src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentAnnotation;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.datamodel.features.FeatureMatcherSetI;
   9 import jalview.io.AnnotationFile;
  10 import jalview.io.DataSourceType;
  11 import jalview.io.FeaturesFile;
  12 import jalview.util.MessageManager;
  13 import jalview.ws.api.JobId;
  14 import jalview.ws.api.SequenceAnnotationServiceI;
  15 import jalview.ws.params.ArgumentI;
  16 import jalview.ws.params.WsParamSetI;
  17 import jalview.ws.uimodel.AlignAnalysisUIText;
  18
  19 import java.io.IOError;
  20 import java.io.IOException;
  21 import java.util.Arrays;
  22 import java.util.Collection;
  23 import java.util.List;
  24 import java.util.Map;
  25
  26 import compbio.data.msa.Category;
  27 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  28 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  29 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  30
  31 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  32 {
  33   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  34           SlivkaService service, String category)
  35   {
  36     super(client, service, category);
  37     if (category == Category.CATEGORY_CONSERVATION)
  38     {
  39       /* FIXME: the category name is hardcoded for AACon, names other than
  40        * "AAConWS" doesn't work. */
  41       setAlignAnalysisUI(new AlignAnalysisUIText(getName(),
  42               SlivkaAnnotationServiceInstance.class,
  43               "Slivka.AACons", false, true, true, true, true, 2,
  44               MessageManager.getString("label.aacon_calculations"),
  45               MessageManager.getString("tooltip.aacon_calculations"),
  46               MessageManager.getString("label.aacon_settings"),
  47               MessageManager.getString("tooltip.aacon_settings")));
  48     }
  49     style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  50   }
  51
  52   @Override
  53   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  54   {
  55     return super.submit(seqs, preset, paramset);
  56   }
  57
  58   @Override
  59   public List<AlignmentAnnotation> getAnnotationResult(JobId jobId,
  60           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  61           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  62   {
  63     RemoteFile annotFile = null;
  64     RemoteFile featFile = null;
  65     try
  66     {
  67       var slivkaJob = client.getJob(jobId.getJobId());
  68       Collection<RemoteFile> files = slivkaJob.getResults();
  69       for (RemoteFile f : files)
  70       {
  71         if (f.getMediaType().equals("application/jalview-annotations"))
  72         {
  73           annotFile = f;
  74         }
  75         else if (f.getMediaType().equals("application/jalview-features"))
  76         {
  77           featFile = f;
  78         }
  79       }
  80     } catch (IOException e)
  81     {
  82       throw new IOError(e);
  83     }
  84     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
  85     if (annotFile == null
  86         || !new AnnotationFile().readAnnotationFile(aln, annotFile.getContentUrl().toString(), DataSourceType.URL))
  87     {
  88       Cache.log.debug("No annotation from slivka job\n" + annotFile);
  89     }
  90     else {
  91       Cache.log.debug("Annotation file loaded " + annotFile);
  92     }
  93     if (featFile == null
  94         || !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true))
  95     {
  96       Cache.log.debug("No features from slivka job\n" + featFile);
  97     }
  98     else {
  99       Cache.log.debug("Features feil loaded " + featFile);
 100     }
 101     return Arrays.asList(aln.getAlignmentAnnotation());
 102   }
 103 }