Changeset 3009

Timestamp:

Dec 8, 2006, 10:47:53 AM (16 years ago)

Author:

dominic

Message:

 

File:

• branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageExporter.java (modified) (24 diffs)

branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageExporter.java

@@ -19 +19 @@
 */
 package net.sf.basedb.plugins;
+
 
 import java.io.BufferedWriter;
@@ -255 +256 @@
     Set<String>  protocolHybSectionHeader= new LinkedHashSet<String>();
     Set<String>  parameterHybSectionHeader= new LinkedHashSet<String>();
-    
     Map<AnnotationType, Annotation> factorValues= new HashMap<AnnotationType,Annotation>();
     List<String> protocolRefId= new LinkedList<String>();
     List<String> hybridizationDataRows=new LinkedList<String>();
     List<String> parameterValues= new LinkedList<String>();
+    List<Annotation> expFactorValues= new LinkedList<Annotation>();
+    
+    List<String> twoColorHybDataRowsFirstSection=new LinkedList<String>();
+    List<String> twoColorHybDataRowsSecondSection=new LinkedList<String>();
+  
     
     boolean overwrite = false;
+    boolean twoColorHyb= false; 
     try
     {
@@ -289 +295 @@
       //  check if the logged in user owned the experiment
       if (!(experiment.getOwner().equals(user))) return; //if not the logged in user do not own the experiment. This can be re-coded to return a message for usability
-      //  get the release date string and convert it into date format
-      String releaseDate= (String)job.getValue("releaseDate");
+      String releaseDate= (String)job.getValue("releaseDate"); // get the release date string and convert it into date format
       //create an output stream writer to the file
       //We use OutputStreamWriter so that characters written to it are encoded into bytes using a specified charset for all 
       //System.out.println("The java runtime default char set is  :" +Charset.defaultCharset());
       Writer out= new BufferedWriter(new OutputStreamWriter(file.getUploadStream(false),"ISO-8859-1")); 
-    
+      
+      // Header section
+      out.write("# This file contains an experiment exported in tab2mage specification from BASE2\n\n");
       // Experiment Section
-      //outputExperimentSection(out,experiment,releaseDate, response);
       out.write("Experiment section \n");
       out.write("domain\t"+Application.getHostName()+"\n");
       out.write("accession\tE-BASE-"+experiment.getId()+"\n");
+      out.write("quality_control\t\n");
       out.write("experiment_design_type\t"+ Values.getEmptyStringIfNull(experiment.getExperimentDesign())+"\n");
       out.write("name\t"+experiment.getName() +"\n");
@@ -307 +314 @@
       out.write("release_date\t"+Values.getEmptyStringIfNull(releaseDate)+"\n");
       out.write("submission_date\t"+Values.formatDate(new Date())+"\n");
-      out.write("submitter\t"+experiment.getOwner().getName() +" email: "+Values.getEmptyStringIfNull(experiment.getOwner().getEmail()) +"\n");
+      out.write("submitter\t"+experiment.getOwner().getName()+"\n");
+      out.write("submitter_email\t"+Values.getEmptyStringIfNull(experiment.getOwner().getEmail())+"\n");
       out.write("organization\t"+ Values.getEmptyStringIfNull(experiment.getOwner().getOrganisation()) +"\n");
+      out.write("publication_title\t"+Values.getEmptyStringIfNull(experiment.getTitle()) +"\n");  
       out.write("authors\t"+Values.getEmptyStringIfNull(experiment.getAuthors())+"\n");
       out.write("journal\t"+Values.getEmptyStringIfNull(experiment.getPublication())+"\n"); 
-      out.write("year\t"+ String.format("%1$tY", experiment.getPublicationDate())+"\n");
-      out.write("pubmed_id\t"+Values.getEmptyStringIfNull(experiment.getPubMedId())+"\n");
-      out.write("quality_control\t\n");
-      out.write("publication_title\t\n"); 
       out.write("volume\t\n");  
       out.write("issue\t\n");
       out.write("pages\t\n");
+      out.write("year\t"+ String.format("%1$tY", experiment.getPublicationDate())+"\n");
+      out.write("pubmed_id\t"+Values.getEmptyStringIfNull(experiment.getPubMedId())+"\n");
       out.write("\n");
       out.flush();
+      
       
