Changeset 5612


Ignore:
Timestamp:
Apr 18, 2011, 1:23:57 PM (11 years ago)
Author:
Nicklas Nordborg
Message:

References #1592: Unified installation procedure for plug-ins, extensions and more...

Moved remaining core plug-in definitions to the xml file. Removed the getAbout() method from all plugins.

Location:
trunk
Files:
3 deleted
49 edited

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r5611 r5612  
    732732    >
    733733    <jar
    734       jarfile="${test.build}/JarPluginAbout.jar"
    735       basedir="${test.build}"
    736       includes="JarPluginAbout.class"
    737     />
    738     <jar
    739734      jarfile="${test.build}/JarPlugin.jar"
    740735      basedir="${test.build}"
    741736      includes="JarPlugin*,NullPlugin*,Base1*"
    742       excludes="JarPlugin.jar,JarPluginAbout.*"
     737      excludes="JarPlugin.jar"
    743738      manifest="${test.src}/data/JarPluginManifest.txt"
    744739      >
    745       <metainf file="${test.src}/base-plugins.xml"></metainf>
    746        <metainf file="${test.src}/base-configurations.xml"></metainf>
    747740    </jar>
    748741    <delete>
  • trunk/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java

    r5481 r5612  
    4646import net.sf.basedb.core.Type;
    4747import net.sf.basedb.core.Unit;
    48 import net.sf.basedb.core.Version;
    4948
    5049import net.sf.basedb.core.Job.ExecutionTime;
     
    5251import net.sf.basedb.core.data.RawData;
    5352import net.sf.basedb.core.data.ReporterListScoreData;
    54 import net.sf.basedb.core.plugin.About;
    55 import net.sf.basedb.core.plugin.AboutImpl;
    5653import net.sf.basedb.core.plugin.AbstractExporterPlugin;
    5754import net.sf.basedb.core.plugin.ExportOutputStream;
     
    10097{
    10198
    102   /**
    103      Plugin description
    104   */
    105   private static final About about =
    106     new AboutImpl
    107     (
    108       "Table exporter",
    109       "Export all table listings in the web interface as tab-separated text files " +
    110       "or as XML. This plugin only works from within the web client, since it depends " +
    111       "on context and table information.",
    112       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    113       "2006, Base 2 development team",
    114       null,
    115       null,
    116       "http://base.thep.lu.se"
    117     );
    118 
    11999  private static final Set<GuiContext> guiContexts = new HashSet<GuiContext>();
    120100  private RequestInformation configureJob;
     
    126106    -------------------------------------------
    127107  */
    128   public About getAbout()
    129   {
    130     return about;
    131   }
    132108  public Plugin.MainType getMainType()
    133109  {
  • trunk/src/core/net/sf/basedb/core/Install.java

    r5610 r5612  
    693693      createPluginDefinitions("/core-plugins.xml", keyEveryoneUse, update);
    694694     
    695       /*
    696       createPluginDefinition("net.sf.basedb.plugins.Base1PluginExecuter", null, null, true, null, false);
    697       createPluginDefinition("net.sf.basedb.plugins.BaseFileExporterPlugin", null, keyEveryoneUse, true, null, true);
    698       createPluginDefinition("net.sf.basedb.plugins.BfsExporterPlugin", null, keyEveryoneUse, true, null, true);
    699       createPluginDefinition("net.sf.basedb.plugins.FormulaFilter", null, keyEveryoneUse, true, null, false);
    700       createPluginDefinition("net.sf.basedb.plugins.HelpExporter", null, null, true, null, true);
    701       createPluginDefinition("net.sf.basedb.plugins.HelpImporter", null, null, true, null, false);
    702      
    703       createPluginDefinition("net.sf.basedb.plugins.IntensityCalculatorPlugin", null, keyEveryoneUse, true, null, false);
    704       createPluginDefinition("net.sf.basedb.plugins.JepExtraValueCalculator", null, keyEveryoneUse, true, null, false);
    705       createPluginDefinition("net.sf.basedb.plugins.JepIntensityTransformer", null, keyEveryoneUse, true, null, false);
    706       createPluginDefinition("net.sf.basedb.plugins.LowessNormalization", null, keyEveryoneUse, true, null, false);
    707       createPluginDefinition("net.sf.basedb.plugins.MedianRatioNormalization", null, keyEveryoneUse, true, null, false);
    708       createPluginDefinition("net.sf.basedb.plugins.PlateFlatFileImporter", null, null, true, null, false);
    709       createPluginDefinition("net.sf.basedb.plugins.PlateMappingExporter", null, null, true, null, true);
    710       createPluginDefinition("net.sf.basedb.plugins.PlateMappingImporter", null, null, true, null, false);
    711       createPluginDefinition("net.sf.basedb.plugins.PrintMapFlatFileImporter", null, null, true, null, false);
    712       createPluginDefinition("net.sf.basedb.plugins.RawDataFlatFileImporter", null, keyEveryoneUse, true, null, false);
    713       createPluginDefinition("net.sf.basedb.plugins.ReporterFlatFileImporter", null, keyEveryoneUse, true, null, false);
    714       createPluginDefinition("net.sf.basedb.plugins.ReporterMapFlatFileImporter", null, null, true, null, false);
    715       createPluginDefinition("net.sf.basedb.plugins.SpotImageCreator", null, keyEveryoneUse, true, null, false);
    716       createPluginDefinition("net.sf.basedb.plugins.ZipFileUnpacker", null, keyEveryoneUse, true, null, true);
    717       createPluginDefinition("net.sf.basedb.plugins.TarFileUnpacker", null, keyEveryoneUse, true, null, true);
    718       createPluginDefinition("net.sf.basedb.plugins.PluginConfigurationExporter", null, keyEveryoneUse, true, null, true);
    719       createPluginDefinition("net.sf.basedb.plugins.PluginConfigurationImporter", null, null, true, null, false);
    720       createPluginDefinition("net.sf.basedb.plugins.CdfFileReporterImporter", null, null, true, null, false);
    721       createPluginDefinition("net.sf.basedb.plugins.PackedFileExporter", null, keyEveryoneUse, true, null, true);
    722       createPluginDefinition("net.sf.basedb.plugins.AnnotationFlatFileImporter", null, keyEveryoneUse, true, null, false);
    723       createPluginDefinition("net.sf.basedb.plugins.IlluminaRawDataImporter", null, keyEveryoneUse, true, null, false);
    724       createPluginDefinition("net.sf.basedb.plugins.GalExporter", null, keyEveryoneUse, true, null, true);
    725       createPluginDefinition("net.sf.basedb.plugins.ManualTransformCreator", null, keyEveryoneUse, true, null, true);
    726       createPluginDefinition("net.sf.basedb.plugins.batchimport.BioSourceImporter", null, keyEveryoneUse, true, null, false);
    727       createPluginDefinition("net.sf.basedb.plugins.batchimport.SampleImporter", null, keyEveryoneUse, true, null, false);
    728       createPluginDefinition("net.sf.basedb.plugins.batchimport.ExtractImporter", null, keyEveryoneUse, true, null, false);
    729       createPluginDefinition("net.sf.basedb.plugins.batchimport.LabeledExtractImporter", null, keyEveryoneUse, true, null, false);
    730       createPluginDefinition("net.sf.basedb.plugins.batchimport.HybridizationImporter", null, keyEveryoneUse, true, null, false);
    731       createPluginDefinition("net.sf.basedb.plugins.batchimport.ScanImporter", null, keyEveryoneUse, true, null, false);
    732       createPluginDefinition("net.sf.basedb.plugins.batchimport.RawBioAssayImporter", null, keyEveryoneUse, true, null, false);
    733       createPluginDefinition("net.sf.basedb.plugins.batchimport.ArrayDesignImporter", null, null, true, null, false);
    734       createPluginDefinition("net.sf.basedb.plugins.batchimport.ArrayBatchImporter", null, null, true, null, false);
    735       createPluginDefinition("net.sf.basedb.plugins.batchimport.ArraySlideImporter", null, null, true, null, false);
    736       createPluginDefinition("net.sf.basedb.plugins.batchimport.BioPlateImporter", null, keyEveryoneUse, true, null, false);
    737       createPluginDefinition("net.sf.basedb.plugins.executor.ExternalProgramExecutor", null, keyEveryoneUse, true, null, false);
    738       createPluginDefinition("net.sf.basedb.plugins.executor.BfsExporterSupport", null, keyEveryoneUse, true, null, false);
    739       createPluginDefinition("net.sf.basedb.plugins.executor.BfsImporterSupport", null, keyEveryoneUse, true, null, false);
    740       createPluginDefinition("net.sf.basedb.plugins.executor.BaseFileExporterSupport", null, keyEveryoneUse, true, null, false);
    741       createPluginDefinition("net.sf.basedb.plugins.executor.BaseFileImporterSupport", null, keyEveryoneUse, true, null, false);
    742       createPluginDefinition("net.sf.basedb.plugins.executor.FileOnlyImporterSupport", null, keyEveryoneUse, true, null, false);
    743       */
    744      
    745695      // Plugin configurations
    746696      progressStep++;
    747697      if (progress != null) progress.display((int)(progressStep*progress_factor), "--Creating example plugin configurations...");
    748       /*
    749698      createPluginConfigurations("/plugin_configfile.xml", update);
    750699      createPluginConfigurations("/illumina.configurations.xml", update);
    751       */
    752700     
    753701      // Formulas
  • trunk/src/install/net/sf/basedb/install/Webclient.java

    r4889 r5612  
    3838import net.sf.basedb.core.BaseException;
    3939import net.sf.basedb.core.ItemNotFoundException;
     40import net.sf.basedb.core.Version;
     41import net.sf.basedb.core.plugin.AboutImpl;
    4042import net.sf.basedb.plugins.HelpImporter;
    4143
     
