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common-queries.xml @ 8099

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Last change on this file since 8099 was 8099, checked in by Nicklas Nordborg, 9 months ago

References #2290: Allow plug-in configurations to be disabled

Added a filter to get rid of disabled plug-in configurations when starting a new job.

Property svn:eol-style set to native
Property svn:keywords set to Id

File size: 98.5 KB

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1	<?xml version="1.0" encoding="UTF-8" ?>
2	<!DOCTYPE predefined-queries SYSTEM "predefined-queries.dtd" >
3	<!--
4	$Id: common-queries.xml 8099 2022-12-20 13:16:51Z nicklas $
5
6	Copyright (C) 2005 Samuel Andersson, Johan Enell, Nicklas Nordborg
7	Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
8	Copyright (C) 2007 Johan Enell, Nicklas Nordborg, Martin Svensson
9
10	This file is part of BASE - BioArray Software Environment.
11	Available at http://base.thep.lu.se/
12
13	BASE is free software; you can redistribute it and/or
14	modify it under the terms of the GNU General Public License
15	as published by the Free Software Foundation; either version 3
16	of the License, or (at your option) any later version.
17
18	BASE is distributed in the hope that it will be useful,
19	but WITHOUT ANY WARRANTY; without even the implied warranty of
20	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21	GNU General Public License for more details.
22
23	You should have received a copy of the GNU General Public License
24	along with BASE. If not, see <http://www.gnu.org/licenses/>.
25	-->
26	<!--
27	This XML file contains HQL and SQL queries that are common
28	to all databases. If one of them happens to fail on your
29	particular database, do not modify this file. Instead, you
30	should add an entry into the file that is specific for your
31	particular database that overrides the query in this file.
32	For example, for PostgreSQL modify the postgresql-queries.xml.
33	-->
34	<predefined-queries>
35
36	<query id="LOAD_SYSTEM_ITEMS" type="HQL">
37	<sql>
38	SELECT item.id, item.systemId
39	FROM net.sf.basedb.core.data.SystemData item
40	WHERE NOT item.systemId IS NULL
41	</sql>
42	<description>
43	Load the ID and systemID, in that order, of all SystemData
44	items.
45	</description>
46	</query>
47
48	<query id="LOAD_ROLE_KEY_IDS" type="HQL">
49	<sql>
50	SELECT rk.id, rk.itemType
51	FROM RoleKeyData rk
52	</sql>
53	<description>
54	Load the ID and itemType, in that order, of all RoleKeyData
55	items.
56	</description>
57	</query>
58
59	<query id="GET_USER_FOR_LOGIN" type="HQL">
60	<sql>
61	SELECT usr
62	FROM UserData usr
63	WHERE usr.login = :login
64	</sql>
65	<description>
66	Load a user when you know the login.
67	</description>
68	</query>
69
70	<query id="GET_USER_FOR_EXTERNAL_ID" type="HQL">
71	<sql>
72	SELECT usr
73	FROM UserData usr
74	WHERE usr.externalId = :externalId
75	</sql>
76	<description>
77	Load a user when you know the external id.
78	</description>
79	</query>
80
81	<query id="GET_CLIENT_FOR_EXTERNAL_ID" type="HQL">
82	<sql>
83	SELECT cli
84	FROM ClientData cli
85	WHERE cli.externalId = :externalId
86	</sql>
87	<description>
88	Load a client when you know the external ID.
89	</description>
90	</query>
91
92	<query id="GET_ROLE_IDS_FOR_USER" type="HQL">
93	<sql>
94	SELECT ur.roleId
95	FROM UserRoles ur
96	WHERE ur.userId = :userId
97	</sql>
98	<description>
99	Load the ID of all roles where the given user is a member.
100	</description>
101	</query>
102
103	<query id="GET_GROUP_IDS_FOR_USER" type="HQL">
104	<sql>
105	SELECT ug.groupId
106	FROM UserGroups ug
107	WHERE ug.userId = :userId
108	</sql>
109	<description>
110	Load the ID of all groups where the given user is a direct member.
111	</description>
112	</query>
113
114	<query id="GET_QUOTA_GROUP_ID_FOR_USER" type="HQL">
115	<sql>
116	SELECT usr.quotaGroup.id
117	FROM UserData usr
118	WHERE usr.id = :userId
119	</sql>
120	<description>
121	Load the ID of a user's quota group.
122	</description>
123	</query>
124
125	<query id="GET_PARENTGROUPS_IDS_FOR_GROUPS" type="HQL">
126	<sql>
127	SELECT DISTINCT gg.parentId
128	FROM GroupGroups gg
129	WHERE gg.childId IN (:groups)
130	AND gg.parentId NOT IN (:groups)
131	</sql>
132	<description>
133	Load the ID of all groups that are parents to at least one of
134	the given groups, excluding the given groups.
135	</description>
136	</query>
137
138	<query id="GET_CHILDGROUPS_IDS_FOR_GROUPS" type="HQL">
139	<sql>
140	SELECT DISTINCT gg.childId
141	FROM GroupGroups gg
142	WHERE gg.parentId IN (:groups)
143	AND gg.childId NOT IN (:groups)
144	</sql>
145	<description>
146	Load the ID of all groups that are children to at least one of
147	the given groups, excluding the given groups.
148	</description>
149	</query>
150
151	<query id="GET_PROJECT_IDS_FOR_OWNER" type="HQL">
152	<sql>
153	SELECT p.id
154	FROM ProjectData p
155	WHERE p.owner = :userId
156	</sql>
157	<description>
158	Load the ID of all projects where the given user is the owner.
159	</description>
160	</query>
161
162	<query id="GET_PROJECTINFO_FOR_USER" type="HQL">
163	<sql>
164	SELECT up
165	FROM UserProjects up
166	WHERE up.userId = :userId
167	</sql>
168	<description>
169	Load the UserProjects of all projects where the given user is a member.
170	</description>
171	</query>
172
173	<query id="GET_PROJECTINFO_FOR_GROUPS" type="HQL">
174	<sql>
175	SELECT DISTINCT gp
176	FROM GroupProjects gp
177	WHERE gp.groupId IN (:groups)
178	</sql>
179	<description>
180	Load the GroupProjects of all projects where at least one of the given groups
181	is a member.
182	</description>
183	</query>
184
185	<query id="GET_USER_IDS_FOR_GROUPS" type="HQL">
186	<sql>
187	SELECT ug.userId
188	FROM UserGroups ug
189	WHERE ug.groupId IN (:groups)
190	</sql>
191	<description>
192	Load the ID of all users which is a member of at least one of the given groups.
193	</description>
194	</query>
195
196	<query id="GET_USER_IDS_FOR_QUOTAGROUPS" type="HQL">
197	<sql>
198	SELECT usr.id
199	FROM UserData usr
200	WHERE usr.quotaGroup.id IN (:groups)
201	</sql>
202	<description>
203	Load the ID of all users which has a quota group from one of the given groups.
204	</description>
205	</query>
206
207	<query id="GET_USER_IDS_FOR_PROJECT" type="HQL">
208	<sql>
209	SELECT up.userId
210	FROM UserProjects up
211	WHERE up.projectId = :projectId
212	</sql>
213	<description>
214	Load the ID of all users which are direct member of the given project
215	</description>
216	</query>
217
218	<query id="GET_GROUP_IDS_FOR_PROJECT" type="HQL">
219	<sql>
220	SELECT gp.groupId
221	FROM GroupProjects gp
222	WHERE gp.projectId = :projectId
223	</sql>
224	<description>
225	Load the ID of all groups which are direct member of the given project
226	</description>
227	</query>
228
229	<query id="GET_USERKEYS_FOR_USER" type="HQL">
230	<sql>
231	SELECT uk
232	FROM UserKeys uk
233	WHERE uk.userId = :userId
234	</sql>
235	<description>
236	Load the UserKeys for the given user.
237	</description>
238	</query>
239
240	<query id="GET_GROUPKEYS_FOR_GROUPS" type="HQL">
241	<sql>
242	SELECT gk
243	FROM GroupKeys gk
244	WHERE gk.groupId IN (:groups)
245	</sql>
246	<description>
247	Load the GroupKeys for the given groups.
248	</description>
249	</query>
250
251	<query id="GET_ROLEKEYS_FOR_USER" type="HQL">
252	<sql>
253	SELECT rk
254	FROM RoleKeys rk, UserRoles ur
255	WHERE rk.roleId = ur.roleId AND ur.userId = :userId
256	ORDER BY rk.keyId
257	</sql>
258	<description>
259	Load the RoleKeys for the roles where the given user is a member.
260	</description>
261	</query>
262
263	<query id="GET_PROJECTKEYS_FOR_PROJECT" type="HQL">
264	<sql>
265	SELECT pk
266	FROM ProjectKeys pk
267	WHERE pk.projectId = :projectId
268	ORDER BY pk.keyId
269	</sql>
270	<description>
271	Load the ProjectKeys for the given project. Sort by
272	keyId for fast lookup in array (Keyring class).
273	</description>
274	</query>
275
276	<query id="GET_PROJECTKEYIDS_FOR_PROJECT" type="HQL">
277	<sql>
278	SELECT pk.keyId
279	FROM ProjectKeys pk
280	WHERE pk.projectId = :projectId
281	</sql>
282	<description>
283	Load the ID of ProjectKeys for the given project.
284	</description>
285	</query>
286
287	<query id="GET_PROJECTKEY_IDS_FOR_COUNT" type="HQL">
288	<sql>
289	SELECT pk.keyId FROM ProjectKeys pk
290	GROUP BY pk.keyId
291	HAVING count(pk.projectId) = :numPermissions
292	</sql>
293	<description>
294	Load the ID of all project keys which have permissions for the
295	specified number of projects.
296	</description>
297	</query>
298
299	<query id="FIND_USED_PROJECTKEY_IDS" type="HQL">
300	<sql>
301	SELECT DISTINCT sd.projectKey.id
302	FROM net.sf.basedb.core.data.ShareableData sd
303	WHERE NOT sd.projectKey IS NULL
304	</sql>
305	<description>
306	Load the ID of all project keys which are used by at least one
307	shareable item.
308	</description>
309	</query>
310
311	<query id="SELECT_UNUSED_PROJECTKEYS" type="HQL">
312	<sql>
313	SELECT pk FROM ProjectKeyData pk
314	WHERE pk.id NOT IN (:used)
315	</sql>
316	<description>
317	Load all unused project keys given a list of the ID:s of all used
318	keys.
319	</description>
320	</query>
321
322	<query id="GET_ITEMKEY_IDS_FOR_USERCOUNT" type="HQL">
323	<sql>
324	SELECT ik.id FROM ItemKeyData ik
325	LEFT JOIN ik.users u
326	GROUP BY ik.id
327	HAVING COUNT(u.index) = :numPermissions
328	</sql>
329	<description>
330	Load the ID of all item keys which have permissions for the
331	specified number of users.
332	</description>
333	</query>
334
335	<query id="GET_ITEMKEY_IDS_FOR_GROUPCOUNT" type="HQL">
336	<sql>
337	SELECT ik.id FROM ItemKeyData ik
338	LEFT JOIN ik.groups g
339	WHERE ik.id IN (:candidates)
340	GROUP BY ik.id
341	HAVING count(g.index) = :numPermissions
342	</sql>
343	<description>
344	Load the ID of all item keys which have permissions for the
345	specified number of groups and are among the list of candidates.
346	</description>
347	</query>
348
349	<query id="FIND_USED_ITEMKEY_IDS" type="HQL">
350	<sql>
351	SELECT DISTINCT sd.itemKey.id
352	FROM net.sf.basedb.core.data.ShareableData sd
353	WHERE NOT sd.itemKey IS NULL
354	</sql>
355	<description>
356	Load the ID of all item keys which are used by at least one
357	shareable item.
358	</description>
359	</query>
360
361	<query id="SELECT_UNUSED_ITEMKEYS" type="HQL">
362	<sql>
363	SELECT ik FROM ItemKeyData ik
364	WHERE ik.id NOT IN (:used)
365	</sql>
366	<description>
367	Load all unused item keys given a list of the ID:s of all used
368	keys.
369	</description>
370	</query>
371
372	<query id="GET_USERS_FOR_QUOTAGROUP" type="HQL">
373	<sql>
374	SELECT {1}
375	FROM UserData usr
376	WHERE usr.quotaGroup = :theGroup
377	</sql>
378	<description>
379	Get users having the specified group as
380	their quota group.
381	</description>
382	</query>
383
384	<query id="GET_USERS_FOR_QUOTA" type="HQL">
385	<sql>
386	SELECT {1}
387	FROM UserData u
388	WHERE u.quota = :quota
389	</sql>
390	<description>
391	A Hibernate query that gets users
392	that has been assigned a given quota.
393	</description>
394	</query>
395
396	<query id="GET_GROUPS_FOR_QUOTA" type="HQL">
397	<sql>
398	SELECT {1}
399	FROM GroupData g
400	WHERE g.quota = :quota
401	</sql>
402	<description>
403	A Hibernate query that gets groups
404	that has been assigned a given quota.
405	</description>
406	</query>
407
408	<query id="GET_SHAREABLE_ITEMS_FOR_ITEMKEY" type="HQL">
409	<sql>
410	SELECT s
411	FROM net.sf.basedb.core.data.ShareableData s
412	WHERE s.itemKey = :itemKey
413	</sql>
414	<description>
415	Get all items beeing shared to the specified item key.
416	</description>
417	</query>
418
419	<query id="GET_SHAREABLE_ITEMS_FOR_PROJECTKEY" type="HQL">
420	<sql>
421	SELECT s
422	FROM net.sf.basedb.core.data.ShareableData s
423	WHERE s.projectKey = :projectKey
424	</sql>
425	<description>
426	Get all items beeing shared to the specified project key.
427	</description>
428	</query>
429
430	<query id="GET_OWNABLE_ITEMS_FOR_USER" type="HQL">
431	<sql>
432	SELECT o
433	FROM net.sf.basedb.core.data.OwnableData o
434	WHERE o.owner = :user
435	</sql>
436	<description>
437	Get all items that are owned by the specified user.
438	</description>
439	</query>
440
441	<query id="LOAD_USER_CLIENT_SETTINGS" type="HQL">
442	<sql>
443	SELECT s
444	FROM UserClientSettingData s
445	WHERE s.user = :user AND s.client = :client
446	</sql>
447	<description>
448	Load all settings for the specified user and client application.
449	</description>
450	</query>
451
452	<query id="LOAD_USER_DEFAULT_SETTINGS" type="HQL">
453	<sql>
454	SELECT s
455	FROM UserDefaultSettingData s
456	WHERE s.user = :user
457	</sql>
458	<description>
459	Load all default settings for the specified user.
460	</description>
461	</query>
462
463	<query id="LOAD_CLIENT_DEFAULT_SETTINGS" type="HQL">
464	<sql>
465	SELECT s
466	FROM ClientDefaultSettingData s
467	WHERE s.client = :client
468	</sql>
469	<description>
470	Load all default settings for the specified client application.
471	</description>
472	</query>
473
474	<query id="GET_MIME_TYPE_FROM_EXTENSION" type="HQL">
475	<sql>
476	SELECT s
477	FROM net.sf.basedb.core.data.MimeTypeData s
478	WHERE LOWER(s.extension) = LOWER(:extension)
479	</sql>
480	<description>
481	A Hibernate query that returns a MimeType given an extension.
482	</description>
483	</query>
484
485	<query id="GET_TOTAL_DISKUSAGE_FOR_USER" type="HQL">
486	<sql>
487	SELECT sum(du.bytes)
488	FROM DiskUsageData du
489	WHERE du.user = :user
490	AND du.location = :location
491	</sql>
492	<description>
493	A Hibernate query that returns the total used quota
494	for the specified user at the specified location.
495	</description>
496	</query>
497
498	<query id="GET_SPECIFIC_DISKUSAGE_FOR_USER" type="HQL">
499	<sql>
500	SELECT sum(du.bytes)
501	FROM DiskUsageData du
502	WHERE du.user = :user
503	AND du.location = :location
504	AND du.quotaType = :quotaType
505	</sql>
506	<description>
507	A Hibernate query that returns the used quota for the
508	specific quota type for the specified user at the
509	specified location.
510	</description>
511	</query>
512
513	<query id="GET_TOTAL_DISKUSAGE_FOR_GROUP" type="HQL">
514	<sql>
515	SELECT sum(du.bytes)
516	FROM DiskUsageData du
517	WHERE du.group = :group
518	AND du.location = :location
519	</sql>
520	<description>
521	A Hibernate query that returns the total used quota
522	for the specified group at the specified location.
523	</description>
524	</query>
525
526	<query id="GET_SPECIFIC_DISKUSAGE_FOR_GROUP" type="HQL">
527	<sql>
528	SELECT sum(du.bytes)
529	FROM DiskUsageData du
530	WHERE du.group = :group
531	AND du.location = :location
532	AND du.quotaType = :quotaType
533	</sql>
534	<description>
535	A Hibernate query that returns the used quota for the
536	specific quota type for the specified group at the
537	specified location.
