Merge pull request #1863 from Mailaender/mzml-dad

Added mzML HPLC-DAD read/write support
eclipse · Sep 11, 2024 · eea47ad · eea47ad
2 parents 6852b64 + 9e7cfb4
commit eea47ad
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Showing 216 changed files with 3,231 additions and 1,231 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/...io/exception/UnknownVersionException.java → ...r/exceptions/UnknownVersionException.java b/...io/exception/UnknownVersionException.java → ...r/exceptions/UnknownVersionException.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2018 Lablicate GmbH.
+ * Copyright (c) 2016, 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
@@ -9,7 +9,7 @@
  * Contributors:
  * Dr. Alexander Kerner - initial API and implementation
  *******************************************************************************/
-package org.eclipse.chemclipse.xxd.converter.supplier.io.exception;
+package org.eclipse.chemclipse.converter.exceptions;
 
 import java.io.IOException;
 

diff --git a/...pse.chemclipse.converter/src/org/eclipse/chemclipse/converter/l10n/ConverterMessages.java b/...pse.chemclipse.converter/src/org/eclipse/chemclipse/converter/l10n/ConverterMessages.java
@@ -37,6 +37,7 @@ public class ConverterMessages extends NLS {
 	public static String readPeaks;
 	public static String readDatabase;
 	public static String writeMassSpectra;
+	public static String noMassSpectraStored;
 	//
 	static {
 		NLS.initializeMessages(BUNDLE_NAME, ConverterMessages.class);

diff --git a/...clipse.chemclipse.converter/src/org/eclipse/chemclipse/converter/l10n/messages.properties b/...clipse.chemclipse.converter/src/org/eclipse/chemclipse/converter/l10n/messages.properties
@@ -17,4 +17,5 @@ writeChromatogram=Write Chromatogram
 writeScans=Write Scans
 readPeaks=Read Peaks
 readDatabase=Read Database
-writeMassSpectra=Write Mass Spectra
+writeMassSpectra=Write Mass Spectra
+noMassSpectraStored=No mass spectra are stored.
diff --git a/...pse.chemclipse.converter/src/org/eclipse/chemclipse/converter/l10n/messages_de.properties b/...pse.chemclipse.converter/src/org/eclipse/chemclipse/converter/l10n/messages_de.properties
@@ -17,4 +17,5 @@ writeChromatogram=Schreibe Chromatogramm
 writeScans=Schreibe Scans
 readPeaks=Lese Peaks
 readDatabase=Lese Datenbank
-writeMassSpectra=Schreibe Massenspektren
+writeMassSpectra=Schreibe Massenspektren
+noMassSpectraStored=Keine Massenspektren enthalten.
diff --git a/...clipse/chemclipse/msd/converter/supplier/amdis/converter/fin/DatabaseImportConverter.java b/...clipse/chemclipse/msd/converter/supplier/amdis/converter/fin/DatabaseImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2020, 2022 Lablicate GmbH.
+ * Copyright (c) 2020, 2024 Lablicate GmbH.
  *
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -12,14 +12,20 @@
 package org.eclipse.chemclipse.msd.converter.supplier.amdis.converter.fin;
 
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 
+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.database.AbstractDatabaseImportConverter;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
 import org.eclipse.chemclipse.msd.converter.supplier.amdis.io.FINReader;
 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 DatabaseImportConverter extends AbstractDatabaseImportConverter {
 
@@ -37,11 +43,20 @@ public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor monitor
 				if(massSpectra != null && !massSpectra.isEmpty()) {
 					processingInfo.setProcessingResult(massSpectra);
 				} else {
-					processingInfo.addErrorMessage(DESCRIPTION, "No mass spectra were extracted." + file.getAbsolutePath());
+					processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.noMassSpectraStored, file.getAbsolutePath()));
 				}
-			} catch(Exception e) {
+			} catch(FileNotFoundException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(DESCRIPTION, "Exception parsing the file: " + file.getAbsolutePath());
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath()));
+			} catch(FileIsNotReadableException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotReadable, file.getAbsolutePath()));
+			} catch(FileIsEmptyException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.emptyFile, file.getAbsolutePath()));
+			} catch(IOException e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
 			}
 		}
 		return processingInfo;

diff --git a/...pse/chemclipse/msd/converter/supplier/amdis/converter/msl/MSLDatabaseImportConverter.java b/...pse/chemclipse/msd/converter/supplier/amdis/converter/msl/MSLDatabaseImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2022 Lablicate GmbH.
+ * Copyright (c) 2008, 2024 Lablicate GmbH.
  *
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -18,6 +18,7 @@
 
