Example usage for org.apache.commons.pipeline StageException StageException

Introduction

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

Prototype

public StageException(Stage source, Throwable cause) 

Source Link

Document

Constructs an instance of StageException with the specified detail message and cause

Usage

From source file:edu.scripps.fl.pubchem.app.relations.DeleteRelationsStage.java

@Override
public void process(Object obj) throws StageException {
    Integer id = (Integer) obj;
    try {/*from w  ww . ja  va 2 s.c  om*/
        Query query = getSession().createQuery("delete from Relation where fromId = ? and fromDb = ?");
        query.setInteger(0, id);
        query.setString(1, "pcassay");
        query.executeUpdate();
        emit(id);
    } catch (Exception ex) {
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.summary.NodesStage.java

@Override
public void innerProcess(Object obj) throws StageException {
    Document document = (Document) obj;
    try {//from w  w w . j av a 2s.  c  om
        Element setElem = (Element) document.selectSingleNode("/eSummaryResult/DocumentSummarySet");
        Iterator<Node> iter = setElem.nodeIterator();
        for (; iter.hasNext();) {
            Node node = iter.next();
            if ("DocumentSummary".equals(node.getName())) // eUtils version 2.0 
                emit(node);
        }
    } catch (Exception ex) {
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pipeline.DocumentStage.java

@Override
public void innerProcess(Object obj) throws StageException {
    File file = (File) obj;
    try {//from   w w  w . j  ava 2s.com
        Document document = EUtilsWebSession.getInstance().getDocument(new FileInputStream(file));
        file.deleteOnExit();
        emit(document);
    } catch (Exception ex) {
        log.error(String.format("Problem with file %s: %s", file, ex.getMessage()));
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.cids.FetchSDFStage.java

@Override
public void process(Object obj) throws StageException {
    List<Number> ids = (List<Number>) obj;
    try {//from   w w w . j  a  va2 s .  c om
        int[] list = (int[]) ConvertUtils.convert(ids, int[].class);
        URL url = PUGSoapFactory.getInstance().getSDFilefromCIDs(list);
        System.out.println("SDF File URL: " + url);
        emit(url);
    } catch (Exception ex) {
        ex.printStackTrace();
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.relations.ProcessRelationsStage.java

@Override
public void process(Object obj) throws StageException {
    Document document = (Document) obj;
    try {/*  ww w .  j  a  va2 s  .  co  m*/
        int relations = PubChemFactory.getInstance().populateRelations(getSession(), document);
    } catch (Exception ex) {

        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.results.DownloadCsvStage.java

@Override
public void process(Object obj) throws StageException {
    Integer aid = (Integer) obj;
    try {/*from w ww.java  2  s . c  om*/
        InputStream is = PubChemFactory.getInstance().getCsv(getDataUrl(), aid);
        emit(new Object[] { aid, is });
    } catch (IOException ex) {
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.relations.ELinkStage.java

@Override
public void preprocess() throws StageException {
    try {//from w w  w  . j a v  a2  s .  com
        Set<String> dbs = EUtilsWebSession.getInstance().getDatabases();
        dbs.remove("pccompound");
        dbs.remove("pcsubstance");
        databases = StringUtils.join(dbs, ",");
    } catch (Exception ex) {
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.results.DeleteResultsStage.java

@Override
public void process(Object obj) throws StageException {
    Integer aid = (Integer) obj;
    try {/*w ww .j  a  v a  2 s  .c  om*/
        Query query = getSession().createQuery("from PCAssay where AID = :aid");
        query.setParameter("aid", aid);
        PCAssay assay = (PCAssay) query.uniqueResult();
        query = getSession().createQuery("delete from PCAssayResult where assay.id = :id");
        query.setParameter("id", assay.getId());
        int deleted = query.executeUpdate();
        emit(aid);
    } catch (Exception ex) {
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pubchem.app.summary.ESummaryStage.java

@Override
public void innerProcess(Object obj) throws StageException {
    try {/*w  ww  .  ja v  a  2s.c  o m*/
        Thread.sleep(333);
        List<Long> aids = (List<Long>) obj;
        InputStream in = EUtilsWebSession.getInstance().getSummaries(aids, "pcassay");
        File file = File.createTempFile("pubchem", "summary.xml");
        log.info(String.format("Downloaded %s summaries to %s", aids.size(), file));
        IOUtils.copy(in, new FileOutputStream(file));
        emit(file);
    } catch (Exception ex) {
        throw new StageException(this, ex);
    }
}

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From source file:edu.scripps.fl.pipeline.StatelessCommitStage.java

@Override
public void process(Object obj) throws StageException {
    try {/*  www .j  a va2  s. c om*/
        StatelessSession session = getStatelessSession();
        int count = counter.incrementAndGet();
        doSave(obj);
        if (count % getCommitFrequency() == 0) {
            getTransaction().commit();
            setTransaction(session.beginTransaction());
        }
    } catch (Exception ex) {
        throw new StageException(this, ex);
    }
}

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