Added basic read support for RDML

chemclipse/features/org.eclipse.chemclipse.pcr.converter.supplier.rdml.feature/.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>org.eclipse.chemclipse.pcr.converter.supplier.rdml.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>

chemclipse/features/org.eclipse.chemclipse.pcr.converter.supplier.rdml.feature/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=utf8

chemclipse/features/org.eclipse.chemclipse.pcr.converter.supplier.rdml.feature/build.properties

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

chemclipse/features/org.eclipse.chemclipse.pcr.converter.supplier.rdml.feature/feature.xml

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+ id="org.eclipse.chemclipse.pcr.converter.supplier.rdml.feature"
+ label="RDML Converter"
+ version="0.9.0.qualifier"
+ provider-name="ChemClipse"
+ plugin="org.eclipse.chemclipse.feature.branding"
+ license-feature="org.eclipse.license"
+ license-feature-version="1.0.0.qualifier">
+
+ <description url="http://www.chemclipse.net/">
+ This is the Real-Time PCR Data Markup Language qPCR converter.
+ </description>
+
+ <copyright url="http://www.chemclipse.net/">
+ Copyright (c) 2023 Lablicate GmbH.
+ </copyright>
+
+ <license url="%licenseURL">
+ %license
+ </license>
+
+ <url>
+ <discovery label="RDML" url="http://rdml.org/"/>
+ </url>
+
+ <plugin
+ id="org.eclipse.chemclipse.pcr.converter.supplier.rdml"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+</feature>

chemclipse/features/org.eclipse.chemclipse.rcp.app.compilation.core.feature/feature.xml

@@ -300,4 +300,8 @@
  id="org.eclipse.chemclipse.chromatogram.xxd.report.supplier.image.feature"
  version="0.0.0"/>
 
+ <includes
+ id="org.eclipse.chemclipse.pcr.converter.supplier.rdml.feature"
+ version="0.0.0"/>
+
 </feature>

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/.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-17"/>
+ <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+ <classpathentry kind="src" path="src"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/.gitignore

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

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/.project

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>org.eclipse.chemclipse.pcr.converter.supplier.rdml</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>

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=utf8

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/.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=17
+org.eclipse.jdt.core.compiler.compliance=17
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=17

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/META-INF/MANIFEST.MF

@@ -0,0 +1,22 @@
+Manifest-Version: 1.0
+Automatic-Module-Name: org.eclipse.chemclipse.pcr.converter.supplier.rdml
+Bundle-ManifestVersion: 2
+Bundle-Name: RDML PCR Converter
+Bundle-SymbolicName: org.eclipse.chemclipse.pcr.converter.supplier.rdml;singleton:=true
+Bundle-Version: 0.9.0.qualifier
+Bundle-Activator: org.eclipse.chemclipse.pcr.converter.supplier.rdml.Activator
+Bundle-Vendor: ChemClipse
+Require-Bundle: org.eclipse.core.runtime,
+ org.eclipse.chemclipse.converter;bundle-version="0.8.0",
+ org.eclipse.chemclipse.pcr.converter;bundle-version="0.8.0",
+ org.eclipse.chemclipse.model;bundle-version="0.8.0",
+ org.eclipse.chemclipse.pcr.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.support;bundle-version="0.8.0",
+ jakarta.xml.bind-api;bundle-version="4.0.0"
+Bundle-RequiredExecutionEnvironment: JavaSE-17
+Bundle-ActivationPolicy: lazy
+Import-Package: jakarta.xml.bind,
+ jakarta.xml.bind.annotation,
+ jakarta.xml.bind.annotation.adapters

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/OSGI-INF/l10n/bundle_en.properties

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

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/build.properties

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

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/plugin.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+ <extension
+ point="org.eclipse.chemclipse.pcr.converter.plateSupplier">
+ <PlateSupplier
+ description="Reads Real-time PCR Data Markup Language (RDML) qPCR experiments."
+ exportConverter="org.eclipse.chemclipse.pcr.converter.supplier.rdml.core.PCRExportConverter"
+ fileExtension=".rdml"
+ fileName=""
+ filterName="qPCR experiments (*.rdml)"
+ id="org.eclipse.chemclipse.pcr.converter.supplier.rdml"
+ importConverter="org.eclipse.chemclipse.pcr.converter.supplier.rdml.core.PCRImportConverter"
+ importMagicNumberMatcher="org.eclipse.chemclipse.pcr.converter.supplier.rdml.core.MagicNumberMatcher"
+ isExportable="false"
+ isImportable="true">
+ </PlateSupplier>
+ </extension>
+</plugin>

