1 package jalview.ws.slivkaws;
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;
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;
24 import org.apache.http.entity.ContentType;
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;
33 public class ClustaloWS extends ServiceWithParameters
34 implements MultipleSequenceAlignmentI, JalviewServiceEndpointProviderI
36 private SlivkaClient client;
37 private Service service;
39 private EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
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);
51 ClustaloWS(SlivkaClient client)
53 super("ClustalO", "Alignment", "ClustalO", "foo", "http://foo.foo");
58 service = client.getService("clustalo");
59 } catch (IOException e)
61 throw new RuntimeException(e);
66 public void updateStatus(WsJob job)
70 job.setState(stateMap.get(client.getJobState(job.getJobId())));
71 } catch (IOException e)
73 throw new RuntimeException(e);
78 public boolean updateJobProgress(WsJob job)
84 public boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
90 public boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
96 public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws FormValidationException, IOException
98 StringBuilder builder = new StringBuilder();
99 for (SequenceI seq : toalign)
101 builder.append(">").append(seq.getName()).append("\n");
102 builder.append(seq.getSequence()).append("\n\n");
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);
113 public AlignmentI getAlignmentFor(JobId jobId)
115 List<RemoteFile> files;
118 files = client.getJobResults(jobId.getJobId());
119 for (RemoteFile f: files) {
120 if (f.getMimeType().equals("application/clustal"))
122 return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
125 } catch (IOException e1)
127 // TODO Auto-generated catch block
128 e1.printStackTrace();
134 public void initParamStore(ParamManager userParameterStore)
140 public Object getEndpoint()