source: extensions/net.sf.basedb.varsearch/trunk/META-INF/extensions.xml @ 6767

<?xml version="1.0" encoding="UTF-8" ?>
<extensions xmlns="http://base.thep.lu.se/extensions.xsd">
  <about safe-resources="1" safe-scripts="1">
    <name>Variant Search Engine</name>
    <description>
      A package implementing an indexing service
      and search engine for variants in VCF files.
      The implementation works with VCF files produced by
      the variant calling pipeline in Reggie and with the
      released data in Relax.
    </description>
    <version>1.7-dev</version>
    <min-base-version>3.19.0</min-base-version>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>https://baseplugins.thep.lu.se/wiki/net.sf.basedb.varsearch</url>
  </about>

  <extension
    id="net.sf.basedb.varsearch.service"
    extends="net.sf.basedb.clients.web.services"
    >
    <about>
      <name>Variant Indexing Service</name>
      <description>
        A service for maintaining an index of variants discovered
        by the variant calling pipeline.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.varsearch.service.VarSearchServiceFactory
      </factory-class>
    </action-factory>
  </extension>


  <extension
    id="net.sf.basedb.varsearch.lucene-query"
    extends="net.sf.basedb.query.entity-query-filter"
    >
    <about>
      <name>Lucene query filter</name>
      <description>
        Implements Lucene query againts variants. Triggered
        on filter expressions starting with "!x.lucene".
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>
        net.sf.basedb.varsearch.query.LuceneQueryFactory
      </factory-class>
    </action-factory>
  </extension>
  
  <extension
    id="net.sf.basedb.varsearch.lucene-column"
    extends="net.sf.basedb.clients.web.listcolumn.rawbioassay"
    >
    <index>6</index>
    <about safe-scripts="1">
      <name>Lucene</name>
      <description>
        Adds a Lucene column to the raw bioassays table. 
        It will only display information that is matching
        the filter.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.varsearch.LuceneColumnFactory
      </factory-class>
      <parameters>
        <stylesheet>~/css/varsearch.css</stylesheet>
        <script>~/varsearch.js</script>
      </parameters>
    </action-factory>
  </extension>

  <extension
    id="net.sf.basedb.varsearch.admin"
    extends="net.sf.basedb.clients.web.menu.extensions"
    >
    <index>90</index>
    <about safe-scripts="1">
      <name>Variant Search (admin)</name>
      <description>
        Menu entry for Variant Search administrators.
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.varsearch.extensions.RequireRoleMenuItemFactory
      </factory-class>
      <parameters>
        <title>Variant Search (admin)</title>
        <tooltip>Variant Search administration</tooltip>
        <data-url>~/admin/index.jsp?ID=$SESSION-ID$</data-url>
        <role>net.sf.basedb.core.Role.ADMINISTRATOR</role>
      </parameters>
    </action-factory>
  </extension>

  <extension 
    id="net.sf.basedb.varsearch.vcf-actions"
    extends="net.sf.basedb.clients.web.file-viewer"
    >
    <about>
      <name>Genotype and variant call VCF viewer</name>
      <description>
        Add links for viewing the genotype VCF (genotype_*.vcf) 
        file and the filtered variant call VCF file (variants-filtered.vcf).
      </description>
    </about>
    <action-factory>
      <factory-class>
        net.sf.basedb.varsearch.extensions.VcfViewerActionFactory
      </factory-class>
      <parameters>
        <script>~/scripts/vcf-actions.js</script>
      </parameters>
    </action-factory>
  </extension>

</extensions>