source: trunk/src/core/common-queries.xml @ 4383

<?xml version="1.0" ?>
<!DOCTYPE predefined-queries SYSTEM "predefined-queries.dtd" >
<!--
  $Id: common-queries.xml 4380 2008-08-06 11:30:07Z nicklas $

  Copyright (C) 2005 Samuel Andersson, Johan Enell, Nicklas Nordborg
  Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 Johan Enell, Nicklas Nordborg, Martin Svensson

  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 2
  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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
-->
<!--
  This XML file contains HQL and SQL queries that are common
  to all databases. If one of them happens to fail on your
  particular database, do not modify this file. Instead, you
  should add an entry into the file that is specific for your
  particular database that overrides the query in this file.
  For example, for MySQL modify the mysql-queries.xml.
-->
<predefined-queries>

  <query id="LOAD_SYSTEM_ITEMS" type="HQL">
    <sql>
      SELECT item.id, item.systemId
      FROM net.sf.basedb.core.data.SystemData item
      WHERE NOT item.systemId IS NULL
    </sql>
    <description>
      Load the ID and systemID, in that order, of all SystemData
      items.
    </description>
  </query>

  <query id="LOAD_ROLE_KEY_IDS" type="HQL">
    <sql>
      SELECT rk.id, rk.itemType
      FROM RoleKeyData rk
    </sql>
    <description>
      Load the ID and itemType, in that order, of all RoleKeyData
      items.
    </description>
  </query>

  <query id="GET_USER_FOR_LOGIN" type="HQL">
    <sql>
      SELECT usr
      FROM UserData usr
      WHERE usr.login = :login
    </sql>
    <description>
      Load a user when you know the login.
    </description>
  </query>
  
  <query id="GET_USER_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT usr
      FROM UserData usr
      WHERE usr.externalId = :externalId
    </sql>
    <description>
      Load a user when you know the external id.
    </description>
  </query>

  <query id="GET_CLIENT_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT cli
      FROM ClientData cli
      WHERE cli.externalId = :externalId
    </sql>
    <description>
      Load a client when you know the external ID.
    </description>
  </query>
  
  <query id="GET_ROLE_IDS_FOR_USER" type="HQL">
    <sql>
      SELECT ur.roleId
      FROM UserRoles ur
      WHERE ur.userId = :userId
    </sql>
    <description>
      Load the ID of all roles where the given user is a member.
    </description>
  </query>

  <query id="GET_GROUP_IDS_FOR_USER" type="HQL">
    <sql>
      SELECT ug.groupId
      FROM UserGroups ug
      WHERE ug.userId = :userId
    </sql>
    <description>
      Load the ID of all groups where the given user is a direct member.
    </description>
  </query>
  
  <query id="GET_QUOTA_GROUP_ID_FOR_USER" type="HQL">
    <sql>
      SELECT usr.quotaGroup.id
      FROM UserData usr
      WHERE usr.id = :userId
    </sql>
    <description>
      Load the ID of a user's quota group.
    </description>
  </query>

  <query id="GET_PARENTGROUPS_IDS_FOR_GROUPS" type="HQL">
    <sql>
      SELECT DISTINCT gg.parentId
      FROM GroupGroups gg
      WHERE gg.childId IN (:groups)
      AND gg.parentId NOT IN (:groups)
    </sql>
    <description>
      Load the ID of all groups that are parents to at least one of
      the given groups, excluding the given groups.
    </description>
  </query>
  
  <query id="GET_CHILDGROUPS_IDS_FOR_GROUPS" type="HQL">
    <sql>
      SELECT DISTINCT gg.childId
      FROM GroupGroups gg
      WHERE gg.parentId IN (:groups)
      AND gg.childId NOT IN (:groups)
    </sql>
    <description>
      Load the ID of all groups that are children to at least one of
      the given groups, excluding the given groups.
    </description>
  </query>

  <query id="GET_PROJECT_IDS_FOR_OWNER" type="HQL">
    <sql>
      SELECT p.id
      FROM ProjectData p
      WHERE p.owner = :userId
    </sql>
    <description>
      Load the ID of all projects where the given user is the owner.
    </description>
  </query>

  <query id="GET_PROJECTINFO_FOR_USER" type="HQL">
    <sql>
      SELECT up
      FROM UserProjects up
      WHERE up.userId = :userId
    </sql>
    <description>
      Load the UserProjects of all projects where the given user is a member.
    </description>
  </query>

  <query id="GET_PROJECTINFO_FOR_GROUPS" type="HQL">
    <sql>
      SELECT DISTINCT gp
      FROM GroupProjects gp
      WHERE gp.groupId IN (:groups)
    </sql>
    <description>
      Load the GroupProjects of all projects where at least one of the given groups 
      is a member.
    </description>
  </query>

  <query id="GET_USER_IDS_FOR_GROUPS" type="HQL">
    <sql>
      SELECT ug.userId
      FROM UserGroups ug
      WHERE ug.groupId IN (:groups)
    </sql>
    <description>
      Load the ID of all users which is a member of at least one of the given groups.
    </description>
  </query>

  <query id="GET_USER_IDS_FOR_QUOTAGROUPS" type="HQL">
    <sql>
      SELECT usr.id
      FROM UserData usr
      WHERE usr.quotaGroup.id IN (:groups)
    </sql>
    <description>
      Load the ID of all users which has a quota group from one of the given groups.
    </description>
  </query>

  <query id="GET_USER_IDS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT up.userId
      FROM UserProjects up
      WHERE up.projectId = :projectId
    </sql>
    <description>
      Load the ID of all users which are direct member of the given project
    </description>
  </query>

  <query id="GET_GROUP_IDS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT gp.groupId
      FROM GroupProjects gp
      WHERE gp.projectId = :projectId
    </sql>
    <description>
      Load the ID of all groups which are direct member of the given project
    </description>
  </query>

  <query id="GET_USERKEYS_FOR_USER" type="HQL">
    <sql>
      SELECT uk
      FROM UserKeys uk
      WHERE uk.userId = :userId
    </sql>
    <description>
      Load the UserKeys for the given user.
    </description>
  </query>

  <query id="GET_GROUPKEYS_FOR_GROUPS" type="HQL">
    <sql>
      SELECT gk
      FROM GroupKeys gk
      WHERE gk.groupId IN (:groups)
    </sql>
    <description>
      Load the GroupKeys for the given groups.
    </description>
  </query>

  <query id="GET_ROLEKEYS_FOR_USER" type="HQL">
    <sql>
      SELECT rk
      FROM RoleKeys rk, UserRoles ur
      WHERE rk.roleId = ur.roleId AND ur.userId = :userId
      ORDER BY rk.keyId
    </sql>
    <description>
      Load the RoleKeys for the roles where the given user is a member.
    </description>
  </query>

  <query id="GET_PROJECTKEYS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT pk
      FROM ProjectKeys pk
      WHERE pk.projectId = :projectId
      ORDER BY pk.keyId
    </sql>
    <description>
      Load the ProjectKeys for the given project. Sort by
      keyId for fast lookup in array (Keyring class).
    </description>
  </query>
  
  <query id="GET_PROJECTKEYIDS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT pk.keyId
      FROM ProjectKeys pk
      WHERE pk.projectId = :projectId
    </sql>
    <description>
      Load the ID of ProjectKeys for the given project.
    </description>
  </query>

  <query id="GET_PERMISSION_FOR_USER_IN_PROJECT" type="HQL">
    <sql>
      SELECT up.permission
      FROM UserProjects up
      WHERE up.userId = :userId
      AND up.projectId = :projectId
    </sql>
    <description>
      Load the permission for the given user in the given project.
    </description>
  </query>

  <query id="GET_PERMISSIONS_FOR_GROUPS_IN_PROJECT" type="HQL">
    <sql>
      SELECT gp.permission
      FROM GroupProjects gp
      WHERE gp.groupId IN (:groups)
      AND gp.projectId = :projectId
    </sql>
    <description>
      Load the permissions for the given groups in the given project.
    </description>
  </query>

  <query id="GET_PROJECTKEY_IDS_FOR_COUNT" type="HQL">
    <sql>
      SELECT pk.keyId FROM ProjectKeys pk
      GROUP BY pk.keyId
      HAVING count(pk.projectId) = :numPermissions
    </sql>
    <description>
      Load the ID of all project keys which have permissions for the 
      specified number of projects.
    </description>
  </query>

  <query id="FIND_USED_PROJECTKEY_IDS" type="HQL">
    <sql>
      SELECT DISTINCT sd.projectKey.id
      FROM net.sf.basedb.core.data.ShareableData sd
      WHERE NOT sd.projectKey IS NULL
    </sql>
    <description>
      Load the ID of all project keys which are used by at least one 
      shareable item.
    </description>
  </query>
  
  <query id="SELECT_UNUSED_PROJECTKEYS" type="HQL">
    <sql>
      SELECT pk FROM ProjectKeyData pk 
      WHERE pk.id NOT IN (:used)
    </sql>
    <description>
      Load all unused project keys given a list of the ID:s of all used
      keys.
    </description>
  </query>

  <query id="GET_ITEMKEY_IDS_FOR_USERCOUNT" type="HQL">
    <sql>
      SELECT ik.id FROM ItemKeyData ik
      LEFT JOIN ik.users u
      GROUP BY ik.id
      HAVING COUNT(u.index) = :numPermissions
    </sql>
    <description>
      Load the ID of all item keys which have permissions for the 
      specified number of users.
    </description>
  </query>

  <query id="GET_ITEMKEY_IDS_FOR_GROUPCOUNT" type="HQL">
    <sql>
      SELECT ik.id FROM ItemKeyData ik
      LEFT JOIN ik.groups g
      WHERE ik.id IN (:candidates)
      GROUP BY ik.id
      HAVING count(g.index) = :numPermissions
    </sql>
    <description>
      Load the ID of all item keys which have permissions for the 
      specified number of groups and are among the list of candidates.
    </description>
  </query>
  
  <query id="FIND_USED_ITEMKEY_IDS" type="HQL">
    <sql>
      SELECT DISTINCT sd.itemKey.id
      FROM net.sf.basedb.core.data.ShareableData sd
      WHERE NOT sd.itemKey IS NULL
    </sql>
    <description>
      Load the ID of all item keys which are used by at least one 
      shareable item.
    </description>
  </query>
  
  <query id="SELECT_UNUSED_ITEMKEYS" type="HQL">
    <sql>
      SELECT ik FROM ItemKeyData ik 
      WHERE ik.id NOT IN (:used)
    </sql>
    <description>
      Load all unused item keys given a list of the ID:s of all used
      keys.
    </description>
  </query>

  <query id="GET_USERS_FOR_QUOTAGROUP" type="HQL">
    <sql>
      SELECT {1}
      FROM UserData usr
      WHERE usr.quotaGroup = :theGroup
    </sql>
    <description>
      Get users having the specified group as
      their quota group.
    </description>
  </query>
  
  <query id="GET_USERS_FOR_QUOTA" type="HQL">
    <sql>
      SELECT {1}
      FROM UserData u
      WHERE u.quota = :quota
    </sql>
    <description>
      A Hibernate query that gets users
      that has been assigned a given quota.
    </description>
  </query>
  
