Add mzDB export.

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

@@ -4,13 +4,14 @@
    <extension
          point="org.eclipse.chemclipse.msd.converter.chromatogramSupplier">
       <ChromatogramSupplier
-            description="Reads mzDB Chromatograms"
+            description="Reads and writes mzDB chromatograms"
             fileExtension=".mzDB"
             filterName="mzDB Chromatogram (*.mzDB)"
             id="net.openchrom.msd.converter.supplier.mzdb"
-            importConverter="net.openchrom.msd.converter.supplier.mzdb.converter.ChromatogramImportConverter"
             importMagicNumberMatcher="net.openchrom.msd.converter.supplier.mzdb.converter.MagicNumberMatcher"
-            isExportable="false"
+            importConverter="net.openchrom.msd.converter.supplier.mzdb.converter.ChromatogramImportConverter"
+            exportConverter="net.openchrom.msd.converter.supplier.mzdb.converter.ChromatogramExportConverter"
+            isExportable="true"
             isImportable="true">
       </ChromatogramSupplier>
    </extension>

openchrom/plugins/net.openchrom.msd.converter.supplier.mzdb/src/net/openchrom/msd/converter/supplier/mzdb/converter/ChromatogramExportConverter.java

@@ -0,0 +1,49 @@
+/*******************************************************************************
+ * Copyright (c) 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 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.mzdb.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.mzdb.io.ChromatogramWriter;
+
+public class ChromatogramExportConverter extends AbstractChromatogramExportConverter implements IChromatogramExportConverter {
+
+	private static final Logger logger = Logger.getLogger(ChromatogramExportConverter.class);
+	private static final String DESCRIPTION = "mzDB Export Converter";
+
+	@Override
+	public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> chromatogram, IProgressMonitor monitor) {
+
+		IProcessingInfo<File> processingInfo = super.validate(file);
+		if(!processingInfo.hasErrorMessages() && chromatogram instanceof IChromatogramMSD chromatogramMSD) {
+			IChromatogramMSDWriter writer = new ChromatogramWriter();
+			try {
+				writer.writeChromatogram(file, chromatogramMSD, monitor);
+			} catch(Exception e) {
+				logger.warn(e);
+				processingInfo.addErrorMessage(DESCRIPTION, "Failed to write file: " + file.getAbsolutePath());
+			}
+			processingInfo.setProcessingResult(file);
+		}
+		return processingInfo;
+	}
+}

openchrom/plugins/net.openchrom.msd.converter.supplier.mzdb/src/net/openchrom/msd/converter/supplier/mzdb/io/ChromatogramWriter.java

@@ -1,30 +1,214 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2021 Lablicate GmbH.
+ * Copyright (c) 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
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Matthias Mailänder - initial API and implementation
  *******************************************************************************/
 package net.openchrom.msd.converter.supplier.mzdb.io;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
 
 import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException;
 import org.eclipse.chemclipse.converter.io.AbstractChromatogramWriter;
+import org.eclipse.chemclipse.converter.l10n.ConverterMessages;
+import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.model.core.IScan;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
+import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.IScanMSD;
+import org.eclipse.chemclipse.support.history.IEditInformation;
 import org.eclipse.core.runtime.IProgressMonitor;
 
+import net.openchrom.msd.converter.supplier.mzdb.Activator;
+
 public class ChromatogramWriter extends AbstractChromatogramWriter implements IChromatogramMSDWriter {
 
