Changeset 3510

Timestamp:

Jun 19, 2007, 8:56:23 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #470

Location:

trunk

Files:

• bin/set_classpath.bat (modified) (1 diff)
• bin/set_classpath.sh (modified) (1 diff)
• doc/3rd-party-components.txt (modified) (1 diff)
• doc/licenses/tar.license.txt (added)
• lib/dist/bzip2.jar (added)
• lib/dist/tar.jar (added)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/util/FileUtil.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/InputStreamTracker.java (added)
• src/core/net/sf/basedb/util/zip/AbstractFileUnpacker.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java (added)
• src/test/set_classpath.bat (modified) (1 diff)
• src/test/set_classpath.sh (modified) (1 diff)

trunk/bin/set_classpath.bat

@@ -86 +86 @@
 REM Affymetrix Fusion SDK
 SET CP=%CP%;%WEBINF%/lib/AffxFusion.jar
+
+REM TAR and BZIP
+SET CP=%CP%;%WEBINF%/lib/tar.jar
+SET CP=%CP%;%WEBINF%/lib/bzip2.jar

trunk/bin/set_classpath.sh

@@ -85 +85 @@
 # Affymetrix Fusion SDK
 CP=$CP:$WEBINF/lib/AffxFusion.jar
+
+# TAR and BZIP
+CP=$CP:$WEBINF/lib/tar.jar
+CP=$CP:$WEBINF/lib/bzip2.jar

trunk/doc/3rd-party-components.txt

@@ -238 +238 @@
 Files    : AffxFusion.jar
 
+TAR file support
+----------------
+Package for reading and writing TAR files.
+
+More info: http://www.trustice.com/java/tar/
+Version  : 2.5
+License  : tar.license.txt
+Files    : tar.jar
+
+BZIP file support
+-----------------
+Package for reading and writing BZIP files.
+
+More info: http://www.kohsuke.org/bzip2/
+Version  : unknown
+License  : Apache software license (apache.license.txt)
+Files    : bzip2.jar
+
+
+

trunk/src/core/net/sf/basedb/core/Install.java

@@ -602 +602 @@
       createPluginDefinition("net.sf.basedb.plugins.SpotImageCreator", null, keyEveryoneUse, true, null, false);
       createPluginDefinition("net.sf.basedb.plugins.ZipFileUnpacker", null, keyEveryoneUse, true, null, true);
+      createPluginDefinition("net.sf.basedb.plugins.TarFileUnpacker", null, keyEveryoneUse, true, null, true);
       createPluginDefinition("net.sf.basedb.plugins.PluginConfigurationExporter", null, keyEveryoneUse, true, null, true);
       createPluginDefinition("net.sf.basedb.plugins.PluginConfigurationImporter", null, null, true, null, false);

trunk/src/core/net/sf/basedb/util/FileUtil.java

@@ -36 +36 @@
 import net.sf.basedb.core.query.Orders;
 
+import java.util.Arrays;
 import java.util.List;
 import java.util.LinkedList;
@@ -49 +50 @@
 import java.io.FileInputStream;
 import java.io.BufferedInputStream;
+import java.io.PushbackInputStream;
 
 /**
@@ -118 +120 @@
   
   /**
+    Take a peek at an input stream and check if the first few bytes
+    matches the bCheck parameter. After the check the bytes are
+    pushed back to the stream again. This method is useful to check
+    the file format of a file, which can often be done by checing
+    the first few bytes at the start of the file. For example
+    to check if the file is gzip file:
+    <p>
+    <code>bCheck = new byte[] { 0x1f, (byte)0x8b };</code>
+    
+    @param pin The input stream to read from which must have
+      large enough buffer to be able to unread the bytes
+    @param bCheck The byte values to use for comparison
+    @return TRUE if the file matches the specified bytes, 
+      FALSE otherwise
+    @throws IOException If there is an error reading or unreading
+      the bytes
+    @throws NullPointerException If pin or bCheck is null
+    @throws IllegalArgumentException If bCheck is zero length
+    @since 2.4
+  */
+  public static boolean checkMagicNumber(PushbackInputStream pin, byte[] bCheck)
+    throws IOException
+  {
+    if (pin == null) throw new NullPointerException("pin");
+    if (bCheck == null) throw new NullPointerException("bCheck");
+    if (bCheck.length == 0) throw new IllegalArgumentException("bCheck has zero length");
+    byte[] b = new byte[bCheck.length];
+    pin.read(b);
+    boolean match = Arrays.equals(b, bCheck);
+    pin.unread(b);
+    return match;
+  }
+  
+  /**
     Get the complete tree of subdirectories from a given directory.
     @param directory The directory to start with