538	</description>
539	</query>
540
541	<query id="GET_TOTAL_DISKUSAGE_SUMMARY" type="HQL">
542	<sql>
543	SELECT SUM(du.bytes), du.location, du.quotaType.systemId
544	FROM DiskUsageData du
545	GROUP BY du.location, du.quotaType.systemId
546	</sql>
547	<description>
548	A Hibernate query that returns the total disk usage grouped
549	by location and quota type system id.
550	</description>
551	</query>
552
553	<query id="GET_DISKUSAGE_SUMMARY_FOR_USER" type="HQL">
554	<sql>
555	SELECT SUM(du.bytes), du.location, du.quotaType.systemId
556	FROM DiskUsageData du
557	WHERE du.user = :user
558	GROUP BY du.location, du.quotaType.systemId
559	</sql>
560	<description>
561	A Hibernate query that returns the disk usage for a user grouped
562	by location and quota type system id.
563	</description>
564	</query>
565
566	<query id="GET_DISKUSAGE_SUMMARY_FOR_GROUP" type="HQL">
567	<sql>
568	SELECT SUM(du.bytes), du.location, du.quotaType.systemId
569	FROM DiskUsageData du
570	WHERE du.group = :group
571	GROUP BY du.location, du.quotaType.systemId
572	</sql>
573	<description>
574	A Hibernate query that returns the disk usage for a group grouped
575	by location and quota type system id.
576	</description>
577	</query>
578
579	<query id="GET_FILES_IN_DIRECTORY" type="HQL">
580	<sql>
581	SELECT {1}
582	FROM FileData f
583	WHERE f.directory = :directory
584	</sql>
585	<description>
586	A Hibernate query that gets the files
587	in a given directory.
588	</description>
589	</query>
590
591	<query id="GET_FILES_FOR_FILESERVER" type="HQL">
592	<sql>
593	SELECT {1}
594	FROM FileData f
595	WHERE f.fileServer = :fileServer
596	</sql>
597	<description>
598	A Hibernate query that gets the files
599	with a given file server.
600	</description>
601	</query>
602
603
604	<query id="GET_SUBDIRECTORIES_IN_DIRECTORY" type="HQL">
605	<sql>
606	SELECT {1}
607	FROM DirectoryData d
608	WHERE d.parent = :directory
609	</sql>
610	<description>
611	A Hibernate query that gets the subdirectories
612	in a given directory.
613	</description>
614	</query>
615
616	<query id="GET_HOME_DIRECTORIES" type="HQL">
617	<sql>
618	SELECT {1}
619	FROM UserData usr
620	WHERE usr.homeDirectory = :directory
621	</sql>
622	<description>
623	A Hibernate query that gets the users having
624	the specified directory as home directory.
625	</description>
626	</query>
627
628	<query id="GET_EXPERIMENT_DIRECTORIES" type="HQL">
629	<sql>
630	SELECT {1}
631	FROM ExperimentData xpr
632	WHERE xpr.directory = :directory
633	</sql>
634	<description>
635	A Hibernate query that gets the experiments having
636	the specified directory as the plugin directory.
637	</description>
638	</query>
639
640	<query id="GET_SUBDIRECTORIES" type="HQL">
641	<sql>
642	SELECT dir
643	FROM DirectoryData dir
644	WHERE dir.parent = :parent
645	</sql>
646	<description>
647	A Hibernate query that returns all subdirectories in a directory.
648	</description>
649	</query>
650
651	<query id="GET_SUBDIRECTORY_WITH_NAME" type="HQL">
652	<sql>
653	SELECT dir
654	FROM DirectoryData dir
655	WHERE dir.name = :name
656	AND dir.parent = :parent
657	</sql>
658	<description>
659	A Hibernate query that returns the a subdirectory with the
660	specified name in a given directory.
661	</description>
662	</query>
663
664	<query id="GET_QUOTA_TYPE_WITH_NAME" type="HQL">
665	<sql>
666	SELECT qt
667	FROM QuotaTypeData qt
668	WHERE qt.name = :name
669	</sql>
670	<description>
671	A Hibernate query that returns the quota type with the specified
672	name.
673	</description>
674	</query>
675
676	<query id="GET_QUOTA_WITH_NAME" type="HQL">
677	<sql>
678	SELECT q
679	FROM QuotaData q
680	WHERE q.name = :name
681	</sql>
682	<description>
683	A Hibernate query that returns the quota with the specified
684	name.
685	</description>
686	</query>
687
688	<query id="GET_GROUP_WITH_NAME" type="HQL">
689	<sql>
690	SELECT grp
691	FROM GroupData grp
692	WHERE grp.name = :name
693	</sql>
694	<description>
695	A Hibernate query that returns the group with the specified
696	name.
697	</description>
698	</query>
699
700	<query id="GET_ROLE_WITH_NAME" type="HQL">
701	<sql>
702	SELECT rle
703	FROM RoleData rle
704	WHERE rle.name = :name
705	</sql>
706	<description>
707	A Hibernate query that returns the role with the specified
708	name.
709	</description>
710	</query>
711
712	<query id="GET_SOFTWARE_WITH_NAME" type="HQL">
713	<sql>
714	SELECT sw
715	FROM SoftwareData sw
716	WHERE sw.name = :name
717	</sql>
718	<description>
719	A Hibernate query that returns the software with the specified
720	name.
721	</description>
722	</query>
723
724	<query id="GET_HARDWARE_WITH_NAME" type="HQL">
725	<sql>
726	SELECT hw
727	FROM HardwareData hw
728	WHERE hw.name = :name
729	</sql>
730	<description>
731	A Hibernate query that returns the hardware with the specified
732	name.
733	</description>
734	</query>
735
736	<query id="GET_PLATE_GEOMETRY_WITH_SIZE" type="HQL">
737	<sql>
738	SELECT pg
739	FROM PlateGeometryData pg
740	WHERE pg.rows = :rows AND pg.columns = :columns
741	</sql>
742	<description>
743	A Hibernate query that returns the plate geometry with the specified
744	size (rows and columns).
745	</description>
746	</query>
747
748	<query id="GET_PLATE_MAPPING_WITH_PROPERTIES" type="HQL">
749	<sql>
750	SELECT pm
751	FROM PlateMappingData pm
752	WHERE pm.sourceCount = :sourceCount AND pm.sourceGeometry = :sourceGeometry
753	AND pm.destinationCount = :destinationCount AND pm.destinationGeometry = :destinationGeometry
754	</sql>
755	<description>
756	A Hibernate query that returns the plate mapping with the specified
757	source and destination properties.
758	</description>
759	</query>
760
761	<query id="GET_TAG_WITH_NAME" type="HQL">
762	<sql>
763	SELECT tag
764	FROM TagData tag
765	WHERE tag.name = :name
766	</sql>
767	<description>
768	A Hibernate query that returns the tag with the specified
769	name.
770	</description>
771	</query>
772
773	<query id="GET_ANNOTATION_TYPE_WITH_NAME" type="HQL">
774	<sql>
775	SELECT at
776	FROM AnnotationTypeData at
777	WHERE at.name = :name
778	</sql>
779	<description>
780	A Hibernate query that returns the annotation type with the specified
781	name.
782	</description>
783	</query>
784
785	<query id="GET_NEWS_WITH_NAME" type="HQL">
786	<sql>
787	SELECT nws
788	FROM NewsData nws
789	WHERE nws.name = :name
790	</sql>
791	<description>
792	A Hibernate query that returns the news with the specified
793	name.
794	</description>
795	</query>
796
797	<query id="GET_FILE_IN_DIRECTORY" type="HQL">
798	<sql>
799	SELECT f
800	FROM FileData f
801	WHERE f.directory = :directory
802	AND f.name = :name
803	</sql>
804	<description>
805	A Hibernate query that returns the file with the specified
806	name in a given directory.
807	</description>
808	</query>
809
810	<query id="GET_PLATEEVENTTYPES_FOR_PROTOCOLTYPE" type="HQL">
811	<sql>
812	SELECT {1}
813	FROM PlateEventTypeData pet
814	WHERE pet.protocolType = :subtype
815	</sql>
816	<description>
817	Get the plate events types that uses a protocol type.
818	</description>
819	</query>
820
821	<query id="GET_BIOMATERIALEVENTS_FOR_PROTOCOL" type="HQL">
822	<sql>
823	SELECT {1}
824	FROM BioMaterialEventData bme
825	WHERE bme.protocol = :protocol
826	</sql>
827	<description>
828	A Hibernate query that gets biomaterial
829	events using a protocol.
830	</description>
831	</query>
832
833	<query id="GET_PLATEEVENTS_FOR_PROTOCOL" type="HQL">
834	<sql>
835	SELECT {1}
836	FROM PlateEventData pe
837	WHERE pe.protocol = :protocol
838	</sql>
839	<description>
840	A Hibernate query thatgets plate events
841	using a protocol.
842	</description>
843	</query>
844
845	<query id="GET_ARRAYBATCHES_FOR_PROTOCOL" type="HQL">
846	<sql>
847	SELECT {1}
848	FROM ArrayBatchData ab
849	WHERE ab.protocol = :protocol
850	</sql>
851	<description>
852	A Hibernate query that gets array batches
853	using a protocol.
854	</description>
855	</query>
856
857	<query id="GET_DERIVEDBIOASSAY_FOR_PROTOCOL" type="HQL">
858	<sql>
859	SELECT {1}
860	FROM DerivedBioAssayData dba
861	WHERE dba.protocol = :protocol
862	</sql>
863	<description>
864	A Hibernate query that gets derived bioassays
865	using a protocol.
866	</description>
867	</query>
868
869	<query id="GET_RAWBIOASSAYS_FOR_PROTOCOL" type="HQL">
870	<sql>
871	SELECT {1}
872	FROM RawBioAssayData rba
873	WHERE rba.protocol = :protocol
874	</sql>
875	<description>
876	A Hibernate query that gets raw bioassays
877	using a protocol.
878	</description>
879	</query>
880
881	<query id="GET_BIOMATERIALEVENTS_FOR_KIT" type="HQL">
882	<sql>
883	SELECT {1}
884	FROM BioMaterialEventData bme
885	WHERE bme.kit = :kit
886	</sql>
887	<description>
888	A Hibernate query that gets biomaterial
889	events using a kit.
890	</description>
891	</query>
892
893	<query id="GET_BIOPLATEEVENTS_FOR_KIT" type="HQL">
894	<sql>
895	SELECT {1}
896	FROM BioPlateEventData bpe
897	WHERE bpe.kit = :kit
898	</sql>
899	<description>
900	A Hibernate query that gets bioplate events
901	events using a kit.
902	</description>
903	</query>
904
905	<query id="GET_DERIVEDBIOASSAYS_FOR_KIT" type="HQL">
906	<sql>
907	SELECT {1}
908	FROM DerivedBioAssayData dba
909	WHERE dba.kit = :kit
910	</sql>
911	<description>
912	A Hibernate query that gets derived bioassays using a kit.
913	</description>
914	</query>
915
916	<query id="FIND_USED_FILES" type="HQL">
917	<sql>
918	SELECT fad
919	FROM net.sf.basedb.core.data.FileAttachableData fad
920	WHERE fad.file = :file
921	</sql>
922	<description>
923	Load the files that is used by any FileAttachableData.
924	</description>
925	</query>
926
927	<query id="GET_FILESETMEMBERS_FOR_FILE" type="HQL">
928	<sql>
929	SELECT {1}
930	FROM FileSetMemberData fsm
931	WHERE fsm.file = :file
932	</sql>
933	<description>
934	A Hibernate query that gets file set membership
935	for a given file
936	</description>
937	</query>
938
939	<query id="GET_DERIVEDBIOASSAYS_FOR_HARDWARE" type="HQL">
940	<sql>
941	SELECT {1}
942	FROM DerivedBioAssayData dba
943	WHERE dba.hardware = :hardware
944	</sql>
945	<description>
946	A Hibernate query that gets derived bioassays which
947	uses a given hardware.
948	</description>
949	</query>
950
951	<query id="GET_ARRAYBATCHES_FOR_PRINTROBOT" type="HQL">
952	<sql>
953	SELECT {1}
954	FROM ArrayBatchData ab
955	WHERE ab.printRobot = :printrobot
956	</sql>
957	<description>
958	A Hibernate query that gets array batches which
959	uses a given print robot (hardware).
960	</description>
961	</query>
962
963	<query id="GET_BIOMATERIALEVENTS_FOR_HARDWARE" type="HQL">
964	<sql>
965	SELECT {1}
966	FROM BioMaterialEventData bme
967	WHERE bme.hardware = :hardware
968	</sql>
969	<description>
970	A Hibernate query that gets biomaterial events which
971	uses a given hardware.
972	</description>
973	</query>
974
975	<query id="GET_PLATEEVENTS_FOR_HARDWARE" type="HQL">
976	<sql>
977	SELECT {1}
978	FROM PlateEventData ple
979	WHERE ple.hardware = :hardware
980	</sql>
981	<description>
982	A Hibernate query that gets plates events which
983	uses a given hardware.
984	</description>
985	</query>
986
987	<query id="GET_REPORTERS_FOR_REPORTERTYPE" type="HQL">
988	<sql>
989	SELECT {1}
990	FROM ReporterData rpt
991	WHERE rpt.reporterType = :reporterType
992	</sql>
993	<description>
994	A Hibernate query that gets reporter items
995	of the given reporter type.
996	</description>
997	</query>
998
999	<query id="GET_REPORTER_FOR_EXTERNAL_ID" type="HQL">
1000	<sql>
1001	SELECT rpt
1002	FROM ReporterData rpt
1003	WHERE rpt.externalId = :externalId
1004	</sql>
1005	<description>
1006	A Hibernate query that finds the reporter with a given external id.
1007	</description>
1008	</query>
1009
1010	<query id="GET_RAWBIOASSAYS_FOR_SOFTWARE" type="HQL">
1011	<sql>
1012	SELECT {1}
1013	FROM RawBioAssayData rba
1014	WHERE rba.software = :software
1015	</sql>
1016	<description>
1017	A Hibernate query that gets the raw bioassays
1018	produced from a given software.
1019	</description>
1020	</query>
1021
1022	<query id="GET_DERIVEDBIOASSAYS_FOR_SOFTWARE" type="HQL">
1023	<sql>
1024	SELECT {1}
1025	FROM DerivedBioAssayData dba
1026	WHERE dba.software = :software
1027	</sql>
1028	<description>
1029	A Hibernate query that gets the derived bioassay
1030	using a given software.
1031	</description>
1032	</query>
1033
1034
1035	<query id="GET_ANNOTATIONS_FOR_ANNOTATIONTYPE" type="HQL">
1036	<sql>
1037	SELECT {1}
1038	FROM AnnotationData a
1039	WHERE a.annotationType = :annotationType
1040	</sql>
1041	<description>
1042	A Hibernate query that gets annotations
1043	of the given annotation type.
1044	</description>
1045	</query>
1046
1047	<query id="GET_EXPERIMENTS_FOR_ANNOTATIONTYPE" type="HQL">
1048	<sql>
1049	SELECT {1}
1050	FROM ExperimentData exp
1051	JOIN exp.experimentalFactors ef
1052	WHERE ef = :annotationType
1053	</sql>
1054	<description>
1055	A Hibernate query that gets experiments
1056	where the given annotation type is used as an experimental factor.
1057	</description>
1058	</query>
1059
1060	<query id="GET_PROTOCOLS_FOR_ANNOTATIONTYPE" type="HQL">
1061	<sql>
1062	SELECT {1}
1063	FROM ProtocolData prt
1064	JOIN prt.parameters pp
1065	WHERE pp = :annotationType
1066	</sql>
1067	<description>
1068	A Hibernate query that gets protocols
1069	where the given annotation type is used as a protocol parameter.
1070	</description>
1071	</query>
1072
1073	<query id="GET_SAMPLES_FOR_BIOSOURCE" type="HQL">
1074	<sql>
1075	SELECT {1}
1076	FROM SampleData s
1077	WHERE s.parent = :biosource
1078	</sql>
1079	<description>
1080	A Hibernate query that gets samples
1081	created from a given biosource.
1082	</description>
1083	</query>
1084
1085	<query id="GET_EXTRACTS_FOR_SAMPLE" type="HQL">
1086	<sql>
1087	SELECT {1}
1088	FROM ExtractData e
1089	WHERE e.parent = :sample
1090	</sql>
1091	<description>
1092	A Hibernate query that gets extracts
1093	created from a given sample.
