/**
* 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());
}
}