Changeset 449

Timestamp:

Oct 30, 2007, 3:54:31 PM (15 years ago)

Author:

dominic

Message:

added tab2mage export version 2

Location:

trunk/uk/ac/ebi/Tab2MageExporter/src/uk/ac/ebi/nugo

Files:

• common/Helper.java (modified) (7 diffs)
• common/Tab2MageConstants.java (modified) (3 diffs)
• common/ValueFormatter.java (modified) (1 diff)
• common/ZipUnpacker.java (modified) (5 diffs)
• plugins/Tab2MageExporter.java (modified) (14 diffs)
• plugins/ta2mageexport/ExportHelper.java (added)
• plugins/ta2mageexport/Tab2MageFileWriter.java (added)
• plugins/ta2mageexport/Tab2MageHybridization.java (added)
• plugins/ta2mageexport/Tab2MageHybridizationLine.java (added)
• plugins/ta2mageexport/Tab2MageSubHybLine.java (added)
• plugins/ta2mageexport/Tab2MageValidator.java (modified) (3 diffs)

trunk/uk/ac/ebi/Tab2MageExporter/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/Tab2MageExporter/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/Tab2MageExporter/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/Tab2MageExporter/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/Tab2MageExporter/src/uk/ac/ebi/nugo/plugins/Tab2MageExporter.java

@@ -1 @@
-/* $Id: Tab2MageExporter.java 2006-10-22 dominic $
-
-  Copyright (C) Authors contributing to this file.
+/* $Id: Tab2MageExporter.java 2007-09-01 dominic $
+
+  Copyright (C) 2007 Authors contributing to this file.
 
   This file is for NutriBASE - Nutrigenomics BioArray Software Environment.
@@ -22 +22 @@
 */
 package uk.ac.ebi.nugo.plugins;
+
+
 import java.io.Writer;
 import java.util.ArrayList;
@@ -28 +30 @@
 import java.util.Collections;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.LinkedHashSet;
-import java.util.LinkedList;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
@@ -81 +80 @@
 import uk.ac.ebi.nugo.common.Helper;
 import uk.ac.ebi.nugo.common.Tab2MageConstants;
-import uk.ac.ebi.nugo.plugins.ta2mageexport.ExporHelper;
-import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageWriter;
-
+import uk.ac.ebi.nugo.plugins.ta2mageexport.ExportHelper;
+import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageFileWriter;
+import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageHybridization;
+import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageHybridizationLine;
+import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageSubHybLine;
+import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageValidator;
 
 /**
   A plugin that exports an experiment in tab2mage specification for submission to ArrayExpress public repository.
   @author Dominic Oyeniran
+  @email oyeniran@ebi.ac.uk /doyeniran@gmail.com
   @version 1.0
-  @base.modified $Date$
+
 */
-
-public class Tab2MageExporter 
-  extends AbstractPlugin
-  implements InteractivePlugin
+public class Tab2MageExporter extends AbstractPlugin
+                implements InteractivePlugin
 {
   private static final About about=
     new AboutImpl 
     (
-        "Tab2MAGE exporter",
-        "This plugin is used to export an experiment in the tab2mage format specfication. The tab2mage specification " +
+        "Tab2Mage exporter",
+        "This plugin is for exporting an experiment in the tab2mage format specfication. The tab2mage specification " +
         "is provided by the microarray informatics team at the EBI, Cambridge. The exported experiment can later be " +
-        "imported by the corresponding import plugin.",
-        "2.0",
+        "imported into BASE by the corresponding import plugin.",
+        "1.0",
         "2006, NutriBase development team",
         null,
         "oyeniran@ebi.ac.uk",
-        "http://base.thep.lu.se"
+        "http://www.ebi.ac.uk/~oyeniran"
     );
   
@@ -114 +115 @@
   
   private PluginParameter<String> pathParameter; 
-  private static final String pathDefaultValue="/home/tab2mage.txt";
   private PluginParameter<String> statusPathParameter;
-  private static final String statusPathDefaultValue="/home/statusreport.txt";
   private PluginParameter<Experiment> experimentParameter;
   private BooleanParameterType overwriteType= new BooleanParameterType(false, false);;
@@ -138 +137 @@
           "Save as",
           "Please specify the file name where the plugin should store it's output", 
-          new PathParameterType(Path.Type.FILE, pathDefaultValue, true)); 
+          new PathParameterType(Path.Type.FILE, Helper.getUserDefaultDirectory(sc)+"/tab2mage.txt", true)); 
       
       statusPathParameter = new PluginParameter<String>(
@@ -144 +143 @@
           "Save Status File as",
           "Please specify the file name where the plugin should store causes for failure and errors", 
-          new PathParameterType(Path.Type.FILE, statusPathDefaultValue, true));
+          new PathParameterType(Path.Type.FILE, Helper.getUserDefaultDirectory(sc)+"/statusreport.txt", true));
       
       experimentParameter = new PluginParameter<Experiment>(
@@ -259 +258 @@
     return about;
   }
+  @Override
   public boolean supportsConfigurations()
   {
     return false;
   }
+  @Override
   public boolean requiresConfiguration()
   {
@@ -272 +273 @@
   { 
     DbControl dc=null;
-    Set<Protocol> protocols = new LinkedHashSet<Protocol>(); //to get protocols as they are entered
-      
+    //use a linked list to get objects e.g. protocols as they are entered.
+    Set<Protocol> protocols = new LinkedHashSet<Protocol>(); 
     Set<String> hybSectionHeader= new LinkedHashSet<String>();
     Set<String>  protocolHybSectionHeader= new LinkedHashSet<String>();
-    List<String> protocolRefId= new LinkedList<String>();
-    List<String> hybridizationDataRows=new LinkedList<String>();
-    List<String> parameterValues= new LinkedList<String>();
-    
-    List<Annotation> expFactorValues= new LinkedList<Annotation>();
-    Map<AnnotationType, Annotation> factorValues= new HashMap<AnnotationType,Annotation>();
-    List<String> twoColorHybDataRows=new LinkedList<String>();
-    List<String> twoColorParameterValues=new LinkedList<String>();
-    List<String> twoColorFirstParameterValues=new LinkedList<String>();
-    List<String> twoColorProtocolRefId= new LinkedList<String>();
-    List<String> twoColorFirstProtocolRefId= new LinkedList<String>();
-    
-    //pooling data strutures - //NOTE:Pooling is not fully supported at the moment
-    List<String> poolSampleHeader=new LinkedList<String>();
-    List<String> poolSampleTail= new LinkedList<String>();
-    List<String> poolHybDataRows=new LinkedList<String>();
-        
+  
     boolean overwrite = false;
-    boolean twoColorHyb= false; 
-    //pooling attributes
-    boolean pooledSampleFlag= false;
-    
+      
     try 
     {
@@ -309 +291 @@
       Experiment experiment= (Experiment)job.getValue("experiment");
       experiment= Experiment.getById(dc,experiment.getId());
+                
       //  check if the logged in user owned the experiment, if not the export exit with a message.
+      
       if (!(experiment.getOwner().equals(user))) 
       {
-        response.setDone("[EXPORT FAILED: User - "+user.getName()+ " do not own this experiment or have permission to export it].");
+        response.setError("[EXPORT FAILED: User - "+user.getName()+ " do not own this experiment or have permission to export it].", Arrays.asList(new Throwable()));
         return; 
       }
        if (experiment.getExperimentalFactors().list(dc).size()==0)
       {
-        response.setError("[Export Failed] Experimental factors have not been specified for this experiment].", Arrays.asList(new Throwable()));
+        response.setError("[EXPORT FAILED: Experimental factors have not been specified for this experiment].", Arrays.asList(new Throwable()));
         return;  
-  
-      }
-      //initialise, count resources used, create concurrentmap for all parameter headers
-      getResourceCounter(experiment,dc);
+      }
             