1094	</description>
1095	</query>
1096
1097	<query id="GET_EXTRACTS_FOR_TAG" type="HQL">
1098	<sql>
1099	SELECT {1}
1100	FROM ExtractData ext
1101	WHERE ext.tag = :tag
1102	</sql>
1103	<description>
1104	A Hibernate query that gets extracts with a given tag.
1105	</description>
1106	</query>
1107
1108	<query id="GET_SOURCEEVENTS_FOR_BIOMATERIAL" type="HQL">
1109	<sql>
1110	SELECT {1}
1111	FROM BioMaterialEventData bme
1112	JOIN bme.sources src
1113	WHERE src.bioMaterial = :bioMaterial
1114	</sql>
1115	<description>
1116	A Hibernate query that gets the events where a given
1117	biomaterial has been part of as a source biomaterial, ie. the number
1118	of pooled biomaterials that have been created from it.
1119	</description>
1120	</query>
1121
1122	<query id="GET_DERIVEDBIOASSAYS_FOR_EXTRACT" type="HQL">
1123	<sql>
1124	SELECT {1}
1125	FROM DerivedBioAssayData dba
1126	WHERE dba.extract = :extract
1127	</sql>
1128	<description>
1129	A Hibernate query that gets the derived bioassays
1130	that are referencing a given extract.
1131	</description>
1132	</query>
1133
1134	<query id="GET_RAWBIOASSAYS_FOR_EXTRACT" type="HQL">
1135	<sql>
1136	SELECT {1}
1137	FROM RawBioAssayData rba
1138	WHERE rba.parentExtract = :extract
1139	</sql>
1140	<description>
1141	A Hibernate query that gets the raw bioassays
1142	that are referencing a given extract.
1143	</description>
1144	</query>
1145
1146	<query id="COUNT_UNREAD_MESSAGES_FOR_USER" type="HQL">
1147	<sql>
1148	SELECT count(*)
1149	FROM MessageData msg
1150	WHERE msg.to = :user AND msg.read = false AND msg.removedBy IS NULL
1151	</sql>
1152	<description>
1153	A Hibernate query that counts the number of
1154	unread messages for a given user
1155	</description>
1156	</query>
1157
1158	<query id="GET_PLATETYPES_FOR_PLATEGEOMETRY" type="HQL">
1159	<sql>
1160	SELECT {1}
1161	FROM PlateTypeData pt
1162	WHERE pt.plateGeometry = :plateGeometry
1163	</sql>
1164	<description>
1165	A Hibernate query that gets the
1166	plate types using a given plate geometry
1167	</description>
1168	</query>
1169
1170	<query id="GET_PLATEMAPPINGS_FOR_PLATEGEOMETRY" type="HQL">
1171	<sql>
1172	SELECT {1}
1173	FROM PlateMappingData pm
1174	WHERE pm.sourceGeometry = :plateGeometry
1175	OR pm.destinationGeometry = :plateGeometry
1176	</sql>
1177	<description>
1178	A Hibernate query that gets the
1179	plate mappings using a given plate geometry as source or destination
1180	</description>
1181	</query>
1182
1183	<query id="GET_BIOPLATES_FOR_PLATEGEOMETRY" type="HQL">
1184	<sql>
1185	SELECT {1}
1186	FROM BioPlateData bp
1187	WHERE bp.plateGeometry = :plateGeometry
1188	</sql>
1189	<description>
1190	A Hibernate query that gets the
1191	bioplates using of given plate geometry
1192	</description>
1193	</query>
1194
1195	<query id="GET_PLATES_FOR_PLATETYPE" type="HQL">
1196	<sql>
1197	SELECT {1}
1198	FROM PlateData p
1199	WHERE p.plateType = :plateType
1200	</sql>
1201	<description>
1202	A Hibernate query that gets
1203	plates of a specific plate type.
1204	</description>
1205	</query>
1206
1207	<query id="GET_PLATEEVENTS_FOR_PLATEEVENTTYPE" type="HQL">
1208	<sql>
1209	SELECT {1}
1210	FROM PlateEventData pe
1211	WHERE pe.plateEventType = :plateEventType
1212	</sql>
1213	<description>
1214	A Hibernate query that gets
1215	plate events of the given plate event type.
1216	</description>
1217	</query>
1218
1219	<query id="GET_CHILDPLATES_FOR_PLATE" type="HQL">
1220	<sql>
1221	SELECT {1}
1222	FROM PlateData p
1223	JOIN p.parents pp
1224	WHERE pp = :plate
1225	</sql>
1226	<description>
1227	A Hibernate query that gets the
1228	child plates for a given plate.
1229	</description>
1230	</query>
1231
1232	<query id="GET_ARRAYDESIGNS_FOR_PLATE" type="HQL">
1233	<sql>
1234	SELECT {1}
1235	FROM ArrayDesignData ad
1236	JOIN ad.plates p
1237	WHERE p = :plate
1238	</sql>
1239	<description>
1240	A Hibernate query that gets the
1241	array designs that has used a given plate.
1242	</description>
1243	</query>
1244
1245	<query id="GET_PLATES_FOR_PLATEMAPPING" type="HQL">
1246	<sql>
1247	SELECT {1}
1248	FROM PlateData p
1249	WHERE p.plateMapping = :plateMapping
1250	</sql>
1251	<description>
1252	A Hibernate query that gets the
1253	plates that has been created from a given plate mapping.
1254	</description>
1255	</query>
1256
1257	<query id="GET_FEATURES_FOR_WELL" type="HQL">
1258	<sql>
1259	SELECT {1}
1260	FROM FeatureData f
1261	WHERE f.well = :well
1262	</sql>
1263	<description>
1264	A Hibernate query that gets the
1265	features using a given well.
1266	</description>
1267	</query>
1268
1269	<query id="COUNT_FEATURES_FOR_ARRAYDESIGN" type="HQL">
1270	<sql>
1271	SELECT count(*)
1272	FROM FeatureData f
1273	WHERE f.arrayDesignBlock.arrayDesign = :arrayDesign
1274	</sql>
1275	<description>
1276	A Hibernate query that counts the number of
1277	features on a given array design
1278	</description>
1279	</query>
1280
1281
1282	<query id="GET_CHILDWELLS_FOR_WELL" type="HQL">
1283	<sql>
1284	SELECT {1}
1285	FROM Well w
1286	WHERE w.parent = :well
1287	</sql>
1288	<description>
1289	A Hibernate query that gets the
1290	child wells of a given well.
1291	</description>
1292	</query>
1293
1294	<query id="GET_PLUGINCONFIGURATIONS_FOR_PLUGINDEFINITION" type="HQL">
1295	<sql>
1296	SELECT {1}
1297	FROM PluginConfigurationData pc
1298	WHERE pc.pluginDefinition = :pluginDefinition
1299	</sql>
1300	<description>
1301	A Hibernate query that gets plugin configurations
1302	using a plugin definition.
1303	</description>
1304	</query>
1305
1306	<query id="GET_JOBS_FOR_PLUGINCONFIGURATION" type="HQL">
1307	<sql>
1308	SELECT {1}
1309	FROM JobData j
1310	WHERE j.pluginConfiguration = :pluginConfiguration
1311	</sql>
1312	<description>
1313	A Hibernate query that gets the jobs
1314	using a specific plugin configuration.
1315	</description>
1316	</query>
1317
1318	<query id="GET_JOBS_FOR_PLUGINDEFINITION" type="HQL">
1319	<sql>
1320	SELECT {1}
1321	FROM JobData j
1322	WHERE j.pluginDefinition = :pluginDefinition
1323	</sql>
1324	<description>
1325	A Hibernate query that gets the jobs
1326	using a specific plugin definition.
1327	</description>
1328	</query>
1329
1330	<query id="FIND_JOBS_IN_QUEUE" type="HQL">
1331	<sql>
1332	SELECT job
1333	FROM JobData job
1334	WHERE job.status = :status
1335	AND job.type = :type
1336	AND job.removedBy IS NULL
1337	ORDER BY job.priority ASC, job.scheduled ASC
1338	</sql>
1339	<description>
1340	A Hibernate query that loads plugin jobs in the job queue waiting to be
1341	executed sorted by priority and waiting time. The query should return all
1342	jobs, ignoring all settings specifying that the internal job queue should
1343	not be used.
1344	</description>
1345	</query>
1346
1347	<query id="FIND_INTERNAL_JOBS_IN_QUEUE" type="HQL">
1348	<sql>
1349	SELECT job
1350	FROM JobData job
1351	WHERE job.status = :status
1352	AND job.type = :type
1353	AND job.removedBy IS NULL
1354	AND job.pluginDefinition.useInternalJobQueue = true
1355	AND job.jobAgentId IS NULL
1356	ORDER BY job.priority ASC, job.scheduled ASC
1357	</sql>
1358	<description>
1359	A Hibernate query that loads plugin jobs in the job queue waiting to be
1360	executed sorted by priority and waiting time. It should only return
1361	jobs where the plug-in setting useInternalJobQueue=true and no
1362	specific job agent has been selected for the job.
1363	</description>
1364	</query>
1365
1366	<query id="FIND_EXTERNAL_JOBS_FOR_STATUS_UPDATE" type="HQL">
1367	<sql>
1368	SELECT job
1369	FROM JobData job
1370	WHERE job.type = :type
1371	AND job.removedBy IS NULL
1372	AND NOT job.signalTransporter IS NULL
1373	</sql>
1374	<description>
1375	A Hibernate query that loads external jobs in the job queue that
1376	has a non-null signal transporter so that it may be possible to
1377	send a signal request for status update to them,
1378	</description>
1379	</query>
1380
1381	<query id="GET_ARRAYSLIDES_FOR_BATCH" type="HQL">
1382	<sql>
1383	SELECT {1}
1384	FROM ArraySlideData a
1385	WHERE a.arrayBatch = :arrayBatch
1386	</sql>
1387	<description>
1388	A Hibernate query that gets the array slides
1389	in an array batch.
1390	</description>
1391	</query>
1392
1393	<query id="GET_ARRAYSLIDES_WITH_BARCODE" type="HQL">
1394	<sql>
1395	SELECT {1}
1396	FROM ArraySlideData ars
1397	WHERE ars.barcode = :barcode
1398	</sql>
1399	<description>
1400	A Hibernate query that gets the array slides
1401	with a given barcode.
1402	</description>
1403	</query>
1404
1405
1406	<query id="GET_ARRAYBATCHES_FOR_ARRAYDESIGN" type="HQL">
1407	<sql>
1408	SELECT {1}
1409	FROM ArrayBatchData a
1410	WHERE a.arrayDesign = :arrayDesign
1411	</sql>
1412	<description>
1413	A Hibernate query that gets array batches
1414	that uses a specific array design.
1415	</description>
1416	</query>
1417
1418	<query id="GET_RAWBIOASSAYS_FOR_ARRAYDESIGN" type="HQL">
1419	<sql>
1420	SELECT {1}
1421	FROM RawBioAssayData rba
1422	WHERE rba.arrayDesign = :arrayDesign
1423	</sql>
1424	<description>
1425	A Hibernate query that gets raw bioassays
1426	that uses a specific array design.
1427	</description>
1428	</query>
1429
1430	<query id="GET_ROOT_DERIVEDBIOASSAYS_FOR_PHYSICALBIOASSAY" type="HQL">
1431	<sql>
1432	SELECT {1}
1433	FROM DerivedBioAssayData dba
1434	INNER JOIN dba.physicalBioAssays pba
1435	WHERE pba = :bioAssay
1436	AND dba.root = true
1437	</sql>
1438	<description>
1439	A Hibernate query that gets root derived bioassays
1440	created from a specific physical bioassay.
1441	</description>
1442	</query>
1443
1444	<query id="GET_CHILD_DERIVEDBIOASSAYS_FOR_DERIVEDBIOASSAY" type="HQL">
1445	<sql>
1446	SELECT {1}
1447	FROM DerivedBioAssayData dba
1448	INNER JOIN dba.parents p
1449	WHERE p = :bioAssay
1450	</sql>
1451	<description>
1452	A Hibernate query that gets child derived bioassays
1453	created from a specific derived bioassay.
1454	</description>
1455	</query>
1456
1457
1458	<query id="GET_RAWBIOASSAYS_FOR_DERIVEDBIOASSAY" type="HQL">
1459	<sql>
1460	SELECT {1}
1461	FROM RawBioAssayData rba
1462	WHERE rba.parentBioAssay = :bioAssay
1463	</sql>
1464	<description>
1465	A Hibernate query that gets raw bioassays
1466	created from a specific derived bioassay.
1467	</description>
1468	</query>
1469
1470	<query id="PRELOAD_FEATURES" type="HQL">
1471	<sql>
1472	SELECT f
1473	FROM FeatureData f
1474	JOIN FETCH f.arrayDesignBlock b
1475	LEFT JOIN FETCH f.reporter
1476	WHERE b.arrayDesign = :arrayDesign
1477	</sql>
1478	<description>
1479	A Hibernate query that loads features, blocks and reporters
1480	for a single array design.
1481	</description>
1482	</query>
1483
1484	<query id="DELETE_FEATURES_FOR_ARRAYDESIGN" type="HQL">
1485	<sql>
1486	DELETE FROM Features f, ArrayDesignBlocks adb
1487	WHERE adb.id = f.arraydesignblock_id AND adb.arraydesign_id = ?
1488	</sql>
1489	<description>
1490	A Hibernate query that deletes all features for an array design.
1491	</description>
1492	</query>
1493
1494	<query id="GET_PLUGINTYPE_FOR_INTERFACENAME" type="HQL">
1495	<sql>
1496	SELECT plt
1497	FROM PluginTypeData plt
1498	WHERE plt.interfaceName = :interfaceName
1499	</sql>
1500	<description>
1501	Load a plugin type when you know the interface name.
1502	</description>
1503	</query>
1504
1505	<query id="GET_PLUGINDEFINITION_FOR_CLASSNAME" type="HQL">
1506	<sql>
1507	SELECT pd
1508	FROM PluginDefinitionData pd
1509	WHERE pd.className = :className
1510	</sql>
1511	<description>
1512	Load a plugin definition when you know the class name.
1513	</description>
1514	</query>
1515
1516	<query id="GET_PLUGINCONFIGURATION_FOR_PLUGIN_WITH_NAME" type="HQL">
1517	<sql>
1518	SELECT pc
1519	FROM PluginConfigurationData pc
1520	WHERE pc.pluginDefinition.className = :className
1521	AND pc.name = :name
1522	</sql>
1523	<description>
1524	Load a plugin configuration for a given plug-in and with a given name
1525	</description>
1526	</query>
1527
1528
1529	<query id="GET_EXPERIMENTS_FOR_RAWBIOASSAY" type="HQL">
1530	<sql>
1531	SELECT {1}
1532	FROM ExperimentData xp
1533	JOIN xp.rawBioAssays rba
1534	WHERE rba = :rawBioAssay
1535	</sql>
1536	<description>
1537	A Hibernate query that gets the experiments
1538	using a specific raw bioassay.
1539	</description>
1540	</query>
1541
1542	<query id="GET_TRANSFORMATIONS_FOR_RAWBIOASSAY" type="HQL">
1543	<sql>
1544	SELECT {1}
1545	FROM TransformationData trf
1546	JOIN trf.rawSources rba
1547	WHERE rba = :rawBioAssay
1548	</sql>
1549	<description>
1550	A Hibernate query that gets the transformations
1551	using a specifiec raw bioassay.
1552	</description>
1553	</query>
1554
1555	<query id="GET_TRANSFORMATIONS_FOR_JOB" type="HQL">
1556	<sql>
1557	SELECT {1}
1558	FROM TransformationData trf
1559	WHERE trf.job = :job
1560	</sql>
1561	<description>
1562	A Hibernate query that gets transformations
1563	linked to a job.
1564	</description>
1565	</query>
1566
1567	<query id="GET_RAWBIOASSAYS_FOR_JOB" type="HQL">
1568	<sql>
1569	SELECT {1}
1570	FROM RawBioAssayData rba
1571	WHERE rba.job = :job
1572	</sql>
1573	<description>
1574	A Hibernate query that gets raw bioassays
1575	linked to a job.
1576	</description>
1577	</query>
1578
1579	<query id="GET_ARRAYDESIGNS_FOR_JOB" type="HQL">
1580	<sql>
1581	SELECT {1}
1582	FROM ArrayDesignData ad
1583	WHERE ad.job = :job
1584	</sql>
1585	<description>
1586	A Hibernate query that gets array designs
1587	linked to a job.
1588	</description>
1589	</query>
1590
1591	<query id="GET_DERIVEDBIOASSAYS_FOR_JOB" type="HQL">
1592	<sql>
1593	SELECT {1}
1594	FROM DerivedBioAssayData dba
1595	WHERE dba.job = :job
1596	</sql>
1597	<description>
1598	A Hibernate query that gets derived bioassays
1599	linked to a job.
1600	</description>
1601	</query>
1602
1603	<query id="FIND_CHILD_BIOASSAYSETS" type="HQL">
1604	<sql>
1605	SELECT bas
1606	FROM BioAssaySetData bas
1607	WHERE bas.transformation.source = :parent
1608	</sql>
1609	<description>
1610	A Hibernate query that returns all bioassaysets that are
1611	children to a specified parent bioassayset.