  <query id="GET_GROUPS_FOR_QUOTA" type="HQL">
    <sql>
      SELECT {1}
      FROM GroupData g
      WHERE g.quota = :quota
    </sql>
    <description>
      A Hibernate query that gets groups
      that has been assigned a given quota.
    </description>
  </query>

  <query id="GET_SHAREABLE_ITEMS_FOR_ITEMKEY" type="HQL">
    <sql>
      SELECT s
      FROM net.sf.basedb.core.data.ShareableData s
      WHERE s.itemKey = :itemKey
    </sql>
    <description>
      Get all items beeing shared to the specified item key.
    </description>
  </query>

  <query id="GET_SHAREABLE_ITEMS_FOR_PROJECTKEY" type="HQL">
    <sql>
      SELECT s
      FROM net.sf.basedb.core.data.ShareableData s
      WHERE s.projectKey = :projectKey
    </sql>
    <description>
      Get all items beeing shared to the specified project key.
    </description>
  </query>
  
  <query id="GET_SHARED_ITEMS" type="HQL">
    <sql>
      SELECT s
      FROM net.sf.basedb.core.data.ShareableData s
    </sql>
    <description>
      Get all shared items.
    </description>
  </query>

  <query id="GET_OWNABLE_ITEMS_FOR_USER" type="HQL">
    <sql>
      SELECT o
      FROM net.sf.basedb.core.data.OwnableData o
      WHERE o.owner = :user
    </sql>
    <description>
      Get all items that are owned by the specified user.
    </description>
  </query>
  
  <query id="GET_DISKCONSUMABLE_ITEMS_FOR_USER" type="HQL">
    <sql>
      SELECT o
      FROM net.sf.basedb.core.data.DiskConsumableData o
      WHERE o.owner = :user
    </sql>
    <description>
      Get all diskconsumable items that are owned by the specified user.
    </description>
  </query>

  
  <query id="LOAD_USER_CLIENT_SETTINGS" type="HQL">
    <sql>
      SELECT s 
      FROM UserClientSettingData s
      WHERE s.user = :user AND s.client = :client
    </sql>
    <description>
      Load all settings for the specified user and client application.
    </description>
  </query>
  
  <query id="LOAD_USER_DEFAULT_SETTINGS" type="HQL">
    <sql>
      SELECT s 
      FROM UserDefaultSettingData s
      WHERE s.user = :user
    </sql>
    <description>
      Load all default settings for the specified user.
    </description>
  </query>

  <query id="LOAD_CLIENT_DEFAULT_SETTINGS" type="HQL">
    <sql>
      SELECT s 
      FROM ClientDefaultSettingData s
      WHERE s.client = :client
    </sql>
    <description>
      Load all default settings for the specified client application.
    </description>
  </query>
  
  <query id="GET_MIME_TYPE_FROM_EXTENSION" type="HQL">
    <sql>
      SELECT s
      FROM net.sf.basedb.core.data.MimeTypeData s
      WHERE LOWER(s.extension) = LOWER(:extension)
    </sql>
    <description>
      A Hibernate query that returns a MimeType given an extension.
    </description>
  </query>
  
  <query id="GET_TOTAL_DISKUSAGE_FOR_USER" type="HQL">
    <sql>
      SELECT sum(du.bytes)
      FROM DiskUsageData du
      WHERE du.user = :user
      AND du.location = :location
    </sql>
    <description>
      A Hibernate query that returns the total used quota
      for the specified user at the specified location.
    </description>
  </query>
  
  <query id="GET_SPECIFIC_DISKUSAGE_FOR_USER" type="HQL">
    <sql>
      SELECT sum(du.bytes)
      FROM DiskUsageData du
      WHERE du.user = :user
      AND du.location = :location
      AND du.quotaType = :quotaType
    </sql>
    <description>
      A Hibernate query that returns the used quota for the
      specific quota type for the specified user at the
      specified location.
    </description>
  </query>

  <query id="GET_TOTAL_DISKUSAGE_FOR_GROUP" type="HQL">
    <sql>
      SELECT sum(du.bytes)
      FROM DiskUsageData du
      WHERE du.group = :group
      AND du.location = :location
    </sql>
    <description>
      A Hibernate query that returns the total used quota
      for the specified group at the specified location.
    </description>
  </query>

  <query id="GET_SPECIFIC_DISKUSAGE_FOR_GROUP" type="HQL">
    <sql>
      SELECT sum(du.bytes)
      FROM DiskUsageData du
      WHERE du.group = :group
      AND du.location = :location
      AND du.quotaType = :quotaType
    </sql>
    <description>
      A Hibernate query that returns the used quota for the
      specific quota type for the specified group at the
      specified location.
    </description>
  </query>

  <query id="GET_TOTAL_DISKUSAGE_SUMMARY" type="HQL">
    <sql>
      SELECT SUM(du.bytes), du.location, du.quotaType.systemId
      FROM DiskUsageData du
      GROUP BY du.location, du.quotaType.systemId
    </sql>
    <description>
      A Hibernate query that returns the total disk usage grouped
      by location and quota type system id.
    </description>
  </query>

  <query id="GET_DISKUSAGE_SUMMARY_FOR_USER" type="HQL">
    <sql>
      SELECT SUM(du.bytes), du.location, du.quotaType.systemId
      FROM DiskUsageData du
      WHERE du.user = :user
      GROUP BY du.location, du.quotaType.systemId
    </sql>
    <description>
      A Hibernate query that returns the disk usage for a user grouped
      by location and quota type system id.
    </description>
  </query>

  <query id="GET_DISKUSAGE_SUMMARY_FOR_GROUP" type="HQL">
    <sql>
      SELECT SUM(du.bytes), du.location, du.quotaType.systemId
      FROM DiskUsageData du
      WHERE du.group = :group
      GROUP BY du.location, du.quotaType.systemId
    </sql>
    <description>
      A Hibernate query that returns the disk usage for a group grouped
      by location and quota type system id.
    </description>
  </query>
  
  <query id="GET_FILES_IN_DIRECTORY" type="HQL">
    <sql>
      SELECT {1}
      FROM FileData f
      WHERE f.directory = :directory
    </sql>
    <description>
      A Hibernate query that gets the files
      in a given directory.
    </description>
  </query>
  
  <query id="GET_FILES_FOR_FILETYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM FileData f
      WHERE f.fileType = :filetype
    </sql>
    <description>
      A Hibernate query that gets the files
      with a given filetype.
    </description>
  </query>

  <query id="GET_SUBDIRECTORIES_IN_DIRECTORY" type="HQL">
    <sql>
      SELECT {1}
      FROM DirectoryData d
      WHERE d.parent = :directory
    </sql>
    <description>
      A Hibernate query that gets the subdirectories
      in a given directory.
    </description>
  </query>
  
  <query id="GET_HOME_DIRECTORIES" type="HQL">
    <sql>
      SELECT {1}
      FROM UserData usr
      WHERE usr.homeDirectory = :directory
    </sql>
    <description>
      A Hibernate query that gets the users having
      the specified directory as home directory.
    </description>
  </query>
  
  <query id="GET_EXPERIMENT_DIRECTORIES" type="HQL">
    <sql>
      SELECT {1}
      FROM ExperimentData xpr
      WHERE xpr.directory = :directory
    </sql>
    <description>
      A Hibernate query that gets the experiments having
      the specified directory as the plugin directory.
    </description>
  </query>

  <query id="GET_SUBDIRECTORIES" type="HQL">
    <sql>
      SELECT dir
      FROM DirectoryData dir
      WHERE dir.parent = :parent
    </sql>
    <description>
      A Hibernate query that returns all subdirectories in a directory.
    </description>
  </query>
  
  <query id="GET_SUBDIRECTORY_WITH_NAME" type="HQL">
    <sql>
      SELECT dir
      FROM DirectoryData dir
      WHERE dir.name = :name
      AND dir.parent = :parent
    </sql>
    <description>
      A Hibernate query that returns the a subdirectory with the
      specified name in a given directory.
    </description>
  </query>

  <query id="GET_FILE_TYPE_WITH_NAME" type="HQL">
    <sql>
      SELECT ft
      FROM FileTypeData ft
      WHERE ft.name = :name
    </sql>
    <description>
      A Hibernate query that returns the file type with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_QUOTA_TYPE_WITH_NAME" type="HQL">
    <sql>
      SELECT qt
      FROM QuotaTypeData qt
      WHERE qt.name = :name
    </sql>
    <description>
      A Hibernate query that returns the quota type with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_QUOTA_WITH_NAME" type="HQL">
    <sql>
      SELECT q
      FROM QuotaData q
      WHERE q.name = :name
    </sql>
    <description>
      A Hibernate query that returns the quota with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_GROUP_WITH_NAME" type="HQL">
    <sql>
      SELECT grp
      FROM GroupData grp
      WHERE grp.name = :name
    </sql>
    <description>
      A Hibernate query that returns the group with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_ROLE_WITH_NAME" type="HQL">
    <sql>
      SELECT rle
      FROM RoleData rle
      WHERE rle.name = :name
    </sql>
    <description>
      A Hibernate query that returns the role with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_PROTOCOL_TYPE_WITH_NAME" type="HQL">
    <sql>
      SELECT pt
      FROM ProtocolTypeData pt
      WHERE pt.name = :name
    </sql>
    <description>
      A Hibernate query that returns the protocol type with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_SOFTWARE_TYPE_WITH_NAME" type="HQL">
    <sql>
      SELECT st
      FROM SoftwareTypeData st
      WHERE st.name = :name
    </sql>
    <description>
      A Hibernate query that returns the software type with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_SOFTWARE_WITH_NAME" type="HQL">
    <sql>
      SELECT sw
      FROM SoftwareData sw
      WHERE sw.name = :name
    </sql>
    <description>
      A Hibernate query that returns the software with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_HARDWARE_TYPE_WITH_NAME" type="HQL">
    <sql>
      SELECT ht
      FROM HardwareTypeData ht
      WHERE ht.name = :name
    </sql>
    <description>
      A Hibernate query that returns the hardware type with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_HARDWARE_WITH_NAME" type="HQL">
    <sql>
      SELECT hw
      FROM HardwareData hw
      WHERE hw.name = :name
    </sql>
    <description>
      A Hibernate query that returns the hardware with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_PLATE_GEOMETRY_WITH_NAME" type="HQL">
    <sql>
      SELECT pg
      FROM PlateGeometryData pg
      WHERE pg.name = :name
    </sql>
    <description>
      A Hibernate query that returns the plate geometry with the specified 
      name.
    </description>
  </query>

  <query id="GET_PLATE_MAPPING_WITH_NAME" type="HQL">
    <sql>
      SELECT pm
      FROM PlateMappingData pm
      WHERE pm.name = :name
    </sql>
    <description>
      A Hibernate query that returns the plate mapping with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_LABEL_WITH_NAME" type="HQL">
    <sql>
      SELECT lbl
      FROM LabelData lbl
      WHERE lbl.name = :name
    </sql>
    <description>
      A Hibernate query that returns the label with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_ANNOTATION_TYPE_WITH_NAME" type="HQL">
    <sql>
      SELECT at
      FROM AnnotationTypeData at
      WHERE at.name = :name
    </sql>
    <description>
      A Hibernate query that returns the annotation type with the specified 
      name.
    </description>
  </query>
  