    149151    }
    150152   
     153    simpleExport.setAbout(
     154        new AboutImpl
     155        (
     156            "Table exporter",
     157            "Export all table listings in the web interface as tab-separated text files " +
     158            "or as XML. This plugin only works from within the web client, since it depends " +
     159            "on context and table information.",
     160            Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
     161            "2006, Base 2 development team",
     162            null,
     163            null,
     164            "http://base.thep.lu.se"
     165          ), false);
     166   
    151167    dc.commit();
    152168   
  • trunk/src/plugins/core/core-plugins.xml

    r5610 r5612  
    118118  </plugin-definition>
    119119 
     120  <plugin-definition id="IntensityCalculator">
     121    <about>
     122      <name>Formula intensity calculator</name>
     123      <description>
     124        This plugin is used to calculate intensities from raw data creating an initial root bioassay set.
     125        The intensities are calculated using Formula objects registered for the experiment's raw data type.
     126        Thus, the functionality of this plugin can be extended by adding more formula objects to the database.
     127      </description>
     128    </about>
     129    <plugin-class>net.sf.basedb.plugins.IntensityCalculatorPlugin</plugin-class>
     130    <settings>
     131      <property name="everyone-use">1</property>
     132    </settings>
     133  </plugin-definition>
    120134 
     135  <plugin-definition id="JepExtraValueCalculator">
     136    <about>
     137      <name>Formula extra value calculator</name>
     138      <description>
     139        This plugin is used to calculate extra values for a bioassay set using
     140        formulas entered by the user.
     141      </description>
     142    </about>
     143    <plugin-class>net.sf.basedb.plugins.JepExtraValueCalculator</plugin-class>
     144    <settings>
     145      <property name="everyone-use">1</property>
     146    </settings>
     147  </plugin-definition>
     148 
     149  <plugin-definition id="JepIntensityTransformer">
     150    <about>
     151      <name>Formula intensity transformer</name>
     152      <description>
     153        This plugin is used to transform the intensities of a bioassayset using
     154        formulas entered by the user.
     155      </description>
     156    </about>
     157    <plugin-class>net.sf.basedb.plugins.JepIntensityTransformer</plugin-class>
     158    <settings>
     159      <property name="everyone-use">1</property>
     160    </settings>
     161  </plugin-definition>
     162 
     163  <plugin-definition id="LowessNormalization">
     164    <about>
     165      <name>Normalization: Lowess</name>
     166      <description>
     167        This is an efficient java implementation by Johan Enell
     168        of the LOWESS algorithm. It provides intensity-based normalization.
     169        The window size is the only smoothness parameter available
     170        in this implementation. The higher it is, the smoother the
     171        function will be. Tweaking the other two parameters allows
     172        you to gain performance at the price of a small precision loss.
     173        The default values are usually good.
     174       
     175        This plug-in supports the use of reporter lists for exclusion of
     176        reporters in the LOWESS calculation. The option to select reporter
     177        lists is visible for users with access to defined reporter lists.
     178
     179        For more info on LOWESS:
     180        Cleveland WS, Devlin SJ: Locally weighted regression: an
     181        approach to regression analysis by local fitting. J Am Stat
     182        Assoc 1988, 83:596-610.
     183        Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP:
     184        Normalization for cDNA microarray data: a robust composite
     185        method addressing single and multiple slide systematic
     186        variation. Nucleic Acids Res 2002, 30:e15.
     187      </description>
     188    </about>
     189    <plugin-class>net.sf.basedb.plugins.LowessNormalization</plugin-class>
     190    <settings>
     191      <property name="everyone-use">1</property>
     192    </settings>
     193  </plugin-definition>
     194 
     195  <plugin-definition id="MedianRatioNormalization">
     196    <about>
     197      <name>Normalization: Median ratio</name>
     198      <description>
     199        This normalizer behaves differently depending on the array type.
     200
     201        1-channel arrays: Intensities are changed in two different ways
     202        depending on user selection.
     203        a) For absolute intensity data the intensities should be scaled
     204        with the median intensity, Inew=Iold/Imedian, such that resulting
     205        median is 1.
     206        b) For log intensity data the intensities should be subtracted with
     207        the median intensity, log(Inew)=log(Iold)-log(Imedian), such that
     208        resulting median is 0.
     209
     210        2-channel arrays: Intensities are scaled such that their geometric
     211        mean (sqrt(i1 * i2)) is kept constant but the median of their ratios
     212        (i1/i2) is shifted to 1.
     213
     214        All array types: The user can optionally exclude spots; all spots
     215        with at least one intensity below a user selectable threshold are
     216        removed. User selectable (low/high intensity) fractions of the
     217        remaining spots are ignored in median calculation.
     218      </description>
     219    </about>
     220    <plugin-class>net.sf.basedb.plugins.MedianRatioNormalization</plugin-class>
     221    <settings>
     222      <property name="everyone-use">1</property>
     223    </settings>
     224  </plugin-definition>
     225
     226  <plugin-definition id="PlateFlatFileImporter">
     227    <about>
     228      <name>Plate importer</name>
     229      <description>
     230        This plugin is used to import plates from a simple flat file.
     231      </description>
     232    </about>
     233    <plugin-class>net.sf.basedb.plugins.PlateFlatFileImporter</plugin-class>
     234  </plugin-definition>
     235
     236  <plugin-definition id="PlateMappingExporter">
     237    <about>
     238      <name>Plate mapping exporter</name>
     239      <description>
     240        This plugin is used to export plate mappings, which maps the
     241        coordinates of one or more source plates to coordinates on
     242        one or more destination plates. Use the "Plate mapping importer"
     243        to import the files produced by this plugin.
     244      </description>
     245    </about>
     246    <plugin-class>net.sf.basedb.plugins.PlateMappingExporter</plugin-class>
     247    <settings>
     248      <property name="immediate-execution">1</property>
     249    </settings>
     250  </plugin-definition>
     251
     252  <plugin-definition id="PlateMappingImporter">
     253    <about>
     254      <name>Plate mapping importer</name>
     255      <description>
     256        This plugin is used to import plate mapping files created
     257        by the "Plate mapping exporter". The file maps the
     258        coordinates of one or more source plates to coordinates
     259        on one or more destination plates.
     260      </description>
     261    </about>
     262    <plugin-class>net.sf.basedb.plugins.PlateMappingImporter</plugin-class>
     263  </plugin-definition>
     264
     265  <plugin-definition id="RawDataFlatFileImporter">
     266    <about>
     267      <name>Raw data importer</name>
     268      <description>
     269        This plugin is used to import raw data from a simple text file.
     270      </description>
     271    </about>
     272    <plugin-class>net.sf.basedb.plugins.RawDataFlatFileImporter</plugin-class>
     273    <settings>
     274      <property name="everyone-use">1</property>
     275    </settings>
     276  </plugin-definition>
     277
     278  <plugin-definition id="ReporterFlatFileImporter">
     279    <about>
     280      <name>Reporter importer</name>
     281      <description>
     282        This plugin is used to import reporters from a simple flat file.
     283      </description>
     284    </about>
     285    <plugin-class>net.sf.basedb.plugins.ReporterFlatFileImporter</plugin-class>
     286    <settings>
     287      <property name="everyone-use">1</property>
     288    </settings>
     289  </plugin-definition>
     290
     291  <plugin-definition id="ReporterMapFlatFileImporter">
     292    <about>
     293      <name>Reporter map importer</name>
     294      <description>
     295        This plugin is used to import features to an ArrayDesign from a simple flat file.
     296      </description>
     297    </about>
     298    <plugin-class>net.sf.basedb.plugins.ReporterMapFlatFileImporter</plugin-class>
     299  </plugin-definition>
     300
     301  <plugin-definition id="SpotImageCreator">
     302    <about>
     303      <name>Spot images creator</name>
     304      <description>
     305        Converts a full-size scanned image into smaller preview jpg images for each individual spot.
     306      </description>
     307    </about>
     308    <plugin-class>net.sf.basedb.plugins.SpotImageCreator</plugin-class>
     309    <settings>
     310      <property name="everyone-use">1</property>
     311    </settings>
     312  </plugin-definition>
     313
     314  <plugin-definition id="ZipFileUnpacker">
     315    <about>
     316      <name>ZIP file unpacker</name>
     317      <description>
     318        This plugin unpacks a zip file on the BASE file system.
     319        It supports zip and jar files.
     320      </description>
     321    </about>
     322    <plugin-class>net.sf.basedb.plugins.ZipFileUnpacker</plugin-class>
     323    <settings>
     324      <property name="everyone-use">1</property>
     325      <property name="immediate-execution">1</property>
     326    </settings>
     327  </plugin-definition>
     328
     329  <plugin-definition id="TarFileUnpacker">
     330    <about>
     331      <name>TAR file unpacker</name>
     332      <description>
     333        This plugin unpacks a tar file on the BASE file system.
     334        It also supports TAR files compressed with the GZIP and
     335        BZIP algorithms.
     336      </description>
     337    </about>
     338    <plugin-class>net.sf.basedb.plugins.TarFileUnpacker</plugin-class>
     339    <settings>
     340      <property name="everyone-use">1</property>
     341      <property name="immediate-execution">1</property>
     342    </settings>
     343  </plugin-definition>
     344
     345  <plugin-definition id="PluginConfigurationExporter">
     346    <about>
     347      <name>Plugin configuration exporter</name>
     348      <description>
     349        This plugin is used to export selected plugin configurations
     350        to an XML-file. The plugin configurations can later be imported
     351        by the "Plugin configuration importer".
     352      </description>
     353    </about>
     354    <plugin-class>net.sf.basedb.plugins.PluginConfigurationExporter</plugin-class>
     355    <settings>
     356      <property name="everyone-use">1</property>
     357      <property name="immediate-execution">1</property>
     358    </settings>
     359  </plugin-definition>
     360
     361  <plugin-definition id="PluginConfigurationImporter">
     362    <about>
     363      <name>Plugin configuration importer</name>
     364      <description>
     365        This plugin is used to import configuration for a BASE plugin from
     366        an XML-file created by the "Plugin configuration exporter".
     367      </description>
     368    </about>
     369    <plugin-class>net.sf.basedb.plugins.PluginConfigurationImporter</plugin-class>
     370  </plugin-definition>
     371
     372  <plugin-definition id="CdfFileReporterImporter">
     373    <about>
     374      <name>Affymetrix CDF probeset importer</name>
     375      <description>
     376        This plug-in is used to import probesets from an Affymetrix
     377        CDF file as reporters. It can be used in import mode from the
     378        reporter list view and from the array design view and in
     379        verification mode from the array design view. The plug-in can
     380        only set the name and ID of the reporters, since the CDF file
     381        doesn't contains any annotation information. Probesets already
     382        in BASE will not be affected by the import.
     383      </description>
     384    </about>
     385    <plugin-class>net.sf.basedb.plugins.CdfFileReporterImporter</plugin-class>
     386  </plugin-definition>
     387
     388  <plugin-definition id="PackedFileExporter">
     389    <about>
     390      <name>Packed file exporter</name>
     391      <description>
