zip file documents

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13728 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/util/ZipFileDocument.java

+/* ZipFileDocument
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2010  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+
+package uk.ac.sanger.artemis.util;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+public class ZipFileDocument extends FileDocument
+{
+  private File zipFile;
+  private String zipEntryName;
+  
+  public ZipFileDocument(File zipFile, String zipEntryName)
+  {
+    super(zipFile);
+    this.zipFile = zipFile;
+    this.zipEntryName = zipEntryName;
+  }
+  
+  /**
+   *  Return the name of this Document.
+   **/
+  public String getName () {
+    return zipEntryName;
+  }
+  
+  /**
+   *  Create a new InputStream object from this Document.  The contents of the
+   *  Document can be read from the InputStream.
+   *  @exception IOException Thrown if the Document can't be read from
+   *    (for example if it doesn't exist).
+   **/
+  public InputStream getInputStream() throws IOException
+  {
+    System.out.println(zipEntryName);
+    
+    if(!zipFile.getName().endsWith(".zip"))
+      return super.getInputStream();
+    
+    System.out.println(zipEntryName);
+    byte b[] = getEntryContent(zipFile, zipEntryName);
+    
+    if(b == null)
+    {
+      if(!zipEntryName.endsWith(".gz"))
+      {
+        zipEntryName = zipEntryName + ".gz";
+        b = getEntryContent(zipFile, zipEntryName);
+      }
+      
+      if(b == null)
+      {
+        return null;
+      }
+    }
+    if(zipEntryName.endsWith(".gz"))
+      return new WorkingGZIPInputStream(new ByteArrayInputStream(b));
+    return new ByteArrayInputStream(b);
+  }
+  
+  /**
+   * Returns true if the zip file contains the entry name.
+   * @return
+   */
+  private boolean containsEntry()
+  {
+    try
+    {
+      ZipInputStream zis = new ZipInputStream(
+          new FileInputStream(zipFile));
+      ZipEntry ze;
+      
+      while ((ze=zis.getNextEntry())!=null)
+      {
+        if( !ze.isDirectory() && 
+            (ze.getName().equals(zipEntryName) || ze.getName().equals(zipEntryName+".gz")))
+        {
+          if(ze.getName().equals(zipEntryName+".gz"))
+            zipEntryName = ze.getName();
+          zis.close();
+          return true;
+        }
+      }
+      zis.close();
+    }
+    catch (IOException e){}
+    
+    return false;
+  }
+  
+  /**
+   *  Return true if and only if the Document referred to by this object exists
+   *  and is readable.
+   **/
+  public boolean readable() 
+  {
+    if(getFile().exists() && 
+       getFile ().canWrite() && 
+       zipFile.getName().endsWith(".zip")) 
+    {
+      if(containsEntry())
+        return true;
+    } 
+    return false;
+  }
+  
+  private static byte[] getEntryContent(File zipFile, String zipEntryName) throws IOException
+  {
+    ZipInputStream zis= new ZipInputStream(
+                     new FileInputStream(zipFile));
+      
+    ZipEntry ze;
+    while ((ze=zis.getNextEntry())!=null)
+    {
+      if(ze.isDirectory() || !ze.getName().equals(zipEntryName))
+        continue;
+
+      ByteBuffer buff = new ByteBuffer();
+      byte[] b = new byte[1];
+      while(zis.read(b,0,1) != -1)
+        buff.append(b);
+      return buff.getBytes();
+    }
+    return null;
+  }
+
+  public static void main(String[] args)
+  {
+    System.out.println(args[1]);
+
+    try
+    {
+      ZipFileDocument document = new ZipFileDocument(new File(args[0]), args[1]);
+      InputStream in = document.getInputStream();
+      StringBuffer out = new StringBuffer();
+      byte[] b = new byte[4096];
+      for (int n; (n = in.read(b)) != -1;) {
+          out.append(new String(b, 0, n));
+      }
+      System.out.println(new String(out));
+      
+    }
+    catch (IOException e)
+    {
+      e.printStackTrace();
+    }
+  }
+}
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