-      Tab2MageWriter.createFileWriters(file, statusFile);
-                
-      // Get all protocols and hybs   
+      // check that raw bio assays have been added to experiment, otherwise fails 
+      
       ItemQuery<RawBioAssay> rawBioAssaysQuery = experiment.getRawBioAssays();
       rawBioAssaysQuery.order(Orders.asc(Hql.property("name")));
@@ -335 +315 @@
         return; 
       }
+      
+      // create all the required writers for the status file and the export file
+      
+      Tab2MageFileWriter.createFileWriters(file, statusFile);
+      
+      //initialise, count resources used, create concurrentmap for all parameter and biomaterial headers
+      Tab2MageValidator validator = new Tab2MageValidator (experiment, sc, response);
+      
+      //Tab2MageHybridization hybridization= new Tab2MageHybridization ();
+      
       for (RawBioAssay rba : rawBioAssays)
       {
-        initialiseMaps(parameterMap,true);
-        initialiseMaps(twoColorParameterMap,true);
-        initialiseMaps(twoColorFirstParameterMap,true);
-        initialiseMaps(bioXterParameterMap,false);
-        initialiseMaps(twoColorBioXterParameterMap,false);
-        
-        twoColorHybDataRows.add("-done-"); 
+        // create the Tab2MageHybridization object
+        Tab2MageHybridization hybridization= new Tab2MageHybridization ();
+        // create the Tab2MageHybridizationLine object
+        Tab2MageHybridizationLine hybRow = new Tab2MageHybridizationLine();
+        
+        // set the number of channels for the Hybridization
+        hybridization.setChannelNumber(validator.getChannelNumber()); // mainly useful during the writing stage
+                        
         /*
-          Data files and array information section//
-         */
+          Experimental Factor Section
+        */
+        AnnotationSet annotationSet =rba.isAnnotated() ? rba.getAnnotationSet() : null;
+        ItemQuery<AnnotationType> experimentalFactorsQuery= experiment.getExperimentalFactors();
+        experimentalFactorsQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT, Include.NOT_REMOVED);
+        ItemResultList<AnnotationType> experimentalFactors = experimentalFactorsQuery.list(dc);
+        for (AnnotationType exprFactor :experimentalFactors)
+        {
+          if (!exprFactor.isRemoved())
+          {
+            if (annotationSet!=null)
+            {
+              Annotation an= annotationSet.findAnnotation(exprFactor);
+              if (an!=null) //exprFacor has annotations
+              {
+                List<?> values=  an.getValues();
+                hybRow.set("FactorValue", exprFactor.getName(), values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
+              }
+              else // exprFactor has no annotations
+              {
+                hybRow.set("FactorValue", exprFactor.getName(), "" );
+              }
+            }
+            else //The raw bio assay is not annotated
+            {
+              hybRow.set("FactorValue", exprFactor.getName(), "" );
+            }
+          }
+        }
+        
             //Array Design
-        ArrayDesign arrayDesign= rba.getArrayDesign();
-        if (arrayDesign.isAffyChip())
+        ArrayDesign arrayDesign = null;
+        try
         {
-          File cdfFile= Affymetrix.getCdfFile(arrayDesign);
-          File celFile=Affymetrix.getCelFile(rba);
-          hybSectionHeader.add(Tab2MageConstants.raw_file.getName());
-          hybridizationDataRows.add(celFile.getName());
-          twoColorHybDataRows.add(celFile.getName());
-          hybSectionHeader.add(Tab2MageConstants.cdf_file.getName());
-          hybridizationDataRows.add(cdfFile.getName());
-          twoColorHybDataRows.add(cdfFile.getName());
+          arrayDesign= rba.getArrayDesign();
         }
-        else
+        catch(Throwable tr)
         {
-          hybSectionHeader.add(Tab2MageConstants.raw_file.getName());
-          hybridizationDataRows.add(rba.getName());
-          twoColorHybDataRows.add(rba.getName());
+          response.setError("[EXPORT FAILED: All Array Design(s) must be provided in BASE to continue].",Arrays.asList(tr));
         }
-        hybSectionHeader.add(Tab2MageConstants.array_accession.getName());
-        hybridizationDataRows.add(arrayDesign.getName());
-        twoColorHybDataRows.add(arrayDesign.getName());
-        
-          //Raw BioAssay protocol
-        protocols.add(rba.getProtocol());
-        if (extractionProtocolCount>0)
-        {
-          protocolHybSectionHeader.add(Tab2MageConstants.protocol_featureextraction.getName());
-          protocolRefId.add(getFormattedProtocolId(rba.getProtocol()));
-          twoColorFirstProtocolRefId.add(getFormattedProtocolId(rba.getProtocol()));
-        }
-                
-        // rba protocol parameters
-        if (rba.isAnnotated())  setParameterValues(rba,dc);
-          
-        //Scanning Protocol
+        // Populate the Array file map in HybLine
+        setArraysAttributes(hybRow, arrayDesign );
+        
+        // Populate the Data file map in HybLine
+        setFileAttributes(hybRow, arrayDesign, rba, response);
+        
+        //Raw BioAssay protocol and parameter
+        setProtocolAndParameterAtrributes(hybRow,rba,Tab2MageValidator.getFeProtocolCount(), 
+            Tab2MageConstants.protocol_featureextraction.getName(), response, dc);
+        
+        //Scanning Protocol and Parameters
         Scan scan= rba.getScan();
-        if (scanningProtocolCount>0)
-        {
-          protocolHybSectionHeader.add(Tab2MageConstants.protocol_scanning.getName());
-          protocolRefId.add(getFormattedProtocolId(scan.getProtocol()));
-          twoColorFirstProtocolRefId.add(getFormattedProtocolId(scan.getProtocol()));
-        }
-        protocols.add(scan.getProtocol());  // add scanning protocol
-          //  Scanning protocol parameter
-        if (scan.isAnnotated()) setParameterValues(scan,dc);
-        
-          //Hybridization
+        setProtocolAndParameterAtrributes(hybRow,scan,Tab2MageValidator.getScanningProtocolCount(), 
+            Tab2MageConstants.protocol_scanning.getName(),response, dc);
+        
+        /*
+          Array Slide
+         */ 
         Hybridization hyb= scan.getHybridization();
         if (hyb.getArraySlide()==null)
@@ -403 +402 @@
         else
         {
-          hybSectionHeader.add("Array[serial]");
-          hybridizationDataRows.add(hyb.getArraySlide().getName());
-          twoColorHybDataRows.add(hyb.getArraySlide().getName());
+          hybRow.set("Array","serial", hyb.getArraySlide().getName());
         }
           
         /*
-          Names of materials and processes section
+          Hybridization
          */
-        hybSectionHeader.add(Tab2MageConstants.hybridization.getName());
-        hybridizationDataRows.add(hyb.getName());
-        twoColorHybDataRows.add(hyb.getName()); 
-        
+        hybRow.set(Tab2MageConstants.hybridization.getName(), null,hyb.getName());
         BioMaterialEvent bioMaterialEvent= hyb.getCreationEvent(); // an event that created the hyridization
-        
-        Protocol hybProtocol= bioMaterialEvent.getProtocol(); //hybridization protocol
-        protocols.add(hybProtocol); 
-        
-        if (hybridizationProtocolCount>0)
-        {
-          protocolHybSectionHeader.add(Tab2MageConstants.protocol_hyb.getName());
-          protocolRefId.add(getFormattedProtocolId(hybProtocol));
-          twoColorFirstProtocolRefId.add(getFormattedProtocolId(hybProtocol));
-        }
-        //  Hybridization protocol parameter
-        if (hyb.isAnnotated()) setParameterValues(hyb,dc);
-          
+      
+        // Hybridization protocol and parameter
+        setProtocolAndParameterAtrributes(hybRow,hyb,Tab2MageValidator.getHybridizationProtocolCount(), 
+            Tab2MageConstants.protocol_hyb.getName(), response, dc);
+        
         ItemQuery<LabeledExtract> labeledExtractQuery =(ItemQuery<LabeledExtract>) bioMaterialEvent.getSources(); // get all the labeled extract
         ItemResultList<LabeledExtract> labeledExtracts= labeledExtractQuery .list(dc);
-        int hybsize=labeledExtracts.size();
-        int count=1;
-        for (LabeledExtract labeledExtract :labeledExtracts) // can have more than one labeled extract (2 color experiments)
+        int size = labeledExtracts.size();
+        
+        // create the Tab2MageSubHybLine object List
+        List<Tab2MageSubHybLine> subLines = new ArrayList<Tab2MageSubHybLine>();
+        
+        int count=1; // initialise the count variable to 1
+        // Loop through all the labeled extracts
+        for (LabeledExtract labeledExtract :labeledExtracts) // can have more than one labeled extract (e.g. 2 color experiments)
         {
-          //  labeled extract
-          hybSectionHeader.add(Tab2MageConstants.labeledextract.getName());
+          //create the new SubHyb Line
+          Tab2MageSubHybLine subLine = new Tab2MageSubHybLine();
+          
+          /*
+            labeled extract
+           */
           Protocol lbExtractProtocol= labeledExtract.getCreationEvent().getProtocol();
-          protocols.add(lbExtractProtocol); // labeled extract protocol
-          if (labelingProtocolCount>0)protocolHybSectionHeader.add(Tab2MageConstants.protocol_labeling.getName());
-          if (count<hybsize || count==1)
-          {
-            hybridizationDataRows.add(labeledExtract.getName());
-            if (labelingProtocolCount>0) protocolRefId.add(getFormattedProtocolId(lbExtractProtocol));
-          }
-          else if (count==2)
-          {
-            twoColorHyb=true;
-            twoColorHybDataRows.add(labeledExtract.getName());
-            if (labelingProtocolCount>0)twoColorProtocolRefId.add(getFormattedProtocolId(lbExtractProtocol));
-          }
-            //  labelling protocol parameter
-          setParameterValues(labeledExtract,dc, count, hybsize);
-          
-          // Label 
+          subLine.set(Tab2MageConstants.labeledextract.getName(), null, labeledExtract.getName());
+          
+            // labelling protocol and parameter
+          setProtocolAndParameterAtrributes(dc, subLine,labeledExtract,Tab2MageValidator.getLabelingProtocolCount(), 
+              Tab2MageConstants.protocol_labeling.getName(),lbExtractProtocol, response);
+          /*
+            Label 
+           */
           String labelName= labeledExtract.getLabel().getName(); // the name of the label
-          hybSectionHeader.add(Tab2MageConstants.dye.getName());
-          if (count < hybsize || count==1)
-          {
-            hybridizationDataRows.add(labelName);
-          }
-          else if (count==2)
-          {
-            twoColorHybDataRows.add(labelName);
-          }
-          
-          //  Extract
-          Extract extract= labeledExtract.getExtract();
+          subLine.set(Tab2MageConstants.dye.getName(), null,labelName); 
+                          
+          /*
+            Extract
+          */
+          
+          Extract extract= ExportHelper.getExtract(labeledExtract, dc);
           if (extract!=null)
           {
-            hybSectionHeader.add(Tab2MageConstants.extract.getName());
             Protocol extractProtocol =extract.getCreationEvent().getProtocol(); //extract protocol
-            if (extractProtocolCount>0) protocolHybSectionHeader.add(Tab2MageConstants.protocol_extraction.getName());
-            protocols.add(extractProtocol); 
-            if (count < hybsize || count==1)
-            {
-              hybridizationDataRows.add(extract.getName());
-              if (extractProtocolCount>0)protocolRefId.add(getFormattedProtocolId(extractProtocol));
-            }
-            else if (count==2)
-            {
-              twoColorHybDataRows.add(extract.getName());
-              if (extractProtocolCount>0)twoColorProtocolRefId.add(getFormattedProtocolId(extractProtocol));
-            }
-              //  extraction protocol parameter
-            setParameterValues(extract,dc,count,hybsize);
+            subLine.set(Tab2MageConstants.extract.getName(), null, extract.getName());
+            
+            // extraction protocol  and parameter
+            setProtocolAndParameterAtrributes(dc, subLine,extract,Tab2MageValidator.getExtractProtocolCount(), 
+                Tab2MageConstants.protocol_extraction.getName(), extractProtocol, response);
           }
           
