Merge pull request #140 from Mailaender/animl-msd

Added support for MSD .animl chromatograms

openchrom/features/net.openchrom.xxd.converter.supplier.animl.feature/feature.xml

@@ -43,4 +43,11 @@ http://www.eclipse.org/legal/epl-v10.html
          version="0.0.0"
          unpack="false"/>
 
+   <plugin
+         id="net.openchrom.msd.converter.supplier.animl"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
 </feature>

openchrom/plugins/net.openchrom.csd.converter.supplier.animl/plugin.xml

@@ -7,7 +7,7 @@
             description="Writes AnIML Chromatograms."
             exportConverter="net.openchrom.csd.converter.supplier.animl.converter.ChromatogramExportConverter"
             fileExtension=".animl"
-            filterName="AnIML Chromatogram (*.animl)"
+            filterName="AnIML FID Chromatogram (*.animl)"
             id="net.openchrom.csd.converter.supplier.animl"
             importConverter="net.openchrom.csd.converter.supplier.animl.converter.ChromatogramImportConverter"
             importMagicNumberMatcher="net.openchrom.csd.converter.supplier.animl.converter.MagicNumberMatcher"

openchrom/plugins/net.openchrom.csd.converter.supplier.animl/src/net/openchrom/csd/converter/supplier/animl/converter/ChromatogramExportConverter.java

@@ -23,9 +23,9 @@
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
 
-import net.openchrom.csd.converter.supplier.animl.internal.converter.IConstants;
-import net.openchrom.csd.converter.supplier.animl.internal.converter.SpecificationValidator;
 import net.openchrom.csd.converter.supplier.animl.io.ChromatogramWriter;
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.SpecificationValidator;
 
 public class ChromatogramExportConverter extends AbstractChromatogramExportConverter implements IChromatogramExportConverter {
 

openchrom/plugins/net.openchrom.csd.converter.supplier.animl/src/net/openchrom/csd/converter/supplier/animl/converter/ChromatogramImportConverter.java

@@ -22,8 +22,8 @@
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
 
-import net.openchrom.csd.converter.supplier.animl.internal.converter.IConstants;
 import net.openchrom.csd.converter.supplier.animl.io.ChromatogramReader;
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
 
 public class ChromatogramImportConverter extends AbstractChromatogramImportConverter<IChromatogramCSD> {
 

openchrom/plugins/net.openchrom.csd.converter.supplier.animl/src/net/openchrom/csd/converter/supplier/animl/converter/MagicNumberMatcher.java

@@ -13,14 +13,50 @@
 
 import java.io.File;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
 import org.eclipse.chemclipse.converter.core.AbstractMagicNumberMatcher;
 import org.eclipse.chemclipse.converter.core.IMagicNumberMatcher;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
+
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.SpecificationValidator;
 
 public class MagicNumberMatcher extends AbstractMagicNumberMatcher implements IMagicNumberMatcher {
 
 	@Override
 	public boolean checkFileFormat(File file) {
 
-		return checkFileExtension(file, ".animl");
+		boolean isValidFormat = false;
+		try {
+			file = SpecificationValidator.validateSpecification(file);
+			if(!file.exists()) {
+				return isValidFormat;
+			}
+			if(!checkFileExtension(file, ".animl")) {
+				return isValidFormat;
+			}
+			DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
+			DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
+			Document document = documentBuilder.parse(file);
+			NodeList root = document.getElementsByTagName(IConstants.NODE_ANIML);
+			if(root.getLength() != 1) {
+				return isValidFormat;
+			}
+			NodeList techniquesList = document.getElementsByTagName(IConstants.NODE_TECHNIQUE);
+			int techniques = techniquesList.getLength();
+			for(int t = 0; t < techniques; t++) {
+				Element element = (Element)techniquesList.item(t);
+				if(element.getAttribute("name").equals("Flame Ionization Detector")) {
+					isValidFormat = true;
+				}
+			}
+		} catch(Exception e) {
+			// fail silently
+		}
+		return isValidFormat;
 	}
 }

openchrom/plugins/net.openchrom.csd.converter.supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramReader.java

