Changeset 472

Timestamp:

Nov 12, 2007, 5:50:07 PM (16 years ago)

Author:

dominic

Message:

added newly changed code. This source code is not in sycn with the current released version of the tab2mage importer.

Location:

trunk/uk/ac/ebi/Tab2MageImporter

Files:

• README.txt (modified) (1 diff)
• src/uk/ac/ebi/nugo/plugins/Helper.java (modified) (3 diffs)
• src/uk/ac/ebi/nugo/plugins/ZipUnpacker.java (modified) (13 diffs)

trunk/uk/ac/ebi/Tab2MageImporter/README.txt

@@ -63 +63 @@
   When the import has finished, you can check and review the uploaded experiment by navigating through base2 web client, using the menu. If you have provided your email server name. You would receive an email message on the status of the import.
 
+=========================================================
+Pooling Implementation
+--------------------------------
+The tab2mage importer runs in a pooled or non- pooled state.
+A pooling protocol - Protocol[pool] must be specified for experiments that involve pooling, otherwise the importer would run in a non-pool state.
+
+One stage pooling - > biosource to sample, sample to extract or extract to labeled extract is fully supported
+
+Multiple stage pooling: biosource to sample and sample to extract supported.  Note that Multi stage pooling involving labeled extract is not supported.
+
+Please check pooling notes link on the download page for more information
+
+For usability and consistency on the biomaterial user interface, do run the same experiment twice. An imported experiment (with raw data and meta-data) that involves pooling may only be loaded once.
+
  ===========================================================
 AnnotationTypes and Cv Importer

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Helper.java

@@ -82 +82 @@
       }
       Path path = new Path(pathString, Path.Type.FILE);   
-      
       file= File.getByPath(dc, path, true); 
       file.setMimeType("text/plain"); //set the type of the file
@@ -135 +134 @@
    {
      String fileName= file.getName();
-     //System.out.println("\nThe file name is: " + fileName );
      String ext= fileName.substring(fileName.lastIndexOf(".") + 1);
      ext = ext.toLowerCase();
-     //System.out.printf("The file ext is: %s\n", ext);
-     return ext;
+      return ext;
    }
    
@@ -370 +367 @@
     return p;
   }
+  
+  /**
+    validates the directory parameter specified by user
+    @param file, the zip file. its directory, is checked for the existence of directoryName given by the user
+    @param directoryName, the name of the directory specified by the user
+    @return TRUE if directory exist and FALSE otherwise
+  */
+  public static boolean validateDirectory (SessionControl sc ,File file, String directoryName)
+  {
+    DbControl dc = sc.newDbControl();
+    try
+    {
+      file = File.getById(dc, file.getId());
+      return Directory.exists(dc, file.getDirectory(), directoryName);
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    } 
+  }
 }

