Examples with PropertyEnricherException org.eol.globi.service.PropertyEnricherException used on opensource projects

Example 11 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class TaxonCacheService method initTaxonCache.

private void initTaxonCache() throws PropertyEnricherException {
    DB db = initDb("taxonCache");
    String taxonCacheName = "taxonCacheById";
    if (db.exists(taxonCacheName)) {
        LOG.info("re-using pre-existing cache");
        resolvedIdToTaxonMap = db.getTreeMap(taxonCacheName);
    } else {
        LOG.info("no pre-existing cache found, rebuilding...");
        LOG.info("taxon cache loading [" + taxonCacheResource + "]...");
        StopWatch watch = new StopWatch();
        watch.start();
        try {
            resolvedIdToTaxonMap = db.createTreeMap(taxonCacheName).pumpPresort(100000).pumpIgnoreDuplicates().pumpSource(taxonCacheIterator(taxonCacheResource, new LineSkipper() {

                @Override
                public boolean shouldSkipLine(LabeledCSVParser parser) {
                    final Taxon taxon = TaxonCacheParser.parseLine(parser);
                    return StringUtils.isBlank(taxon.getPath());
                }
            })).keySerializer(BTreeKeySerializer.STRING).make();
        } catch (IOException e) {
            throw new PropertyEnricherException("failed to instantiate taxonCache: [" + e.getMessage() + "]", e);
        }
        watch.stop();
        LOG.info("taxon cache loading [" + taxonCacheResource + "] done.");
        logCacheLoadStats(watch.getTime(), resolvedIdToTaxonMap.size());
        watch.reset();
    }
}

Example 12 with PropertyEnricherException

use of org.eol.globi.service.PropertyEnricherException in project eol-globi-data by jhpoelen.

the class XmlUtil method extractPathNoJoin.

public static List<String> extractPathNoJoin(String xmlContent, String elementName, String valuePrefix, String valueSuffix) throws PropertyEnricherException {
    List<String> ranks = new ArrayList<String>();
    try {
        InputStream is = IOUtils.toInputStream(xmlContent, "UTF-8");
        String xpathExpr = "//*[local-name() = '" + elementName + "']";
        NodeList nodes = (NodeList) applyXPath(is, xpathExpr, XPathConstants.NODESET);
        for (int i = 0; i < nodes.getLength(); i++) {
            Node item = nodes.item(i);
            Node firstChild = item.getFirstChild();
            if (null != firstChild) {
                String nodeValue = firstChild.getNodeValue();
                if (StringUtils.isNotBlank(nodeValue)) {
                    ranks.add(valuePrefix + nodeValue + valueSuffix);
                }
            }
        }
    } catch (Exception e) {
        throw new PropertyEnricherException("failed to handle response [" + xmlContent + "]", e);
    }
    return ranks;
}