trunk/src/core/net/sf/basedb/util/zip/AbstractFileUnpacker.java

@@ -198 +198 @@
       if (!getMimeTypes().contains(mimeType))
       {
-        int dotIndex = name.lastIndexOf('.');
-        String extension = name.substring(dotIndex + 1);
-        if (dotIndex ==  -1 || !getExtensions().contains(extension))
+        for (String extension : getExtensions())
         {
-          message = "Unsupported file: " + f.getPath().toString();
+          if (name.endsWith(extension)) return null;
         }
+        message = "Unsupported file: " + f.getPath().toString();
       }
     }
@@ -277 +276 @@
     @return The packed file or null
     @see #getZipFileParameter(String, String)
+    @see #getCurrentFile(DbControl)
   */
   protected File getZipFile(DbControl dc)
@@ -304 +304 @@
     if (label == null) label = "Save in";
     if (description == null) description = "The directory where the unpacked files should be saved.";
-    return new PluginParameter<String>(UNPACK_DIRECTORY, label, description , unpackType); 
-  }
+    DbControl dc = sc.newDbControl();
+    String defaultDir = null;
+    try
+    {
+      Directory dir = getCurrentDirectory(dc);
+      if (dir != null) defaultDir = dir.getPath().toString();
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+    return new PluginParameter<String>(UNPACK_DIRECTORY, label, description , defaultDir, unpackType); 
+  }
+  
+  /**
+    Get the current directory or null there is no current or it can't be loaded.
+    This method will first try to load the current file and use the file's
+    directory as the current. If there is no current file, the current directory
+    is loaded from the session context.
+    The current directory is only available in the configuration phase.
+    
+    @param dc A DbControl to use for database access
+    @return A directory or null
+    @since 2.4
+    @see #getUnpackDirectory(DbControl)
+  */
+  protected Directory getCurrentDirectory(DbControl dc)
+  {
+    File currentFile = getCurrentFile(dc);
+    if (currentFile != null) return currentFile.getDirectory();
+    int directoryId = sc.getCurrentContext(Item.DIRECTORY).getId();
+    if (directoryId != 0)
+    {
+      try
+      {
+        return Directory.getById(dc, directoryId);
+      }
+      catch (Throwable t)
+      {}
+    }
+    return null;
+  }
+  
+  /**
+    Get the current file or null there is no current or it can't be loaded.
+    The current file is only available in the configuration phase.
+    @param dc A DbControl to use for database access
+    @return A file or null
+    @since 2.4
+    @see #getZipFile(DbControl)
+  */
+  protected File getCurrentFile(DbControl dc)
+  {
+    int fileId = sc.getCurrentContext(Item.FILE).getId();
+    if (fileId != 0)
+    {
+      try
+      {
+        return File.getById(dc, fileId);
+      }
+      catch (Throwable t)
+      {}
+    }
+    return null;
+  } 
   
   /**
@@ -314 +377 @@
     @return The directory or null
     @see #getDirectoryParameter(String, String)
+    @see #getCurrentDirectory(DbControl)
   */
   protected Directory getUnpackDirectory(DbControl dc)

trunk/src/test/set_classpath.bat

@@ -81 +81 @@
 REM Affymetrix Fusion SDK
 SET CP=%CP%;../../lib/dist/AffxFusion.jar
+
+REM TAR and BZIP
+SET CP=%CP%;../../lib/dist/tar.jar
+SET CP=%CP%;../../lib/dist/bzip2.jar
+

trunk/src/test/set_classpath.sh

@@ -82 +82 @@
 # Affymetrix Fusion SDK
 CP=$CP:$LIB/AffxFusion.jar
+
+# TAR and BZIP
+CP=$CP:$LIB/tar.jar
+CP=$CP:$LIB/bzip2.jar