Changeset 3209


Ignore:
Timestamp:
Mar 26, 2007, 10:54:26 AM (14 years ago)
Author:
dominic
Message:

default export file names and added annotations

File:
1 edited

Legend:

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

    r3204 r3209  
    114114 
    115115  private PluginParameter<String> pathParameter;
     116  private static final String pathDefaultValue="/home/tab2mage.txt";
    116117  private PluginParameter<String> statusPathParameter;
     118  private static final String statusPathDefaultValue="/home/statusreport.txt";
    117119  private PluginParameter<Experiment> experimentParameter;
    118120  private BooleanParameterType overwriteType= new BooleanParameterType(false, false);;
     
    136138          "Save as",
    137139          "Please specify the file name where the plugin should store it's output",
    138           new PathParameterType(Path.Type.FILE, null, true));
     140          new PathParameterType(Path.Type.FILE, pathDefaultValue, true));
    139141     
    140142      statusPathParameter = new PluginParameter<String>(
     
    142144          "Save Status File as",
    143145          "Please specify the file name where the plugin should store causes for failure and errors",
    144           new PathParameterType(Path.Type.FILE, null, true));
     146          new PathParameterType(Path.Type.FILE, statusPathDefaultValue, true));
    145147     
    146148      experimentParameter = new PluginParameter<Experiment>(
     
    422424          twoColorFirstProtocolRefId.add(getFormattedProtocolId(rba.getProtocol()));
    423425        }
    424         //Protocol rbapro= rba.getProtocol() ;
    425        
     426               
    426427        // rba protocol parameters
    427428        if (rba.isAnnotated())   
     
    835836            out.write(Values.getEmptyStringIfNull(protocol.getProtocolType().getName())+"\t");
    836837            ItemQuery<AnnotationType> parameterQuery= protocol.getParameters();
     838            parameterQuery.include(Include.MINE, Include.SHARED,Include.IN_PROJECT);
    837839            ItemResultList<AnnotationType> parameters= parameterQuery.list(dc);
    838840            for (AnnotationType parameter: parameters)
     
    965967  }
    966968  /**
    967     add more commenets and annnotations later
    968       @param experiment
     969    Set all resource counters used within an experiment
     970      @param experiment, the experiment
     971      @param dc, the database control object
    969972   */
    970973  @SuppressWarnings({"deprecation","unchecked"})
     
    10141017  }
    10151018  /**
    1016     Get new parameter section header method
    1017     [TODO] add more comments later and anotations
     1019      Gets the used annotation types (parameters) for an annotatable item
     1020      @param annotatable, an item that implements annotatable
     1021      @param dc, the database control object
    10181022   */
    10191023 
     
    10321036    }
    10331037  }
    1034 /**
    1035  [TODO] ANNOTATE THIS METHOD
    1036  * @param anotatable
    1037  * @param dc
    1038  */
     1038  /**
     1039    Gets the annotation types used as biomaterial characteristics for an annotatable item
     1040    @param annotatable, an item that implements annotatable
     1041      @param dc, the database control object
     1042  */
    10391043 
    10401044  private static void setAllBioMatXteristicsHeader(Annotatable anotatable, DbControl dc)
     
    10501054 
    10511055  /**
    1052     [TODO]
    1053     Add ANNOTATIONS TO THIS METHOD  AS WELL
     1056    initialises the maps required to manage tab2mage data 
     1057    @param map, the map to be intitialised
     1058    @param isForParameter, TRUE if map is for parameters and FALSE otherwise
    10541059   */
    10551060   
     
    11491154 
    11501155  /**
    1151     Display the content of the map
     1156    Displays the content of the map. Helps to check that content displayed is correct.
     1157    Note: this can be removed
     1158    @param map to be displayed.
    11521159   */
    11531160   private static void displayMaps (ConcurrentHashMap map)
     
    11601167   
    11611168 /**
    1162    [TODO] ADD ANNOTATION TO THIS METHOD
     1169   creates the exports files and throws an exception if the file is already exisiting
     1170   @param user, the logged in user
     1171   @param overwrite, false if an existing file should not be overwritten and true otherwise
     1172   @param pathString, the file path
     1173   @throws ItemAlreadyExistsException
    11631174 */
     1175   
    11641176   private static File processFilePath (User user,boolean overwrite, DbControl dc, String pathString)
    11651177   {
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