Preparations for 4.9.0 release

Author: gfrn

HISTORY.rst

@@ -5,6 +5,22 @@ History
 Unreleased / master
 -------------------
 
+4.10.0 (2025-11-20)
+-------------------
+
+Thank you so much, Karl! / Tusen takk, Karl!
+
+Lookups:
+
+- Add ``CLEM`` experiment type
+- Add ``FIB`` experiment type
+
+New or modified tables, columns, lookup values:
+
+- New table ``LaserParameters``
+- New table ``LaserPoint``
+- Add ``LASER`` to ``RobotAction`` ``actionType`` column
+
 4.9.0 (2025-10-01)
 -------------------
 

schemas/ispyb/data.sql

@@ -332,19 +332,19 @@ INSERT INTO `ComponentLattice` (`componentLatticeId`, `componentId`, `spaceGroup
 /*!40000 ALTER TABLE `Component_has_SubType` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `Container` DISABLE KEYS */;
-INSERT INTO `Container` (`containerId`, `dewarId`, `code`, `containerType`, `capacity`, `sampleChangerLocation`, `containerStatus`, `bltimeStamp`, `beamlineLocation`, `screenId`, `scheduleId`, `barcode`, `imagerId`, `sessionId`, `ownerId`, `requestedImagerId`, `requestedReturn`, `comments`, `experimentType`, `storageTemperature`, `containerRegistryId`, `scLocationUpdated`, `priorityPipelineId`, `experimentTypeId`, `containerTypeId`, `currentDewarId`, `parentContainerId`, `source`) VALUES (1326,573,'Container-1-cm0001-1','Puck-16',16,'3','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000001',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,4,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(1329,573,'Container-2-cm0001-1','Puck-16',16,'4','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000002',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(1332,576,'Container-3-cm0001-1','Puck-16',16,'5','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000003',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(1335,579,'Container-4-cm0001-2','Puck-16',16,'6','processing',NULL,'i03',NULL,NULL,'container-cm0001-2-0001335',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(1338,582,'Container-5-cm0001-3','Puck-16',16,'7','processing',NULL,'i03',NULL,NULL,'container-cm0001-3-0001338',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(1341,573,'Manual',NULL,NULL,'9',NULL,NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(33049,8287,'cm14451-1_i03r-002','Puck',16,NULL,'at DLS',NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(34864,8572,'I03R-001','Puck',16,'29','processing','2016-02-24 12:13:05','i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(34874,8572,'test_plate2','CrystalQuickX',192,'3','in_storage','2016-02-12 09:20:44','i03',NULL,2,'test_plate2',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(34877,8572,'test_plate3','CrystalQuickX',192,'3','in_storage','2016-10-04 10:50:05','i03',NULL,2,'test_plate3',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(34879,8572,'test_plate4','CrystalQuickX',192,'4','processing',NULL,'i02-2',NULL,2,'test_plate4',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(34883,NULL,'XPDF-container-1','XPDF container',NULL,NULL,'processing',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),
-(34888,8578,'TestSim01','CrystalQuickX',192,'1','in_storage',NULL,'i02-2',NULL,2,'VMXiSim-001',7,339535,1,7,0,NULL,NULL,NULL,5,NULL,NULL,NULL,NULL,NULL,NULL,'root@%');
+INSERT INTO `Container` (`containerId`, `dewarId`, `code`, `containerType`, `capacity`, `sampleChangerLocation`, `containerStatus`, `bltimeStamp`, `beamlineLocation`, `screenId`, `scheduleId`, `barcode`, `imagerId`, `sessionId`, `ownerId`, `requestedImagerId`, `requestedReturn`, `comments`, `experimentType`, `storageTemperature`, `containerRegistryId`, `scLocationUpdated`, `priorityPipelineId`, `experimentTypeId`, `containerTypeId`, `currentDewarId`, `parentContainerId`, `source`, `parentContainerLocation`) VALUES (1326,573,'Container-1-cm0001-1','Puck-16',16,'3','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000001',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,4,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(1329,573,'Container-2-cm0001-1','Puck-16',16,'4','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000002',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(1332,576,'Container-3-cm0001-1','Puck-16',16,'5','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000003',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(1335,579,'Container-4-cm0001-2','Puck-16',16,'6','processing',NULL,'i03',NULL,NULL,'container-cm0001-2-0001335',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(1338,582,'Container-5-cm0001-3','Puck-16',16,'7','processing',NULL,'i03',NULL,NULL,'container-cm0001-3-0001338',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(1341,573,'Manual',NULL,NULL,'9',NULL,NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(33049,8287,'cm14451-1_i03r-002','Puck',16,NULL,'at DLS',NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(34864,8572,'I03R-001','Puck',16,'29','processing','2016-02-24 12:13:05','i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(34874,8572,'test_plate2','CrystalQuickX',192,'3','in_storage','2016-02-12 09:20:44','i03',NULL,2,'test_plate2',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(34877,8572,'test_plate3','CrystalQuickX',192,'3','in_storage','2016-10-04 10:50:05','i03',NULL,2,'test_plate3',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(34879,8572,'test_plate4','CrystalQuickX',192,'4','processing',NULL,'i02-2',NULL,2,'test_plate4',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(34883,NULL,'XPDF-container-1','XPDF container',NULL,NULL,'processing',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),
+(34888,8578,'TestSim01','CrystalQuickX',192,'1','in_storage',NULL,'i02-2',NULL,2,'VMXiSim-001',7,339535,1,7,0,NULL,NULL,NULL,5,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL);
 /*!40000 ALTER TABLE `Container` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ContainerHistory` DISABLE KEYS */;
@@ -560,6 +560,12 @@ INSERT INTO `ImageQualityIndicators` (`dataCollectionId`, `imageNumber`, `imageI
 /*!40000 ALTER TABLE `Laboratory` DISABLE KEYS */;
 /*!40000 ALTER TABLE `Laboratory` ENABLE KEYS */;
 