1612	</description>
1613	</query>
1614
1615	<query id="FIND_DATACUBES_FOR_BIOASSAYSETS" type="HQL">
1616	<sql>
1617	SELECT DISTINCT cbe
1618	FROM BioAssaySetData bas
1619	JOIN bas.dataCubeLayer.dataCube cbe
1620	WHERE bas IN (:basList)
1621	</sql>
1622	<description>
1623	A Hibernate query that returns all data cubes that are
1624	used by the specified list of bioassaysets
1625	</description>
1626	</query>
1627
1628	<query id="FIND_DATACUBES_USED_BY_OTHERS" type="HQL">
1629	<sql>
1630	SELECT DISTINCT cbe
1631	FROM BioAssaySetData bas
1632	JOIN bas.dataCubeLayer.dataCube cbe
1633	WHERE bas NOT IN (:basList)
1634	AND cbe IN (:possibleCubes)
1635	</sql>
1636	<description>
1637	A Hibernate query that, given a list of data cubes and bioassaysets,
1638	returns all of those data cubes that are also used by other bioassaysets.
1639	</description>
1640	</query>
1641
1642	<query id="FIND_DATACUBELAYERS_FOR_BIOASSAYSETS" type="HQL">
1643	<sql>
1644	SELECT lay
1645	FROM BioAssaySetData bas
1646	JOIN bas.dataCubeLayer lay
1647	WHERE bas IN (:basList)
1648	</sql>
1649	<description>
1650	A Hibernate query that returns all data cube layers that are
1651	used by the specified list of bioassaysets
1652	</description>
1653	</query>
1654
1655	<query id="FIND_DATACUBELAYERS_FOR_BIOASSAYSETS_IGNORE_DELETED_DATACUBES" type="HQL">
1656	<sql>
1657	SELECT lay
1658	FROM BioAssaySetData bas
1659	JOIN bas.dataCubeLayer lay
1660	WHERE bas IN (:basList)
1661	AND lay.dataCube NOT IN (:deletedCubes)
1662	</sql>
1663	<description>
1664	A Hibernate query that returns all data cube layers that are
1665	used by the specified list of bioassaysets but not are part of the
1666	list of already deleted data cubes.
1667	</description>
1668	</query>
1669
1670	<query id="FIND_DATACUBELAYERS_USED_BY_OTHERS" type="HQL">
1671	<sql>
1672	SELECT lay
1673	FROM BioAssaySetData bas
1674	JOIN bas.dataCubeLayer lay
1675	WHERE bas NOT IN (:basList)
1676	AND lay IN (:possibleLayers)
1677	</sql>
1678	<description>
1679	A Hibernate query that, given a list of data cube layers and bioassaysets,
1680	returns all of those data cube layers that are also used by other bioassaysets.
1681	</description>
1682	</query>
1683
1684	<query id="FIND_DATACUBEFILTERS_FOR_BIOASSAYSETS" type="HQL">
1685	<sql>
1686	SELECT flt
1687	FROM BioAssaySetData bas
1688	JOIN bas.dataCubeFilter flt
1689	WHERE bas IN (:basList)
1690	</sql>
1691	<description>
1692	A Hibernate query that returns all data cube filters that are
1693	used by the specified list of bioassaysets
1694	</description>
1695	</query>
1696
1697	<query id="FIND_DATACUBEFILTERS_FOR_BIOASSAYSETS_IGNORE_DELETED_DATACUBES" type="HQL">
1698	<sql>
1699	SELECT flt
1700	FROM BioAssaySetData bas
1701	JOIN bas.dataCubeFilter flt
1702	WHERE bas IN (:basList)
1703	AND flt.dataCube NOT IN (:deletedCubes)
1704	</sql>
1705	<description>
1706	A Hibernate query that returns all data cube filters that are
1707	used by the specified list of bioassaysets but not are part of the
1708	list of already deleted data cubes.
1709	</description>
1710	</query>
1711
1712	<query id="FIND_DATACUBEFILTERS_USED_BY_OTHERS" type="HQL">
1713	<sql>
1714	SELECT flt
1715	FROM BioAssaySetData bas
1716	JOIN bas.dataCubeFilter flt
1717	WHERE bas NOT IN (:basList)
1718	AND flt IN (:possibleFilters)
1719	</sql>
1720	<description>
1721	A Hibernate query that, given a list of data cube filters and bioassaysets,
1722	returns all of those data cube filters that are also used by other bioassaysets.
1723	</description>
1724	</query>
1725
1726	<query id="FIND_DATACUBEEXTRAVALUES_FOR_BIOASSAYSETS" type="HQL">
1727	<sql>
1728	SELECT dcev
1729	FROM BioAssaySetData bas
1730	JOIN bas.extraValues ev
1731	JOIN ev.dataCubeExtraValue dcev
1732	WHERE bas IN (:basList)
1733	</sql>
1734	<description>
1735	A Hibernate query that returns all data cube extra values that are
1736	used by the specified list of bioassaysets
1737	</description>
1738	</query>
1739
1740	<query id="FIND_DATACUBEEXTRAVALUES_FOR_BIOASSAYSETS_IGNORE_DELETED_DATACUBES" type="HQL">
1741	<sql>
1742	SELECT dcev
1743	FROM BioAssaySetData bas
1744	JOIN bas.extraValues ev
1745	JOIN ev.dataCubeExtraValue dcev
1746	WHERE bas IN (:basList)
1747	AND dcev.dataCube NOT IN (:deletedCubes)
1748	</sql>
1749	<description>
1750	A Hibernate query that returns all data cube extra values that are
1751	used by the specified list of bioassaysets but not are part of the
1752	list of already deleted data cubes.
1753	</description>
1754	</query>
1755
1756	<query id="FIND_DATACUBEEXTRAVALUES_USED_BY_OTHERS" type="HQL">
1757	<sql>
1758	SELECT dcev
1759	FROM BioAssaySetData bas
1760	JOIN bas.extraValues ev
1761	JOIN ev.dataCubeExtraValue dcev
1762	WHERE bas NOT IN (:basList)
1763	AND dcev IN (:possibleExtraValues)
1764	</sql>
1765	<description>
1766	A Hibernate query that, given a list of data cube extra values and bioassaysets,
1767	returns all of those data cube extra values that are also used by other bioassaysets.
1768	</description>
1769	</query>
1770
1771	<query id="GET_EXTRAVALUETYPE_FOR_EXTERNAL_ID" type="HQL">
1772	<sql>
1773	SELECT evt
1774	FROM ExtraValueTypeData evt
1775	WHERE evt.externalId = :externalId
1776	</sql>
1777	<description>
1778	Load an extra value type when you know the external id.
1779	</description>
1780	</query>
1781
1782	<query id="GET_EXTRAVALUES_FOR_EXTRAVALUETYPE" type="HQL">
1783	<sql>
1784	SELECT {1}
1785	FROM ExtraValueData ev
1786	WHERE ev.extraValueType = :extraValueType
1787	</sql>
1788	<description>
1789	A Hibernate query that gets extra values
1790	of a specific type.
1791	</description>
1792	</query>
1793
1794	<query id="LOAD_CONTEXT_NAMES" type="HQL">
1795	<sql>
1796	SELECT ctx.id, ctx.name
1797	FROM ContextData ctx
1798	WHERE ctx.client = :client AND
1799	(ctx.user = :user OR ctx.public = true)
1800	AND ctx.itemType = :itemType
1801	AND ctx.subContext = :subContext
1802	ORDER BY ctx.name
1803	</sql>
1804	<description>
1805	A Hibernate query that selects the id and name of all contexts for
1806	a user and item type. The names should be sorted in ascending order.
1807	</description>
1808	</query>
1809
1810	<query id="LOAD_CONTEXT_BY_NAME" type="HQL">
1811	<sql>
1812	SELECT ctx
1813	FROM ContextData ctx
1814	WHERE ctx.user = :user
1815	AND ctx.client = :client
1816	AND ctx.itemType = :itemType
1817	AND ctx.subContext = :subContext
1818	AND ctx.name = :name
1819	</sql>
1820	<description>
1821	A Hibernate query that load a context given the user, client,
1822	item type, subcontext and name of the context.
1823	</description>
1824	</query>
1825
1826	<query id="LOAD_USER_CONTEXTS" type="HQL">
1827	<sql>
1828	SELECT ctx
1829	FROM ContextData ctx
1830	WHERE ctx.user.id = :user
1831	AND ctx.client.id = :client
1832	AND ctx.name = :name
1833	</sql>
1834	<description>
1835	A Hibernate query that loads all saved context information
1836	with a given name for a specific user/client.
1837	</description>
1838	</query>
1839
1840	<query id="COUNT_PLUGINS_BY_TYPE_FOR_CONTEXT" type="HQL">
1841	<sql>
1842	SELECT plg.mainType, count(DISTINCT plg.id)
1843	FROM PluginDefinitionData plg
1844	JOIN plg.guiContexts gcx
1845	LEFT JOIN plg.configurations cfg
1846	WITH true = :hasConfigPermission OR cfg.owner.id = :owner
1847	OR cfg.itemKey.id IN (:itemKeys) OR cfg.projectKey.id IN (:projectKeys)
1848	WHERE
1849	(true = :hasPluginPermission OR plg.owner.id = :owner
1850	OR plg.itemKey.id IN (:itemKeys) OR plg.projectKey.id IN (:projectKeys))
1851	AND gcx.itemType = :itemType AND gcx.contextType = :contextType
1852	AND (
1853	(plg.requiresConfiguration = false)
1854	OR
1855	(plg.requiresConfiguration = true AND cfg.parameterVersion > 0)
1856	)
1857	AND plg.disabled = false
1858	AND (cfg.id IS NULL OR cfg.disabled = false)
1859	GROUP BY plg.mainType
1860	</sql>
1861	<description>
1862	A Hibernate query that counts the number of plugins available for a
1863	given GUI context grouped by the main type of the plugins taking
1864	the requirement of configurations and user permissions into account.
1865	</description>
1866	</query>
1867
1868	<query id="GET_FORMULA_WITH_NAME_AND_CHANNELS" type="HQL">
1869	<sql>
1870	SELECT fml
1871	FROM FormulaData fml
1872	WHERE fml.name = :name
1873	AND fml.channels = :channels
1874	</sql>
1875	<description>
1876	A Hibernate query that loads a formula with a given name and number
1877	of channels.
1878	</description>
1879	</query>
1880
1881	<query id="GET_FORMULA_WITH_NAME_AND_TYPE" type="HQL">
1882	<sql>
1883	SELECT fml
1884	FROM FormulaData fml
1885	WHERE fml.name = :name
1886	AND fml.rawDataType = :rawDataType
1887	</sql>
1888	<description>
1889	A Hibernate query that loads a formula with a given name and raw data type.
1890	</description>
1891	</query>
1892
1893	<query id="GET_HELP_FOR_EXTERNAL_ID" type="HQL">
1894	<sql>
1895	SELECT hlp
1896	FROM HelpData hlp
1897	WHERE hlp.externalId = :externalId AND hlp.client = :client
1898	</sql>
1899	<description>
1900	A Hibernate query that loads a help text.
1901	</description>
1902	</query>
1903
1904	<query id="GET_SCHEMA_VERSION_FOR_APP" type="HQL">
1905	<sql>
1906	SELECT sv
1907	FROM SchemaVersionData sv
1908	WHERE sv.appId = :appId
1909	</sql>
1910	<description>
1911	A Hibernate query that loads the schema version for a
1912	given application (there should only be one record since appId is unique).
1913	</description>
1914	</query>
1915
1916	<query id="SET_SCHEMA_VERSION_FOR_APP" type="HQL">
1917	<sql>
1918	UPDATE SchemaVersionData sv
1919	SET sv.schemaVersion = :schemaVersion,
1920	sv.build = :build
1921	WHERE sv.appId = :appId
1922	</sql>
1923	<description>
1924	A Hibernate query that updates the schema version and build number.
1925	</description>
1926	</query>
1927
1928	<query id="GET_PRIMARY_ANNOTATION" type="HQL">
1929	<sql>
1930	SELECT ad
1931	FROM AnnotationData ad
1932	WHERE ad.annotationType = :annotationType
1933	AND ad.annotationSet = :annotationSet
1934	AND ad.source = 0
1935	</sql>
1936	<description>
1937	A Hibernate query that loads the primary annotation of a specific
1938	annotation type for a given annotation set.
1939	</description>
1940	</query>
1941
1942	<query id="LOAD_ANNOTATIONSET_INHERITING_ANNOTATIONTYPE" type="SQL">
1943	<sql>
1944	SELECT [a].[annotationset_id] FROM [Annotations] [a]
1945	WHERE [a].[annotationtype_id] = :annotationType
1946	AND [a].[source] != 0
1947	</sql>
1948	<description>
1949	An SQL query that load the ID of all annotation sets that
1950	are inheriting a given annotation type.
1951	</description>
1952	</query>
1953
1954	<query id="DELETE_INHERITED_ANNOTATIONS" type="SQL">
1955	<sql>
1956	DELETE FROM [Annotations]
1957	WHERE [annotationtype_id] = :annotationType
1958	AND [source] != 0
1959	</sql>
1960	<description>
1961	An SQL query that delete all inherited annotations of the specified
1962	annotation type.
1963	</description>
1964	</query>
1965
1966	<query id="NULLIFY_LINK_FROM_CLONES" type="HQL">
1967	<sql>
1968	UPDATE AnnotationData ad
1969	SET ad.inheritedFrom = null
1970	WHERE ad.inheritedFrom = :targetId
1971	AND ad.source = 2
1972	</sql>
1973	<description>
1974	A HQL query that nullify the link from all cloned annotations
1975	to a specified target annotation.
1976	</description>
1977	</query>
1978
1979	<query id="UPDATE_BYTES_FOR_EXPERIMENT" type="HQL">
1980	<sql>
1981	UPDATE ExperimentData xpm
1982	SET xpm.bytes = xpm.bytes + :addedBytes
1983	WHERE xpm.id = :experiment
1984	</sql>
1985	<description>
1986	A Hibernate query that updates the number of bytes used by an experiment.
1987	</description>
1988	</query>
1989
1990	<query id="UPDATE_BYTES_FOR_DATACUBE" type="HQL">
1991	<sql>
1992	UPDATE DataCubeData dcd
1993	SET dcd.bytes = dcd.bytes + :addedBytes
1994	WHERE dcd.id = :dataCube
1995	</sql>
1996	<description>
1997	A Hibernate query that updates the number of bytes used by a data cube.
1998	</description>
1999	</query>
2000
2001	<query id="GET_REMOVED_ITEMS" type="HQL">
2002	<sql>
2003	SELECT trash
2004	FROM net.sf.basedb.core.data.RemovableData trash
2005	WHERE NOT trash.removedBy IS NULL
2006	</sql>
2007	<description>
2008	A Hibernate query that loads all items flagged for deletion.
2009	</description>
2010	</query>
2011
2012	<query id="UPDATE_REMAINING_QUANTITY" type="HQL">
2013	<sql>
2014	UPDATE MeasuredBioMaterialData mbm
2015	SET mbm.remainingQuantity = mbm.remainingQuantity - :used
2016	WHERE mbm = :bioMaterial
2017	</sql>
2018	<description>
2019	A Hibernate query that adds/removes the remaining quantity on a
2020	measuered biomaterial.
2021	</description>
2022	</query>
2023
2024	<query id="GET_REMAINING_QUANTITY" type="HQL">
2025	<sql>
2026	SELECT mbm.remainingQuantity
2027	FROM MeasuredBioMaterialData mbm
2028	WHERE mbm = :bioMaterial
2029	</sql>
2030	<description>
2031	A Hibernate query that load the remaining quantity for a
2032	measuered biomaterial.
2033	</description>
2034	</query>
2035
2036	<query id="GET_ANYTOANY_FOR_NAME" type="HQL">
2037	<sql>
2038	SELECT ata
2039	FROM AnyToAnyData ata
2040	WHERE ata.fromId = :fromId AND ata.fromType = :fromType AND ata.name = :name
2041	</sql>
2042	<description>
2043	A Hibernate query that loads the any-to-any link with the specified name
2044	for an item.
2045	</description>
2046	</query>
2047
2048	<query id="DELETE_ANYTOANY_FROM" type="HQL">
2049	<sql>
2050	DELETE FROM AnyToAnyData ata
2051	WHERE ata.fromId = :fromId AND ata.fromType = :fromType AND ata.name = :name
2052	</sql>
2053	<description>
2054	A Hibernate query that deletes a names any-to-any link leading out from
2055	an item.