-          //Sample
-          Sample sample =extract.getSample(); // The sample, extract is created from
+          /*
+            Sample
+          */
+          
+          Sample sample= ExportHelper.getSample(extract, dc);
           if (sample != null)
           {
-            hybSectionHeader.add(Tab2MageConstants.sample.getName());
             Protocol sampleProtocol=sample.getCreationEvent().getProtocol();    //sampling protocol
-            if (samplingProtocolCount>0)protocolHybSectionHeader.add(Tab2MageConstants.protocol_treatment.getName());
-            protocols.add(sampleProtocol); 
-            if (count < hybsize || count==1)
+            subLine.set(Tab2MageConstants.sample.getName(), null, sample.getName());
+            
+            // sampling protocol and parameter
+            setProtocolAndParameterAtrributes(dc, subLine,sample,Tab2MageValidator.getSamplingProtocolCount(), 
+                Tab2MageConstants.protocol_treatment.getName(),sampleProtocol, response );
+          }
+          
+          /*  
+            Biosource
+           */ 
+          
+          BioSource  bioSource=ExportHelper.getBioSource(sample, dc);
+          if (bioSource != null)
+          {
+            subLine.set(Tab2MageConstants.biosource.getName(), null, bioSource.getName());
+            
+            //section for biomaterial xterixtics
+            ItemQuery<Annotation> query = bioSource.getAnnotationSet().getAnnotations();
+            query.include(Include.MINE, Include.NOT_REMOVED, Include.IN_PROJECT,Include.SHARED);
+            List<Annotation> annotations = query.list(dc); 
+            for (Annotation annotation: annotations)
             {
-              hybridizationDataRows.add(sample.getName());
-              if (samplingProtocolCount>0)protocolRefId.add(getFormattedProtocolId(sampleProtocol));
-            }
-            else if (count==2)
-            {
-              twoColorHybDataRows.add(sample.getName());
-              if (samplingProtocolCount>0) twoColorProtocolRefId.add(getFormattedProtocolId(sampleProtocol));
-            }
-              // sampling protocol parameter
-            setParameterValues(sample,dc,count,hybsize);
-          }
-          
-          // Biosource
-          Set<BioSource> bioSources= new LinkedHashSet();
-          if (sample.isPooled())
-          { 
-            pooledSampleFlag=true;
-            poolSampleHeader.addAll(hybridizationDataRows);
-            
-            bioSources.addAll(ExporHelper.getBiosources(sample, dc));
-          }
-          else if (!sample.isPooled())
-          {
-            bioSources.add(sample.getBioSource());
-          }
-          int bioSourceCount=1;
-          for (BioSource bioSource: bioSources)
-          {
-            if (bioSource!=null)
-            {
-              hybSectionHeader.add(Tab2MageConstants.biosource.getName());
-              if (count < hybsize || count==1)
+              AnnotationType at=annotation.getAnnotationType();
+              if(!at.isRemoved()) 
               {
-                if (bioSourceCount==1) // this caters for the the first Biosource for pooling and non pooling
-                {
-                  hybridizationDataRows.add(bioSource.getName());
-                }
-                else if (pooledSampleFlag && bioSourceCount>1) // this cater for other biources when samples were pooled
-                {
-                  poolSampleTail.add(bioSource.getName());
-                }
-              }
-              else if(count==2)
-              {
-                twoColorHybDataRows.add(bioSource.getName());
-                if (pooledSampleFlag && bioSourceCount>1) poolSampleTail.add(bioSource.getName());
-              }
-              
-              //section for biomaterial xterixtics
-              List<Annotation> annotations = bioSource.getAnnotationSet().getAnnotations().list(dc); 
-              for (Annotation annotation: annotations)
-              {
-                AnnotationType at=annotation.getAnnotationType();
-                if(!at.isRemoved()) 
-                {
-                  List<?> values= annotation==null? null:annotation.getValues();
-                  if (count < hybsize || count==1)
-                  {
-                    if (bioSourceCount==1) // this caters for the the first Biosource for pooling and non pooling
-                    {
-                      for (String header : bioXterParameterMap.keySet())
-                      {
-                        if (header.equals(annotation.getAnnotationType().getName()))
-                        {
-                          bioXterParameterMap.replace(header, values==null || values.size()==0 ? getDefaultValue(at) : Values.getString(values, ", ", true));
-                        }
-                      }
-                    }
-                    else if (pooledSampleFlag && bioSourceCount>1) // this cater for other biources when samples were pooled
-                    {
-                      poolSampleTail.add(values==null || values.size()==0 ? getDefaultValue(at) : Values.getString(values, ", ", true));
-                    }
-                  }
-                  else if(count==2)
-                  {
-                    for (String header : twoColorBioXterParameterMap.keySet())
-                    {
-                      if (header.equals(annotation.getAnnotationType().getName()))
-                      {
-                        twoColorBioXterParameterMap.replace(header, values==null || values.size()==0 ? getDefaultValue(at) : Values.getString(values, ", ", true));
-                      }
-                    }
-                    if (pooledSampleFlag && bioSourceCount>1) poolSampleTail.add(values==null || values.size()==0 ? getDefaultValue(at) : Values.getString(values, ", ", true));
-                  }
-                }
-              }
-            }
-            if (pooledSampleFlag && bioSourceCount>1) poolSampleTail.add("--*poolend*--");
-            bioSourceCount++;
-          }
-          count++;
-          
-        } //end of labeled extract loop
-        
-        /*
-          Populate the Hyb data row before display
-         */ 
-        for (Map.Entry<String, String> e: bioXterParameterMap.entrySet())
-        {
-          hybridizationDataRows.add(e.getValue());
-          bioXterHybSectionHeader.add(e.getKey());
-        }
-        if (twoColorHyb)
-        {
-          for (Map.Entry<String, String> e: twoColorBioXterParameterMap.entrySet())
-          {
-            twoColorHybDataRows.add(e.getValue());
-          }
-        }
-        // add protocol hyb ref ids
-        for (String protcolId : protocolRefId) //add protocol id
-        {
-          hybridizationDataRows.add(protcolId);
-        }
-        if (twoColorHyb)
-        {
-          twoColorFirstProtocolRefId.addAll(twoColorProtocolRefId);
-          for (String protocolId : twoColorFirstProtocolRefId )
-          {
-            twoColorHybDataRows.add(protocolId);
-          }
-        }
-          //  add parameter values
-        
-        for (Map.Entry<String, String> entry: parameterMap.entrySet())
-        {
-          hybridizationDataRows.add(entry.getValue());
-          parameterHybSectionHeader.add(entry.getKey());
-        }
-        if (twoColorHyb)
-        {
-          for (Map.Entry<String, String> firstMapE :twoColorFirstParameterMap.entrySet())
-          {
-            for (Map.Entry<String, String> mapE :twoColorParameterMap.entrySet())
-            {
-              if (firstMapE.getKey().equals(mapE.getKey()))
-              {
-                twoColorFirstParameterMap.replace(firstMapE.getKey(), firstMapE.getValue()==""? mapE.getValue():"" ) ;
+                List<?> values= annotation==null? null:annotation.getValues();
+                subLine.set(Tab2MageConstants.bio_mat_charact.getName(), annotation.getAnnotationType().getName(), 
+                    values==null || values.size()==0 ? ExportHelper.getDefaultValue(at) : Values.getString(values, ", ", true));
               }
             }
           }
-          for (String paramValue : twoColorFirstParameterMap.values())
-          {
-            twoColorHybDataRows.add(paramValue);
-          }
+        
+          subLines.add(subLine);  //make a list of subLines
+          count++;
+        } //end of labeled extract loop
+      
+        hybRow.addHybSubLines(size, hybRow.getName(), subLines); // add the subLines (i.e. Tab2MageSubHybLine objectc list to Tab2MageHybridizationLine Object
+          
+        hybridization.addLine(hybRow);  // add Tab2MageHybridizationLine Object to Tab2MageHybridization object
+        if(!hybs.contains(hybridization)) 
+          hybs.add(hybridization);    // add Tab2MageHybridization Object to the List of Tab2MageHybridization object
+      
+      }// end of raw biossay for loop 
+      
+      // create headers for biomaterial xteristics
+      Set<String> bioMatHeaders = new LinkedHashSet<String>();
+      
+      //create  headers for the parameters
+      Set<String> paramHeaders = new LinkedHashSet<String>();
+      
+      //create headers for experimental factor values
+      Set<String> factorValueHeaders = new LinkedHashSet<String>();
+      
+      for (Tab2MageHybridization h : hybs)
+      {
+        
+        Tab2MageHybridizationLine l = h.getLine();
+              
+        // add headers to main parameter header list
+        paramHeaders.addAll(ExportHelper.getHeaderWithValuesOnly(l.getParameter()));
+        
+        for (Tab2MageSubHybLine sl: l.getSubLineSet())
+        {
+          // get the headers for biomaterial xteristics and add to  biomaterial xteristics header set
+          bioMatHeaders.addAll(ExportHelper.getHeaderWithValuesOnly(sl.getBioMaterialCharacteristics()));
+          // get the parameter values headers and add to the set of parameter headers
+          paramHeaders.addAll(ExportHelper.getHeaderWithValuesOnly(sl.getParameter()));
+          
         }
         
