source: trunk/src/core/core-extensions.xml @ 7312

<?xml version="1.0" encoding="UTF-8" ?>
<!--
  $Id: core-extensions.xml 6432 2014-03-14 07:23:38Z nicklas $

  Copyright (C) Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
-->
<extensions
  xmlns="http://base.thep.lu.se/extensions.xsd"
  >
  <about>
    <version></version>
    <name>Core extensions points and extensions</name>
    <description>
      This file defines core extension points and extensions. 
      Core extensions are always loaded when BASE starts up and
      are available in all context, no matter if BASE is running
      as a job agent, web server, etc.
    </description>
    <copyright>BASE development team</copyright>
    <email>basedb-users@lists.sourceforge.net</email>
    <url>http://base.thep.lu.se/</url>
  </about>
  
  <extension-point
    id="net.sf.basedb.core.authentication-manager"
    >
    <action-class>net.sf.basedb.core.authentication.AuthenticationManager</action-class>
    <name>Authentication manager</name>
    <description>
      Extension point for authentication of users when logging in to BASE.
      Installed authentication managers are invoked in the index order.
      An authentication manager have three possible options:
      1) Decide that the login/password is valid and return an 
         AuthenticationInformation object. No further authentication managers
         are invoked and the user is logged in to BASE.
      2) Decide that the login/password is invalid and throw an
         Exception. No further authentication managers
         are invoked and the user is NOT logged in to BASE.
      3) Decide that it doesn't know if the login/password is valid or not
         and return null. The next authentication manager is invoked.
         If this was the last authentication manager, internal authentication
         is used.
    </description>
  </extension-point>
  
  <extension-point
    id="net.sf.basedb.core.uri.connection-manager"
    >
    <action-class>net.sf.basedb.util.uri.ConnectionManagerFactory</action-class>
    <name>Connection manager</name>
    <description>
      Extension point for external file support. A connection manager is
      something that knows how to access an external file pointed to by an
      URI. Actions are ConnectionManagerFactory instances and are typically
      used in two ways. 
      1) In a single-file context when getting metadata or the contents of
      a single File item. The ClientContext object is populated with an active 
      DbControl and the current item is the file.
      2) A standalone context with the external reference as an URI. No 
      DbControl is used and no current item.
      Extensions to this extension point must not return more than one
      factory since we need to associate each factory with the id
      of the extension.
    </description>
  </extension-point>
  
  <extension-point 
    id="net.sf.basedb.core.filehandler.validator"
    >
    <action-class>net.sf.basedb.util.fileset.ValidationAction</action-class>
    <name>File set validators</name>
    <description>
      Extension point for validating and extracting metadata from files in a FileSet. 
      Extensions can be invoked in three different contexts:
      1) Validation of a file set: The current item in the context is the owner of
        the file set (eg. the FileStoreEnabled item). 
      2) Removing a file from a file set: The current item in the context
        is the owner of the file set (eg. the FileStoreEnabled item). The 
        extension is supposed to remove metadata that was extracted from the 
        given file.
      3) Checking if a given data file type can be validated or not: The current
        item in the context is a DataFileType and the core will only check if
        the action factory returns TRUE from the prepareContext method. The
        extensions will not actually be invoked.
    </description>
  </extension-point>
  
  <extension-point 
    id="net.sf.basedb.util.overview.loader">
    <action-class>net.sf.basedb.util.overview.extensions.ChildNodeLoaderAction</action-class>
    <name>Item overview - loader</name>
    <description>
      Extension point for extending the item overview by
      loading child nodes to existing nodes. Each registered action factory
      is asked to create child items for every node in the item overview.
      The ClientContext is populated with an active DbControl and the current
      item is the parent node for which child nodes should be loaded.
    </description>
  </extension-point>

  <extension-point 
    id="net.sf.basedb.util.overview.validator">
    <action-class>net.sf.basedb.util.overview.extensions.NodeValidatorAction</action-class>
    <name>Item overview - validator</name>
    <description>
      Extension point for adding validation checks to the item overview. Each registered
      action factory is asked to create a validator for every node in the item overview.
      The ClientContext is populated with an active DbControl and the key used by the
      validator factory to create the validators. Typically, this is a value from
      the Item enumeration (eg. Item.SAMPLE, etc).
    </description>
  </extension-point>
  
  <extension-point 
    id="net.sf.basedb.util.overview.validationrule">
    <action-class>net.sf.basedb.util.overview.extensions.ValidationRuleAction</action-class>
    <name>Item overview - validation rule</name>
    <description>
      Extension point for adding validation rules to the item overview. This extension
      point is used in the "Validation options" dialog and allows a user to set the
      severity level for each registered rule. The ClientContext is populated with
      an active DbControl and the current item is the GenericOverview that is currently
      in use.
    </description>
  </extension-point>
  