 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.database.AbstractDatabaseImportConverter;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
@@ -26,6 +27,7 @@
 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 MSLDatabaseImportConverter extends AbstractDatabaseImportConverter {
 
@@ -44,20 +46,20 @@ public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor 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/...pse/chemclipse/msd/converter/supplier/amdis/converter/msp/MSPDatabaseImportConverter.java b/...pse/chemclipse/msd/converter/supplier/amdis/converter/msp/MSPDatabaseImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016, 2022 Lablicate GmbH.
+ * Copyright (c) 2016, 2024 Lablicate GmbH.
  *
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -18,6 +18,7 @@
 
 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.database.AbstractDatabaseImportConverter;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
@@ -26,6 +27,7 @@
 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 MSPDatabaseImportConverter extends AbstractDatabaseImportConverter {
 
@@ -44,20 +46,20 @@ public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor 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.getLocalizedMessage());
-				processingInfo.addErrorMessage(DESCRIPTION, "The file couldn't be found: " + file.getAbsolutePath());
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath()));
 			} catch(FileIsNotReadableException e) {
-				logger.warn(e.getLocalizedMessage());
-				processingInfo.addErrorMessage(DESCRIPTION, "The file is not readable: " + file.getAbsolutePath());
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotReadable, file.getAbsolutePath()));
 			} catch(FileIsEmptyException e) {
-				logger.warn(e.getLocalizedMessage());
-				processingInfo.addErrorMessage(DESCRIPTION, "The file is empty: " + file.getAbsolutePath());
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.emptyFile, file.getAbsolutePath()));
 			} catch(IOException e) {
-				logger.warn(e.getLocalizedMessage(), e);
-				processingInfo.addErrorMessage(DESCRIPTION, "Something has gone completely wrong: " + file.getAbsolutePath());
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
 			}
 		}
 		return processingInfo;

diff --git a/.../org/eclipse/chemclipse/msd/converter/supplier/cml/converter/DatabaseExportConverter.java b/.../org/eclipse/chemclipse/msd/converter/supplier/cml/converter/DatabaseExportConverter.java
@@ -16,6 +16,7 @@
 import java.io.IOException;
 
 import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException;
+import org.eclipse.chemclipse.converter.l10n.ConverterMessages;
 import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.msd.converter.database.AbstractDatabaseExportConverter;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraWriter;
@@ -43,13 +44,13 @@ public IProcessingInfo<File> convert(File file, IScanMSD massSpectrum, boolean a
 				processingInfo.setProcessingResult(file);
 			} catch(FileNotFoundException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.fileNotFound, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath()));
 			} catch(FileIsNotWriteableException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.fileNotWriteable, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.fileNotWritable, file.getAbsolutePath()));
 			} catch(IOException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.ioError, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.failedToWriteFile, file.getAbsolutePath()));
 			}
 		}
 		return processingInfo;

diff --git a/.../org/eclipse/chemclipse/msd/converter/supplier/cml/converter/DatabaseImportConverter.java b/.../org/eclipse/chemclipse/msd/converter/supplier/cml/converter/DatabaseImportConverter.java
@@ -17,6 +17,7 @@
 
 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.database.AbstractDatabaseImportConverter;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
@@ -49,20 +50,20 @@ public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor monitor
 				if(massSpectra != null && !massSpectra.isEmpty()) {
 					processingInfo.setProcessingResult(massSpectra);
 				} else {
-					processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.noMassSpectraStored, file.getAbsolutePath()));
+					processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.noMassSpectraStored, file.getAbsolutePath()));
 				}
 			} catch(FileNotFoundException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.fileNotFound, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath()));
 			} catch(FileIsNotReadableException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.fileNotReadable, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.fileNotReadable, file.getAbsolutePath()));
 			} catch(FileIsEmptyException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.fileIsEmpty, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.emptyFile, file.getAbsolutePath()));
 			} catch(IOException e) {
 				logger.warn(e);
-				processingInfo.addErrorMessage(Messages.description, NLS.bind(Messages.ioError, file.getAbsolutePath()));
+				processingInfo.addErrorMessage(Messages.description, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
 			}
 		}
 		return processingInfo;

