Makefile

.PHONY:all
PROXY1= ## -httpproxy:host:port
PROXY2= ## -Dhttp.proxyHost=host -Dhttp.proxyPort=port

all: Test.class
	java ${PROXY2} -cp tmp:. Test


Test.class : Test.java tmp/uk/ac/ebi/webservices/whatizit/ws/ObjectFactory.java tmp/gov/nih/nlm/ncbi/eutils/entrez/eutils/esearch/ObjectFactory.java
	javac -sourcepath tmp:. $<
		
tmp/uk/ac/ebi/webservices/whatizit/ws/ObjectFactory.java:
	mkdir -p tmp
	wsimport -d tmp -keep ${PROXY1} "http://www.ebi.ac.uk/webservices/whatizit/ws?wsdl"
	
tmp/gov/nih/nlm/ncbi/eutils/entrez/eutils/esearch/ObjectFactory.java:
	mkdir -p tmp
	curl -o tmp/esearch.xsd "https://raw.github.com/lindenb/xsd-sandbox/master/schemas/bio/ncbi/esearch.xsd"
	xjc -d tmp  -p gov.nih.nlm.ncbi.eutils.entrez.eutils.esearch tmp/esearch.xsd

Test.java

import java.io.InputStream;
import java.net.URL;
import java.net.URLEncoder;
import java.util.HashSet;
import java.util.Set;
import java.util.logging.Logger;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;

import javax.xml.transform.stream.StreamSource;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpression;
import javax.xml.xpath.XPathFactory;

import org.w3c.dom.Document;
import org.w3c.dom.Node;

/* generated with wsimport */
import uk.ac.ebi.webservices.whatizit.ws.*;
import gov.nih.nlm.ncbi.eutils.entrez.eutils.esearch.*;


public class Test
{
private static Logger LOG=Logger.getLogger("testwhatizit");
private gov.nih.nlm.ncbi.eutils.entrez.eutils.esearch.ObjectFactory _foo_javac=null;
public void run(String[] args) throws Exception
	{
	final String errorPrefix="################################################################## ";
	XPath xpath=XPathFactory.newInstance().newXPath();
	XPathExpression abstractExpr=xpath.compile(
		"/PubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract"
		);
	
	Whatizit_Service service=new Whatizit_Service();
	
	LOG.info("getting pipelines");
	Whatizit whatizit=service.getPipeline();
	
	LOG.info("getting enabled pipelines");
	Set<String> pipelines=new HashSet<String>();
	for(SelectItem status:whatizit.getPipelinesStatus())
		{
		if(status.isDisabled()) continue;
		System.out.println("adding pipeline "+status.getLabel()+" "+status.getDescription());
		pipelines.add(status.getLabel());
		}
	
	
	DocumentBuilderFactory factory=DocumentBuilderFactory.newInstance();
	factory.setCoalescing(true);
	factory.setExpandEntityReferences(true);
	factory.setValidating(false);
	factory.setIgnoringComments(true);
	DocumentBuilder builder=factory.newDocumentBuilder();
	
	
	String terms="Exome[title]";
	LOG.info("searching pubmed for "+terms);
	String uri="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="+
			URLEncoder.encode(terms,"UTF-8")
			;
	javax.xml.bind.JAXBContext jaxbCtxt=javax.xml.bind.JAXBContext.newInstance(ESearchResult.class);
	javax.xml.bind.Unmarshaller unmarshaller=jaxbCtxt.createUnmarshaller();
	InputStream in=new URL(uri).openStream();
	ESearchResult eSearchResult=unmarshaller.unmarshal(new StreamSource(in),ESearchResult.class).getValue();
	in.close();
	
	IdList idList=eSearchResult.getIdList();
	if(idList==null) return ;
	for(Integer pmid:idList.getId())
		{
		LOG.info("PMID is:"+pmid);
		
		Document dom=builder.parse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id="+pmid);
		Node abstractNode=(Node)abstractExpr.evaluate(dom, XPathConstants.NODE);
		if(abstractNode==null) continue;
		String content=abstractNode.getTextContent();
		if(content==null || content.trim().isEmpty()) continue;
		
		LOG.info("content is "+content);
		
		for(String pipeline:pipelines)
			{
			  try
		    		{
				LOG.info("contact MID "+pmid+" vs pipeline:"+pipeline);
				String result = whatizit.contact(pipeline, content, false);
			    System.out.println("contact output is :"+result); 
			    	}
			    catch(Exception err)
			    	{
			    	err.printStackTrace();
			    	LOG.severe(errorPrefix+err.getMessage()+" content:"+content);
			    	}
		    
			    try
			    	{
			    	LOG.info("queryPmid : PMID "+pmid+" vs pipeline:"+pipeline);
			    	String xml = whatizit.queryPmid(pipeline, ""+pmid);
				    System.err.println(pipeline+":\n"+xml);
			    	}
			    catch(Exception err)
			    	{
			    	err.printStackTrace();
			    	LOG.severe(errorPrefix+pipeline+":"+err.getMessage()+" content:"+content);
			    	}
		    	
		    
			    
			     try
			    	{
			    	LOG.info("invoking whatizit.search with pipeline:"+pipeline);
				Search search=new Search();
			
				search.setPipelineName(pipeline);
				search.setQuery(content);
				search.setLimit(10);
				SearchResponse src=whatizit.search(search);
				 System.out.println("SearchResponse:"+src); 
				}
			  catch(Exception err)
			    	{
			    	err.printStackTrace();
			    	LOG.severe(errorPrefix+pipeline+":"+err.getMessage()+" content:"+content);
			    	}
			}
		}
	 
	}
	
	
public static void main(String[] args) throws Exception
	{
	new Test().run(args);
	}
}