  <extension-point 
    id="net.sf.basedb.core.log-manager">
    <action-class>net.sf.basedb.core.log.LogManagerFactory</action-class>
    <name>Log managers</name>
    <description>
      Extension point for logging changes that are made to items. This
      extension point is invoked for every access and the ClientContext
      is populated with the current SessionControl.
    </description>
  </extension-point>
  
  <extension-point 
    id="net.sf.basedb.core.signal.job">
    <action-class>net.sf.basedb.core.signal.SignalHandler</action-class>
    <name>Job signal handler</name>
    <description>
      Extension point for sending signals to jobs. Intended for jobs 
      running on external servers outside of direct control for BASE.
      The ClientContext is populated with the current SessionControl and
      Job item, and the "signal-uri" attribute is set to the URI registered
      with Job.setSignalTransporter. It is recommended that implementations
      return quickly. If the action takes a long time the handler should spawn
      a new thread.
    </description>
  </extension-point>
  
  <extension 
    id="net.sf.basedb.core.uri.http-connection-manager"
    extends="net.sf.basedb.core.uri.connection-manager"
    >
    <about>
      <name>HTTP(s) connection manager</name>
      <description>
        Provides support for regular HTTP and HTTPS including Basic 
        and Digest authentication as well as server- and client-side
        certificates. Auto-detection matches all URI:s with 'http' 
        or 'https' scheme.
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory</factory-class>
    </action-factory>
  </extension>
  
  <extension 
    id="net.sf.basedb.util.affymetrix.cel-validator"
    extends="net.sf.basedb.core.filehandler.validator"
    >
    <about>
      <name>CEL file validator</name>
      <description>
        Validator and metadata extractor implementation for Affymetrix CEL files.
        The validation is done by trying to open the file with the Affymetrix 
        Fusion SDK. If this was successful some metadata information is extracted
        from the headers including chip type and algorithm parameters. The number
        of spots for the raw bioassay is set to the number of cells in the file.
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>net.sf.basedb.util.affymetrix.CelValidationFactory</factory-class>
    </action-factory>
  </extension>

  <extension 
    id="net.sf.basedb.util.affymetrix.cdf-validator"
    extends="net.sf.basedb.core.filehandler.validator"
    >
    <about>
      <name>CDF file validator</name>
      <description>
        Validator and metadata extractor implementation for Affymetrix CDF files.
        The validation is done by trying to open the file with the Affymetrix 
        Fusion SDK. If this was successful some metadata information is extracted
        from the headers including 
        
        chip type and algoritm parameters. The number
        of spots for the raw bioassay is set to the number of cells in the file.
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>net.sf.basedb.util.affymetrix.CdfValidationFactory</factory-class>
    </action-factory>
  </extension>

  <extension 
    id="net.sf.basedb.util.gtf.gtf-validator"
    extends="net.sf.basedb.core.filehandler.validator"
    >
    <about>
      <name>GTF file validator</name>
      <description>
        Validator for GTF reference files. The validation checks that
        the first few lines follow the GTF specification. 
        See http://mblab.wustl.edu/GTF22.html
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>net.sf.basedb.util.gtf.GtfValidationFactory</factory-class>
    </action-factory>
  </extension>

  <extension 
    id="net.sf.basedb.core.db-log-manager"
    extends="net.sf.basedb.core.log-manager"
    >
    <about>
      <name>Database log manager</name>
      <description>
        Information about changes to items are logged in the
        database. Some configuration options can be set in base.config.
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>net.sf.basedb.core.log.db.DbLogManagerFactory</factory-class>
    </action-factory>
  </extension>
  
  <extension 
    id="net.sf.basedb.core.authentication.old-auth-manager"
    extends="net.sf.basedb.core.authentication-manager"
    >
    <about>
      <name>Old authentication manager</name>
      <description>
        Wrapper implementation for supporting the old external
        authentication style. The implemention is only enabled if
        the 'auth.driver' settings exists in 'base.config'.
      </description>
    </about>
    <index>999</index>
    <action-factory>
      <factory-class>net.sf.basedb.core.authentication.OldAuthenticationWrapperFactory</factory-class>
    </action-factory>
  </extension>

  <!-- 
  <extension 
    id="net.sf.basedb.core.filehandler.cdf-validator"
    extends="net.sf.basedb.core.filehandler.affymetrix.cdf"
    >
    <about>
      <name>CDF file validator</name>
      <description>
        Validator and metadata extractor implementation for Affymetrix CDF files.
        The validation is done by trying to open the file with the Affymetrix 
        Fusion SDK. If this was successful the number of features for the array design 
        is set to the number of probesets in the file.
      </description>
    </about>
    <index>1</index>
    <action-factory>
      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
      <parameters>
        <beanClassName>net.sf.basedb.core.filehandler.CdfFileHandler</beanClassName>
      </parameters>
    </action-factory>
  </extension>
  -->
</extensions>