diff --git a/...ter.supplier.cml/src/org/eclipse/chemclipse/msd/converter/supplier/cml/l10n/Messages.java b/...ter.supplier.cml/src/org/eclipse/chemclipse/msd/converter/supplier/cml/l10n/Messages.java
@@ -18,12 +18,6 @@ public class Messages extends NLS {
 	private static final String BUNDLE_NAME = "org.eclipse.chemclipse.msd.converter.supplier.cml.l10n.messages"; //$NON-NLS-1$
 	//
 	public static String description;
-	public static String noMassSpectraStored;
-	public static String fileNotFound;
-	public static String fileNotReadable;
-	public static String fileIsEmpty;
-	public static String ioError;
-	public static String fileNotWriteable;
 	public static String singleSpectrum;
 	//
 	static {

diff --git a/...pplier.cml/src/org/eclipse/chemclipse/msd/converter/supplier/cml/l10n/messages.properties b/...pplier.cml/src/org/eclipse/chemclipse/msd/converter/supplier/cml/l10n/messages.properties
@@ -1,8 +1,2 @@
 massSpectrumImport=CML Mass Spectrum Import
-noMassSpectraStored=No mass spectra are stored.
-fileNotFound=The file couldn't be found: {0}
-fileNotReadable=The file is not readable: {0}
-fileIsEmpty=The file is empty: {0}
-ioError=An error occurred while reading the file: {0}
-fileNotWriteable=The file is not writable: {0}
 singleSpectrum=Only one spectrum per file supported.
diff --git a/...eclipse/chemclipse/msd/converter/supplier/massbank/converter/MassBankImportConverter.java b/...eclipse/chemclipse/msd/converter/supplier/massbank/converter/MassBankImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2022 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
@@ -13,8 +13,13 @@
 package org.eclipse.chemclipse.msd.converter.supplier.massbank.converter;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 
+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.database.IDatabaseImportConverter;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
 import org.eclipse.chemclipse.msd.converter.massspectrum.IMassSpectrumImportConverter;
@@ -23,9 +28,11 @@
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.chemclipse.processing.core.ProcessingInfo;
 import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.osgi.util.NLS;
 
 public class MassBankImportConverter implements IDatabaseImportConverter, IMassSpectrumImportConverter {
 
+	private static final Logger logger = Logger.getLogger(MassBankImportConverter.class);
 	private static final String DESCRIPTION = "MassBank MassSpectrum Import";
 
 	@Override
@@ -38,10 +45,20 @@ public IProcessingInfo<IMassSpectra> convert(File file, IProgressMonitor monitor
 			if(massSpectra != null && !massSpectra.isEmpty()) {
 				processingInfo.setProcessingResult(massSpectra);
 			} else {
-				processingInfo.addErrorMessage(DESCRIPTION, "No mass spectra are stored in" + file.getAbsolutePath());
+				processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.noMassSpectraStored, file.getAbsolutePath()));
 			}
+		} catch(FileNotFoundException e) {
+			logger.warn(e);
+			processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotFound, file.getAbsolutePath()));
+		} catch(FileIsNotReadableException e) {
+			logger.warn(e);
+			processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.fileNotReadable, file.getAbsolutePath()));
+		} catch(FileIsEmptyException e) {
+			logger.warn(e);
+			processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.emptyFile, file.getAbsolutePath()));
 		} catch(IOException e) {
-			processingInfo.addErrorMessage(DESCRIPTION, "Error reading file: " + file.getAbsolutePath(), e);
+			logger.warn(e);
+			processingInfo.addErrorMessage(DESCRIPTION, NLS.bind(ConverterMessages.failedToReadFile, file.getAbsolutePath()));
 		}
 		return processingInfo;
 	}

diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/META-INF/MANIFEST.MF
@@ -15,8 +15,7 @@ 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="1.16.0"
+ org.apache.commons.commons-codec;bundle-version="1.16.0",
+ org.apache.commons.lang3;bundle-version="3.13.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Bundle-ActivationPolicy: lazy
-Import-Package: org.apache.commons.lang3.tuple;version="3.1.0",
- org.eclipse.chemclipse.xxd.converter.supplier.io.exception