Changeset 1347


Ignore:
Timestamp:
Apr 18, 2011, 2:50:19 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #309: Merge example plug-ins and extensions into one package

Moved the two example plug-ins to this package. Since there is no way to install plug-ins yet in BASE 3, it can't be tested.

Location:
extensions/net.sf.basedb.examples/trunk
Files:
1 added
2 edited
2 copied

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.examples/trunk/META-INF/extensions.xml

    r1346 r1347  
    1515    <email>basedb-users@lists.sourceforge.net</email>
    1616  </about>
     17 
     18  <plugin-definition id="ExampleAnalyzer">
     19    <about>
     20      <name>Example: Copy spot intensity</name>
     21      <description>
     22        An example analysis plugin that creates a new bioassay set
     23        by multiplying each intensitity value with the same factor,
     24        filtering out intensities below a cutoff value.
     25      </description>
     26    </about>
     27    <plugin-class>net.sf.basedb.examples.plugins.ExampleAnalyzer</plugin-class>
     28  </plugin-definition>
     29 
     30  <plugin-definition id="ExampleImporter">
     31    <about>
     32      <name>Example: sample importer</name>
     33      <description>
     34        An example plugin that pretends to import samples.
     35        It can't be configured, but will ask for a file to
     36        import from and if existing samples should be updated
     37        or not. It won't actually import any samples, but
     38        will report that a few samples has been imported.
     39      </description>
     40    </about>
     41    <plugin-class>net.sf.basedb.examples.plugins.ExampleImporter</plugin-class>
     42  </plugin-definition>
     43 
    1744  <extension
    1845    id="menu.helloworld"
  • extensions/net.sf.basedb.examples/trunk/README

    r1346 r1347  
    3434   logging feature that stores information about the last update to an item.
    3535
     36This package contains the following plug-ins:
     37
     38 * An importer that pretends to be able to import samples. It will
     39   accept any file, but doesn't do anything. Main purpose is to
     40   show parameter handling with plug-ins.
     41 * An analyser plug-in that does some bogus calculations on a
     42   bioassay set. Main purpose is to show how a plug-in can access
     43   analysed data, do some calculations and store the result as
     44   a new bioassay set.
     45
     46
    3647== Installation ==
    3748
     
    4051    configured in base.config[plugins.dir] setting.
    4152 3. Run the ''Extensions -> Manual scan'' command and click the 'Start'
    42     button. If all goes well several new extensions and more should
     53    button. If all goes well several new extensions and plug-ins should
    4354    now be installed.
    4455 4. If you are logged in, you may have to logout and then login again to see
  • extensions/net.sf.basedb.examples/trunk/src/net/sf/basedb/examples/plugins/ExampleAnalyzer.java

    r1346 r1347  
    2020  Boston, MA  02111-1307, USA.
    2121*/
    22 package net.sf.basedb.exampleplugins;
     22package net.sf.basedb.examples.plugins;
    2323
    2424import net.sf.basedb.core.BaseException;
     
    4545import net.sf.basedb.core.signal.ThreadSignalHandler;
    4646
    47 import net.sf.basedb.core.plugin.About;
    48 import net.sf.basedb.core.plugin.AboutImpl;
    4947import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
    5048import net.sf.basedb.core.plugin.InteractivePlugin;
     
    7371  implements InteractivePlugin, SignalTarget
    7472{
    75 
    76   private static final About about =
    77     new AboutImpl
    78     (
    79       "Copy spot intensity",
    80       "An example analysis plugin that creates a new bioassay set " +
    81       "by multiplying each intensitity value with the same factor, filtering " +
    82       "out intensities below a cutoff value.",
    83       "2.17",
    84       "2006, Base 2 development team",
    85       null,
    86       null,
    87       "http://base.thep.lu.se"
    88     );
    89 
    9073  private static final Set<GuiContext> guiContexts = Collections.singleton(
    9174    new GuiContext(Item.BIOASSAYSET, GuiContext.Type.ITEM)
     
    11497    -------------------------------------------
    11598  */
    116   @Override
    117   public About getAbout()
    118   {
    119     return about;
    120   }
    12199  @Override
    122100  public boolean supportsConfigurations()
     
    343321          Request.COMMAND_CONFIGURE_JOB,
    344322          "Specify multiplication factor and cutoff",
    345           about.getDescription(),
     323          "An example analysis plugin that creates a new bioassay set " +
     324          "by multiplying each intensitity value with the same factor, " +
     325          "filtering out intensities below a cutoff value.",
    346326          parameters
    347327        );
  • extensions/net.sf.basedb.examples/trunk/src/net/sf/basedb/examples/plugins/ExampleImporter.java

    r1346 r1347  
    2121
    2222*/
    23 package net.sf.basedb.exampleplugins;
     23package net.sf.basedb.examples.plugins;
    2424
    2525import net.sf.basedb.core.BooleanParameterType;
     
    114114    -------------------------------------------
    115115  */
    116   @Override
    117   public About getAbout()
    118   {
    119     return about;
    120   }
    121116  @Override
    122117  public Plugin.MainType getMainType()
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