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 @WebService(endpointInterface = "compbio.ws.jpred.Jpred", targetNamespace = "http://server.proteocache.ws", serviceName = "ProteoCacheWS", portName = "ProteoCacheWSPort")
  17 public class JpredWS implements Jpred {
  18         private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
  19         String jobid;
  20
  21         private List<String> findJobs(String sequence, String program, String version) {
  22                 CassandraNativeConnector dbconnector = new CassandraNativeConnector();
  23                 SequenceReader reader = new SequenceReader();
  24                 reader.setSession(dbconnector.getSession());
  25                 log.debug("ProteoCacheWS is connected:\n search for sequence: " + sequence + "\ncalculated with  " + program + " (version: "
  26                                 + version + ")");
  27                 List<String> jobs = new ArrayList<String>();
  28                 List<ProteinBean> result = reader.readProteins(sequence, "whole");
  29                 if (null != result) {
  30                         for (ProteinBean protein : result) {
  31                                 List<String> thejobs = protein.getJobid();
  32                                 jobid = thejobs.get(0);
  33                                 for (String job : thejobs) {
  34                                         jobs.add(job);
  35                                 }
  36                         }
  37                 }
  38                 return jobs;
  39         }
  40
  41         @Override
  42         public String findSequence(String sequence, String program, String version) {
  43                 List<String> jobs = findJobs(sequence, program, version);
  44                 if (null != jobs) {
  45                         return jobs.size() + " jobs found";
  46                 }
  47                 return "no jobs found";
  48         }
  49
  50         @Override
  51         public String findJobForSequence(String sequence, String program, String version) {
  52                 List<String> jobs = findJobs(sequence, program, version);
  53                 if (null != jobs) {
  54                         for (String job : jobs) {
  55                                 String link = null;
  56                                 ArchivedJob aj = new ArchivedJob(job);
  57                                 try {
  58                                         link = aj.prepareJobArchiveToWeb();
  59                                 } catch (IOException e) {
  60                                         log.error("JpredWS.findSequence: IO exception with job archive file");
  61                                         log.error(e.getLocalizedMessage(), e.getCause());
  62                                 }
  63                                 if (null != link) {
  64                                         return job;
  65                                 }
  66                         }
  67                         return "";
  68                 }
  69                 return "";
  70         }
  71
  72         @Override
  73         public String getArchive(String jobid) {
  74                 String link = "undefined";
  75                 ArchivedJob aj = new ArchivedJob(jobid);
  76                 try {
  77                         link = aj.prepareJobArchiveToWeb();
  78                 } catch (IOException e) {
  79                         log.error("JpredWS.findSequence: IO exception with job archive file");
  80                         log.error(e.getLocalizedMessage(), e.getCause());
  81                 }
  82                 return link;
  83         }
  84
  85 }