src/jalview/ws/slivkaws/ClustaloWS.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.gui.WebserviceInfo;
   6 import jalview.io.DataSourceType;
   7 import jalview.io.FileFormat;
   8 import jalview.io.FormatAdapter;
   9 import jalview.ws.api.JalviewServiceEndpointProviderI;
  10 import jalview.ws.api.JobId;
  11 import jalview.ws.api.MultipleSequenceAlignmentI;
  12 import jalview.ws.api.ServiceWithParameters;
  13 import jalview.ws.gui.WsJob;
  14 import jalview.ws.params.ArgumentI;
  15 import jalview.ws.params.ParamManager;
  16 import jalview.ws.params.WsParamSetI;
  17
  18 import java.io.ByteArrayInputStream;
  19 import java.io.IOException;
  20 import java.io.InputStream;
  21 import java.util.EnumMap;
  22 import java.util.List;
  23
  24 import uk.ac.dundee.compbio.slivkaclient.Form;
  25 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  26 import uk.ac.dundee.compbio.slivkaclient.JobState;
  27 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  28 import uk.ac.dundee.compbio.slivkaclient.Service;
  29 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  30
  31 public class ClustaloWS extends ServiceWithParameters
  32     implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
  33 {
  34   private SlivkaClient client;
  35   private Service service;
  36
  37   private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  38   {
  39     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
  40     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
  41     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
  42     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
  43     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
  44     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
  45     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  46   }
  47
  48
  49   ClustaloWS(SlivkaClient client)
  50   {
  51     super("ClustalO", "Alignment", "ClustalO", "foo", "http://foo.foo");
  52
  53     this.client = client;
  54     try
  55     {
  56       service = client.getService("clustalo");
  57     } catch (IOException e)
  58     {
  59       throw new RuntimeException(e);
  60     }
  61   }
  62
  63   @Override
  64   public void updateStatus(WsJob job)
  65   {
  66     try
  67     {
  68       job.setState(stateMap.get(client.getJobState(job.getJobId())));
  69     } catch (IOException e)
  70     {
  71       throw new RuntimeException(e);
  72     }
  73   }
  74
  75   @Override
  76   public boolean updateJobProgress(WsJob job)
  77   {
  78     return false;
  79   }
  80
  81   @Override
  82   public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
  83   {
  84     return false;
  85   }
  86
  87   @Override
  88   public boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
  89   {
  90     return false;
  91   }
  92
  93   @Override
  94   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws FormValidationException, IOException
  95   {
  96     StringBuilder builder = new StringBuilder();
  97     for (SequenceI seq : toalign)
  98     {
  99       builder.append(">").append(seq.getName()).append("\n");
 100       builder.append(seq.getSequence()).append("\n\n");
 101     }
 102     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
 103     RemoteFile file = client.uploadFile(stream, "input.fasta",
 104             "application/fasta");
 105     Form form = service.getForm();
 106     form.insert("input", file);
 107     String jobUUID = form.submit();
 108     return new JobId("clustalo", "clustalo", jobUUID);
 109   }
 110
 111   @Override
 112   public AlignmentI getAlignmentFor(JobId jobId)
 113   {
 114     List<RemoteFile> files;
 115     try
 116     {
 117       files = client.getJobResults(jobId.getJobId());
 118       for (RemoteFile f: files) {
 119         if (f.getMimeType().equals("application/clustal"))
 120         {
 121           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
 122         }
 123       }
 124     } catch (IOException e1)
 125     {
 126       // TODO Auto-generated catch block
 127       e1.printStackTrace();
 128     }
 129     return null;
 130   }
 131
 132   @Override
 133   public void initParamStore(ParamManager userParameterStore)
 134   {
 135
 136   }
 137
 138   @Override
 139   public Object getEndpoint()
 140   {
 141     return this;
 142   }
 143 }