     392        This plugin is used to pack one or more files/directories
     393        into a single file. Items should be selected before starting
     394        the plug-in and they must all be located in the same parent
     395        directory. The compressed file can be downloaded immediately
     396        or stored in the BASE file system. The user can choose to have
     397        the selected files and directories removed after they've been
     398        packed.
     399      </description>
     400    </about>
     401    <plugin-class>net.sf.basedb.plugins.PackedFileExporter</plugin-class>
     402    <settings>
     403      <property name="everyone-use">1</property>
     404      <property name="immediate-execution">1</property>
     405    </settings>
     406  </plugin-definition>
     407
     408  <plugin-definition id="AnnotationFlatFileImporter">
     409    <about>
     410      <name>Annotation importer</name>
     411      <description>
     412        This plugin is used to import annotations to any annotatable items.
     413      </description>
     414    </about>
     415    <plugin-class>net.sf.basedb.plugins.AnnotationFlatFileImporter</plugin-class>
     416    <settings>
     417      <property name="everyone-use">1</property>
     418    </settings>
     419  </plugin-definition>
     420
     421  <plugin-definition id="IlluminaRawDataImporter">
     422    <about>
     423      <name>Illumina raw data importer</name>
     424      <description>
     425        This plugin is used to import raw data from Illumina data files.
     426        The plug-in can be executed from the list of raw bioassays and
     427        will then only create new raw bioassays, or from within an experiment,
     428        in which case the imported data will also be associated with
     429        the experiment.
     430      </description>
     431    </about>
     432    <plugin-class>net.sf.basedb.plugins.IlluminaRawDataImporter</plugin-class>
     433    <settings>
     434      <property name="everyone-use">1</property>
     435    </settings>
     436  </plugin-definition>
     437
     438  <plugin-definition id="GalExporter">
     439    <about>
     440      <name>GAL exporter</name>
     441      <description>
     442        This plugin exports the features of an array design to a
     443        GAL file. The plugin only works for array designs that
     444        has features in the database and is disabled for other
     445        array designs.
     446      </description>
     447    </about>
     448    <plugin-class>net.sf.basedb.plugins.GalExporter</plugin-class>
     449    <settings>
     450      <property name="everyone-use">1</property>
     451      <property name="immediate-execution">1</property>
     452    </settings>
     453  </plugin-definition>
     454
     455  <plugin-definition id="ManualTransformCreator">
     456    <about>
     457      <name>Manual transform</name>
     458      <description>
     459        This plug-in allows a user to manually register an external
     460        analysis procedure that has happened outside of BASE and to
     461        register the parameters used and the output files that was
     462        generated. Before this plug-in can be used a configuration
     463        that represents the external tool must be created. The
     464        configuration will be used to register possible parameters
     465        and output files.
     466      </description>
     467    </about>
     468    <plugin-class>net.sf.basedb.plugins.ManualTransformCreator</plugin-class>
     469    <settings>
     470      <property name="everyone-use">1</property>
     471      <property name="immediate-execution">1</property>
     472    </settings>
     473  </plugin-definition>
     474
     475  <plugin-definition id="BioSourceImporter">
     476    <about>
     477      <name>Biosource importer</name>
     478      <description>
     479        Imports and updates biosources in a batch.
     480      </description>
     481    </about>
     482    <plugin-class>net.sf.basedb.plugins.batchimport.BioSourceImporter</plugin-class>
     483    <settings>
     484      <property name="everyone-use">1</property>
     485    </settings>
     486  </plugin-definition>
     487 
     488  <plugin-definition id="BioPlateImporter">
     489    <about>
     490      <name>Bioplate importer</name>
     491      <description>
     492        Imports and updates bioplates in a batch.
     493      </description>
     494    </about>
     495    <plugin-class>net.sf.basedb.plugins.batchimport.BioPlateImporter</plugin-class>
     496    <settings>
     497      <property name="everyone-use">1</property>
     498    </settings>
     499  </plugin-definition>
     500
     501  <plugin-definition id="SampleImporter">
     502    <about>
     503      <name>Sample importer</name>
     504      <description>
     505        Imports and updates samples in a batch.
     506      </description>
     507    </about>
     508    <plugin-class>net.sf.basedb.plugins.batchimport.SampleImporter</plugin-class>
     509    <settings>
     510      <property name="everyone-use">1</property>
     511    </settings>
     512  </plugin-definition>
     513
     514  <plugin-definition id="ExtractImporter">
     515    <about>
     516      <name>Extract importer</name>
     517      <description>
     518        Imports and updates extracts in a batch.
     519      </description>
     520    </about>
     521    <plugin-class>net.sf.basedb.plugins.batchimport.ExtractImporter</plugin-class>
     522    <settings>
     523      <property name="everyone-use">1</property>
     524    </settings>
     525  </plugin-definition>
     526
     527  <plugin-definition id="LabeledExtractImporter">
     528    <about>
     529      <name>Labeled extract importer</name>
     530      <description>
     531        Imports and updates labeled extracts in a batch.
     532      </description>
     533    </about>
     534    <plugin-class>net.sf.basedb.plugins.batchimport.LabeledExtractImporter</plugin-class>
     535    <settings>
     536      <property name="everyone-use">1</property>
     537    </settings>
     538  </plugin-definition>
     539
     540  <plugin-definition id="HybridizationImporter">
     541    <about>
     542      <name>Hybridization importer</name>
     543      <description>
     544        Imports and updates hybridizations in a batch.
     545      </description>
     546    </about>
     547    <plugin-class>net.sf.basedb.plugins.batchimport.HybridizationImporter</plugin-class>
     548    <settings>
     549      <property name="everyone-use">1</property>
     550    </settings>
     551  </plugin-definition>
     552
     553  <plugin-definition id="ScanImporter">
     554    <about>
     555      <name>Scan importer</name>
     556      <description>
     557        Imports and updates scans in a batch.
     558      </description>
     559    </about>
     560    <plugin-class>net.sf.basedb.plugins.batchimport.ScanImporter</plugin-class>
     561    <settings>
     562      <property name="everyone-use">1</property>
     563    </settings>
     564  </plugin-definition>
     565
     566  <plugin-definition id="RawBioAssayImporter">
     567    <about>
     568      <name>Raw bioassay importer</name>
     569      <description>
     570        Imports and updates raw bioassays in a batch.
     571      </description>
     572    </about>
     573    <plugin-class>net.sf.basedb.plugins.batchimport.RawBioAssayImporter</plugin-class>
     574    <settings>
     575      <property name="everyone-use">1</property>
     576    </settings>
     577  </plugin-definition>
     578
     579  <plugin-definition id="ArrayDesignImporter">
     580    <about>
     581      <name>Array design importer</name>
     582      <description>
     583        Imports and updates array designs in a batch.
     584      </description>
     585    </about>
     586    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayDesignImporter</plugin-class>
     587  </plugin-definition>
     588
     589  <plugin-definition id="ArrayBatchImporter">
     590    <about>
     591      <name>Array batch importer</name>
     592      <description>
     593        Imports and updates array batches in a batch.
     594      </description>
     595    </about>
     596    <plugin-class>net.sf.basedb.plugins.batchimport.ArrayBatchImporter</plugin-class>
     597  </plugin-definition>
     598
     599  <plugin-definition id="ArraySlideImporter">
     600    <about>
     601      <name>Array slide importer</name>
     602      <description>
     603        Imports and updates array slides in a batch.
     604      </description>
     605    </about>
     606    <plugin-class>net.sf.basedb.plugins.batchimport.ArraySlideImporter</plugin-class>
     607  </plugin-definition>
     608
     609  <plugin-definition id="ExternalProgramExecutor">
     610    <about>
     611      <name>External program executor</name>
     612      <description>
     613        This plug-in is used to export data from BASE to an external
     614        program, run the program, and import the result back into BASE.
     615        The export and import format is set by the user but must be a
     616        format supported by the external program. The export also handles
     617        the parameters needed to run the external program.
     618      </description>
     619    </about>
     620    <plugin-class>net.sf.basedb.plugins.executor.ExternalProgramExecutor</plugin-class>
     621    <settings>
     622      <property name="everyone-use">1</property>
     623    </settings>
     624  </plugin-definition>
     625
     626  <plugin-definition id="BfsExporterSupport">
     627    <about>
     628      <name>BFS exporter for the ExternalProgramExecutor</name>
     629      <description>
     630        Support plug-in for the external program executor that
     631        exports data to the external program in BFS format. This
     632        plug-in can't be used as a standalone plug-in.
     633      </description>
     634    </about>
     635    <plugin-class>net.sf.basedb.plugins.executor.BfsExporterSupport</plugin-class>
     636    <settings>
     637      <property name="everyone-use">1</property>
     638    </settings>
     639  </plugin-definition>
     640
     641  <plugin-definition id="BfsImporterSupport">
     642    <about>
     643      <name>BFS importer for the ExternalProgramExecutor</name>
     644      <description>
     645        Support plug-in for the external program executor that
     646        imports BFS formatted data from the external program to
     647        BASE. This plug-in can't be used as a standalone plug-in.
     648      </description>
     649    </about>
     650    <plugin-class>net.sf.basedb.plugins.executor.BfsImporterSupport</plugin-class>
     651    <settings>
     652      <property name="everyone-use">1</property>
     653    </settings>
     654  </plugin-definition>
     655
     656  <plugin-definition id="BaseFileExporterSupport">
     657    <about>
     658      <name>BASEFile exporter for the ExternalProgramExecutor</name>
     659      <description>
     660        Support plug-in for the external program executor that
     661        exports data to the external program in BASEFile format.
     662        This plug-in can't be used as a standalone plug-in.
     663      </description>
     664    </about>
     665    <plugin-class>net.sf.basedb.plugins.executor.BaseFileExporterSupport</plugin-class>
     666    <settings>
     667      <property name="everyone-use">1</property>
     668    </settings>
     669  </plugin-definition>
     670
     671  <plugin-definition id="BaseFileImporterSupport">
     672    <about>
     673      <name>BASEfile importer for the ExternalProgramExecutor</name>
     674      <description>
     675        Support plug-in for the external program executor that
     676        imports BASEfile formatted data from the external program
     677        to BASE. This plug-in can't be used as a standalone plug-in.
     678      </description>
     679    </about>
     680    <plugin-class>net.sf.basedb.plugins.executor.BaseFileImporterSupport</plugin-class>
     681    <settings>
     682      <property name="everyone-use">1</property>
     683    </settings>
     684  </plugin-definition>
     685
     686  <plugin-definition id="FileOnlyImporterSupport">
     687    <about>
     688      <name>File-only importer for the ExternalProgramExecutor</name>
     689      <description>
     690        Support plug-in for the external program executor that
     691        uploads all created files to BASE and attaches them to
     692        a child bioassay set. This plug-in can't be used as a
     693        standalone plug-in.
     694      </description>
     695    </about>
     696    <plugin-class>net.sf.basedb.plugins.executor.FileOnlyImporterSupport</plugin-class>
     697    <settings>
     698      <property name="everyone-use">1</property>
     699    </settings>
     700  </plugin-definition>
     701
    121702  <!--
    122703  <plugin-definition id="">
     