-        /*
-          Experimental Factor Section
-        */
-        expFactorValues=getExperimentalFactorValues(dc,experiment,rba);
-        for(Annotation value: expFactorValues)  
-        {
-          if (value!=null)
-          {
-            List<?> values= value.getValues();
-            hybridizationDataRows.add(values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
-            if (twoColorHyb) twoColorHybDataRows.add(values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
-          }
-          else
-          {
-            hybridizationDataRows.add("");
-            if (twoColorHyb) twoColorHybDataRows.add("");
-          }
-        }
-        
-        if (twoColorHyb)hybridizationDataRows.addAll(twoColorHybDataRows);
-        
-        
-        // clear all necessary data holder for reuse
-        parameterMap.clear();
-        twoColorParameterMap.clear();
-        twoColorFirstParameterMap.clear();
-        bioXterParameterMap.clear();
-        twoColorBioXterParameterMap.clear();
-        protocolRefId.clear();
-        parameterValues.clear();
-        factorValues.clear();
-        twoColorParameterValues.clear();
-        twoColorFirstParameterValues.clear();
-        twoColorFirstProtocolRefId.clear();
-        twoColorProtocolRefId.clear();
-        
-        if (!twoColorHybDataRows.isEmpty()) 
-        {
-          twoColorHybDataRows.clear();
-          twoColorHyb=false;
-        } 
-        
-        poolSampleHeader.clear();
-        poolSampleTail.clear();
-        
-        hybridizationDataRows.add(Tab2MageConstants.hybrow_delimeter.getName());
-      }// end of raw biossay for loop
-      
-      //add headers
-      for (String bioXterHeader: bioXterHybSectionHeader)
-      {
-        hybSectionHeader.add("BioMaterialCharacteristics["+bioXterHeader+"]");
-      }
-      for (String protocolHeader: protocolHybSectionHeader)
-      {
-        hybSectionHeader.add(protocolHeader);
-      }
-      for (String parameterHeader :parameterHybSectionHeader) 
-      {
-        hybSectionHeader.add("Parameter["+parameterHeader+"]");
-      }
-      for (String factorValueHeader :factorValuesHybSectionHeader)
-      {
-        hybSectionHeader.add(factorValueHeader);
+        // get the headers for the experiment factor values and add to experimental factor values header set
+        factorValueHeaders.addAll(ExportHelper.getHeaderWithValuesOnly(l.getFactorValues()));
       }
       
       /*
-        Write the tab2mage file
+        Create all the used protocols objects
        */
-      Tab2MageWriter.writeTab2MageFile(experiment, protocols, hybSectionHeader, hybridizationDataRows, job, response, dc);
-            
+      protocols = ExportHelper.createProtocols(rawBioAssays, dc);
+      
+      /*
+        create all used Tab2Mage Hybridization sections protocol headers
+       */
+      protocolHybSectionHeader= Tab2MageValidator.getProtocolHybSectionHeader();
+      
+      /*
+        Create Tab2Mage Hybridization Section Header
+       */
+          
+      hybSectionHeader= ExportHelper.createHybridizationSectionHeader(dc,hybs,bioMatHeaders,
+                                  protocolHybSectionHeader,  paramHeaders, factorValueHeaders);
+      /*
+          Write the tab2mage file
+       */
+          
+      Tab2MageFileWriter.writeTab2MageFile(experiment, protocols,hybs, hybSectionHeader,bioMatHeaders, 
+                      protocolHybSectionHeader, paramHeaders,factorValueHeaders, job, response, dc);
+      
       //statusOut.close();
-      Writer out= Tab2MageWriter.getOut();
+      Writer out= Tab2MageFileWriter.getOut();
       out.flush();
       out.close();
@@ -730 +578 @@
     {
       if (dc != null) dc.close();
-      scanningProtocolCount=0;
-      extractionProtocolCount=0;
-      hybridizationProtocolCount=0;
-      labelingProtocolCount=0;
-      extractProtocolCount=0;
-      samplingProtocolCount=0;
-      newParameterHybSectionHeader.clear();
-      bioMatXteristicsHeader.clear();
-      bioXterHybSectionHeader.clear();
-      factorValuesHybSectionHeader.clear();
-      parameterHybSectionHeader.clear();
     }       
   }
   
   /**
-     get all the experimental factors for an experiments
-     @param DcControl dc, the database control
-     @param Experiment experiment, the experiment
-     @param RawBioassay, the rawbioassay that the experimental factors are obtained from
-     @return List, list of annotations
-   */ 
-  private static List<Annotation> getExperimentalFactorValues(DbControl dc, Experiment experiment, RawBioAssay rba)
-  {
-    List<Annotation> values= new LinkedList<Annotation>();
-    AnnotationSet annotationSet = rba.isAnnotated() ? rba.getAnnotationSet() : null;
-    ItemQuery<AnnotationType> experimentalFactorsQuery= experiment.getExperimentalFactors();
-    experimentalFactorsQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
-    ItemResultList<AnnotationType> experimentalFactors = experimentalFactorsQuery.list(dc);
-    if (annotationSet!=null) 
-    {
-      for (AnnotationType exprFactor :experimentalFactors)
-      {
-        if (!exprFactor.isRemoved())
-        {
-          //factorValuesHybSectionHeader.add("FactorValue["+exprFactor.getName()+"]");
-          values.add(annotationSet.findAnnotation(exprFactor));
-          if (annotationSet.findAnnotation(exprFactor)!=null)factorValuesHybSectionHeader.add("FactorValue["+exprFactor.getName()+"]");
-        }
-      }
-    }
-    return values;
+    set the array attributes  of the the <code>Tab2MageHybridizationLine</code> object
+      @param hybRow, the <code>Tab2MageHybridizationLine</code> object
+      @param arrayDesign, the Array Design
+   */
+  private void setArraysAttributes (Tab2MageHybridizationLine hybRow, ArrayDesign arrayDesign )
+  {
+    hybRow.set("Array",Tab2MageConstants.array_accession.getName(),arrayDesign.getName());
   }
   
