Changeset 1109 for extensions/net.sf.basedb.genepattern/trunk/src/net

Timestamp:

Jun 4, 2009, 11:35:59 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #222: Utility for transfering file between BASE and a GenePattern? server

Added support for downloading files. The files are downloaded to a temporary working directory and exposed as InputStream/OutputStream objects since that suits the BASE API better. I first tried to use JobResult.getURLForFileName() but that issues a request outside the web services session and only results in downloading a HTML page asking for a login/password.

File:

• extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/file/FileTransferGateway.java (modified) (7 diffs)

extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/file/FileTransferGateway.java

@@ -1 +1 @@
 package net.sf.basedb.genepattern.file;
 
+import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileFilter;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -17 +19 @@
 import net.sf.basedb.util.formatter.DateFormatter;
 
+import org.genepattern.webservice.JobResult;
 import org.genepattern.webservice.Parameter;
 
 /**
-  Handles file transfers to a GenePattern server. One getaway instance can
+  Handles file transfers to and from a GenePattern server. One getaway instance can
   handle file for one GenePattern job. The files that are needed for the
   job should be added to the gateway with {@link #addFile(String, FileProxy)}
   which returns a {@link Parameter} object that can be used when invoking
   GenePattern.
+  <p>
+  Once the job has finished the result files can be downloaded with
+  {@link #downloadResultFile(JobResult, String, OutputStream)} or
+  {@link #downloadResultFile(JobResult, String)}.
+  <p>
+  After the gateway has been used it is recommended to call {@link #cleanUp()}
+  to make sure that any temporary files are deleted.
     
   @author nicklas
@@ -40 +50 @@
   private final String id;
   private final String baseUrl;
-  private final Set<String> files;
+  private final Set<String> uploadFiles;
+  private final Set<File> downloadFiles;
+  private final File workDir;
   private final Set<String> directories;
   private final String subDir;
@@ -56 +68 @@
     this.id = "gp-" + System.identityHashCode(this);
     this.subDir = new DateFormatter("yyyy-MM-dd").format(new Date());
-    this.files = new HashSet<String>();
+    this.uploadFiles = new HashSet<String>();
     this.directories = new HashSet<String>();
+    this.downloadFiles = new HashSet<File>();
+    this.workDir = new File(new File(System.getProperty("java.io.tmpdir")), getId());
     directories.add(cacheRoot);
     directories.add(subDir);
@@ -97 +111 @@
   {
     String filename = file.getFileName();
-    if (files.contains(filename))
+    if (uploadFiles.contains(filename))
     {
       throw new ItemAlreadyExistsException("File already exists: " + filename);
@@ -134 +148 @@
       FileUtil.close(fromProxy);
     }
-    files.add(filename);
+    uploadFiles.add(filename);
     return new Parameter(gpParameterName, baseUrl + "/Download/" + downloadPath + ".servlet");
   }
   
   /**
-    Clean up and remove all files that has been added to this gateway.
+    Download a GenePattern result file and make it available as a InputStream.
+    Downloaded file are cached and subseqent calls to this method requesting
+    the same filename will use the cached file.
+    
+    @param result The job result information
+    @param filename A filename that is part of the job result
+    @return An input stream that reads from the downloaded file or null if the
+      file doesn't exists as part of the job result
+    @throws IOException
+  */
+  public InputStream downloadResultFile(JobResult result, String filename)
+    throws IOException
+  {
+    File workDir = getWorkingDirectory();
+    File tmpFile = new File(workDir, filename);
+    if (!tmpFile.exists())
+    {
+      tmpFile = result.downloadFile(filename, workDir.getAbsolutePath(), true);
+      if (tmpFile != null) downloadFiles.add(tmpFile);
+    }
+    InputStream in = null;
+    if (tmpFile != null)
+    {
+      in = new BufferedInputStream(new FileInputStream(tmpFile));
+    }
+    return in;
+  }
+  
+  /**
+    Download a GenePattern result file and copy it to the given ouput stream.
+    Downloaded file are cached and subseqent calls to this method requesting
+    the same filename will use the cached file.
+    
+    @param result The job result information
+    @param filename A filename that is part of the job result
+    @param to The output stream to write to
+    @throws IOException
+  */
+  public long downloadResultFile(JobResult result, String filename, OutputStream to)
+    throws IOException
+  {
+    return FileUtil.copy(downloadResultFile(result, filename), to);
+  }
+  
+  private File getWorkingDirectory()
+  {
+    workDir.mkdirs();
+    return workDir;
+  }
+  
+  /**
+    Clean up and remove all files that has been added or downloaded 
+    to this gateway.
   */
   public void cleanUp()
   {
-    if (files.size() > 0)
+    if (uploadFiles.size() > 0)
     {
       StaticCache cache = Application.getStaticCache();
@@ -153 +219 @@
           {
             String name = file.getName();
-            boolean accept = file.isDirectory() ?directories.contains(name) :
-              id.equals(file.getParentFile().getName()) && files.contains(name);
+            boolean accept = file.isDirectory() ? directories.contains(name) :
+              id.equals(file.getParentFile().getName()) && uploadFiles.contains(name);
             return accept;
           }
         }
       );
-      files.clear();
+      uploadFiles.clear();
+    }
+    if (downloadFiles.size() > 0)
+    {
+      for (File f : downloadFiles)
+      {
+        f.delete();
+      }
+      workDir.delete();
+      downloadFiles.clear();
     }
   }