       // Get all protocols and hybs   
@@ -327 +335 @@
       for (RawBioAssay rba : rawBioAssays)
       {
+        twoColorHybDataRowsFirstSection.add("-done-"); //initialise the twocolor hyb row with -done- as the delimeter
         /*
           Data files and array information section//
@@ -339 +348 @@
           hybSectionHeader.add("File[raw]");
           hybridizationDataRows.add(celFile.getName());
+          twoColorHybDataRowsFirstSection.add(celFile.getName());
           hybSectionHeader.add("File[cdf]");
           hybridizationDataRows.add(cdfFile.getName());
+          twoColorHybDataRowsFirstSection.add(cdfFile.getName());
         }
         else
@@ -346 +357 @@
           hybSectionHeader.add("File[raw]");
           hybridizationDataRows.add(rba.getName());
+          twoColorHybDataRowsFirstSection.add(rba.getName());
         }
         hybSectionHeader.add("Array[accession]");
         hybridizationDataRows.add(arrayDesign.getName());
+        twoColorHybDataRowsFirstSection.add(arrayDesign.getName());
         
             //Raw BioAssay protocol
         protocolRefId.add(getFormattedProtocolId(rba.getProtocol()));
         protocolHybSectionHeader.add("Protocol[image_analysis]");
-        protocols.add(rba.getProtocol()); //rawbioassay protocol
+        //if (rba.getProtocol()!=null)
+        //{
+          protocols.add(rba.getProtocol()); //rawbioassay protocol
+          
+        //  System.out.println("raw bioassay protocol: P-BASE-"+rba.getProtocol().getId());
+        //}
         if (rba.isAnnotated())
         {
@@ -363 +381 @@
             {
               parameterHybSectionHeader.add("Parameter["+annotation.getAnnotationType().getName()+"]");
-              parameterValues.add(annotation.getValues().toString());
-            }
+              for (int i=0; i<annotation.getValues().size(); i++)
+              {
+                parameterValues.add(annotation.getValues().get(i).toString());
+              }
+            }
+            //else
+            //{
+            //  parameterValues.add("\t");
+            //}
           }
         } 
@@ -382 +407 @@
             {
               parameterHybSectionHeader.add("Parameter["+annotation.getAnnotationType().getName()+"]");
-              parameterValues.add(annotation.getValues().toString());
-            }
-            
+              for (int i=0; i<annotation.getValues().size(); i++)
+              {
+                parameterValues.add(annotation.getValues().get(i).toString());
+              }
+            }
+            //else
+            //{
+          //    parameterValues.add("\t");
+          //  }
           }
         }
         