    129710    <settings>
    130711      <property name="everyone-use">1</property>
     712      <property name="immediate-execution">1</property>
    131713    </settings>
    132714  </plugin-definition>
  • trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

    r5481 r5612  
    6767import net.sf.basedb.core.Type;
    6868import net.sf.basedb.core.Unit;
    69 import net.sf.basedb.core.Version;
    70 import net.sf.basedb.core.plugin.About;
    71 import net.sf.basedb.core.plugin.AboutImpl;
    7269import net.sf.basedb.core.plugin.GuiContext;
    7370import net.sf.basedb.core.plugin.InteractivePlugin;
     
    123120{
    124121
    125  
    126   private static final About about =
    127     new AboutImpl
    128     (
    129       "Annotation importer",
    130       "This plugin is used to import annotations to any annotatable items.",
    131       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    132       "2007, Base 2 development team",
    133       null,
    134       null,
    135       "http://base.thep.lu.se"
    136     );
    137  
    138122  private static volatile Set<GuiContext> guiContexts;
    139123  private static final Set<Permissions> permissions = new HashSet<Permissions>();
     
    329313    -------------------------------------------
    330314  */
    331   public About getAbout()
    332   {
    333     return about;
    334   }
    335315  @Override
    336316  public boolean requiresConfiguration()
  • trunk/src/plugins/core/net/sf/basedb/plugins/CdfFileReporterImporter.java

    r5481 r5612  
    6666import net.sf.basedb.core.StringParameterType;
    6767import net.sf.basedb.core.Type;
    68 import net.sf.basedb.core.Version;
    6968import net.sf.basedb.core.filehandler.CdfFileHandler;
    70 import net.sf.basedb.core.plugin.About;
    71 import net.sf.basedb.core.plugin.AboutImpl;
    7269import net.sf.basedb.core.plugin.AbstractPlugin;
    7370import net.sf.basedb.core.plugin.AutoDetectingImporter;
     
    10198  implements InteractivePlugin, AutoDetectingImporter, SignalTarget
    10299{
    103 
    104   /**
    105      Plugin description
    106   */
    107   private static final About about =
    108     new AboutImpl
    109     (
    110       "Affymetrix CDF probeset importer",
    111       "This plug-in is used to import probesets from an Affymetrix CDF file as reporters. " +
    112       "It can be used in import mode from the reporter list view and from the array design view " +
    113       "and in verification mode from the array design view. " +
    114       "The plug-in can only set the name and ID of the reporters, since the CDF file doesn't " +
    115       "contains any annotation information. Probesets already in BASE will not " +
    116       "be affected by the import",
    117       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    118       "2007, Base 2 development team",
    119       null,
    120       null,
    121       "http://base.thep.lu.se"
    122     );
    123100 
    124101  private static final Set<GuiContext> guiContexts =
     
    146123    -------------------------------------------
    147124  */
    148   public About getAbout()
    149   {
    150     return about;
    151   }
    152125  public boolean supportsConfigurations()
    153126  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/GalExporter.java

    r5610 r5612  
    6161import net.sf.basedb.core.ProgressReporter;
    6262import net.sf.basedb.core.RequestInformation;
    63 import net.sf.basedb.core.Version;
    6463import net.sf.basedb.core.Job.ExecutionTime;
    6564import net.sf.basedb.core.data.FeatureData;
    6665import net.sf.basedb.core.data.ReporterData;
    67 import net.sf.basedb.core.plugin.About;
    68 import net.sf.basedb.core.plugin.AboutImpl;
    6966import net.sf.basedb.core.plugin.AbstractExporterPlugin;
    7067import net.sf.basedb.core.plugin.ExportOutputStream;
     
    9491  implements SignalTarget, InteractivePlugin
    9592{
    96 
    97   private static final About about =
    98     new AboutImpl
    99   (
    100       "GAL exporter",
    101       "This plugin exports the features of an array design to a GAL file. The plugin " +
    102       "only works for array designs that has features in the database and is disabled " +
    103       "for other array designs.",
    104       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    105       "2008, Base 2 development team",
    106       null,
    107       null,
    108       "http://base.thep.lu.se"
    109   );
    110  
    11193 
    11294  private static final Set<GuiContext> guiContexts = 
  • trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java

    r5481 r5612  
    6868import net.sf.basedb.core.SystemItems;
    6969import net.sf.basedb.core.Trashcan;
    70 import net.sf.basedb.core.Version;
    7170import net.sf.basedb.core.data.RawData;
    72 import net.sf.basedb.core.plugin.About;
    73 import net.sf.basedb.core.plugin.AboutImpl;
    7471import net.sf.basedb.core.plugin.GuiContext;
    7572import net.sf.basedb.core.plugin.InteractivePlugin;
     
    131128{
    132129
    133   private static final About about =
    134     new AboutImpl
    135     (
    136       "Illumina raw data importer",
    137       "This plugin is used to import raw data from Illumina data files. The plug-in can " +
    138       "be executed from the list of raw bioassays and will then only create new raw bioassays, " +
    139       "or from within an experiment, in which case the imported data will also be associated with " +
    140       "the experiment.",
    141       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    142       "2007, Base 2 development team",
    143       null,
    144       null,
    145       "http://base.thep.lu.se"
    146     );
    147130 
    148131  private static final Set<GuiContext> guiContexts =
     
    228211    -------------------------------------------
    229212  */
    230   public About getAbout()
    231   {
    232     return about;
    233   }
    234213  public boolean supportsConfigurations()
    235214  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java

    r5481 r5612  
    4343import net.sf.basedb.core.StringParameterType;
    4444import net.sf.basedb.core.Transformation;
    45 import net.sf.basedb.core.Version;
    46 import net.sf.basedb.core.plugin.About;
    47 import net.sf.basedb.core.plugin.AboutImpl;
    4845import net.sf.basedb.core.plugin.AbstractPlugin;
    4946import net.sf.basedb.core.plugin.GuiContext;
     
    9491{
    9592
    96   /**
    97      Plugin description
    98   */
    99   private static final About about =
    100           new AboutImpl
    101     (
    102       "Formula intensity calculator",
    103       "This plugin is used to calculate intensities from raw data creating an initial root bioassay set. "+
    104       "The intensities are calculated using Formula objects registered for the experiment's raw data type. " +
    105       "Thus, the functionality of this plugin can be extended by adding more formula objects to the database.",
    106       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    107       "2006, Base 2 development team",
    108       null,
    109       null,
    110       "http://base.thep.lu.se"
    111     );
    11293
    11394  private static final Set<GuiContext> guiContexts =
     
    143124    -------------------------------------------
    144125  */
    145   public About getAbout()
    146   {
    147     return about;
    148   }
    149126  /**
    150127     Returns the main plugin type this plugin belongs to.
  • trunk/src/plugins/core/net/sf/basedb/plugins/JepExtraValueCalculator.java

    r5481 r5612  
    3939import net.sf.basedb.core.SpotExtraValueBatcher;
    4040import net.sf.basedb.core.StringParameterType;
    41 import net.sf.basedb.core.Version;
    4241import net.sf.basedb.core.VirtualColumn;
    43 import net.sf.basedb.core.plugin.About;
    44 import net.sf.basedb.core.plugin.AboutImpl;
    4542import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
    4643import net.sf.basedb.core.plugin.GuiContext;
     
    8077  implements InteractivePlugin, SignalTarget
    8178{
    82 
    83   /**
    84      Plugin description
    85   */
    86   private static final About about =
    87     new AboutImpl
    88     (
    89       "JEP extra value calculator",
    90       "This plugin is used to calculate extra values for a bioassay set using "+
    91       "expressions entered by the user. The expressions are parsed with the JEP package.",
    92       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    93       "2006, Base 2 development team",
    94       null,
    95       null,
    96       "http://base.thep.lu.se"
    97     );
    9879 
    9980  private static final Set<Permissions> permissions = new HashSet<Permissions>();
     
    120101    -------------------------------------------
    121102  */
    122   public About getAbout()
    123   {
    124     return about;
    125   }
    126103  public boolean supportsConfigurations()
    127104  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/JepIntensityTransformer.java

    r5481 r5612  
    4949import net.sf.basedb.core.StringUtil;
    5050import net.sf.basedb.core.Transformation;
    51 import net.sf.basedb.core.Version;
    5251import net.sf.basedb.core.VirtualColumn;
    53 import net.sf.basedb.core.plugin.About;
    54 import net.sf.basedb.core.plugin.AboutImpl;
    5552import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
    5653import net.sf.basedb.core.plugin.GuiContext;
     
    8279{
    8380
    84   /**
    85      Plugin description
    86   */
    87   private static final About about =
    88     new AboutImpl
    89     (
    90       "JEP intensity transformer",
    91       "This plugin is used to transform the intensities of a bioassayset using "+
    92       "expressions entered by the user. The expressions are parsed with the JEP package.",
    93       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    94       "2006, Base 2 development team",
    95       null,
    96       null,
    97       "http://base.thep.lu.se"
    98     );
    99 
    10081  private static final Set<Permissions> permissions = new HashSet<Permissions>();
    10182  private static final Set<GuiContext> guiContexts = Collections.unmodifiableSet(
     
    11697    -------------------------------------------
    11798  */
    118   public About getAbout()
    119   {
    120     return about;
    121   }
    12299  public boolean supportsConfigurations()
    123100  {
     
    154131      String childDescription = (String)job.getValue(CHILD_DESCRIPTION);
    155132      String transformationName = (String)job.getValue(TRANSFORMATION_NAME);
    156       transformationName = getAbout().getName() + ": " + (transformationName == null ? "" : transformationName);
    157133      String resultTransform = (String)job.getValue("resultTransform");
    158134      RawDataType rdt = source.getRawDataType();
  • trunk/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java

    r5481 r5612  
    4545import net.sf.basedb.core.Transformation;
    4646import net.sf.basedb.core.Type;
    47 import net.sf.basedb.core.Version;
    4847import net.sf.basedb.core.VirtualColumn;
    49 import net.sf.basedb.core.plugin.About;
    50 import net.sf.basedb.core.plugin.AboutImpl;
    5148import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
    5249import net.sf.basedb.core.plugin.GuiContext;
     
