JAL-3878 Set job status to cancelled on job cancellation.

[jalview.git] / src / jalview / ws2 / slivka / SlivkaWebService.java

diff --git a/src/jalview/ws2/slivka/SlivkaWebService.java b/src/jalview/ws2/slivka/SlivkaWebService.java
index bd4cb61..5da7be3 100644 (file)
--- a/src/jalview/ws2/slivka/SlivkaWebService.java
+++ b/src/jalview/ws2/slivka/SlivkaWebService.java
@@ -12,10 +12,15 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
 import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
@@ -211,6 +216,7 @@ public class SlivkaWebService implements WebServiceI
   @Override
   public void cancel(WSJob job) throws IOException
   {
+    job.setStatus(WSJobStatus.CANCELLED);
     Cache.log.warn("Slivka does not support job cancellation yet.");
   }
 
@@ -232,7 +238,8 @@ public class SlivkaWebService implements WebServiceI
     return false;
   }
 
-  public AlignmentI getAlignment(WSJob job) throws IOException
+  public AlignmentI getAlignment(WSJob job, List<SequenceI> dataset,
+      AlignViewportI viewport) throws IOException
   {
     Collection<RemoteFile> files;
     var slivkaJob = client.getJob(job.getJobId());
@@ -253,6 +260,48 @@ public class SlivkaWebService implements WebServiceI
     return null;
   }
 
+  public FeaturesFile getFeaturesFile(WSJob job,
+      List<SequenceI> dataset, AlignViewportI viewport) throws IOException
+  {
+    var slivkaJob = client.getJob(job.getJobId());
+    Collection<RemoteFile> files = slivkaJob.getResults();
+    for (RemoteFile f : files)
+    {
+      if (f.getMediaType().equals("application/jalview-features"))
+      {
+        return new FeaturesFile(f.getContentUrl().toString(), DataSourceType.URL);
+      }
+    }
+    return null;
+  }
+
+  public List<AlignmentAnnotation> getAnnotationFile(WSJob job,
+      List<SequenceI> dataset, AlignViewportI viewport) throws IOException
+  {
+    var slivkaJob = client.getJob(job.getJobId());
+    Collection<RemoteFile> files = slivkaJob.getResults();
+    for (RemoteFile f : files)
+    {
+      if (f.getMediaType().equals("application/jalview-annotations"))
+      {
+        Alignment aln = new Alignment(dataset.toArray(new SequenceI[0]));
+        AnnotationFile af = new AnnotationFile();
+        boolean valid = af.readAnnotationFileWithCalcId(aln, service.getId(),
+            f.getContentUrl().toString(), DataSourceType.URL);
+        if (valid)
+        {
+          return Arrays.asList(aln.getAlignmentAnnotation());
+        }
+        else
+        {
+          throw new IOException("Unable to read annotations from file " +
+              f.getContentUrl().toString());
+        }
+      }
+    }
+    return null;
+  }
+
   @Override
   public String toString()
   {