-          //Hybridization
+        //Hybridization
         Hybridization hyb= scan.getHybridization();
         hybSectionHeader.add("Array[serial]");
         hybridizationDataRows.add(hyb.getArraySlide().getName());
-              
+        twoColorHybDataRowsFirstSection.add(hyb.getArraySlide().getName());     
         /*
           Names of materials and processes section
@@ -398 +429 @@
         hybSectionHeader.add("Hybridization");
         hybridizationDataRows.add(hyb.getName());
-      
+        twoColorHybDataRowsFirstSection.add(hyb.getName()); 
+        
         System.out.println("The number of scans: "+hyb.countScans()); // count scans that created the hyb
         BioMaterialEvent bioMaterialEvent= hyb.getCreationEvent(); // event that created the hyridization
@@ -415 +447 @@
             {
               parameterHybSectionHeader.add("Parameter["+annotation.getAnnotationType().getName()+"]");
-              parameterValues.add(annotation.getValues().toString());
-            }
-            
-          }
-        }
-        
-        
+              for (int i=0; i<annotation.getValues().size(); i++)
+              {
+                parameterValues.add(annotation.getValues().get(i).toString());
+              }
+            }
+            //else
+            //{
+            //  parameterValues.add("\t");
+            //}
+          }
+        }
+          
         ItemQuery<LabeledExtract> labeledExtractQuery =(ItemQuery<LabeledExtract>) bioMaterialEvent.getSources(); // get all the labeled extract
         ItemResultList<LabeledExtract> labeledExtracts= labeledExtractQuery .list(dc);
-        for (LabeledExtract labeledExtract :labeledExtracts) // can have more that one labeled extract
-        {
+        int hybsize=labeledExtracts.size();
+        int count=1;
+        //STOPPED HERE (LAST CODE) TRYING TO IMPLEMENT TWO COLOR HYBS
+        //if (hybsize==2 && !hybridizationDataRows.contains("-done-")) 
+        //{
+        //  twoColorHybDataRowsFirstSection.addAll(hybridizationDataRows); //create anew data row for 2 color experiment
+        //  twoColorHybDataRowsSecondSection.addAll(hybridizationDataRows);
+        //  twoColorHyb=true;
+        //}else if(hybsize==2 && twoColorHyb )
+        //{ //NOTE THE OUTPUT SHOWS THAT i AM ADDING THE LAST INFORMATION, SO FIX THIS
+        //  twoColorHybDataRowsFirstSection.addAll(twoColorHybDataRowsSecondSection);
+        //}
+        // END OF LAST CODE
+        System.out.println("The size of the two color data hyb data row before the labeled extract section: " +twoColorHybDataRowsFirstSection.size());
+        System.out.println("The size of the hyb data row before adding to tow color hyb row: " +hybridizationDataRows.size());
+        System.out.println(hybsize ==1 ? "Affy Expriment. Hyb size:"+hybsize :"2 - color Expreriment. Hyb size : "+hybsize );
+        for (LabeledExtract labeledExtract :labeledExtracts) // can have more than one labeled extract (2 color experiments)
+        {
+          
             //  labeled extract
           hybSectionHeader.add("LabeledExtract");
-          hybridizationDataRows.add(labeledExtract.getName());
-          
+          if (count<hybsize)
+          {
+            hybridizationDataRows.add(labeledExtract.getName());
+          }
+          else if (count==2)
+          {
+            twoColorHyb=true;
+            twoColorHybDataRowsFirstSection.add(labeledExtract.getName());
+          }
+        
           Protocol lbExtractProtocol= labeledExtract.getCreationEvent().getProtocol();
           protocols.add(lbExtractProtocol); // labeled extract protocol
           protocolRefId.add(getFormattedProtocolId(lbExtractProtocol));
           protocolHybSectionHeader.add("Protocol[labeling]");
-          
           if (labeledExtract.isAnnotated())
           {
@@ -444 +505 @@
               {
                 parameterHybSectionHeader.add("Parameter["+annotation.getAnnotationType().getName()+"]");
-                parameterValues.add(annotation.getValues().toString());
+                for (int i=0; i<annotation.getValues().size(); i++)
+                {
+                  parameterValues.add(annotation.getValues().get(i).toString());
+                }
               }
-              
-            }
-          }
-                  
+              //else
+              //{
+              //  parameterValues.add("\t");
+              //}
+            }
+          }
           String labelName= labeledExtract.getLabel().getName(); // the name of the label
           hybSectionHeader.add("Dye");
-          hybridizationDataRows.add(labelName);
-          
+          if (count < hybsize)
+          {
+            hybridizationDataRows.add(labelName);
+          }
+          else if (count==2)
+          {
+            twoColorHybDataRowsFirstSection.add(labelName);
+          }
             //  Extract
-          Set <Annotatable> extractOrPooledLabeledExtract= labeledExtract.getAnnotatableParents(); //get extract or pooled labelled extract
+          //Set <Annotatable> extractOrPooledLabeledExtract= labeledExtract.getAnnotatableParents(); //get extract or pooled labelled extract
           //if (extractOrPooledLabeledExtract instanceof Extract)
           Extract extract= labeledExtract.getExtract();
@@ -461 +533 @@
           {
             hybSectionHeader.add("Extract");
-            hybridizationDataRows.add(extract.getName());
+            if (count < hybsize)
+            {
+              hybridizationDataRows.add(extract.getName());
+            }
+            else if (count==2)
+            {
+              twoColorHybDataRowsFirstSection.add(extract.getName());
+            }
             