    103100{
    104101
    105   /**
    106      Plugin description
    107   */
    108   private static final About about = new AboutImpl
    109   (
    110     "Normalization: Lowess",
    111     "This is an efficient java implementation by Johan Enell " +
    112     "of the LOWESS algorithm. It provides intensity-based normalization.\n" +
    113     "The window size is the only smoothness parameter available " +
    114     "in this implementation. The higher it is, the smoother the " +
    115     "function will be. Tweaking the other two parameters allows you to gain " +
    116     "performance at the price of a small precision loss. The default values are usually good.\n" +
    117     "This plug-in supports the use of reporter lists for exclusion of " +
    118     "reporters in the LOWESS calculation. The option to select reporter " +
    119     "lists is visible for users with access to defined reporter lists.\n\n" +
    120     "For more info on LOWESS:\n" +
    121     "Cleveland WS, Devlin SJ: Locally weighted regression: an " +
    122     "approach to regression analysis by local fitting. J Am Stat " +
    123     "Assoc 1988, 83:596-610.\n" +
    124     "Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: " +
    125     "Normalization for cDNA microarray data: a robust composite " +
    126     "method addressing single and multiple slide systematic " +
    127     "variation. Nucleic Acids Res 2002, 30:e15.",
    128     Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    129     "2006, Base 2 development team",
    130     null,
    131     null,
    132     "http://base.thep.lu.se"
    133   );
    134102 
    135103  private static final Set<Permissions> permissions = new HashSet<Permissions>();
     
    187155    -------------------------------------------
    188156  */
    189   public About getAbout()
    190   {
    191     return about;
    192   }
    193157  public boolean supportsConfigurations()
    194158  {
     
    399363    // Create Transformation
    400364    Transformation t = source.newTransformation(job);
    401     t.setName(about.getName());
     365    t.setName("Normalization: Lowess");
    402366    dc.saveItem(t);
    403367   
  • trunk/src/plugins/core/net/sf/basedb/plugins/ManualTransformCreator.java

    r5610 r5612  
    9494    -------------------------------------------
    9595  */
    96   /*
    97   @Override
    98   public About getAbout()
    99   {
    100     return new AboutImpl(
    101       "Manual transform",
    102       "This plug-in allows a user to manually register an external analysis " +
    103       "procedure that has happened outside of BASE and to register the parameters " +
    104       "used and the output files that was generated. Before this plug-in can be " +
    105       "used a configuration that represents the external tool must be created. " +
    106       "The configuration will be used to register possible parameters and output " +
    107       "files.",
    108       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    109       "2009, Base 2 development team",
    110       null,
    111       null,
    112       "http://base.thep.lu.se"
    113     );
    114   }
    115   */
    11696  @Override
    11797  public boolean supportsConfigurations()
  • trunk/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

    r5481 r5612  
    5454import net.sf.basedb.core.Transformation;
    5555import net.sf.basedb.core.Type;
    56 import net.sf.basedb.core.Version;
    5756import net.sf.basedb.core.VirtualColumn;
    58 import net.sf.basedb.core.plugin.About;
    59 import net.sf.basedb.core.plugin.AboutImpl;
    6057import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
    6158import net.sf.basedb.core.plugin.GuiContext;
     
    8885{
    8986
    90   /**
    91      Plugin description
    92   */
    93   private static final About about = new AboutImpl
    94   (
    95     "Normalization: Median ratio",
    96     ("This normalizer behaves differently depending on the array type.\n\n" +
    97 
    98      "1-channel arrays: Intensities are changed in two different ways depending " +
    99      "on user selection.\n" +
    100      "a) For absolute intensity data the intensities should be scaled with the " +
    101      "median intensity, Inew=Iold/Imedian, such that resulting median is 1.\n" +
    102      "b) For log intensity data the intensities should be subtracted with the median " +
    103      "intensity, log(Inew)=log(Iold)-log(Imedian), such that resulting median is 0.\n\n" +
    104 
    105      "2-channel arrays: Intensities are scaled such " +
    106      "that their geometric mean (sqrt(i1 * i2)) is kept constant but " +
    107      "the median of their ratios (i1/i2) is shifted to 1.\n\n" +
    108 
    109      "All array types: The user can optionally exclude spots; all spots " +
    110      "with at least one intensity below a user selectable threshold are " +
    111      "removed. User selectable (low/high intensity) fractions of the " +
    112      "remaining spots are ignored in median calculation."),
    113      Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    114     "2006-8, Base 2 development team",
    115     null,
    116     null,
    117     "http://base.thep.lu.se"
    118   );
    119 
    12087  private static final Set<Permissions> permissions = new HashSet<Permissions>();
    12188
     
    205172    -------------------------------------------
    206173  */
    207   public About getAbout()
    208   {
    209     return about;
    210   }
    211174  public boolean supportsConfigurations()
    212175  {
     
    416379    // Create Transformation
    417380    Transformation t = source.newTransformation(job);
    418     t.setName(about.getName());
     381    t.setName("Normalization: Median ratio");
    419382    dc.saveItem(t);
    420383
     
    541504    // Create Transformation
    542505    Transformation t = source.newTransformation(job);
    543     t.setName(about.getName());
     506    t.setName("Normalization: Median ratio");
    544507    dc.saveItem(t);
    545508   
  • trunk/src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java

    r5481 r5612  
    4444import net.sf.basedb.core.RequestInformation;
    4545import net.sf.basedb.core.StringParameterType;
    46 import net.sf.basedb.core.Version;
    4746import net.sf.basedb.core.Job.ExecutionTime;
    48 import net.sf.basedb.core.plugin.About;
    49 import net.sf.basedb.core.plugin.AboutImpl;
    5047import net.sf.basedb.core.plugin.AbstractExporterPlugin;
    5148import net.sf.basedb.core.plugin.ExportOutputStream;
     
    9491  implements InteractivePlugin, SignalTarget
    9592{
    96 
    97   private static final About about = new AboutImpl
    98     (
    99         "Packed file exporter",
    100         "This plugin is used to pack one or more files/directories " +
    101         "into a single file. Items should be selected before starting the plug-in and " +
    102         "they must all be located in the same parent directory. " +
    103         "The compressed file can be downloaded immediately " +
    104         "or stored in the BASE file system. The user can choose to have the selected files and " +
    105         "directories removed after they've been packed.",
    106         Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    107         "2007, Base 2 development team",
    108         null,
    109         null,
    110         "http://base.thep.lu.se"
    111     );
    11293 
    11394  private static final GuiContext fileGui = new GuiContext(Item.FILE, GuiContext.Type.LIST);
     
    142123    --------------------------------
    143124  */
    144   public About getAbout()
    145   {
    146     return about;
    147   }
    148125  public boolean supportsConfigurations()
    149126  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/PlateFlatFileImporter.java

    r5481 r5612  
    4747import net.sf.basedb.core.RequestInformation;
    4848import net.sf.basedb.core.StringParameterType;
    49 import net.sf.basedb.core.Version;
    5049import net.sf.basedb.core.Well;
    5150import net.sf.basedb.core.data.ReporterData;
    52 import net.sf.basedb.core.plugin.About;
    53 import net.sf.basedb.core.plugin.AboutImpl;
    5451import net.sf.basedb.core.plugin.GuiContext;
    5552import net.sf.basedb.core.plugin.InteractivePlugin;
     
    8986  implements InteractivePlugin, ConfigureByExample
    9087{
    91   private static final About about =
    92     new AboutImpl
    93     (
    94       "Plate importer",
    95       "This plugin is used to import plates from a simple flat file.",
    96       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    97       "2006, Base 2 development team",
    98       null,
    99       null,
    100       "http://base.thep.lu.se"
    101     );
    10288
    10389  private static final Set<GuiContext> guiContexts =
     
    219205    -------------------------------------------
    220206  */
    221   public About getAbout()
    222   {
    223     return about;
    224   }
    225207  public boolean supportsConfigurations()
    226208  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/PlateMappingExporter.java

    r5481 r5612  
    4747import net.sf.basedb.core.ProgressReporter;
    4848import net.sf.basedb.core.RequestInformation;
    49 import net.sf.basedb.core.Version;
    5049import net.sf.basedb.core.Job.ExecutionTime;
    5150import net.sf.basedb.core.data.MappingCoordinate;
    52 import net.sf.basedb.core.plugin.About;
    53 import net.sf.basedb.core.plugin.AboutImpl;
    5451import net.sf.basedb.core.plugin.AbstractExporterPlugin;
    5552import net.sf.basedb.core.plugin.ExportOutputStream;
     
    9491{
    9592
    96   private static final About about =
    97     new AboutImpl
    98     (
    99       "Plate mapping exporter",
    100       "This plugin is used to export plate mappings, which maps the coordinates of one or more source plates " +
    101       "to coordinates on one or more destination plates.",
    102       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    103       "2006, Base 2 development team",
    104       null,
    105       null,
    106       "http://base.thep.lu.se"
    107     );
    10893 
    10994  private static final Set<GuiContext> guiContexts =
     
    129114    -------------------------------------------
    130115  */
    131   public About getAbout()
    132   {
    133     return about;
    134   }
    135116  public boolean supportsConfigurations()
    136117  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/PlateMappingImporter.java

    r5481 r5612  
    4545import net.sf.basedb.core.RequestInformation;
    4646import net.sf.basedb.core.StringParameterType;
    47 import net.sf.basedb.core.Version;
    4847import net.sf.basedb.core.data.MappingCoordinate;
    49 import net.sf.basedb.core.plugin.About;
    50 import net.sf.basedb.core.plugin.AboutImpl;
    5148import net.sf.basedb.core.plugin.GuiContext;
    5249import net.sf.basedb.core.plugin.InteractivePlugin;
     
    9188  implements InteractivePlugin
    9289{
    93 
    94   private static final About about =
    95     new AboutImpl
    96     (
    97       "Plate mapping importer",
    98       "This plugin is used to import plate mappings, which maps the coordinates of one or more source plates " +
    99       "to coordinates on one or more destination plates.",
    100       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    101       "2006, Base 2 development team",
    102       null,
    103       null,
    104       "http://base.thep.lu.se"
    105     );
    10690 
    10791  private static final Set<GuiContext> guiContexts =
     
    140124    -------------------------------------------
    141125  */
    142   public About getAbout()
    143   {
    144     return about;
    145   }
    146126  public boolean supportsConfigurations()
    147127  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/PluginConfigurationExporter.java

    r5481 r5612  
    4040import net.sf.basedb.core.RequestInformation;
    4141import net.sf.basedb.core.Type;
    42 import net.sf.basedb.core.Version;
    4342import net.sf.basedb.core.Job.ExecutionTime;
    44 import net.sf.basedb.core.plugin.About;
    45 import net.sf.basedb.core.plugin.AboutImpl;
    4643import net.sf.basedb.core.plugin.AbstractExporterPlugin;
    4744import net.sf.basedb.core.plugin.ExportOutputStream;
     
