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.util.MessageManager;
  12 import jalview.ws.api.JobId;
  13 import jalview.ws.api.SequenceAnnotationServiceI;
  14 import jalview.ws.params.ArgumentI;
  15 import jalview.ws.params.WsParamSetI;
  16 import jalview.ws.uimodel.AlignAnalysisUIText;
  17
  18 import java.io.BufferedReader;
  19 import java.io.ByteArrayInputStream;
  20 import java.io.IOError;
  21 import java.io.IOException;
  22 import java.io.InputStream;
  23 import java.io.InputStreamReader;
  24 import java.util.Arrays;
  25 import java.util.HashMap;
  26 import java.util.List;
  27 import java.util.Map;
  28
  29 import uk.ac.dundee.compbio.slivkaclient.FormField;
  30 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  31 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  32 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  33 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  34
  35 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  36 {
  37   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  38           SlivkaService service, boolean conservation)
  39   {
  40     super(client, service, !conservation ? "Annotations disorder"
  41             : "Alignment Conservation");
  42     if (conservation)
  43     {
  44       setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
  45               SlivkaAnnotationServiceInstance.class,
  46               "Slivka.AACons", false, true, true, true, true, 2,
  47               MessageManager.getString("label.aacon_calculations"),
  48               MessageManager.getString("tooltip.aacon_calculations"),
  49               MessageManager.getString("label.aacon_settings"),
  50               MessageManager.getString("tooltip.aacon_settings")));
  51     }
  52     style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  53   }
  54
  55   @Override
  56   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  57   {
  58     StringBuilder builder = new StringBuilder();
  59     for (SequenceI seq : seqs)
  60     {
  61       builder.append(">").append(seq.getName()).append("\n");
  62       builder.append(seq.getSequence()).append("\n");
  63     }
  64     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  65     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  66     SlivkaForm form = service.getForm();
  67     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  68     if (paramset != null)
  69     {
  70       for (ArgumentI arg : paramset)
  71       {
  72         values.put(arg.getName(), arg.getValue());
  73       }
  74     }
  75     for (FormField field : form.getFields())
  76     {
  77       switch (field.getType())
  78       {
  79       case FILE:
  80         form.insert(field.getName(), file);
  81         break;
  82       case BOOLEAN:
  83         String value = values.get(field.getName());
  84         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  85         break;
  86       default:
  87         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  88       }
  89     }
  90     return new JobId(service.getName(), service.getName(), form.submit());
  91   }
  92
  93   @Override
  94   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  95           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  96           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  97   {
  98     RemoteFile annotFile = null;
  99     RemoteFile featFile = null;
 100     try
 101     {
 102       List<RemoteFile> files = client.getJobResults(job.getJobId());
 103       for (RemoteFile f : files)
 104       {
 105         if (f.getMimeType().equals("application/jalview-annotations"))
 106         {
 107           annotFile = f;
 108         }
 109         else if (f.getMimeType().equals("application/jalview-features"))
 110         {
 111           featFile = f;
 112         }
 113       }
 114     } catch (IOException e)
 115     {
 116       throw new IOError(e);
 117     }
 118     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
 119     BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
 120     new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
 121     if (featFile != null)
 122     {
 123       new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
 124     }
 125     return Arrays.asList(aln.getAlignmentAnnotation());
 126   }
 127 }