Fixed #789 - Import *.msl, *.msp files - Support Charset

eclipse · Oct 20, 2021 · 212f9a3 · 212f9a3
1 parent 0b40353
commit 212f9a3
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Showing 14 changed files with 344 additions and 44 deletions.
diff --git a/...lipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis.ui/META-INF/MANIFEST.MF b/...lipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis.ui/META-INF/MANIFEST.MF
@@ -1,7 +1,7 @@
 Manifest-Version: 1.0
 Automatic-Module-Name: org.eclipse.chemclipse.msd.converter.supplier.amdis.ui
 Bundle-ManifestVersion: 2
-Bundle-Name: Ui
+Bundle-Name: AMDIS Converter UI
 Bundle-SymbolicName: org.eclipse.chemclipse.msd.converter.supplier.amdis.ui;singleton:=true
 Bundle-Version: 0.9.0.qualifier
 Bundle-Activator: org.eclipse.chemclipse.msd.converter.supplier.amdis.ui.Activator

diff --git a/...rc/org/eclipse/chemclipse/msd/converter/supplier/amdis/ui/preferences/PreferencePage.java b/...rc/org/eclipse/chemclipse/msd/converter/supplier/amdis/ui/preferences/PreferencePage.java
@@ -13,7 +13,10 @@
 
 import org.eclipse.chemclipse.msd.converter.supplier.amdis.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.msd.converter.supplier.amdis.ui.Activator;
+import org.eclipse.chemclipse.support.text.CharsetNIO;
+import org.eclipse.chemclipse.support.ui.preferences.fieldeditors.SpacerFieldEditor;
 import org.eclipse.jface.preference.BooleanFieldEditor;
+import org.eclipse.jface.preference.ComboFieldEditor;
 import org.eclipse.jface.preference.FieldEditorPreferencePage;
 import org.eclipse.ui.IWorkbench;
 import org.eclipse.ui.IWorkbenchPreferencePage;
@@ -24,7 +27,8 @@ public PreferencePage() {
 
 		super(GRID);
 		setPreferenceStore(Activator.getDefault().getPreferenceStore());
-		setDescription("AMDIS Settings.");
+		setTitle("AMDIS Converter");
+		setDescription("");
 	}
 
 	/**
@@ -42,6 +46,12 @@ public void createFieldEditors() {
 		addField(new BooleanFieldEditor(PreferenceSupplier.P_EXPORT_INTENSITIES_AS_INTEGER, "Export intensities as Integer", getFieldEditorParent()));
 		addField(new BooleanFieldEditor(PreferenceSupplier.P_PARSE_COMPOUND_INFORMATION, "Parse Compound Information (*.CID)", getFieldEditorParent()));
 		addField(new BooleanFieldEditor(PreferenceSupplier.P_PARSE_MOL_INFORMATION, "Parse MOL Information (*.MOL)", getFieldEditorParent()));
+		//
+		addField(new SpacerFieldEditor(getFieldEditorParent()));
+		addField(new ComboFieldEditor(PreferenceSupplier.P_CHARSET_IMPORT_MSL, "Charset Import MSL", CharsetNIO.getOptions(), getFieldEditorParent()));
+		addField(new ComboFieldEditor(PreferenceSupplier.P_CHARSET_IMPORT_MSP, "Charset Import MSP", CharsetNIO.getOptions(), getFieldEditorParent()));
+		addField(new ComboFieldEditor(PreferenceSupplier.P_CHARSET_IMPORT_FIN, "Charset Import FIN", CharsetNIO.getOptions(), getFieldEditorParent()));
+		addField(new ComboFieldEditor(PreferenceSupplier.P_CHARSET_IMPORT_ELU, "Charset Import ELU", CharsetNIO.getOptions(), getFieldEditorParent()));
 	}
 