2056	</description>
2057	</query>
2058
2059
2060	<query id="DELETE_ALL_ANYTOANY_FROM" type="HQL">
2061	<sql>
2062	DELETE FROM AnyToAnyData ata
2063	WHERE ata.fromId = :fromId AND ata.fromType = :fromType
2064	</sql>
2065	<description>
2066	A Hibernate query that deletes all any-to-any links leading out from
2067	an item.
2068	</description>
2069	</query>
2070
2071	<query id="DELETE_ALL_ANYTOANY_TO" type="HQL">
2072	<sql>
2073	DELETE FROM AnyToAnyData ata
2074	WHERE ata.toId = :toId AND ata.toType = :toType
2075	</sql>
2076	<description>
2077	A Hibernate query that deletes all any-to-any links leading in to an item.
2078	</description>
2079	</query>
2080
2081	<query id="DELETE_UNUSED_ANYTOANY_TO" type="HQL">
2082	<sql>
2083	DELETE FROM AnyToAnyData ata
2084	WHERE ata.toId = :toId AND ata.toType = :toType AND ata.usingTo = false
2085	</sql>
2086	<description>
2087	A Hibernate query that deletes all any-to-any links leading in to
2088	an item that doesn't count as using the item.
2089	</description>
2090	</query>
2091
2092	<query id="COUNT_USED_ANYTOANY_TO" type="HQL">
2093	<sql>
2094	SELECT count(*)
2095	FROM AnyToAnyData ata
2096	WHERE ata.toId = :toId AND ata.toType = :toType AND ata.usingTo = true
2097	</sql>
2098	<description>
2099	A Hibernate query that counts the number of any-to-any links
2100	to a given item that counts as using the item.
2101	</description>
2102	</query>
2103
2104	<query id="FIND_USING_ANYTOANY" type="HQL">
2105	<sql>
2106	SELECT ana.fromId, ana.fromType
2107	FROM AnyToAnyData ana
2108	WHERE ana.toId = :toId AND ana.toType = :toType AND ana.usingTo = true
2109	</sql>
2110	<description>
2111	A Hibernate query that finds the any-to-any links
2112	to a given item that counts as using the item.
2113	</description>
2114	</query>
2115
2116
2117	<query id="UPDATE_DATACUBENO_FOR_VIRTUALDB" type="HQL">
2118	<sql>
2119	UPDATE VirtualDbData vdb
2120	SET vdb.cubes = vdb.cubes + 1
2121	WHERE vdb.id = :virtualDb
2122	</sql>
2123	<description>
2124	A Hibernate query that updates the number of data cubes
2125	for the specified virtual database.
2126	</description>
2127	</query>
2128
2129	<query id="GET_DATACUBENO_FOR_VIRTUALDB" type="HQL">
2130	<sql>
2131	SELECT vdb.cubes
2132	FROM VirtualDbData vdb
2133	WHERE vdb.id = :virtualDb
2134	</sql>
2135	<description>
2136	A Hibernate query that gets the current number of data cubes
2137	for the specified virtual database.
2138	</description>
2139	</query>
2140
2141	<query id="UPDATE_FILTERNO_FOR_DATACUBE" type="HQL">
2142	<sql>
2143	UPDATE DataCubeData dcb
2144	SET dcb.numFilters = dcb.numFilters + 1
2145	WHERE dcb.id = :dataCube
2146	</sql>
2147	<description>
2148	A Hibernate query that updates the number of filters
2149	for the specified data cube.
2150	</description>
2151	</query>
2152
2153	<query id="GET_FILTERNO_FOR_DATACUBE" type="HQL">
2154	<sql>
2155	SELECT dcb.numFilters
2156	FROM DataCubeData dcb
2157	WHERE dcb.id = :dataCube
2158	</sql>
2159	<description>
2160	A Hibernate query that gets the current number of filters
2161	for the specified data cube.
2162	</description>
2163	</query>
2164
2165	<query id="UPDATE_EXTRAVALUENO_FOR_DATACUBE" type="HQL">
2166	<sql>
2167	UPDATE DataCubeData dcb
2168	SET dcb.numExtraValues = dcb.numExtraValues + 1
2169	WHERE dcb.id = :dataCube
2170	</sql>
2171	<description>
2172	A Hibernate query that updates the number of extra values
2173	for the specified data cube.
2174	</description>
2175	</query>
2176
2177	<query id="GET_EXTRAVALUENO_FOR_DATACUBE" type="HQL">
2178	<sql>
2179	SELECT dcb.numExtraValues
2180	FROM DataCubeData dcb
2181	WHERE dcb.id = :dataCube
2182	</sql>
2183	<description>
2184	A Hibernate query that gets the current number of extra values
2185	for the specified data cube.
2186	</description>
2187	</query>
2188
2189	<query id="UPDATE_LAYERNO_FOR_DATACUBE" type="HQL">
2190	<sql>
2191	UPDATE DataCubeData dcb
2192	SET dcb.numLayers = dcb.numLayers + 1
2193	WHERE dcb.id = :dataCube
2194	</sql>
2195	<description>
2196	A Hibernate query that updates the number of layers
2197	for the specified data cube.
2198	</description>
2199	</query>
2200
2201	<query id="GET_LAYERNO_FOR_DATACUBE" type="HQL">
2202	<sql>
2203	SELECT dcb.numLayers
2204	FROM DataCubeData dcb
2205	WHERE dcb.id = :dataCube
2206	</sql>
2207	<description>
2208	A Hibernate query that gets the current number of layers
2209	for the specified data cube.
2210	</description>
2211	</query>
2212
2213	<query id="UPDATE_COLUMNNO_FOR_DATACUBE" type="HQL">
2214	<sql>
2215	UPDATE DataCubeData dcb
2216	SET dcb.numColumns = dcb.numColumns + 1
2217	WHERE dcb.id = :dataCube
2218	</sql>
2219	<description>
2220	A Hibernate query that updates the number of columns
2221	for the specified data cube.
2222	</description>
2223	</query>
2224
2225	<query id="GET_COLUMNNO_FOR_DATACUBE" type="HQL">
2226	<sql>
2227	SELECT dcb.numColumns
2228	FROM DataCubeData dcb
2229	WHERE dcb.id = :dataCube
2230	</sql>
2231	<description>
2232	A Hibernate query that gets the current number of columns
2233	for the specified data cube.
2234	</description>
2235	</query>
2236
2237	<query id="GET_JOBAGENT_FOR_EXTERNALID" type="HQL">
2238	<sql>
2239	SELECT jag
2240	FROM JobAgentData jag
2241	WHERE jag.externalId = :externalId
2242	</sql>
2243	<description>
2244	A Hibernate query that loads the job agent with the specified external ID.
2245	</description>
2246	</query>
2247
2248	<query id="GET_KEYS_FOR_PLUGIN" type="HQL">
2249	<sql>
2250	SELECT pdk
2251	FROM PluginKeys pdk
2252	WHERE pdk.pluginDefinitionId = :pluginId
2253	ORDER BY pdk.keyId
2254	</sql>
2255	<description>
2256	A Hibernate query that loads all PluginDefinitionKeys for a specified plugin ID.
2257	</description>
2258	</query>
2259
2260	<query id="LOAD_DEFAULT_GROUPS" type="HQL">
2261	<sql>
2262	SELECT grp
2263	FROM GroupData grp
2264	WHERE grp.default = true
2265	</sql>
2266	<description>
2267	A HQL query that loads all groups which are marked as default
2268	groups.
2269	</description>
2270	</query>
2271
2272	<query id="LOAD_DEFAULT_ROLES" type="HQL">
2273	<sql>
2274	SELECT rle
2275	FROM RoleData rle
2276	WHERE rle.default = true
2277	</sql>
2278	<description>
2279	A HQL query that loads all roles which are marked as default
2280	roles.
2281	</description>
2282	</query>
2283
2284	<query id="GET_RAWBIOASSAYS_FOR_PLATFORM" type="HQL">
2285	<sql>
2286	SELECT {1}
2287	FROM RawBioAssayData rba
2288	WHERE rba.platform = :platform
2289	</sql>
2290	<description>
2291	A Hibernate query that gets raw bioassays
2292	with a given platform.
2293	</description>
2294	</query>
2295
2296	<query id="GET_ARRAYDESIGNS_FOR_PLATFORM" type="HQL">
2297	<sql>
2298	SELECT {1}
2299	FROM ArrayDesignData ad
2300	WHERE ad.platform = :platform
2301	</sql>
2302	<description>
2303	A Hibernate query that gets array designs
2304	with a given platform.
2305	</description>
2306	</query>
2307
2308	<query id="GET_RAWBIOASSAYS_FOR_VARIANT" type="HQL">
2309	<sql>
2310	SELECT {1}
2311	FROM RawBioAssayData rba
2312	WHERE rba.variant = :variant
2313	</sql>
2314	<description>
2315	A Hibernate query that gets raw bioassays
2316	with a given platform variant.
2317	</description>
2318	</query>
2319
2320	<query id="GET_ARRAYDESIGNS_FOR_VARIANT" type="HQL">
2321	<sql>
2322	SELECT {1}
2323	FROM ArrayDesignData ad
2324	WHERE ad.variant = :variant
2325	</sql>
2326	<description>
2327	A Hibernate query that gets array designs
2328	with a given platform variant.
2329	</description>
2330	</query>
2331
2332	<query id="GET_PLATFORM_FOR_EXTERNAL_ID" type="HQL">
2333	<sql>
2334	SELECT plf
2335	FROM PlatformData plf
2336	WHERE plf.externalId = :externalId
2337	</sql>
2338	<description>
2339	A Hibernate query that loads a platform by external ID.
2340	</description>
2341	</query>
2342
2343	<query id="GET_PLATFORMVARIANT_FOR_EXTERNAL_ID" type="HQL">
2344	<sql>
2345	SELECT plv
2346	FROM PlatformVariantData plv
2347	WHERE plv.externalId = :externalId
2348	</sql>
2349	<description>
2350	A Hibernate query that loads a platform variant by external ID.
2351	</description>
2352	</query>
2353
2354	<query id="GET_DATAFILETYPE_FOR_EXTERNAL_ID" type="HQL">
2355	<sql>
2356	SELECT dft
2357	FROM DataFileTypeData dft
2358	WHERE dft.externalId = :externalId
2359	</sql>
2360	<description>
2361	A Hibernate query that loads a data file type by external ID.
2362	</description>
2363	</query>
2364
2365	<query id="GET_FILESETMEMBERS_FOR_DATAFILETYPE" type="HQL">
2366	<sql>
2367	SELECT {1}
2368	FROM FileSetMemberData mbr
2369	WHERE mbr.dataFileType = :dataFileType
2370	</sql>
2371	<description>
2372	A Hibernate query that gets file set members of a specific
2373	data file type.
2374	</description>
2375	</query>
2376
2377	<query id="GET_PLATFORMFILETYPE_FOR_DATAFILETYPE" type="HQL">
2378	<sql>
2379	SELECT {1}
2380	FROM PlatformFileTypeData pft
2381	WHERE pft.dataFileType = :dataFileType
2382	</sql>
2383	<description>
2384	A Hibernate query that gets platform file types of a specific
2385	data file type.
2386	</description>
2387	</query>
2388
2389	<query id="GET_ITEMSUBTYPES_FOR_DATAFILETYPE" type="HQL">
2390	<sql>
2391	SELECT {1}
2392	FROM ItemSubtypeFileTypeData sft
2393	WHERE sft.dataFileType = :dataFileType
2394	</sql>
2395	<description>
2396	A Hibernate query that gets item subtype file types for a specific
2397	data file type.
2398	</description>
2399	</query>
2400
2401
2402	<query id="GET_FILESETMEMBER_FOR_DATAFILETYPE" type="HQL">
2403	<sql>
2404	SELECT mbr
2405	FROM FileSetMemberData mbr
2406	WHERE mbr.dataFileType.externalId = :externalId
2407	AND mbr.fileSet = :fileSet
2408	</sql>
2409	<description>
2410	A Hibernate query that loads a member in a given file set
2411	if we know the external ID of the data file type.
2412	</description>
2413	</query>
2414
2415
2416	<query id="UPDATE_JOB_STATUS" type="HQL">
2417	<sql>
2418	UPDATE JobData job
2419	SET
2420	job.percentComplete = :percent,
2421	job.statusMessage = :statusMessage
2422	WHERE job.id = :id
2423	</sql>
2424	<description>
2425	A HQL query that updates the progress information on a specific job.
2426	</description>
2427	</query>
2428
2429	<query id="APPEND_JOB_STATUS" type="HQL">
2430	<sql>
2431	UPDATE JobData job
2432	SET
2433	job.statusMessage = job.statusMessage \|\| :statusMessage
2434	WHERE job.id = :id
2435	</sql>
2436	<description>
2437	A HQL query that appends a string to the status message on a specific job.
2438	</description>
2439	</query>
2440
2441	<query id="LOAD_RAWBIOASSAY_JOBS_IN_EXPERIMENT" type="HQL">
2442	<sql>
2443	SELECT DISTINCT rba.job.id
2444	FROM RawBioAssayData rba
2445	WHERE rba.job.experiment = :experiment
2446	</sql>
2447	<description>
2448	A HQL query that loads the ID:s of all jobs that are part
2449	of a given experiment and also has been assigned to at
2450	least one raw bioassay.
2451	</description>
2452	</query>
2453
2454	<query id="LOAD_ARRAYDESIGN_JOBS_IN_EXPERIMENT" type="HQL">
2455	<sql>
2456	SELECT ad.job.id
2457	FROM ArrayDesignData ad
2458	WHERE ad.job.experiment = :experiment
2459	</sql>
2460	<description>
2461	A HQL query that loads the ID:s of all jobs that are part
2462	of a given experiment and also has been assigned to at
2463	least one array design.
2464	</description>
2465	</query>
2466
2467	<query id="UNLINK_JOBS_FROM_EXPERIMENT" type="HQL">
2468	<sql>
2469	UPDATE JobData job
2470	SET job.experiment = null
2471	WHERE job.id IN (:list)
2472	</sql>
2473	<description>
2474	A HQL query that set the experiment property to null for
2475	a given set of jobs.
2476	</description>
2477	</query>
2478
2479	<query id="GET_UNIT_WITH_NAME_FOR_QUANTITY" type="HQL">
2480	<sql>
2481	SELECT unt
2482	FROM UnitData unt
2483	WHERE unt.quantity = :quantity
2484	AND unt.name = :name
2485	</sql>
2486	<description>
2487	A HQL query that finds the unit for a quantity
2488	with a given name.
2489	</description>
2490	</query>
2491
2492	<query id="GET_UNITS_FOR_QUANTITY" type="HQL">
2493	<sql>
2494	SELECT {1}
2495	FROM UnitData unt
2496	WHERE unt.quantity = :quantity
2497	</sql>
2498	<description>
2499	A Hibernate query that gets units
2500	for a given quantity.
2501	</description>
2502	</query>
2503
2504	<query id="GET_ANNOTATIONTYPES_FOR_QUANTITY" type="HQL">
2505	<sql>
2506	SELECT {1}
2507	FROM AnnotationTypeData at
2508	WHERE at.quantity = :quantity
2509	</sql>
2510	<description>
2511	A Hibernate query that gets annotation types
2512	that are using a given quantity.
2513	</description>
2514	</query>
2515
2516	<query id="GET_ANNOTATIONTYPES_FOR_UNIT" type="HQL">
2517	<sql>
2518	SELECT {1}
2519	FROM AnnotationTypeData at
2520	WHERE at.defaultUnit = :unit
2521	</sql>
2522	<description>
2523	A Hibernate query that gets annotation types
2524	that are using a given unit as default unit.
2525	</description>
2526	</query>
2527
2528	<query id="GET_ANNOTATIONS_FOR_UNIT" type="HQL">
2529	<sql>
2530	SELECT {1}
2531	FROM AnnotationData a
2532	WHERE a.unit = :unit
2533	</sql>
2534	<description>
2535	A Hibernate query that gets annotations
2536	that are using a given unit.
2537	</description>
2538	</query>
2539
2540	<query id="GET_UNIT_WITH_SYMBOL_FOR_QUANTITY" type="HQL">
2541	<sql>
2542	SELECT unt
2543	FROM UnitData unt
2544	JOIN unt.symbols smb
2545	WHERE unt.quantity = :quantity
2546	AND smb.symbol = :symbol
2547	</sql>
2548	<description>
2549	A HQL query that finds the unit for a quantity
2550	with a given symbol.
2551	</description>
2552	</query>
2553
2554	<query id="GET_UNIT_WITH_SYMBOL_FOR_UNIT" type="HQL">
2555	<sql>
2556	SELECT smb.unit
2557	FROM UnitSymbolData smb
2558	JOIN smb.quantity qnt
2559	JOIN qnt.units unt
2560	WHERE unt = :unit
2561	AND smb.symbol = :symbol
2562	</sql>
2563	<description>
2564	A HQL query that finds the unit with a given symbol
2565	that has the same quantity as another unit.