  <query id="GET_NEWS_WITH_NAME" type="HQL">
    <sql>
      SELECT nws
      FROM NewsData nws
      WHERE nws.name = :name
    </sql>
    <description>
      A Hibernate query that returns the news with the specified 
      name.
    </description>
  </query>

  <query id="GET_FILE_IN_DIRECTORY" type="HQL">
    <sql>
      SELECT f
      FROM FileData f
      WHERE f.directory = :directory
      AND f.name = :name
    </sql>
    <description>
      A Hibernate query that returns the file with the specified 
      name in a given directory.
    </description>
  </query>

  <query id="GET_PROTOCOLS_FOR_PROTOCOLTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM ProtocolData p
      WHERE p.protocolType = :protocolType
    </sql>
    <description>
      Get the protocols the uses a protocol type.
    </description>
  </query>

  <query id="GET_PLATEEVENTTYPES_FOR_PROTOCOLTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateEventTypeData pet
      WHERE pet.protocolType = :protocolType
    </sql>
    <description>
      Get the plate events types that uses a protocol type.
    </description>
  </query>
  
  <query id="GET_BIOMATERIALEVENTS_FOR_PROTOCOL" type="HQL">
    <sql>
      SELECT {1}
      FROM BioMaterialEventData bme
      WHERE bme.protocol = :protocol
    </sql>
    <description>
      A Hibernate query that gets biomaterial
      events using a protocol.
    </description>
  </query>

  <query id="GET_PLATEEVENTS_FOR_PROTOCOL" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateEventData pe
      WHERE pe.protocol = :protocol
    </sql>
    <description>
      A Hibernate query thatgets plate events
      using a protocol.
    </description>
  </query>

  <query id="GET_ARRAYBATCHES_FOR_PROTOCOL" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayBatchData ab
      WHERE ab.protocol = :protocol
    </sql>
    <description>
      A Hibernate query that gets array batches
      using a protocol.
    </description>
  </query>

  <query id="GET_SCANS_FOR_PROTOCOL" type="HQL">
    <sql>
      SELECT {1}
      FROM ScanData sc
      WHERE sc.protocol = :protocol
    </sql>
    <description>
      A Hibernate query that gets scans
      using a protocol.
    </description>
  </query>

  <query id="GET_RAWBIOASSAYS_FOR_PROTOCOL" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.protocol = :protocol
    </sql>
    <description>
      A Hibernate query that gets raw bioassays
      using a protocol.
    </description>
  </query>

  <query id="FIND_USED_FILES" type="HQL">
    <sql>
      SELECT fad
      FROM net.sf.basedb.core.data.FileAttachableData fad
      WHERE fad.file = :file
    </sql>
    <description>
      Load the files that is used by any FileAttachableData.
    </description>
  </query>

  <query id="GET_SPOTIMAGES_FOR_FILE" type="HQL">
    <sql>
      SELECT {1}
      FROM SpotImagesData spi
      WHERE spi.redImageFile = :file 
      OR spi.greenImageFile = :file 
      OR spi.blueImageFile = :file 
      OR spi.spotImagesFile = :file 
    </sql>
    <description>
      A Hibernate query that gets spot images where a given 
      file is used as one of the color components or holds the generated spot images.
    </description>
  </query>
  
  <query id="GET_FILESETMEMBERS_FOR_FILE" type="HQL">
    <sql>
      SELECT {1}
      FROM FileSetMemberData fsm
      WHERE fsm.file = :file
    </sql>
    <description>
      A Hibernate query that gets file set membership
      for a given file
    </description>
  </query>
  
  <query id="GET_HARDWARE_FOR_TYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM HardwareData hw
      WHERE hw.hardwareType = :hardwaretype
    </sql>
    <description>
      A Hibernate query that gets hardware items
      of the given hardware type.
    </description>
  </query>

  <query id="GET_SCANS_FOR_SCANNER" type="HQL">
    <sql>
      SELECT {1}
      FROM ScanData scn
      WHERE scn.scanner = :scanner
    </sql>
    <description>
      A Hibernate query that gets scans which
      uses a given scanner (hardware).
    </description>
  </query>
  
  <query id="GET_ARRAYBATCHES_FOR_PRINTROBOT" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayBatchData ab
      WHERE ab.printRobot = :printrobot
    </sql>
    <description>
      A Hibernate query that gets array batches which
      uses a given print robot (hardware).
    </description>
  </query>
  
  <query id="GET_BIOMATERIALEVENTS_FOR_HARDWARE" type="HQL">
    <sql>
      SELECT {1}
      FROM BioMaterialEventData bme
      WHERE bme.hardware = :hardware
    </sql>
    <description>
      A Hibernate query that gets biomaterial events which
      uses a given hardware.
    </description>
  </query>
  
  <query id="GET_PLATEEVENTS_FOR_HARDWARE" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateEventData ple
      WHERE ple.hardware = :hardware
    </sql>
    <description>
      A Hibernate query that gets plates events which
      uses a given hardware.
    </description>
  </query>

  <query id="GET_REPORTERS_FOR_REPORTERTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM ReporterData rpt
      WHERE rpt.reporterType = :reporterType
    </sql>
    <description>
      A Hibernate query that gets reporter items
      of the given reporter type.
    </description>
  </query>

  <query id="GET_REPORTER_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT rpt
      FROM ReporterData rpt
      WHERE rpt.externalId = :externalId
    </sql>
    <description>
      A Hibernate query that finds the reporter with a given external id.
    </description>
  </query>
  
  <query id="GET_SOFTWARE_FOR_SOFTWARETYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM SoftwareData sw
      WHERE sw.softwareType = :softwaretype
    </sql>
    <description>
      A Hibernate query that gets software items
      of the given software type.
    </description>
  </query>

  <query id="GET_RAWBIOASSAYS_FOR_SOFTWARE" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.software = :software
    </sql>
    <description>
      A Hibernate query that gets the raw bioassays
      produced from a given software.
    </description>
  </query>

  <query id="GET_ANNOTATIONS_FOR_ANNOTATIONTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM AnnotationData a
      WHERE a.annotationType = :annotationType
    </sql>
    <description>
      A Hibernate query that gets annotations 
      of the given annotation type.
    </description>
  </query>
  
  <query id="GET_EXPERIMENTS_FOR_ANNOTATIONTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM ExperimentData exp
      JOIN exp.experimentalFactors ef
      WHERE ef = :annotationType
    </sql>
    <description>
      A Hibernate query that gets experiments
      where the given annotation type is used as an experimental factor.
    </description>
  </query>
  
  <query id="GET_PROTOCOLS_FOR_ANNOTATIONTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM ProtocolData prt
      JOIN prt.parameters pp
      WHERE pp = :annotationType
    </sql>
    <description>
      A Hibernate query that gets protocols
      where the given annotation type is used as a protocol parameter.
    </description>
  </query>

  <query id="GET_SAMPLES_FOR_BIOSOURCE" type="HQL">
    <sql>
      SELECT {1}
      FROM SampleData s
      WHERE s.parent = :biosource
    </sql>
    <description>
      A Hibernate query that gets samples 
      created from a given biosource.
    </description>
  </query>

  <query id="GET_EXTRACTS_FOR_SAMPLE" type="HQL">
    <sql>
      SELECT {1}
      FROM ExtractData e
      WHERE e.parent = :sample
    </sql>
    <description>
      A Hibernate query that gets extracts 
      created from a given sample.
    </description>
  </query>
  
  <query id="GET_LABELED_EXTRACTS_FOR_EXTRACT" type="HQL">
    <sql>
      SELECT {1}
      FROM LabeledExtractData le
      WHERE le.parent = :extract
    </sql>
    <description>
      A Hibernate query that gets labeled extracts 
      created from a given extract.
    </description>
  </query>

  <query id="GET_LABELED_EXTRACTS_FOR_LABEL" type="HQL">
    <sql>
      SELECT {1}
      FROM LabeledExtractData le
      WHERE le.label = :label
    </sql>
    <description>
      A Hibernate query that gets labeled extracts 
      with a given label.
    </description>
  </query>

  <query id="GET_SOURCEEVENTS_FOR_BIOMATERIAL" type="HQL">
    <sql>
      SELECT {1}
      FROM BioMaterialEventData bme
      JOIN bme.sources src
      WHERE index(src) = :bioMaterial
    </sql>
    <description>
      A Hibernate query that gets the events where a given
      biomaterial has been part of as a source biomaterial, ie. the number 
      of pooled biomaterials that have been created from it.
    </description>
  </query>

  <query id="GET_CREATION_EVENT_FOR_BIOMATERIAL" type="HQL">
    <sql>
      SELECT evt
      FROM BioMaterialEventData evt
      WHERE evt.bioMaterial = :bioMaterial
      AND evt.eventType = 1
    </sql>
    <description>
      A Hibernate query that returns the creation event for
      a biomaterial.
    </description>
  </query>
  
  <query id="COUNT_UNREAD_MESSAGES_FOR_USER" type="HQL">
    <sql>
      SELECT count(*) 
      FROM MessageData msg
      WHERE msg.to = :user AND msg.read = false AND msg.removed = false
    </sql>
    <description>
      A Hibernate query that counts the number of
      unread messages for a given user
    </description>
  </query>
  
  <query id="GET_PLATETYPES_FOR_PLATEGEOMETRY" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateTypeData pt
      WHERE pt.plateGeometry = :plateGeometry
    </sql>
    <description>
      A Hibernate query that gets the
      plate types using a given plate geometry
    </description>
  </query>
  
  <query id="GET_PLATEMAPPINGS_FOR_PLATEGEOMETRY" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateMappingData pm
      WHERE pm.sourceGeometry = :plateGeometry
      OR pm.destinationGeometry = :plateGeometry
    </sql>
    <description>
      A Hibernate query that gets the
      plate mappings using a given plate geometry as source or destination
    </description>
  </query>

  <query id="GET_PLATES_FOR_PLATETYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateData p
      WHERE p.plateType = :plateType
    </sql>
    <description>
      A Hibernate query that gets
      plates of a specific plate type.
    </description>
  </query>

  <query id="GET_PLATEEVENTS_FOR_PLATEEVENTTYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateEventData pe
      WHERE pe.plateEventType = :plateEventType
    </sql>
    <description>
      A Hibernate query that gets
      plate events of the given plate event type.
    </description>
  </query>

  <query id="GET_CHILDPLATES_FOR_PLATE" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateData p
      JOIN p.parents pp
      WHERE pp = :plate
    </sql>
    <description>
      A Hibernate query that gets the
      child plates for a given plate.
    </description>
  </query>

  <query id="GET_ARRAYDESIGNS_FOR_PLATE" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayDesignData ad
      JOIN ad.plates p
      WHERE p = :plate
    </sql>
    <description>
      A Hibernate query that gets the
      array designs that has used a given plate.
    </description>
  </query>

  <query id="GET_PLATES_FOR_PLATEMAPPING" type="HQL">
    <sql>
      SELECT {1}
      FROM PlateData p
      WHERE p.plateMapping = :plateMapping
    </sql>
    <description>
      A Hibernate query that gets the
      plates that has been created from a given plate mapping.
    </description>
  </query>
  
  <query id="GET_FEATURES_FOR_WELL" type="HQL">
    <sql>
      SELECT {1}
      FROM FeatureData f
      WHERE f.well = :well
    </sql>
    <description>
      A Hibernate query that gets the
      features using a given well.
    </description>
  </query>