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/Activator.java

@@ -0,0 +1,37 @@
+/*******************************************************************************
+ * Copyright (c) 2023 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 org.eclipse.chemclipse.pcr.converter.supplier.rdml;
+
+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;
+ }
+
+ @Override
+ public void start(BundleContext bundleContext) throws Exception {
+
+ Activator.context = bundleContext;
+ }
+
+ @Override
+ public void stop(BundleContext bundleContext) throws Exception {
+
+ Activator.context = null;
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/PathResolver.java

@@ -0,0 +1,46 @@
+/*******************************************************************************
+ * Copyright (c) 2016, 2023 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
+ * Dr. Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.chemclipse.pcr.converter.supplier.rdml;
+
+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/test.rdml
+ * 
+ * @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();
+ } catch(IOException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/core/MagicNumberMatcher.java

@@ -0,0 +1,26 @@
+/*******************************************************************************
+ * Copyright (c) 2023 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 org.eclipse.chemclipse.pcr.converter.supplier.rdml.core;
+
+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, ".rdml");
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/core/PCRExportConverter.java

@@ -0,0 +1,39 @@
+/*******************************************************************************
+ * Copyright (c) 2023 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 org.eclipse.chemclipse.pcr.converter.supplier.rdml.core;
+
+import java.io.File;
+
+import org.eclipse.chemclipse.pcr.converter.core.AbstractPlateExportConverter;
+import org.eclipse.chemclipse.pcr.converter.core.IPlateExportConverter;
+import org.eclipse.chemclipse.pcr.model.core.IPlate;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+
+public class PCRExportConverter extends AbstractPlateExportConverter implements IPlateExportConverter {
+
+ private static IPlateExportConverter instance = null;
+
+ @Override
+ public IProcessingInfo<File> convert(File file, IPlate plate, IProgressMonitor monitor) {
+
+ throw new UnsupportedOperationException();
+ }
+
+ public static IPlateExportConverter getInstance() {
+
+ if(instance == null) {
+ instance = new PCRExportConverter();
+ }
+ return instance;
+ }
+}

chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/core/PCRImportConverter.java

@@ -0,0 +1,68 @@
+/*******************************************************************************
+ * Copyright (c) 2023 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 org.eclipse.chemclipse.pcr.converter.supplier.rdml.core;
+
+import java.io.File;
+import java.io.IOException;
+import java.security.InvalidParameterException;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.pcr.converter.core.AbstractPlateImportConverter;
+import org.eclipse.chemclipse.pcr.converter.core.IPlateImportConverter;
+import org.eclipse.chemclipse.pcr.converter.supplier.rdml.io.PCRReader;
+import org.eclipse.chemclipse.pcr.model.core.IPlate;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.xml.sax.SAXException;
+
+import jakarta.xml.bind.JAXBException;
+
+public class PCRImportConverter extends AbstractPlateImportConverter implements IPlateImportConverter {
+
+ private static final Logger logger = Logger.getLogger(PCRImportConverter.class);
+ private static final String DESCRIPTION = "RDML Converter";
+ private static IPlateImportConverter instance = null;
+
+ @Override
+ public IProcessingInfo<IPlate> convert(File file, IProgressMonitor monitor) {
+
+ IProcessingInfo<IPlate> processingInfo = super.validate(file);
+ if(!processingInfo.hasErrorMessages()) {
+ PCRReader qPCR = new PCRReader();
+ try {
+ IPlate plate = qPCR.read(file);
+ processingInfo.setProcessingResult(plate);
+ } catch(IOException e) {
+ logger.warn(e);
+ processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file: " + file.getAbsolutePath(), e);
+ } catch(SAXException | JAXBException
+ | ParserConfigurationException e) {
+ logger.warn(e);
+ processingInfo.addErrorMessage(DESCRIPTION, "Failed to read file contents: " + file.getAbsolutePath(), e);
+ } catch(InvalidParameterException e) {
+ logger.warn(e);
+ processingInfo.addErrorMessage(DESCRIPTION, "Unsupported data in file: " + file.getAbsolutePath(), e);
+ }
+ }
+ return processingInfo;
+ }
+
+ public static IPlateImportConverter getInstance() {
+
+ if(instance == null) {
+ instance = new PCRImportConverter();
+ }
+ return instance;
+ }
+}