server/compbio/ws/jpred/JpredWS.java

   1 package compbio.ws.jpred;
   2
   3 import java.io.IOException;
   4 import java.util.ArrayList;
   5 import java.util.List;
   6
   7 import javax.jws.WebService;
   8
   9 import org.apache.log4j.Logger;
  10
  11 import compbio.beans.ProteinBean;
  12 import compbio.cassandra.CassandraNativeConnector;
  13 import compbio.cassandra.readers.SequenceReader;
  14 import compbio.engine.archive.ArchivedJob;
  15
  16 /**
  17  * Implementation of the Jpred web service in ProteoCache
  18  *
  19  * @author Alexander Sherstnev
  20  * @author Natasha Sherstneva
  21  *
  22  * @version 1.0
  23  * @since Jan 2014
  24  */
  25 @WebService(endpointInterface = "compbio.ws.jpred.Jpred", targetNamespace = "http://server.proteocache.ws", serviceName = "ProteoCacheWS", portName = "ProteoCacheWSPort")
  26 public class JpredWS implements Jpred {
  27         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  28         String jobid;
  29
  30         private List<String> findJobs(String sequence, String program, String version) {
  31                 CassandraNativeConnector dbconnector = new CassandraNativeConnector();
  32                 SequenceReader reader = new SequenceReader();
  33                 reader.setSession(dbconnector.getSession());
  34                 log.debug("ProteoCacheWS is connected:\n search for sequence: " + sequence + "\ncalculated with  " + program + " (version: "
  35                                 + version + ")");
  36                 List<String> jobs = new ArrayList<String>();
  37                 List<ProteinBean> result = reader.readProteins(sequence, "whole");
  38                 if (null != result) {
  39                         for (ProteinBean protein : result) {
  40                                 List<String> thejobs = protein.getJobid();
  41                                 jobid = thejobs.get(0);
  42                                 for (String job : thejobs) {
  43                                         jobs.add(job);
  44                                 }
  45                         }
  46                 }
  47                 return jobs;
  48         }
  49
  50         @Override
  51         public String findSequence(String sequence, String program, String version) {
  52                 List<String> jobs = findJobs(sequence, program, version);
  53                 if (null != jobs) {
  54                         return jobs.size() + " jobs found";
  55                 }
  56                 return "no jobs found";
  57         }
  58
  59         @Override
  60         public String findJobForSequence(String sequence, String program, String version) {
  61                 List<String> jobs = findJobs(sequence, program, version);
  62                 if (null != jobs) {
  63                         for (String job : jobs) {
  64                                 String link = null;
  65                                 ArchivedJob aj = new ArchivedJob(job);
  66                                 try {
  67                                         link = aj.prepareJobArchiveToWeb();
  68                                 } catch (IOException e) {
  69                                         log.error("JpredWS.findSequence: IO exception with job archive file");
  70                                         log.error(e.getLocalizedMessage(), e.getCause());
  71                                 }
  72                                 if (null != link) {
  73                                         return job;
  74                                 }
  75                         }
  76                         return "";
  77                 }
  78                 return "";
  79         }
  80
  81         @Override
  82         public String getArchive(String jobid) {
  83                 String link = null;
  84                 ArchivedJob aj = new ArchivedJob(jobid);
  85                 try {
  86                         link = aj.prepareJobArchiveToWeb();
  87                 } catch (IOException e) {
  88                         log.error("JpredWS.findSequence: IO exception with job archive file");
  89                         log.error(e.getLocalizedMessage(), e.getCause());
  90                 }
  91                 // if the archive file is not available null is returned
  92                 return link;
  93         }
  94
  95 }