JAL-3848 Update slivka client library.

[jalview.git] / src / jalview / ws / slivkaws / SlivkaAnnotationServiceInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
index b3509b0..3c80fbc 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -19,6 +19,7 @@ import jalview.ws.uimodel.AlignAnalysisUIText;
 import java.io.IOError;
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
@@ -55,7 +56,7 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
   }
 
   @Override
-  public List<AlignmentAnnotation> getAnnotationResult(JobId job,
+  public List<AlignmentAnnotation> getAnnotationResult(JobId jobId,
           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
   {
@@ -63,14 +64,15 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
     RemoteFile featFile = null;
     try
     {
-      List<RemoteFile> files = client.getJobResults(job.getJobId());
+      var slivkaJob = client.getJob(jobId.getJobId());
+      Collection<RemoteFile> files = slivkaJob.getResults();
       for (RemoteFile f : files)
       {
-        if (f.getMimeType().equals("application/jalview-annotations"))
+        if (f.getMediaType().equals("application/jalview-annotations"))
         {
           annotFile = f;
         }
-        else if (f.getMimeType().equals("application/jalview-features"))
+        else if (f.getMediaType().equals("application/jalview-features"))
         {
           featFile = f;
         }
@@ -81,15 +83,21 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
     }
     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
     if (annotFile == null
-        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
+        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getContentUrl().toString(), DataSourceType.URL))
     {
       Cache.log.debug("No annotation from slivka job\n" + annotFile);
     }
+    else {
+      Cache.log.debug("Annotation file loaded " + annotFile);
+    }
     if (featFile == null
-        || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
+        || !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true))
     {
       Cache.log.debug("No features from slivka job\n" + featFile);
     }
+    else {
+      Cache.log.debug("Features feil loaded " + featFile);
+    }
     return Arrays.asList(aln.getAlignmentAnnotation());
   }
 }