JAL-1700 Improved the error handling mechanism for the PDB Rest client

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 358412d..142028a 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -46,6 +46,7 @@ import java.util.List;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
+import javax.swing.JOptionPane;
 import javax.swing.table.DefaultTableModel;
 
 
@@ -139,6 +140,7 @@ public class StructureChooser extends GStructureChooser
             .getStructureSummaryFields();
 
     discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+    HashSet<String> errors = new HashSet<String>();
     for (SequenceI seq : selectedSequences)
     {
       PDBRestRequest pdbRequest = new PDBRestRequest();
@@ -149,7 +151,15 @@ public class StructureChooser extends GStructureChooser
       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
       pdbRequest.setAssociatedSequence(seq.getName());
       pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      PDBRestResponse resultList;
+      try
+      {
+        resultList = pdbRestCleint.executeRequest(pdbRequest);
+      } catch (Exception e)
+      {
+        errors.add(e.getMessage());
+        continue;
+      }
       lastPdbRequest = pdbRequest;
       if (resultList.getSearchSummary() != null
               && !resultList.getSearchSummary().isEmpty())
@@ -160,6 +170,8 @@ public class StructureChooser extends GStructureChooser
     }
 
     int noOfStructuresFound = 0;
+    String totalTime = (System.currentTimeMillis() - startTime)
+            + " milli secs";
     if (discoveredStructuresSet != null
             && !discoveredStructuresSet.isEmpty())
     {
@@ -167,11 +179,25 @@ public class StructureChooser extends GStructureChooser
               discoveredStructuresSet));
       structuresDiscovered = true;
       noOfStructuresFound = discoveredStructuresSet.size();
+      mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+              + " Found (" + totalTime + ")");
+    }
+    else
+    {
+      mainFrame
+.setTitle("Structure Chooser - Manual association");
+      if (errors.size() > 0)
+      {
+        StringBuilder errorMsg = new StringBuilder(
+                "Operation was unsucessful due to the following: \n");
+        for (String error : errors)
+        {
+          errorMsg.append(error).append("\n");
+        }
+        JOptionPane.showMessageDialog(this, errorMsg.toString(),
+                "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+      }
     }
-    String totalTime = (System.currentTimeMillis() - startTime)
-            + " milli secs";
-    mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
-            + " Found (" + totalTime + ")");
   }
 
   public void loadLocalCachedPDBEntries()
@@ -326,60 +352,77 @@ public class StructureChooser extends GStructureChooser
       public void run()
       {
         long startTime = System.currentTimeMillis();
-        try
+        lbl_loading.setVisible(true);
+        Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+                .getStructureSummaryFields();
+        Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+        HashSet<String> errors = new HashSet<String>();
+        for (SequenceI seq : selectedSequences)
         {
-          lbl_loading.setVisible(true);
-
-          Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
-                  .getStructureSummaryFields();
-          Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
-          for (SequenceI seq : selectedSequences)
+          PDBRestRequest pdbRequest = new PDBRestRequest();
+          pdbRequest.setAllowEmptySeq(false);
+          pdbRequest.setResponseSize(1);
+          pdbRequest.setFieldToSearchBy("(text:");
+          pdbRequest.setFieldToSortBy(fieldToFilterBy,
+                  !chk_invertFilter.isSelected());
+          pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+          pdbRequest.setWantedFields(wantedFields);
+          pdbRequest.setAssociatedSequence(seq.getName());
+          pdbRestCleint = new PDBRestClient();
+          PDBRestResponse resultList;
+          try
           {
-            PDBRestRequest pdbRequest = new PDBRestRequest();
-            pdbRequest.setAllowEmptySeq(false);
-            pdbRequest.setResponseSize(1);
-            pdbRequest.setFieldToSearchBy("(text:");
-            pdbRequest.setFieldToSortBy(fieldToFilterBy,
-                    !chk_invertFilter.isSelected());
-            pdbRequest.setSearchTerm(buildQuery(seq) + ")");
-            pdbRequest.setWantedFields(wantedFields);
-            pdbRequest.setAssociatedSequence(seq.getName());
-            pdbRestCleint = new PDBRestClient();
-            PDBRestResponse resultList = pdbRestCleint
-                    .executeRequest(pdbRequest);
-            lastPdbRequest = pdbRequest;
-            if (resultList.getSearchSummary() != null
-                    && !resultList.getSearchSummary().isEmpty())
-            {
-              filteredResponse.addAll(resultList.getSearchSummary());
-            }
+            resultList = pdbRestCleint.executeRequest(pdbRequest);
+          } catch (Exception e)
+          {
+            errors.add(e.getMessage());
+            continue;
           }
-
-          if (!filteredResponse.isEmpty())
+          lastPdbRequest = pdbRequest;
+          if (resultList.getSearchSummary() != null
+                  && !resultList.getSearchSummary().isEmpty())
           {
-            final int filterResponseCount = filteredResponse.size();
-            Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
-            reorderedStructuresSet.addAll(filteredResponse);
-            reorderedStructuresSet.addAll(discoveredStructuresSet);
-            tbl_summary.setModel(PDBRestResponse.getTableModel(
-                    lastPdbRequest, reorderedStructuresSet));
+            filteredResponse.addAll(resultList.getSearchSummary());
+          }
+        }
 
