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 org.apache.http.entity.ContentType;
  25
  26 import uk.ac.dundee.compbio.slivkaclient.Form;
  27 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  28 import uk.ac.dundee.compbio.slivkaclient.JobState;
  29 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  30 import uk.ac.dundee.compbio.slivkaclient.Service;
  31 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  32
  33 public class ClustaloWS extends ServiceWithParameters
  34     implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
  35 {
  36   private SlivkaClient client;
  37   private Service service;
  38
  39   private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  40   {
  41     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
  42     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
  43     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
  44     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
  45     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
  46     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
  47     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  48   }
  49
  50
  51   ClustaloWS(SlivkaClient client)
  52   {
  53     super("ClustalO", "Alignment", "ClustalO", "foo", "http://foo.foo");
  54
  55     this.client = client;
  56     try
  57     {
  58       service = client.getService("clustalo");
  59     } catch (IOException e)
  60     {
  61       throw new RuntimeException(e);
  62     }
  63   }
  64
  65   @Override
  66   public void updateStatus(WsJob job)
  67   {
  68     try
  69     {
  70       job.setState(stateMap.get(client.getJobState(job.getJobId())));
  71     } catch (IOException e)
  72     {
  73       throw new RuntimeException(e);
  74     }
  75   }
  76
  77   @Override
  78   public boolean updateJobProgress(WsJob job)
  79   {
  80     return false;
  81   }
  82
  83   @Override
  84   public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
  85   {
  86     return false;
  87   }
  88
  89   @Override
  90   public boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
  91   {
  92     return false;
  93   }
  94
  95   @Override
  96   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws FormValidationException, IOException
  97   {
  98     StringBuilder builder = new StringBuilder();
  99     for (SequenceI seq : toalign)
 100     {
 101       builder.append(">").append(seq.getName()).append("\n");
 102       builder.append(seq.getSequence()).append("\n\n");
 103     }
 104     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
 105     RemoteFile file = client.uploadFile(stream, "input.fasta", ContentType.create("application/fasta"));
 106     Form form = service.getForm();
 107     form.insert("input", file);
 108     String jobUUID = form.submit();
 109     return new JobId("clustalo", "clustalo", jobUUID);
 110   }
 111
 112   @Override
 113   public AlignmentI getAlignmentFor(JobId jobId)
 114   {
 115     List<RemoteFile> files;
 116     try
 117     {
 118       files = client.getJobResults(jobId.getJobId());
 119       for (RemoteFile f: files) {
 120         if (f.getMimeType().equals("application/clustal"))
 121         {
 122           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
 123         }
 124       }
 125     } catch (IOException e1)
 126     {
 127       // TODO Auto-generated catch block
 128       e1.printStackTrace();
 129     }
 130     return null;
 131   }
 132
 133   @Override
 134   public void initParamStore(ParamManager userParameterStore)
 135   {
 136
 137   }
 138
 139   @Override
 140   public Object getEndpoint()
 141   {
 142     return this;
 143   }
 144 }