2566	</description>
2567	</query>
2568
2569	<query id="SET_UNIT_TO_NULL_ON_PROPERTY_FILTERS" type="SQL">
2570	<sql>
2571	UPDATE [PropertyFilters]
2572	SET [unit_id] = null
2573	WHERE [unit_id] = :unit
2574	</sql>
2575	<description>
2576	A SQL query that sets the unit to null for all properties
2577	with a given unit (about to be deleted).
2578	</description>
2579	</query>
2580
2581	<query id="RECALCULATE_ANNOTATIONS_WITH_ANNOTATIONTYPE" type="SQL">
2582	<sql>
2583	UPDATE [{1}]
2584	SET [value] = [value] * :factor + :offset
2585	WHERE [id] IN
2586	(
2587	SELECT [value_id]
2588	FROM [Annotations]
2589	WHERE [annotationtype_id] = :annotationType
2590	)
2591	</sql>
2592	<description>
2593	A SQL query that recalculates the annotation values for
2594	a given annotation type.
2595	</description>
2596	</query>
2597
2598	<query id="SET_UNIT_ON_ANNOTATIONS_WITH_ANNOTATIONTYPE" type="HQL">
2599	<sql>
2600	UPDATE AnnotationData a
2601	SET a.unit = :unit
2602	WHERE a.annotationType = :annotationType
2603	</sql>
2604	<description>
2605	A HQL query that changes the unit for all annotations with a given
2606	annotation type.
2607	</description>
2608	</query>
2609
2610	<query id="RECALCULATE_ANNOTATIONS_FOR_UNIT" type="SQL">
2611	<sql>
2612	UPDATE [{1}] SET [value] = [value] * :factor + :offset
2613	WHERE [id] IN
2614	(
2615	SELECT [a].[value_id]
2616	FROM [Annotations] [a]
2617	JOIN [AnnotationTypes] [at] ON [at].[id] = [a].[annotationtype_id]
2618	WHERE [at].[value_type] = :valueType
2619	AND
2620	(
2621	(:case = 1 AND [a].[unit_id] = :unit AND [at].[default_unit_id] <> :unit)
2622	OR
2623	(:case = 2 AND [a].[unit_id] <> :unit AND [at].[default_unit_id] = :unit)
2624	)
2625	)
2626	</sql>
2627	<description>
2628	A SQL query that recalculates the annotation values for
2629	when reference factor and/or offset changes. The query must handle
2630	two cases where either the annotation type's default unit
2631	or the annotation's unit matched. More info in doc for the
2632	Unit.changeReferenceFactorAndOffset() method.
2633	</description>
2634	</query>
2635
2636	<query id="UPDATE_ITEMLIST_SIZE" type="SQL">
2637	<sql>
2638	UPDATE [ItemLists]
2639	SET [size] = [size] + :delta
2640	WHERE [member_type] = :memberType
2641	AND [id] = ANY(
2642	SELECT [list_id]
2643	FROM [ItemListMembers]
2644	WHERE [item_id] = :itemId
2645	)
2646	</sql>
2647	<description>
2648	An update query that changes the size for all item lists
2649	where a given item is a member. Mainly used to decrease
2650	the size when an item is deleted.
2651	</description>
2652	</query>
2653
2654	<query id="DELETE_ITEMLIST_MEMBER" type="SQL">
2655	<sql>
2656	DELETE FROM [ItemListMembers]
2657	WHERE [item_id] = :itemId
2658	AND [list_id] = ANY(
2659	SELECT [id]
2660	FROM [ItemLists]
2661	WHERE [member_type] = :memberType
2662	)
2663	</sql>
2664	<description>
2665	An update query that delete the list member entries
2666	for all lists where the given item is a member.
2667	</description>
2668	</query>
2669
2670	<query id="GET_BIOMATERIAL_ON_PLATE" type="HQL">
2671	<sql>
2672	SELECT {1}
2673	FROM MeasuredBioMaterialData mbm
2674	JOIN mbm.bioWell bw
2675	WHERE bw.bioPlate = :bioPlate
2676	</sql>
2677	<description>
2678	A HQL query that gets MeasuredBioMaterial:s
2679	located on a given bioplate.
2680	</description>
2681	</query>
2682	<query id="FIND_USED_TYPES_IN_ANYTOANY" type="SQL">
2683	<sql>
2684	SELECT [a].[from_type] FROM [AnyToAny] [a]
2685	UNION
2686	SELECT [a].[to_type] FROM [AnyToAny] [a]
2687	</sql>
2688	<description>
2689	An SQL query that selects all used item types in any-to-any
2690	links. It must select both the the 'from' and 'to' item type.
2691	</description>
2692	</query>
2693	<query id="SELECT_STRAY_ANYTOANY" type="SQL">
2694	<sql>
2695	SELECT [a].[id]
2696	FROM [AnyToAny] [a]
2697	LEFT JOIN [{1}] [t]
2698	ON ([t].[id] = [a].[from_id] AND [a].[from_type] = :type)
2699	OR ([t].[id] = [a].[to_id] AND [a].[to_type] = :type)
2700	WHERE [t].[id] IS NULL
2701	AND ([a].[from_type] = :type OR [a].[to_type] = :type)
2702	</sql>
2703	<description>
2704	An SQL query that selects the ID of all any-to-any links were
2705	either the 'from' or 'to' item is missing. A single query
2706	is used to delete all items of a specific type (both
2707	'from' and 'to).
2708	</description>
2709	</query>
2710	<query id="DELETE_STRAY_ANYTOANY" type="HQL">
2711	<sql>
2712	DELETE FROM AnyToAnyData
2713	WHERE id IN (:ids)
2714	</sql>
2715	<description>
2716	A HQL query that deletes all any-to-any links with the
2717	id's given in the list.
2718	</description>
2719	</query>
2720	<query id="FIND_USED_TYPES_IN_CHANGEHISTORY" type="HQL">
2721	<sql>
2722	SELECT DISTINCT ch.itemType FROM ChangeHistoryDetailData ch
2723	</sql>
2724	<description>
2725	An HQL query that selects all used item types in the change
2726	history table.
2727	</description>
2728	</query>
2729	<query id="DELETE_STRAY_CHANGEHISTORY" type="HQL">
2730	<sql>
2731	DELETE FROM ChangeHistoryDetailData
2732	WHERE id IN (:ids)
2733	</sql>
2734	<description>
2735	A HQL query that deletes all change history entries with the
2736	id's given in the list.
2737	</description>
2738	</query>
2739	<query id="SELECT_STRAY_CHANGEHISTORY" type="SQL">
2740	<sql>
2741	SELECT [ch].[id]
2742	FROM [ChangeHistoryDetails] [ch]
2743	LEFT JOIN [{1}] [t]
2744	ON ([t].[id] = [ch].[item_id] AND [ch].[item_type] = :type)
2745	WHERE [t].[id] IS NULL
2746	AND [ch].[item_type] = :type
2747	</sql>
2748	<description>
2749	An SQL query that selects the ID of all change history entries
2750	that references a missing item of a specified type.
2751	</description>
2752	</query>
2753	<query id="DBLOG_GET_ANNOTATIONTYPE_INFO" type="HQL">
2754	<sql>
2755	SELECT at.name, at.valueType, at.disableLogOfValues, at.projectAnnotations
2756	FROM AnnotationTypeData at
2757	WHERE at.id = :annotationTypeId
2758	</sql>
2759	<description>
2760	An HQL query that loads the 'name', 'valueType', 'disableLogOfValues' and
2761	the 'projectAnnotations' flag for an annotation type given the ID.
2762	</description>
2763	</query>
2764	<query id="DBLOG_GET_ANNOTATION_ITEMTYPE" type="HQL">
2765	<sql>
2766	SELECT a.itemType
2767	FROM AnnotationSetData a
2768	WHERE a.id = :annotationSetId
2769	</sql>
2770	<description>
2771	An HQL query that loads the item type value an annotation
2772	set with a given ID belongs to.
2773	</description>
2774	</query>
2775	<query id="DBLOG_GET_ITEMID_WITH_ANNOTATION" type="HQL">
2776	<sql>
2777	SELECT i.id
2778	FROM {1} i
2779	WHERE i.annotationSet = :annotationSetId
2780	</sql>
2781	<description>
2782	An HQL query that loads the ID of the item that
2783	is associated with a given annotation set.
2784	</description>
2785	</query>
2786	<query id="DBLOG_GET_NAME_FOR_ITEM" type="HQL">
2787	<sql>
2788	SELECT i.name
2789	FROM {1} i
2790	WHERE i.id = :id
2791	</sql>
2792	<description>
2793	An HQL query that loads the name of a an item.
2794	</description>
2795	</query>
2796	<query id="DBLOG_GET_FILESET_ITEMTYPE" type="HQL">
2797	<sql>
2798	SELECT fs.itemType
2799	FROM FileSetData fs
2800	WHERE fs.id = :fileSetId
2801	</sql>
2802	<description>
2803	An HQL query that loads the item type value a file set
2804	set with a given ID belongs to.
2805	</description>
2806	</query>
2807	<query id="DBLOG_GET_ITEMID_WITH_FILESET" type="HQL">
2808	<sql>
2809	SELECT i.id
2810	FROM {1} i
2811	WHERE i.fileSet = :fileSetId
2812	</sql>
2813	<description>
2814	An HQL query that loads the ID of the item that
2815	is associated with a given file set.
2816	</description>
2817	</query>
2818	<query id="DBLOG_INSERT_INTO_CHANGEHISTORYDETAILS" type="SQL">
2819	<sql>
2820	INSERT INTO [ChangeHistoryDetails]
2821	([id], [version], [history_id], [change_type], [item_id], [item_type], [change_info], [old_value], [new_value])
2822	VALUES (nextval('hibernate_sequence'), 0, ?, ?, ?, ?, ?, ?, ?)
2823	</sql>
2824	<description>
2825	SQL query for inserting rows into the ChangeHistoryDetails table.
2826	The primary key (id) must be auto-generated.
2827	Parameters: history_id, change_type, item_id, item_type, change_info, old_value, new_value
2828	</description>
2829	</query>
2830	<query id="GET_GROUPS_WITH_NONHIDDENMEMBERS" type="HQL">
2831	<sql>
2832	SELECT grp.id
2833	FROM GroupData grp
2834	WHERE grp.hiddenMembers = false
2835	AND grp.id IN (:groups)
2836	</sql>
2837	<description>
2838	A HQL query that selects the ID of the groups among a given set of
2839	groups that has 'hiddenMembers=false'
2840	</description>
2841	</query>
2842	<query id="GET_BIOPLATES_FOR_BIOPLATETYPE" type="HQL">
2843	<sql>
2844	SELECT {1}
2845	FROM BioPlateData bpl
2846	WHERE bpl.bioPlateType = :bioPlateType
2847	</sql>
2848	<description>
2849	A HQL query that gets the bioplates using a given type.
2850	</description>
2851	</query>
2852
2853	<query id="GET_BIOPLATETYPE_WITH_NAME" type="HQL">
2854	<sql>
2855	SELECT bpt
2856	FROM BioPlateTypeData bpt
2857	WHERE bpt.name = :name
2858	</sql>
2859	<description>
2860	A HQL query that gets the bioplate type with a given name.
2861	</description>
2862	</query>
2863	<query id="GET_PROJECTS_FOR_PERMISSION_TEMPLATE" type="HQL">
2864	<sql>
2865	SELECT {1}
2866	FROM ProjectData prj
2867	WHERE prj.permissionTemplate = :permissionTemplate
2868	</sql>
2869	<description>
2870	A HQL query that gets the projects that are using a given permission
2871	template.
2872	</description>
2873	</query>
2874
2875	<query id="SET_GROUP_TO_NULL_ON_DISK_USAGE" type="HQL">
2876	<sql>
2877	UPDATE DiskUsageData du
2878	SET du.group = null
2879	WHERE du.group = :group
2880	</sql>
2881	<description>
2882	An HQL update-query that sets group to null on all
2883	diskusage that are associated with a given group.
2884	</description>
2885	</query>
2886
2887	<query id="CLEAR_ORIGINAL_BIOMATERIAL_ON_BIOWELLS" type="HQL">
2888	<sql>
2889	UPDATE BioWellData bw
2890	SET bw.originalBioMaterial = null
2891	WHERE bw.originalBioMaterial = :bioMaterial
2892	</sql>
2893	<description>
2894	An HQL update-query that for a given biomaterial clears the
2895	link on all biowells were it is set as the original biomaterial.
2896	</description>
2897	</query>
2898
2899	<query id="CLEAR_PARTICIPANT_ON_BIOMATERIALEVENTS_FOR_BIOPLATEEVENT" type="HQL">
2900	<sql>
2901	UPDATE BioMaterialEventData bme
2902	SET bme.bioPlateEventParticipant = null
2903	WHERE bme.bioPlateEventParticipant =ANY (
2904	SELECT bep FROM BioPlateEventParticipantData bep
2905	WHERE bep.event = :event
2906	)
2907	</sql>
2908	<description>
2909	An HQL update-query that clears the references to a given
2910	bioplate event on all biomaterial events that links to it
2911	(via the bioplate event participant table).
2912	</description>
2913	</query>
2914
2915	<query id="CLEAR_PARTICIPANT_ON_BIOMATERIALEVENTS_FOR_BIOPLATE" type="HQL">
2916	<sql>
2917	UPDATE BioMaterialEventData bme
2918	SET bme.bioPlateEventParticipant = null
2919	WHERE bme.bioPlateEventParticipant =ANY (
2920	SELECT bep FROM BioPlateEventParticipantData bep
2921	WHERE bep.bioPlate = :bioPlate
2922	)
2923	</sql>
2924	<description>
2925	An HQL update-query that clears the references to all bioplate
2926	event participants on biomaterial events for a given bioplate.
2927	</description>
2928	</query>
2929
2930	<query id="CLEAR_PARTICIPANT_ON_BIOMATERIALEVENTS_FOR_PARTICIPANT" type="HQL">
2931	<sql>
2932	UPDATE BioMaterialEventData bme
2933	SET bme.bioPlateEventParticipant = null
2934	WHERE bme.bioPlateEventParticipant = :participant
2935	</sql>
2936	<description>
2937	An HQL update-query that clears the references to a given bioplate
2938	event participant on all related biomaterial events.
2939	</description>
2940	</query>
2941
2942	<query id="GET_BIOPLATEEVENTS_FOR_BIOPLATEEVENTTYPE" type="HQL">
2943	<sql>
2944	SELECT {1}
2945	FROM BioPlateEventData bpe
2946	WHERE bpe.eventType = :eventType
2947	</sql>
2948	<description>
2949	An HQL update-query that gets the bioplate events that are
2950	of a given bioplate event type.
2951	</description>
2952	</query>
2953
2954	<query id="GET_JAR_PATH_FROM_TABLE" type="SQL">
2955	<sql>
2956	SELECT [id], [jar_path] FROM [{1}] [t]
2957	where [t].[jar_file] IS NULL AND NOT [t].[jar_path] IS NULL
2958	</sql>
2959	<description>
2960	An SQL query that selects the ID and JAR_PATH column from a given table
2961	where the existing JAR_PATH has a value and the existing JAR_FILE is
2962	null.
