Changeset 1129 for extensions/net.sf.basedb.genepattern

Timestamp:

Jun 16, 2009, 1:33:33 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

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

Separated adding and copying of files to two separate steps. Added a convenience method
for downloading a file and reading it into a string.

File:

• extensions/net.sf.basedb.genepattern/trunk/src/net/sf/basedb/genepattern/file/FileTransferGateway.java (modified) (9 diffs)

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

@@ -2 +2 @@
 
 import java.io.BufferedInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileFilter;
@@ -8 +9 @@
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
@@ -15 +18 @@
 import net.sf.basedb.core.ConfigurationException;
 import net.sf.basedb.core.ItemAlreadyExistsException;
+import net.sf.basedb.core.ProgressReporter;
+import net.sf.basedb.core.signal.ThreadSignalHandler;
 import net.sf.basedb.genepattern.wrapper.JobResult;
 import net.sf.basedb.util.FileUtil;
@@ -27 +32 @@
   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.
+  GenePattern. After all files has been added to the gateway, {@link #prepareForUpload()}
+  must be called. This method makes a copy of all added files to a temporary
+  location that is accessible by the GenePattern server via the BASE web server
+  (even if the file transfer is initialized from a job agent). 
   <p>
   Once the job has finished the result files can be downloaded with
@@ -52 +60 @@
   private final Set<String> uploadFiles;
   private final Set<File> downloadFiles;
+  private final List<FileProxy> proxies;
   private final File workDir;
   private final Set<String> directories;
@@ -69 +78 @@
     this.directories = new HashSet<String>();
     this.downloadFiles = new HashSet<File>();
+    this.proxies = new ArrayList<FileProxy>();
     this.workDir = new File(new File(System.getProperty("java.io.tmpdir")), getId());
     directories.add(cacheRoot);
@@ -113 +123 @@
       throw new ItemAlreadyExistsException("File already exists: " + filename);
     }
+    uploadFiles.add(filename);
+    proxies.add(file);
+    String downloadPath = subDir + "/" + id + "/" + filename;
+    return new Parameter(gpParameterName, downloadServletUrl + "/" + downloadPath);
+  }
+  
+  /**
+    Prepare all added files for upload. The preparation includes
+    copying the files to a temporary location so this method may
+    take some time if the files are large.
+    @param progress An optional progress reporter
+    @return The number of files copied
+  */
+  public int prepareUpload(ProgressReporter progress)
+  {
     StaticCache cache = Application.getStaticCache();
     if (cache.isDisabled())
@@ -120 +145 @@
     }
     
-    String downloadPath = subDir + "/" + id + "/" + filename;
-    String cacheKey = cacheRoot + "/" + downloadPath;
-    OutputStream toCache = null;
-    InputStream fromProxy = null;
-    try
-    {
-      fromProxy = file.getInputStream();
-      if (fromProxy != null)
-      {
-        cache.write(cacheKey, fromProxy, 1000);
-      }
-      else
-      {
-        toCache = cache.write(cacheKey, 1000);
-        file.writeTo(toCache);
-      }
-    }
-    catch (IOException ex)
-    {
-      throw new RuntimeException(ex);
-    }
-    finally
-    {
-      FileUtil.close(toCache);
-      FileUtil.close(fromProxy);
-    }
-    uploadFiles.add(filename);
-    return new Parameter(gpParameterName, downloadServletUrl + "/" + downloadPath);
+    int numFiles = proxies.size();
+    int currentFile = 0;
+    for (FileProxy file : proxies)
+    {
+      ThreadSignalHandler.checkInterrupted();
+      String filename = file.getFileName();
+      String downloadPath = subDir + "/" + id + "/" + filename;
+      String cacheKey = cacheRoot + "/" + downloadPath;
+      OutputStream toCache = null;
+      InputStream fromProxy = null;
+      if (progress != null)
+      {
+        progress.display(100 * currentFile / numFiles, "Copying '" + filename + "'");
+      }
+      try
+      {
+        fromProxy = file.getInputStream();
+        if (fromProxy != null)
+        {
+          cache.write(cacheKey, fromProxy, 1000);
+        }
+        else
+        {
+          toCache = cache.write(cacheKey, 1000);
+          file.writeTo(toCache);
+        }
+      }
+      catch (IOException ex)
+      {
+        throw new RuntimeException(ex);
+      }
+      finally
+      {
+        FileUtil.close(toCache);
+        FileUtil.close(fromProxy);
+      }
+    }
+    proxies.clear();
+    return numFiles;
   }
   
@@ -193 +229 @@
   {
     return FileUtil.copy(downloadResultFile(result, filename), to);
+  }
+  
+  /**
+    Download a GenePattern result file and read it in as a string.
+    @param result The job result information
+    @param filename The name of a (text) file that is part of the job result
+    @param charset The character set used in the file
+    @return The file contents as a string
+    @throws IOException
+  */
+  public String downloadAsString(JobResult result, String filename, String charset)
+    throws IOException
+  {
+    ByteArrayOutputStream to = new ByteArrayOutputStream();
+    downloadResultFile(result, filename, to);
+    return to.toString(charset);
   }