source: trunk/api/core/conf/common-queries.xml @ 4475

<?xml version="1.0" ?>
<!DOCTYPE predefined-queries SYSTEM "predefined-queries.dtd" >
<!--
  $Id: common-queries.xml 1618 2007-05-09 13:53:02Z fredrik $

  Copyright (C) 2007 Gregory Vincic

  This file is part of Proteios.
  Available at http://www.proteios.org/

  Proteios 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.

  Proteios 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 org.proteios.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_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_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_UNIQUE_SCORE_TYPES_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.scoreType
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.scoreType
    </sql>
    <description>
      Load all distinct (unique) score types in the Hits table for a project 
    </description>
  </query>

  <query id="GET_UNIQUE_PLATEIDS_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.plateId
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.plateId
    </sql>
    <description>
      Load all distinct (unique) plateIds in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_GELEXTERNALIDS_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.gelExternalId
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.gelExternalId
    </sql>
    <description>
      Load all distinct (unique) gelIds in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_LOCALSAMPLEIDS_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.localSampleId
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.localSampleId
    </sql>
    <description>
      Load all distinct (unique) localSampleIds in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_FRACTIONIDS_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.fractionId
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.fractionId
    </sql>
    <description>
      Load all distinct (unique) fractionIds in the Hits table for a project.
    </description>
  </query>
  
  <query id="GET_UNIQUE_REPLICATEIDS_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.replicateId
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.replicateId
    </sql>
    <description>
      Load all distinct (unique) replicateIds in the Hits table for a project.
    </description>
  </query>
  
  <query id="GET_UNIQUE_REPLICATEIDS_IN_HITS_FOR_LOCALSAMPLEID_IN_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.replicateId
      FROM HitData h
      WHERE h.project = :project AND h.localSampleId = :localSampleId
      ORDER by h.replicateId
    </sql>
    <description>
      Load all distinct (unique) replicateIds for a sampleLocalId in the Hits table for a project.
    </description>
  </query>
  
  <query id="GET_UNIQUE_PEPTIDE_SEQUENCES_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.description
      FROM HitData h
      WHERE h.project = :project AND h.protein = false
      ORDER by h.description
    </sql>
    <description>
      Load all distinct (unique) peptide sequences in the Hits table for a project.
    </description>
  </query>
  
  <query id="GET_UNIQUE_CHARGES_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.charge
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.charge
    </sql>
    <description>
      Load all distinct (unique) charges in the Hits table for a project.
    </description>
  </query>
  
  <query id="GET_UNIQUE_EXTERNALIDS_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.externalId
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.externalId
    </sql>
    <description>
      Load all distinct (unique) external Ids in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_IDENTIFICATIONRESULTFILES_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.identificationResultFile
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.identificationResultFile
    </sql>
    <description>
      Load all distinct (unique) identification result file Ids in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_PEAKLISTFILES_IN_HITS_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.peakListFile
      FROM HitData h
      WHERE h.project = :project
      ORDER by h.peakListFile
    </sql>
    <description>
      Load all distinct (unique) peakList file Ids in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_PEAKLISTFILES_IN_HITS_FOR_IDENTIFICATIONRESULTFILE_IN_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.peakListFile
      FROM HitData h
      WHERE h.project = :project AND h.identificationResultFile = :identificationResultFile
      ORDER by h.peakListFile
    </sql>
    <description>
      Load all distinct (unique) peakList file Ids for an identification result file in the Hits table for a project.
    </description>
  </query>

  <query id="GET_UNIQUE_IDENTIFICATIONRESULTFILES_IN_HITS_FOR_PEAKLISTFILE_IN_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.identificationResultFile
      FROM HitData h
      WHERE h.project = :project AND h.peakListFile = :peakListFile
      ORDER by h.identificationResultFile
    </sql>
    <description>
      Load all distinct (unique) identification result file Ids for a peakList file in the Hits table for a project.
    </description>
  </query>