    8885  implements InteractivePlugin, SignalTarget
    8986{
    90  
    91   private static final About about =
    92     new AboutImpl
    93   (
    94       "Plugin configuration exporter",
    95       "This plugin is used to export selected plugin configurations to an XML-file. The plugin " +
    96       "configurations can later be imported by the corresponding import plugin.",
    97       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    98       "2006, Base 2 development team",
    99       null,
    100       null,
    101       "http://base.thep.lu.se"
    102   );
    103  
     87   
    10488  private static final GuiContext configList = new GuiContext(Item.PLUGINCONFIGURATION, GuiContext.Type.LIST);
    10589  private static final Set<GuiContext> guiContexts = new HashSet<GuiContext>(Arrays.asList(configList));
     
    188172      response.setError(ex.getMessage(), Arrays.asList(ex));
    189173    }
    190   }
    191 
    192   /**
    193     Returns information about this plugin
    194   */
    195   public About getAbout()
    196   {
    197     return about;
    198174  }
    199175 
  • trunk/src/plugins/core/net/sf/basedb/plugins/PluginConfigurationImporter.java

    r5481 r5612  
    4646import net.sf.basedb.core.RequestInformation;
    4747import net.sf.basedb.core.StringParameterType;
    48 import net.sf.basedb.core.Version;
    49 import net.sf.basedb.core.plugin.About;
    50 import net.sf.basedb.core.plugin.AboutImpl;
    5148import net.sf.basedb.core.plugin.AbstractPlugin;
    5249import net.sf.basedb.core.plugin.AutoDetectingImporter;
     
    9895  private static final String COMMAND_SELECT_CONFIGURATIONS = "select_configurations";
    9996 
    100   private static final About about = new AboutImpl
    101   (
    102       "Plugin configuration importer",
    103       "This plugin is used to import configuration for a BASE plugin from an XML-file.",
    104       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    105       "2006, Base 2 development team",
    106       null,
    107       null,
    108       "http://base.thep.lu.se"
    109   );
    110  
    11197  private static final String dtdFileName = "plugin-configuration-file.dtd";
    11298 
     
    246232  {
    247233    return MainType.IMPORT;
    248   }
    249 
    250   public About getAbout()
    251   {
    252     return about;
    253234  }
    254235 
  • trunk/src/plugins/core/net/sf/basedb/plugins/PrintMapFlatFileImporter.java

    r5481 r5612  
    5252import net.sf.basedb.core.RequestInformation;
    5353import net.sf.basedb.core.StringParameterType;
    54 import net.sf.basedb.core.Version;
    5554import net.sf.basedb.core.Well;
    5655import net.sf.basedb.core.data.FeatureData;
    57 import net.sf.basedb.core.plugin.About;
    58 import net.sf.basedb.core.plugin.AboutImpl;
    5956import net.sf.basedb.core.plugin.GuiContext;
    6057import net.sf.basedb.core.plugin.InteractivePlugin;
     
    9390  implements InteractivePlugin
    9491{
    95   private static final About about =
    96     new AboutImpl
    97     (
    98       "Print map importer",
    99       "This plugin is used to import arraydesign from a print map.",
    100       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    101       "2006, Base 2 development team",
    102       null,
    103       null,
    104       "http://base.thep.lu.se"
    105     );
    10692
    10793  private static final Set<GuiContext> guiContexts =
     
    146132    From the Plugin interface
    147133    -------------------------------------------
    148   */ 
    149   public About getAbout()
    150   {
    151     return about;
    152   }
     134  */
    153135  public boolean supportsConfigurations()
    154136  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java

    r5574 r5612  
    6060import net.sf.basedb.core.SystemItems;
    6161import net.sf.basedb.core.UnsupportedFileFormatException;
    62 import net.sf.basedb.core.Version;
    6362import net.sf.basedb.core.data.FeatureData;
    6463import net.sf.basedb.core.data.RawData;
    6564import net.sf.basedb.core.data.ReporterData;
    66 import net.sf.basedb.core.plugin.About;
    67 import net.sf.basedb.core.plugin.AboutImpl;
    6865import net.sf.basedb.core.plugin.AnnotationSetterPlugin;
    6966import net.sf.basedb.core.plugin.GuiContext;
     
    113110{
    114111 
    115   private static final About about =
    116     new AboutImpl
    117     (
    118       "Raw data importer",
    119       "This plugin is used to import raw data from a simple text file.",
    120       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    121       "2006, Base 2 development team",
    122       null,
    123       null,
    124       "http://base.thep.lu.se"
    125     );
    126112 
    127113  private static final Set<GuiContext> guiContexts =
     
    317303    -------------------------------------------
    318304  */
    319   public About getAbout()
    320   {
    321     return about;
    322   }
    323305  public boolean supportsConfigurations()
    324306  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/ReporterFlatFileImporter.java

    r5480 r5612  
    5050import net.sf.basedb.core.Job;
    5151import net.sf.basedb.core.Type;
    52 import net.sf.basedb.core.Version;
    5352import net.sf.basedb.core.query.Expressions;
    5453import net.sf.basedb.core.query.Orders;
     
    6261import net.sf.basedb.core.plugin.Request;
    6362import net.sf.basedb.core.plugin.Response;
    64 import net.sf.basedb.core.plugin.About;
    65 import net.sf.basedb.core.plugin.AboutImpl;
    6663import net.sf.basedb.core.plugin.GuiContext;
    6764
     
    9794{
    9895
    99   private static final About about =
    100     new AboutImpl
    101     (
    102       "Reporter importer",
    103       "This plugin is used to import reporters from a simple flat file.",
    104       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    105       "2006, Base 2 development team",
    106       null,
    107       null,
    108       "http://base.thep.lu.se"
    109     );
    110 
    11196  private static final Set<GuiContext> guiContexts =
    11297    new HashSet<GuiContext>(Arrays.asList(
     
    201186    -------------------------------------------
    202187  */
    203   public About getAbout()
    204   {
    205     return about;
    206   }
    207188  public boolean supportsConfigurations()
    208189  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/ReporterMapFlatFileImporter.java

    r5481 r5612  
    5252import net.sf.basedb.core.StringParameterType;
    5353import net.sf.basedb.core.Item;
    54 import net.sf.basedb.core.Version;
    5554import net.sf.basedb.core.data.FeatureData;
    5655import net.sf.basedb.core.data.ReporterData;
    5756import net.sf.basedb.core.plugin.InteractivePlugin;
    58 import net.sf.basedb.core.plugin.About;
    59 import net.sf.basedb.core.plugin.AboutImpl;
    6057import net.sf.basedb.core.plugin.GuiContext;
    6158import net.sf.basedb.core.plugin.Permissions;
     
    9289  implements InteractivePlugin, ConfigureByExample
    9390{
    94 
    95   private static final About about =
    96     new AboutImpl
    97     (
    98       "Reporter map importer",
    99       "This plugin is used to import features to an ArrayDesign from a simple flat file.",
    100       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    101       "2006, Base 2 development team",
    102       null,
    103       null,
    104       "http://base.thep.lu.se"
    105     );
    10691
    10792  private static final Set<GuiContext> guiContexts =
     
    273258    -------------------------------------------
    274259  */
    275   public About getAbout()
    276   {
    277     return about;
    278   }
    279260  public boolean supportsConfigurations()
    280261  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/SpotImageCreator.java

    r4889 r5612  
    3131import net.sf.basedb.core.Path;
    3232import net.sf.basedb.core.ItemAlreadyExistsException;
    33 import net.sf.basedb.core.Version;
    34 import net.sf.basedb.core.plugin.About;
    35 import net.sf.basedb.core.plugin.AboutImpl;
    3633import net.sf.basedb.core.plugin.AbstractPlugin;
    3734import net.sf.basedb.core.plugin.Permissions;
     
    5956{
    6057
    61   /**
    62      Plugin description
    63   */
    64   private static final About about =
    65     new AboutImpl
    66     (
    67       "Spot images creator",
    68       "Converts a full-size scanned image into smaller preview jpg images for each individual spot.",
    69       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    70       "2006, Base 2 development team",
    71       null,
    72       null,
    73       "http://base.thep.lu.se"
    74     );
    75 
    7658  private static final Set<Permissions> permissions = new HashSet<Permissions>();
    7759
     
    8264    -------------------------------------------
    8365  */
    84   public About getAbout()
    85   {
    86     return about;
    87   }
    8866  public Plugin.MainType getMainType()
    8967  {
  • trunk/src/plugins/core/net/sf/basedb/plugins/TarFileUnpacker.java

    r5405 r5612  
    4646import net.sf.basedb.core.Location;
    4747import net.sf.basedb.core.Path;
    48 import net.sf.basedb.core.Version;
    49 import net.sf.basedb.core.plugin.About;
    50 import net.sf.basedb.core.plugin.AboutImpl;
    5148import net.sf.basedb.core.signal.ThreadSignalHandler;
    5249import net.sf.basedb.util.FileUtil;
     
    6764  extends AbstractFileUnpacker
    6865{
    69  
    70   /**
    71      Plugin description
    72   */
    73   private static final About about =
    74     new AboutImpl
    75     (
    76       "TAR file unpacker",
    77       "This plugin unpacks a tar file on the BASE file system. It also supports TAR " +
    78       "files compressed with the GZIP and BZIP algorithms.",
    79       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    80       "2007, Base 2 development team",
    81       null,
    82       null,
    83       "http://base.thep.lu.se"
    84     );
    8566
    8667  private static final Set<String> extensions = 
     
    9273
    9374  private Map<String, Directory> paths;
    94  
    95   /*
    96     From the Plugin interface
    97     -------------------------------------------
    98   */
    99   public About getAbout()
    100   {
    101     return about;
    102   }
    103   // -------------------------------------------
    10475 
    10576  /*
  • trunk/src/plugins/core/net/sf/basedb/plugins/ZipFileUnpacker.java

    r4513 r5612  
    3232import net.sf.basedb.core.DbControl;
    3333import net.sf.basedb.core.Directory;
    34 import net.sf.basedb.core.Version;
    35 import net.sf.basedb.core.plugin.About;
    36 import net.sf.basedb.core.plugin.AboutImpl;
    3734import net.sf.basedb.util.zip.AbstractFileUnpacker;
    3835import net.sf.basedb.util.zip.ZipUnpacker;
     