  <query id="COUNT_FEATURES_FOR_ARRAYDESIGN" type="HQL">
    <sql>
      SELECT count(*)
      FROM FeatureData f
      WHERE f.arrayDesignBlock.arrayDesign = :arrayDesign
    </sql>
    <description>
      A Hibernate query that counts the number of
      features on a given array design
    </description>
  </query>


  <query id="GET_CHILDWELLS_FOR_WELL" type="HQL">
    <sql>
      SELECT {1}
      FROM Well w
      WHERE w.parent = :well
    </sql>
    <description>
      A Hibernate query that gets the
      child wells of a given well.
    </description>
  </query>

  <query id="GET_PLUGINCONFIGURATIONS_FOR_PLUGINDEFINITION" type="HQL">
    <sql>
      SELECT {1}
      FROM PluginConfigurationData pc
      WHERE pc.pluginDefinition = :pluginDefinition
    </sql>
    <description>
      A Hibernate query that gets plugin configurations
      using a plugin definition.
    </description>
  </query>
  
  <query id="GET_JOBS_FOR_PLUGINCONFIGURATION" type="HQL">
    <sql>
      SELECT {1}
      FROM JobData j
      WHERE j.pluginConfiguration = :pluginConfiguration
    </sql>
    <description>
      A Hibernate query that gets the jobs
      using a specific plugin configuration.
    </description>
  </query>
  
  <query id="GET_JOBS_FOR_PLUGINDEFINITION" type="HQL">
    <sql>
      SELECT {1}
      FROM JobData j
      WHERE j.pluginDefinition = :pluginDefinition
    </sql>
    <description>
      A Hibernate query that gets the jobs
      using a specific plugin definition.
    </description>
  </query>

  <query id="FIND_JOBS_IN_QUEUE" type="HQL">
    <sql>
      SELECT job
      FROM JobData job
      WHERE job.status = :status
      AND job.type = :type
      ORDER BY job.priority ASC, job.created ASC
    </sql>
    <description>
      A Hibernate query that loads plugin jobs in the job queue waiting to be
      executed sorted by priority and waiting type. The query should return all
      jobs, ignoring all settings specifying that the internal job queue should
      not be used.
    </description>
  </query>
  
  <query id="FIND_INTERNAL_JOBS_IN_QUEUE" type="HQL">
    <sql>
      SELECT job
      FROM JobData job
      WHERE job.status = :status
      AND job.type = :type
      AND job.pluginDefinition.useInternalJobQueue = true
      AND job.jobAgentId IS NULL
      ORDER BY job.priority ASC, job.created ASC
    </sql>
    <description>
      A Hibernate query that loads plugin jobs in the job queue waiting to be
      executed sorted by priority and waiting type. It should only return
      jobs where the plug-in setting useInternalJobQueue=true and no
      specific job agent has been selected for the job.
    </description>
  </query>
  
  <query id="GET_ARRAYSLIDES_FOR_BATCH" type="HQL">
    <sql>
      SELECT {1}
      FROM ArraySlideData a
      WHERE a.arrayBatch = :arrayBatch
    </sql>
    <description>
      A Hibernate query that gets the array slides
      in an array batch.
    </description>
  </query>

  <query id="GET_ARRAYSLIDES_WITH_BARCODE" type="HQL">
    <sql>
      SELECT {1}
      FROM ArraySlideData ars
      WHERE ars.barcode = :barcode
    </sql>
    <description>
      A Hibernate query that gets the array slides
      with a given barcode.
    </description>
  </query>


  <query id="GET_ARRAYBATCHES_FOR_ARRAYDESIGN" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayBatchData a
      WHERE a.arrayDesign = :arrayDesign
    </sql>
    <description>
      A Hibernate query that gets array batches
      that uses a specific array design.
    </description>
  </query>

  <query id="GET_RAWBIOASSAYS_FOR_ARRAYDESIGN" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.arrayDesign = :arrayDesign
    </sql>
    <description>
      A Hibernate query that gets raw bioassays
      that uses a specific array design.
    </description>
  </query>

  <query id="GET_SCANS_FOR_HYBRIDIZATION" type="HQL">
    <sql>
      SELECT {1}
      FROM ScanData scn
      WHERE scn.hybridization = :hybridization
    </sql>
    <description>
      A Hibernate query that gets scans
      that uses a specific hybridization.
    </description>
  </query>

  <query id="GET_RAWBIOASSAYS_FOR_SCAN" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.scan = :scan
    </sql>
    <description>
      A Hibernate query that gets raw bioassays
      created from a specific scan.
    </description>
  </query>

  <query id="GET_IMAGES_FOR_SCAN" type="HQL">
    <sql>
      SELECT {1}
      FROM ImageData img
      WHERE img.scan = :scan
    </sql>
    <description>
      A Hibernate query that gets images
      created from a specific scan.
    </description>
  </query>

  <query id="GET_FEATURE_BY_ALL_COORDINATES" type="HQL">
    <sql>
      SELECT f
      FROM FeatureData f
      WHERE f.arrayDesignBlock.arrayDesign = :arrayDesign
      AND f.row = :row
      AND f.column = :column
      AND 
      ( 
        (f.arrayDesignBlock.blockNumber = :block AND :block &lt;&gt; 0)
        OR 
        (:block = 0 AND f.arrayDesignBlock.metaGridX = :metaGridX
        AND f.arrayDesignBlock.metaGridY = :metaGridY)
      )
    </sql>
    <description>
      A Hibernate query that finds a feature on a given array design
      with specified block and coordinates.
    </description>
  </query>
  
  <query id="PRELOAD_FEATURES" type="HQL">
    <sql>
      SELECT f
      FROM FeatureData f
      JOIN FETCH f.arrayDesignBlock b
      LEFT JOIN FETCH f.reporter
      WHERE b.arrayDesign = :arrayDesign
    </sql>
    <description>
      A Hibernate query that loads features, blocks and reporters
      for a single array design.
    </description>
  </query>
  
  <query id="DELETE_FEATURES_FOR_ARRAYDESIGN" type="HQL">
    <sql>
      DELETE FROM Features f, ArrayDesignBlocks adb
      WHERE adb.id = f.arraydesignblock_id AND adb.arraydesign_id = ?
    </sql>
    <description>
      A Hibernate query that deletes all features for an array design.
    </description>
  </query>

  <query id="GET_PLUGINTYPE_FOR_INTERFACENAME" type="HQL">
    <sql>
      SELECT plt
      FROM PluginTypeData plt
      WHERE plt.interfaceName = :interfaceName
    </sql>
    <description>
      Load a plugin type when you know the interface name.
    </description>
  </query>

  <query id="GET_PLUGINDEFINITION_FOR_CLASSNAME" type="HQL">
    <sql>
      SELECT pd
      FROM PluginDefinitionData pd
      WHERE pd.className = :className
    </sql>
    <description>
      Load a plugin definition when you know the class name.
    </description>
  </query>

  <query id="GET_PLUGINCONFIGURATION_FOR_PLUGIN_WITH_NAME" type="HQL">
    <sql>
      SELECT pc
      FROM PluginConfigurationData pc
      WHERE pc.pluginDefinition.className = :className
      AND pc.name = :name
    </sql>
    <description>
      Load a plugin configuration for a given plug-in and with a given name
    </description>
  </query>


  <query id="GET_EXPERIMENTS_FOR_RAWBIOASSAY" type="HQL">
    <sql>
      SELECT {1}
      FROM ExperimentData xp
      JOIN xp.rawBioAssays rba
      WHERE rba = :rawBioAssay
    </sql>
    <description>
      A Hibernate query that gets the experiments
      using a specific raw bioassay.
    </description>
  </query>
  
  <query id="GET_TRANSFORMATIONS_FOR_RAWBIOASSAY" type="HQL">
    <sql>
      SELECT {1}
      FROM TransformationData trf
      JOIN trf.rawSources rba
      WHERE rba = :rawBioAssay
    </sql>
    <description>
      A Hibernate query that gets the transformations
      using a specifiec raw bioassay.
    </description>
  </query>
  
  <query id="GET_TRANSFORMATIONS_FOR_JOB" type="HQL">
    <sql>
      SELECT {1}
      FROM TransformationData trf
      WHERE trf.job = :job
    </sql>
    <description>
      A Hibernate query that gets transformations
      linked to a job.
    </description>
  </query>
  
  <query id="GET_RAWBIOASSAYS_FOR_JOB" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.job = :job
    </sql>
    <description>
      A Hibernate query that gets raw bioassays
      linked to a job.
    </description>
  </query>
  
  <query id="GET_ARRAYDESIGNS_FOR_JOB" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayDesignData ad
      WHERE ad.job = :job
    </sql>
    <description>
      A Hibernate query that gets array designs
      linked to a job.
    </description>
  </query>

  <query id="FIND_CHILD_BIOASSAYSETS" type="HQL">
    <sql>
      SELECT bas 
      FROM BioAssaySetData bas
      WHERE bas.transformation.source = :parent
    </sql>
    <description>
      A Hibernate query that returns all bioassaysets that are 
      children to a specified parent bioassayset.
    </description>
  </query>
  
  <query id="FIND_DATACUBES_FOR_BIOASSAYSETS" type="HQL">
    <sql>
      SELECT DISTINCT cbe
      FROM BioAssaySetData bas
      JOIN bas.dataCubeLayer.dataCube cbe
      WHERE bas IN (:basList)
    </sql>
    <description>
      A Hibernate query that returns all data cubes that are 
      used by the specified list of bioassaysets
    </description>
  </query>
  
  <query id="FIND_DATACUBES_USED_BY_OTHERS" type="HQL">
    <sql>
      SELECT DISTINCT cbe
      FROM BioAssaySetData bas
      JOIN bas.dataCubeLayer.dataCube cbe
      WHERE bas NOT IN (:basList)
      AND cbe IN (:possibleCubes)
    </sql>
    <description>
      A Hibernate query that, given a list of data cubes and bioassaysets,
      returns all of those data cubes that are also used by other bioassaysets.
    </description>
  </query>

  <query id="FIND_DATACUBELAYERS_FOR_BIOASSAYSETS" type="HQL">
    <sql>
      SELECT lay
      FROM BioAssaySetData bas
      JOIN bas.dataCubeLayer lay
      WHERE bas IN (:basList)
    </sql>
    <description>
      A Hibernate query that returns all data cube layers that are 
      used by the specified list of bioassaysets
    </description>
  </query>
  
  <query id="FIND_DATACUBELAYERS_FOR_BIOASSAYSETS_IGNORE_DELETED_DATACUBES" type="HQL">
    <sql>
      SELECT lay
      FROM BioAssaySetData bas
      JOIN bas.dataCubeLayer lay
      WHERE bas IN (:basList)
      AND lay.dataCube NOT IN (:deletedCubes)
    </sql>
    <description>
      A Hibernate query that returns all data cube layers that are 
      used by the specified list of bioassaysets but not are part of the
      list of already deleted data cubes.
    </description>
  </query>

  <query id="FIND_DATACUBELAYERS_USED_BY_OTHERS" type="HQL">
    <sql>
      SELECT lay
      FROM BioAssaySetData bas
      JOIN bas.dataCubeLayer lay
      WHERE bas NOT IN (:basList)
      AND lay IN (:possibleLayers)
    </sql>
    <description>
      A Hibernate query that, given a list of data cube layers and bioassaysets,
      returns all of those data cube layers that are also used by other bioassaysets.
    </description>
  </query>

