source: extensions/net.sf.basedb.meludi/trunk/META-INF/extensions.xml @ 3521

<?xml version="1.0" encoding="UTF-8" ?>
<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
  <about safe-resources="1">
    <name>MeLuDi package</name>
    <description>
      A package for simplified registration of biosources
      and samples.
    </description>
    <version>1.3.3</version>
    <min-base-version>3.5.0</min-base-version>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.meludi</url>
  </about>

<!--
  <plugin-definition id="CaliperSampleNameExporter">
    <about>
      <name>Caliper sample name exporter</name>
      <description>
        Plug-in that export the sample names on a bioplate to a
        CSV file that can be used by the Caliper software. The
        exported file has one line for each non-empty well with
        five columns. Only the first two columns are used:
        Well coordinate, sample name.
      </description>
    </about>
    <plugin-class>net.sf.basedb.meludi.plugins.CaliperSampleNameExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="CaliperRunParametersExporter">
    <about>
      <name>Caliper run parameters exporter</name>
      <description>
        Plug-in that export run file parameters that can be used by the
        Caliper software. The run file include information about Assay Type,
        Plate Name, selected wells, etc.
      </description>
    </about>
    <plugin-class>net.sf.basedb.meludi.plugins.CaliperRunParametersExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="CaliperLibPrepParametersExporter">
    <about>
      <name>Caliper library preparation parameters exporter</name>
      <description>
        Plug-in that export run file parameters that can be used by the
        Caliper software. The run file include information about Assay Type,
        Plate Name, selected wells, etc.
      </description>
    </about>
    <plugin-class>net.sf.basedb.meludi.plugins.CaliperLibPrepParametersExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="QubitSampleNameExporter">
    <about>
      <name>Qubit sample name exporter</name>
      <description>
        Plug-in that export the sample names on a bioplate to a
        tab-separated file that the operator can use to fill in
        concentration measurements from the Qubit. When all data
        has been filled in, the file can be uploaded to BASE and
        the concentration values are imported as annotations.
      </description>
    </about>
    <plugin-class>net.sf.basedb.meludi.plugins.QubitSampleNameExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>

  <plugin-definition id="FlowCellSampleSheetExporter">
    <about>
      <name>Flow cell sample sheet exporter</name>
      <description>
        Plug-in for exporting information about libraries used in a flow cell.
        The generated tab-separated text file used used by analysis software
        to pick up data from the sequencing.
      </description>
    </about>
    <plugin-class>net.sf.basedb.meludi.plugins.FlowCellSampleSheetExporter</plugin-class>
    <settings>
      <property name="everyone-use">1</property>
      <property name="immediate-execution">1</property>
    </settings>
  </plugin-definition>
-->

  <extension
    id="net.sf.basedb.meludi"
    extends="net.sf.basedb.clients.web.menu.extensions"
    >
    <index>10</index>
    <about safe-scripts="1">
      <name>MeLuDi</name>
      <description>
        Menu entry for accessing MeLuDi-specific operations.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
      </factory-class>
      <parameters>
        <title>MeLuDi</title>
        <tooltip>Access MeLuDi operations</tooltip>
        <icon>~/images/musical_note.png</icon>
        <data-url>~/index.jsp?ID=$SESSION-ID$</data-url>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.meludi.toolbar.case-summary"
    >
    <extends>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref>
      <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref>
    </extends>
    <about safe-scripts="1">
      <name>Case summary</name>
      <description>
        Adds a button to the toolbar of sample and extracts pages
        that opens the 'case summary' for the case that the current
        item is part of. Works for all items that have a name pattern
        that starts with 7 digits.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.extensions.CaseSummaryButtonFactory
      </factory-class>
      <parameters>
        <title>Case summary</title>
        <clazz>button auto-init</clazz>
        <data-auto-init>meludi-case-summary-link</data-auto-init>
        <data-home>$HOME$</data-home>
        <icon>~/images/case_summary.png</icon>
        <script>~/scripts/case-summary.js</script>
      </parameters>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.meludi.list-column"
    >
    <extends>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref>
      <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref>
    </extends>
    <index>2</index>
    <about safe-scripts="1">
      <name>MeLuDi column</name>
      <description>
        Add a column to the list page of samples, extract and bioplates
        for including some MeLuDi-specific links.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.extensions.MeludiListColumnsFactory
      </factory-class>
    </action-factory>
  </extension>
  
  
  <extension
    id="net.sf.basedb.meludi.overview.case-summary"
    extends="net.sf.basedb.clients.web.overview.info-details"
    >
    <index>1</index>
    <about safe-scripts="1">
      <name>Case overview</name>
      <description>
        Adds a section to the information pane in the "Item overview"
        functionality that display a link to the "Case summary" 
        function in MeLuDi for all items that have a name pattern
        that starts with 7 digits.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.extensions.CaseSummarySectionFactory
      </factory-class>
      <parameters>
        <id>meludi.case-summary</id>
        <title>MeLuDi</title>
        <include>~/reports/case_summary_hook.jsp</include>
      </parameters>
    </action-factory>
  </extension>

<!--  
  <extension
    id="net.sf.basedb.meludi.toolbar.histology-score"
    extends="net.sf.basedb.clients.web.toolbar.item.bioplate"
    >
    <about safe-scripts="1">
      <name>Histology score</name>
      <description>
        Adds a button to the toolbar of paraffin blocks and
        HE stain bioplates that start the 'histology scoring wizard'.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.extensions.HistologyScoreButtonFactory
      </factory-class>
      <parameters>
        <title>Score HE glass</title>
        <clazz>button auto-init</clazz>
        <data-auto-init>meludi-he-score-link</data-auto-init>
        <data-home>$HOME$</data-home>
        <icon>~/images/microscope.png</icon>
        <script>~/scripts/he-score.js</script>
      </parameters>
    </action-factory>
  </extension>
-->

<!--
  <extension
    id="net.sf.basedb.meludi.grid.ogs-service"
    extends="net.sf.basedb.clients.web.services"
    >
    <about>
      <name>Open Grid Scheduler service</name>
      <description>
        A service for managing Open Grid Scheduler hosts
        which makes it possible to connect to, execute commands,
        control jobs, etc. on configured hosts.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.grid.OpenGridServiceFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.meludi.grid.job-signal"
    extends="net.sf.basedb.core.signal.job"
    >
    <about>
      <name>Open Grid Scheduler signal handler</name>
      <description>
        Responds to signals sent from BASE. Support
        for ABORT and STATUS signals.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.grid.OpenGridSignalHandlerFactory
      </factory-class>
    </action-factory>
  </extension>
-->

  <extension
    id="net.sf.basedb.meludi.counter-service"
    extends="net.sf.basedb.clients.web.services"
    >
    <about>
      <name>Auto-confirm service</name>
      <description>
        A service that count the number of items at
        various stages in the lab and analysis process.
        The counters are presented on the MeLuDi index page.
        If this service is stopped the counter will not
        be updated.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.meludi.counter.CounterServiceFactory
      </factory-class>
    </action-factory>
  </extension>
  
</extensions>