   /**
-    Gets the base format id for the protocol, if protocol is null an empty string is returned
-    this is required to have consistent tab delimited format
-    @param protocol, the protocol used in the experiment
-    @return protocol id, an empty string is returned when the protocol is null 
-   */ 
-  private static String getFormattedProtocolId (Protocol protocol)
-  {
-    String tab="";
-    String protocolId;
-    if (protocol!=null)
-    {
-      protocolId = "P-BASE-"+protocol.getId();
-    }
-    else
-    {
-      protocolId= tab;
-    }
-    return  protocolId ; 
+    set the file attributes  of the the <code>Tab2MageHybridizationLine</code> object
+      @param hybRow, the Tab2MageHybridizationLine object
+      @param arrayDesign, the Array Design
+      @param rba, the raw bio assay
+      @param response, the response object to return errors in case of failure during the setting of file values
+   */
+  private void setFileAttributes(Tab2MageHybridizationLine hybRow, ArrayDesign arrayDesign, RawBioAssay rba, Response response)
+  {
+    try 
+    {
+      if (arrayDesign.isAffyChip())
+      {
+        File cdfFile= Affymetrix.getCdfFile(arrayDesign);
+        File celFile=Affymetrix.getCelFile(rba);
+        hybRow.set("File", Tab2MageConstants.raw_file.getName(), celFile.getName());
+        hybRow.set("File",Tab2MageConstants.cdf_file.getName(), cdfFile.getName());
+      }
+      else
+      {
+        hybRow.set("File", Tab2MageConstants.raw_file.getName(), rba.getName());
+      }
+      
+    }
+    catch(Throwable tr)
+    {
+      response.setError(tr.getMessage(), Arrays.asList(tr));
+    }
   }
   /**
-    Set all resource counters used within an experiment
-      @param experiment, the experiment
-      @param dc, the database control object
+    set the protocol and parameters attributes/values for Labeling -to- Sampling protocol and parameters
+    @param dc, the database control
+      @param subLine, the <code>Tab2MageSubHybLine</code> object
+      @param anotatable, the annotatable item to extract protocol and parameters from
+      @param protocolCount, the number of protocols already identified for the annotatable item
+      @param keyEntry, the header to set for the protocol in the <code>SubHybridizationLine</code> protocol map attributes
+      @param protocol, the protocol object
+      @param response, the response object to return errors in case of failure during the setting of parameter values
    */
-  @SuppressWarnings({"deprecation","unchecked"})
-  private static void getResourceCounter(Experiment experiment,DbControl dc)
-  {
-    ItemResultList<RawBioAssay> rbas= experiment.getRawBioAssays().list(dc);
-    for (RawBioAssay rba : rbas)
-    {
-      if (rba.getProtocol()!=null) 
-      {
-        extractionProtocolCount++ ;
-        getParameterSectionHeader(rba, dc );
-      }
-      if (rba.getScan().getProtocol()!=null)
-      {
-        scanningProtocolCount++;
-        getParameterSectionHeader(rba.getScan(), dc );
-      }
-      if (rba.getScan().getHybridization().getProtocol()!=null)
-      {
-        hybridizationProtocolCount++;
-        getParameterSectionHeader(rba.getScan().getHybridization(), dc );
-      }
-      ItemResultList<LabeledExtract>labeledExtracts = (ItemResultList<LabeledExtract>)
-                              rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);
-      for (LabeledExtract labeledExtract :labeledExtracts)
-      {
-        if (labeledExtract.getProtocol()!=null)
-        {
-          labelingProtocolCount++;
-          getParameterSectionHeader(labeledExtract, dc );
-        }
-        if (labeledExtract.getExtract().getProtocol()!=null)
-        {
-          extractProtocolCount++;
-          getParameterSectionHeader(labeledExtract.getExtract(), dc );
-        }
-        if  (labeledExtract.getExtract().getSample().getProtocol()!=null) 
-        { 
-          samplingProtocolCount++;
-          getParameterSectionHeader(labeledExtract.getExtract().getSample(), dc );
-        }
-        if (labeledExtract.getExtract().getSample().getBioSource()!=null)
-        setAllBioMatXteristicsHeader(labeledExtract.getExtract().getSample().getBioSource(),dc);
-      }
-    }
-  }
+  private void setProtocolAndParameterAtrributes(DbControl dc,Tab2MageSubHybLine subLine, Annotatable anotatable, int protocolCount, String keyEntry, Protocol protocol, Response response)
+  { 
+    if (protocolCount>0)
+    {
+      subLine.set("Protocol",keyEntry,ExportHelper.getFormattedProtocolId(protocol));
+    }
+            
+    // MeasuredBioMaterial protocol parameters
+    if (anotatable.isAnnotated()) setParameterValues(anotatable,dc, null,subLine, response);
+  }
+  
   /**
-      Gets the used annotation types (parameters) for an annotatable item 
-      @param annotatable, an item that implements annotatable
-      @param dc, the database control object
+    set the protocol and parameters attributes/values for Image_Analysis -to- Hybridization protocol and parameters
+      @param hybRow, the Tab2MageHybridizationLine object
+      @param anotatable, the annotatable item to extract protocol and parameters from
+      @param protocolCount, the number of protocols already identified for the annotatable item
+      @param keyEntry, the header to set for the protocol in the <code>SubHybridizationLine</code> protocol map attributes
+      @param protocol, the protocol object
+      @param response, the response object to return errors in case of failure during the setting of parameter values
+      @param dc, the database control
    */
-  
-  private static void getParameterSectionHeader(Annotatable anotatable, DbControl dc )
-  {
-    ItemResultList<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc);
-    for (Annotation annotation: annotations)
-    {
-      if (anotatable.getProtocol().isParameter(annotation.getAnnotationType()) && !annotation.getAnnotationType().isRemoved())
-        newParameterHybSectionHeader.add(annotation.getAnnotationType().getName());
-    }
-    //Helper.displayParameterHeader(newParameterHybSectionHeader);
-  }
-  /**
-    Gets the annotation types used as biomaterial characteristics for an annotatable item
-    @param annotatable, an item that implements annotatable
-      @param dc, the database control object
-   */
-  
-  private static void setAllBioMatXteristicsHeader(Annotatable anotatable, DbControl dc)
-  {
-    List<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc); 
-    for (Annotation annotation: annotations)
-    {
-      AnnotationType at=annotation.getAnnotationType();
-      if(!at.isRemoved()) 
-        bioMatXteristicsHeader.add(at.getName());
-    }
-  }
-  
-  /**
-    initialises the maps required to manage tab2mage data  
-    @param map, the map to be intitialised
-    @param isForParameter, TRUE if map is for parameters and FALSE otherwise
-   */
-   
-  private static void initialiseMaps(ConcurrentHashMap<String,String> map, boolean isForParameter)
-  {
-    if (map.isEmpty())
-    {
-      if (isForParameter)
-      {
-        for (String param: newParameterHybSectionHeader)
-        {
-          if (param!=null) map.put(param, "");
-        }
-      }
-      else if (!isForParameter)
-      {
-        for (String bioXterParam: bioMatXteristicsHeader)
-        {
-          if (bioXterParam!=null) map.put(bioXterParam, "");
-        }
-      }
-    }
-  }
+  private void setProtocolAndParameterAtrributes(Tab2MageHybridizationLine hybRow, Annotatable anotatable, int protocolCount,String keyEntry, Response response, DbControl dc)
+  {
+    if (protocolCount>0)
+    {
+      hybRow.set("Protocol", keyEntry, ExportHelper.getFormattedProtocolId(anotatable.getProtocol()));
+    }
+      //  protocol parameter
+    if (anotatable.isAnnotated()) setParameterValues(anotatable,dc, hybRow,null, response);
+    
+  }
+  
   /**
     sets protocol parameter values
@@ -907 +667 @@
       @param dc, the dabatabase control
    */
-  private static void setParameterValues(Annotatable anotatable, DbControl dc)
-  {
-    ItemResultList<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc);
-    for (Annotation annotation: annotations)
-    {
-      if (anotatable.getProtocol()!=null) // only check if the annotation is not null, watch this!
-      {   
-        if (anotatable.getProtocol().isParameter(annotation.getAnnotationType()) && !annotation.getAnnotationType().isRemoved())
-        {
-          List<?> values= annotation.getValues();
-          for (String header : parameterMap.keySet())
+  private static void setParameterValues(Annotatable anotatable, DbControl dc, Tab2MageHybridizationLine hybRow, Tab2MageSubHybLine subLine, Response response)
+  {
+    try
+    {
+      ItemResultList<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc);
+      for (Annotation annotation: annotations)
+      {
+        if (anotatable.getProtocol()!=null) // only check if the annotation is not null, watch this!
+        {   
+          if (anotatable.getProtocol().isParameter(annotation.getAnnotationType()) && !annotation.getAnnotationType().isRemoved())
           {
-            if (header.equals(annotation.getAnnotationType().getName()))
-            {
-              parameterMap.replace(header, "", values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
-            }
-          }
-          for (String twoColorFirstHeader : twoColorFirstParameterMap.keySet())
-          {
-            if (twoColorFirstHeader.equals(annotation.getAnnotationType().getName()))
-            {
-              twoColorFirstParameterMap.replace(twoColorFirstHeader, "", values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
-            }
+            List<?> values= annotation.getValues();
+            AnnotationType at= annotation.getAnnotationType();
+            if (hybRow!=null) 
+              hybRow.set("Parameter", at.getName(), values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
+            if (subLine!=null)
+              subLine.set("Parameter", at.getName(), values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
           }
         }
       }
     }
-  }
+    catch(Throwable tr)
+    {
+      response.setError(tr.getMessage(), Arrays.asList(tr));
+    }
+    
+  }
+  
   /**
-    sets protocol parameter values
-      @param anotatable, the annotatable item
-    @param dc, the database control
-    @param count, the two channel count
-    @param hybsize, the number of labeled extract to a Hybridization. 
+    get headers from the concurrent hasp maps
+    @return set of string : headers 
    */
-  private static void setParameterValues (Annotatable anotatable, DbControl dc, int count, int hybsize )
-  {
-    ItemResultList<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc);
-    for (Annotation annotation: annotations)
-    { 
-      if (anotatable.getProtocol()!=null)
-      {
-        if (anotatable.getProtocol().isParameter(annotation.getAnnotationType()) && !annotation.getAnnotationType().isRemoved())
-        {
-          List<?> values= annotation.getValues();
-          if (count < hybsize || count==1)
-          {
-            for (String header : parameterMap.keySet())
-            {
-              if (header.equals(annotation.getAnnotationType().getName()))
-              {
-                parameterMap.replace(header, "", values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
-              }
-            }
-          }
-          else if(count==2)
-          {
-            for (String twoColorHeader : twoColorParameterMap.keySet())
-            {
-              if (twoColorHeader.equals(annotation.getAnnotationType().getName()))
-              {
-                twoColorParameterMap.replace(twoColorHeader, "", values==null || values.size()==0 ? "" : Values.getString(values, ", ", true));
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-  
+  public static Set<String> getHeaders(ConcurrentHashMap<String,String> map)
+  {
+    Set<String> headers= new LinkedHashSet<String>();
+    headers.addAll(map.keySet());
+    return headers;
+  }
+    
   /**
-    gets the default value of an annotation type, used when annotation value is null
-    @param at, annotation type to obtain the default value from
-    @return string, deafult value or an empty string if the default value is null
+    List of Hybridizations
    */
-  private static String getDefaultValue(AnnotationType at)
-  {
-    
-    return at.getDefaultValue()!=null? at.getDefaultValue():"";
-  }
-  private static int scanningProtocolCount=0;
-  private static int extractionProtocolCount=0;
-  private static int hybridizationProtocolCount=0;
-  private static int labelingProtocolCount=0;
-  private static int extractProtocolCount=0;
-  private static int samplingProtocolCount=0;
-  private static ConcurrentHashMap<String,String> parameterMap = new ConcurrentHashMap<String, String>();
-  private static ConcurrentHashMap<String,String> twoColorParameterMap = new ConcurrentHashMap<String, String>();
-  private static ConcurrentHashMap<String,String> twoColorFirstParameterMap = new ConcurrentHashMap<String, String>();
-  private static ConcurrentHashMap<String,String> bioXterParameterMap = new ConcurrentHashMap<String, String>();
-  private static ConcurrentHashMap<String,String> twoColorBioXterParameterMap = new ConcurrentHashMap<String, String>();
-  private static Set<String> factorValuesHybSectionHeader= new LinkedHashSet<String>();
-  private static Set<String> parameterHybSectionHeader= new LinkedHashSet<String>();
-  private static Set<String> newParameterHybSectionHeader= new LinkedHashSet<String>();
-  private static Set<String> bioMatXteristicsHeader=  new LinkedHashSet<String>();
-  private static Set<String> bioXterHybSectionHeader=  new LinkedHashSet<String>();
+  private List<Tab2MageHybridization> hybs = new ArrayList<Tab2MageHybridization>();    
+
 }
+

