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Preparations for release 4.13.0
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-47
lines changed

4 files changed

+201
-47
lines changed

‎schemas/ispyb/data.sql‎

Lines changed: 125 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -322,6 +322,124 @@ INSERT INTO `BeamLineSetup` (`beamLineSetupId`, `detectorId`, `synchrotronMode`,
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/*!40000 ALTER TABLE `CalendarHash` ENABLE KEYS */;
323323

324324
/*!40000 ALTER TABLE `Component` DISABLE KEYS */;
325+
INSERT INTO `Component` (`componentId`, `componentTypeId`, `proposalId`, `name`, `composition`) VALUES (1,8,NULL,'H','Hydrogen'),
326+
(2,8,NULL,'He','Helium'),
327+
(3,8,NULL,'Li','Lithium'),
328+
(4,8,NULL,'Be','Beryllium'),
329+
(5,8,NULL,'B','Boron'),
330+
(6,8,NULL,'C','Carbon'),
331+
(7,8,NULL,'N','Nitrogen'),
332+
(8,8,NULL,'O','Oxygen'),
333+
(9,8,NULL,'F','Fluorine'),
334+
(10,8,NULL,'Ne','Neon'),
335+
(11,8,NULL,'Na','Sodium'),
336+
(12,8,NULL,'Mg','Magnesium'),
337+
(13,8,NULL,'Al','Aluminum'),
338+
(14,8,NULL,'Si','Silicon'),
339+
(15,8,NULL,'P','Phosphorus'),
340+
(16,8,NULL,'S','Sulfur'),
341+
(17,8,NULL,'Cl','Chlorine'),
342+
(18,8,NULL,'Ar','Argon'),
343+
(19,8,NULL,'K','Potassium'),
344+
(20,8,NULL,'Ca','Calcium'),
345+
(21,8,NULL,'Sc','Scandium'),
346+
(22,8,NULL,'Ti','Titanium'),
347+
(23,8,NULL,'V','Vanadium'),
348+
(24,8,NULL,'Cr','Chromium'),
349+
(25,8,NULL,'Mn','Manganese'),
350+
(26,8,NULL,'Fe','Iron'),
351+
(27,8,NULL,'Co','Cobalt'),
352+
(28,8,NULL,'Ni','Nickel'),
353+
(29,8,NULL,'Cu','Copper'),
354+
(30,8,NULL,'Zn','Zinc'),
355+
(31,8,NULL,'Ga','Gallium'),
356+
(32,8,NULL,'Ge','Germanium'),
357+
(33,8,NULL,'As','Arsenic'),
358+
(34,8,NULL,'Se','Selenium'),
359+
(35,8,NULL,'Br','Bromine'),
360+
(36,8,NULL,'Kr','Krypton'),
361+
(37,8,NULL,'Rb','Rubidium'),
362+
(38,8,NULL,'Sr','Strontium'),
363+
(39,8,NULL,'Y','Yttrium'),
364+
(40,8,NULL,'Zr','Zirconium'),
365+
(41,8,NULL,'Nb','Niobium'),
366+
(42,8,NULL,'Mo','Molybdenum'),
367+
(43,8,NULL,'Tc','Technetium'),
368+
(44,8,NULL,'Ru','Ruthenium'),
369+
(45,8,NULL,'Rh','Rhodium'),
370+
(46,8,NULL,'Pd','Palladium'),
371+
(47,8,NULL,'Ag','Silver'),
372+
(48,8,NULL,'Cd','Cadmium'),
373+
(49,8,NULL,'In','Indium'),
374+
(50,8,NULL,'Sn','Tin'),
375+
(51,8,NULL,'Sb','Antimony'),
376+
(52,8,NULL,'Te','Tellurium'),
377+
(53,8,NULL,'I','Iodine'),
378+
(54,8,NULL,'Xe','Xenon'),
379+
(55,8,NULL,'Cs','Cesium'),
380+
(56,8,NULL,'Ba','Barium'),
381+
(57,8,NULL,'La','Lanthanum'),
382+
(58,8,NULL,'Ce','Cerium'),
383+
(59,8,NULL,'Pr','Praseodymium'),
384+
(60,8,NULL,'Nd','Neodymium'),
385+
(61,8,NULL,'Pm','Promethium'),
386+
(62,8,NULL,'Sm','Samarium'),
387+
(63,8,NULL,'Eu','Europium'),
388+
(64,8,NULL,'Gd','Gadolinium'),
389+
(65,8,NULL,'Tb','Terbium'),
390+
(66,8,NULL,'Dy','Dysprosium'),
391+
(67,8,NULL,'Ho','Holmium'),
392+
(68,8,NULL,'Er','Erbium'),
393+
(69,8,NULL,'Tm','Thulium'),
394+
(70,8,NULL,'Yb','Ytterbium'),
395+
(71,8,NULL,'Lu','Lutetium'),
396+
(72,8,NULL,'Hf','Hafnium'),
397+
(73,8,NULL,'Ta','Tantalum'),
398+
(74,8,NULL,'W','Tungsten'),
399+
(75,8,NULL,'Re','Rhenium'),
400+
(76,8,NULL,'Os','Osmium'),
401+
(77,8,NULL,'Ir','Iridium'),
402+
(78,8,NULL,'Pt','Platinum'),
403+
(79,8,NULL,'Au','Gold'),
404+
(80,8,NULL,'Hg','Mercury'),
405+
(81,8,NULL,'Tl','Thallium'),
406+
(82,8,NULL,'Pb','Lead'),
407+
(83,8,NULL,'Bi','Bismuth'),
408+
(84,8,NULL,'Po','Polonium'),
409+
(85,8,NULL,'At','Astatine'),
410+
(86,8,NULL,'Rn','Radon'),
411+
(87,8,NULL,'Fr','Francium'),
412+
(88,8,NULL,'Ra','Radium'),
413+
(89,8,NULL,'Ac','Actinium'),
414+
(90,8,NULL,'Th','Thorium'),
415+
(91,8,NULL,'Pa','Protactinium'),
416+
(92,8,NULL,'U','Uranium'),
417+
(93,8,NULL,'Np','Neptunium'),
418+
(94,8,NULL,'Pu','Plutonium'),
419+
(95,8,NULL,'Am','Americium'),
420+
(96,8,NULL,'Cm','Curium'),
421+
(97,8,NULL,'Bk','Berkelium'),
422+
(98,8,NULL,'Cf','Californium'),
423+
(99,8,NULL,'Es','Einsteinium'),
424+
(100,8,NULL,'Fm','Fermium'),
425+
(101,8,NULL,'Md','Mendelevium'),
426+
(102,8,NULL,'No','Nobelium'),
427+
(103,8,NULL,'Lr','Lawrencium'),
428+
(104,8,NULL,'Rf','Rutherfordium'),
429+
(105,8,NULL,'Db','Dubnium'),
430+
(106,8,NULL,'Sg','Seaborgium'),
431+
(107,8,NULL,'Bh','Bohrium'),
432+
(108,8,NULL,'Hs','Hassium'),
433+
(109,8,NULL,'Mt','Meitnerium'),
434+
(110,8,NULL,'Ds','Darmstadtium'),
435+
(111,8,NULL,'Rg','Roentgenium'),
436+
(112,8,NULL,'Cn','Copernicium'),
437+
(113,8,NULL,'Nh','Nihonium'),
438+
(114,8,NULL,'Fl','Flerovium'),
439+
(115,8,NULL,'Mc','Moscovium'),
440+
(116,8,NULL,'Lv','Livermorium'),
441+
(117,8,NULL,'Ts','Tennessine'),
442+
(118,8,NULL,'Og','Oganesson');
325443
/*!40000 ALTER TABLE `Component` ENABLE KEYS */;
326444

