io.github.msdk.io.nativeformats.ThermoRawImportMethod.java Source code

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Here is the source code for io.github.msdk.io.nativeformats.ThermoRawImportMethod.java

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/* 
 * (C) Copyright 2015-2016 by MSDK Development Team
 *
 * This software is dual-licensed under either
 *
 * (a) the terms of the GNU Lesser General Public License version 2.1
 * as published by the Free Software Foundation
 *
 * or (per the licensee's choosing)
 *
 * (b) the terms of the Eclipse Public License v1.0 as published by
 * the Eclipse Foundation.
 */

package io.github.msdk.io.nativeformats;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import org.apache.commons.io.FileUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import io.github.msdk.MSDKException;
import io.github.msdk.MSDKMethod;
import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.files.FileType;
import io.github.msdk.datamodel.impl.MSDKObjectBuilder;
import io.github.msdk.datamodel.rawdata.RawDataFile;

/**
 * <p>
 * ThermoRawImportMethod class.
 * </p>
 */
public class ThermoRawImportMethod implements MSDKMethod<RawDataFile> {

    private final Logger logger = LoggerFactory.getLogger(this.getClass());

    private final @Nonnull File sourceFile;
    private final @Nonnull FileType fileType = FileType.THERMO_RAW;
    private final @Nonnull DataPointStore dataStore;

    private RawDataFile newRawFile;
    private boolean canceled = false;

    private Process dumperProcess = null;
    private RawDumpParser parser = null;

    /**
     * <p>
     * Constructor for ThermoRawImportMethod.
     * </p>
     *
     * @param sourceFile
     *            a {@link java.io.File} object.
     * @param dataStore
     *            a {@link io.github.msdk.datamodel.datastore.DataPointStore}
     *            object.
     */
    public ThermoRawImportMethod(@Nonnull File sourceFile, @Nonnull DataPointStore dataStore) {
        this.sourceFile = sourceFile;
        this.dataStore = dataStore;
    }

    /** {@inheritDoc} */
    @SuppressWarnings("null")
    @Override
    public RawDataFile execute() throws MSDKException {

        String osName = System.getProperty("os.name").toUpperCase();
        if (!osName.contains("WINDOWS")) {
            throw new MSDKException("Native data format import only works on MS Windows");
        }

        logger.info("Started parsing file " + sourceFile);

        try {

            // Decompress the thermo raw dump executable to a temporary folder
            File tempFolder = Files.createTempDirectory("msdk").toFile();
            tempFolder.deleteOnExit();
            InputStream dumpArchive = this.getClass().getClassLoader().getResourceAsStream("thermorawdump.zip");
            if (dumpArchive == null)
                throw new MSDKException("Failed to load the thermorawdump.zip archive from the MSDK jar");
            ZipUtils.extractStreamToFolder(dumpArchive, tempFolder);

            // Path to the rawdump executable
            File rawDumpPath = new File(tempFolder, "ThermoRawDump.exe");

            if (!rawDumpPath.canExecute())
                throw new MSDKException("Cannot execute program " + rawDumpPath);

            // Create a separate process and execute RAWdump.exe
            final String cmdLine[] = new String[] { rawDumpPath.getPath(), sourceFile.getPath() };
            dumperProcess = Runtime.getRuntime().exec(cmdLine);

            // Get the stdout of RAWdump process as InputStream
            InputStream dumpStream = dumperProcess.getInputStream();

            // Create the new RawDataFile
            String fileName = sourceFile.getName();
            newRawFile = MSDKObjectBuilder.getRawDataFile(fileName, sourceFile, fileType, dataStore);

            // Read the dump data
            parser = new RawDumpParser(newRawFile, dataStore);
            parser.readRAWDump(dumpStream);

            // Cleanup
            dumpStream.close();
            dumperProcess.destroy();

            try {
                FileUtils.deleteDirectory(tempFolder);
            } catch (IOException e) {
                // Ignore errors while deleting the tmp folder
            }

            if (canceled)
                return null;

        } catch (Throwable e) {
            if (dumperProcess != null)
                dumperProcess.destroy();

            throw new MSDKException(e);
        }

        logger.info("Finished parsing " + sourceFile);

        return newRawFile;

    }

    /** {@inheritDoc} */
    @Override
    @Nullable
    public RawDataFile getResult() {
        return newRawFile;
    }

    /** {@inheritDoc} */
    @Override
    public Float getFinishedPercentage() {
        if (parser == null)
            return 0f;
        else
            return parser.getFinishedPercentage();
    }

    /** {@inheritDoc} */
    @Override
    public void cancel() {
        this.canceled = true;
        if (parser != null) {
            parser.cancel();
        }
    }

}