 	/*

diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis/.project b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis/.project
@@ -20,6 +20,11 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ds.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>

diff --git a/...se.chemclipse.msd.converter.supplier.amdis/.settings/org.eclipse.pde.ds.annotations.prefs b/...se.chemclipse.msd.converter.supplier.amdis/.settings/org.eclipse.pde.ds.annotations.prefs
@@ -0,0 +1,6 @@
+eclipse.preferences.version=1
+enabled=true
+generateBundleActivationPolicyLazy=true
+path=OSGI-INF
+validationErrorLevel=error
+validationErrorLevel.missingImplicitUnbindMethod=error
diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.amdis/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Automatic-Module-Name: org.eclipse.chemclipse.msd.converter.supplier.amdis
 Eclipse-RegisterBuddy: 	org.eclipse.chemclipse.model, org.eclipse.chemclipse.msd.model
 Bundle-ManifestVersion: 2
-Bundle-Name: Amdis Plug-in
+Bundle-Name: AMDIS Converter
 Bundle-SymbolicName: org.eclipse.chemclipse.msd.converter.supplier.amdis;singleton:=true
 Bundle-Version: 0.9.0.qualifier
 Bundle-Activator: org.eclipse.chemclipse.msd.converter.supplier.amdis.Activator
@@ -15,10 +15,13 @@ Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.chemclipse.model;bundle-version="0.8.0",
  org.apache.commons.io;bundle-version="2.2.0",
  org.eclipse.chemclipse.support;bundle-version="0.8.0",
- org.eclipse.chemclipse.numeric;bundle-version="0.8.0"
+ org.eclipse.chemclipse.numeric;bundle-version="0.8.0",
+ com.fasterxml.jackson.core.jackson-annotations;bundle-version="2.9.9"
 Bundle-ActivationPolicy: lazy
+Import-Package: org.osgi.service.component.annotations;version="1.2.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: ChemClipse
 Export-Package: org.eclipse.chemclipse.msd.converter.supplier.amdis.converter.misc,
  org.eclipse.chemclipse.msd.converter.supplier.amdis.model,
  org.eclipse.chemclipse.msd.converter.supplier.amdis.preferences
+Service-Component: OSGI-INF/org.eclipse.chemclipse.msd.converter.supplier.amdis.system.ConverterProcessor.xml
diff --git a/...SGI-INF/org.eclipse.chemclipse.msd.converter.supplier.amdis.system.ConverterProcessor.xml b/...SGI-INF/org.eclipse.chemclipse.msd.converter.supplier.amdis.system.ConverterProcessor.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.eclipse.chemclipse.msd.converter.supplier.amdis.system.ConverterProcessor">
+   <service>
+      <provide interface="org.eclipse.chemclipse.processing.supplier.IProcessTypeSupplier"/>
+   </service>
+   <implementation class="org.eclipse.chemclipse.msd.converter.supplier.amdis.system.ConverterProcessor"/>
+</scr:component>
diff --git a/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/ELUReader.java b/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/ELUReader.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2020 Lablicate GmbH.
+ * Copyright (c) 2014, 2021 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -15,7 +15,7 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
+import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -73,8 +73,9 @@ public class ELUReader implements IPeakReader {
 	@Override
 	public IProcessingInfo<IPeaks<?>> read(File file, IProgressMonitor monitor) throws FileNotFoundException, FileIsNotReadableException, FileIsEmptyException, IOException {
 
+		Charset charset = PreferenceSupplier.getCharsetImportELU();
 		IProcessingInfo<IPeaks<?>> processingInfo = new ProcessingInfo<IPeaks<?>>();
-		String content = FileUtils.readFileToString(file, StandardCharsets.US_ASCII);
+		String content = FileUtils.readFileToString(file, charset);
 		int numberOfHits = getNumberOfHits(content);
 		if(numberOfHits <= 0) {
 			processingInfo.addErrorMessage("AMDIS ELU Parser", "There seems to be no peak in the file.");

diff --git a/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/FINReader.java b/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/FINReader.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2020 Lablicate GmbH.
+ * Copyright (c) 2020, 2021 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -13,15 +13,18 @@
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.charset.Charset;
 
