AsyncFetchTask for SequenceFetcher

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 549d198..ae4fffd 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -437,7 +437,6 @@ public class SequenceFetcher extends JPanel
 
   public void fetch(String ids, boolean isAsync)
   {
-    isAsync &= Platform.isJS();
     if (ids == null)
     {
       ids = textArea.getText();
@@ -477,33 +476,39 @@ public class SequenceFetcher extends JPanel
   private class AsyncFetchTask extends AsyncSwingWorker
   {
 
-    private boolean addToLast = false;
+    protected boolean addToLast = false;
 
-    private List<String> aresultq = new ArrayList<>();
+    protected List<String> aresultq = new ArrayList<>();
 
-    private List<String> presultTitle = new ArrayList<>();
+    protected List<String> presultTitle = new ArrayList<>();
 
-    private List<AlignmentI> presult = new ArrayList<>();
+    protected List<AlignmentI> presult = new ArrayList<>();
 
-    private List<AlignmentI> aresult = new ArrayList<>();
+    protected List<AlignmentI> aresult = new ArrayList<>();
 
-    private FeatureSettingsModelI preferredFeatureColours = null;
+    protected FeatureSettingsModelI preferredFeatureColours = null;
 
-    private List<DbSourceProxy> sources;
+    protected List<DbSourceProxy> sources;
 
-    private Iterator<DbSourceProxy> sourceIterator;
+    protected Iterator<DbSourceProxy> sourceIterator;
 
-    private String[] fetchArray;
+    protected String[] fetchArray;
 
-    private List<String> fetchList;
+    protected List<String> fetchList;
 
-    private Iterator<String> fetchIterator;
+    protected Iterator<String> fetchIterator;
 
-    private int fetchCount;
+    protected int fetchCount;
 
-    private DbSourceProxy source;
+    protected DbSourceProxy source;
 
-    private String ids;
+    protected String ids;
+
+    protected long myID;
+
+    protected boolean isAsync;
+
+    protected Throwable taskError;
 
     public AsyncFetchTask(String ids, Component owner, String title,
             int delayMillis,
@@ -511,6 +516,8 @@ public class SequenceFetcher extends JPanel
     {
       super(owner, title, delayMillis, min, max);
       this.ids = ids;
+      isAsync = (delayMillis != 0);
+      myID = Thread.currentThread().getId();
     }
 
     @Override
@@ -537,9 +544,14 @@ public class SequenceFetcher extends JPanel
 
     private final static int STATE_DONE = 100;
 
+    protected static final int STATE_TASK_ERROR = 99;
+
     @Override
     public int doInBackgroundAsync(int progress)
     {
+      System.out.println("SequenceFetcher.AsyncFetchTask " + isAsync + " "
+              + progress + " "
+              + taskError);
       switch (progress)
       {
       case STATE_INIT:
@@ -574,43 +586,55 @@ public class SequenceFetcher extends JPanel
       case STATE_FETCH_SINGLE:
         if (fetchIterator.hasNext())
         {
-          // source only handles one accession id at a time
-          try
+          return runSubtask(new Runnable()
           {
-            if (delayMillis == 0)
-            {
-              // for CrossRef2xmlTest only
-              Thread.sleep(5);
-            }
-            String accession = fetchIterator.next();
-            if (!fetchSingleAccession(source, accession, aresultq, aresult))
-            {
-              fetchList.add(accession);
-            }
-          } catch (Throwable e)
-          {
-            if (!showError(e))
+
+            @Override
+            public void run()
             {
-              return STATE_DONE;
+              // source only handles one accession id at a time
+              try
+              {
+                if (!isAsync)
+                {
+                  // for CrossRef2xmlTest only; to "allow the server to breathe"
+                  // (but we are doing that already when isAsync is true)
+                  Thread.sleep(5);
+                }
+                String notFound = fetchSingleAccession(source,
+                        fetchIterator.next(), aresultq, aresult);
+                if (notFound != null)
+                {
+                  fetchList.add(notFound);
+                }
+              } catch (Throwable e)
+              {
+                taskError = e;
+              }
             }
-          }
-          return STATE_FETCH_SINGLE;
+          });
         }
         return STATE_PROCESS;
       case STATE_FETCH_MULTIPLE:
         // proxy can fetch multiple accessions at one time
-        try
+        setProgressAsync(STATE_PROCESS);
+        return runSubtask(new Runnable()
         {
-          fetchMultipleAccessions(source, fetchIterator, aresultq, aresult,
-                  fetchList);
-        } catch (Throwable e)
-        {
-          if (!showError(e))
+
+          @Override
+          public void run()
           {
-            return STATE_DONE;
+            try
+            {
+              fetchMultipleAccessions(source, fetchIterator, aresultq,
+                      aresult, fetchList);
+            } catch (Throwable e)
+            {
+              taskError = e;
+            }
           }
-        }
-        return STATE_PROCESS;
+
+        });
       case STATE_PROCESS:
         // Stack results ready for opening in alignment windows
         if (aresult != null && aresult.size() > 0)
@@ -668,13 +692,63 @@ public class SequenceFetcher extends JPanel
                   preferredFeatureColours);
         }
         break;
+      case STATE_TASK_ERROR:
+        showProgress(null);
+        super.cancelAsync();
+        return 0; // arbitrary; ignored
       }
       return STATE_DONE;
     }
 
