org.openscience.cdk.applications.taverna.io.ARFFFileReaderActivity.java Source code

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Here is the source code for org.openscience.cdk.applications.taverna.io.ARFFFileReaderActivity.java

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/*
 * Copyright (C) 2010 by Andreas Truszkowski <ATruszkowski@gmx.de>
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 */
package org.openscience.cdk.applications.taverna.io;

import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;

import net.sf.taverna.t2.reference.ExternalReferenceSPI;
import net.sf.taverna.t2.reference.impl.external.file.FileReference;
import net.sf.taverna.t2.reference.impl.external.object.InlineStringReference;

import org.openscience.cdk.applications.taverna.AbstractCDKActivity;
import org.openscience.cdk.applications.taverna.CDKTavernaConstants;
import org.openscience.cdk.applications.taverna.CDKTavernaException;
import org.openscience.cdk.applications.taverna.basicutilities.ErrorLogger;

import weka.core.Instances;
import weka.core.converters.ConverterUtils.DataSource;

/**
 * Class which represents the ARFF file reader activity.
 * 
 * @author Andreas Truzskowski
 * 
 */
public class ARFFFileReaderActivity extends AbstractCDKActivity {

    public static final String ARFF_FILE_READER_ACTIVITY = "ARFF File Reader";

    /**
     * Creates a new instance.
     */
    public ARFFFileReaderActivity() {
        this.INPUT_PORTS = new String[] { "Files" };
        this.OUTPUT_PORTS = new String[] { "Weka Datasets" };
    }

    @Override
    protected void addInputPorts() {
        List<Class<? extends ExternalReferenceSPI>> expectedReferences = new ArrayList<Class<? extends ExternalReferenceSPI>>();
        expectedReferences.add(FileReference.class);
        expectedReferences.add(InlineStringReference.class);
        addInput(this.INPUT_PORTS[0], 1, false, expectedReferences, null);
    }

    @Override
    protected void addOutputPorts() {
        addOutput(this.OUTPUT_PORTS[0], 1);
    }

    @Override
    public void work() throws Exception {
        // Get input
        List<File> files = this.getInputAsFileList(this.INPUT_PORTS[0]);
        // Do work
        List<Instances> datasets = new LinkedList<Instances>();
        for (File file : files) {
            try {
                Instances instances = DataSource.read(file.getPath());
                int lastAttr = instances.numAttributes() - 1;
                if (instances.classIndex() == -1 && instances.attribute(lastAttr).name().equals("Class")) {
                    instances.setClassIndex(lastAttr);
                }
                datasets.add(instances);
            } catch (Exception e) {
                ErrorLogger.getInstance().writeError(CDKTavernaException.READ_FILE_ERROR + file,
                        this.getActivityName(), e);
            }
        }
        // Set output
        this.setOutputAsObjectList(datasets, this.OUTPUT_PORTS[0]);
    }

    @Override
    public String getActivityName() {
        return ARFFFileReaderActivity.ARFF_FILE_READER_ACTIVITY;
    }

    @Override
    public HashMap<String, Object> getAdditionalProperties() {
        HashMap<String, Object> properties = new HashMap<String, Object>();
        return properties;
    }

    @Override
    public String getDescription() {
        return "Description: " + ARFFFileReaderActivity.ARFF_FILE_READER_ACTIVITY;
    }

    @Override
    public String getFolderName() {
        return CDKTavernaConstants.IO_FOLDER_NAME;
    }

}