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.JobReader;
  14 import compbio.cassandra.readers.SequenceReader;
  15 import compbio.engine.archive.ArchivedJob;
  16
  17 /**
  18  * Implementation of the Jpred web service in ProteoCache
  19  *
  20  * @author Alexander Sherstnev
  21  * @author Natasha Sherstneva
  22  *
  23  * @version 1.0
  24  * @since Jan 2014
  25  */
  26 @WebService(endpointInterface = "compbio.ws.jpred.Jpred", targetNamespace = "http://server.proteocache.ws", serviceName = "ProteoCacheWS", portName = "ProteoCacheWSPort")
  27 public class JpredWS implements Jpred {
  28         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  29         String jobid;
  30
  31         private List<String> findJobs(String sequence, String program, String version) {
  32                 CassandraNativeConnector dbconnector = new CassandraNativeConnector();
  33                 SequenceReader reader = new SequenceReader();
  34                 reader.setSession(dbconnector.getSession());
  35                 log.debug("ProteoCacheWS is connected:\n search for sequence: " + sequence + "\ncalculated with  " + program + " (version: "
  36                                 + version + ")");
  37                 List<String> jobs = new ArrayList<String>();
  38                 List<ProteinBean> result = reader.readProteins(sequence, "whole");
  39                 if (null != result) {
  40                         for (ProteinBean protein : result) {
  41                                 List<String> thejobs = protein.getJobid();
  42                                 jobid = thejobs.get(0);
  43                                 for (String job : thejobs) {
  44                                         jobs.add(job);
  45                                 }
  46                         }
  47                 }
  48                 return jobs;
  49         }
  50
  51         @Override
  52         public int findSequence(String sequence, String program, String version) {
  53                 List<String> jobs = findJobs(sequence, program, version);
  54                 if (null != jobs) {
  55                         return jobs.size();
  56                 }
  57                 return 0;
  58         }
  59
  60         @Override
  61         public String findJobForSequence(String sequence, String program, String version) {
  62                 List<String> jobs = findJobs(sequence, program, version);
  63                 if (null != jobs) {
  64                         for (String job : jobs) {
  65                                 String link = null;
  66                                 ArchivedJob aj = new ArchivedJob(job);
  67                                 try {
  68                                         link = aj.prepareJobArchiveToWeb();
  69                                 } catch (IOException e) {
  70                                         log.error("JpredWS.findSequence: IO exception with job archive file");
  71                                         log.error(e.getLocalizedMessage(), e.getCause());
  72                                 }
  73                                 if (null != link) {
  74                                         return job;
  75                                 }
  76                         }
  77                         return "";
  78                 }
  79                 return "";
  80         }
  81
  82         @Override
  83         public String getArchive(String jobid) {
  84                 String link = null;
  85                 ArchivedJob aj = new ArchivedJob(jobid);
  86                 try {
  87                         link = aj.prepareJobArchiveToWeb();
  88                 } catch (IOException e) {
  89                         log.error("JpredWS.findSequence: IO exception with job archive file");
  90                         log.error(e.getLocalizedMessage(), e.getCause());
  91                 }
  92                 // if the archive file is not available null is returned
  93                 return link;
  94         }
  95
  96         @Override
  97         public int jobExists(String jobid) {
  98                 CassandraNativeConnector dbconnector = new CassandraNativeConnector();
  99                 JobReader reader = new JobReader();
 100                 reader.setSession(dbconnector.getSession());
 101                 if (null != reader.readJobLog(jobid)) {
 102                         return 1;
 103                 }
 104                 return 0;
 105         }
 106
 107 }