  <query id="GET_HIT_FOR_FEATURE_MSFILE_FOR_PROJECT" type="HQL">
    <sql>
      SELECT h
      FROM HitData h
      WHERE h.feature.msFile = :msFile AND h.project = :project
    </sql>
    <description>
      Load all hits which have features with the given msFile in the Feature table for a project 
    </description>
  </query>

  <query id="GET_UNIQUE_MSFILES_IN_FEATURES_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.msFile
      FROM FeatureData h
      WHERE h.project = :project
    </sql>
    <description>
      Load all distinct (unique) ms files in the Feature table for a project 
    </description>
  </query>

  <query id="GET_UNIQUE_FEATUREFILES_IN_FEATURES_FOR_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.featureFile
      FROM FeatureData h
      WHERE h.project = :project
      ORDER by h.featureFile
    </sql>
    <description>
      Load all distinct (unique) feature files in the Feature table for a project 
    </description>
  </query>

  <query id="GET_UNIQUE_MSFILES_IN_FEATURES_FOR_FEATUREFILE_IN_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.msFile
      FROM FeatureData h
      WHERE h.project = :project AND h.featureFile = :featureFile
    </sql>
    <description>
      Load all distinct (unique) ms files for a feature file in the Feature table for a project 
    </description>
  </query>

  <query id="GET_UNIQUE_FEATUREFILES_IN_FEATURES_FOR_MSFILE_IN_PROJECT" type="HQL">
    <sql>
      SELECT DISTINCT h.featureFile
      FROM FeatureData h
      WHERE h.project = :project AND h.msFile = :msFile
    </sql>
    <description>
      Load all distinct (unique) feature files for an ms file in the Feature table for a project 
    </description>
  </query>

  <query id="DELETE_FEATURES_FOR_MSFILE_IN_PROJECT" type="HQL">
    <sql>
      DELETE FeatureData f
      WHERE f.project = :project AND f.msFile = :msFile
    </sql>
    <description>
      Delete all features for an ms file in the Feature table for a project 
    </description>
  </query>

  <query id="GET_IDS_FOR_SEPARATION_METHODS_WITH_SEPARATION_EVENTS" type="HQL">
    <sql>
      SELECT separationMethod.id
      FROM SeparationEventData bme
      WHERE NOT bme.separationMethod IS NULL
    </sql>
    <description>
      Load all separationMethod ids for separation methods with associated seapration events.
    </description>
  </query>
  
  <query id="GET_SEPARATIONMETHOD_FOR_EXTERNAL_ID" type="HQL">
    <sql>
      SELECT sm 
      FROM SeparationMethodData sm 
      WHERE sm.externalId = :externalId
    </sql>
    <description>
      Load Separationmethod by the given externalId.
    </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_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.
    </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 org.proteios.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 org.proteios.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="COUNT_USERS_FOR_QUOTAGROUP" type="HQL">
    <sql>
      SELECT count(*)
      FROM UserData usr
      WHERE usr.quotaGroup = :theGroup
    </sql>
    <description>
      Count the number of users having the specified group as
      their quota group.
    </description>
  </query>
  
  <query id="COUNT_USERS_FOR_QUOTA" type="HQL">
    <sql>
      SELECT count(*)
      FROM UserData u
      WHERE u.quota = :quota
    </sql>
    <description>
      A Hibernate query that counts the number of users
      that has been assigned a given quota.
    </description>
  </query>
  
  <query id="COUNT_GROUPS_FOR_QUOTA" type="HQL">
    <sql>
      SELECT count(*)
      FROM GroupData g
      WHERE g.quota = :quota
    </sql>
    <description>
      A Hibernate query that counts the number of groups
      that has been assigned a given quota.
    </description>
  </query>

