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.io.DataSourceType;
  10 import jalview.io.FeaturesFile;
  11 import jalview.ws.api.JobId;
  12 import jalview.ws.api.SequenceAnnotationServiceI;
  13 import jalview.ws.params.ArgumentI;
  14 import jalview.ws.params.WsParamSetI;
  15
  16 import java.io.BufferedReader;
  17 import java.io.ByteArrayInputStream;
  18 import java.io.IOError;
  19 import java.io.IOException;
  20 import java.io.InputStream;
  21 import java.io.InputStreamReader;
  22 import java.util.Arrays;
  23 import java.util.HashMap;
  24 import java.util.List;
  25 import java.util.Map;
  26
  27 import uk.ac.dundee.compbio.slivkaclient.FormField;
  28 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  29 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  30 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  31 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  32
  33 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  34 {
  35   public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
  36   {
  37     super(client, service, "Annotations disorder");
  38   }
  39
  40   @Override
  41   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  42   {
  43     StringBuilder builder = new StringBuilder();
  44     for (SequenceI seq : seqs)
  45     {
  46       builder.append(">").append(seq.getName()).append("\n");
  47       builder.append(seq.getSequence()).append("\n");
  48     }
  49     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  50     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  51     SlivkaForm form = service.getForm();
  52     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  53     if (paramset != null)
  54     {
  55       for (ArgumentI arg : paramset)
  56       {
  57         values.put(arg.getName(), arg.getValue());
  58       }
  59     }
  60     for (FormField field : form.getFields())
  61     {
  62       switch (field.getType())
  63       {
  64       case FILE:
  65         form.insert(field.getName(), file);
  66         break;
  67       case BOOLEAN:
  68         String value = values.get(field.getName());
  69         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  70         break;
  71       default:
  72         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  73       }
  74     }
  75     return new JobId(service.getName(), service.getName(), form.submit());
  76   }
  77
  78   @Override
  79   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  80           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  81           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  82   {
  83     RemoteFile annotFile = null;
  84     RemoteFile featFile = null;
  85     try
  86     {
  87       List<RemoteFile> files = client.getJobResults(job.getJobId());
  88       for (RemoteFile f : files)
  89       {
  90         if (f.getMimeType().equals("application/jalview-annotations"))
  91         {
  92           annotFile = f;
  93         }
  94         else if (f.getMimeType().equals("application/jalview-features"))
  95         {
  96           featFile = f;
  97         }
  98       }
  99     } catch (IOException e)
 100     {
 101       throw new IOError(e);
 102     }
 103     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
 104     BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
 105     new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
 106     if (featFile != null)
 107     {
 108       new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
 109     }
 110     return Arrays.asList(aln.getAlignmentAnnotation());
 111   }
 112 }