 import org.eclipse.chemclipse.converter.exceptions.FileIsEmptyException;
 import org.eclipse.chemclipse.converter.exceptions.FileIsNotReadableException;
 import org.eclipse.chemclipse.msd.converter.io.AbstractMassSpectraReader;
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
 import org.eclipse.chemclipse.msd.converter.supplier.amdis.model.IVendorLibraryMassSpectrum;
+import org.eclipse.chemclipse.msd.converter.supplier.amdis.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
 import org.eclipse.chemclipse.msd.model.implementation.MassSpectra;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -64,7 +67,8 @@ private void parse(IMassSpectra massSpectra, File file, IProgressMonitor monitor
 		 * ...
 		 */
 		if(file != null && file.exists()) {
-			try (BufferedReader bufferedReader = new BufferedReader(new FileReader(file))) {
+			Charset charset = PreferenceSupplier.getCharsetImportFIN();
+			try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), charset))) {
 				/*
 				 * Settings and builder.
 				 */

diff --git a/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSLReader.java b/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSLReader.java
@@ -64,7 +64,6 @@ public class MSLReader extends AbstractMassSpectraReader implements IMassSpectra
 	private static final Pattern DATA = Pattern.compile("(.*)(Num Peaks:)(\\s*)(\\d*)(.*)", Pattern.CASE_INSENSITIVE | Pattern.MULTILINE | Pattern.DOTALL);
 	private static final Pattern IONS = Pattern.compile("([+]?\\d+\\.?\\d*)(\\s+)([+-]?\\d+\\.?\\d*([eE][+-]?\\d+)?)"); // "(\\d+)(\\s+)(\\d+)" or "(\\d+)(\\s+)([+-]?\\d+\\.?\\d*([eE][+-]?\\d+)?)"
 	//
-	private static final String CHARSET_US = "US-ASCII";
 	private static final String RETENTION_INDICES_DELIMITER = ", ";
 	private static final String LINE_DELIMITER = "\r\n";
 
@@ -160,7 +159,7 @@ protected IVendorLibraryMassSpectrum extractMassSpectrum(String massSpectrumData
 	 */
 	private List<String> getMassSpectraData(File file) throws IOException {
 
-		Charset charset = Charset.forName(CHARSET_US);
+		Charset charset = PreferenceSupplier.getCharsetImportMSL();
 		List<String> massSpectraData = new ArrayList<String>();
 		//
 		try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), charset))) {
@@ -186,7 +185,6 @@ private List<String> getMassSpectraData(File file) throws IOException {
 			 * Don't forget to add the last mass spectrum.
 			 */
 			addMassSpectrumData(builder, massSpectraData);
-			bufferedReader.close();
 		}
 		//
 		return massSpectraData;

diff --git a/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSPReader.java b/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSPReader.java
@@ -11,7 +11,6 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.converter.supplier.amdis.io;
 
-import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -114,39 +113,34 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws FileNotFoun
 	 */
 	private List<String> getMassSpectraData(File file) throws IOException {
 