  <query id="GET_SHAREABLE_ITEMS_FOR_ITEMKEY" type="HQL">
    <sql>
      SELECT s
      FROM org.proteios.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 org.proteios.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_OWNABLE_ITEMS_FOR_USER" type="HQL">
    <sql>
      SELECT o
      FROM org.proteios.core.data.OwnableData o
      WHERE o.owner = :user
    </sql>
    <description>
      Get all 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 org.proteios.core.data.MimeTypeData s
      WHERE s.extension = :extension
    </sql>
    <description>
      A Hibernate query that returns a MimeType given an extension.
    </description>
  </query>
  
  <query id="GET_MIME_TYPE_DATA_LIST" type="HQL">
    <sql>
      SELECT mt
      FROM MimeTypeData mt
    </sql>
    <description>
      A Hibernate query that returns a list of available MimeTypeData.
    </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="COUNT_FILES_IN_DIRECTORY" type="HQL">
    <sql>
      SELECT count(*)
      FROM FileData f
      WHERE f.directory = :directory
    </sql>
    <description>
      A Hibernate query that counts the number of files
      in a given directory.
    </description>
  </query>
  
  <query id="COUNT_FILES_FOR_FILETYPE" type="HQL">
    <sql>
      SELECT count(*)
      FROM FileData f
      WHERE f.fileType = :filetype
    </sql>
    <description>
      A Hibernate query that counts the number of files
      with a given filetype.
    </description>
  </query>

  <query id="COUNT_SUBDIRECTORIES_IN_DIRECTORY" type="HQL">
    <sql>
      SELECT count(*)
      FROM DirectoryData d
      WHERE d.parent = :directory
    </sql>
    <description>
      A Hibernate query that counts the number of subdirectories
      in a given directory.
    </description>
  </query>
  
  <query id="COUNT_HOME_DIRECTORIES" type="HQL">
    <sql>
      SELECT COUNT(*)
      FROM UserData usr
      WHERE usr.homeDirectory = :directory
    </sql>
    <description>
      A Hibernate query that counts the number of users having
      the specified directory as home directory.
    </description>
  </query>

  <query id="IS_PROJECT_DIRECTORY" type="HQL">
    <sql>
      SELECT count(*)
      FROM ProjectData d
      WHERE d.projectDirectory = :directory
    </sql>
    <description>
      A Hibernate query that checks if the given directory is 
      connected to any project as it's main 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_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="COUNT_PROTOCOLS_FOR_PROTOCOLTYPE" type="HQL">
    <sql>
      SELECT count(*)
      FROM ProtocolData p
      WHERE p.protocolType = :protocolType
    </sql>
    <description>
      Counts the protocols the uses a protocol type.
    </description>
  </query>

  <query id="COUNT_BIOMATERIALEVENTS_FOR_PROTOCOL" type="HQL">
    <sql>
      SELECT count(*)
      FROM BioMaterialEventData bme
      WHERE bme.protocol = :protocol
    </sql>
    <description>
      A Hibernate query that counts the number of biomaterial
      events using a protocol.
    </description>
  </query>

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

  <query id="COUNT_HARDWARE_FOR_TYPE" type="HQL">
    <sql>
      SELECT count(*)
      FROM HardwareData hw
      WHERE hw.hardwareType = :hardwaretype
    </sql>
    <description>
      A Hibernate query that counts the number of hardware items
      of the given hardware type.
    </description>
  </query>

  <query id="COUNT_SOFTWARE_FOR_SOFTWARETYPE" type="HQL">
    <sql>
      SELECT count(*)
      FROM SoftwareData sw
      WHERE sw.softwareType = :softwaretype
    </sql>
    <description>
      A Hibernate query that counts the number of software items
      of the given software type.
    </description>
  </query>

  <query id="COUNT_ANNOTATIONS_FOR_ANNOTATIONTYPE" type="HQL">
    <sql>
      SELECT count(*)
      FROM AnnotationData a
      WHERE a.annotationType = :annotationType
    </sql>
    <description>
      A Hibernate query that counts the number of annotations 
      of the given annotation type.
    </description>
  </query>

