Added support for reading .mzMLb chromatograms

openchrom/features/net.openchrom.msd.converter.supplier.mzmlb.feature/.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>net.openchrom.msd.converter.supplier.mzmlb.feature</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.pde.FeatureBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.FeatureNature</nature>
+	</natures>
+</projectDescription>

openchrom/features/net.openchrom.msd.converter.supplier.mzmlb.feature/build.properties

@@ -0,0 +1 @@
+bin.includes = feature.xml

openchrom/features/net.openchrom.msd.converter.supplier.mzmlb.feature/feature.xml

@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+      id="net.openchrom.msd.converter.supplier.mzmlb.feature"
+      label="mzMLb converter"
+      version="1.4.0.qualifier"
+      provider-name="OpenChrom"
+      plugin="net.openchrom.feature.branding">
+
+   <description url="http://www.openchrom.net">
+      This is the mzMLb chromatogram converter.
+   </description>
+
+   <copyright url="http://www.openchrom.net">
+      Copyright (c) 2014, 2021 Lablicate GmbH.
+   </copyright>
+
+   <license url="http://www.eclipse.org/legal/epl-v10.html">
+      Copyright (c) 2014, 2021 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, and is available at
+http://www.eclipse.org/legal/epl-v10.html
+   </license>
+
+   <url>
+      <discovery label="mzMLb Converter" url="http://www.openchrom.net"/>
+   </url>
+
+   <plugin
+         id="net.openchrom.msd.converter.supplier.mzmlb"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+   <plugin
+         id="net.openchrom.msd.converter.supplier.mzmlb.ui"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+</feature>

openchrom/features/net.openchrom.platform.feature/feature.xml

@@ -141,6 +141,10 @@
          id="net.openchrom.nmr.converter.supplier.nmrml.feature"
          version="0.0.0"/>
 
+   <includes
+         id="net.openchrom.msd.converter.supplier.mzmlb.feature"
+         version="0.0.0"/>
+
    <plugin
          id="net.openchrom.rcp.compilation.community.ui"
          download-size="0"

openchrom/features/pom.xml

@@ -64,5 +64,6 @@
 		<module>net.openchrom.msd.converter.supplier.mz5.feature</module>
 		<module>net.openchrom.xxd.converter.supplier.gaml.feature</module>
 		<module>net.openchrom.nmr.converter.supplier.nmrml.feature</module>
+		<module>net.openchrom.msd.converter.supplier.mzmlb.feature</module>
 	</modules>
 </project>

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/.classpath

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/.gitignore

@@ -0,0 +1 @@
+/bin/

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/.project

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>net.openchrom.msd.converter.supplier.mzmlb</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ManifestBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.SchemaBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.PluginNature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,7 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/META-INF/MANIFEST.MF

@@ -0,0 +1,24 @@
+Manifest-Version: 1.0
+Automatic-Module-Name: net.openchrom.msd.converter.supplier.mz5
+Bundle-ManifestVersion: 2
+Bundle-Name: mzMLb
+Bundle-SymbolicName: net.openchrom.msd.converter.supplier.mzmlb;singleton:=true
+Bundle-Version: 1.4.0.qualifier
+Bundle-Activator: net.openchrom.msd.converter.supplier.mzmlb.Activator
+Bundle-Vendor: OpenChrom
+Require-Bundle: org.eclipse.core.runtime,
+ org.eclipse.chemclipse.msd.converter;bundle-version="0.8.0",
+ org.eclipse.chemclipse.msd.model;bundle-version="0.8.0",
+ org.eclipse.chemclipse.logging;bundle-version="0.8.0",
+ org.eclipse.chemclipse.processing;bundle-version="0.8.0",
+ 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",
+ net.openchrom.thirdpartylibraries.jhdf5,
+ org.eclipse.chemclipse.msd.converter.supplier.mzml
+Bundle-RequiredExecutionEnvironment: JavaSE-1.8
+Bundle-ActivationPolicy: lazy
+Export-Package: net.openchrom.msd.converter.supplier.mzmlb,
+ net.openchrom.msd.converter.supplier.mzmlb.converter,
+ net.openchrom.msd.converter.supplier.mzmlb.io,
+ net.openchrom.msd.converter.supplier.mzmlb.model

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/OSGI-INF/l10n/bundle_en.properties

@@ -0,0 +1,12 @@
+###############################################################################
+# Copyright (c) 2015, 2017 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, and is available at
+# http://www.eclipse.org/legal/epl-v10.html
+#
+# Contributors:
+#     Dr. Philip Wenig - initial API and implementation
+###############################################################################
+#Properties file

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/build.properties

@@ -0,0 +1,6 @@
+source.. = src/
+output.. = bin/
+bin.includes = META-INF/,\
+               .,\
+               OSGI-INF/,\
+               plugin.xml

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/plugin.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+   <extension
+         point="org.eclipse.chemclipse.msd.converter.chromatogramSupplier">
+      <ChromatogramSupplier
+            description="Reads mzMLb Chromatograms"
+            fileExtension=".mzMLb"
+            filterName="mzML Chromatogram (*.mzMLb)"
+            id="net.openchrom.msd.converter.supplier.mzmlb"
+            importConverter="net.openchrom.msd.converter.supplier.mzmlb.converter.ChromatogramImportConverter"
+            importMagicNumberMatcher="net.openchrom.msd.converter.supplier.mzmlb.converter.MagicNumberMatcher"
+            isExportable="false"
+            isImportable="true">
+      </ChromatogramSupplier>
+   </extension>
+</plugin>