trunk/uk/ac/ebi/Tab2MageExporter/src/uk/ac/ebi/nugo/plugins/ta2mageexport/Tab2MageValidator.java

@@ +1 @@
+/* $Id: Tab2MageValidator.java 2007-10-01 dominic $
+
+  Copyright (C) 2007 Authors contributing to this file.
+
+  This file is for NutriBASE - Nutrigenomics BioArray Software Environment.
+  A customisation of the BASE SOFTWARE.
+  
+  BASE is free software; you can redistribute it and/or
+  modify it under the terms of the GNU General Public License
+  as published by the Free Software Foundation; either version 2
+  of the License, or (at your option) any later version.
+
+  BASE is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program; if not, write to the Free Software
+  Foundation, Inc., 59 Temple Place - Suite 330,
+  Boston, MA  02111-1307, USA.
+*/
 package uk.ac.ebi.nugo.plugins.ta2mageexport;
 
+import java.util.Arrays;
 import java.util.LinkedHashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 
 import net.sf.basedb.core.Annotatable;
 import net.sf.basedb.core.Annotation;
+import net.sf.basedb.core.AnnotationSet;
 import net.sf.basedb.core.AnnotationType;
+import net.sf.basedb.core.BioSource;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
+import net.sf.basedb.core.Extract;
+import net.sf.basedb.core.Include;
+import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemResultList;
 import net.sf.basedb.core.LabeledExtract;
 import net.sf.basedb.core.RawBioAssay;
-
-/*
-  What the validation class should do: (for next implementation)
-  Export NO FAILURE
-    ----
-    if raw bioassay data have no protocol, export but report 'missing feature extraction protocol'
-    
-    if raw bioassay data are of type 'Affymetrix' but have no CEL file, export but report missing CEL file (AE may refuse your submission)
-    
-    if scan has no protocol or no scanner, export but report 'missing scanning protocol (MIAME data)' and/or 'missing scanner'
-    
-    if hybridization has no protocol or no hardware, export report 'missing hybridization protocol (MIAME data)' and/or 'missing hardware'
-    
-    if hybridization has no ArraySlide, export but report 'missing ArraySlide (barcode) information'
-    
-    Note: There is no need to fail here as the ArrayDesign information can be rescued from the Scan (please check)
-    
-    if labeled extract has no protocol, export but report 'missing labeling protocol (MIAME data)'
-    
-    if extract has no protocol, export but report 'missing extraction protocol (MIAME data)'
-    
-    if sample has no protocol, export but report 'missing sampling protocol (MIAME data)'
-    
-    IMPORTANT: There is probably a need for keeping track of how many protocols are missing for every records, so that if no protocols are used, then the export should output a BIG error message:
-    'Tab2mage submission incomplete: you must provide which protocols have been used and with which item '
-    
-    This is where the Experiment overview if a complementary effort to the tab2mage plugin: it already has a facility for checking all missing items)
-    
-    
-    if biosource has no annotationtype 'Species' reported, export but report 'Key MIAME annotation missing: AE may refuse your submission'
-    
-    if Experiment has no Experimental Factor declared and Experimental design and experiment design type are missing, export but report missing information (AE may refuse your submission)
-    
-    if Protocol description is empty or less than 25 characters in length, export but report 'description is too short and may compromise MIAME compliance'
-  FAILURE - No Export
-    ----
-    if raw bioassay data has no ArrayDesign or no Scan associated, then FAIL and report cause of failure=link missing between Raw Bioassay and Scan, or/and. Raw Bioassay data and ArrayDesign
-
-    (scan and hyb are automatically associated so no risk of breakage here)
-
-    if hybridization has no labeled extract associated, then FAIL and report cause of failure=link missing between Hyb and Labeled Extract
-    if labeled extract has no parent 'Extract', FAIL and report cause of failure=link missing between extracts and labeled extract
-    if extract has no parent 'Sample',  FAIL and report cause of failure=link missing between sample and extract
-    if sample has no parent 'BioSource', FAIL and report cause of failure=link missing between biosource and sample
-
+import net.sf.basedb.core.Sample;
+import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.plugin.Response;
+
+import org.apache.log4j.Logger;
+
+import uk.ac.ebi.nugo.common.Tab2MageConstants;
+
+
+/**
+  The tab2mage export validator
+  @author Dominic Oyeniran
+    @email  oyeniran@ebi.ac.uk/doyeniran@gmail.com
+  @version 1.0
  */
-
 public class Tab2MageValidator 
 {
-  
+  // logger
+  private static Logger log = Logger.getLogger(Tab2MageValidator.class);
+    
+  // counts the number of feature extraction protocol used in the experiment
+  private static int feProtocolCount=0;
+  
+  // counts the number of scanning protocols used in the experiment
   private static int scanningProtocolCount=0;
-  private static int extractionProtocolCount=0;
+  
+  // counts the number of hybridization protocol used in the experiment
   private static int hybridizationProtocolCount=0;
+  
+  // counts the number of labelling protocol used in the experiment
   private static int labelingProtocolCount=0;
+  
+  // counts the number of extraction protocol used in the experiment
   private static int extractProtocolCount=0;
+  
+  // counts the number of extraction protocol used in the experiment
   private static int samplingProtocolCount=0;
-  private static Set<String> newParameterHybSectionHeader= new LinkedHashSet<String>();
-  private static Set<String> bioMatXteristicsHeader=  new LinkedHashSet<String>();
+  
+  private Set<String> parameterHeaders= new LinkedHashSet<String>();
+  
+  private Set<String> bioMaterialXteristicsHeaders=  new LinkedHashSet<String>();
+  
+  private static Set<String> factorValuesHybSectionHeader= new LinkedHashSet<String>();
+  
+  private static Set<String>  protocolHybSectionHeader= new LinkedHashSet<String>();
+  
+  /* channel number to indicate platforms
+    1-- affymetrix
+    2-- agilent. genepix etc
+    3-- ......
+   */
+  private int channelNumber = 0;
+  // the experiment
   private Experiment experiment;
   
