Changeset 3042


Ignore:
Timestamp:
Dec 19, 2006, 4:18:11 PM (15 years ago)
Author:
dominic
Message:

tab2mage export with the systen out messages revoved

File:
1 edited

Legend:

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

    r3038 r3042  
    103103        "is provided by the microarray informatics team at the EBI, Cambridge. The exported experiment can later be " +
    104104        "imported by the corresponding import plugin.",
    105         "1.0",
    106         "@Copyright 2006. EBI, NUGO Nutrigenomics Project",
     105        "2.0",
     106        "2006, Base 2 development team",
    107107        null,
    108108        "oyeniran@ebi.ac.uk",
    109         "http://www.ebi.ac.uk/~oyeniran"
     109        "http://base.thep.lu.se"
    110110    );
    111111 
     
    295295      Path path = new Path(p, Path.Type.FILE);   
    296296      if ((Boolean)job.getValue("overwrite") != null) overwrite = (Boolean)job.getValue("overwrite");
    297       File file = File.getByPath(dc, path, true); // Get the file by path and set an error if the file already exist and shouldn't be overwritten
     297      File file = File.getByPath(dc, path, true);
    298298      file.setMimeType("text/plain"); //set the type of the file
    299299      if (file.isInDatabase() && !overwrite && !file.isRemoved())
     
    307307      Experiment experiment= (Experiment)job.getValue("experiment");
    308308      experiment= Experiment.getById(dc,experiment.getId());
    309       //  check if the logged in user owned the experiment
    310       if (!(experiment.getOwner().equals(user))) return; //if not return. This can be re-coded to return a message for usability
     309      //  check if the logged in user owned the experiment //if not return. This can be re-coded to return a message for usability
     310      if (!(experiment.getOwner().equals(user))) return;
    311311     
    312312      //create an output stream writer to the file
    313313      //We use OutputStreamWriter so that characters written to it are encoded into bytes using a specified charset for all
    314       //System.out.println("The java runtime default char set is  :" +Charset.defaultCharset());
     314     
    315315      Writer out= new BufferedWriter(new OutputStreamWriter(file.getUploadStream(false),"ISO-8859-1"));
    316316     
     
    353353      for (RawBioAssay rba : rawBioAssays)
    354354      {
    355         twoColorHybDataRows.add("-done-"); //initialise the twocolor hyb row with -done- as the delimeter
     355        twoColorHybDataRows.add("-done-");
    356356        /*
    357357          Data files and array information section//
     
    474474        int hybsize=labeledExtracts.size();
    475475        int count=1;
    476         //System.out.println("The size of the two color data hyb data row before the labeled extract section: " +twoColorHybDataRows.size());
    477         //System.out.println("The size of the tow color param value before adding the labeled extract section is: " +twoColorFirstParameterValues.size());
    478         //System.out.println(hybsize ==1 ? "Affy Expriment. Hyb size:"+hybsize :"2 - color Expreriment. Hyb size : "+hybsize );
    479476        for (LabeledExtract labeledExtract :labeledExtracts) // can have more than one labeled extract (2 color experiments)
    480477        {
     
    500497          if (lbprotocolParameters!=null )
    501498          {
    502             //System.out.println("Labeled Extract protocol parameters size is: "+lbprotocolParameters.size());
    503499            if (lbprotocolParameters.size()!=0)
    504500            {
     
    554550            if (protocolParameters!=null )
    555551            {
    556               //System.out.println("Extract protocol parameters size is: "+protocolParameters.size());
    557552              if (protocolParameters.size()!=0)
    558553              {
     
    599594            if (protocolParameters!=null )
    600595            {
    601               //System.out.println("Sample protocol parameters size is: "+protocolParameters.size());
    602596              if (protocolParameters.size()!=0)
    603597              {
     
    872866      protocolParameters=protocolParametersQuery.list(dc);
    873867    }
    874     else
    875     {
    876       System.out.println("protocol is null");
    877     }
    878868    return protocolParameters;
    879869   
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