Changeset 3212


Ignore:
Timestamp:
Mar 26, 2007, 2:30:41 PM (14 years ago)
Author:
dominic
Message:

constants and sample pooling

Location:
branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins
Files:
1 added
1 edited

Legend:

Unmodified
Added
Removed
  • branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageExporter.java

    r3209 r3212  
    340340      Writer statusOut= new BufferedWriter(new OutputStreamWriter(statusFile.getUploadStream(false),"ISO-8859-1"));
    341341      statusOut.write(" Please check the messages below for the status of the export");
    342       /*
    343         Tab2Mage Header section
    344        */
    345       out.write("# This file contains an experiment exported in tab2mage specification from NutriBASE\n\n");
    346      
    347       /*
    348         Tab2Mage Experiment Section
    349        */
    350       out.write("Experiment section \n");
    351       out.write("domain\t"+Application.getHostName()+"\n");
    352       out.write("accession\tE-BASE-"+experiment.getId()+"\n");
    353       out.write("quality_control\t\n");
    354       out.write("experiment_design_type\t"+ Values.getEmptyStringIfNull(experiment.getExperimentDesign())+"\n");
    355       out.write("name\t"+experiment.getName() +"\n");
    356       String description = experiment.getDescription()!=null && experiment.getDescription().length()!=0 ? experiment.getDescription(): Values.getEmptyStringIfNull(experiment.getAbstract()).toString();
    357       out.write("description\t"+description +"\n");
    358       out.write("release_date\t"+Values.getEmptyStringIfNull(job.getValue("releaseDate"))+"\n");
    359       out.write("submission_date\t"+Values.formatDate(new Date())+"\n");
    360       out.write("submitter\t"+experiment.getOwner().getName()+"\n");
    361       out.write("submitter_email\t"+Values.getEmptyStringIfNull(experiment.getOwner().getEmail())+"\n");
    362       out.write("organization\t"+ Values.getEmptyStringIfNull(experiment.getOwner().getOrganisation()) +"\n");
    363       out.write("publication_title\t"+Values.getEmptyStringIfNull(experiment.getTitle()) +"\n"); 
    364       out.write("authors\t"+Values.getEmptyStringIfNull(experiment.getAuthors())+"\n");
    365       out.write("journal\t"+Values.getEmptyStringIfNull(experiment.getPublication())+"\n");
    366       out.write("volume\t\n"); 
    367       out.write("issue\t\n");
    368       out.write("pages\t\n");
    369       out.write("year\t"+ String.format("%1$tY", experiment.getPublicationDate())+"\n");
    370       out.write("pubmed_id\t"+Values.getEmptyStringIfNull(experiment.getPubMedId())+"\n");
    371       out.write("\n");
    372       out.flush();
    373          
     342               
    374343      // Get all protocols and hybs   
    375344      ItemQuery<RawBioAssay> rawBioAssaysQuery = experiment.getRawBioAssays();
     
    820789     
    821790      /*
     791        Tab2Mage Header section
     792      */
     793      out.write("# This file contains an experiment exported in tab2mage specification from NutriBASE\n\n");
     794     
     795      /*
     796        Tab2Mage Experiment Section
     797      */
     798      out.write("Experiment section \n");
     799      out.write("domain\t"+Application.getHostName()+"\n");
     800      out.write("accession\tE-BASE-"+experiment.getId()+"\n");
     801      out.write("quality_control\t\n");
     802      out.write("experiment_design_type\t"+ Values.getEmptyStringIfNull(experiment.getExperimentDesign())+"\n");
     803      out.write("name\t"+experiment.getName() +"\n");
     804      String description = experiment.getDescription()!=null && experiment.getDescription().length()!=0 ? experiment.getDescription(): Values.getEmptyStringIfNull(experiment.getAbstract()).toString();
     805      out.write("description\t"+description +"\n");
     806      out.write("release_date\t"+Values.getEmptyStringIfNull(job.getValue("releaseDate"))+"\n");
     807      out.write("submission_date\t"+Values.formatDate(new Date())+"\n");
     808      out.write("submitter\t"+experiment.getOwner().getName()+"\n");
     809      out.write("submitter_email\t"+Values.getEmptyStringIfNull(experiment.getOwner().getEmail())+"\n");
     810      out.write("organization\t"+ Values.getEmptyStringIfNull(experiment.getOwner().getOrganisation()) +"\n");
     811      out.write("publication_title\t"+Values.getEmptyStringIfNull(experiment.getTitle()) +"\n"); 
     812      out.write("authors\t"+Values.getEmptyStringIfNull(experiment.getAuthors())+"\n");
     813      out.write("journal\t"+Values.getEmptyStringIfNull(experiment.getPublication())+"\n");
     814      out.write("volume\t\n"); 
     815      out.write("issue\t\n");
     816      out.write("pages\t\n");
     817      out.write("year\t"+ String.format("%1$tY", experiment.getPublicationDate())+"\n");
     818      out.write("pubmed_id\t"+Values.getEmptyStringIfNull(experiment.getPubMedId())+"\n");
     819      out.write("\n");
     820      out.flush();
     821      /*
    822822        Tab2Mage Protocol Section
    823823       */
Note: See TracChangeset for help on using the changeset viewer.