             Protocol extractProtocol =extract.getCreationEvent().getProtocol(); //extract protocol
@@ -476 +555 @@
                 {
                   parameterHybSectionHeader.add("Parameter["+annotation.getAnnotationType().getName()+"]");
-                  parameterValues.add(annotation.getValues().toString());
+                  for (int i=0; i<annotation.getValues().size(); i++)
+                  {
+                    System.out.println("The extract protocol parameter is :" + annotation.getValues().get(i).toString());
+                    parameterValues.add(annotation.getValues().get(i).toString());
+                  }
                 }
-                
+                //else
+                //{
+                //  parameterValues.add("\t");
+                //}
               }
             }
@@ -489 +575 @@
           {
             hybSectionHeader.add("Sample");
-            hybridizationDataRows.add(sample.getName());
+            if (count < hybsize)
+            {
+              hybridizationDataRows.add(sample.getName());
+            }
+            else if (count==2)
+            {
+              twoColorHybDataRowsFirstSection.add(sample.getName());
+            }
             
             Protocol sampleProtocol=sample.getCreationEvent().getProtocol();      //sampling protocol
@@ -505 +598 @@
                 {
                   parameterHybSectionHeader.add("Parameter["+annotation.getAnnotationType().getName()+"]");
-                  parameterValues.add(annotation.getValues().toString());
+                  for (int i=0; i<annotation.getValues().size(); i++)
+                  {
+                    System.out.println("The sample protocl parameter is :" + annotation.getValues().get(i).toString());
+                    parameterValues.add(annotation.getValues().get(i).toString());
+                  }
                 }
-                
+                //else
+                //{
+                //  parameterValues.add("\t");
+                //}
               }
             }
           }
             // Biosource
-          
+          //sample.getAnnotatableParents(); //get the biosource or pooled samples
           BioSource bioSource=sample.getBioSource();
           if (bioSource!=null) //get the biosource
           {
-            hybridizationDataRows.add(bioSource.getName());
+            
             hybSectionHeader.add("Biosource");
+            if (count < hybsize)
+            {
+              hybridizationDataRows.add(bioSource.getName());
+            }
+            else if(count==2)
+            {
+              twoColorHybDataRowsFirstSection.add(bioSource.getName());
+            }
             AnnotationSet bsAnnotationSet =bioSource.getAnnotationSet();
             ItemQuery<Annotation> annotationsQuery= bsAnnotationSet.getAnnotations();
@@ -529 +637 @@
                 for (int i=0; i<annotation.getValues().size(); i++)
                 {
-            
-                  hybridizationDataRows.add(annotation.getValues().get(i).toString());
-              
+                  if (count < hybsize)
+                  {
+                    hybridizationDataRows.add(annotation.getValues().get(i).toString());
+                  }
+                  else if(count==2)
+                  {
+                    twoColorHybDataRowsFirstSection.add(annotation.getValues().get(i).toString());
+                  }
+                  
                 }
               }
             }
-          } 
+          }
+          System.out.println("The count before increament is :" +count);
+          count++;
           