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/Activator.java

@@ -0,0 +1,43 @@
+/*******************************************************************************
+ * Copyright (c) 2014, 2021 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,
+ * and is available at http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Dr. Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.msd.converter.supplier.mzmlb;
+
+import org.osgi.framework.BundleActivator;
+import org.osgi.framework.BundleContext;
+
+public class Activator implements BundleActivator {
+
+	private static BundleContext context;
+
+	public static BundleContext getContext() {
+
+		return context;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * @see org.osgi.framework.BundleActivator#start(org.osgi.framework.BundleContext)
+	 */
+	public void start(BundleContext bundleContext) throws Exception {
+
+		Activator.context = bundleContext;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * @see org.osgi.framework.BundleActivator#stop(org.osgi.framework.BundleContext)
+	 */
+	public void stop(BundleContext bundleContext) throws Exception {
+
+		Activator.context = null;
+	}
+}

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/PathResolver.java

@@ -0,0 +1,45 @@
+/*******************************************************************************
+ * Copyright (c) 2014, 2021 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,
+ * and is available at http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Dr. Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.msd.converter.supplier.mzmlb;
+
+import java.io.IOException;
+import java.net.URL;
+
+import org.eclipse.core.runtime.FileLocator;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.Path;
+import org.eclipse.core.runtime.Platform;
+import org.osgi.framework.Bundle;
+
+public class PathResolver {
+
+	/**
+	 * Returns a absolute path of the specified Folder. For example
+	 * TESTDATA_IMPORT_EMPTY as an absolute Path:
+	 * $PluginPath$/testData/files/data.mzMLb
+	 * 
+	 * @param string
+	 * @return String absolutePath
+	 */
+	public static String getAbsolutePath(String string) {
+
+		Bundle bundle = Platform.getBundle(Activator.getContext().getBundle().getSymbolicName());
+		IPath path = new Path(string);
+		URL url = FileLocator.find(bundle, path, null);
+		try {
+			return FileLocator.resolve(url).getPath().toString();
+		} catch(IOException e) {
+			e.printStackTrace();
+		}
+		return null;
+	}
+}

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/converter/ChromatogramImportConverter.java

@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2021 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, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Dr. Philip Wenig - initial API and implementation
+ * Christoph Läubrich - add generics
+ *******************************************************************************/
+package net.openchrom.msd.converter.supplier.mzmlb.converter;
+
+import java.io.File;
+
+import org.eclipse.chemclipse.converter.chromatogram.AbstractChromatogramImportConverter;
+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.model.core.IChromatogramMSD;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+
+import net.openchrom.msd.converter.supplier.mzmlb.internal.support.IConstants;
+import net.openchrom.msd.converter.supplier.mzmlb.io.ChromatogramReader;
+
+public class ChromatogramImportConverter extends AbstractChromatogramImportConverter<IChromatogramMSD> {
+
+	private static final Logger logger = Logger.getLogger(ChromatogramImportConverter.class);
+	private static final String DESCRIPTION = "mzMLb Import Converter";
+
+	@Override
+	public IProcessingInfo<IChromatogramMSD> convert(File file, IProgressMonitor monitor) {
+
+		IProcessingInfo<IChromatogramMSD> processingInfo = super.validate(file);
+		if(!processingInfo.hasErrorMessages()) {
+			/*
+			 * Read the chromatogram.
+			 */
+			IChromatogramMSDReader reader = new ChromatogramReader();
+			monitor.subTask(IConstants.IMPORT_CHROMATOGRAM);
+			try {
+				IChromatogramMSD chromatogram = reader.read(file, monitor);
+				processingInfo.setProcessingResult(chromatogram);
+			} catch(Exception e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "Something has definitely gone wrong with the file: " + file.getAbsolutePath());
+			}
+		}
+		return processingInfo;
+	}
+
+	@Override
+	public IProcessingInfo<IChromatogramOverview> convertOverview(File file, IProgressMonitor monitor) {
+
+		IProcessingInfo<IChromatogramOverview> processingInfo = super.validate(file);
+		if(!processingInfo.hasErrorMessages()) {
+			IChromatogramMSDReader reader = new ChromatogramReader();
+			monitor.subTask(IConstants.IMPORT_CHROMATOGRAM_OVERVIEW);
+			try {
+				IChromatogramOverview chromatogramOverview = reader.readOverview(file, monitor);
+				processingInfo.setProcessingResult(chromatogramOverview);
+			} catch(Exception e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "Something has definitely gone wrong with the file: " + file.getAbsolutePath());
+			}
+		}
+		return processingInfo;
+	}
+}

openchrom/plugins/net.openchrom.msd.converter.supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/converter/MagicNumberMatcher.java

@@ -0,0 +1,26 @@
+/*******************************************************************************
+ * Copyright (c) 2021 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, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.msd.converter.supplier.mzmlb.converter;
+
+import java.io.File;
+
+import org.eclipse.chemclipse.converter.core.AbstractMagicNumberMatcher;
+import org.eclipse.chemclipse.converter.core.IMagicNumberMatcher;
+
+public class MagicNumberMatcher extends AbstractMagicNumberMatcher implements IMagicNumberMatcher {
+
+	@Override
+	public boolean checkFileFormat(File file) {
+
+		return checkFileExtension(file, ".mzMLb");
+	}
+}