    4946{
    5047 
    51   /**
    52      Plugin description
    53   */
    54   private static final About about =
    55     new AboutImpl
    56     (
    57       "ZIP file unpacker",
    58       "This plugin unpacks a zip file on the BASE file system. It supports zip and jar files.",
    59       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    60       "2006, Base 2 development team",
    61       null,
    62       null,
    63       "http://base.thep.lu.se"
    64     );
    65 
    6648  private static final Set<String> extensions = 
    6749    new LinkedHashSet<String>(Arrays.asList("zip", "jar"));
     
    6951  private static final Set<String> mimeTypes = 
    7052    new LinkedHashSet<String>(Arrays.asList("application/zip", "application/java-archive"));
    71 
    72   /*
    73     From the Plugin interface
    74     -------------------------------------------
    75   */
    76   public About getAbout()
    77   {
    78     return about;
    79   }
    80   // -------------------------------------------
    8153 
    8254  /*
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ArrayBatchImporter.java

    r5610 r5612  
    3636import net.sf.basedb.core.ProtocolType;
    3737import net.sf.basedb.core.SystemItems;
    38 import net.sf.basedb.core.Version;
    39 import net.sf.basedb.core.plugin.About;
    40 import net.sf.basedb.core.plugin.AboutImpl;
    4138import net.sf.basedb.core.plugin.GuiContext;
    4239import net.sf.basedb.util.parser.FlatFileParser;
     
    5855    Collections.singleton(new GuiContext(Item.ARRAYBATCH, GuiContext.Type.LIST));
    5956
    60   private static final About about =
    61     new AboutImpl
    62   (
    63       "Array batch importer",
    64       "Imports and updates array batches in a batch.",
    65       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    66       "2008, Base 2 development team",
    67       null,
    68       null,
    69       "http://base.thep.lu.se"
    70   );
    71 
    72  
    7357  protected static final PluginParameter<String> hardwareColumnMapping = new PluginParameter<String>(
    7458      "hardwareColumnMapping",
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ArrayDesignImporter.java

    r5610 r5612  
    3838import net.sf.basedb.core.PlatformVariant;
    3939import net.sf.basedb.core.PluginParameter;
    40 import net.sf.basedb.core.Version;
    41 import net.sf.basedb.core.plugin.About;
    42 import net.sf.basedb.core.plugin.AboutImpl;
    4340import net.sf.basedb.core.plugin.GuiContext;
    4441import net.sf.basedb.util.parser.FlatFileParser;
     
    5956  private static final Set<GuiContext> guiContexts = 
    6057    Collections.singleton(new GuiContext(Item.ARRAYDESIGN, GuiContext.Type.LIST));
    61 
    62   private static final About about =
    63     new AboutImpl
    64   (
    65       "Array design importer",
    66       "Imports and updates array designs in a batch.",
    67       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    68       "2008, Base 2 development team",
    69       null,
    70       null,
    71       "http://base.thep.lu.se"
    72   );
    7358
    7459  protected static final PluginParameter<String> numArraysColumnMapping =
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ArraySlideImporter.java

    r5610 r5612  
    3333import net.sf.basedb.core.LabeledExtract;
    3434import net.sf.basedb.core.PluginParameter;
    35 import net.sf.basedb.core.Version;
    36 import net.sf.basedb.core.plugin.About;
    37 import net.sf.basedb.core.plugin.AboutImpl;
    3835import net.sf.basedb.core.plugin.GuiContext;
    3936import net.sf.basedb.util.Values;
     
    5552  private static final Set<GuiContext> guiContexts = 
    5653    Collections.singleton(new GuiContext(Item.ARRAYSLIDE, GuiContext.Type.LIST));
    57 
    58   private static final About about =
    59     new AboutImpl
    60   (
    61       "Array slide importer",
    62       "Imports and updates array slides in a batch.",
    63       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    64       "2008, Base 2 development team",
    65       null,
    66       null,
    67       "http://base.thep.lu.se"
    68   );
    6954
    7055  protected static final PluginParameter<String> arrayBatchColumnMapping = new PluginParameter<String>(
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/BioPlateImporter.java

    r5610 r5612  
    3636import net.sf.basedb.core.PlateGeometry;
    3737import net.sf.basedb.core.PluginParameter;
    38 import net.sf.basedb.core.Version;
    39 import net.sf.basedb.core.plugin.About;
    40 import net.sf.basedb.core.plugin.AboutImpl;
    4138import net.sf.basedb.core.plugin.GuiContext;
    4239import net.sf.basedb.util.parser.FlatFileParser;
     
    5754  private static final Set<GuiContext> guiContexts = 
    5855    Collections.singleton(new GuiContext(Item.BIOPLATE, GuiContext.Type.LIST));
    59 
    60   private static final About about =
    61     new AboutImpl
    62   (
    63       "Bioplate importer",
    64       "Imports and updates bioplates in a batch.",
    65       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    66       "2010, Base 2 development team",
    67       null,
    68       null,
    69       "http://base.thep.lu.se"
    70   );
    7156
    7257  protected static final PluginParameter<String> bioPlateTypeColumnMapping = new PluginParameter<String>(
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/BioSourceImporter.java

    r5610 r5612  
    3131import net.sf.basedb.core.ItemQuery;
    3232import net.sf.basedb.core.PluginParameter;
    33 import net.sf.basedb.core.Version;
    34 import net.sf.basedb.core.plugin.About;
    35 import net.sf.basedb.core.plugin.AboutImpl;
    3633import net.sf.basedb.core.plugin.GuiContext;
    3734import net.sf.basedb.util.parser.FlatFileParser;
     
    5249  private static final Set<GuiContext> guiContexts = 
    5350    Collections.singleton(new GuiContext(Item.BIOSOURCE, GuiContext.Type.LIST));
    54 
    55  
    56   private static final About about =
    57     new AboutImpl
    58   (
    59       "Biosource importer",
    60       "Imports and updates biosources in a batch.",
    61       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    62       "2008, Base 2 development team",
    63       null,
    64       null,
    65       "http://base.thep.lu.se"
    66   );
    67 
    6851 
    6952  public BioSourceImporter()
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java

    r5610 r5612  
    3838import net.sf.basedb.core.Sample;
    3939import net.sf.basedb.core.SystemItems;
    40 import net.sf.basedb.core.Version;
    41 import net.sf.basedb.core.plugin.About;
    42 import net.sf.basedb.core.plugin.AboutImpl;
    4340import net.sf.basedb.core.plugin.GuiContext;
    4441import net.sf.basedb.util.Values;
     
    6057  private static final Set<GuiContext> guiContexts = 
    6158    Collections.singleton(new GuiContext(Item.EXTRACT, GuiContext.Type.LIST));
    62 
    63 
    64   private static final About about =
    65     new AboutImpl
    66   (
    67       "Extract importer",
    68       "Imports and updates extracts in a batch.",
    69       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    70       "2008, Base 2 development team",
    71       null,
    72       null,
    73       "http://base.thep.lu.se"
    74   );
    75 
    7659 
    7760  public ExtractImporter()
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/HybridizationImporter.java

    r5610 r5612  
    4343import net.sf.basedb.core.StringParameterType;
    4444import net.sf.basedb.core.SystemItems;
    45 import net.sf.basedb.core.Version;
    46 import net.sf.basedb.core.plugin.About;
    47 import net.sf.basedb.core.plugin.AboutImpl;
    4845import net.sf.basedb.core.plugin.GuiContext;
    4946import net.sf.basedb.util.parser.FlatFileParser;
     
    6461  private static final Set<GuiContext> guiContexts = 
    6562    Collections.singleton(new GuiContext(Item.HYBRIDIZATION, GuiContext.Type.LIST));
    66 
    67   private static final About about =
    68     new AboutImpl
    69   (
    70       "Hybridization importer",
    71       "Imports and updates hybridizations in a batch.",
    72       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    73       "2008, Base 2 development team",
    74       null,
    75       null,
    76       "http://base.thep.lu.se"
    77   );
    78 
    7963 
    8064  protected static final PluginParameter<String> hardwareColumnMapping = new PluginParameter<String>(
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java

    r5610 r5612  
    3939import net.sf.basedb.core.ProtocolType;
    4040import net.sf.basedb.core.SystemItems;
    41 import net.sf.basedb.core.Version;
    42 import net.sf.basedb.core.plugin.About;
    43 import net.sf.basedb.core.plugin.AboutImpl;
    4441import net.sf.basedb.core.plugin.GuiContext;
    4542import net.sf.basedb.util.Values;
     
    7269      optionalColumnMapping
    7370      );
    74  
    75   private static final About about =
    76     new AboutImpl
    77   (
    78       "Labeled extract importer",
    79       "Imports and updates labeled extracts in a batch.",
    80       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    81       "2008, Base 2 development team",
    82       null,
    83       null,
    84       "http://base.thep.lu.se"
    85   );
    86 
    8771 
    8872  public LabeledExtractImporter()
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java

    r5610 r5612  
    4545import net.sf.basedb.core.Software;
    4646import net.sf.basedb.core.SystemItems;
    47 import net.sf.basedb.core.Version;
    48 import net.sf.basedb.core.plugin.About;
    49 import net.sf.basedb.core.plugin.AboutImpl;
    5047import net.sf.basedb.core.plugin.GuiContext;
    5148import net.sf.basedb.util.parser.FlatFileParser;
     
    6663  private static final Set<GuiContext> guiContexts = 
    6764    Collections.singleton(new GuiContext(Item.RAWBIOASSAY, GuiContext.Type.LIST));
    68 
    69   private static final About about =
    70     new AboutImpl
    71   (
    72       "Raw bioassay importer",
    73       "Imports and updates raw bioassays in a batch.",
    74       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    75       "2008, Base 2 development team",
    76       null,
    77       null,
    78       "http://base.thep.lu.se"
    79   );
    8065
    8166  protected static final PluginParameter<String> platformColumnMapping = new PluginParameter<String>(
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java

    r5610 r5612  
    3838import net.sf.basedb.core.Sample;
    3939import net.sf.basedb.core.SystemItems;
    40 import net.sf.basedb.core.Version;
    41 import net.sf.basedb.core.plugin.About;
    42 import net.sf.basedb.core.plugin.AboutImpl;
    4340import net.sf.basedb.core.plugin.GuiContext;
    4441import net.sf.basedb.util.Values;
     
