Changeset 441

Timestamp:

Oct 30, 2007, 2:05:17 PM (16 years ago)

Author:

dominic

Message:

added changed the ebi-utils- apis, readme.txt,changelog and dependent jars

Location:

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter

Files:

• AffyArrayDesignBatchImporter.jar (modified) (previous)
• ChangeLog.txt (modified) (1 diff)
• README.txt (modified) (1 diff)
• credit.txt (modified) (1 diff)
• lib (added)
• lib/BASE2Core.jar (added)
• lib/BASE2CorePlugins.jar (added)
• lib/log4j-1.2.9.jar (added)
• src/uk/ac/ebi/nugo/common/Helper.java (modified) (7 diffs)
• src/uk/ac/ebi/nugo/common/Tab2MageConstants.java (modified) (3 diffs)
• src/uk/ac/ebi/nugo/common/ValueFormatter.java (modified) (1 diff)
• src/uk/ac/ebi/nugo/common/ZipUnpacker.java (modified) (5 diffs)
• src/uk/ac/ebi/nugo/plugins/AffyArrayDesignBatchImporter.java (modified) (2 diffs)

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/ChangeLog.txt

@@ -1 @@
-,____First release
+,____This file will contain information about changes iin subsequent releases.
 
-This file will contain information about changes iin subsequent releases.
+The ebi-utils-plugins.jar has been updated.

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

@@ -23 +23 @@
   The new plugins appears under the name "Affymetrix Array Design Batch Importer" in the plugins list and is now ready for use. 
 
-  6. For other base users to use the plugin as detailed in the next section, please share them to the appropriate users by manually setting the permissions on the  plugin.
-
   General Installation instruction is available at:  
 http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/credit.txt

@@ -1 @@
-At this release, Nutribase developement team is :
+At this release, Nutribase developement team are :
 
- - Dominic Oyeniran (oyeniran@ebi.ac.uk)
- - Philippe Rocca- Serra (rocca@ebi.ac.uk)
+ - Dominic Oyeniran (oyeniran@ebi.ac.uk): Author
+ - Philippe Rocca- Serra (rocca@ebi.ac.uk): Techinical Director
 
 both based at the European Bioinformatics Institute, Cambridge, UK 

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/common/Helper.java

@@ -11 +11 @@
 import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.ArraySlide;
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioSource;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Directory;
 import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.File;
@@ -23 +25 @@
 import net.sf.basedb.core.Path;
 import net.sf.basedb.core.Sample;
+import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.User;
@@ -31 +34 @@
 /**
   A plugin utils class for the tab2mage export and export.  
-  [TODO] This class may be merged to other utils in the main base 2 source code
-  @author Dominic Oyeniran
+  @author Dominic Oyeniran
   @version 1.0
 */
@@ -68 +70 @@
   
     
+   public static File processFilePath (User user,boolean overwrite, SessionControl sc, String pathString)
+   {
+    DbControl dc= null;
+    File file =null;
+     try
+     {
+      dc= sc.newDbControl();
+      if (pathString.startsWith("~/"))
+      {
+       pathString = "~"+user.getLogin()+pathString.substring(1);
+      }
+      Path path = new Path(pathString, Path.Type.FILE);   
+      
+      file= File.getByPath(dc, path, true); 
+      file.setMimeType("text/plain"); //set the type of the file
+      if (file.isInDatabase() && !overwrite && !file.isRemoved())
+      { 
+        throw new ItemAlreadyExistsException("File[path="+path+"]");      
+      }
+      else if(!file.isInDatabase())
+      {
+        dc.saveItem(file);
+      }
+      dc.commit();
+    }
+    catch(Exception e)
+    {
+      dc.close();
+    }
+    finally
+    {
+      if (dc!=null)
+        dc.close();
+    }
+     
+    return file;
+   }
   /**
     Displays the content of the map. Helps to check that the content displayed is correct. 
@@ -109 +148 @@
     of a tab2mage file
     @param atName , annotation type name
-    @return annotationTypes,  <code>AnnotationType</code> 
+    @return annotationType,  <code>AnnotationType</code> 
    */
   public static AnnotationType getAnnotationTypeByName(String atName, DbControl dc)
@@ -211 +250 @@
     return  ar;
   }
-  /**
-    writes a string to standard output
-      @param o
-   */
-  public static void write(String o)
-  {
-    System.out.println("&& DEBUG : "+o);
-  }
-  
+
   
   /**
@@ -311 +342 @@
       return le;    
   }
+  
+
+  /**
+    gets the currently looged in user default directory
+      @param sc, the seesion control
+      @return path of the user directory as a string object
+   */
+  public static String getUserDefaultDirectory( SessionControl sc)
+  {
+    DbControl  dc = sc.newDbControl();
+    String p ="";
+    try
+    {
+      User user = User.getById(dc, sc.getLoggedInUserId());
+      Directory dir= user.getHomeDirectory();
+      Path path = dir.getPath();
+      p=path.toString();
+    }
+    catch(Exception e)
+    {
+      new BaseException(e.getMessage());
+    }
+    finally
+    {
+      if (dc!=null) dc.close();
+    }
+    return p;
+  }
 }