2963	</description>
2964	</query>
2965
2966	<query id="SET_JAR_FILE_IN_TABLE" type="SQL">
2967	<sql>
2968	UPDATE [{1}] SET [jar_file] = :file WHERE id = :id
2969	</sql>
2970	<description>
2971	An SQL query that updates the JAR_FILE with the given value.
2972	</description>
2973	</query>
2974
2975	<query id="DROP_COLUMN" type="SQL">
2976	<sql>
2977	ALTER TABLE [{1}] DROP COLUMN [{2}]
2978	</sql>
2979	<description>
2980	An SQL query that drops a column (2) from a table (1).
2981	</description>
2982	</query>
2983
2984	<query id="DROP_NOT_NULL_CONSTRAINT" type="SQL">
2985	<sql>
2986	ALTER TABLE [{1}] ALTER COLUMN [{2}] DROP NOT NULL
2987	</sql>
2988	<description>
2989	An SQL query that drops a NOT NULL contraint from column (2) in a table (1).
2990	</description>
2991	</query>
2992
2993	<query id="DROP_TABLE" type="SQL">
2994	<sql>
2995	DROP TABLE [{1}]
2996	</sql>
2997	<description>
2998	An SQL query that drops a table (1).
2999	</description>
3000	</query>
3001
3002	<query id="CONVERT_LABELEDEXTRACTS_TO_EXTRACTS" type="SQL">
3003	<sql>
3004	UPDATE [BioMaterials]
3005	SET [discriminator] = 3
3006	WHERE [discriminator] = 4
3007	</sql>
3008	<description>
3009	An SQL query that convert labeled extract to extract.
3010	</description>
3011	</query>
3012
3013	<query id="GET_HYBRIDIZATIONS" type="SQL">
3014	<sql>
3015	SELECT
3016	[id], [version],
3017	[arrayslide_id], [num_arrays],
3018	[annotationset_id], [name],
3019	[description], [removed],
3020	[itemkey_id], [projectkey_id],
3021	[owner]
3022	FROM
3023	[Hybridizations]
3024	</sql>
3025	<description>
3026	An SQL query that load all BASE 2.17 hybridizations.
3027	</description>
3028	</query>
3029
3030	<query id="UPDATE_BIOASSAYID_FROM_HYBID" type="SQL">
3031	<sql>
3032	UPDATE [BioMaterialEvents]
3033	SET [physicalbioassay_id] = :bioAssayId
3034	WHERE [hybridization_id] = :hybId
3035	</sql>
3036	<description>
3037	An SQL query that sets the physicalbioassay_id
3038	for a given hybridization_id
3039	</description>
3040	</query>
3041
3042	<query id="GET_SCANS" type="SQL">
3043	<sql>
3044	SELECT
3045	[id], [version],
3046	[entry_date], [hybridization_id],
3047	[hardware_id], [protocol_id],
3048	[annotationset_id], [name],
3049	[description], [removed],
3050	[itemkey_id], [projectkey_id],
3051	[owner]
3052	FROM
3053	[Scans]
3054	</sql>
3055	<description>
3056	An SQL query that load all BASE 2.17 scans.
3057	</description>
3058	</query>
3059
3060	<query id="GET_IMAGES" type="SQL">
3061	<sql>
3062	SELECT
3063	[id], [version],
3064	[file_id]
3065	FROM
3066	[Images]
3067	WHERE [scan_id] = :scanId
3068	</sql>
3069	<description>
3070	An SQL query that load BASE 2.17 image files for a given scan.
3071	</description>
3072	</query>
3073
3074	<query id="GET_PROTOCOLTYPES" type="SQL">
3075	<sql>
3076	SELECT
3077	[id], [version],
3078	[entry_date], [name],
3079	[description], [removed],
3080	[system_id]
3081	FROM
3082	[ProtocolTypes]
3083	</sql>
3084	<description>
3085	An SQL query that load all BASE 2.17 protocol types.
3086	</description>
3087	</query>
3088
3089	<query id="GET_HARDWARETYPES" type="SQL">
3090	<sql>
3091	SELECT
3092	[id], [version],
3093	[entry_date], [name],
3094	[description], [removed],
3095	[system_id]
3096	FROM
3097	[HardwareTypes]
3098	</sql>
3099	<description>
3100	An SQL query that load all BASE 2.17 hardware types.
3101	</description>
3102	</query>
3103
3104	<query id="GET_SOFTWARETYPES" type="SQL">
3105	<sql>
3106	SELECT
3107	[id], [version],
3108	[entry_date], [name],
3109	[description], [system_id]
3110	FROM
3111	[SoftwareTypes]
3112	</sql>
3113	<description>
3114	An SQL query that load all BASE 2.17 software types.
3115	</description>
3116	</query>
3117
3118	<query id="GET_FILETYPES" type="SQL">
3119	<sql>
3120	SELECT
3121	[id], [version],
3122	[entry_date], [name],
3123	[description], [system_id]
3124	FROM
3125	[FileTypes]
3126	</sql>
3127	<description>
3128	An SQL query that load all BASE 2.17 file types.
3129	</description>
3130	</query>
3131
3132	<query id="GET_RAWBIOASSAYS" type="SQL">
3133	<sql>
3134	SELECT
3135	[id], [scan_id],
3136	[array_num]
3137	FROM [RawBioAssays]
3138	WHERE NOT [scan_id] IS NULL
3139	</sql>
3140	<description>
3141	An SQL query that load scan and array num for all raw bioassays
3142	that has a scan parent.
3143	</description>
3144	</query>
3145
3146	<query id="FIND_EXTRACT_FOR_RAWBIOASSAY_POSITION" type="SQL">
3147	<sql>
3148	SELECT bm2.[biomaterial_id]
3149	FROM [DerivedBioAssays] dba
3150	INNER JOIN [ParentPhysicalBioAssays] pba ON pba.[derivedbioassay_id] = dba.[id]
3151	INNER JOIN [BioMaterialEvents] bme ON bme.[physicalbioassay_id] = pba.[physicalbioassay_id]
3152	INNER JOIN [BioMaterialEventSources2] bm2 ON bm2.[event_id]=bme.[id]
3153	WHERE bm2.[position] = :position AND dba.[id] = :derivedBioAssayId
3154	</sql>
3155	<description>
3156	An SQL query that tries to find the extract id given a
3157	derived bioassay and the bioassay position.
3158	</description>
3159	</query>
3160
3161	<query id="UPDATE_RAWBIOASSAY" type="SQL">
3162	<sql>
3163	UPDATE [RawBioAssays]
3164	SET [bioassay_id] = :parentBioAssayId,
3165	[extract_id] = :extractId
3166	WHERE [id] = :rawBioAssayId
3167	</sql>
3168	<description>
3169	An SQL query that update the parent bioassay and extract
3170	for a given raw bioassay.
3171	</description>
3172	</query>
3173
3174
3175	<query id="COPY_BIOMATERIALEVENTSOURCES" type="SQL">
3176	<sql>
3177	INSERT INTO [BioMaterialEventSources2]
3178	(
3179	[id], [version],
3180	[biomaterial_id], [event_id],
3181	[used_quantity], [position]
3182	)
3183	SELECT
3184	{1}, 0,
3185	[biomaterial_id], [event_id],
3186	[used_quantity], [dummy]
3187	FROM [BioMaterialEventSources]
3188	</sql>
3189	<description>
3190	An SQL query that load copy BASE 2.17 biomaterial
3191	event sources to the new table.
3192	</description>
3193	</query>
3194
3195	<query id="COPY_SAMPLE_BIOSOURCE_PARENT_LINK" type="SQL">
3196	<sql>
3197	INSERT INTO [BioMaterialEventSources2]
3198	(
3199	[id], [version],
3200	[biomaterial_id], [event_id],
3201	[used_quantity], [position]
3202	)
3203	SELECT
3204	{1}, 0,
3205	bm.[parent_id], evt.[id],
3206	null, 1
3207	FROM [BioMaterials] bm
3208	INNER JOIN [BioMaterialEvents] evt ON bm.[id]=evt.[biomaterial_id] AND evt.[event_type]=1
3209	WHERE bm.[discriminator] = 2 AND NOT bm.[parent_id] IS NULL
3210	</sql>
3211	<description>
3212	An SQL query that copy Sample--BioSource parent
3213	links to the BioMaterialEventSources2 table.
3214	</description>
3215	</query>
3216
3217	<query id="NULLIFY_ALL_BIOMATERIAL_PARENTS" type="SQL">
3218	<sql>
3219	UPDATE [BioMaterials]
3220	SET [parent_type] = NULL, [parent_id] = NULL
3221	</sql>
3222	<description>
3223	An SQL query that nullify all biomaterial parent
3224	information.
3225	</description>
3226	</query>
3227
3228	<query id="GET_BIOMATERIAL_PARENT_INFO" type="SQL">
3229	<sql>
3230	SELECT bm.[id], bm.[discriminator], evt.[biomaterial_id]
3231	FROM [BioMaterialEventSources2] bm2
3232	INNER JOIN [BioMaterialEvents] evt ON bm2.[event_id]=evt.[id] AND evt.[event_type]=1
3233	INNER JOIN [BioMaterials] bm ON bm2.[biomaterial_id]=bm.[id]
3234	ORDER BY evt.[biomaterial_id]
3235	</sql>
3236	<description>
3237	An SQL query that get parent biomaterial information. We need
3238	parent_id, parent_type and child_id ordered by child_id
3239	</description>
3240	</query>
3241
3242
3243	<query id="SET_BIOMATERIAL_PARENT" type="SQL">
3244	<sql>
3245	UPDATE [BioMaterials]
3246	SET [parent_type] = :parentType, [parent_id] = :parentId
3247	WHERE [id] = :childId
3248	</sql>
3249	<description>
3250	An SQL query that set the biomaterial parent info for a single
3251	biomaterial.
3252	</description>
3253	</query>
3254
3255	<query id="SET_LABELEDEXTRACT_SUBTYPE" type="SQL">
3256	<sql>
3257	UPDATE [BioMaterials]
3258	SET [subtype_id]=:subtype
3259	WHERE [label_id] IS NOT NULL
3260	</sql>
3261	<description>
3262	An SQL query that sets the subtype of labeled extracts
3263	</description>
3264	</query>
3265
3266	<query id="SET_SUBTYPE_ON_ALL" type="SQL">
3267	<sql>
3268	UPDATE [{1}]
3269	SET [subtype_id]=:subtype
3270	</sql>
3271	<description>
3272	An SQL query that sets the subtype
3273	of all items in a table
3274	</description>
3275	</query>
3276
3277	<query id="UPDATE_ANNOTATIONSET_ITEM" type="SQL">
3278	<sql>
3279	UPDATE [AnnotationSets]
3280	SET [item_id] = :newId, [item_type] = {1}
3281	WHERE [id] = :id
3282	</sql>
3283	<description>
3284	An SQL query that update the item_type and item_id
3285	on annotation set.
3286	</description>
3287	</query>
3288
3289	<query id="UPDATE_ANYTOANY_FROMITEM" type="SQL">
3290	<sql>
3291	UPDATE [AnyToAny]
3292	SET [from_id] = :newId, [from_type] = {2}
3293	WHERE [from_id] = :oldId AND [from_type] = {1}
3294	</sql>
3295	<description>
3296	An SQL query that update the from_type and from_id
3297	on any-to-any.
3298	</description>
3299	</query>
3300
3301	<query id="UPDATE_ANYTOANY_TOITEM" type="SQL">
3302	<sql>
3303	UPDATE [AnyToAny]
3304	SET [to_id] = :newId, [to_type] = {2}
3305	WHERE [to_id] = :oldId AND [to_type] = {1}
3306	</sql>
3307	<description>
3308	An SQL query that update the to_type and to_id
3309	on any-to-any.
3310	</description>
3311	</query>
3312
3313	<query id="UPDATE_CHANGEHISTORYDETAILS_ITEM" type="SQL">
3314	<sql>
3315	UPDATE [ChangeHistoryDetails]
3316	SET [item_id] = :newId, [item_type] = {2}
3317	WHERE [item_id] = :oldId AND [item_type] = {1}
3318	</sql>
3319	<description>
3320	An SQL query that update the item_type and item_id
3321	on change history details.
3322	</description>
3323	</query>
3324
3325	<query id="UPDATE_ITEMVALUES_ITEM" type="SQL">
3326	<sql>
3327	UPDATE [ItemValues]
3328	SET [data_class_id] = :newId, [data_class] = :newClass
3329	WHERE [data_class_id] = :oldId AND [data_class] = :oldClass
3330	</sql>
3331	<description>
3332	An SQL query that update the data_class_id and data_class
3333	on item values.
3334	</description>
3335	</query>
3336
3337	<query id="UPDATE_ITEMVALUES_CLASS" type="SQL">
3338	<sql>
3339	UPDATE [ItemValues]
3340	SET [data_class] = :newClass
3341	WHERE [data_class] = :oldClass
3342	</sql>
3343	<description>
3344	An SQL query that update the data_class
3345	on item values.
3346	</description>
3347	</query>
3348
3349	<query id="UPDATE_ITEMTYPE" type="SQL">
3350	<sql>
3351	UPDATE [{1}]
3352	SET [{2}] = {4}
3353	WHERE [{2}] = {3}
3354	</sql>
3355	<description>
3356	An SQL query that update the item-type column on
3357	a generic table.
3358	</description>
3359	</query>
3360
3361	<query id="UPDATE_SUBTYPEID_FROM_OLDTYPEID" type="SQL">
3362	<sql>
3363	UPDATE [{1}]
3364	SET [{2}] = :subtypeId
3365	WHERE [{3}] = :oldTypeId
3366	</sql>
3367	<description>
3368	An SQL query that update the subtype_id column on
3369	a generic table.
3370	</description>
3371	</query>
3372
3373
3374	<query id="DELETE_PLUGINGUICONTEXTS_FOR_ITEMTYPE" type="SQL">
3375	<sql>
3376	DELETE FROM [PluginDefinitionGuiContexts]
3377	WHERE [item_type] = :itemType
3378	</sql>
3379	<description>
3380	An SQL query that delete plug-in gui contexts for
3381	a given item type.
3382	</description>
3383	</query>
3384
3385	<query id="DELETE_PLUGINKEYS_FOR_ITEMTYPE" type="SQL">
3386	<sql>
3387	DELETE FROM [PluginKeys]
3388	WHERE [key_id] IN (
3389	SELECT k.[id]
3390	FROM [Keys] k
3391	WHERE k.[item_type] = :itemType
3392	)
3393	</sql>
3394	<description>
3395	An SQL query that delete plug-in keys referencing keys
3396	for a given item type.
3397	</description>
3398	</query>
3399
3400
3401	<query id="GET_SUBTYPABLE_ITEMS_FOR_SUBTYPE_OF_CLASS" type="HQL">
3402	<sql>
3403	SELECT {1}
3404	FROM {2} sub
3405	WHERE sub.itemSubtype = :subtype
3406	</sql>
3407	<description>
3408	Get all items that are subtyped with a subtype for a given class.
3409	</description>
3410	</query>
3411
3412	<query id="GET_ITEMLISTS_FOR_SUBTYPE" type="HQL">
3413	<sql>
3414	SELECT {1}
3415	FROM ItemListData il
3416	WHERE il.itemSubtype = :subtype
3417	</sql>
3418	<description>
3419	A Hibernate query that gets ITEMLISTS for a given item subtype.
3420	</description>
3421	</query>
3422
3423	<query id="GET_MIMETYPES_FOR_FILETYPE" type="HQL">
3424	<sql>
3425	SELECT {1}
3426	FROM MimeTypeData mt
3427	WHERE mt.fileType = :subtype
3428	</sql>
3429	<description>
3430	A Hibernate query that gets MIME types for a given item subtype.
3431	</description>
3432	</query>
3433
3434	<query id="GET_DATAFILETYPES_FOR_FILETYPE" type="HQL">
3435	<sql>
3436	SELECT {1}
3437	FROM DataFileTypeData dft
3438	WHERE dft.genericType = :subtype
3439	</sql>
3440	<description>
3441	A Hibernate query that gets Data file types for a given item subtype.
3442	</description>
3443	</query>
3444
3445	<query id="UPDATE_FILESETMEMBER_FILETYPE" type="HQL">
3446	<sql>
3447	UPDATE FileSetMemberData mbr
3448	SET mbr.dataFileType = :newType
3449	WHERE mbr.dataFileType = :oldType
3450	</sql>
3451	<description>
3452	A Hibernate query that update the data file type of all
3453	file set members with a given old data file type.
3454	</description>
3455	</query>
3456
3457	<query id="DISABLE_ALL_PLUGINS" type="HQL">
3458	<sql>
3459	UPDATE PluginDefinitionData pl
3460	SET pl.disabled = true
3461	</sql>
3462	<description>
3463	A Hibernate query that disable all plug-ins.
3464	</description>
3465	</query>
3466
3467	<query id="GET_PROJECT_DEFAULT_ANYTOANY" type="HQL">
3468	<sql>
3469	SELECT a FROM AnyToAnyData a
3470	WHERE a.fromType = 24 AND a.name LIKE 'default_%'
3471	</sql>
3472	<description>
3473	A Hibernate query that load all any-to-any links containing
3474	project default items.
3475	</description>
3476	</query>
3477
3478	<query id="GET_MD5_PASSWORDS" type="SQL">
3479	<sql>
3480	SELECT [id], [md5password] FROM [Passwords]
3481	</sql>
3482	<description>
3483	An SQL query that load all md5 passwords.
3484	</description>
3485	</query>
3486
3487	<query id="SET_ENCRYPTED_PASSWORD" type="SQL">
3488	<sql>
3489	UPDATE [Passwords]
3490	SET [crypted_password] = :cryptedPassword
3491	WHERE [id] = :id
3492	</sql>
3493	<description>
3494	An SQL query that set the encrypted password for a given entry.
3495	</description>
3496	</query>
3497
3498	<query id="GET_VIRTUALDBS_FOR_REPORTERCLONETEMPLATE" type="HQL">
3499	<sql>
3500	SELECT {1}
3501	FROM VirtualDbData vdb
3502	WHERE vdb.reporterCloneTemplate = :reporterCloneTemplate
3503	</sql>
3504	<description>
3505	A Hibernate query that get virtual databases
3506	that are using a given reporter clone template.