-		Charset charSet = Charset.forName("US-ASCII");
-		BufferedInputStream bufferedInputStream = new BufferedInputStream(new FileInputStream(file));
-		InputStreamReader inputStreamReader = new InputStreamReader(bufferedInputStream, charSet);
-		BufferedReader bufferedReader = new BufferedReader(inputStreamReader);
+		Charset charset = PreferenceSupplier.getCharsetImportMSP();
 		List<String> massSpectraData = new ArrayList<String>();
-		StringBuilder builder = new StringBuilder();
-		String line;
-		while((line = bufferedReader.readLine()) != null) {
+		//
+		try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), charset))) {
+			StringBuilder builder = new StringBuilder();
+			String line;
+			while((line = bufferedReader.readLine()) != null) {
+				/*
+				 * The mass spectra are divided by empty lines. If the builder has
+				 * at least 1 char, then add a new potential mass spectrum to the
+				 * mass spectra data list. Don't forget to build a new
+				 * StringBuilder. In all other cases append the found lines to the
+				 * StringBuilder.
+				 */
+				if(line.length() == 0) {
+					addMassSpectrumData(builder, massSpectraData);
+					builder = new StringBuilder();
+				} else {
+					builder.append(line);
+					builder.append(LINE_END);
+				}
+			}
 			/*
-			 * The mass spectra are divided by empty lines. If the builder has
-			 * at least 1 char, then add a new potential mass spectrum to the
-			 * mass spectra data list. Don't forget to build a new
-			 * StringBuilder. In all other cases append the found lines to the
-			 * StringBuilder.
+			 * Don't forget to add the last mass spectrum.
 			 */
-			if(line.length() == 0) {
-				addMassSpectrumData(builder, massSpectraData);
-				builder = new StringBuilder();
-			} else {
-				builder.append(line);
-				builder.append(LINE_END);
-			}
+			addMassSpectrumData(builder, massSpectraData);
 		}
-		/*
-		 * Don't forget to add the last mass spectrum.
-		 */
-		addMassSpectrumData(builder, massSpectraData);
-		/*
-		 * Close the streams.
-		 */
-		bufferedReader.close();
-		inputStreamReader.close();
-		bufferedInputStream.close();
+		//
 		return massSpectraData;
 	}
 

diff --git a/...c/org/eclipse/chemclipse/msd/converter/supplier/amdis/preferences/PreferenceSupplier.java b/...c/org/eclipse/chemclipse/msd/converter/supplier/amdis/preferences/PreferenceSupplier.java
@@ -11,17 +11,23 @@
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.converter.supplier.amdis.preferences;
 
+import java.nio.charset.Charset;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.msd.converter.supplier.amdis.Activator;
 import org.eclipse.chemclipse.support.preferences.IPreferenceSupplier;
+import org.eclipse.chemclipse.support.text.CharsetNIO;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.core.runtime.preferences.IScopeContext;
 import org.eclipse.core.runtime.preferences.InstanceScope;
+import org.osgi.service.prefs.BackingStoreException;
 
 public class PreferenceSupplier implements IPreferenceSupplier {
 
+	private static final Logger logger = Logger.getLogger(PreferenceSupplier.class);
+	//
 	public static final String P_SPLIT_LIBRARY = "splitLibrary";
 	public static final boolean DEF_SPLIT_LIBRARY = false;
 	public static final String P_EXCLUDE_UNCERTAIN_IONS = "excludeUncertainIons";
@@ -39,6 +45,15 @@ public class PreferenceSupplier implements IPreferenceSupplier {
 	public static final String P_PARSE_MOL_INFORMATION = "parseMolInformation";
 	public static final boolean DEF_PARSE_MOL_INFORMATION = true;
 	//
+	public static final String P_CHARSET_IMPORT_MSL = "charsetImportMSL";
+	public static final String DEF_CHARSET_IMPORT_MSL = CharsetNIO.US_ASCII.name();
+	public static final String P_CHARSET_IMPORT_MSP = "charsetImportMSP";
+	public static final String DEF_CHARSET_IMPORT_MSP = CharsetNIO.US_ASCII.name();
+	public static final String P_CHARSET_IMPORT_FIN = "charsetImportFIN";
+	public static final String DEF_CHARSET_IMPORT_FIN = CharsetNIO.US_ASCII.name();
+	public static final String P_CHARSET_IMPORT_ELU = "charsetImportELU";
+	public static final String DEF_CHARSET_IMPORT_ELU = CharsetNIO.US_ASCII.name();
+	//
 	private static IPreferenceSupplier preferenceSupplier;
 
 	public static IPreferenceSupplier INSTANCE() {
@@ -65,6 +80,7 @@ public String getPreferenceNode() {
 	public Map<String, String> getDefaultValues() {
 
