src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.datamodel.Alignment;
   5 import jalview.datamodel.AlignmentAnnotation;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.datamodel.features.FeatureMatcherSetI;
   8 import jalview.io.AnnotationFile;
   9 import jalview.ws.api.JobId;
  10 import jalview.ws.api.SequenceAnnotationServiceI;
  11 import jalview.ws.params.ArgumentI;
  12 import jalview.ws.params.WsParamSetI;
  13
  14 import java.io.BufferedReader;
  15 import java.io.ByteArrayInputStream;
  16 import java.io.IOError;
  17 import java.io.IOException;
  18 import java.io.InputStream;
  19 import java.io.InputStreamReader;
  20 import java.util.Arrays;
  21 import java.util.HashMap;
  22 import java.util.List;
  23 import java.util.Map;
  24
  25 import uk.ac.dundee.compbio.slivkaclient.FormField;
  26 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  27 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  28 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  29 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  30
  31 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  32 {
  33   public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
  34   {
  35     super(client, service, "Annotations disorder");
  36   }
  37
  38   @Override
  39   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  40   {
  41     StringBuilder builder = new StringBuilder();
  42     for (SequenceI seq : seqs)
  43     {
  44       builder.append(">").append(seq.getName()).append("\n");
  45       builder.append(seq.getSequence()).append("\n");
  46     }
  47     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  48     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  49     SlivkaForm form = service.getForm();
  50     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  51     if (paramset != null)
  52     {
  53       for (ArgumentI arg : paramset)
  54       {
  55         values.put(arg.getName(), arg.getValue());
  56       }
  57     }
  58     for (FormField field : form.getFields())
  59     {
  60       switch (field.getType())
  61       {
  62       case FILE:
  63         form.insert(field.getName(), file);
  64         break;
  65       case BOOLEAN:
  66         String value = values.get(field.getName());
  67         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  68         break;
  69       default:
  70         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  71       }
  72     }
  73     return new JobId(service.getName(), service.getName(), form.submit());
  74   }
  75
  76   @Override
  77   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  78           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  79           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  80   {
  81     RemoteFile annotFile = null;
  82     RemoteFile featFile = null;
  83     try
  84     {
  85       List<RemoteFile> files = client.getJobResults(job.getJobId());
  86       for (RemoteFile f : files)
  87       {
  88         if (f.getMimeType().equals("application/jalview-annotations"))
  89         {
  90           annotFile = f;
  91         }
  92         else if (f.getMimeType().equals("application/jalview-features"))
  93         {
  94           featFile = f;
  95         }
  96       }
  97     } catch (IOException e)
  98     {
  99       throw new IOError(e);
 100     }
 101     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
 102     BufferedReader in = new BufferedReader(new InputStreamReader(annotFile.getContent()));
 103     AnnotationFile f = new AnnotationFile();
 104     f.parseAnnotationFrom(aln, null, in);
 105     return Arrays.asList(aln.getAlignmentAnnotation());
 106   }
 107 }