-  /**
-    creates a new Tab2Mage Validator
-   * @param experiment
-   */
-  public Tab2MageValidator(Experiment experiment)
+  private SessionControl sc;
+  
+  private Response response;
+  
+  /**
+      creates a new Tab2Mage Validator
+      @param experiment
+      @param sc
+      @param response
+   */
+  public Tab2MageValidator(Experiment experiment, SessionControl sc, Response response)
   {
     this.experiment=experiment;
-    getResourceCounter(experiment,experiment.getDbControl());
-  }
-  
-  /**
-  Set all resource counters used within an experiment
-    @param experiment, the experiment
-    @param dc, the database control object
- */
+    this.sc = sc;
+    this.response= response;
+    countProtocols();
+    createHeaders();
+  }
+  
+  /**
+    counts all protocols used in the experiment and initialise protocol variables
+   */
+  @SuppressWarnings("unchecked")
+  private void countProtocols()
+  {
+    DbControl dc =null;
+    try
+    {
+      dc = sc.newDbControl();
+      ItemResultList<RawBioAssay> rbas= experiment.getRawBioAssays().list(dc);
+      for (RawBioAssay rba : rbas)
+      {
+        if (rba.getProtocol()!=null) 
+          feProtocolCount++ ;
+        
+        if (rba.getScan().getProtocol()!=null)
+          scanningProtocolCount++;
+      
+        if (rba.getScan().getHybridization().getProtocol()!=null)
+          hybridizationProtocolCount++;
+        
+        ItemResultList<LabeledExtract>labeledExtracts = (ItemResultList<LabeledExtract>)
+                                rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);
+        if (channelNumber==0)
+              setChannelNumber(labeledExtracts.size());
+        for (LabeledExtract labeledExtract :labeledExtracts)
+        {
+          if (labeledExtract.getProtocol()!=null)
+            labelingProtocolCount++;  
+          
+          //Extract extract = labeledExtract.getExtract(); // RefExtract
+          Extract extract = ExportHelper.getExtract(labeledExtract, dc);
+          if (extract.getProtocol()!=null)
+            extractProtocolCount++;
+                    
+          //sample
+          Sample sample = ExportHelper.getSample(extract, dc);
+          if (sample.getProtocol()!=null)
+            samplingProtocolCount++;
+          
+        } 
+      }
+    }
+    catch(Throwable tr)
+    {
+      log.error("the protocol count was not successful", tr);
+      response.setError("the protocol counting was not successful", Arrays.asList(tr));
+      dc.close();
+    }
+    finally
+    {
+      if (dc!=null)
+        dc.close();
+    }
+  }
+  
+  /**
+    create both the parameter [AT] header and BioMaterialCharactertistic[AT] headers found in the whole experiment
+   */
   @SuppressWarnings({"deprecation","unchecked"})
-  private static void getResourceCounter(Experiment experiment,DbControl dc)
-  {
-    ItemResultList<RawBioAssay> rbas= experiment.getRawBioAssays().list(dc);
-    for (RawBioAssay rba : rbas)
-    {
-      if (rba.getProtocol()!=null) 
-      {
-        extractionProtocolCount++ ;
-        getParameterSectionHeader(rba, dc );
-      }
-      if (rba.getScan().getProtocol()!=null)
-      {
-        scanningProtocolCount++;
-        getParameterSectionHeader(rba.getScan(), dc );
-      }
-      if (rba.getScan().getHybridization().getProtocol()!=null)
-      {
-        hybridizationProtocolCount++;
-        getParameterSectionHeader(rba.getScan().getHybridization(), dc );
-      }
-      ItemResultList<LabeledExtract>labeledExtracts = (ItemResultList<LabeledExtract>)
-                              rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);
-      for (LabeledExtract labeledExtract :labeledExtracts)
-      {
-        if (labeledExtract.getProtocol()!=null)
-        {
-          labelingProtocolCount++;
-          getParameterSectionHeader(labeledExtract, dc );
-        }
-        if (labeledExtract.getExtract().getProtocol()!=null)
-        {
-          extractProtocolCount++;
-          getParameterSectionHeader(labeledExtract.getExtract(), dc );
-        }
-        if  (labeledExtract.getExtract().getSample().getProtocol()!=null) 
-        { 
-          samplingProtocolCount++;
-          getParameterSectionHeader(labeledExtract.getExtract().getSample(), dc );
-        }
-        if (labeledExtract.getExtract().getSample().getBioSource()!=null)
-        setAllBioMatXteristicsHeader(labeledExtract.getExtract().getSample().getBioSource(),dc);
-      }
-    }
-  }
-  /**
-      Gets the used annotation types (parameters) for an annotatable item 
+  private void createHeaders()
+  {
+    DbControl dc =null;
+    try
+    {
+      dc = sc.newDbControl();
+      ItemResultList<RawBioAssay> rbas= experiment.getRawBioAssays().list(dc);
+      for (RawBioAssay rba : rbas)
+      {
+        if (rba.getProtocol()!=null) 
+        {
+          createParameterSectionHeaders(rba, dc );
+          createProtocolHybSectionHeader(Tab2MageValidator.getFeProtocolCount(),Tab2MageConstants.protocol_featureextraction.getName());
+        }
+        if (rba.getScan().getProtocol()!=null)
+        {
+          createParameterSectionHeaders(rba.getScan(), dc );
+          createProtocolHybSectionHeader(Tab2MageValidator.getScanningProtocolCount(), Tab2MageConstants.protocol_scanning.getName());
+        }
+        if (rba.getScan().getHybridization().getProtocol()!=null)
+        {
+          createParameterSectionHeaders(rba.getScan().getHybridization(), dc );
+          createProtocolHybSectionHeader(Tab2MageValidator.getHybridizationProtocolCount(), Tab2MageConstants.protocol_hyb.getName());
+        }
+        ItemResultList<LabeledExtract>labeledExtracts = (ItemResultList<LabeledExtract>)
+                                rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);
+        for (LabeledExtract labeledExtract :labeledExtracts)
+        {
+          if (labeledExtract.getProtocol()!=null)
+          {
+            createParameterSectionHeaders(labeledExtract, dc );
+            createProtocolHybSectionHeader(Tab2MageValidator.getLabelingProtocolCount(), Tab2MageConstants.protocol_labeling.getName());
+          }
+          //Extract extract= labeledExtract.getExtract();
+          Extract extract = ExportHelper.getExtract(labeledExtract, dc);
+          if (extract.getProtocol()!=null)
+          {
+            createParameterSectionHeaders(labeledExtract.getExtract(), dc );
+            createProtocolHybSectionHeader(Tab2MageValidator.getExtractProtocolCount(), Tab2MageConstants.protocol_extraction.getName());
+          }
+          Sample sample = ExportHelper.getSample(extract, dc);
+          if  (sample.getProtocol()!=null) 
+          { 
+            createParameterSectionHeaders(sample, dc );
+            createProtocolHybSectionHeader(Tab2MageValidator.getSamplingProtocolCount(), Tab2MageConstants.protocol_treatment.getName());
+          }
+          BioSource bioSource= ExportHelper.getBioSource(sample, dc);
+          if (bioSource!=null)
+            createBioMatXteristicsSectionHeader(bioSource,dc);
+        }
+      }
+    }
+    catch(Throwable tr)
+    {
+      log.error("cannot create / set parameters headers and biomaterials headers", tr );
+      response.setError("cannot create / set parameters headers and biomaterials headers", Arrays.asList(tr));
+      dc.close();
+    }
+    finally
+    {
+      if (dc!=null)
+        dc.close();
+    }
+    
+  }
+  /**
+      Gets the used annotation types (parameters) for an annotatable item and add it to a set of PARAMETER[AT] headers
       @param annotatable, an item that implements annotatable
       @param dc, the database control object
    */
   
