ch.javasoft.metabolic.generate.ConfiguredGenerator.java Source code

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Here is the source code for ch.javasoft.metabolic.generate.ConfiguredGenerator.java

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/*
 * =============================================================================
 * Simplified BSD License, see http://www.opensource.org/licenses/
 * -----------------------------------------------------------------------------
 * Copyright (c) 2008-2009, Marco Terzer, Zurich, Switzerland
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without 
 * modification, are permitted provided that the following conditions are met:
 * 
 *     * Redistributions of source code must retain the above copyright notice, 
 *       this list of conditions and the following disclaimer.
 *     * Redistributions in binary form must reproduce the above copyright 
 *       notice, this list of conditions and the following disclaimer in the 
 *       documentation and/or other materials provided with the distribution.
 *     * Neither the name of the Swiss Federal Institute of Technology Zurich 
 *       nor the names of its contributors may be used to endorse or promote 
 *       products derived from this software without specific prior written 
 *       permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
 * POSSIBILITY OF SUCH DAMAGE.
 * =============================================================================
 */
package ch.javasoft.metabolic.generate;

import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;

import org.dom4j.Element;

import ch.javasoft.io.Print;
import ch.javasoft.metabolic.MetabolicNetwork;
import ch.javasoft.xml.config.StreamConfigParser;
import ch.javasoft.xml.config.XmlConfigException;
import ch.javasoft.xml.config.XmlNode;
import ch.javasoft.xml.config.XmlUtil;

/**
 * The <tt>ConfiguredGenerator</tt> reads from the xml config what to generate
 * (which format, which output sources and options).
 * 
 * Snipplet from such a config file:
 * <pre>
  <generate type="sbml">
     <output type="file">
        <file name="{-out[1]}"/>
     </output>
     <model name="{-name[1]}"/>
  </generate>
  <generate type="matlab">
     <output type="file">
        <file name="{-out[1]}"/>
     </output>
  </generate>
 * </pre>
 */
public class ConfiguredGenerator {
    public static enum XmlElements implements XmlNode {
        metabolic_generate, generate, output, model, struct;
        public String getXmlName() {
            return name().replaceAll("_", "-");
        }
    }

    public static enum XmlAttributes implements XmlNode {
        type, name;
        public String getXmlName() {
            return name().replaceAll("_", "-");
        }
    }

    public static enum GenerateType {
        sbml, matlab;
        String getXmlName() {
            return name().replaceAll("_", "-");
        }

        static GenerateType find(String type) {
            for (GenerateType gType : values()) {
                if (gType.getXmlName().equals(type))
                    return gType;
            }
            return null;
        }
    }

    /**
     * @param parentElement         the element which contains the metabolic_parse child
     * @throws XmlConfigException   if an xml configuration exception occurs,
     *                         for instance due to invalid xml structure
      * @throws IOException         if an i/o exception occurs, for instance 
      *                         caused by file access
     */
    public static void generateConfig(Element parentElement, MetabolicNetwork net)
            throws XmlConfigException, IOException {
        Element parseElement = XmlUtil.getRequiredSingleChildElement(parentElement, XmlElements.metabolic_generate);
        generate(parseElement, net);
    }

    public static void generate(Element metabolicParseElement, MetabolicNetwork net)
            throws XmlConfigException, IOException {
        XmlUtil.checkExpectedElementName(metabolicParseElement, XmlElements.metabolic_generate);
        Element parseElement = XmlUtil.getRequiredSingleChildElement(metabolicParseElement, XmlElements.generate);
        String type = parseElement.attributeValue(XmlAttributes.type.getXmlName());
        GenerateType gType = GenerateType.find(type);
        if (gType == null) {
            throw new XmlConfigException("unknown generate type '" + type + "'", parseElement);
        }
        switch (gType) {
        case sbml:
            generateSbml(parseElement, net);
            return;
        case matlab:
            generateMatlab(parseElement, net);
            return;
        default:
            //should not happen
            throw new XmlConfigException("internal error: unknown parse type " + gType, parseElement);
        }
    }

    /**
     * Generates sbml configured like this:
     * 
     * <pre>
       <generate type="sbml">
     <output type="file">
        <file name="{-out[1]}"/>
     </output>
     <model name="{-name[1]}"/>
       </generate>
     * </pre>
     * @throws XmlConfigException 
     * @throws IOException 
     */
    private static void generateSbml(Element parseElement, MetabolicNetwork net)
            throws XmlConfigException, IOException {
        Element elOutput = XmlUtil.getRequiredSingleChildElement(parseElement, XmlElements.output);
        Element elModel = XmlUtil.getRequiredSingleChildElement(parseElement, XmlElements.model);
        OutputStream out = StreamConfigParser.parseOutputStream(elOutput);
        String modelName = XmlUtil.getRequiredAttributeValue(elModel, XmlAttributes.name);
        new SbmlGenerator(net, modelName).write(out);
    }

    /**
     * Generates matlab configured like this:
     * 
     * <pre>
       <generate type="matlab">
     <output type="file">
        <file name="{-out[1]}"/>
     </output>
     <struct name="metanet"/>
       </generate>
     * </pre>
     * 
     * @throws XmlConfigException 
     * @throws IOException 
     */
    private static void generateMatlab(Element parseElement, MetabolicNetwork net)
            throws XmlConfigException, IOException {
        Element elOutput = XmlUtil.getRequiredSingleChildElement(parseElement, XmlElements.output);
        Element elStruct = XmlUtil.getRequiredSingleChildElement(parseElement, XmlElements.struct);
        OutputStream out = StreamConfigParser.parseOutputStream(elOutput);
        String structName = XmlUtil.getRequiredAttributeValue(elStruct, XmlAttributes.name);
        PrintWriter pw = Print.createWriter(out);
        new MatlabGenerator(structName).writeAll(net, pw);
        pw.flush();
        pw.close();
    }

}