Java tutorial
/** * The contents of this file are subject to the license and copyright * detailed in the LICENSE and NOTICE files at the root of the source * tree and available online at * * http://www.dspace.org/license/ */ package org.dspace.submit.lookup; import gr.ekt.bte.core.Record; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.io.InputStream; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.List; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import org.apache.commons.lang.StringUtils; import org.apache.http.HttpException; import org.apache.http.HttpResponse; import org.apache.http.HttpStatus; import org.apache.http.StatusLine; import org.apache.http.client.HttpClient; import org.apache.http.client.methods.HttpGet; import org.apache.http.client.utils.URIBuilder; import org.apache.http.impl.client.DefaultHttpClient; import org.apache.http.params.CoreConnectionPNames; import org.apache.log4j.Logger; import org.dspace.app.util.XMLUtils; import org.dspace.core.ConfigurationManager; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.xml.sax.SAXException; /** * @author Andrea Bollini * @author Kostas Stamatis * @author Luigi Andrea Pascarelli * @author Panagiotis Koutsourakis */ public class PubmedService { private static final Logger log = Logger.getLogger(PubmedService.class); protected int timeout = 1000; public void setTimeout(int timeout) { this.timeout = timeout; } public Record getByPubmedID(String pubmedid) throws HttpException, IOException, ParserConfigurationException, SAXException { List<String> ids = new ArrayList<String>(); ids.add(pubmedid.trim()); List<Record> items = getByPubmedIDs(ids); if (items != null && items.size() > 0) { return items.get(0); } return null; } public List<Record> search(String title, String author, int year) throws HttpException, IOException { StringBuffer query = new StringBuffer(); if (StringUtils.isNotBlank(title)) { query.append("((").append(title).append("[TI]) OR ("); // [TI] does not always work, book chapter title query.append("(").append(title).append("[book]))"); } if (StringUtils.isNotBlank(author)) { // [FAU] if (query.length() > 0) query.append(" AND "); query.append("(").append(author).append("[AU])"); } if (year != -1) { // [DP] if (query.length() > 0) query.append(" AND "); query.append(year).append("[DP]"); } return search(query.toString()); } public List<Record> search(String query) throws IOException, HttpException { List<Record> results = new ArrayList<>(); if (!ConfigurationManager.getBooleanProperty(SubmissionLookupService.CFG_MODULE, "remoteservice.demo")) { HttpGet method = null; try { HttpClient client = new DefaultHttpClient(); client.getParams().setIntParameter(CoreConnectionPNames.CONNECTION_TIMEOUT, timeout); URIBuilder uriBuilder = new URIBuilder("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"); uriBuilder.addParameter("db", "pubmed"); uriBuilder.addParameter("datetype", "edat"); uriBuilder.addParameter("retmax", "10"); uriBuilder.addParameter("term", query); method = new HttpGet(uriBuilder.build()); // Execute the method. HttpResponse response = client.execute(method); StatusLine statusLine = response.getStatusLine(); int statusCode = statusLine.getStatusCode(); if (statusCode != HttpStatus.SC_OK) { throw new RuntimeException("WS call failed: " + statusLine); } DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setIgnoringComments(true); factory.setIgnoringElementContentWhitespace(true); DocumentBuilder builder; try { builder = factory.newDocumentBuilder(); Document inDoc = builder.parse(response.getEntity().getContent()); Element xmlRoot = inDoc.getDocumentElement(); Element idList = XMLUtils.getSingleElement(xmlRoot, "IdList"); List<String> pubmedIDs = XMLUtils.getElementValueList(idList, "Id"); results = getByPubmedIDs(pubmedIDs); } catch (ParserConfigurationException e1) { log.error(e1.getMessage(), e1); } catch (SAXException e1) { log.error(e1.getMessage(), e1); } } catch (Exception e1) { log.error(e1.getMessage(), e1); } finally { if (method != null) { method.releaseConnection(); } } } else { InputStream stream = null; try { File file = new File(ConfigurationManager.getProperty("dspace.dir") + "/config/crosswalks/demo/pubmed-search.xml"); stream = new FileInputStream(file); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setIgnoringComments(true); factory.setIgnoringElementContentWhitespace(true); DocumentBuilder builder = factory.newDocumentBuilder(); Document inDoc = builder.parse(stream); Element xmlRoot = inDoc.getDocumentElement(); Element idList = XMLUtils.getSingleElement(xmlRoot, "IdList"); List<String> pubmedIDs = XMLUtils.getElementValueList(idList, "Id"); results = getByPubmedIDs(pubmedIDs); } catch (Exception e) { throw new RuntimeException(e.getMessage(), e); } finally { if (stream != null) { try { stream.close(); } catch (IOException e) { e.printStackTrace(); } } } } return results; } public List<Record> getByPubmedIDs(List<String> pubmedIDs) throws HttpException, IOException, ParserConfigurationException, SAXException { List<Record> results = new ArrayList<Record>(); HttpGet method = null; try { HttpClient client = new DefaultHttpClient(); client.getParams().setIntParameter(CoreConnectionPNames.CONNECTION_TIMEOUT, 5 * timeout); try { URIBuilder uriBuilder = new URIBuilder("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"); uriBuilder.addParameter("db", "pubmed"); uriBuilder.addParameter("retmode", "xml"); uriBuilder.addParameter("rettype", "full"); uriBuilder.addParameter("id", StringUtils.join(pubmedIDs.iterator(), ",")); method = new HttpGet(uriBuilder.build()); } catch (URISyntaxException ex) { throw new RuntimeException("Request not sent", ex); } // Execute the method. HttpResponse response = client.execute(method); StatusLine statusLine = response.getStatusLine(); int statusCode = statusLine.getStatusCode(); if (statusCode != HttpStatus.SC_OK) { throw new RuntimeException("WS call failed: " + statusLine); } DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setIgnoringComments(true); factory.setIgnoringElementContentWhitespace(true); DocumentBuilder builder = factory.newDocumentBuilder(); Document inDoc = builder.parse(response.getEntity().getContent()); Element xmlRoot = inDoc.getDocumentElement(); List<Element> pubArticles = XMLUtils.getElementList(xmlRoot, "PubmedArticle"); for (Element xmlArticle : pubArticles) { Record pubmedItem = null; try { pubmedItem = PubmedUtils.convertPubmedDomToRecord(xmlArticle); results.add(pubmedItem); } catch (Exception e) { throw new RuntimeException("PubmedID is not valid or not exist: " + e.getMessage(), e); } } return results; } finally { if (method != null) { method.releaseConnection(); } } } public List<Record> search(String doi, String pmid) throws HttpException, IOException { StringBuffer query = new StringBuffer(); if (StringUtils.isNotBlank(doi)) { query.append(doi); query.append("[AID]"); } if (StringUtils.isNotBlank(pmid)) { // [FAU] if (query.length() > 0) query.append(" OR "); query.append(pmid).append("[PMID]"); } return search(query.toString()); } }