+	private static final Logger logger = Logger.getLogger(ChromatogramWriter.class);
+
 	@Override
-	public void writeChromatogram(File file, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws FileNotFoundException, FileIsNotWriteableException, IOException {
+	public void writeChromatogram(File file, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws FileIsNotWriteableException, IOException {
+
+		try {
+			Class.forName("org.sqlite.JDBC");
+		} catch(ClassNotFoundException e) {
+			logger.error(e);
+			return;
+		}
+		if(file.exists()) {
+			if(!file.delete()) { // otherwise it would try to append
+				logger.error("Failed to delete file.");
+			}
+		}
+		try (Connection connection = DriverManager.getConnection("jdbc:sqlite:" + file.toString())) {
+			connection.setAutoCommit(false);
+			createMzDB(connection, chromatogram);
+			createSample(connection, chromatogram);
+			createSoftware(connection);
+			createDataProcessing(connection, chromatogram);
+			createSpectrum(connection, chromatogram, monitor);
+			connection.commit();
+			connection.setAutoCommit(true);
+		} catch(SQLException e) {
+			logger.error(e);
+		}
+	}
+
+	private void createDataProcessing(Connection connection, IChromatogramMSD chromatogram) throws SQLException {
+
+		String createDataProcessing = """
+				CREATE TABLE data_processing (
+				  id INTEGER PRIMARY KEY AUTOINCREMENT,
+				  name TEXT NOT NULL
+				)
+				""";
+		try (var statement = connection.createStatement()) {
+			statement.execute(createDataProcessing);
+		}
+		String insert = "INSERT INTO data_processing(id,name) VALUES(?,?)";
+		try (var prepareStatement = connection.prepareStatement(insert)) {
+			for(IEditInformation editInformation : chromatogram.getEditHistory()) {
+				prepareStatement.setString(2, editInformation.getDescription());
+				prepareStatement.addBatch();
+			}
+			prepareStatement.setString(2, "Convert to mzDB");
+			prepareStatement.addBatch();
+			prepareStatement.executeBatch();
+		}
+	}
+
+	private void createMzDB(Connection connection, IChromatogramMSD chromatogram) throws SQLException {
+
+		String createMzDB = """
+				CREATE TABLE mzdb (
+				  version TEXT(10) NOT NULL,
+				  creation_timestamp TEXT NOT NULL,
+				  file_content TEXT NOT NULL,
+				  contacts TEXT NOT NULL,
+				  param_tree TEXT NOT NULL,
+				  PRIMARY KEY (version)
+				)
+				""";
+		try (var statement = connection.createStatement()) {
+			statement.execute(createMzDB);
+		}
+		String insert = "INSERT INTO mzdb(version,creation_timestamp,file_content,contacts,param_tree) VALUES(?,?,?,?,?)";
+		try (var prepareStatement = connection.prepareStatement(insert)) {
+			prepareStatement.setString(1, "0.7");
+			prepareStatement.setLong(2, chromatogram.getDate().getTime());
+			prepareStatement.setString(3, ""); // TODO
+			prepareStatement.setString(4, chromatogram.getOperator());
+			prepareStatement.setString(5, ""); // TODO
+			prepareStatement.executeUpdate();
+		}
+	}
+
+	private void createSample(Connection connection, IChromatogramMSD chromatogram) throws SQLException {
+
+		String createSample = """
+				CREATE TABLE sample (
+				  id INTEGER PRIMARY KEY AUTOINCREMENT,
+				  name TEXT NOT NULL,
+				  param_tree TEXT,
+				  shared_param_tree_id INTEGER,
+				  FOREIGN KEY (shared_param_tree_id) REFERENCES shared_param_tree (id)
+				)
+				 """;
+		try (var statement = connection.createStatement()) {
+			statement.execute(createSample);
+		}
+		String insert = "INSERT INTO sample(id,name,param_tree,shared_param_tree_id) VALUES(?,?,?,?)";
+		try (var prepareStatement = connection.prepareStatement(insert)) {
+			prepareStatement.setString(2, chromatogram.getSampleName());
+			prepareStatement.executeUpdate();
+		}
+	}
+
+	private void createSoftware(Connection connection) throws SQLException {
+
+		String createSoftware = """
+				CREATE TABLE software (
+				  id INTEGER PRIMARY KEY AUTOINCREMENT,
+				  name TEXT NOT NULL,
+				  version TEXT NOT NULL,
+				  param_tree TEXT NOT NULL,
+				  shared_param_tree_id INTEGER,
+				  FOREIGN KEY (shared_param_tree_id) REFERENCES shared_param_tree (id)
+				)
+				""";
+		try (var statement = connection.createStatement()) {
+			statement.execute(createSoftware);
+		}
+		String insert = "INSERT INTO software(id,name,version,param_tree,shared_param_tree_id) VALUES(?,?,?,?,?)";
+		try (var prepareStatement = connection.prepareStatement(insert)) {
+			prepareStatement.setString(2, "OpenChrom");
+			prepareStatement.setString(3, Activator.getContext().getBundle().getVersion().toString());
+			prepareStatement.setString(4, "");// TODO
+			prepareStatement.setInt(5, 0); // TODO
+			prepareStatement.executeUpdate();
+		}
+	}
+
+	private void createSpectrum(Connection connection, IChromatogramMSD chromatogram, IProgressMonitor monitor) throws SQLException {
 
+		String createSpectrum = """
+				CREATE TABLE spectrum(
+				  id INT,
+				  initial_id INT,
+				  title TEXT,
+				  cycle INT,
+				  time REAL,
+				  ms_level INT,
+				  activation_type TEXT,
+				  tic REAL,
+				  base_peak_mz REAL,
+				  base_peak_intensity REAL,
+				  main_precursor_mz REAL,
+				  main_precursor_charge INT,
+				  data_points_count INT,
+				  param_tree TEXT,
+				  scan_list TEXT,
+				  precursor_list TEXT,
+				  product_list TEXT,
+				  shared_param_tree_id INT,
+				  instrument_configuration_id INT,
+				  source_file_id INT,
+				  run_id INT,
+				  data_processing_id INT,
+				  data_encoding_id INT,
+				  bb_first_spectrum_id INT
+				)
+				""";
+		try (var statement = connection.createStatement()) {
+			statement.execute(createSpectrum);
+		}
+		monitor.beginTask(ConverterMessages.writeScans, chromatogram.getNumberOfScans());
+		String insert = "INSERT INTO spectrum(cycle,title,time,ms_level,tic,main_precursor_mz) VALUES(?,?,?,?,?,?)";
+		try (var prepareStatement = connection.prepareStatement(insert)) {
+			for(IScan scan : chromatogram.getScans()) {
+				prepareStatement.setFloat(5, scan.getTotalSignal());
+				if(scan instanceof IScanMSD scanMSD) {
+					prepareStatement.setInt(1, scanMSD.getScanNumber());
+					prepareStatement.setString(2, scanMSD.getIdentifier());
+					prepareStatement.setFloat(3, scanMSD.getRetentionTime() / 1000f); // ms to s
+					if(scanMSD instanceof IRegularMassSpectrum regularMassSpectrum) {
+						prepareStatement.setShort(4, regularMassSpectrum.getMassSpectrometer());
+						prepareStatement.setDouble(6, regularMassSpectrum.getPrecursorIon());
+					}
+				}
+				prepareStatement.addBatch();
+				monitor.worked(1);
+			}
+			prepareStatement.executeBatch();
+		}
 	}
 }