-            // Update table selection model here
-            tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+        String totalTime = (System.currentTimeMillis() - startTime)
+                + " milli secs";
+        if (!filteredResponse.isEmpty())
+        {
+          final int filterResponseCount = filteredResponse.size();
+          Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+          reorderedStructuresSet.addAll(filteredResponse);
+          reorderedStructuresSet.addAll(discoveredStructuresSet);
+          tbl_summary.setModel(PDBRestResponse.getTableModel(
+                  lastPdbRequest, reorderedStructuresSet));
 
-          }
+          // Update table selection model here
+          tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
 
-          lbl_loading.setVisible(false);
-          String totalTime = (System.currentTimeMillis() - startTime)
-                  + " milli secs";
           mainFrame.setTitle("Structure Chooser - Filter time ("
                   + totalTime + ")");
-
-          validateSelections();
-        } catch (Exception e)
+        }
+        else
         {
-          e.printStackTrace();
+          mainFrame.setTitle("Structure Chooser - Filter time ("
+                  + totalTime + ")");
+          if (errors.size() > 0)
+          {
+            StringBuilder errorMsg = new StringBuilder(
+                    "Operation unsucessful due to the following: \n");
+            for (String error : errors)
+            {
+              errorMsg.append(error).append("\n");
+            }
+            JOptionPane.showMessageDialog(null, errorMsg.toString(),
+                    "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+          }
         }
+
+        lbl_loading.setVisible(false);
+
+        validateSelections();
       }
     });
     filterThread.start();
@@ -460,6 +503,7 @@ public class StructureChooser extends GStructureChooser
     else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
             || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
     {
+      mainFrame.setTitle(filterTitle);
       idInputAssSeqPanel.loadCmbAssSeq();
       fileChooserAssSeqPanel.loadCmbAssSeq();
     }
@@ -737,7 +781,20 @@ public class StructureChooser extends GStructureChooser
       pdbRequest.setSearchTerm(txt_search.getText() + ")");
       pdbRequest.setAssociatedSequence(selectedSequence.getName());
       pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      PDBRestResponse resultList;
+      try
+      {
+        resultList = pdbRestCleint.executeRequest(pdbRequest);
+      } catch (Exception e)
+      {
+        JOptionPane.showMessageDialog(this, e.getMessage(),
+                "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+        return;
+      } finally
+      {
+        System.out.println(">>>>> executing finally block");
+        validateSelections();
+      }
       if (resultList.getSearchSummary() != null
               && resultList.getSearchSummary().size() > 0)
       {