolutePath());
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotReadable, file.getAbsolutePath()));
 			} catch(FileIsEmptyException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(DESCRIPTION, "The file is empty: " + file.getAbsolutePath());
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.emptyFile, file.getAbsolutePath()));
 			} catch(IOException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(DESCRIPTION, "Something has gone completely wrong: " + file.getAbsolutePath());
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
 			}
 		}
 		return processingInfo;

diff --git a/...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramReader.java b/...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramReader.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2023 Lablicate GmbH.
+ * Copyright (c) 2014, 2024 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -16,15 +16,15 @@
 import java.io.FileReader;
 import java.io.IOException;
 
+import org.eclipse.chemclipse.converter.exceptions.UnknownVersionException;
 import org.eclipse.chemclipse.model.core.IChromatogramOverview;
 import org.eclipse.chemclipse.msd.converter.io.AbstractChromatogramMSDReader;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader10;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramReaderVersion10;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramReaderVersion110;
+import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.ChromatogramReaderVersion10;
+import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.ChromatogramReaderVersion110;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
-import org.eclipse.chemclipse.xxd.converter.supplier.io.exception.UnknownVersionException;
+import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader10;
+import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 public class ChromatogramReader extends AbstractChromatogramMSDReader implements IChromatogramMSDReader {

diff --git a/...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramWriter.java b/...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/ChromatogramWriter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2023 Lablicate GmbH.
+ * Copyright (c) 2014, 2024 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -18,10 +18,10 @@
 import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException;
 import org.eclipse.chemclipse.converter.io.AbstractChromatogramWriter;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.ChromatogramWriterVersion110;
+import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.ChromatogramWriterVersion110;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
+import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 public class ChromatogramWriter extends AbstractChromatogramWriter implements IChromatogramMSDWriter {

diff --git a/...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/MassSpectrumReader.java b/...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/converter/io/MassSpectrumReader.java
@@ -1,6 +1,6 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2023 Lablicate GmbH.
- * 
+ * Copyright (c) 2013, 2024 Lablicate GmbH.
+ *
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
@@ -15,12 +15,12 @@
 import java.io.FileReader;
 import java.io.IOException;
 
+import org.eclipse.chemclipse.converter.exceptions.UnknownVersionException;
 import org.eclipse.chemclipse.msd.converter.io.AbstractMassSpectraReader;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter.XmlReader110;
-import org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.io.MassSpectrumReaderVersion110;
+import org.eclipse.chemclipse.msd.converter.supplier.mzml.io.MassSpectrumReaderVersion110;
 import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
-import org.eclipse.chemclipse.xxd.converter.supplier.io.exception.UnknownVersionException;
+import org.eclipse.chemclipse.xxd.converter.supplier.mzml.io.XmlReader110;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 public class MassSpectrumReader extends AbstractMassSpectraReader implements IMassSpectraReader {