src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.io.DataSourceType;
   6 import jalview.io.FileFormat;
   7 import jalview.io.FormatAdapter;
   8 import jalview.ws.api.JobId;
   9 import jalview.ws.api.MultipleSequenceAlignmentI;
  10 import jalview.ws.params.ArgumentI;
  11 import jalview.ws.params.InvalidArgumentException;
  12 import jalview.ws.params.WsParamSetI;
  13
  14 import java.io.ByteArrayInputStream;
  15 import java.io.IOError;
  16 import java.io.IOException;
  17 import java.io.InputStream;
  18 import java.rmi.ServerError;
  19 import java.util.List;
  20 import java.util.Optional;
  21
  22 import uk.ac.dundee.compbio.slivkaclient.FieldType;
  23 import uk.ac.dundee.compbio.slivkaclient.FormField;
  24 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  25 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  26 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  27 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  28
  29 public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements MultipleSequenceAlignmentI
  30 {
  31   SlivkaMsaServiceInstance(SlivkaClient client, SlivkaService service) {
  32     super(client, service, "Sequence Alignment");
  33     style = ServiceClient.MSAWSCLIENT;
  34   }
  35
  36   @Override
  37   public JobId align(List<SequenceI> toalign, WsParamSetI parameters, List<ArgumentI> list) throws Throwable
  38   {
  39     StringBuilder builder = new StringBuilder();
  40     for (SequenceI seq : toalign)
  41     {
  42       builder.append(">").append(seq.getName()).append("\n");
  43       builder.append(seq.getSequence()).append("\n");
  44     }
  45     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  46     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  47     SlivkaForm form = service.getForm();
  48     Optional<FormField> inputField = form.getFields().stream()
  49         .filter(f -> f.getType() == FieldType.FILE).findFirst();
  50     if (inputField.isPresent())
  51     {
  52       form.insert(inputField.get().getName(), file);
  53     }
  54     if (list != null)
  55     {
  56       for (ArgumentI arg : list)
  57       {
  58         FormField field = form.getField(arg.getName());
  59         if (field.getType() == FieldType.BOOLEAN)
  60         {
  61           form.insert(arg.getName(), (arg.getValue() != null && !arg.getValue().isBlank()) ? true : false);
  62         }
  63         else
  64         {
  65           form.insert(arg.getName(), field.valueOf(arg.getValue()));
  66         }
  67       }
  68     }
  69     return new JobId(service.getName(), service.getName(), form.submit());
  70   }
  71
  72   @Override
  73   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
  74   {
  75     List<RemoteFile> files;
  76     try
  77     {
  78       files = client.getJobResults(jobId.getJobId());
  79       for (RemoteFile f : files)
  80       {
  81         if (f.getMimeType().equals("application/clustal"))
  82         {
  83           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
  84         }
  85         else if (f.getMimeType().equals("application/fasta"))
  86         {
  87           return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
  88         }
  89       }
  90     } catch (IOException e)
  91     {
  92       throw new IOError(e);
  93     }
  94     return null;
  95   }
  96 }