Changeset 513 for branches/uk_ac_ebi_Tab2MageImporter/src/uk

Timestamp:

Dec 6, 2007, 1:04:50 PM (14 years ago)

Author:

mbayer

Message:

have implemented a skeleton writer class which writes a dummy tab2mage file

Location:

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins

Files:

• DataBean.java (modified) (2 diffs)
• Tab2MageImporter.java (modified) (14 diffs)

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

@@ -43 +43 @@
   String pooling;
   String zipFile;
+  String experimentId;
   
   
@@ -356 +357 @@
   {
     this.zipFile = zipFile;
+  }
+  public String getExperimentId()
+  {
+    return experimentId;
+  }
+  public void setExperimentId(String experimentId)
+  {
+    this.experimentId = experimentId;
   }
   

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

@@ -9 +9 @@
 import java.io.InputStream;
 import java.util.Arrays;
+import java.util.Calendar;
 import java.util.Collections;
 import java.util.LinkedList;
@@ -25 +26 @@
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.Job;
+import net.sf.basedb.core.Path;
 import net.sf.basedb.core.PluginConfigurationRequest;
 import net.sf.basedb.core.PluginParameter;
@@ -41 +43 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
+import net.sf.basedb.util.formatter.DateFormatter;
 import uk.ac.ebi.nugo.common.Helper;
 import uk.ac.ebi.nugo.common.ZipUnpacker;
@@ -101 +104 @@
 
   private static final Set<GuiContext> guiContexts = Collections.singleton(experimentItemGuiContext);
+  
 
 //  =====================================================c'tor==================================  
@@ -120 +124 @@
   {   
     //add all the parameter names to a String array for processing
-    String [] paramNames = new String []{"domain","accession","qualityControl","experimentalDesign",
+    String [] paramNames = new String []{"experimentId","domain","accession","qualityControl","experimentalDesign",
             "experimentName","description","releaseDate","submissionDate","submitter","organization",
             "publicationTitle","authors","journal","volume","issue","pages","year","pubmedId","treatmentProtocol",
@@ -129 +133 @@
             "tissues","pooling","zipFile"};
         
-    // next create the parameter type
+    // next create the parameter type - everyone is a String here
     StringParameterType stringPT = new StringParameterType(255, null, true);
     
@@ -188 +192 @@
       }
     }
-    catch (Throwable ex)
-    {
+    catch (Exception ex)
+    {
+      System.out.println("exception in configure method");
       ex.printStackTrace();
-      response.setError(ex.getMessage(), Arrays.asList(ex));
+      //response.setError(ex.getMessage(), Arrays.asList(ex));
     }
 
@@ -213 +218 @@
   public String isInContext(GuiContext context, Object item)
   {
+    System.out.println("isInContext called");
+    
     String message = null;
     if (item == null)
@@ -224 +231 @@
     }
     else
-    {
-      Experiment exp = (Experiment) item;
-      RawDataType rawDataType = exp.getRawDataType();
+    {   
+      Experiment exp = (Experiment)item;
+      RawDataType rawDataType = exp.getRawDataType(); 
       if (!Tab2MageHelper.supportedPlatforms(rawDataType.getId().toLowerCase()))
       {
@@ -342 +349 @@
     System.out.println("running Tab2MageImporter plugin");
     response.setDone("Import plugin ended successfully");
-    /*
+
     
     DbControl dc=null;
@@ -354 +361 @@
       User user= User.getById(dc, sc.getLoggedInUserId());
 
-
-       //obtain all job parameters
-
-      File file = (File) job.getValue("file");
-      file= File.getById(dc, file.getId());
-
-      String directoryName = (String)job.getValue("directory");
-
-      String tab2MageFileName= (String) job.getValue("tab2mageFileName");
-      hostName= (String) job.getValue("emailHost");
-
-      if ((Boolean)job.getValue("overwrite") != null) overwrite = (Boolean)job.getValue("overwrite");
-      if ((Boolean)job.getValue("validation") != null)  validation = (Boolean)job.getValue("validation");
-
-      Experiment experiment= (Experiment)job.getValue("experiment");
-      experiment= Experiment.getById(dc,experiment.getId());
+      String tab2MageFileName= "tab2mage.txt";
+      String zipFileName = (String)job.getValue("zipFile");
+      
+      File zipFile = File.getByPath(dc, new Path(zipFileName, Path.Type.FILE), false);
+      
+      // figure out where the zip file is located
+      Directory zipFileDir = zipFile.getDirectory();
+      System.out.println("zipFile is located in dir " + zipFileDir.toString());
+
+      // make a new subdir in that dir
+      // the zip file should then be unzipped in here
+      // give it the same name as that of the zip file plus a timestamp
+      String timeStamp = new DateFormatter("ddMMyy_HHmmss").format(Calendar.getInstance().getTime());
+      Directory subDir = Directory.getNew(dc, zipFileDir);
+      String fileNameNoExt = zipFile.getName().substring(0, zipFile.getName().indexOf("."));
+      System.out.println("new subDir = " + fileNameNoExt + timeStamp);
+      subDir.setName(fileNameNoExt + timeStamp);
+
+      // save the new subDir
+      dc.saveItem(subDir);
+
+//      String directoryName = (String)job.getValue("directory");
+//      hostName= (String) job.getValue("emailHost");
+//      if ((Boolean)job.getValue("overwrite") != null) overwrite = (Boolean)job.getValue("overwrite");
+//      if ((Boolean)job.getValue("validation") != null)  validation = (Boolean)job.getValue("validation");
+
+      //get the experiment object that our data is meant to be imported into
+      //this will be the experiment that the user is running the import from
+      String experimentId= (String)job.getValue("experimentId");
+      Experiment experiment= Experiment.getById(dc,Integer.parseInt(experimentId));
+            
       RawDataType rdt= experiment.getRawDataType(); // experiment platform
 
-      String statusp=(String)job.getValue("statusPath");
-      File statusFile=Helper.processFilePath(user,overwrite, sc,statusp);
+//      String statusp=(String)job.getValue("statusPath");
+//      File statusFile=Helper.processFilePath(user,overwrite, sc,statusp);
 
         //FILE UNZIP MODULE: unzip the files into user specified directory
          
-      ZipUnpacker importUnpacker = new ZipUnpacker(file, user, sc);
-      importUnpacker.unpack(directoryName);
+      ZipUnpacker importUnpacker = new ZipUnpacker(zipFile, user, sc);
+      importUnpacker.unpack(subDir.getName());
       Directory dir= importUnpacker.getUnzippedFilesDirectory(); // this may return the id of the unzipped file directory instead
       if (dir==null)
@@ -396 +418 @@
       //use code from tab2mage exporter to do so
       
+      //PluginConfigurationRequest pcRequest = (PluginConfigurationRequest) sc.getSessionSetting("plugin.configure.request");     
+      Tab2MageWriter t2mWriter = new Tab2MageWriter(request, dir,dc);
+      t2mWriter.writeTab2MageFile();
+      
+      
       /////////////////////////////////////////////////////////////////////////////////////////////////
       
-
+/*
 
         //VALIDATION MODULE
@@ -539 +566 @@
       }
       // -- end of messaging module
-      
+      */
       dc.commit();
       response.setDone("Import plugin ended successfully");
@@ -553 +580 @@
     }
     
-    */
+    
 
   }