Example usage for org.xml.sax SAXException SAXException

Introduction

In this page you can find the example usage for org.xml.sax SAXException SAXException.

Prototype

public SAXException(Exception e)

Source Link

Document

Create a new SAXException wrapping an existing exception.

Usage

From source file:org.intermine.bio.dataconversion.KeggConverter.java

private void processMapTitleFile(Reader reader) throws IOException, ObjectStoreException, SAXException {
    Iterator lineIter = FormattedTextParser.parseTabDelimitedReader(reader);

    while (lineIter.hasNext()) {
        String[] line = (String[]) lineIter.next();
        String pathwayKey = line[0];
        String pathwayName = line[1];
        if (!StringUtils.isEmpty(pathwayKey)) {
            Item pathway = getPathway(pathwayKey);
            pathway.setAttribute("name", pathwayName);
            try {
                store(pathway);//  w  ww  . java  2s . c  om
            } catch (ObjectStoreException e) {
                throw new SAXException(e);
            }
        }
    }
}

From source file:org.intermine.bio.dataconversion.KeggConverter.java

private void processGeneMapFile(Reader reader) throws Exception {

    Iterator lineIter = FormattedTextParser.parseDelimitedReader(reader, '|');

    while (lineIter.hasNext()) {
        String[] line = (String[]) lineIter.next();
        String entrezId = line[0];
        String[] pathwayIds = line[4].split(" ");
        String geneId = line[2];/* ww  w  .  ja  v  a2 s  . c  om*/
        Item gene = getGene(geneId);
        gene.setAttribute("secondaryIdentifier", entrezId);

        for (int i = 0; i < pathwayIds.length; i++) {
            //System.out.println("test "+geneId+" "+i);
            String pathwayId = pathwayIds[i];
            if (!StringUtils.isEmpty(pathwayId)) {
                //System.out.println("pathwayId found: "+pathwayId);
                Item pathway = getPathway(pathwayId);
                if (pathway == null) {
                    System.out.println("pathway not found: " + geneId + " " + pathwayId);
                }
                gene.addToCollection("pathways", pathway);
            }
        }

        try {
            store(gene);
        } catch (ObjectStoreException e) {
            throw new SAXException(e);
        }
    }
}

From source file:validation.xslt.handler.XsltResultHandler.java

/** SAX handling, Receive notification of the end of an element.
 * // w w  w. ja  v  a 2s.  com
 * @param namespaceURI The Namespace URI, or the empty string if the element has no Namespace URI or if Namespace processing is not being performed.
 * @param localName The local name (without prefix), or the empty string if Namespace processing is not being performed.
 * @param qName The qualified name (with prefix), or the empty string if qualified names are not available.
 * @throws SAXException Any SAX exception, possibly wrapping another exception.
 */
@Override
public void endElement(String namespaceURI, String localName, String qName) throws SAXException {
    if (qName.compareTo(FAILED) == 0) {
        if (failed) {
            buffer.append("</");
            buffer.append(qName);
            buffer.append(">");
            throw new SAXException(NORMAL_STATUS);
        }
    }
}