-        }
-        for (String protcolId : protocolRefId)
-        {
-          System.out.println("----Test protocol id added----");
-          System.out.println("Id: "+protcolId);
-          hybridizationDataRows.add(protcolId);
-        }
-        for (String paramValue : parameterValues )
-        {
-          System.out.println("----Test parametervalue added----");
-          hybridizationDataRows.add(paramValue);
-        }
+        } //end of labeled extract loop
+        
+        System.out.println("THE VALUE OF COUNT IS: "+ count);
+        //for (String protcolId : protocolRefId) //add protocol id
+        //{
+          //System.out.println("----Test protocol id added----");
+          //System.out.println("Id: "+protcolId);
+        /// hybridizationDataRows.add(protcolId);
+        //}
+        //for (String paramValue : parameterValues ) //add parameter values
+        //{
+          //System.out.println("----Test parametervalue added----");
+        //  hybridizationDataRows.add(paramValue);
+        //}
         /*
           Experimental Factor Section
         */
-        factorValues= getExperimentalFactors(dc,experiment,rba);
-        for(Annotation value: factorValues.values())
+        expFactorValues=getExperimentalFactorValues(dc,experiment,rba);
+        for(Annotation value: expFactorValues)  //add factor values
         {
           if (value!=null)
@@ -562 +680 @@
             }
           }
-        }
-        
+          else
+          {
+            hybridizationDataRows.add("\t");
+          }
+        }
+        if (twoColorHyb)
+        {
+          //twoColorHybDataRowsFirstSection.add("-done-");
+          hybridizationDataRows.addAll(twoColorHybDataRowsFirstSection);
+          //hybridizationDataRows.add("-done-");
+        }
         protocolRefId.clear();
         parameterValues.clear();
         factorValues.clear();
-        System.out.println("done");
+        if (!twoColorHybDataRowsFirstSection.isEmpty()) 
+        {
+          twoColorHybDataRowsFirstSection.clear();
+          twoColorHyb=false;
+        } 
         hybridizationDataRows.add("-done-");
+        System.out.println("done - end of rawbioassay :" + rba.getName());
       }// end of raw biossay for loop
       
@@ -579 +711 @@
         hybSectionHeader.add(parameterHeader);
       }
+      for (String factorValueHeader :factorValuesHybSectionHeader)
+      {
+        hybSectionHeader.add(factorValueHeader);
+      }
+      
       //Protocol Section
       out.write("Protocol section \n");
@@ -614 +751 @@
         out.write(header.toString()+"\t");
       }
-      if (factorValues!=null)
-      {
-        for (AnnotationType fv : factorValues.keySet())
-        {
-          out.write("FactorValue["+fv.getName()+"]\t");
-        }
-      }
+      
       out.write("\n");
       //values
@@ -634 +765 @@
         }
       }
+      //for (String twoColor :twoColorHybDataRowsFirstSection )
+      //{
+      //  if (twoColor!="-done-")
+      //  {
+      //    out.write(twoColor+"\t");
+      //  }
+      //  else if("-done-".equals(twoColor))
+      //  {
+      //    out.write("\n");
+      //  }
+      //}
       out.write("\n");
     
@@ -650 +792 @@
     }       
   }
-  
-  
   //   get all the experimental factors for this experiments,
-  private static Map<AnnotationType, Annotation> getExperimentalFactors(DbControl dc, Experiment experiment, RawBioAssay rba)
-  {
-    Map<AnnotationType, Annotation> values= new HashMap<AnnotationType,Annotation>();
+  private static List<Annotation> getExperimentalFactorValues(DbControl dc, Experiment experiment, RawBioAssay rba)
+  {
+    List<Annotation> values= new LinkedList<Annotation>();
     ItemQuery<AnnotationType> experimentalFactorsQuery= experiment.getExperimentalFactors();
     experimentalFactorsQuery.include(Include.MINE,Include.IN_PROJECT, Include.SHARED, Include.OTHERS);
@@ -661 +801 @@
     for (AnnotationType exprFactor :experimentalFactors) //create the factor value for this experiment obtaining annotations from rawbioassay
     {
+      factorValuesHybSectionHeader.add("FactorValue["+exprFactor.getName()+"]");
       AnnotationSet annotationSet = rba.isAnnotated() ? rba.getAnnotationSet() : null;
       if (annotationSet!=null)
       {
-        values.put(exprFactor,annotationSet.findAnnotation(exprFactor));
+        values.add(annotationSet.findAnnotation(exprFactor));
+        
       }         
     }
     return values;
   }
-  
-  // get the base format id for the protocol if protocol is null and empty string is returned , this helps the mainatin the tab delim format
+  // get the base format id for the protocol if protocol is null and empty string is returned , this helps to  mentain the tab delim format
   private static String getFormattedProtocolId (Protocol protocol)
   {
@@ -685 +826 @@
     return  protocolId ; 
   }
+   
+  private static Set<String>  factorValuesHybSectionHeader= new LinkedHashSet<String>();
 }