-    private void showProgress(String msg)
+    protected void resume()
     {
-      guiWindow.setProgressBar(msg, Thread.currentThread().hashCode());
+      if (!isAsync)
+      {
+        return;
+      }
+      super.setPaused(false);
+      super.stateLoop();
+    }
+
+    private int runSubtask(Runnable subtask)
+    {
+
+      Runnable r = new Runnable()
+      {
+
+        @Override
+        public void run()
+        {
+          try
+          {
+            subtask.run();
+          } catch (Throwable e)
+          {
+            taskError = e;
+          }
+          if (checkError(taskError))
+          {
+            setProgressAsync(STATE_TASK_ERROR);
+          }
+          else
+          {
+            taskError = null;
+          }
+          if (isAsync)
+          {
+            resume();
+          }
+        }
+      };
+
+      if (isAsync)
+      {
+        super.setPaused(true);
+        new Thread(r).start();
+        return 0; // arbitrary return -- ignored because we are paused.
+      }
+      r.run();
+      return super.getProgressAsync();
     }
 
     @Override
@@ -706,8 +780,17 @@ public class SequenceFetcher extends JPanel
       resetDialog();
     }
 
-    private boolean showError(Throwable e)
+    /**
+     * 
+     * @param e
+     * @return true if there was an error and we need to STOP
+     */
+    protected boolean checkError(Throwable e)
     {
+      if (e == null)
+      {
+        return false;
+      }
       String problem = "retrieving " + ids + " from "
               + database.getSelectedItem();
       if (e instanceof Exception)
@@ -733,6 +816,11 @@ public class SequenceFetcher extends JPanel
       return true;
     }
 
+    private void showProgress(String msg)
+    {
+      guiWindow.setProgressBar(msg, myID);
+    }
+
   }
 
   /**
@@ -800,49 +888,19 @@ public class SequenceFetcher extends JPanel
    *          a list of successful queries to add to
    * @param aresult
    *          a list of retrieved alignments to add to
-   * @return true if the fetch was successful, else false
+   * @return null if the fetch was successful; the accession if not
    */
-  boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
-          List<String> aresultq, List<AlignmentI> aresult)
+  String fetchSingleAccession(DbSourceProxy proxy, String accession,
+          List<String> aresultq, List<AlignmentI> aresult) throws Throwable
   {
-    boolean success = false;
-    try
-    {
-      // BH no longer necessary; we are doing 5-ms asynchronous delays all along
-      // if (aresult != null)
-      // {
-      // try
-      // {
-      // // give the server a chance to breathe
-      // Thread.sleep(5);
-      // } catch (Exception e)
-      // {
-      // //
-      // }
-      // }
-      //
-      AlignmentI indres = null;
-      try
-      {
-        indres = proxy.getSequenceRecords(accession);
-      } catch (OutOfMemoryError oome)
-      {
-        new OOMWarning(
-                "fetching " + accession + " from " + proxy.getDbName(),
-                oome, this);
-      }
-      if (indres != null)
-      {
-        aresultq.add(accession);
-        aresult.add(indres);
-        success = true;
-      }
-    } catch (Exception e)
+    AlignmentI indres = proxy.getSequenceRecords(accession);
+    if (indres == null)
     {
-      Cache.log.info("Error retrieving " + accession + " from "
-              + proxy.getDbName(), e);
+      return accession;
     }
-    return success;
+    aresultq.add(accession);
+    aresult.add(indres);
+    return null;
   }
 
   /**