Changeset 378 for trunk/uk/ac/ebi/AnnotationTypeCvImporter

Timestamp:

Aug 8, 2007, 12:42:55 PM (16 years ago)

Author:

dominic

Message:

 

Location:

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

Files:

• AnnotationTypeCvImporter.java (modified) (2 diffs)
• util/Helper.java (added)
• util/Tab2MageHelper.java (deleted)
• util/ValueFormatter.java (added)
• util/Values.java (deleted)
• util/ZipUnpacker.java (modified) (7 diffs)

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

@@ -34 +34 @@
 import net.sf.basedb.util.parser.FlatFileParser;
 import net.sf.basedb.util.parser.Mapper;
-import uk.ac.ebi.nugo.plugins.util.Values;
+import net.sf.basedb.util.Values;
 
 
@@ -419 +419 @@
   private ItemResultList<AnnotationTypeCategory> categories;
   private ItemQuery<AnnotationTypeCategory> categoryQuery;
-  private boolean updateExisting, enumeration,found;
+  private boolean updateExisting, enumeration;
   private String separator;
   private int numInserted;

trunk/uk/ac/ebi/AnnotationTypeCvImporter/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;