Changeset 515

Timestamp:

Dec 7, 2007, 11:56:19 AM (14 years ago)

Author:

mbayer

Message:

problem with file writing fixed - file is now actually written to directory where the zip file shave been unzipped

Location:

branches/uk_ac_ebi_Tab2MageImporter

Files:

• Tab2MageImporter.jar (modified) (previous)
• build.xml (modified) (1 diff)
• lib/ebi-plugins-utils.jar (modified) (previous)
• src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java (modified) (5 diffs)
• src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java (modified) (5 diffs)

branches/uk_ac_ebi_Tab2MageImporter/build.xml

@@ -69 +69 @@
 
   <target name="copyToServer" depends="build.plugin,copyJSPs">
-    <copy file="${plugin.name}.jar" todir="C:\tomcat\apache-tomcat-6.0.13\webapps\base\WEB-INF\lib" verbose="true" />
+    <copy file="${plugin.name}.jar" todir="${tomcat.home}\webapps\base\WEB-INF\lib" verbose="true" />
     <!-- now restart tomcat to reload the application -->
     <echo message="tomcat home = "/>

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

@@ -153 +153 @@
     System.out.println("configure()");
     String command = request.getCommand();
-    System.out.println("command = " + command);
+    System.out.println(" configure request = "  +request + ", command = " + request.getCommand());
 
     try
@@ -348 +348 @@
   {
     System.out.println("running Tab2MageImporter plugin");
-    response.setDone("Import plugin ended successfully");
-
+    System.out.println(" run request = "  +request + ", command = " + request.getCommand());
+    
     
     DbControl dc=null;
@@ -381 +381 @@
       // save the new subDir
       dc.saveItem(subDir);
+      
+      if(dc==null)
+        dc = sc.newDbControl();
 
 //      String directoryName = (String)job.getValue("directory");
@@ -415 +418 @@
       //now write the tab2mage file to the user's home dir on the server so it can be consumed by the plugin
       //this takes all the inputs provided by the user on the custom interface (input.jsp)
-      //give the file a unique name so we don't get any conflicts
-      //use code from tab2mage exporter to do so
-      
-      //PluginConfigurationRequest pcRequest = (PluginConfigurationRequest) sc.getSessionSetting("plugin.configure.request");     
-      Tab2MageWriter t2mWriter = new Tab2MageWriter(request, dir,dc);
+      //give the file a unique name so we don't get any conflicts 
+      Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc);
       t2mWriter.writeTab2MageFile();
-      
+
       
       /////////////////////////////////////////////////////////////////////////////////////////////////
@@ -567 +567 @@
       // -- end of messaging module
       */
-      dc.commit();
+      //dc.commit();
       response.setDone("Import plugin ended successfully");
     }

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java

@@ -9 +9 @@
 import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.PluginConfigurationRequest;
+import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.plugin.ParameterValues;
 import net.sf.basedb.core.plugin.Request;
 
@@ -15 +17 @@
 //===================================================vars================================================ 
   
-  int numSubjects;
+  int numReplicates;
   int numTissues;
   int numTreatments;
-  Request pcRequest ;
   Directory dir;
-  DbControl dc;
+  SessionControl sc;
   
 //  ===================================================c'tor================================================
   
-  public Tab2MageWriter(Request pcRequest,Directory dir,DbControl dc )
+  public Tab2MageWriter(ParameterValues job,Directory dir,SessionControl sc)
   {
-    this.pcRequest = pcRequest;
     this.dir = dir;
-    this.dc = dc;
+    this.sc = sc;
+
+    //get values for the parameters we need here
+    int numReplicates = Integer.parseInt((String)job.getValue("numReplicates"));
+    int numTreatments = Integer.parseInt((String)job.getValue("numTreatments"));    
+    String tissues = (String)job.getValue("tissues");
+    int numTissues = tissues.split(",").length;
     
-    //get values for the parameters we need here
-    int numSubjects = Integer.parseInt((String)pcRequest.getParameterValue("numReplicates"));
-    int numTreatments = Integer.parseInt((String)pcRequest.getParameterValue("numTreatments"));   
-    String tissues = (String)pcRequest.getParameterValue("tissues");
-    int numTissues = tissues.split(",").length;
+    System.out.println("numReplicates extracted from job = " +numReplicates);
   }
 
@@ -48 +50 @@
     {
       //set up a file writer
+      DbControl dc = sc.newDbControl();
       net.sf.basedb.core.File t2mFile = net.sf.basedb.core.File.getNew(dc, dir);    
-      t2mFile.setName("tab2mage.txt");
+      System.out.println("dir for writing new tab2mage file = "+dir.getName());
+      t2mFile.setName("tab2mage.txt");      
+      dc.saveItem(t2mFile);
+      
+      if(dc==null)
+        dc = sc.newDbControl();
+      
       Writer out= new BufferedWriter(new OutputStreamWriter(t2mFile.getUploadStream(false),"ISO-8859-1"));
       
@@ -57 +66 @@
       //close writer
       if (out!= null) out.close();
+      
+      dc.commit();
+      if(dc!=null)
+        dc.close();
     }
     catch (Exception e)
@@ -67 +80 @@
   {
     //Number of hybridizations (NH) = Number of subjects (NS) x Number of Target Tissue (NTT) x Number of Study groups (NSG)
-    return numSubjects * numTissues * numTreatments;
+    return numReplicates * numTissues * numTreatments;
 
   }