  <query id="FIND_DATACUBEFILTERS_FOR_BIOASSAYSETS" type="HQL">
    <sql>
      SELECT flt
      FROM BioAssaySetData bas
      JOIN bas.dataCubeFilter flt
      WHERE bas IN (:basList)
    </sql>
    <description>
      A Hibernate query that returns all data cube filters that are 
      used by the specified list of bioassaysets
    </description>
  </query>
  
  <query id="FIND_DATACUBEFILTERS_FOR_BIOASSAYSETS_IGNORE_DELETED_DATACUBES" type="HQL">
    <sql>
      SELECT flt
      FROM BioAssaySetData bas
      JOIN bas.dataCubeFilter flt
      WHERE bas IN (:basList)
      AND flt.dataCube NOT IN (:deletedCubes)
    </sql>
    <description>
      A Hibernate query that returns all data cube filters that are 
      used by the specified list of bioassaysets but not are part of the
      list of already deleted data cubes.
    </description>
  </query>

  <query id="FIND_DATACUBEFILTERS_USED_BY_OTHERS" type="HQL">
    <sql>
      SELECT flt
      FROM BioAssaySetData bas
      JOIN bas.dataCubeFilter flt
      WHERE bas NOT IN (:basList)
      AND flt IN (:possibleFilters)
    </sql>
    <description>
      A Hibernate query that, given a list of data cube filters and bioassaysets,
      returns all of those data cube filters that are also used by other bioassaysets.
    </description>
  </query>

  <query id="FIND_DATACUBEEXTRAVALUES_FOR_BIOASSAYSETS" type="HQL">
    <sql>
      SELECT dcev
      FROM BioAssaySetData bas
      JOIN bas.extraValues ev
      JOIN ev.dataCubeExtraValue dcev
      WHERE bas IN (:basList)
    </sql>
    <description>
      A Hibernate query that returns all data cube extra values that are 
      used by the specified list of bioassaysets
    </description>
  </query>
  
  <query id="FIND_DATACUBEEXTRAVALUES_FOR_BIOASSAYSETS_IGNORE_DELETED_DATACUBES" type="HQL">
    <sql>
      SELECT dcev
      FROM BioAssaySetData bas
      JOIN bas.extraValues ev
      JOIN ev.dataCubeExtraValue dcev
      WHERE bas IN (:basList)
      AND dcev.dataCube NOT IN (:deletedCubes)
    </sql>
    <description>
      A Hibernate query that returns all data cube extra values that are 
      used by the specified list of bioassaysets but not are part of the
      list of already deleted data cubes.
    </description>
  </query>

  <query id="FIND_DATACUBEEXTRAVALUES_USED_BY_OTHERS" type="HQL">
    <sql>
      SELECT dcev
      FROM BioAssaySetData bas
      JOIN bas.extraValues ev
      JOIN ev.dataCubeExtraValue dcev
      WHERE bas NOT IN (:basList)
      AND dcev IN (:possibleExtraValues)
    </sql>
    <description>
      A Hibernate query that, given a list of data cube extra values and bioassaysets,
      returns all of those data cube extra values that are also used by other bioassaysets.
    </description>
  </query>

  <query id="GET_EXTRAVALUETYPE_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT evt
      FROM ExtraValueTypeData evt
      WHERE evt.externalId = :externalId
    </sql>
    <description>
      Load an extra value type when you know the external id.
    </description>
  </query>

  <query id="GET_EXTRAVALUES_FOR_EXTRAVALUETYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM ExtraValueData ev
      WHERE ev.extraValueType = :extraValueType
    </sql>
    <description>
      A Hibernate query that gets extra values
      of a specific type.
    </description>
  </query>
  
  <query id="LOAD_CONTEXT_NAMES" type="HQL">
    <sql>
      SELECT ctx.id, ctx.name
      FROM ContextData ctx
      WHERE ctx.client = :client AND 
      (ctx.user = :user OR ctx.public = true) 
      AND ctx.itemType = :itemType
      AND ctx.subContext = :subContext
      ORDER BY ctx.name
    </sql>
    <description>
      A Hibernate query that selects the id and name of all contexts for
      a user and item type. The names should be sorted in ascending order.
    </description>
  </query>
  
  <query id="LOAD_CONTEXT_BY_NAME" type="HQL">
    <sql>
      SELECT ctx
      FROM ContextData ctx
      WHERE ctx.user = :user
      AND ctx.client = :client
      AND ctx.itemType = :itemType
      AND ctx.subContext  = :subContext
      AND ctx.name = :name
    </sql>
    <description>
      A Hibernate query that load a context given the user, client,
      item type, subcontext and name of the context.
    </description>
  </query>
  
  <query id="LOAD_USER_CONTEXTS" type="HQL">
    <sql>
      SELECT ctx
      FROM ContextData ctx
      WHERE ctx.user.id = :user
      AND ctx.client.id = :client
      AND ctx.name = :name
    </sql>
    <description>
      A Hibernate query that loads all saved context information
      with a given name for a specific user/client.
    </description>
  </query>

  <query id="COUNT_PLUGINS_BY_TYPE_FOR_CONTEXT" type="HQL">
    <sql>
      SELECT plg.mainType, count(DISTINCT plg.id)
      FROM PluginDefinitionData plg
      JOIN plg.guiContexts gcx
      LEFT JOIN plg.configurations cfg
      WITH true = :hasConfigPermission OR cfg.owner.id = :owner 
        OR cfg.itemKey.id IN (:itemKeys) OR cfg.projectKey.id IN (:projectKeys)
      WHERE 
        (true = :hasPluginPermission OR plg.owner.id = :owner 
        OR plg.itemKey.id IN (:itemKeys) OR plg.projectKey.id IN (:projectKeys))
      AND gcx.itemType = :itemType AND gcx.contextType = :contextType
      AND (
        (plg.requiresConfiguration = false)
        OR
        (plg.requiresConfiguration = true AND NOT cfg.id IS NULL)
      )
      GROUP BY plg.mainType
    </sql>
    <description>
      A Hibernate query that counts the number of plugins available for a 
      given GUI context grouped by the main type of the plugins taking
      the requirement of configurations and user permissions into account.
    </description>
  </query>
  
  <query id="GET_FORMULA_WITH_NAME_AND_CHANNELS" type="HQL">
    <sql>
      SELECT fml 
      FROM FormulaData fml
      WHERE fml.name = :name
      AND fml.channels = :channels
    </sql>
    <description>
      A Hibernate query that loads a formula with a given name and number
      of channels.
    </description>
  </query>

  <query id="GET_FORMULA_WITH_NAME_AND_TYPE" type="HQL">
    <sql>
      SELECT fml 
      FROM FormulaData fml
      WHERE fml.name = :name
      AND fml.rawDataType = :rawDataType
    </sql>
    <description>
      A Hibernate query that loads a formula with a given name and raw data type.
    </description>
  </query>
  
  <query id="GET_HELP_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT hlp
      FROM HelpData hlp
      WHERE hlp.externalId = :externalId AND hlp.client = :client
    </sql>
    <description>
      A Hibernate query that loads a help text.
    </description>
  </query>
  
  <query id="GET_SCHEMA_VERSION" type="HQL">
    <sql>
      SELECT sv
      FROM SchemaVersionData sv
    </sql>
    <description>
      A Hibernate query that loads the schema version (there should only be one record).
    </description>
  </query>
  
  <query id="SET_SCHEMA_VERSION" type="HQL">
    <sql>
      UPDATE SchemaVersionData sv
      SET sv.schemaVersion = :schemaVersion,
      sv.build = :build
    </sql>
    <description>
      A Hibernate query that updates the schema version and build number.
    </description>
  </query>
  
  <query id="SET_PROJECT_ID_FOR_JOBS" type="HQL">
    <sql>
      UPDATE JobData job
      SET job.activeProjectId = 0
      WHERE job.activeProjectId IS NULL
    </sql>
    <description>
      A Hibernate query that sets the active project ID for all
      jobs to 0 if they have a null value.
    </description>
  </query>

  <query id="GET_PRIMARY_ANNOTATION" type="HQL">
    <sql>
      SELECT ad
      FROM AnnotationData ad
      WHERE ad.annotationType = :annotationType
      AND ad.annotationSet = :annotationSet
    </sql>
    <description>
      A Hibernate query that loads the primary annotation of a specific
      annotation type for a given annotation set.
    </description>
  </query>
  
  <query id="GET_DIRECTLY_INHERITED_ANNOTATION" type="HQL">
    <sql>
      SELECT ad 
      FROM AnnotationData ad
      JOIN ad.inheritingSets ans
      WHERE ad.annotationType = :annotationType
      AND ans = :annotationSet
    </sql>
    <description>
      A Hibernate query that loads an directly inherited annotation of a specific
      annotation type for a given annotation set. A directly inhertited annotation
      is an annotation that is linked to the specified annotation set.
    </description>
  </query>

  <query id="GET_INDIRECTLY_INHERITED_ANNOTATION" type="HQL">
    <sql>
      SELECT ad
      FROM AnnotationData ad
      JOIN ad.annotationSet.inheritingSets ians
      WHERE ad.annotationType = :annotationType
      AND ians = :annotationSet
    </sql>
    <description>
      A Hibernate query that loads an indirectly inherited annotation of a specific
      annotation type for a given annotation set. An indirectly inherited annotation
      is an annotation which belongs to an annotation set which is inherited by 
      the given annotation set.
    </description>
  </query>
  
  <query id="UPDATE_BYTES_FOR_EXPERIMENT" type="HQL">
    <sql>
      UPDATE ExperimentData xpm
      SET xpm.bytes = xpm.bytes + :addedBytes
      WHERE xpm.id = :experiment
    </sql>
    <description>
      A Hibernate query that updates the number of bytes used by an experiment.
    </description>
  </query>

  <query id="UPDATE_BYTES_FOR_DATACUBE" type="HQL">
    <sql>
      UPDATE DataCubeData dcd
      SET dcd.bytes = dcd.bytes + :addedBytes
      WHERE dcd.id = :dataCube
    </sql>
    <description>
      A Hibernate query that updates the number of bytes used by a data cube.
    </description>
  </query>
  
  <query id="GET_REMOVED_ITEMS" type="HQL">
    <sql>
      SELECT trash
      FROM net.sf.basedb.core.data.RemovableData trash
      WHERE trash.removed = true
    </sql>
    <description>
      A Hibernate query that loads all items flagged for deletion.
    </description>
  </query>
  
  <query id="UPDATE_REMAINING_QUANTITY" type="HQL">
    <sql>
      UPDATE MeasuredBioMaterialData mbm 
      SET mbm.remainingQuantity = mbm.remainingQuantity - :used
      WHERE mbm = :bioMaterial
    </sql>
    <description>
      A Hibernate query that adds/removes the remaining quantity on a
      measuered biomaterial.
    </description>
  </query>

  <query id="SET_REMAINING_QUANTITY" type="HQL">
    <sql>
      UPDATE MeasuredBioMaterialData mbm 
      SET mbm.remainingQuantity = :remain
      WHERE mbm = :bioMaterial
    </sql>
    <description>
      A Hibernate query that sets the remaining quantity on a
      measuered biomaterial.
    </description>
  </query>