 		Map<String, String> defaultValues = new HashMap<String, String>();
+		//
 		defaultValues.put(P_SPLIT_LIBRARY, Boolean.toString(DEF_SPLIT_LIBRARY));
 		defaultValues.put(P_EXCLUDE_UNCERTAIN_IONS, Boolean.toString(DEF_EXCLUDE_UNCERTAIN_IONS));
 		defaultValues.put(P_USE_UNIT_MASS_RESOLUTION, Boolean.toString(DEF_USE_UNIT_MASS_RESOLUTION));
@@ -73,6 +89,12 @@ public Map<String, String> getDefaultValues() {
 		defaultValues.put(P_EXPORT_INTENSITIES_AS_INTEGER, Boolean.toString(DEF_EXPORT_INTENSITIES_AS_INTEGER));
 		defaultValues.put(P_PARSE_COMPOUND_INFORMATION, Boolean.toString(DEF_PARSE_COMPOUND_INFORMATION));
 		defaultValues.put(P_PARSE_MOL_INFORMATION, Boolean.toString(DEF_PARSE_MOL_INFORMATION));
+		//
+		defaultValues.put(P_CHARSET_IMPORT_MSL, DEF_CHARSET_IMPORT_MSL);
+		defaultValues.put(P_CHARSET_IMPORT_MSP, DEF_CHARSET_IMPORT_MSP);
+		defaultValues.put(P_CHARSET_IMPORT_FIN, DEF_CHARSET_IMPORT_FIN);
+		defaultValues.put(P_CHARSET_IMPORT_ELU, DEF_CHARSET_IMPORT_ELU);
+		//
 		return defaultValues;
 	}
 
@@ -129,4 +151,65 @@ public static boolean isParseMolInformation() {
 		IEclipsePreferences preferences = INSTANCE().getPreferences();
 		return preferences.getBoolean(P_PARSE_MOL_INFORMATION, DEF_PARSE_MOL_INFORMATION);
 	}
-}
+
+	public static Charset getCharsetImportMSL() {
+
+		return getCharset(P_CHARSET_IMPORT_MSL, DEF_CHARSET_IMPORT_MSL);
+	}
+
+	public static void setCharsetImportMSL(CharsetNIO charsetNIO) {
+
+		setCharset(P_CHARSET_IMPORT_MSL, charsetNIO);
+	}
+
+	public static Charset getCharsetImportMSP() {
+
+		return getCharset(P_CHARSET_IMPORT_MSP, DEF_CHARSET_IMPORT_MSP);
+	}
+
+	public static void setCharsetImportMSP(CharsetNIO charsetNIO) {
+
+		setCharset(P_CHARSET_IMPORT_MSP, charsetNIO);
+	}
+
+	public static Charset getCharsetImportFIN() {
+
+		return getCharset(P_CHARSET_IMPORT_FIN, DEF_CHARSET_IMPORT_FIN);
+	}
+
+	public static void setCharsetImportFIN(CharsetNIO charsetNIO) {
+
+		setCharset(P_CHARSET_IMPORT_FIN, charsetNIO);
+	}
+
+	public static Charset getCharsetImportELU() {
+
+		return getCharset(P_CHARSET_IMPORT_ELU, DEF_CHARSET_IMPORT_ELU);
+	}
+
+	public static void setCharsetImportELU(CharsetNIO charsetNIO) {
+
+		setCharset(P_CHARSET_IMPORT_ELU, charsetNIO);
+	}
+
+	private static Charset getCharset(String key, String def) {
+
+		IEclipsePreferences preferences = INSTANCE().getPreferences();
+		try {
+			return CharsetNIO.valueOf(preferences.get(key, def)).getCharset();
+		} catch(Exception e) {
+			return CharsetNIO.US_ASCII.getCharset();
+		}
+	}
+
+	private static void setCharset(String key, CharsetNIO charsetNIO) {
+
+		try {
+			IEclipsePreferences preferences = PreferenceSupplier.INSTANCE().getPreferences();
+			preferences.put(key, charsetNIO.name());
+			preferences.flush();
+		} catch(BackingStoreException e) {
+			logger.warn(e);
+		}
+	}
+}