package ubic.basecode.ontology.ncbo;
   
   import org.apache.commons.lang3.StringUtils;
   import org.apache.commons.lang3.exception.ExceptionUtils;
   import org.slf4j.Logger;
   import org.slf4j.LoggerFactory;
   import org.w3c.dom.Document;
   import org.w3c.dom.Element;
   import org.w3c.dom.Node;
  import org.w3c.dom.NodeList;
  import ubic.basecode.util.Configuration;
  
  import javax.xml.parsers.DocumentBuilder;
  import javax.xml.parsers.DocumentBuilderFactory;
  import java.io.InputStream;
  import java.net.URL;
  import java.util.Collection;
  import java.util.HashSet;
  import java.util.Map;
  
  /**
   * to use the OMIM api
   * TODO Document Me
   *
   * @author Nicolas
   */
  public class OmimAnnotatorClient {
  
      private static String OMIM_API_URL = "http://api.omim.org/api/entry";
  
      // this OMIM_API_KEY needs to be added to basecode.properties
      private static String OMIM_API_KEY = Configuration.getString( "omim.api.key" );
  
      private static Logger log = LoggerFactory.getLogger( OmimAnnotatorClient.class );
  
      /**
       * Giving a set of OMIM id return for each id its list of related publication
       *
       * @param omimIds      the omimIds we want to find the publication
       * @param mimToPubmeds the results, pass by reference for multiple calls, limit of size 10
       */
      public static Map<Long, Collection<Long>> findLinkedPublications( Collection<Long> omimIds,
          Map<Long, Collection<Long>> mimToPubmeds ) throws InterruptedException {
  
          if ( omimIds.size() > 10 || omimIds.isEmpty() ) {
              throw new IllegalArgumentException( "Size of the Omim ids must be between 1 and 10,  Size Found: "
                  + omimIds.size() );
          }
  
          // From OMIM documentation : The rate of requests is currently limited to 4 requests per second.
          // if too many request are made, the ip gets ban, sleep makes this not possible
          Thread.sleep( 700 );
  
          String omimIdsAsString = StringUtils.removeEnd( StringUtils.join( omimIds, "," ), "," );
  
          String url = OMIM_API_URL + "?mimNumber=" + omimIdsAsString + "&format=xml&include=referenceList&apiKey="
              + OMIM_API_KEY;
  
          log.info( "request url: " + url );
  
          try ( InputStream response = new URL( url ).openConnection().getInputStream() ) {
              return findPublications( response, mimToPubmeds );
          } catch ( Exception e ) {
              log.error( ExceptionUtils.getStackTrace( e ) );
              return null;
          }
      }
  
      private static Map<Long, Collection<Long>> findPublications( InputStream response,
          Map<Long, Collection<Long>> mimToPubmeds ) throws Exception {
  
          DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
          DocumentBuilder builder = factory.newDocumentBuilder();
          Document document = builder.parse( response );
          NodeList nodes = document.getElementsByTagName( "reference" );
  
          // for each response receive, populate the return objects
          for ( int temp = 0; temp < nodes.getLength(); temp++ ) {
  
              Node nNode = nodes.item( temp );
              Element eElement = ( Element ) nNode;
  
              if ( eElement.getElementsByTagName( "pubmedID" ).item( 0 ) != null
                  && eElement.getElementsByTagName( "mimNumber" ).item( 0 ) != null ) {
  
                  Long pubmedID = new Long( eElement.getElementsByTagName( "pubmedID" ).item( 0 ).getTextContent() );
                  Long mimNumber = new Long( eElement.getElementsByTagName( "mimNumber" ).item( 0 ).getTextContent() );
  
                  Collection<Long> pubmeds = new HashSet<>();
  
                  if ( mimToPubmeds.get( mimNumber ) != null ) {
                      pubmeds = mimToPubmeds.get( mimNumber );
                  }
                  pubmeds.add( pubmedID );
  
                  mimToPubmeds.put( mimNumber, pubmeds );
              }
          }
          return mimToPubmeds;
     }
 
 }