JAL-4414 Add a FileNotFoundException when identifying URL file formats and catch...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index b6a5a25..5ef32c8 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import java.awt.Color;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.util.ArrayList;
@@ -286,6 +287,10 @@ public class Commands
         try
         {
           format = new IdentifyFile().identify(openFile, protocol);
+        } catch (FileNotFoundException e0)
+        {
+          addError((protocol == DataSourceType.URL ? "File at URL" : "File")
+                  + " '" + openFile + "' not found");
         } catch (FileFormatException e1)
         {
           addError("Unknown file format for '" + openFile + "'");
@@ -1301,18 +1306,22 @@ public class Commands
 
   private void colourAlignFrame(AlignFrame af, ColourSchemeI cs)
   {
-    try {
-    SwingUtilities.invokeAndWait(new Runnable()
+    try
     {
-      @Override
-      public void run()
+      SwingUtilities.invokeAndWait(new Runnable()
       {
-        // Note that cs == null removes colour scheme from af
-        af.changeColour(cs);
-      }
-    }); } catch (Exception x) {
-      Console.trace("Interrupted whilst waiting for colorAlignFrame action",x);
-      
+        @Override
+        public void run()
+        {
+          // Note that cs == null removes colour scheme from af
+          af.changeColour(cs);
+        }
+      });
+    } catch (Exception x)
+    {
+      Console.trace("Interrupted whilst waiting for colorAlignFrame action",
+              x);
+
     }
   }
 

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e343b0f..d8e149d 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,7 @@ package jalview.bin;
 import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -938,9 +939,12 @@ public class Jalview implements JalviewObjectI
       try
       {
         format = new IdentifyFile().identify(file, protocol);
-      } catch (FileFormatException e1)
+      } catch (FileNotFoundException e)
       {
-        // TODO ?
+        Console.error("File at '" + file + "' not found", e);
+      } catch (FileFormatException e)
+      {
+        Console.error("File '" + file + "' format not recognised", e);
       }
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -1211,9 +1215,12 @@ public class Jalview implements JalviewObjectI
         try
         {
           format = new IdentifyFile().identify(file, protocol);
+        } catch (FileNotFoundException e)
+        {
+          Console.error("File at '" + file + "' not found", e);
         } catch (FileFormatException e)
         {
-          // TODO what?
+          Console.error("File '" + file + "' format not recognised", e);
         }
       }
 

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index bc3c0d2..91f8189 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -28,6 +28,7 @@ import java.awt.datatransfer.Transferable;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
+import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -226,6 +227,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     try
     {
       format = new IdentifyFile().identify(text, DataSourceType.PASTE);
+    } catch (FileNotFoundException e0)
+    {
+      // this won't happen
     } catch (FileFormatException e1)
     {
       // leave as null

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index bbd4dae..4c30a06 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -54,6 +54,7 @@ import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyVetoException;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.lang.reflect.Field;
@@ -1400,10 +1401,13 @@ public class Desktop extends jalview.jbgui.GDesktop
         try
         {
           format = new IdentifyFile().identify(url, DataSourceType.URL);
+        } catch (FileNotFoundException e)
+        {
+          jalview.bin.Console.error("URL '" + url + "' not found", e);
         } catch (FileFormatException e)
         {
-          // TODO revise error handling, distinguish between
-          // URL not found and response not valid
+          jalview.bin.Console.error(
+                  "File at URL '" + url + "' format not recognised", e);
         }
 
         if (format == null)

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 76aa2fa..ca0588a 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -426,7 +426,7 @@ public class FileParse
    * @throws IOException
    */
   public FileParse(Object file, DataSourceType sourceType)
-          throws MalformedURLException, IOException
+          throws MalformedURLException, FileNotFoundException, IOException
   {
     if (file instanceof File)
     {
@@ -439,11 +439,12 @@ public class FileParse
   }
 
   private void parse(File file, String fileStr, DataSourceType sourceType,
-          boolean isFileObject) throws IOException
+          boolean isFileObject) throws FileNotFoundException, IOException
   {
     bytes = Platform.getFileBytes(file);
     dataSourceType = sourceType;
     error = false;
+    boolean filenotfound = false;
 
