JAL-3066 Check if annotation and features are present before fetching

[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 80e44ec..ad09f7a 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -1,6 +1,7 @@
 package jalview.ws.slivkaws;
 
 import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
@@ -15,12 +16,10 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
-import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.IOError;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -41,7 +40,7 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
             : "Alignment Conservation");
     if (conservation)
     {
-      setAlignAnalysisUI(new AlignAnalysisUIText(getServiceType(),
+      setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
               SlivkaAnnotationServiceInstance.class,
               "Slivka.AACons", false, true, true, true, true, 2,
               MessageManager.getString("label.aacon_calculations"),
@@ -49,6 +48,7 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
               MessageManager.getString("label.aacon_settings"),
               MessageManager.getString("tooltip.aacon_settings")));
     }
+    style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
   }
 
   @Override
@@ -115,11 +115,15 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
       throw new IOError(e);
     }
     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
-    BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
-    new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
-    if (featFile != null)
+    if (annotFile == null
+        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
     {
-      new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
+      Cache.log.debug("No annotation from slivka job\n" + annotFile);
+    }
+    if (featFile == null
+        || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
+    {
+      Cache.log.debug("No features from slivka job\n" + featFile);
     }
     return Arrays.asList(aln.getAlignmentAnnotation());
   }