327445
/*!40000 ALTER TABLE `ComponentLattice` DISABLE KEYS */;
@@ -726,6 +844,9 @@ INSERT INTO `Protein` (`proteinId`, `proposalId`, `name`, `acronym`, `descriptio
726844
(123497,37027,'XPDF comp1','xpdf-comp-01',NULL,1,1,NULL,NULL,NULL,NULL,'2017-03-23 22:03:40',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL);
727845
/*!40000 ALTER TABLE `Protein` ENABLE KEYS */;
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/*!40000 ALTER TABLE `Protein_has_Component` DISABLE KEYS */;
848+
/*!40000 ALTER TABLE `Protein_has_Component` ENABLE KEYS */;
849+
729850
/*!40000 ALTER TABLE `Protein_has_PDB` DISABLE KEYS */;
730851
INSERT INTO `Protein_has_PDB` (`proteinhaspdbid`, `proteinid`, `pdbid`) VALUES (5,123497,6);
731852
/*!40000 ALTER TABLE `Protein_has_PDB` ENABLE KEYS */;
@@ -950,11 +1071,11 @@ INSERT INTO `Shipping` (`shippingId`, `proposalId`, `shippingName`, `deliveryAge
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/*!40000 ALTER TABLE `Shipping` ENABLE KEYS */;
9511072