  <query id="GET_ANYTOANY_FOR_NAME" type="HQL">
    <sql>
      SELECT ata
      FROM AnyToAnyData ata
      WHERE ata.fromId = :fromId AND ata.fromType = :fromType AND ata.name = :name
    </sql>
    <description>
      A Hibernate query that loads the any-to-any link with the specified name
      for an item.
    </description>
  </query>

  <query id="DELETE_ANYTOANY_FROM" type="HQL">
    <sql>
      DELETE FROM AnyToAnyData ata 
      WHERE ata.fromId = :fromId AND ata.fromType = :fromType AND ata.name = :name
    </sql>
    <description>
      A Hibernate query that deletes a names any-to-any link leading out from
      an item.
    </description>
  </query>


  <query id="DELETE_ALL_ANYTOANY_FROM" type="HQL">
    <sql>
      DELETE FROM AnyToAnyData ata 
      WHERE ata.fromId = :fromId AND ata.fromType = :fromType
    </sql>
    <description>
      A Hibernate query that deletes all any-to-any links leading out from
      an item.
    </description>
  </query>

  <query id="DELETE_ALL_ANYTOANY_TO" type="HQL">
    <sql>
      DELETE FROM AnyToAnyData ata 
      WHERE ata.toId = :toId AND ata.toType = :toType
    </sql>
    <description>
      A Hibernate query that deletes all any-to-any links leading in to
      an item.
    </description>
  </query>
  
  <query id="DELETE_UNUSED_ANYTOANY_TO" type="HQL">
    <sql>
      DELETE FROM AnyToAnyData ata 
      WHERE ata.toId = :toId AND ata.toType = :toType AND ata.usingTo = false
    </sql>
    <description>
      A Hibernate query that deletes all any-to-any links leading in to
      an item that doesn't count as using the item.
    </description>
  </query>

  <query id="COUNT_ANYTOANY_FROM" type="HQL">
    <sql>
      SELECT count(*)
      FROM AnyToAnyData ata
      WHERE ata.fromId = :fromId AND ata.fromType = :fromType
    </sql>
    <description>
      A Hibernate query that counts the number of any-to-any links
      from a given item.
    </description>
  </query>

  <query id="COUNT_ANYTOANY_TO" type="HQL">
    <sql>
      SELECT count(*)
      FROM AnyToAnyData ana
      WHERE ana.toId = :toId AND ana.toType = :toType
    </sql>
    <description>
      A Hibernate query that counts the number of any-to-any links
      to a given item.
    </description>
  </query>

  <query id="COUNT_USED_ANYTOANY_TO" type="HQL">
    <sql>
      SELECT count(*)
      FROM AnyToAnyData ata
      WHERE ata.toId = :toId AND ata.toType = :toType AND ata.usingTo = true
    </sql>
    <description>
      A Hibernate query that counts the number of any-to-any links
      to a given item that counts as using the item.
    </description>
  </query>

  <query id="FIND_USING_ANYTOANY" type="HQL">
    <sql>
      SELECT ana.fromId, ana.fromType
      FROM AnyToAnyData ana
      WHERE ana.toId = :toId AND ana.toType = :toType AND ana.usingTo = true
    </sql>
    <description>
      A Hibernate query that finds the any-to-any links
      to a given item that counts as using the item.
    </description>
  </query>

  
  <query id="UPDATE_DATACUBENO_FOR_VIRTUALDB" type="HQL">
    <sql>
      UPDATE VirtualDbData vdb
      SET vdb.cubes = vdb.cubes + 1
      WHERE vdb.id = :virtualDb
    </sql>
    <description>
      A Hibernate query that updates the number of data cubes
      for the specified virtual database.
    </description>
  </query>

  <query id="GET_DATACUBENO_FOR_VIRTUALDB" type="HQL">
    <sql>
      SELECT vdb.cubes
      FROM VirtualDbData vdb
      WHERE vdb.id = :virtualDb
    </sql>
    <description>
      A Hibernate query that gets the current number of data cubes
      for the specified virtual database.
    </description>
  </query>
  
  <query id="UPDATE_FILTERNO_FOR_DATACUBE" type="HQL">
    <sql>
      UPDATE DataCubeData dcb
      SET dcb.numFilters = dcb.numFilters + 1
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that updates the number of filters
      for the specified data cube.
    </description>
  </query>

  <query id="GET_FILTERNO_FOR_DATACUBE" type="HQL">
    <sql>
      SELECT dcb.numFilters
      FROM DataCubeData dcb
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that gets the current number of filters
      for the specified data cube.
    </description>
  </query>

  <query id="UPDATE_EXTRAVALUENO_FOR_DATACUBE" type="HQL">
    <sql>
      UPDATE DataCubeData dcb
      SET dcb.numExtraValues = dcb.numExtraValues + 1
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that updates the number of extra values
      for the specified data cube.
    </description>
  </query>

  <query id="GET_EXTRAVALUENO_FOR_DATACUBE" type="HQL">
    <sql>
      SELECT dcb.numExtraValues
      FROM DataCubeData dcb
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that gets the current number of extra values
      for the specified data cube.
    </description>
  </query>

  <query id="UPDATE_LAYERNO_FOR_DATACUBE" type="HQL">
    <sql>
      UPDATE DataCubeData dcb
      SET dcb.numLayers = dcb.numLayers + 1
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that updates the number of layers
      for the specified data cube.
    </description>
  </query>

  <query id="GET_LAYERNO_FOR_DATACUBE" type="HQL">
    <sql>
      SELECT dcb.numLayers
      FROM DataCubeData dcb
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that gets the current number of layers
      for the specified data cube.
    </description>
  </query>

  <query id="UPDATE_COLUMNNO_FOR_DATACUBE" type="HQL">
    <sql>
      UPDATE DataCubeData dcb
      SET dcb.numColumns = dcb.numColumns + 1
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that updates the number of columns
      for the specified data cube.
    </description>
  </query>

  <query id="GET_COLUMNNO_FOR_DATACUBE" type="HQL">
    <sql>
      SELECT dcb.numColumns
      FROM DataCubeData dcb
      WHERE dcb.id = :dataCube
    </sql>
    <description>
      A Hibernate query that gets the current number of columns
      for the specified data cube.
    </description>
  </query>

  <query id="SET_HAS_DATA_FOR_RAWBIOASSAYS" type="HQL">
    <sql>
      UPDATE RawBioAssayData rba
      SET rba.hasData = CASE 
        WHEN rba.spots > 0 THEN true
        ELSE false
        END
      WHERE rba.hasData IS NULL
    </sql>
    <description>
      A Hibernate query that sets the hasData property for a
      raw bioassay depending on if it has spots or not.
    </description>
  </query>
  
  <query id="SET_REMOVED_FOR_HARDWARETYPES" type="HQL">
    <sql>
      UPDATE HardwareTypeData hwd
      SET hwd.removed = false
      WHERE hwd.removed IS NULL
    </sql>
    <description>
      A Hibernate query that sets the removed property to false for a
      HardwareTypeData if it has NULL value.
    </description>
  </query>

  <query id="SET_CONFIG_FOR_PLUGINS" type="HQL">
    <sql>
      UPDATE PluginDefinitionData pd
      SET pd.supportsConfigurations = true, pd.requiresConfiguration = false
      WHERE pd.supportsConfigurations IS NULL OR pd.requiresConfiguration IS NULL
    </sql>
    <description>
      A Hibernate query that sets the supportsConfigurations and requiresConfiguration
      properties of PluginDefinitionData items if any of them is null.
    </description>
  </query>

  <query id="GET_INCORRECT_PLATEMAPPINGS" type="HQL">
    <sql>
      SELECT pm
      FROM PlateMappingData pm
      WHERE pm.sourceCount = 4 AND pm.destinationCount = 1
      AND 
      (
        (pm.sourceGeometry.rows = 8 AND pm.sourceGeometry.columns = 12)
        OR
        (pm.sourceGeometry.rows = 16 AND pm.sourceGeometry.columns = 24)
      )
    </sql>
    <description>
      A Hibernate query that finds incorrect plate mappings.
    </description>
  </query>
  
  <query id="GET_PLATES_WITH_MAPPING" type="HQL">
    <sql>
      SELECT p
      FROM PlateData p
      WHERE p.plateMapping = :plateMapping
    </sql>
    <description>
      A Hibernate query that loads all plates with a specific plate mapping.
    </description>
  </query>
  
  <query id="GET_JOBAGENT_FOR_EXTERNALID" type="HQL">
    <sql>
      SELECT jag
      FROM JobAgentData jag
      WHERE jag.externalId = :externalId
    </sql>
    <description>
      A Hibernate query that loads the job agent with the specified external ID.
    </description>
  </query>

  <query id="SET_TRUSTED_FOR_PLUGINDEFINITIONS" type="HQL">
    <sql>
      UPDATE PluginDefinitionData pd
      SET pd.trusted = true
      WHERE pd.trusted IS NULL
    </sql>
    <description>
      A Hibernate query that sets the trusted flag for all plugins with a null value
      to TRUE. 
    </description>
  </query>
  
  <query id="SET_USE_PERMISSION_FOR_PLUGINDEFINITIONS" type="HQL">
    <sql>
      UPDATE PluginDefinitionData pd
      SET pd.usePermissions = false
      WHERE pd.usePermissions IS NULL
    </sql>
    <description>
      A Hibernate query that sets the use permission flag to false 
      for all plugins with a null value.
    </description>
  </query>
  
  <query id="GET_KEYS_FOR_PLUGIN" type="HQL">
    <sql>
      SELECT pdk
      FROM PluginKeys pdk
      WHERE pdk.pluginDefinitionId = :pluginId
      ORDER BY pdk.keyId
    </sql>
    <description>
      A Hibernate query that loads all PluginDefinitionKeys for a specified plugin ID.
    </description>
  </query>
  
  <query id="SET_SENDMESSAGE_FOR_JOBS" type="HQL">
    <sql>
      UPDATE JobData job
      SET job.sendMessage = true
      WHERE job.sendMessage IS NULL
    </sql>
    <description>
      A Hibernate query that sets the send message flag for all jobs with a null value.
    </description>
  </query>

  <query id="SET_PARAMETER_VERSION_FOR_PLUGINCONFIGURATIONS" type="HQL">
    <sql>
      UPDATE PluginConfigurationData pc
      SET pc.parameterVersion = 1 
      WHERE pc.parameterVersion IS NULL
    </sql>
    <description>
      A Hibernate query that sets the parameter version to 1 for all 
      configurations with a null value.
    </description>
  </query>

  <query id="SET_PARAMETER_VERSION_FOR_JOBS" type="HQL">
    <sql>
      UPDATE JobData job
      SET job.parameterVersion = 1 
      WHERE job.parameterVersion IS NULL
    </sql>
    <description>
      A Hibernate query that sets the parameter version to 1 for all 
      jobs with a null value.
    </description>
  </query>

  <query id="COPY_PLUGINCONFIGURATION_PARAMETERS" type="SQL">
    <sql>
      INSERT INTO "VersionedPluginConfigurationValues"
      ("pluginconfiguration_id", "name", "parameter_version", "value_id")
      SELECT "pluginconfiguration_id", "name", 1, "value_id"
      FROM "PluginConfigurationValues"
    </sql>
    <description>
      An SQL query that creates versioned parameters from unversioned.
    </description>
  </query>
  
