edu.scripps.fl.pubchem.app.cids.WriteSDFStage.java Source code

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Here is the source code for edu.scripps.fl.pubchem.app.cids.WriteSDFStage.java

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/*
 * Copyright 2010 The Scripps Research Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.scripps.fl.pubchem.app.cids;

import java.io.File;
import java.net.URL;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.zip.GZIPInputStream;

import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.pipeline.StageException;
import org.apache.commons.pipeline.stage.BaseStage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class WriteSDFStage extends BaseStage {

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

    private AtomicInteger counter = new AtomicInteger();

    private String outputFile = "";

    public String getOutputFile() {
        return outputFile;
    }

    public void setOutputFile(String outputFile) {
        this.outputFile = outputFile;
    }

    @Override
    public void process(Object obj) throws StageException {
        URL url = (URL) obj;
        try {
            File outputFile = newOutputFile(counter.incrementAndGet());
            logger.info("Writing SDF file: " + outputFile);
            IOUtils.copy(new GZIPInputStream(url.openStream()), FileUtils.openOutputStream(outputFile));
            emit(outputFile);
        } catch (Exception ex) {
            throw new StageException(this, ex);
        }
    }

    public File newOutputFile(int index) {
        String outputFile = getOutputFile();
        outputFile = new File(outputFile).getAbsoluteFile().toString();
        String path = FilenameUtils.getFullPath(outputFile);
        String name = FilenameUtils.getBaseName(outputFile);
        String ext = FilenameUtils.getExtension(outputFile);
        File file = new File(path, name + "-" + index + "." + ext);
        return file;
    }
}