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/*!40000 ALTER TABLE `ShippingHasSession` DISABLE KEYS */;
953-
INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (6988,55167),
954-
(7227,55168),
955-
(474,339525),
1074+
INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (474,339525),
9561075
(477,339528),
957-
(480,339531);
1076+
(480,339531),
1077+
(6988,55167),
1078+
(7227,55168);
9581079
/*!40000 ALTER TABLE `ShippingHasSession` ENABLE KEYS */;
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/*!40000 ALTER TABLE `Sleeve` DISABLE KEYS */;

‎schemas/ispyb/lookups.sql‎

Lines changed: 55 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
1212

1313
/*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */;
14-
INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.12.0');
14+
INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.13.0');
1515
/*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */;
1616

1717
/*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */;
@@ -309,12 +309,19 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
309309
(337,'2026_01_13_AdminVar_bump_version.sql','DONE','2026-01-13 15:16:00'),
310310
(338,'2026_01_27_AutoProcProgram_parentAutoProcProgramId.sql','DONE','2026-02-12 10:30:32'),
311311
(339,'2026_02_09_ProcessedTomogram_feature.sql','DONE','2026-02-12 10:30:33'),
312-
(340,'2026_02_10_AdminVar_bump_version.sql','DONE','2026-02-12 10:30:33');
312+
(340,'2026_02_10_AdminVar_bump_version.sql','DONE','2026-02-12 10:30:33'),
313+
(341,'2026_03_02_LaserParameters_unique_contraints.sql','DONE','2026-04-10 12:18:14'),
314+
(342,'2026_03_16_ProcessingPipeline_new_pipelines.sql ','DONE','2026-04-10 12:18:14'),
315+
(343,'2026_03_18_ExperimentType_sxt.sql','DONE','2026-04-10 12:18:14'),
316+
(344,'2026_04_08_Protein_has_Component.sql','DONE','2026-04-10 12:18:14'),
317+
(345,'2026_04_10_Component_element.sql','DONE','2026-04-10 12:18:14'),
318+
(346,'2026_04_10_AdminVar_bump_version.sql','DONE','2026-04-10 12:18:14');
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/*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
314320