  <query id="COUNT_SAMPLES_FOR_BIOSOURCE" type="HQL">
    <sql>
      SELECT count(*)
      FROM SampleData s
      WHERE s.parent = :biosource
    </sql>
    <description>
      A Hibernate query that counts the number of samples 
      created from a given biosource.
    </description>
  </query>

  <query id="COUNT_EXTRACTS_FOR_SAMPLE" type="HQL">
    <sql>
      SELECT count(*)
      FROM ExtractData e
      WHERE e.parent = :sample
    </sql>
    <description>
      A Hibernate query that counts the number of extracts 
      created from a given sample.
    </description>
  </query>
  
  <query id="COUNT_LABELED_EXTRACTS_FOR_EXTRACT" type="HQL">
    <sql>
      SELECT count(*)
      FROM LabeledExtractData le
      WHERE le.parent = :extract
    </sql>
    <description>
      A Hibernate query that counts the number of labeled extracts 
      created from a given extract.
    </description>
  </query>

  <query id="COUNT_LABELED_EXTRACTS_FOR_LABEL" type="HQL">
    <sql>
      SELECT count(*)
      FROM LabeledExtractData le
      WHERE le.label = :label
    </sql>
    <description>
      A Hibernate query that counts the number of labeled extracts 
      with the given label.
    </description>
  </query>

  <query id="COUNT_SOURCEEVENTS_FOR_BIOMATERIAL" type="HQL">
    <sql>
      SELECT count(*)
      FROM BioMaterialEventData bme
      JOIN bme.sources src
      WHERE index(src) = :bioMaterial
    </sql>
    <description>
      A Hibernate query that counts the number of events 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="COUNT_PLUGINCONFIGURATIONS_FOR_PLUGINDEFINITION" type="HQL">
    <sql>
      SELECT count(*)
      FROM PluginConfigurationData pc
      WHERE pc.pluginDefinition = :pluginDefinition
    </sql>
    <description>
      A Hibernate query that counts the number of plugin configurations
      using a plugin definition.
    </description>
  </query>
  
  <query id="COUNT_JOBS_FOR_PLUGINCONFIGURATION" type="HQL">
    <sql>
      SELECT count(*)
      FROM JobData j
      WHERE j.pluginConfiguration = :pluginConfiguration
    </sql>
    <description>
      A Hibernate query that counts the number of jobs
      using a plugin configuration.
    </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.
    </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="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="COUNT_PLUGINS_BY_TYPE_FOR_CONTEXT" type="HQL">
    <sql>
      SELECT plg.mainType, count(*)
      FROM PluginDefinitionData plg
      JOIN plg.guiContexts gcx
      WHERE gcx.itemType = :itemType AND gcx.contextType = :contextType
      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.
    </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_TYPE" type="HQL">
    <sql>
      UPDATE ProjectData pd
      SET pd.projectType = 0
      WHERE pd.projectType IS NULL
    </sql>
    <description>
      A Hibernate query that updates the new column projectType when going from
schema 6 to 7
    </description>
  </query>
  
  <query id="SET_JOBS_ABORTED_BY_SERVER_SHUTDOWN" type="HQL">
    <sql>
      UPDATE JobData job
      SET job.statusMessage = :newStatusMessage,
      job.percentComplete = :newPercentComplete,
      job.status = :newStatus,
      job.ended = :newEnded
      WHERE job.status = :status AND job.type = :type
    </sql>
    <description>
      A Hibernate query that updates job properties.
    </description>
  </query>
  
  <query id="FIND_PENDING_JOBS" type="HQL">
    <sql>
      SELECT job
      FROM JobData job
      WHERE job.type = :type AND job.ended = null
      ORDER BY job.priority ASC, job.created ASC
    </sql>
    <description>
      A Hibernate query that loads pending jobs
      sorted by priority and creation time.
    </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>

</predefined-queries>