  <query id="DELETE_UNVERSIONED_PLUGINCONFIGURATION_PARAMETERS" type="SQL">
    <sql>
      DELETE FROM "PluginConfigurationValues"
    </sql>
    <description>
      An SQL query that deletes unversioned plugin configuration parameters.
    </description>
  </query>

  <query id="SET_COLORING_FOR_FORMULAS" type="HQL">
    <sql>
        UPDATE FormulaData frm
        SET 
          frm.coloring.usingColors = false,
          frm.coloring.logarithmic = false
        WHERE frm.coloring.usingColors IS NULL
    </sql>
    <description>
      A HQL query that sets the usingColors and logarithmic to false
      for all formulas with null values.
    </description>
  </query>
  
  <query id="SET_COLORING_FOR_EXTRAVALUETYPES" type="HQL">
    <sql>
      UPDATE ExtraValueTypeData evt
      SET 
        evt.coloring.usingColors = false,
        evt.coloring.logarithmic = false
        WHERE evt.coloring.usingColors IS NULL
    </sql>
    <description>
      A HQL query that sets the usingColors and logarithmic to false
      for all extra value types with null values.
    </description>
  </query>
  
  <query id="SET_IMMEDIATE_EXECUTION_FOR_PLUGINS" type="HQL">
    <sql>
      UPDATE PluginDefinitionData plg
      SET plg.allowImmediateExecution = false
      WHERE plg.allowImmediateExecution IS NULL
    </sql>
    <description>
      A HQL query that sets the allowImmediateExecution to false
      for all plugins which has a null value.
    </description>
  </query>
  
  <query id="SET_PROTOCOL_PARAMETER_FOR_ANNOTATION_TYPES" type="HQL">
    <sql>
      UPDATE AnnotationTypeData at
      SET at.protocolParameter = false
      WHERE at.protocolParameter IS NULL
    </sql>
    <description>
      A HQL query that sets the protocolParameter flag to false
      for all annotation types with a null value.
    </description>
  </query>

  <query id="CHANGE_FILE_DISCRIMINATOR" type="SQL">
    <sql>
      UPDATE "ParameterValues" 
      SET "discriminator" = 10 
      WHERE "discriminator" = 9
    </sql>
    <description>
      An SQL query that changes the discriminator for file
      parameters
    </description>
  </query>

  <query id="COPY_FILE_PARAMETERS" type="SQL">
    <sql>
      INSERT INTO "ItemValues" ("id", "data_class", "data_class_id")
      SELECT "id", 'net.sf.basedb.core.data.FileData', "value"
      FROM "FileValues"
    </sql>
    <description>
      An SQL query that copies file parameter values into
      the item parameter values table.
    </description>
  </query>

  <query id="DELETE_FILE_PARAMETERS" type="SQL">
    <sql>
      DELETE FROM "FileValues"
    </sql>
    <description>
      An SQL query that deletes old file parameter values (after they have been copied).
    </description>
  </query>

  <query id="SET_ITEMTYPE_ON_DISKUSAGE" type="HQL">
    <sql>
      UPDATE DiskUsageData du
      SET du.itemType = :itemType
      WHERE du.id IN (:itemList)
      AND du.itemType IS NULL
    </sql>
    <description>
      A HQL query that sets the item type for disk usage items.
    </description>
  </query>

  <query id="LOAD_DISKUSAGEID_FOR_FILES" type="HQL">
    <sql>
      SELECT f.diskUsage.id 
      FROM FileData f
    </sql>
    <description>
      A HQL query that loads the disk usage ID for all files.
    </description>
  </query>
  
  <query id="LOAD_DISKUSAGEID_FOR_EXPERIMENTS" type="HQL">
    <sql>
      SELECT xp.diskUsage.id 
      FROM ExperimentData xp
    </sql>
    <description>
      A HQL query that loads the disk usage ID for all experiments.
    </description>
  </query>
  
  <query id="LOAD_DISKUSAGEID_FOR_RAWBIOASSAYS" type="HQL">
    <sql>
      SELECT rba.diskUsage.id 
      FROM RawBioAssayData rba
    </sql>
    <description>
      A HQL query that loads the disk usage ID for all raw bioassays.
    </description>
  </query>

  <query id="SET_MAX_MAPPING_ON_DATACUBES" type="HQL">
    <sql>
      UPDATE DataCubeData dcd
      SET dcd.maxRawMappingsForSpot = -1
      WHERE dcd.maxRawMappingsForSpot IS NULL
    </sql>
    <description>
      A HQL query that sets the maxRawMappingsForSpot on all data cubes with a
      null value to -1. This is required so we can load them by Hibernate.
    </description>
  </query>

  <query id="SET_MAX_MAPPING_ON_DATACUBE" type="HQL">
    <sql>
      UPDATE DataCubeData dcd
      SET dcd.maxRawMappingsForSpot = :mapCount
      WHERE dcd.id = :dataCube
    </sql>
    <description>
      A HQL query that sets the maxRawMappingsForSpot on a data cube.
    </description>
  </query>

  <query id="GET_USED_QUANTITY_EVENTS" type="HQL">
    <sql>
      SELECT evt.bioMaterial, evt.usedQuantity
      FROM BioMaterialEventData evt
    </sql>
    <description>
      A HQL query that loads the biomaterial and the used quantity 
      for all BioMaterialEvent:s.
    </description>
  </query>
  
  <query id="GET_USED_QUANTITY_SOURCES" type="HQL">
    <sql>
      SELECT index(src), src.usedQuantity
      FROM BioMaterialEventData evt
      JOIN evt.sources src
    </sql>
    <description>
      A HQL query that loads the used quantity 
      for all sources to BioMaterialEvent:s.
    </description>
  </query>

  <query id="SET_WRITE_PROTECTED_ON_FILES" type="HQL">
    <sql>
      UPDATE FileData f
      SET f.writeProtected = false
      WHERE f.writeProtected IS NULL
    </sql>
    <description>
      A HQL query that sets the writeProtected on all files with a
      null value to false.
    </description>
  </query>
  
  <query id="SET_REMOVE_JOB_ON_JOBS" type="HQL">
    <sql>
      UPDATE JobData j
      SET j.removeJobWhenFinished = false
      WHERE j.removeJobWhenFinished IS NULL
    </sql>
    <description>
      A HQL query that sets the deleteJobWhenFinished to false 
      on all jobs with a null value.
    </description>
  </query>  
  
  <query id="GET_INTERNAL_FILES_WITH_NO_LAST_UPDATE" type="HQL">
    <sql>
      SELECT f
      FROM FileData f
      WHERE f.lastUpdate IS NULL AND NOT f.internalName IS NULL
    </sql>
    <description>
      A HQL query that sets the writeProtected on all files with a
      null value to false.
    </description>
  </query>
  
  <query id="LOAD_DEFAULT_GROUPS" type="HQL">
    <sql>
      SELECT grp
      FROM GroupData grp
      WHERE grp.default = true
    </sql>
    <description>
      A HQL query that loads all groups which are marked as default
      groups.
    </description>
  </query>
  
  <query id="LOAD_DEFAULT_ROLES" type="HQL">
    <sql>
      SELECT rle
      FROM RoleData rle
      WHERE rle.default = true
    </sql>
    <description>
      A HQL query that loads all roles which are marked as default
      roles.
    </description>
  </query>
  
  <query id="SET_DEFAULT_ON_GROUPS" type="HQL">
    <sql>
      UPDATE GroupData grp
      SET grp.default = false
      WHERE grp.default IS NULL
    </sql>
    <description>
      A HQL query that sets the isDefault flag to false for all 
      groups with a null value.
    </description>
  </query>
  
  <query id="SET_DEFAULT_ON_ROLES" type="HQL">
    <sql>
      UPDATE RoleData rle
      SET rle.default = false
      WHERE rle.default IS NULL
    </sql>
    <description>
      A HQL query that sets the isDefault flag to false for all 
      roles with a null value.
    </description>
  </query>
  
  <query id="SET_ITEM_ID_ON_CONTEXTS" type="HQL">
    <sql>
      UPDATE ContextData ctx
      SET ctx.itemId = 0
      WHERE ctx.itemId IS NULL
    </sql>
    <description>
      A HQL query that sets the itemId to 0 for all 
      contexts with a null value.
    </description>
  </query>
  
  <query id="SET_AVERAGE_METHOD_ON_FORMULAS" type="HQL">
    <sql>
      UPDATE FormulaData f
      SET f.averageMethod = 2
      WHERE f.averageMethod IS NULL
    </sql>
    <description>
      A HQL query that sets the averageMethod to arithmetic mean for all 
      formulas with a null value.
    </description>
  </query>
  
  <query id="SET_AVERAGE_METHOD_ON_EXTRAVALUETYPES" type="HQL">
    <sql>
      UPDATE ExtraValueTypeData evt
      SET evt.averageMethod = 2
      WHERE evt.averageMethod IS NULL
    </sql>
    <description>
      A HQL query that sets the averageMethod to arithmetic mean for all 
      extra value types with a null value.
    </description>
  </query>
  
  <query id="UPDATE_PROPERTY_FILTER" type="SQL">
    <sql>
      UPDATE [PropertyFilters] 
      SET [property] = :newProperty
      WHERE [property] = :oldProperty
      AND [context_id] NOT IN 
      (
         SELECT [context_id] 
         FROM [PropertyFilters]
         WHERE [property] = :newProperty
      )
    </sql>
    <description>
      An SQL query that changes the property for all PropertyFilters
      which filters on a given property. It must ignore any filter that  
      causes a duplicate key violation if a filter with the new
      property already exists for any context.
    </description>
  </query>
  
  <query id="UPDATE_PROPERTY_FILTER_VALUE" type="SQL">
    <sql>
      UPDATE [PropertyFilters]
      SET [value] = :newValue
      WHERE [property] = :property AND [value] = :oldValue
    </sql>
    <description>
      An SQL query that changes the property for all PropertyFilters
      with a given value.
    </description>
  </query>
  
  <query id="SET_AUTOCOMPRESS_ON_MIMETYPES" type="HQL">
    <sql>
      UPDATE MimeTypeData mt
      SET mt.autoCompress = false
      WHERE mt.autoCompress IS NULL
    </sql>
    <description>
      A HQL query that sets the autoCompress property to false for all 
      MIME types with a null value.
    </description>
  </query>
  
  <query id="SET_AUTOCOMPRESS_ON_DIRECTORIES" type="HQL">
    <sql>
      UPDATE DirectoryData dir
      SET dir.autoCompress = false
      WHERE dir.autoCompress IS NULL
    </sql>
    <description>
      A HQL query that sets the autoCompress property to false for all 
      directories with a null value.
    </description>
  </query>

  <query id="SET_COMPRESSED_ON_FILES" type="HQL">
    <sql>
      UPDATE FileData f
      SET 
        f.compressed = false,
        f.compressedSize = f.size
      WHERE f.compressed IS NULL
    </sql>
    <description>
      A HQL query that sets the compressed property to false and the
      compressedSize to size for all files with a null value.
    </description>
  </query>
  