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/common/Tab2MageConstants.java

@@ -1 @@
-/**
- * 
- */
+/* $Id: Tab2MageConstants.java 2006-08-08 dominic $
+
+  This file is for NutriBASE - Nutrigenomics BioArray Software Environment.
+  A customisation of the BASE SOFTWARE.
+  Developed at the EBI , Cambridge.
+  Author: Dominic Oyeniran: oyeniran@ebi.ac.uk
+*/
 package uk.ac.ebi.nugo.common;
 
@@ -13 +17 @@
   @author Dominic Oyeniran
   @version 1.0
-  @base.modified $Date
  */
 public enum Tab2MageConstants 
@@ -193 +196 @@
     The parameter header 
    */
-  parameter(49, "Parameter");
+  parameter(49, "Parameter"),
+  
+  /**
+    The protocol header
+   */
+  protocol(50, "Protocol"),
+  
+  /**
+    nucleic acid extraction
+   */
+  nucleicacidextraction(51, "Nucleic_Acid_Extraction");
+  ;
   
   /**

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/common/ValueFormatter.java

@@ -16 +16 @@
 /**
   A utility class containing static methods for formatting parameter values.
-  [TODO] This class may be merged to util class in the main base 2 source code
   @author Dominic Oyeniran
   @email oyeniran@ebi.ac.uk

trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/common/ZipUnpacker.java

@@ -13 +13 @@
 import java.util.zip.ZipInputStream;
 
+import net.sf.basedb.core.DatabaseException;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Directory;
@@ -31 +32 @@
 /**
     This class unpacks zip file provided by users into the base file structure
-    Note: Parts of the codes are authored by Misha Bayer - email: sbrn@scri.ac.uk,
+    Note: Parts of the codes were authored by Misha Bayer - email: sbrn@scri.ac.uk,
     @author Dominic Oyeniran 
     @email oyeniran@ebi.ac.uk
-    @see BatchDataImport.java and BatchLoader plugin developed by Misha Bayer.
-    
     
  */
@@ -75 +74 @@
       {
         createSubDirectory( file, user);
-        // now call the mathod to unpack the zip files
+        // 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);
@@ -115 +114 @@
     //unlimited storage (e.g. for user root) will return -1
     long quotaValue = quota.getQuotaValue(totalQuotaType, Location.PRIMARY);    
-    //System.out.println("the quota value of the user: " + user.getName()+ " is: "+quotaValue );
+    log.info("the quota value of the user: " + user.getName()+ " is: "+quotaValue );
     long currentDiskUsage = user.getDiskUsage(totalQuotaType, Location.PRIMARY);
       //check whether remaining disk space and zip file size are compatible
     long remainingSpace = quotaValue - currentDiskUsage;
-    //System.out.println("the remaining space for user: " + user.getName()+ " is: "+remainingSpace );
+    log.info("the remaining space for user: " + user.getName()+ " is: "+remainingSpace );
     if(remainingSpace < zipFileSize && quotaValue!=-1)
     {
@@ -172 +171 @@
       //get the parent directory
       Directory zipFileDir = zipFile.getDirectory();
-      //System.out.println("zipFile is located in dir " + zipFile.getPath());
+      log.info("zipFile is located in dir " + zipFile.getPath());
       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());
-        dc.saveItem(subDir);
-        dc.commit();
-        //unzippedFilesDirectory = subDir;
+      if (subDir.isInDatabase())
+      {
+        throw new DatabaseException("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.commit();
         setUnzippedFilesDirectory(subDir);
     }
     catch (Throwable ex)
     {
-      log.error("--Create subdirectory FAILED");
+      log.error("--Create subdirectory FAILED", ex);
     }
     finally

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

@@ -40 +40 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
-import uk.ac.ebi.nugo.common.*;
+import uk.ac.ebi.nugo.common.Helper;
+import uk.ac.ebi.nugo.common.ZipUnpacker;
 import uk.ac.ebi.nugo.plugins.lims.AffymetrixFileFormatTypes;
-
 
 /**
@@ -269 +269 @@
                   
               //share the array design to everyone in based2 or admin does this on the GUI by selecting the plugin and using share button.
-
+          // GroupPermissions groupPermission= new GroupPermissions();
+           //String everyone= Group.EVERYONE;
+           //int id = SystemItems.getId(Group.EVERYONE);
+           //Group everyone = Group.getById(dc, id);
+           //groupPermission.getPermissions(everyone)
+           //ItemKey.getNewOrExisting(dc, null, groupPermissions);
               }
       }