@@ -81,7 +81,7 @@ public IChromatogramCSD read(File file, IProgressMonitor monitor) throws FileNot
 										}
 									}
 									for(EncodedValueSetType encodedValueSet : series.getEncodedValueSet()) {
-										float[] decodedValues = BinaryReader.decodeArray(encodedValueSet.getValue());
+										float[] decodedValues = BinaryReader.decodeFloatArray(encodedValueSet.getValue());
 										for(float f : decodedValues) {
 											retentionTimes.add(multiplicator * f);
 										}
@@ -94,7 +94,7 @@ public IChromatogramCSD read(File file, IProgressMonitor monitor) throws FileNot
 										}
 									}
 									for(EncodedValueSetType encodedValueSet : series.getEncodedValueSet()) {
-										float[] decodedValues = BinaryReader.decodeArray(encodedValueSet.getValue());
+										float[] decodedValues = BinaryReader.decodeFloatArray(encodedValueSet.getValue());
 										for(float f : decodedValues) {
 											signals.add(f);
 										}

openchrom/plugins/net.openchrom.csd.converter.supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramWriter.java

@@ -73,9 +73,6 @@ public void writeChromatogram(File file, IChromatogramCSD chromatogram, IProgres
 			logger.warn(e);
 		} catch(DatatypeConfigurationException e) {
 			logger.warn(e);
-		} catch(Exception e) // TODO remove
-		{
-			e.printStackTrace();
 		}
 	}
 
@@ -148,7 +145,7 @@ private ResultType createResult(IChromatogramCSD chromatogram) {
 			IndividualValueSetType totalSignals = new IndividualValueSetType();
 			for(IScan scan : chromatogram.getScans()) {
 				retentionTimes.getF().add((float)scan.getRetentionTime());
-				totalSignals.getF().add((float)scan.getTotalSignal());
+				totalSignals.getF().add(scan.getTotalSignal());
 			}
 			retentionTimeSeries.getIndividualValueSet().add(retentionTimes);
 			totalSignalSeries.getIndividualValueSet().add(totalSignals);
@@ -186,7 +183,7 @@ private TechniqueType createChromatographyTechnique() {
 
 		TechniqueType technique = new TechniqueType();
 		technique.setName("Chromatography");
-		technique.setUri("https://raw.githubusercontent.com/AnIML/techniques/6e30b1e593e6df661a44ae2a9892b6198def0641/chromatography.atdd");
+		technique.setUri("https://github.com/AnIML/techniques/blob/6e30b1e593e6df661a44ae2a9892b6198def0641/chromatography.atdd");
 		return technique;
 	}
 

openchrom/plugins/net.openchrom.csd.converter.supplier.gaml/src/net/openchrom/csd/converter/supplier/gaml/io/ChromatogramReaderVersion100.java

@@ -55,13 +55,13 @@
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.GAML;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Parameter;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Peaktable;
+import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Peaktable.Peak;
+import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Peaktable.Peak.Baseline;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Technique;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Trace;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Units;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Xdata;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Ydata;
-import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Peaktable.Peak;
-import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Peaktable.Peak.Baseline;
 import net.openchrom.xxd.converter.supplier.gaml.io.Reader100;
 
 public class ChromatogramReaderVersion100 extends AbstractChromatogramReader implements IChromatogramCSDReader {

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

@@ -0,0 +1,11 @@
+<?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">
+		<attributes>
+			<attribute name="module" value="true"/>
+		</attributes>
+	</classpathentry>
+	<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.animl/.gitignore

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

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

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>net.openchrom.msd.converter.supplier.animl</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.animl/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,8 @@
+#Wed Apr 21 08:55:45 CEST 2010
+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.animl/META-INF/MANIFEST.MF