315321
/*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;
316322
INSERT INTO `ComponentType` (`componentTypeId`, `name`) VALUES (6,'Buffer'),
317323
(2,'DNA'),
324+
(8,'Element'),
318325
(7,'JetMaterial'),
319326
(5,'Ligand'),
320327
(1,'Protein'),
@@ -431,7 +438,9 @@ INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `activ
431438
(43,'Metal ID','mx',1),
432439
(44,'Atlas','em',1),
433440
(45,'CLEM','em',1),
434-
(46,'FIB','em',1);
441+
(46,'FIB','em',1),
442+
(47,'Soft X-Ray Tomography','em',1),
443+
(48,'CryoSIM','em',1);
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/*!40000 ALTER TABLE `ExperimentType` ENABLE KEYS */;
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437446
/*!40000 ALTER TABLE `InspectionType` DISABLE KEYS */;
@@ -766,16 +775,19 @@ INSERT INTO `ProcessingPipelineCategory` (`processingPipelineCategoryId`, `name`
766775
INSERT INTO `ProcessingPipeline` (`processingPipelineId`, `processingPipelineCategoryId`, `name`, `discipline`, `pipelineStatus`, `reprocessing`) VALUES (1,1,'Mosflm','MX','automatic',0),
767776
(2,1,'EDNA','MX','automatic',0),
768777
(3,2,'Fast DP','MX','automatic',1),
769-
(4,2,'xia2/3dii','MX','deprecated',0),
778+
(4,2,'xia2/XDS','MX','deprecated',0),
770779
(5,2,'xia2/Multiplex','MX','automatic',1),
771780
(6,2,'xia2/DIALS','MX','optional',1),
772-
(7,2,'xia2/XDS','MX','optional',1),
781+
(7,2,'xia2/3dii','MX','optional',1),
773782
(8,2,'autoPROC','MX','optional',1),
774783
(9,3,'Fast EP','MX','automatic',0),
775784
(10,3,'Dimple','MX','automatic',0),
776785
(11,3,'MrBUMP','MX','automatic',0),
777786
(12,3,'Big EP/XDS','MX','automatic',0),
778-
(13,3,'Big EP/DIALS','MX','automatic',0);
787+
(13,3,'Big EP/DIALS','MX','automatic',0),
788+
(14,2,'autoPROC+STARANISO','MX','automatic',0),
789+
(15,2,'xia2/DIALS (multi)','MX','automatic',0),
790+
(16,2,'xia2/3dii (multi)','MX','automatic',0);
779791
/*!40000 ALTER TABLE `ProcessingPipeline` ENABLE KEYS */;
780792

781793
/*!40000 ALTER TABLE `BLSampleType` DISABLE KEYS */;
@@ -861,63 +873,63 @@ INSERT INTO `Permission` (`permissionId`, `type`, `description`) VALUES (1,'mx_a
861873

862874
/*!40000 ALTER TABLE `UserGroup_has_Permission` DISABLE KEYS */;
863875
INSERT INTO `UserGroup_has_Permission` (`userGroupId`, `permissionId`) VALUES (1,1),
876+
(1,7),
877+
(1,8),
878+
(1,9),
879+
(1,10),
880+
(1,11),
881+
(1,18),
882+
(1,20),
883+
(1,23),
884+
(1,49),
864885
(2,1),
886+
(2,6),
887+
(2,23),
888+
(2,80),
889+
(3,7),
890+
(3,23),
891+
(4,20),
892+
(5,10),
893+
(6,8),
894+
(6,23),
865895
(8,1),
866-
(9,1),
867-
(14,1),
868-
(24,1),
869896
(8,2),
870897
(8,4),
871-
(2,6),
872898
(8,6),
873-
(9,6),
874-
(1,7),
875-
(3,7),
876899
(8,7),
877-
(1,8),
878-
(6,8),
879900
(8,8),
880-
(1,9),
881901
(8,9),
882-
(1,10),
883-
(5,10),
884902
(8,10),
885-
(1,11),
886903
(8,11),
887-
(10,12),
888-
(11,13),
889-
(11,15),
890-
(11,16),
891-
(11,17),
892-
(1,18),
893904
(8,18),
894-
(12,18),
895-
(1,20),
896-
(4,20),
897905
(8,20),
898-
(1,23),
899-
(2,23),
900-
(3,23),
901-
(6,23),
902906
(8,23),
903-
(28,23),
904907
(8,26),
905-
(17,26),
906908
(8,29),
907-
(20,29),
908-
(11,32),
909909
(8,37),
910-
(28,37),
911-
(11,43),
912-
(1,49),
913910
(8,49),
914-
(34,49),
911+
(9,1),
912+
(9,6),
913+
(10,12),
914+
(10,77),
915+
(11,13),
916+
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917+
(11,16),
918+
(11,17),
919+
(11,32),
920+
(11,43),
915921
(11,55),
916922
(11,58),
917923
(11,64),
918-
(39,69),
919-
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920-
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924+
(12,18),
925+
(14,1),
926+
(17,26),
927+
(20,29),
928+
(24,1),
929+
(28,23),
930+
(28,37),
931+
(34,49),
932+
(39,69);
921933
/*!40000 ALTER TABLE `UserGroup_has_Permission` ENABLE KEYS */;
922934

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/*!40000 ALTER TABLE `ScanParametersService` DISABLE KEYS */;

