ch.unibas.fittingwizard.infrastructure.RealBabelScript.java Source code

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Here is the source code for ch.unibas.fittingwizard.infrastructure.RealBabelScript.java

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/*
 * Copyright (c) 2015, Florent Hedin, Markus Meuwly, and the University of Basel
 * All rights reserved.
 *
 * The 3-clause BSD license is applied to this software.
 * see LICENSE.txt
 *
 */
package ch.unibas.fittingwizard.infrastructure;

import ch.unibas.fittingwizard.application.scripts.babel.BabelInput;
import ch.unibas.fittingwizard.application.scripts.babel.BabelOutput;
import ch.unibas.fittingwizard.application.scripts.babel.IBabelScript;
import ch.unibas.fittingwizard.application.scripts.base.ScriptExecutionException;
import ch.unibas.fittingwizard.infrastructure.base.BabelRunner;
import java.io.File;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.FilenameUtils;
import org.apache.log4j.Logger;

/**
 * User: mhelmer Date: 06.12.13 Time: 13:13
 */
public class RealBabelScript implements IBabelScript {

    private final static Logger logger = Logger.getLogger(RealBabelScript.class);

    private static final String sdfExtension = ".sdf";
    private final BabelRunner runner;

    private File moleculesDir;

    public RealBabelScript(File moleculesDir) {
        this.moleculesDir = moleculesDir;
        runner = new BabelRunner();
    }

    @Override
    public BabelOutput execute(BabelInput input) {

        String moleculeName = getMoleculeName(input.getGaussianLogFile());

        File specificMoleculeDir = new File(moleculesDir, moleculeName);

        setWorkingDir(specificMoleculeDir);

        File sdfFile = new File(specificMoleculeDir, moleculeName + sdfExtension);

        List<String> args = Arrays.asList("-ig03", input.getGaussianLogFile().getName(), "-osdf",
                sdfFile.getName());

        logger.info("Running babel: " + args.toString());

        try {
            int retval = runner.exec(args);
            if (retval != 0) {
                logger.error("Babel exited with non-zero return value: " + retval);
                throw new ScriptExecutionException("Babel exited with non-zero return value: " + retval);
            }
        } catch (Exception e) {
            logger.error("Babel file conversion failed.");
            throw new ScriptExecutionException("Babel file conversion failed.", e);
        }

        if (!sdfFile.exists()) {
            logger.error("Babel file conversion did not create SDF output file.");
            throw new ScriptExecutionException("Babel file conversion did not create SDF output file.");
        }

        return new BabelOutput(sdfFile);
    }

    private void setWorkingDir(File workingDir) {
        if (!workingDir.exists()) {
            workingDir.mkdir();
        }

        runner.setWorkingDir(workingDir);
    }

    private String getMoleculeName(File input) {
        return FilenameUtils.removeExtension(input.getName());
    }

}