Changeset 3212

Timestamp:

Mar 26, 2007, 2:30:41 PM (15 years ago)

Author:

dominic

Message:

constants and sample pooling

Location:

branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins

Files:

• Tab2MageConstants.java (added)
• Tab2MageExporter.java (modified) (2 diffs)

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

@@ -340 +340 @@
       Writer statusOut= new BufferedWriter(new OutputStreamWriter(statusFile.getUploadStream(false),"ISO-8859-1"));
       statusOut.write(" Please check the messages below for the status of the export");
-      /*
-        Tab2Mage Header section
-       */ 
-      out.write("# This file contains an experiment exported in tab2mage specification from NutriBASE\n\n");
-      
-      /*
-        Tab2Mage Experiment Section
-       */
-      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");
-      String description = experiment.getDescription()!=null && experiment.getDescription().length()!=0 ? experiment.getDescription(): Values.getEmptyStringIfNull(experiment.getAbstract()).toString(); 
-      out.write("description\t"+description +"\n");
-      out.write("release_date\t"+Values.getEmptyStringIfNull(job.getValue("releaseDate"))+"\n");
-      out.write("submission_date\t"+Values.formatDate(new Date())+"\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("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   
       ItemQuery<RawBioAssay> rawBioAssaysQuery = experiment.getRawBioAssays();
@@ -820 +789 @@
       
       /*
+        Tab2Mage Header section
+      */ 
+      out.write("# This file contains an experiment exported in tab2mage specification from NutriBASE\n\n");
+      
+      /*
+        Tab2Mage Experiment Section
+      */
+      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");
+      String description = experiment.getDescription()!=null && experiment.getDescription().length()!=0 ? experiment.getDescription(): Values.getEmptyStringIfNull(experiment.getAbstract()).toString(); 
+      out.write("description\t"+description +"\n");
+      out.write("release_date\t"+Values.getEmptyStringIfNull(job.getValue("releaseDate"))+"\n");
+      out.write("submission_date\t"+Values.formatDate(new Date())+"\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("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();
+      /*
         Tab2Mage Protocol Section
        */