Example usage for org.apache.commons.pipeline Pipeline getStages

Introduction

In this page you can find the example usage for org.apache.commons.pipeline Pipeline getStages.

Prototype

public final List<Stage> getStages() 

Source Link

Document

Returns an unmodifiable list of stages that have been added to this rendering.

Usage

From source file:edu.scripps.fl.pubchem.app.RelatedCurveProcessor.java

public static void main(String[] args) throws Exception {
    CommandLineHandler clh = new CommandLineHandler();
    args = clh.handle(args);//w ww  . j a va 2 s.co  m

    Integer[] list = (Integer[]) ConvertUtils.convert(args, Integer[].class);
    Integer referenceAid = list[0];
    Integer[] relatedAids = new Integer[list.length - 1];
    System.arraycopy(list, 1, relatedAids, 0, list.length - 1);

    URL url = PipelineUtils.class.getClassLoader()
            .getResource("edu/scripps/fl/pubchem/RelatedCurvesPipeline.xml");
    Pipeline pipeline = new PipelineUtils().createPipeline(url, Arrays.asList(relatedAids));
    List<Stage> stages = pipeline.getStages();
    BeanUtils.setProperty(stages.get(1), "referenceAID", referenceAid);
    pipeline.run();
    new PipelineUtils().logErrors(pipeline);
}

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From source file:edu.scripps.fl.pubchem.app.CIDDownloader.java

public void process(Iterator<?> iterator) throws Exception {
    URL url = getClass().getResource("/edu/scripps/fl/pubchem/SDFDownloadPipeline.xml");
    Pipeline pipeline = new PipelineUtils().createPipeline(url, iterator);
    List<Stage> stages = pipeline.getStages();
    pipeline.run();//w  w  w . ja va2  s  .c  o m
    new PipelineUtils().logErrors(pipeline);
}

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From source file:edu.scripps.fl.pubchem.app.AssayDownloader.java

public Pipeline assayXML(final Set<Long> processAids) throws Exception {
    URL url = PipelineUtils.class.getClassLoader()
            .getResource("edu/scripps/fl/pubchem/BioAssayXMLPipeline.xml");
    Pipeline pipeline = new PipelineUtils().createPipeline(url, processAids);
    for (Stage stage : pipeline.getStages())
        if (stage instanceof ReadDocumentStage)
            ((ReadDocumentStage) stage).setDataUrl(dataUrl);
    pipeline.run();/*from  w w  w . j  ava  2 s  .  c om*/
    new PipelineUtils().logErrors(pipeline);
    return pipeline;

}

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From source file:edu.scripps.fl.pubchem.app.ResultDownloader.java

protected void process(Iterator<Integer> processAids) throws Exception {
    URL url = PipelineUtils.class.getClassLoader()
            .getResource("edu/scripps/fl/pubchem/BioAssayResultsPipeline.xml");
    Pipeline pipeline = new PipelineUtils().createPipeline(url, processAids,
            CollectionUtils.createMap("CsvResultsSource", SourceColumnsInfo.Type.FTP));
    for (Stage stage : pipeline.getStages())
        if (stage instanceof DownloadCsvStage)
            ((DownloadCsvStage) stage).setDataUrl(dataUrl);
    pipeline.run();//  ww  w.j  a v a 2s  .  c  om
    new PipelineUtils().logErrors(pipeline);
}

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