‎schemas/ispyb/tables.sql‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2243,6 +2243,7 @@ CREATE TABLE `LaserParameters` (
22432243
`gonioRotationSpeed` int(10) DEFAULT NULL COMMENT 'Goniometer rotation speed, in deg/s',
22442244
`totalMarkingTime` float DEFAULT NULL COMMENT 'Total marking time, in s',
22452245
PRIMARY KEY (`laserParametersId`),
2246+
UNIQUE KEY `LaserParameters_robotActionId_uc1` (`robotActionId`),
22462247
KEY `LaserParameters_fk_robotActionId` (`robotActionId`),
22472248
CONSTRAINT `LaserParameters_fk_robotActionId` FOREIGN KEY (`robotActionId`) REFERENCES `RobotAction` (`robotActionId`) ON DELETE CASCADE ON UPDATE CASCADE
22482249
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Laser parameters';
@@ -2259,6 +2260,7 @@ CREATE TABLE `LaserPoint` (
22592260
`radius` int(10) unsigned DEFAULT NULL COMMENT 'Radius of point, in microns',
22602261
`laserOn` tinyint(1) DEFAULT 0,
22612262
PRIMARY KEY (`laserPointId`),
2263+
UNIQUE KEY `LaserPoint_laserParametersId_pointIndex_uc1` (`laserParametersId`,`pointIndex`),
22622264
KEY `LaserPoint_fk_laserParametersId` (`laserParametersId`),
22632265
CONSTRAINT `LaserPoint_fk_laserParametersId` FOREIGN KEY (`laserParametersId`) REFERENCES `LaserParameters` (`laserParametersId`) ON DELETE CASCADE ON UPDATE CASCADE
22642266
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Laser points';
@@ -3061,6 +3063,20 @@ CREATE TABLE `Protein` (
30613063
CONSTRAINT `protein_fk4` FOREIGN KEY (`concentrationTypeId`) REFERENCES `ConcentrationType` (`concentrationTypeId`) ON DELETE CASCADE ON UPDATE CASCADE
30623064
) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci;
30633065
/*!40101 SET character_set_client = @saved_cs_client */;
3066+
DROP TABLE IF EXISTS `Protein_has_Component`;
3067+
/*!40101 SET @saved_cs_client = @@character_set_client */;
3068+
/*!40101 SET character_set_client = utf8mb4 */;
3069+
CREATE TABLE `Protein_has_Component` (
3070+
`proteinHasComponentId` int(11) unsigned NOT NULL AUTO_INCREMENT,
3071+
`proteinId` int(10) unsigned NOT NULL COMMENT 'References Protein table',
3072+
`componentId` int(10) unsigned NOT NULL COMMENT 'References Component table',
3073+
PRIMARY KEY (`proteinHasComponentId`),
3074+
KEY `Protein_has_Component_fk_proteinId` (`proteinId`),
3075+
KEY `Protein_has_Component_fk_componentId` (`componentId`),
3076+
CONSTRAINT `Protein_has_Component_fk_componentId` FOREIGN KEY (`componentId`) REFERENCES `Component` (`componentId`) ON DELETE CASCADE ON UPDATE CASCADE,
3077+
CONSTRAINT `Protein_has_Component_fk_proteinId` FOREIGN KEY (`proteinId`) REFERENCES `Protein` (`proteinId`) ON DELETE CASCADE ON UPDATE CASCADE
3078+
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Which elements are contained inside a molecule';
3079+
/*!40101 SET character_set_client = @saved_cs_client */;
30643080
DROP TABLE IF EXISTS `Protein_has_PDB`;
30653081
/*!40101 SET @saved_cs_client = @@character_set_client */;
30663082
/*!40101 SET character_set_client = utf8mb4 */;

‎schemas/ispyb/updates/2026_04_13_AdminVar_bump_version.sql‎

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@@ -0,0 +1,5 @@
1+
INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2026_04_10_AdminVar_bump_version.sql', 'ONGOING');
2+
3+
UPDATE AdminVar SET `value` = '4.13.0' WHERE `name` = 'schemaVersion';
4+
5+
UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2026_04_10_AdminVar_bump_version.sql';

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