-  private static void getParameterSectionHeader(Annotatable anotatable, DbControl dc )
+  private void createParameterSectionHeaders(Annotatable anotatable, DbControl dc )
   {
     ItemResultList<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc);
@@ -145 +255 @@
     {
       if (anotatable.getProtocol().isParameter(annotation.getAnnotationType()) && !annotation.getAnnotationType().isRemoved())
-        newParameterHybSectionHeader.add(annotation.getAnnotationType().getName());
-    }
-    //Tab2MageHelper.displayParameterHeader(newParameterHybSectionHeader);
+        parameterHeaders.add(annotation.getAnnotationType().getName());
+    }
   }
   
@@ -156 +265 @@
    */
   
-  private static void setAllBioMatXteristicsHeader(Annotatable anotatable, DbControl dc)
-  {
-    List<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc); 
+  private void createBioMatXteristicsSectionHeader(Annotatable anotatable, DbControl dc)
+  {
+    
+    List<Annotation> annotations = anotatable.getAnnotationSet().getAnnotations().list(dc);
     for (Annotation annotation: annotations)
     {
-      AnnotationType at=annotation.getAnnotationType();
-      if(!at.isRemoved()) 
-        bioMatXteristicsHeader.add(at.getName());
-    }
-  }
-  
-  public static Set<String> getBioMatXteristicsHeader() 
-  {
-    return bioMatXteristicsHeader;
-  }
-
-  public static int getExtractionProtocolCount() 
-  {
-    return extractionProtocolCount;
-  }
-
+      if (annotation.getValues()!=null && !annotation.getValues().isEmpty())
+      {
+        AnnotationType at=annotation.getAnnotationType();
+        if(!at.isRemoved()) 
+        {
+          bioMaterialXteristicsHeaders.add(at.getName());
+          //("bio header added is :"+ at.getName());
+        } 
+      }
+    }
+    
+  }
+  /**
+    create a list of the protocol headers for the hyridization section of tab2mage file.
+    duplicates are eliminated with the use of linked hash set. 
+      @param count, the number of each protocol used across the raw bio assay.
+      @param header, the header for each protocol used across the raw bio assay
+   */
+  private static void createProtocolHybSectionHeader(int count, String header)
+  {
+    if (count>0)
+    {
+      protocolHybSectionHeader.add(header);
+    }
+  }
+  
+  /**
+    initialises the maps required to manage tab2mage data  
+    @param map, the map to be intitialised
+    @param isForParameter, TRUE if map is for parameters and FALSE otherwise
+   */
+   
+  public ConcurrentHashMap<String,String> initialiseMaps(ConcurrentHashMap<String,String> map, boolean isForParameter)
+  {
+    
+    if (map.isEmpty())
+    {
+      if (isForParameter) // get the parameter[AT] headers and put in a ConcurrentHashMap
+      {
+        for (String param: parameterHeaders)
+        {
+          if (param!=null) map.put(param, "");
+        }
+      }
+      else if (!isForParameter) // get all biomaterial xteristics [AT] headers and put in a ConcurrentHashMap 
+      {
+        for (String bioXterParam: bioMaterialXteristicsHeaders)
+        {
+          if (bioXterParam!=null) map.put(bioXterParam, "");
+        }
+      }
+    }
+    return map;
+  }
+  
+  /**
+     get all the experimental factors for an experiments
+     @param DcControl dc, the database control
+     @param Experiment experiment, the experiment
+     @param RawBioassay, the rawbioassay that the experimental factors are obtained from
+     @return List, list of annotations
+  */  
+  public static List<Annotation> getExperimentalFactorValues(DbControl dc, Experiment experiment, RawBioAssay rba)
+  {
+    List<Annotation> values= new LinkedList<Annotation>();
+    AnnotationSet annotationSet = rba.isAnnotated() ? rba.getAnnotationSet() : null;
+    ItemQuery<AnnotationType> experimentalFactorsQuery= experiment.getExperimentalFactors();
+    experimentalFactorsQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+    ItemResultList<AnnotationType> experimentalFactors = experimentalFactorsQuery.list(dc);
+    if (annotationSet!=null) 
+    {
+      for (AnnotationType exprFactor :experimentalFactors)
+      {
+        if (!exprFactor.isRemoved())
+        {
+          values.add(annotationSet.findAnnotation(exprFactor));
+          if (annotationSet.findAnnotation(exprFactor)!=null)factorValuesHybSectionHeader.add("FactorValue["+exprFactor.getName()+"]");
+        }
+      }
+    }
+    return values;
+  }
+  
+  /**
+     get all the experimental factors headers for an experiments
+     @param DcControl dc, the database control
+     @param Experiment experiment, the experiment
+     @param RawBioassay, the rawbioassay that the experimental factors are obtained from
+     @return List, list of annotations
+  */  
+  public static Set<String> getExperimentalFactorHeader(DbControl dc, Experiment experiment, RawBioAssay rba)
+  {
+    Set<String> headers= new LinkedHashSet<String>();
+    AnnotationSet annotationSet = rba.isAnnotated() ? rba.getAnnotationSet() : null;
+    ItemQuery<AnnotationType> experimentalFactorsQuery= experiment.getExperimentalFactors();
+    experimentalFactorsQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+    ItemResultList<AnnotationType> experimentalFactors = experimentalFactorsQuery.list(dc);
+    if (annotationSet!=null) 
+    {
+      for (AnnotationType exprFactor :experimentalFactors)
+      {
+        if (!exprFactor.isRemoved())
+        {
+    
+          if (annotationSet.findAnnotation(exprFactor)!=null)headers.add("FactorValue["+exprFactor.getName()+"]");
+        }
+      }
+    }
+    return headers;
+  }
+  
+  
+  // get the extraction protocol count
   public static int getExtractProtocolCount() 
   {
     return extractProtocolCount;
   }
-
+  // get the hybidization protocol count
   public static int getHybridizationProtocolCount() 
   {
     return hybridizationProtocolCount;
   }
-
+  // get the labelling protocol count
   public static int getLabelingProtocolCount() 
   {
     return labelingProtocolCount;
   }
-
-  public static Set<String> getNewParameterHybSectionHeader() 
-  {
-    return newParameterHybSectionHeader;
-  }
-
+  // get the sampling protocol count
   public static int getSamplingProtocolCount() 
   {
     return samplingProtocolCount;
   }
-
+  // get the scanning protocol count
   public static int getScanningProtocolCount() 
   {
     return scanningProtocolCount;
   }
-  
-  private static void validateUsers()  //
-  {
-        
-    
-  }
-  
+
+  // get the feature extraction protocol count
+  public static int getFeProtocolCount() 
+  {
+    return feProtocolCount;
+  }
+
+  // get the parameter headers
+  public Set<String> getParameterHeaders() 
+  {
+    return parameterHeaders;
+  }
+  // get the bio material characteristics headers
+  public Set<String> getBioMaterialXteristicsHeaders() 
+  {
+    return bioMaterialXteristicsHeaders;
+  }
+
+  // get the factor values header used in the experiment
+  public static Set<String> getFactorValuesHybSectionHeader() 
+  {
+    return factorValuesHybSectionHeader;
+  }
+
+  // get the protocol Hyb section header
+  public static Set<String> getProtocolHybSectionHeader() 
+  {
+    return protocolHybSectionHeader;
+  }
+
+
+  public int getChannelNumber() 
+  {
+    return channelNumber;
+  }
+
+   void setChannelNumber(int channelNumber) 
+  {
+    this.channelNumber = channelNumber;
+  }
 }