    170167        optionalColumnMapping
    171168    );
    172  
    173   private static final About about =
    174     new AboutImpl
    175   (
    176       "Sample importer",
    177       "Imports and updates samples in a batch.",
    178       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    179       "2008, Base 2 development team",
    180       null,
    181       null,
    182       "http://base.thep.lu.se"
    183   );
    184 
    185169 
    186170  public SampleImporter()
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java

    r5610 r5612  
    3636import net.sf.basedb.core.Scan;
    3737import net.sf.basedb.core.SystemItems;
    38 import net.sf.basedb.core.Version;
    39 import net.sf.basedb.core.plugin.About;
    40 import net.sf.basedb.core.plugin.AboutImpl;
    4138import net.sf.basedb.core.plugin.GuiContext;
    4239import net.sf.basedb.util.parser.FlatFileParser;
     
    6158  private static final Set<GuiContext> guiContexts = 
    6259    Collections.singleton(new GuiContext(Item.SCAN, GuiContext.Type.LIST));
    63 
    64   private static final About about =
    65     new AboutImpl
    66   (
    67       "Scan importer",
    68       "Imports and updates scans in a batch.",
    69       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    70       "2008, Base 2 development team",
    71       null,
    72       null,
    73       "http://base.thep.lu.se"
    74   );
    75 
    7660 
    7761  protected static final PluginParameter<String> hardwareColumnMapping = new PluginParameter<String>(
  • trunk/src/plugins/core/net/sf/basedb/plugins/executor/BaseFileExporterSupport.java

    r5610 r5612  
    4343import net.sf.basedb.core.RequestInformation;
    4444import net.sf.basedb.core.StringParameterType;
    45 import net.sf.basedb.core.Version;
    46 import net.sf.basedb.core.plugin.About;
    47 import net.sf.basedb.core.plugin.AboutImpl;
    4845import net.sf.basedb.core.plugin.GuiContext;
    4946import net.sf.basedb.core.plugin.Plugin;
     
    7875  extends AbstractIOSupport
    7976{
    80 
    81   private static final About about =
    82     new AboutImpl
    83     (
    84       "BASEFile exporter for the ExternalProgramExecutor",
    85       "Support plug-in for the external program executor that exports data to the " +
    86       "external program in BASEFile format. This plug-in can't be used as a standalone " +
    87       "plug-in.",
    88       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    89       "2010, Base 2 development team",
    90       null,
    91       null,
    92       "http://base.thep.lu.se"
    93     );
    94 
    9577 
    9678  public BaseFileExporterSupport()
  • trunk/src/plugins/core/net/sf/basedb/plugins/executor/BaseFileImporterSupport.java

    r5610 r5612  
    4747import net.sf.basedb.core.Transformation;
    4848import net.sf.basedb.core.User;
    49 import net.sf.basedb.core.Version;
    50 import net.sf.basedb.core.plugin.About;
    51 import net.sf.basedb.core.plugin.AboutImpl;
    5249import net.sf.basedb.core.plugin.GuiContext;
    5350import net.sf.basedb.core.plugin.Plugin;
     
    7269  extends AbstractIOSupport
    7370{
    74 
    75   private static final About about =
    76     new AboutImpl
    77     (
    78       "BASEfile importer for the ExternalProgramExecutor",
    79       "Support plug-in for the external program executor that imports BASEfile formatted " +
    80       "data from the external program to BASE. This plug-in can't be used as a standalone " +
    81       "plug-in.",
    82       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    83       "2010, Base 2 development team",
    84       null,
    85       null,
    86       "http://base.thep.lu.se"
    87     );
    88 
    8971 
    9072  public BaseFileImporterSupport()
  • trunk/src/plugins/core/net/sf/basedb/plugins/executor/BfsExporterSupport.java

    r5610 r5612  
    4141import net.sf.basedb.core.RequestInformation;
    4242import net.sf.basedb.core.StringParameterType;
    43 import net.sf.basedb.core.Version;
    44 import net.sf.basedb.core.plugin.About;
    45 import net.sf.basedb.core.plugin.AboutImpl;
    4643import net.sf.basedb.core.plugin.GuiContext;
    4744import net.sf.basedb.core.plugin.Plugin;
     
    8178  extends AbstractIOSupport
    8279{
    83 
    84   private static final About about =
    85     new AboutImpl
    86     (
    87       "BFS exporter for the ExternalProgramExecutor",
    88       "Support plug-in for the external program executor that exports data to the " +
    89       "external program in BFS format. This plug-in can't be used as a standalone " +
    90       "plug-in.",
    91       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    92       "2010, Base 2 development team",
    93       null,
    94       null,
    95       "http://base.thep.lu.se"
    96     );
    97 
    9880 
    9981  public BfsExporterSupport()
  • trunk/src/plugins/core/net/sf/basedb/plugins/executor/BfsImporterSupport.java

    r5610 r5612  
    4343import net.sf.basedb.core.Transformation;
    4444import net.sf.basedb.core.User;
    45 import net.sf.basedb.core.Version;
    46 import net.sf.basedb.core.plugin.About;
    47 import net.sf.basedb.core.plugin.AboutImpl;
    4845import net.sf.basedb.core.plugin.GuiContext;
    4946import net.sf.basedb.core.plugin.Plugin;
     
    6865  extends AbstractIOSupport
    6966{
    70 
    71   private static final About about =
    72     new AboutImpl
    73     (
    74       "BFS importer for the ExternalProgramExecutor",
    75       "Support plug-in for the external program executor that imports BFS formatted " +
    76       "data from the external program to BASE. This plug-in can't be used as a standalone " +
    77       "plug-in.",
    78       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    79       "2010, Base 2 development team",
    80       null,
    81       null,
    82       "http://base.thep.lu.se"
    83     );
    84 
    8567 
    8668  public BfsImporterSupport()
  • trunk/src/plugins/core/net/sf/basedb/plugins/executor/ExternalProgramExecutor.java

    r5610 r5612  
    4444import net.sf.basedb.core.StringParameterType;
    4545import net.sf.basedb.core.StringUtil;
    46 import net.sf.basedb.core.Version;
    4746import net.sf.basedb.core.Job.ExecutionTime;
    48 import net.sf.basedb.core.plugin.About;
    49 import net.sf.basedb.core.plugin.AboutImpl;
    5047import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
    5148import net.sf.basedb.core.plugin.GuiContext;
     
    180177  */
    181178  public static final String NAMESPACE_EXTERNAL = "external";
    182 
    183  
    184   // About this plugin
    185   private static final About about =
    186     new AboutImpl
    187     (
    188       "External program executor",
    189       "This plug-in is used to export data from BASE to an external program, " +
    190       "and import the result back into BASE.\n" +
    191       "The export and import format is set by the user but must be a format " +
    192       "supported by the external plugin.\n" +
    193       "The export also handles the parameters needed to run the external program.",
    194       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    195       "2010, Base 2 development team",
    196       null,
    197       null,
    198       "http://base.thep.lu.se"
    199     );
    200179
    201180  // Command to create parameters for external plugin
  • trunk/src/plugins/core/net/sf/basedb/plugins/executor/FileOnlyImporterSupport.java

    r5610 r5612  
    4545import net.sf.basedb.core.Transformation;
    4646import net.sf.basedb.core.User;
    47 import net.sf.basedb.core.Version;
    48 import net.sf.basedb.core.plugin.About;
    49 import net.sf.basedb.core.plugin.AboutImpl;
    5047import net.sf.basedb.core.plugin.GuiContext;
    5148import net.sf.basedb.core.plugin.Plugin;
     
    6865{
    6966
    70   private static final About about =
    71     new AboutImpl
    72     (
    73       "File-only importer for the ExternalProgramExecutor",
    74       "Support plug-in for the external program executor that uploads all created files " +
    75       "to BASE and attaches them to a child bioassay set. This plug-in can't be " +
    76       "used as a standalone plug-in.",
    77       Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
    78       "2010, Base 2 development team",
    79       null,
    80       null,
    81       "http://base.thep.lu.se"
    82     );
    83 
    84  
    8567  public FileOnlyImporterSupport()
    8668  {}
  • trunk/src/test/JarPlugin.java

    r5596 r5612  
    2222*/
    2323import net.sf.basedb.core.ProgressReporter;
    24 import net.sf.basedb.core.plugin.About;
    2524import net.sf.basedb.core.plugin.AbstractPlugin;
    2625import net.sf.basedb.core.plugin.Request;
     
    4443  }
    4544
    46   public About getAbout()
    47   {
    48     return JarPluginAbout.getAbout();
    49   }
    5045  public boolean supportsConfigurations()
    5146  {
  • trunk/src/test/NullPlugin.java

    r5437 r5612  
    4949import net.sf.basedb.core.plugin.ParameterValues;
    5050import net.sf.basedb.core.plugin.InteractivePlugin;
    51 import net.sf.basedb.core.plugin.About;
    52 import net.sf.basedb.core.plugin.AboutImpl;
    5351import net.sf.basedb.core.plugin.AbstractPlugin;
    5452import net.sf.basedb.core.plugin.GuiContext;
     
    273271  {
    274272    return Plugin.MainType.OTHER;
    275   }
    276 
    277   public About getAbout()
    278   {
    279     return new AboutImpl
    280     (
    281       "Null plugin",
    282       "This plugin does nothing. It is only used for testing purposes.",
    283       "2.0",
    284       "2006, Base 2 development team",
    285       null,
    286       null,
    287       "http://base.thep.lu.se"
    288     );
    289273  }
    290274  public boolean supportsConfigurations()
  • trunk/src/test/PermissionPlugin.java

    r4514 r5612  
    2727import net.sf.basedb.core.PermissionDeniedException;
    2828import net.sf.basedb.core.ProgressReporter;
    29 import net.sf.basedb.core.plugin.About;
    30 import net.sf.basedb.core.plugin.AboutImpl;
    3129import net.sf.basedb.core.plugin.AbstractPlugin;
    3230import net.sf.basedb.core.plugin.Plugin;
     
    4745    return Plugin.MainType.OTHER;
    4846  }
    49  
    50   public About getAbout()
    51   {   
    52     return new AboutImpl
    53     (
    54         "Permission plugin",
    55         "This plugin is testing the plugin permissions.",
    56         "2.0",
    57         "2006, Base 2 development team",
    58         null,
    59         null,
    60         "http://base.thep.lu.se"
    61       );
    62   }
    63 
    6447  public boolean supportsConfigurations()
    6548  {
  • trunk/src/test/data/JarPluginManifest.txt

    r5394 r5612  
    1 Class-Path: JarPluginAbout.jar
    2  ../../lib/dist/AffxFusion.jar
     1Class-Path: ../../lib/dist/AffxFusion.jar
    32 ../../lib/dist/hibernate3.jar
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