Changeset 376 for trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo

Timestamp:

Aug 8, 2007, 12:40:31 PM (16 years ago)

Author:

dominic

Message:

 

Location:

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/plugins

Files:

• AffyArrayDesignBatchImporter.java (modified) (11 diffs)
• lims/AffymetrixFileFormatTypes.java (modified) (1 diff)
• util/ZipUnpacker.java (modified) (7 diffs)

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/plugins/AffyArrayDesignBatchImporter.java

@@ -41 +41 @@
 import net.sf.basedb.core.plugin.Response;
 import uk.ac.ebi.nugo.plugins.lims.AffymetrixFileFormatTypes;
-import uk.ac.ebi.nugo.plugins.util.Tab2MageHelper;
+import uk.ac.ebi.nugo.plugins.util.Helper;
 import uk.ac.ebi.nugo.plugins.util.ZipUnpacker;
 
@@ -56 +56 @@
   
   private RequestInformation configureJob;
-  //private DbControl dc;
+  
   private PluginParameter<File> fileParameter;
     
@@ -64 +64 @@
       "Affymetrix Array Design Batch Importer",
       "This plugin is used to import affymetrix array design into base 2. Running this plugin is a pre-requisite for " +
-      "running the Tab2Mage importer developed at the EBI. The array deisgnare supplied in a zip archive",
+      "running the Tab2Mage importer developed at the EBI. The array deisgns must be supplied in a zip archive",
       "1.0",
       "@Copyright 2007, The EBI NutriBase development team",
@@ -161 +161 @@
     {
       response.setError(ex.getMessage(), Arrays.asList(ex));
-      ex.printStackTrace();
     }   
   }
@@ -197 +196 @@
       for (Role role : roles )
       {
-        //System.out.println("The user role is :"+ role);
         if (role.getName().equalsIgnoreCase("administrator")) validRole = true;
       }
@@ -218 +216 @@
         Unpack Zip files
        */
-      ZipUnpacker affyArrayDesignUnpacker = new ZipUnpacker(file, user, dc);
+      ZipUnpacker affyArrayDesignUnpacker = new ZipUnpacker(file, user, sc);
       affyArrayDesignUnpacker.unpack();
       /*
@@ -233 +231 @@
       {
         // get the file extension and filename
-        String ext= Tab2MageHelper.getFileExtension(affyFile);
+        String ext= Helper.getFileExtension(affyFile);
         
         //  check for validity against an enum file
@@ -252 +250 @@
             }
             
-              // otherwise
-        //  check if an array design with the same name exist. 
+              //  check if an array design with the same name exist. 
         String fileName = affyFile.getName();
         String fileNameWithoutExtension = fileName.substring(0, fileName.indexOf("."));
-              ArrayDesign ad= Tab2MageHelper.getArrayDesign(fileNameWithoutExtension, dc);
+              ArrayDesign ad= Helper.getArrayDesign(fileNameWithoutExtension, dc);
               //if no array design was found create a new one otherwise
               //skip array design creation
@@ -262 +259 @@
               {
                 // create an array design and set the name as filename without the extension
-                if (dc == null || !dc.isConnected())
-              dc = sc.newDbControl();
+                if (dc == null || !dc.isConnected())      dc = sc.newDbControl();
           ArrayDesign arrayDesign= ArrayDesign.getNew(dc, true);
           arrayDesign.setName(fileNameWithoutExtension);
@@ -282 +278 @@
       {
         response.setError(ex.getMessage(), Arrays.asList(ex));
-        ex.printStackTrace();
+        
       }
       finally
@@ -306 +302 @@
       catch (Exception e)
       {
-        Tab2MageHelper.write("File is not a zip file and cannot be imported by this plugin.");
-        e.printStackTrace();
-        
-        return false;
-      }
+         return false;
+      }
       finally
       {

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/plugins/lims/AffymetrixFileFormatTypes.java

@@ -7 +7 @@
 
 
-import java.util.EnumSet;
-import java.util.Set;
 
 public enum AffymetrixFileFormatTypes 

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/plugins/util/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 org.apache.log4j.Logger;
-
-import uk.ac.ebi.nugo.plugins.tab2mageimport.validation.Tab2MageValidationFactory;
 
 import net.sf.basedb.core.DbControl;
@@ -23 +16 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.Location;
-import net.sf.basedb.core.Path;
-import net.sf.basedb.core.SessionControl;
-import net.sf.basedb.core.Path.Type;
+import net.sf.basedb.core.PluginDefinition;
 import net.sf.basedb.core.Quota;
 import net.sf.basedb.core.QuotaType;
+import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.User;
-import net.sf.basedb.core.PluginDefinition;
 import net.sf.basedb.util.zip.FileUnpacker;
+
+import org.apache.log4j.Logger;
 
 
@@ -46 +39 @@
 public class ZipUnpacker 
 {
-  protected static Logger log = Logger.getLogger(Tab2MageValidationFactory.class);
+  protected static Logger log = Logger.getLogger(ZipUnpacker.class);
   private User user;
   private File file; 
@@ -55 +48 @@
   private SessionControl sc;
   
-  public ZipUnpacker(File zipFile, User user, DbControl dc)
+  public ZipUnpacker(File zipFile, User user, SessionControl sc)
   {
     this.user = user;
-    this.dc=dc;
+    this.dc=sc.newDbControl();
     this.file= zipFile;
-    this.sc= dc.getSessionControl();
+    //this.sc= dc.getSessionControl();
   }
   /**
     Unpacks a zip file, checking that there is enough space to accommodate 
     the zip file once it is unpacked. 
-   * @throws NutribasePluginException
+      @throws NutribasePluginException
    */
   public void unpack() throws NutribasePluginException
   {
-    System.out.println("Begin to unpack the files");
+    log.info("Begin to unpack the files");
     try
     {
@@ -94 +87 @@
     catch (Throwable exc)
     {
+      dc.close();
+      log.info("File cannot be unpacked", exc);
       new NutribasePluginException(exc.getMessage());
     }
     finally
     {
-      
+      if (dc!=null)
+        dc.close();
     }
   }
@@ -160 +156 @@
       catch (IOException ioe)
       {
-        ioe.printStackTrace();
+        //ioe.printStackTrace();
+        log.error(ioe.getMessage());
       }
       return totalSize;
     }
-  
+  /**
+    create a sub-directory to contain the unzip files
+    @param zipFile, the zip file to unpack
+    @param user, currently logged-in user
+    @param dc, the database control
+   */
   public void createSubDirectory(File zipFile, User user , DbControl dc)
   {
@@ -170 +172 @@
       
         Directory zipFileDir = zipFile.getDirectory();
-        System.out.println("zipFile is located in dir " + zipFileDir.toString());
+        log.info("zipFile is located in dir " + zipFileDir.toString());
         Directory subDir = Directory.getNew(dc, zipFileDir);
         String fileName = zipFile.getName();
         String fileNameNoExt = fileName.substring(0, fileName.indexOf("."));
-        //System.out.println("new subDir = " + fileNameNoExt );
         subDir.setName(fileNameNoExt);
-  
-        // save the new subDir
         dc.saveItem(subDir);
         unzippedFilesDirectory = subDir;