JAL-3070 detect failed/broken annotation web service jobs using generic JWS2 job...

diff --git a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index 6279ccd..df3a311 100644 (file)
--- a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
+++ b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@ -40,11 +40,13 @@ import jalview.gui.Desktop;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.IProgressIndicatorHandler;
 import jalview.gui.JvOptionPane;
+import jalview.gui.WebserviceInfo;
 import jalview.schemes.FeatureSettingsAdapter;
 import jalview.schemes.ResidueProperties;
 import jalview.util.MapList;
 import jalview.util.MessageManager;
 import jalview.workers.AlignCalcWorker;
+import jalview.ws.JobStateSummary;
 import jalview.ws.api.CancellableI;
 import jalview.ws.api.JalviewServiceEndpointProviderI;
 import jalview.ws.api.JobId;
@@ -238,6 +240,8 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
     final boolean cancellable = CancellableI.class
             .isAssignableFrom(annotService.getClass());
     StringBuffer msg = new StringBuffer();
+    JobStateSummary job = new JobStateSummary();
+    WebserviceInfo info = new WebserviceInfo("foo", "bar", false);
     try
     {
       if (checkDone())
@@ -279,7 +283,7 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
       running.setSeqNames(seqNames);
       running.setStartPos(start);
       running.setSeqs(seqs);
-
+      job.updateJobPanelState(info, "", running);
       if (guiProgress != null)
       {
         guiProgress.registerHandler(progressId,
@@ -309,10 +313,12 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
       {
         Cache.log.debug("Updating status for annotation service.");
         annotService.updateStatus(running);
-
-        if (running.isFinished())
+        job.updateJobPanelState(info, "", running);
+        if (running.isSubjobComplete())
         {
-          Cache.log.debug("Analysis service job reported finished.");
+          Cache.log.debug(
+                  "Finished polling analysis service job: status reported is "
+                          + running.getState());
           finished = true;
         }
         else
@@ -376,6 +382,7 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
         }
       } while (!finished);
 
+      Cache.log.debug("Job poll loop exited. Job is " + running.getState());
       // TODO: need to poll/retry
       if (serverErrorsLeft > 0)
       {
@@ -386,79 +393,85 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
         {
         }
       }
-      // configure job with the associated view's feature renderer, if one
-      // exists.
-      // TODO: here one would also grab the 'master feature renderer' in order
-      // to enable/disable
-      // features automatically according to user preferences
-      running.setFeatureRenderer(
-              ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
-      Cache.log.debug("retrieving job results.");
-      final Map<String, FeatureColourI> featureColours = new HashMap<>();
-      final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
-      List<AlignmentAnnotation> returnedAnnot = annotService
-              .getAnnotationResult(running.getJobHandle(), seqs,
-                      featureColours, featureFilters);
-
-      Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
-              : ("" + returnedAnnot.size())));
-      Cache.log.debug("There were " + featureColours.size()
-              + " feature colours and " + featureFilters.size()
-              + " filters defined.");
-
-      // TODO
-      // copy over each annotation row reurned and also defined on each
-      // sequence, excluding regions not annotated due to gapMap/column
-      // visibility
-
-      running.setAnnotation(returnedAnnot);
-
-      if (running.hasResults())
+      if (running.isFinished())
       {
-        jalview.bin.Cache.log.debug("Updating result annotation from Job "
-                + rslt + " at " + service.getUri());
-        updateResultAnnotation(true);
-        if (running.isTransferSequenceFeatures())
+        // expect there to be results to collect
+        // configure job with the associated view's feature renderer, if one
+        // exists.
+        // TODO: here one would also grab the 'master feature renderer' in order
+        // to enable/disable
+        // features automatically according to user preferences
+        running.setFeatureRenderer(
+                ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
+        Cache.log.debug("retrieving job results.");
+        final Map<String, FeatureColourI> featureColours = new HashMap<>();
+        final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
+        List<AlignmentAnnotation> returnedAnnot = annotService
+                .getAnnotationResult(running.getJobHandle(), seqs,
+                        featureColours, featureFilters);
+
+        Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
+                : ("" + returnedAnnot.size())));
+        Cache.log.debug("There were " + featureColours.size()
+                + " feature colours and " + featureFilters.size()
+                + " filters defined.");
+
+        // TODO
+        // copy over each annotation row reurned and also defined on each
+        // sequence, excluding regions not annotated due to gapMap/column
+        // visibility
+
+        running.setAnnotation(returnedAnnot);
+
+        if (running.hasResults())
         {
-          // TODO
-          // look at each sequence and lift over any features, excluding regions
-          // not annotated due to gapMap/column visibility
-
-          jalview.bin.Cache.log.debug(
-                  "Updating feature display settings and transferring features from Job "
-                          + rslt + " at " + service.getUri());
-          // TODO: consider merge rather than apply here
-          alignViewport.applyFeaturesStyle(new FeatureSettingsAdapter()
+          jalview.bin.Cache.log.debug("Updating result annotation from Job "
+                  + rslt + " at " + service.getUri());
+          updateResultAnnotation(true);
+          if (running.isTransferSequenceFeatures())
           {
-            @Override
-            public FeatureColourI getFeatureColour(String type)
+            // TODO
+            // look at each sequence and lift over any features, excluding
+            // regions
+            // not annotated due to gapMap/column visibility
+
+            jalview.bin.Cache.log.debug(
+                    "Updating feature display settings and transferring features from Job "
+                            + rslt + " at " + service.getUri());
+            // TODO: consider merge rather than apply here
+            alignViewport.applyFeaturesStyle(new FeatureSettingsAdapter()
             {
-              return featureColours.get(type);
-            }
+              @Override
+              public FeatureColourI getFeatureColour(String type)
+              {
+                return featureColours.get(type);
+              }
 
-            @Override
-            public FeatureMatcherSetI getFeatureFilters(String type)
-            {
-              return featureFilters.get(type);
-            }
+              @Override
+              public FeatureMatcherSetI getFeatureFilters(String type)
+              {
+                return featureFilters.get(type);
+              }
 
-            @Override
-            public boolean isFeatureDisplayed(String type)
-            {
-              return featureColours.containsKey(type);
-            }
+              @Override
+              public boolean isFeatureDisplayed(String type)
+              {
+                return featureColours.containsKey(type);
+              }
 
-          });
-          // TODO: JAL-1150 - create sequence feature settings API for defining
-          // styles and enabling/disabling feature overlay on alignment panel
+            });
+            // TODO: JAL-1150 - create sequence feature settings API for
+            // defining
+            // styles and enabling/disabling feature overlay on alignment panel
 
-          if (alignFrame.alignPanel == ap)
-          {
-            alignViewport.setShowSequenceFeatures(true);
-            alignFrame.setMenusForViewport();
+            if (alignFrame.alignPanel == ap)
+            {
+              alignViewport.setShowSequenceFeatures(true);
+              alignFrame.setMenusForViewport();
+            }
           }
+          ap.adjustAnnotationHeight();
         }
-        ap.adjustAnnotationHeight();
       }
       Cache.log.debug("Annotation Service Worker thread finished.");
     }