3507	</description>
3508	</query>
3509
3510	<query id="GET_ALL_ANNOTATIONTYPE_IDS_FOR_USER" type="SQL">
3511	<sql>
3512	SELECT [at].[id]
3513	FROM [AnnotationTypes] [at]
3514	WHERE [at].[owner] = :owner
3515	OR [at].[itemkey_id] IN (:itemKeys)
3516	OR [at].[projectkey_id] IN (:projectKeys)
3517	</sql>
3518	<description>
3519	An SQL query that load the ID of all the annotation types
3520	that the current user has access to. We need to set owner,
3521	item keys and project keys as parameters.
3522	</description>
3523	</query>
3524
3525	<query id="COPY_PARENT_PHYSICAL_BIOASSAYS" type="SQL">
3526	<sql>
3527	INSERT INTO [ParentPhysicalBioAssays] ([physicalbioassay_id], [derivedbioassay_id])
3528	SELECT [bioassay_id], [id] FROM [DerivedBioAssays]
3529	</sql>
3530	<description>
3531	An SQL query that copy the parent physical bioassays
3532	to the new (in BASE 3.2) ParentPhysicalBioAssays table
3533	</description>
3534	</query>
3535
3536
3537	<query id="COPY_PARENT_DERIVED_BIOASSAYS" type="SQL">
3538	<sql>
3539	INSERT INTO [ParentDerivedBioAssays] ([parentbioassay_id], [derivedbioassay_id])
3540	SELECT [parent_id], [id] FROM [DerivedBioAssays] WHERE NOT [parent_id] IS NULL
3541	</sql>
3542	<description>
3543	An SQL query that copy the parent derived bioassays
3544	to the new (in BASE 3.2) ParentDerivedBioAssays table
3545	</description>
3546	</query>
3547
3548	<query id="SET_ISROOT_ON_DERIVED_BIOASSAYS" type="SQL">
3549	<sql>
3550	UPDATE [DerivedBioAssays] SET [is_root] = ([parent_id] IS NULL)
3551	</sql>
3552	<description>
3553	An SQL query that set the is_root property on DerivedBioAssays table.
3554	</description>
3555	</query>
3556
3557	<query id="GET_ITEMSUBTYPE_WITH_NAME_AND_ITEMTYPE" type="HQL">
3558	<sql>
3559	SELECT st FROM ItemSubtypeData st
3560	WHERE st.name = :name AND st.itemType = :itemType
3561	</sql>
3562	<description>
3563	A Hibernate query that load an item subtype given the name
3564	and main item type.
3565	</description>
3566	</query>
3567
3568	<query id="SET_DISABLE_LOG_FOR_ANNOTATION_TYPES" type="HQL">
3569	<sql>
3570	UPDATE AnnotationTypeData at
3571	SET at.disableLogOfValues = false
3572	WHERE at.disableLogOfValues IS NULL
3573	</sql>
3574	<description>
3575	An HQL query that set the disableLogOfValues=false for all annotation types
3576	with a null value.
3577	</description>
3578	</query>
3579
3580	<query id="AB_LOAD_ANNOTATION_INFO" type="SQL">
3581	<sql>
3582	SELECT [annotationtype_id], [id], [version], [unit_id], [value_id], [last_update], [project_id], [override_id]
3583	FROM [Annotations]
3584	WHERE [annotationset_id] = :annotationSet AND [source] = 0 AND ([project_id] = :defaultProject OR [project_id] = :activeProject)
3585	</sql>
3586	<description>
3587	SQL query for loading current (primary) annotations for
3588	a given item.
3589	Used by the AnnotationBatcher as a SQL query via Hibernate.
3590	</description>
3591	</query>
3592
3593	<query id="AB_LOAD_ANNOTATION_VALUES" type="SQL">
3594	<sql>
3595	SELECT [id], [value]
3596	FROM [{1}]
3597	WHERE [id] IN (:listOfIds)
3598	</sql>
3599	<description>
3600	SQL query for loading current annotation values
3601	for a given list of annotation value IDs.
3602	Used by the AnnotationBatcher as a SQL query via Hibernate.
3603	</description>
3604	</query>
3605
3606	<query id="AB_INSERT_INTO_PARAMETERVALUES" type="SQL">
3607	<sql>
3608	INSERT INTO [ParameterValues] ([id], [discriminator], [version])
3609	VALUES (nextval('hibernate_sequence'), ?, 0)
3610	</sql>
3611	<description>
3612	SQL query for inserting rows into the ParameterValues table.
3613	The primary key (id) must be auto-generated.
3614	Parameters: discriminator
3615	</description>
3616	</query>
3617
3618	<query id="AB_INSERT_INTO_ANNOTATIONS" type="SQL">
3619	<sql>
3620	INSERT INTO [Annotations] ([id], [version], [annotationset_id], [annotationtype_id], [unit_id], [value_id], [last_update], [source], [project_id], [override_id])
3621	VALUES (nextval('hibernate_sequence'), 0, ?, ?, ?, ?, ?, 0, ?, ?)
3622	</sql>
3623	<description>
3624	SQL query for inserting rows into the Annotations table.
3625	The primary key (id) must be auto-generated.
3626	Parameters: annotationset_id, annotationtype_id, unit_id, value_id, last_updated, project_id, override_id
3627	</description>
3628	</query>
3629
3630	<query id="AB_UPDATE_ANNOTATIONS" type="SQL">
3631	<sql>
3632	UPDATE [Annotations]
3633	SET [version] = ?, [unit_id] = ?, [last_update] = ?
3634	WHERE [id] = ? AND [version] = ?
3635	</sql>
3636	<description>
3637	SQL query for updating rows into the Annotations table.
3638	Parameters: version (new), unit_id, last_updated, id, version (old)
3639	</description>
3640	</query>
3641
3642	<query id="AB_INSERT_INTO_ANNOTATIONSETS" type="SQL">
3643	<sql>
3644	INSERT INTO [AnnotationSets] ([id], [version], [item_type], [item_id])
3645	VALUES (nextval('hibernate_sequence'), 0, {1}, ?)
3646	</sql>
3647	<description>
3648	SQL query for inserting rows into the AnnotationSets table.
3649	The primary key (id) must be auto-generated.
3650	Parameters: item_id
3651	</description>
3652	</query>
3653
3654	<query id="AB_UPDATE_ITEMTABLE" type="SQL">
3655	<sql>
3656	UPDATE [{1}]
3657	SET [annotationset_id] = ?
3658	WHERE [id] = ?
3659	</sql>
3660	<description>
3661	SQL query for updating the annotationset_id column in any
3662	table it exists in.
3663	Parameters: annotationset_id, item_id
3664	</description>
3665	</query>
3666
3667	<query id="AB_NULLIFY_CLONED_ANNOTATIONS" type="SQL">
3668	<sql>
3669	UPDATE [Annotations]
3670	SET [inherited_id] = null
3671	WHERE [inherited_id] = ? and [source] = 2
3672	</sql>
3673	<description>
3674	SQL query for setting the 'inherited_id' column to null
3675	for cloned annotations that reference the annotation that
3676	is about to be deleted.
3677	Parameters: inherited_id
3678	</description>
3679	</query>
3680
3681	<query id="AB_DELETE_INHERITED_ANNOTATIONS" type="SQL">
3682	<sql>
3683	DELETE FROM [Annotations]
3684	WHERE [inherited_id] = ? and [source] = 1
3685	</sql>
3686	<description>
3687	SQL query for deleting inherited annotations that reference
3688	the annotation that is about to be deleted.
3689	Parameters: inherited_id
3690	</description>
3691	</query>
3692
3693	<query id="AB_DELETE_FROM_ANNOTATIONS" type="SQL">
3694	<sql>
3695	DELETE FROM [Annotations]
3696	WHERE [id] = ?
3697	</sql>
3698	<description>
3699	SQL query for deleting an annotation with a given id.
3700	Used by the AnnotationBatcher as a PreparedStatement.
3701	Parameters: id
3702	</description>
3703	</query>
3704
3705	<query id="AB_DELETE_FROM_PARAMETERVALUES" type="SQL">
3706	<sql>
3707	DELETE FROM [ParameterValues] WHERE [id] = ?
3708	</sql>
3709	<description>
3710	SQL query for deleting a parameter value with a given id.
3711	Used by the AnnotationBatcher as a PreparedStatement.
3712	</description>
3713	</query>
3714
3715	<query id="AB_DELETE_FROM_VALUES" type="SQL">
3716	<sql>
3717	DELETE FROM [{1}] WHERE [id] = ?
3718	</sql>
3719	<description>
3720	SQL query for deleting all actual annotation values with a given id.
3721	The {1} parameter is the table the value are stored in, eg. StringValues,
3722	IntegerValues, FloatValues, etc.
3723	Used by the AnnotationBatcher as a PreparedStatement.
3724	</description>
3725	</query>
3726
3727	<query id="AB_INSERT_INTO_VALUES" type="SQL">
3728	<sql>
3729	INSERT INTO [{1}] ([id], [value]) VALUES (?, ?)
3730	</sql>
3731	<description>
3732	SQL query for inserting annotation values in their respective
3733	table (eg. StringValues, IntegerValues, FloatValues, etc.).
3734	Used by the AnnotationBatcher as a PreparedStatement.
3735	</description>
3736	</query>
3737
3738	<query id="AB_UPDATE_OVERRIDE_ID" type="SQL">
3739	<sql>
3740	UPDATE [Annotations]
3741	SET [override_id] = ?
3742	WHERE [annotationset_id] = ?
3743	AND [annotationtype_id] = ?
3744	AND [source] = 0
3745	AND [project_id] <> 0
3746	</sql>
3747	<description>
3748	Updates the "override_id" column on project-specific annotations
3749	to point to a newly created default annotation of the same
3750	annotation type (PRIMARY annotations only).
3751	Used by the AnnotationBatcher as a PreparedStatement.
3752	Parameters: override_id, annotationset_id, annotationtype_id
3753	</description>
3754	</query>
3755
3756
3757	<query id="PS_UPDATE_PROJECT_ANNOTATION_OVERRIDE_REF" type="SQL">
3758	<sql>
3759	UPDATE [Annotations]
3760	SET [override_id] = :annotationId
3761	WHERE [annotationset_id] = :annotationSetId
3762	AND [annotationtype_id] = :annotationTypeId
3763	AND [source] = 0
3764	AND [project_id] <> 0
3765	</sql>
3766	<description>
3767	Updates the "override_id" column on project-specific annotations
3768	to point to a newly created default annotation of the same
3769	annotation type (PRIMARY annotations only).
3770	</description>
3771	</query>
3772
3773	<query id="PS_FIND_OVERRIDE_ID_FOR_PROJECT_ANNOTATION" type="SQL">
3774	<sql>
3775	UPDATE [Annotations]
3776	SET [override_id] = COALESCE(
3777	(SELECT [id] FROM [Annotations]
3778	WHERE [annotationset_id] = :annotationSetId
3779	AND [annotationtype_id] = :annotationTypeId
3780	AND [source] = 0 AND [project_id] = 0)
3781	, 0)
3782	WHERE id = :annotationId
3783	</sql>
3784	<description>
3785	Updates the "override_id" column on a newly created project-specific
3786	(PRIMARY) annotation to point to the existing default annotation id
3787	or 0 if no default annotation exists.
3788	</description>
3789	</query>
3790
3791	<query id="PS_UPDATE_PROJECT_ANNOTATION_OVERRIDE_REF_INHERITED" type="HQL">
3792	<sql>
3793	UPDATE [Annotations]
3794	SET [override_id] = :annotationId
3795	WHERE [annotationset_id] = :annotationSetId
3796	AND [inherited_id] IN (
3797	SELECT [id] FROM [Annotations]
3798	WHERE [annotationset_id] = :parentSetId
3799	AND [override_id] = :parentId
3800	)
3801	</sql>
3802	<description>
3803	Updates the "override_id" column on project-specific annotations
3804	to point to a newly created default annotation (INHERITED and
3805	CLONED annotations). The subquery will find project-specific annotation
3806	on the parent annotation set that is overriding the inherited annotation.
3807	</description>
3808	</query>
3809
3810	<query id="PS_FIND_OVERRIDE_ID_FOR_PROJECT_ANNOTATION_INHERITED" type="SQL">
3811	<sql>
3812	UPDATE [Annotations]
3813	SET [override_id] = COALESCE(
3814	(SELECT [id] FROM [Annotations]
3815	WHERE [annotationset_id] = :annotationSetId
3816	AND [inherited_id] = :parentOverrideId
3817	AND [source] <> 0
3818	AND [project_id] = 0)
3819	, 0)
3820	WHERE id = :annotationId
3821	</sql>
3822	<description>
3823	Updates the "override_id" column on a newly created project-specific
3824	(CLONED or INHERITED) annotation to point to the existing default
3825	annotation id or 0 if no default annotation exists.
3826	</description>
3827	</query>
3828
3829	<query id="PS_RESET_OVERRIDE_ON_PROJECT_ANNOTATIONS" type="HQL">
3830	<sql>
3831	UPDATE [Annotations]
3832	SET [override_id] = 0
3833	WHERE [override_id] IN (:deletedAnnotations)
3834	OR [inherited_id] IN (
3835	SELECT [id] FROM [Annotations]
3836	WHERE [override_id] IN (:deletedPrimaryAnnotations)
3837	)
3838	</sql>
3839	<description>
3840	Reset the "override_id" column on project-specific annotations
3841	that points to a default annotation that has been removed.
3842	</description>
3843	</query>
3844
3845	<query id="PS_LOAD_ANNOTATIONS_IN_NON_EXISTING_PROJECTS" type="SQL">
3846	<sql>
3847	SELECT a.[id], a.[annotationset_id], a.[value_id], a.[project_id], at.[value_type]
3848	FROM [Annotations] a
3849	INNER JOIN [AnnotationTypes] at ON at.[id] = a.[annotationtype_id]
3850	WHERE a.[project_id] <> 0 AND a.[project_id] NOT IN (SELECT [id] FROM [Projects])
3851	</sql>
3852	<description>
3853	SQL query for loading information about annotations
3854	that are project-specific annotations for a given
3855	list of projects.
3856	Used by the ProjectSpecificAnnotationsManager when
3857	a project has been deleted.
3858	</description>
3859	</query>
3860
3861	<query id="PS_DELETE_FROM_PARAMETERVALUES" type="SQL">
3862	<sql>
3863	DELETE FROM [ParameterValues] WHERE [id] IN (:deletedValues)
3864	</sql>
3865	<description>
3866	SQL query for deleting mutliple parameter values with a given id's.
3867	Used by the ProjectSpecificAnnotationsManager.
3868	</description>
3869	</query>
3870
3871	<query id="PS_DELETE_FROM_VALUES" type="SQL">
3872	<sql>
3873	DELETE FROM [{1}] WHERE [id] IN (:deletedValues)
3874	</sql>
3875	<description>
3876	SQL query for deleting all actual annotation values with given id's.
3877	The {1} parameter is the table the value are stored in, eg. StringValues,
3878	IntegerValues, FloatValues, etc.
3879	Used by the ProjectSpecificAnnotationsManager.
3880	</description>
3881	</query>
3882
3883	<query id="PS_DELETE_FROM_ANNOTATIONS_IN_PROJECTS" type="SQL">
3884	<sql>
3885	DELETE FROM [Annotations] WHERE [project_id] IN (:deletedProjects)
3886	</sql>
3887	<description>
3888	SQL query for deleting all annotation entries referenceing
3889	given list of projects.
3890	Used by the ProjectSpecificAnnotationsManager.
3891	</description>
3892	</query>
3893
3894	<query id="PS_FIND_PROJECT_SPECIFIC_ANNOTATION" type="HQL">
3895	<sql>
3896	SELECT ad FROM AnnotationData ad
3897	WHERE ad.projectId = :activeProject
3898	AND ad.overrideId = :defaultAnnotation
3899	AND ad.annotationSet = :annotationSet
3900	</sql>
3901	<description>
3902	HQL query for locating a project-specific annotation
3903	overriding a specified default annotation.
3904	Used by the ProjectSpecificAnnotationsManager.
3905	</description>
3906	</query>
3907
3908	<query id="COUNT_PROJECT_ANNOTATIONS_FOR_ANNOTATIONTYPE" type="HQL">
3909	<sql>
3910	SELECT count(*)
3911	FROM AnnotationData ad
3912	WHERE ad.annotationType = :annotationType
3913	AND ad.projectId <> 0
3914	</sql>
3915	<description>
3916	HQL query that counts the number of project-specific annotations
3917	for an annotation type.
3918	</description>
3919	</query>
3920
3921	<query id="GET_USER_DEVICE" type="HQL">
3922	<sql>
3923	SELECT dev
3924	FROM UserDeviceData dev
3925	WHERE dev.user = :userId
3926	AND dev.client = :clientId
3927	AND dev.token = :token
3928	</sql>
3929	<description>
3930	HQL query that selects a device for a given user and client
3931	with a given device token.
3932	</description>
3933	</query>
3934
3935	</predefined-queries>

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source: branches/3.19-stable/src/core/common-queries.xml @ 8099

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