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.bin.Console;
   6 import jalview.datamodel.Alignment;
   7 import jalview.datamodel.AlignmentAnnotation;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.datamodel.features.FeatureMatcherSetI;
  10 import jalview.io.AnnotationFile;
  11 import jalview.io.DataSourceType;
  12 import jalview.io.FeaturesFile;
  13 import jalview.util.MessageManager;
  14 import jalview.ws.api.JobId;
  15 import jalview.ws.api.SequenceAnnotationServiceI;
  16 import jalview.ws.params.ArgumentI;
  17 import jalview.ws.params.WsParamSetI;
  18 import jalview.ws.uimodel.AlignAnalysisUIText;
  19
  20 import java.io.IOError;
  21 import java.io.IOException;
  22 import java.util.Arrays;
  23 import java.util.Collection;
  24 import java.util.List;
  25 import java.util.Map;
  26
  27 import compbio.data.msa.Category;
  28 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  29 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  30 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  31
  32 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  33 {
  34   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  35           SlivkaService service, String category)
  36   {
  37     super(client, service, category);
  38     if (category == Category.CATEGORY_CONSERVATION)
  39     {
  40       /* FIXME: the category name is hardcoded for AACon, names other than
  41        * "AAConWS" doesn't work. */
  42       setAlignAnalysisUI(new AlignAnalysisUIText(getName(),
  43               SlivkaAnnotationServiceInstance.class,
  44               "Slivka.AACons", false, true, true, true, true, 2,
  45               MessageManager.getString("label.aacon_calculations"),
  46               MessageManager.getString("tooltip.aacon_calculations"),
  47               MessageManager.getString("label.aacon_settings"),
  48               MessageManager.getString("tooltip.aacon_settings")));
  49     }
  50     style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  51   }
  52
  53   @Override
  54   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  55   {
  56     return super.submit(seqs, preset, paramset);
  57   }
  58
  59   @Override
  60   public List<AlignmentAnnotation> getAnnotationResult(JobId jobId,
  61           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  62           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  63   {
  64     RemoteFile annotFile = null;
  65     RemoteFile featFile = null;
  66     try
  67     {
  68       var slivkaJob = client.getJob(jobId.getJobId());
  69       Collection<RemoteFile> files = slivkaJob.getResults();
  70       for (RemoteFile f : files)
  71       {
  72         if (f.getMediaType().equals("application/jalview-annotations"))
  73         {
  74           annotFile = f;
  75         }
  76         else if (f.getMediaType().equals("application/jalview-features"))
  77         {
  78           featFile = f;
  79         }
  80       }
  81     } catch (IOException e)
  82     {
  83       throw new IOError(e);
  84     }
  85     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
  86     if (annotFile == null
  87         || !new AnnotationFile().readAnnotationFileWithCalcId(aln, service.getId(), annotFile.getContentUrl().toString(), DataSourceType.URL))
  88     {
  89       Console.debug("No annotation from slivka job\n" + annotFile);
  90     }
  91     else {
  92       Console.debug("Annotation file loaded " + annotFile);
  93     }
  94     if (featFile == null
  95         || !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true))
  96     {
  97       Console.debug("No features from slivka job\n" + featFile);
  98     }
  99     else {
 100       Console.debug("Features feil loaded " + featFile);
 101     }
 102     return Arrays.asList(aln.getAlignmentAnnotation());
 103   }
 104 }