     if (sourceType == DataSourceType.FILE)
     {
@@ -502,6 +503,11 @@ public class FileParse
           String suffixLess = extractSuffix(fileStr);
           if (suffixLess == null)
           {
+            if (e instanceof FileNotFoundException)
+            {
+              errormessage = "File at URL '" + fileStr + "' not found";
+              filenotfound = true;
+            }
             throw (e);
           }
           else
@@ -511,7 +517,12 @@ public class FileParse
               checkURLSource(suffixLess);
             } catch (IOException e2)
             {
-              errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+              errormessage = "BAD URL WITH OR WITHOUT SUFFIX '" + fileStr
+                      + "'";
+              if (e instanceof FileNotFoundException)
+              {
+                filenotfound = true;
+              }
               throw (e); // just pass back original - everything was wrong.
             }
           }
@@ -560,6 +571,12 @@ public class FileParse
     if (dataIn == null || error)
     {
       // pass up the reason why we have no source to read from
+      if (filenotfound)
+      {
+        throw new FileNotFoundException(MessageManager
+                .formatMessage("label.url_not_found", new String[]
+                { errormessage }));
+      }
       throw new IOException(MessageManager.formatMessage(
               "exception.failed_to_read_data_from_source", new String[]
               { errormessage }));

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 00e2872..8251c22 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Locale;
 
@@ -38,7 +39,7 @@ public class IdentifyFile
   private static final String XMLHEADER = "<?XML VERSION=\"1.0\" ENCODING=\"UTF-8\" STANDALONE=\"YES\"?>";
 
   public FileFormatI identify(Object file, DataSourceType protocol)
-          throws FileFormatException
+          throws FileFormatException, FileNotFoundException
   {
     // BH 2018
     return (file instanceof File ? identify((File) file, protocol)
@@ -83,10 +84,11 @@ public class IdentifyFile
    * @throws FileFormatException
    */
   public FileFormatI identify(String file, DataSourceType sourceType)
-          throws FileFormatException
+          throws FileFormatException, FileNotFoundException
   {
     String emessage = "UNIDENTIFIED FILE PARSING ERROR";
     FileParse parser = null;
+    FileNotFoundException fnf = null;
     try
     {
       parser = new FileParse(file, sourceType);
@@ -94,6 +96,11 @@ public class IdentifyFile
       {
         return identify(parser);
       }
+    } catch (FileNotFoundException e)
+    {
+      fnf = e;
+      emessage = "Could not find '" + file + "'";
+      Console.error("Could not find '" + file + "'", e);
     } catch (IOException e)
     {
       Console.error("Error whilst trying to read " + file, e);
@@ -106,6 +113,10 @@ public class IdentifyFile
     {
       throw new FileFormatException(parser.errormessage);
     }
+    if (fnf != null)
+    {
+      throw (fnf);
+    }
     throw new FileFormatException(emessage);
   }
 
@@ -497,6 +508,10 @@ public class IdentifyFile
       try
       {
         type = ider.identify(args[i], DataSourceType.FILE);
+      } catch (FileNotFoundException e)
+      {
+        Console.error(String.format("Error '%s' fetching file %s", args[i],
+                e.getMessage()));
       } catch (FileFormatException e)
       {
         Console.error(

diff --git a/test/jalview/io/IdentifyFileTest.java b/test/jalview/io/IdentifyFileTest.java
index 68c099e..6ee3f0e 100644 (file)
--- a/test/jalview/io/IdentifyFileTest.java
+++ b/test/jalview/io/IdentifyFileTest.java
@@ -24,6 +24,8 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.FileNotFoundException;
+
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -43,7 +45,7 @@ public class IdentifyFileTest
 
   @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
   public void testIdentify(String data, FileFormatI expectedFileType)
-          throws FileFormatException
+          throws FileFormatException, FileNotFoundException
   {
     DataSourceType protocol = DataSourceType.FILE;
     IdentifyFile ider = new IdentifyFile();
@@ -58,7 +60,8 @@ public class IdentifyFileTest
    * @throws FileFormatException
    */
   @Test(groups = "Functional")
-  public void testIdentify_featureFile() throws FileFormatException
+  public void testIdentify_featureFile()
+          throws FileFormatException, FileNotFoundException
   {
     IdentifyFile ider = new IdentifyFile();