Merge branch 'alpha/origin_2022_JAL-3066_Jalview_212_slivka-integration' into spike...

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

diff --git a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index 9a33b04..374d2eb 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -1,5 +1,6 @@
 package jalview.ws.slivkaws;
 
+
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -10,13 +11,12 @@ import jalview.ws.api.MultipleSequenceAlignmentI;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.InvalidArgumentException;
 import jalview.ws.params.WsParamSetI;
-
 import java.io.IOError;
 import java.io.IOException;
 import java.rmi.ServerError;
+import java.util.Collection;
 import java.util.List;
 
-import compbio.data.msa.Category;
 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
@@ -37,19 +37,20 @@ public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements Multip
   @Override
   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
   {
-    List<RemoteFile> files;
+    Collection<RemoteFile> files;
     try
     {
-      files = client.getJobResults(jobId.getJobId());
+      var slivkaJob = client.getJob(jobId.getJobId());
+      files = slivkaJob.getResults();
       for (RemoteFile f : files)
       {
-        if (f.getMimeType().equals("application/clustal"))
+        if (f.getMediaType().equals("application/clustal"))
         {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
+          return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
         }
-        else if (f.getMimeType().equals("application/fasta"))
+        else if (f.getMediaType().equals("application/fasta"))
         {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
+          return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
         }
       }
     } catch (IOException e)