  <query id="SET_NUMFEATURES_ON_ARRAYDESIGNS" type="HQL">
    <sql>
      UPDATE ArrayDesignData ad
      SET ad.numDbFeatures = 0, ad.numFileFeatures = 0
      WHERE ad.numDbFeatures IS NULL OR ad.numFileFeatures IS NULL
    </sql>
    <description>
      A HQL query that sets the number of file and db features to 0
      on all array designs with a null value.
    </description>
  </query>
  
  <query id="SET_NUMFILESPOTS_ON_RAWBIOASSAY" type="HQL">
    <sql>
      UPDATE RawBioAssayData rbd
      SET rbd.numFileSpots = 0
      WHERE rbd.numFileSpots IS NULL
    </sql>
    <description>
      A HQL query that sets the number of file aspots to 0
      on all raw bioassays with a null value.
    </description>
  </query>

  <query id="GET_RAWBIOASSAYS_FOR_PLATFORM" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.platform = :platform
    </sql>
    <description>
      A Hibernate query that gets raw bioassays
      with a given platform.
    </description>
  </query>

  <query id="GET_ARRAYDESIGNS_FOR_PLATFORM" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayDesignData ad
      WHERE ad.platform = :platform
    </sql>
    <description>
      A Hibernate query that gets array designs
      with a given platform.
    </description>
  </query>
  
  <query id="GET_RAWBIOASSAYS_FOR_VARIANT" type="HQL">
    <sql>
      SELECT {1}
      FROM RawBioAssayData rba
      WHERE rba.variant = :variant
    </sql>
    <description>
      A Hibernate query that gets raw bioassays
      with a given platform variant.
    </description>
  </query>

  <query id="GET_ARRAYDESIGNS_FOR_VARIANT" type="HQL">
    <sql>
      SELECT {1}
      FROM ArrayDesignData ad
      WHERE ad.variant = :variant
    </sql>
    <description>
      A Hibernate query that gets array designs
      with a given platform variant.
    </description>
  </query>
  
  <query id="GET_PLATFORM_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT plf
      FROM PlatformData plf
      WHERE plf.externalId = :externalId
    </sql>
    <description>
      A Hibernate query that loads a platform by external ID.
    </description>
  </query>
  
  <query id="GET_PLATFORMVARIANT_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT plv
      FROM PlatformVariantData plv
      WHERE plv.externalId = :externalId
    </sql>
    <description>
      A Hibernate query that loads a platform variant by external ID.
    </description>
  </query>
  
  <query id="GET_DATAFILETYPE_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT dft
      FROM DataFileTypeData dft
      WHERE dft.externalId = :externalId
    </sql>
    <description>
      A Hibernate query that loads a data file type by external ID.
    </description>
  </query>

  <query id="GET_FILESETMEMBERS_FOR_DATAFILETYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM FileSetMemberData mbr
      WHERE mbr.dataFileType = :dataFileType
    </sql>
    <description>
      A Hibernate query that gets file set members of a specific 
      data file type.
    </description>
  </query>

  <query id="GET_PLATFORMFILETYPE_FOR_DATAFILETYPE" type="HQL">
    <sql>
      SELECT {1}
      FROM PlatformFileTypeData pft
      WHERE pft.dataFileType = :dataFileType
    </sql>
    <description>
      A Hibernate query that gets platform file types of a specific 
      data file type.
    </description>
  </query>
  
  <query id="GET_FILESETMEMBER_FOR_DATAFILETYPE" type="HQL">
    <sql>
      SELECT mbr
      FROM FileSetMemberData mbr
      WHERE mbr.dataFileType.externalId = :externalId
      AND mbr.fileSet = :fileSet
    </sql>
    <description>
      A Hibernate query that loads a member in a given file set
      if we know the external ID of the data file type.
    </description>
  </query>

  
  <query id="DELETE_PROPERTY_FILTER" type="SQL">
    <sql>
      DELETE FROM [PropertyFilters]
      WHERE [property] = :property
    </sql>
    <description>
      An SQL query that delete all PropertyFilters
      which filter on a given property.
    </description>
  </query>
  
  <query id="GET_PLUGINS_WITH_KEYS" type="HQL">
    <sql>
      SELECT DISTINCT pk.pluginDefinitionId
      FROM PluginKeys pk WHERE pk.keyId IN (:keys)
    </sql>
    <description>
      A HQL query that has been granted a specific permission. Used by 
      update scripts when new item types are added to make sure existing 
      plug-ins can continue to work.
    </description>
  </query>

  <query id="CHANGE_EXPERIMENT_RAWDATATYPE" type="HQL">
    <sql>
      UPDATE ExperimentData
      SET rawDataType = :newRawDataType
      WHERE rawDataType = :oldRawDataType
    </sql>
    <description>
      A HQL query that changes all raw data type for experiments from
      an old value to a new value.
    </description>
  </query>

  <query id="GET_PROJECTS_WITH_DEFAULT" type="HQL">
    <sql>
      SELECT prj
      FROM ProjectData prj
      WHERE prj.projectDefaults[:name] = :value
    </sql>
    <description>
      A HQL query that loads all projects which has a given default value
      for a setting.
    </description>
  </query>

  <query id="SET_USEJOBQUEUE_ON_PLUGINS" type="HQL">
    <sql>
      UPDATE PluginDefinitionData pld
      SET pld.useInternalJobQueue = true
      WHERE pld.useInternalJobQueue IS NULL
    </sql>
    <description>
      A HQL query that set the useInternalJobQueue property to true
      for all plug-ins.
    </description>
  </query>
  
  <query id="SET_FEATUREIDENTIFICATIONMETHOD_ON_ARRAYDESIGNS" type="HQL">
    <sql>
      UPDATE ArrayDesignData ad
      SET ad.featureIdentificationMethod = :method
      WHERE ad.featureIdentificationMethod IS NULL
    </sql>
    <description>
      A HQL query that set the featureIdentificationMethod property 
      on all array designs with a null value.
    </description>
  </query>
  
  <query id="UPDATE_JOB_STATUS" type="HQL">
    <sql>
      UPDATE JobData job
      SET 
        job.percentComplete = :percent,
        job.statusMessage = :statusMessage
      WHERE job.id = :id
    </sql>
    <description>
      A HQL query that updates the progress information on a specific job.
    </description>
  </query>
  
  <query id="APPEND_JOB_STATUS" type="HQL">
    <sql>
      UPDATE JobData job
      SET 
        job.statusMessage = job.statusMessage || :statusMessage
      WHERE job.id = :id
    </sql>
    <description>
      A HQL query that appends a string to the status message on a specific job.
    </description>
  </query>

  <query id="SET_NUMARRAYS_ON_ARRAYDESIGNS" type="HQL">
    <sql>
      UPDATE ArrayDesignData ad
      SET ad.numArrays = :numArrays
      WHERE ad.numArrays IS NULL
    </sql>
    <description>
      A HQL query that set the numArrays property 
      on all array designs with a null value.
    </description>
  </query>
  
  <query id="SET_NUMARRAYS_ON_HYBRIDIZATIONS" type="HQL">
    <sql>
      UPDATE HybridizationData hyb
      SET hyb.numArrays = :numArrays
      WHERE hyb.numArrays IS NULL
    </sql>
    <description>
      A HQL query that set the numArrays property 
      on all hybridizations with a null value.
    </description>
  </query>
  
  <query id="SET_ARRAYNUM_ON_RAWBIOASSAYS" type="HQL">
    <sql>
      UPDATE RawBioAssayData rba
      SET rba.arrayNum = :arrayNum
      WHERE rba.arrayNum IS NULL
    </sql>
    <description>
      A HQL query that set the arrayNum property 
      on all raw bioassays with a null value.
    </description>
  </query>
  
  <query id="SET_FEATUREDIAMETER_ON_ARRAYDESIGNBLOCKS" type="HQL">
    <sql>
      UPDATE ArrayDesignBlockData adb
      SET adb.featureDiameter = :featureDiameter
      WHERE adb.featureDiameter IS NULL
    </sql>
    <description>
      A HQL query that set the featureDiameter property 
      on all array design blocks with a null value.
    </description>
  </query>
  
  <query id="LOAD_RAWBIOASSAY_JOBS_IN_EXPERIMENT" type="HQL">
    <sql>
      SELECT DISTINCT rba.job.id
      FROM RawBioAssayData rba
      WHERE rba.job.experiment = :experiment
    </sql>
    <description>
      A HQL query that loads the ID:s of all jobs that are part
      of a given experiment and also has been assigned to at 
      least one raw bioassay.
    </description>
  </query>
  
  <query id="LOAD_ARRAYDESIGN_JOBS_IN_EXPERIMENT" type="HQL">
    <sql>
      SELECT ad.job.id
      FROM ArrayDesignData ad
      WHERE ad.job.experiment = :experiment
    </sql>
    <description>
      A HQL query that loads the ID:s of all jobs that are part
      of a given experiment and also has been assigned to at 
      least one array design.
    </description>
  </query>

  <query id="UNLINK_JOBS_FROM_EXPERIMENT" type="HQL">
    <sql>
      UPDATE JobData job
      SET job.experiment = null
      WHERE job.id IN (:list)
    </sql>
    <description>
      A HQL query that set the experiment property to null for
      a given set of jobs.
    </description>
  </query>
  
  <query id="SET_REPORTERLIST_SIZE" type="HQL">
    <sql>
      UPDATE ReporterListData rl
      SET rl.size = size(rl.reporterListScores)
      WHERE rl.size IS NULL
    </sql>
    <description>
      A HQL query that set the size of a reporter list
      that is missing this information.
    </description>
  </query>

  <query id="SET_AUTOSHARE_ON_DIRECTORIES" type="HQL">
    <sql>
      UPDATE DirectoryData dir
      SET dir.autoShare = :autoShare
      WHERE dir.autoShare IS NULL
    </sql>
    <description>
      A HQL query that set the autoShare property on all
      directories witha  null value.
    </description>
  </query>

  <query id="SET_NUMFILEVALUES_ON_BIOASSAYSETS" type="HQL">
    <sql>
      UPDATE BioAssaySetData bas
      SET bas.numFileReporters = 0, bas.numFileSpots = 0
      WHERE bas.numFileReporters IS NULL OR bas.numFileSpots IS NULL
    </sql>
    <description>
      A HQL query that set the numFileReporters and numFileSpots properties 
      to 0 on all bioassay sets with a null value.
    </description>
  </query>
  
  <query id="SET_NUMFILEVALUES_ON_BIOASSAYS" type="HQL">
    <sql>
      UPDATE BioAssayData ba
      SET ba.numFileSpots = 0
      WHERE ba.numFileSpots IS NULL
    </sql>
    <description>
      A HQL query that set the numFileSpots property
      to 0 on all bioassay with a null value.
    </description>
  </query>
  
  <query id="SET_NUMFILEVALUES_ON_EXTRAVALUES" type="HQL">
    <sql>
      UPDATE ExtraValueData ev
      SET ev.numFileValues = 0
      WHERE ev.numFileValues IS NULL
    </sql>
    <description>
      A HQL query that set the numFileValues property
      to 0 on all extra values with a null value.
    </description>
  </query>
  
  <query id="SET_DRYRUN_ON_JOBS" type="HQL">
    <sql>
      UPDATE JobData job
      SET job.dryRun = false
      WHERE job.dryRun IS NULL
    </sql>
    <description>
      A HQL query that set the dryRun property
      to false on all jobs with a null value.
    </description>
  </query>


</predefined-queries>