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/ZipUnpacker.java

@@ -9 +9 @@
 import java.io.IOException;
 import java.io.InputStream;
+import java.text.SimpleDateFormat;
 import java.util.Date;
+import java.util.Locale;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
-import net.sf.basedb.core.DatabaseException;
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Directory;
 import net.sf.basedb.core.File;
+import net.sf.basedb.core.ItemAlreadyExistsException;
 import net.sf.basedb.core.Location;
 import net.sf.basedb.core.PluginDefinition;
@@ -57 +60 @@
     Unpacks a zip file, checking that there is enough space to accommodate 
     the zip file once it is unpacked. 
-      @throws NutribasePluginException
-   */
-  public void unpack() throws NutribasePluginException
+    */
+  public void unpack(String dirName)
   {
     log.info("Begin to unpack the files");
@@ -73 +75 @@
       if (hasSpace)
       {
+        createSubDirectory( file, user, dirName);
+        // now call the method to unpack the zip files
+        PluginDefinition zipFilePlugin = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.ZipFileUnpacker");
+        FileUnpacker unpacker = zipFilePlugin.newInstance(net.sf.basedb.plugins.ZipFileUnpacker.class, null, dc.getSessionControl(), null, null);
+        numUnpackedFiles=unpacker.unpack(dc, unzippedFilesDirectory,file.getDownloadStream(0), false,null);
+      }
+      else // if space is not enough
+      {
+        throw new BaseException("User do not have the required Disk Space. Please contact your BASE administrator or remove some files");
+      }
+      dc.commit(); 
+      inStream.close();
+    }
+    catch (Throwable exc)
+    {
+      dc.close();
+      log.info("File cannot be unpacked", exc);
+      new BaseException("File cannot be unpacked :" +exc.getMessage());
+    }
+    finally
+    {
+      if (dc!=null)
+        dc.close();
+    }
+  }
+  
+  
+  /**
+    Unpacks a zip file, checking that there is enough space to accommodate 
+    the zip file once it is unpacked. 
+      @throws NutribasePluginException
+   */
+  public void unpack()
+  {
+    log.info("Begin to unpack the files");
+    DbControl dc=null;
+    try
+    {
+      dc= sc.newDbControl();
+      if (file==null)
+        return;
+      InputStream inStream =  file.getDownloadStream(0);
+      //check if the logged in user has sufficient disk space. if yes go ahead with the unpacking
+      boolean hasSpace= checkUserQuota(inStream, dc);
+      if (hasSpace)
+      {
         createSubDirectory( file, user);
         // now call the method to unpack the zip files
@@ -81 +129 @@
       else // if space is not enough
       {
-        throw new NutribasePluginException("User do not have the required Disk Space. Please contact your NutriBASE administrator or remove some files");
+        throw new BaseException("User do not have the required Disk Space. Please contact your BASE administrator or remove some files");
       }
       dc.commit(); 
@@ -90 +138 @@
       dc.close();
       log.info("File cannot be unpacked", exc);
-      new NutribasePluginException(exc.getMessage());
+      new BaseException(exc.getMessage());
     }
     finally
@@ -98 +146 @@
     }
   }
-  
+
   /**
     checks user quota
@@ -122 +170 @@
     {
       log.error("[disk space: "+remainingSpace+ " ] insufficient for unzipping of file size [" +zipFileSize + "] -- please contact your BASE administrator or remove some files");
-      throw new NutribasePluginException("[disk space: "+remainingSpace+ " ] insufficient for unzipping of file size [" +zipFileSize + "] -- please contact your BASE administrator or remove some files");
+      throw new BaseException("[disk space: "+remainingSpace+ " ] insufficient for unzipping of file size [" +zipFileSize + "] -- please contact your BASE administrator or remove some files");
     }
     else if ( remainingSpace > zipFileSize || quotaValue==-1 )
@@ -153 +201 @@
       catch (IOException ioe)
       {
-        throw new NutribasePluginException("zip file size could not be obtained " + ioe.getMessage());
+        throw new BaseException("zip file size could not be obtained " + ioe.getMessage());
       }
       return totalSize;
@@ -161 +209 @@
       @param zipFile, the zip file to unpack
       @param user, currently logged-in user
+      @param
+    
+   */
+  public void createSubDirectory(File zipFile, User user, String dirName)
+  {
+    DbControl dc=null;
+    try
+    {
+      dc = sc.newDbControl();
+      //get the parent directory
+      Directory zipFileDir = zipFile.getDirectory();
+      log.info("zipFile is located in dir " + zipFile.getPath());
+      Directory d = Directory.getById(dc, zipFileDir.getId());
+      //String timeStamp = getTime("ddMMyy_HHmmss"); // can be added to the time directory name
+      Directory subDir = d.newSubDirectory();
+      subDir.setName(dirName);
+        subDir.setDescription("Unzippped directory created at "+new Date());
+      if (subDir.isInDatabase())
+      {
+        throw new ItemAlreadyExistsException("The Directory ["+ subDir.getPath().toString()+ "] already exists");
+      }
+      else if (!subDir.isInDatabase())
+      {
+        dc.saveItem(subDir);
+      }
+      dc.commit();
+        setUnzippedFilesDirectory(subDir);
+    }
+    catch (Throwable ex)
+    {
+      log.error("--Create subdirectory FAILED", ex);
+    }
+    finally
+    {
+      if (dc!=null) dc.close();
+    }
+            
+   }
+
+  /**
+    create a sub-directory to contain the unzip files
+      @param zipFile, the zip file to unpack
+      @param user, currently logged-in user
+      @param
     
    */
@@ -174 +266 @@
       Directory d = Directory.getById(dc, zipFileDir.getId());
       Directory subDir = d.newSubDirectory();
+      String fileName = zipFile.getName();
+        String fileNameNoExt = fileName.substring(0, fileName.indexOf("."));
+        subDir.setName(fileNameNoExt);
+        subDir.setDescription("Unzippped directory created at "+new Date());
       if (subDir.isInDatabase())
       {
-        throw new DatabaseException("The Directory ["+ subDir.getPath().toString()+ "] already exists");
+        throw new ItemAlreadyExistsException("The Directory ["+ subDir.getPath().toString()+ "] already exists");
       }
       else if (!subDir.isInDatabase())
       {
-        String fileName = zipFile.getName();
-          String fileNameNoExt = fileName.substring(0, fileName.indexOf("."));
-          subDir.setName(fileNameNoExt);
-          subDir.setDescription("Unzippped directory created at "+new Date());
-          dc.saveItem(subDir);
+        dc.saveItem(subDir);
       }
       dc.commit();
@@ -192 +284 @@
     {
       log.error("--Create subdirectory FAILED", ex);
+      //throw new BaseException();
     }
     finally
@@ -200 +293 @@
    }
 
-
   void setUnzippedFilesDirectory(Directory unzippedFilesDirectory) 
   {
@@ -210 +302 @@
     return unzippedFilesDirectory;
   }
+  
+  private String getTime(String pattern)
+  {
+    SimpleDateFormat formatter;
+    Locale currentLocale = Locale.getDefault();
+    formatter = new SimpleDateFormat(pattern, currentLocale);
+    String timeStamp = formatter.format(new Date());
+    return timeStamp;
+  }
 }