@@ -0,0 +1,22 @@
+Manifest-Version: 1.0
+Automatic-Module-Name: net.openchrom.msd.converter.supplier.gaml
+Eclipse-RegisterBuddy: org.eclipse.chemclipse.model, org.eclipse.chemclipse.msd.model
+Bundle-ManifestVersion: 2
+Bundle-Name: AnIML
+Bundle-SymbolicName: net.openchrom.msd.converter.supplier.animl;singleton:=true
+Bundle-Version: 1.4.0.qualifier
+Bundle-Activator: net.openchrom.msd.converter.supplier.animl.Activator
+Bundle-Vendor: OpenChrom
+Require-Bundle: org.eclipse.core.runtime,
+ org.eclipse.chemclipse.logging;bundle-version="0.8.0",
+ org.eclipse.chemclipse.msd.model;bundle-version="0.8.0",
+ org.eclipse.chemclipse.msd.converter;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",
+ org.eclipse.chemclipse.xxd.converter.supplier.chemclipse;bundle-version="0.8.0",
+ net.openchrom.xxd.converter.supplier.gaml,
+ net.openchrom.xxd.converter.supplier.animl
+Bundle-RequiredExecutionEnvironment: JavaSE-1.8
+Bundle-ActivationPolicy: lazy

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

@@ -0,0 +1,12 @@
+###############################################################################
+# 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
+###############################################################################
+#Properties file

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

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

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

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+   <extension
+         point="org.eclipse.chemclipse.msd.converter.chromatogramSupplier">
+      <ChromatogramSupplier
+            description="Reads Analytical Information Markup Language Chromatograms"
+            fileExtension=".animl"
+            filterName="AnIML MSD Chromatogram (*.animl)"
+            id="net.openchrom.msd.converter.supplier.animl.chromatogram"
+            importConverter="net.openchrom.msd.converter.supplier.animl.converter.ChromatogramImportConverter"
+            importMagicNumberMatcher="net.openchrom.msd.converter.supplier.animl.converter.MagicNumberMatcher"
+            exportConverter="net.openchrom.msd.converter.supplier.animl.converter.ChromatogramExportConverter"
+            isExportable="true"
+            isImportable="true">
+      </ChromatogramSupplier>
+   </extension>
+</plugin>

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

@@ -0,0 +1,43 @@
+/*******************************************************************************
+ * Copyright (c) 2008, 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.animl;
+
+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.animl/src/net/openchrom/msd/converter/supplier/animl/converter/ChromatogramExportConverter.java

@@ -0,0 +1,57 @@
+/*******************************************************************************
+ * 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.animl.converter;
+
+import java.io.File;
+
+import org.eclipse.chemclipse.converter.chromatogram.AbstractChromatogramExportConverter;
+import org.eclipse.chemclipse.converter.chromatogram.IChromatogramExportConverter;
+import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.model.core.IChromatogram;
+import org.eclipse.chemclipse.model.core.IPeak;
+import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter;
+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.animl.io.ChromatogramWriter;
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.IConstants;
+import net.openchrom.xxd.converter.supplier.animl.internal.converter.SpecificationValidator;
+
+public class ChromatogramExportConverter extends AbstractChromatogramExportConverter implements IChromatogramExportConverter {
+
+	private static final Logger logger = Logger.getLogger(ChromatogramExportConverter.class);
+	private static final String DESCRIPTION = "AnIML Export Converter";
+
+	@Override
+	public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> chromatogram, IProgressMonitor monitor) {
+
+		file = SpecificationValidator.validateSpecification(file);
+		IProcessingInfo<File> processingInfo = super.validate(file);
+		/*
+		 * Don't process if errors have occurred.
+		 */
+		if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramMSD) {
+			IChromatogramMSD chromatogramMSD = (IChromatogramMSD)chromatogram;
+			monitor.subTask(IConstants.EXPORT_CHROMATOGRAM);
+			IChromatogramMSDWriter writer = new ChromatogramWriter();
+			try {
+				writer.writeChromatogram(file, chromatogramMSD, monitor);
+			} catch(Exception e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "Something has definitely gone wrong with the file: " + file.getAbsolutePath());
+			}
+			processingInfo.setProcessingResult(file);
+		}
+		return processingInfo;
+	}
+}