JAL-2465 fix to prevent files loaded from the system's temporary directory from being...

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 88f9ae5..bd8bc53 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -34,15 +34,18 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.ws.utils.UrlDownloadClient;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
@@ -53,7 +56,8 @@ public class FileLoader implements Runnable
 
   FileFormatI format;
 
-  AlignmentFileI source = null; // alternative specification of where data comes
+  AlignmentFileReaderI source = null; // alternative specification of where data
+                                      // comes
 
   // from
 
@@ -160,7 +164,7 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
           FileFormatI format)
   {
     this.source = source;
@@ -204,6 +208,12 @@ public class FileLoader implements Runnable
       // refer to it as.
       return;
     }
+    if (file != null
+            && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+    {
+      // ignore files loaded from the system's temporary directory
+      return;
+    }
     String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
@@ -237,7 +247,7 @@ public class FileLoader implements Runnable
 
     if (protocol == DataSourceType.FILE)
     {
-      Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
     }
   }
 
@@ -275,13 +285,13 @@ public class FileLoader implements Runnable
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          javax.swing.JOptionPane.showInternalMessageDialog(
+          JvOptionPane.showInternalMessageDialog(
                   Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
-                          + AppletFormatAdapter.SUPPORTED_FORMATS,
+                          + AppletFormatAdapter.getSupportedFormats(),
                   MessageManager.getString("label.couldnt_read_data"),
-                  JOptionPane.WARNING_MESSAGE);
+                  JvOptionPane.WARNING_MESSAGE);
         }
         return;
       }
@@ -298,7 +308,7 @@ public class FileLoader implements Runnable
       loadtime = -System.currentTimeMillis();
       AlignmentI al = null;
 
-      if (format == FileFormat.Jalview)
+      if (FileFormat.Jalview.equals(format))
       {
         if (source != null)
         {
@@ -311,27 +321,41 @@ public class FileLoader implements Runnable
       }
       else
       {
-        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-          try
+        String error = AppletFormatAdapter.getSupportedFormats();
+        try
+        {
+          if (source != null)
+          {
+            // read from the provided source
+            al = new FormatAdapter().readFromFile(source, format);
+          }
+          else
           {
-            if (source != null)
-            {
-              // read from the provided source
-              al = new FormatAdapter().readFromFile(source, format);
-            }
-            else
-            {
 
-              // open a new source and read from it
-              FormatAdapter fa = new FormatAdapter();
-              al = fa.readFile(file, protocol, format);
-              source = fa.getAlignFile(); // keep reference for later if
-                                          // necessary.
+            // open a new source and read from it
+            FormatAdapter fa = new FormatAdapter();
+            boolean downloadStructureFile = format.isStructureFile()
+                    && protocol.equals(DataSourceType.URL);
+            if (downloadStructureFile)
+            {
+              String structExt = format.getExtensions().split(",")[0];
+              String urlLeafName = file.substring(file.lastIndexOf(System
+                      .getProperty("file.separator")), file
+                      .lastIndexOf("."));
+              String tempStructureFileStr = createNamedJvTempFile(
+                      urlLeafName, structExt);
+              UrlDownloadClient.download(file, tempStructureFileStr);
+              file = tempStructureFileStr;
+              protocol = DataSourceType.FILE;
             }
-          } catch (java.io.IOException ex)
-          {
-            error = ex.getMessage();
+            al = fa.readFile(file, protocol, format);
+            source = fa.getAlignFile(); // keep reference for later if
+                                        // necessary.
           }
+        } catch (java.io.IOException ex)
+        {
+          error = ex.getMessage();
+        }
 
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
@@ -455,10 +479,10 @@ public class FileLoader implements Runnable
               @Override
               public void run()
               {
-                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                         errorMessage, MessageManager
                                 .getString("label.error_loading_file"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
               }
             });
           }
@@ -482,12 +506,12 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            javax.swing.JOptionPane.showInternalMessageDialog(
+            JvOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
                             "label.problems_opening_file",
                             new String[] { file }), MessageManager
                             .getString("label.file_open_error"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -504,12 +528,12 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            javax.swing.JOptionPane.showInternalMessageDialog(
+            JvOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }), MessageManager
                             .getString("label.out_of_memory"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -555,6 +579,29 @@ public class FileLoader implements Runnable
 
   }
 
+  /**
+   * This method creates the file -
+   * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+   * file name and extension
+   * 
+   * @param fileName
+   *          the name of the temp file to be created
+   * @param extension
+   *          the extension of the temp file to be created
+   * @return
+   */
+  private static String createNamedJvTempFile(String fileName,
+          String extension) throws IOException
+  {
+    String seprator = System.getProperty("file.separator");
+    String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+            + seprator + System.currentTimeMillis();
+    File tempStructFile = new File(jvTempDir + seprator + fileName + "."
+            + extension);
+    tempStructFile.mkdirs();
+    return tempStructFile.toString();
+  }
+
   /*
    * (non-Javadoc)
    *