+/*!40000 ALTER TABLE `LaserParameters` DISABLE KEYS */;
+/*!40000 ALTER TABLE `LaserParameters` ENABLE KEYS */;
+
+/*!40000 ALTER TABLE `LaserPoint` DISABLE KEYS */;
+/*!40000 ALTER TABLE `LaserPoint` ENABLE KEYS */;
+
 /*!40000 ALTER TABLE `Ligand` DISABLE KEYS */;
 /*!40000 ALTER TABLE `Ligand` ENABLE KEYS */;
 
@@ -694,8 +700,8 @@ INSERT INTO `ProcessingJobParameter` (`processingJobParameterId`, `processingJob
 /*!40000 ALTER TABLE `Project_has_XFEFSpectrum` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `Proposal` DISABLE KEYS */;
-INSERT INTO `Proposal` (`proposalId`, `personId`, `title`, `proposalCode`, `proposalNumber`, `bltimeStamp`, `proposalType`, `externalId`, `state`) VALUES (37027,1,'I03 Commissioning Directory 2016','cm','14451','2015-12-21 15:20:43',NULL,NULL,'Open'),
-(141666,46266,'Test Proposal cm-0001','cm','1','2016-03-16 16:01:34',NULL,NULL,'Open');
+INSERT INTO `Proposal` (`proposalId`, `personId`, `title`, `proposalCode`, `proposalNumber`, `bltimeStamp`, `proposalType`, `externalId`, `state`, `startDate`, `endDate`) VALUES (37027,1,'I03 Commissioning Directory 2016','cm','14451','2015-12-21 15:20:43',NULL,NULL,'Open',NULL,NULL),
+(141666,46266,'Test Proposal cm-0001','cm','1','2016-03-16 16:01:34',NULL,NULL,'Open',NULL,NULL);
 /*!40000 ALTER TABLE `Proposal` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ProposalHasPerson` DISABLE KEYS */;
@@ -944,11 +950,11 @@ INSERT INTO `Shipping` (`shippingId`, `proposalId`, `shippingName`, `deliveryAge
 /*!40000 ALTER TABLE `Shipping` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ShippingHasSession` DISABLE KEYS */;
-INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (474,339525),
+INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (6988,55167),
+(7227,55168),
+(474,339525),
 (477,339528),
-(480,339531),
-(6988,55167),
-(7227,55168);
+(480,339531);
 /*!40000 ALTER TABLE `ShippingHasSession` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `Sleeve` DISABLE KEYS */;

schemas/ispyb/lookups.sql

@@ -11,7 +11,7 @@
 /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
 
 /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */;
-INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.9.0');
+INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.10.0');
 /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */;
@@ -299,7 +299,11 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
 (327,'2025_07_25_Container_parentContainerLocation.sql','DONE','2025-09-24 11:36:21'),
 (328,'2025_09_24_Proposal_start_end_date.sql','DONE','2025-09-24 15:56:17'),
 (329,'2025_10_01_AdminVar_bump_version.sql','DONE','2025-10-01 15:40:02'),
-(330,'2025_07_29_ContainerType_insert.sql','DONE','2025-10-01 15:51:03');
+(330,'2025_07_29_ContainerType_insert.sql','DONE','2025-10-01 15:51:03'),
+(331,'2025_11_03_LaserParameters_tables.sql','DONE','2025-11-20 15:47:48'),
+(332,'2025_11_05_RobotAction_new_type.sql','DONE','2025-11-20 15:47:48'),
+(333,'2025_11_13_ExperimentType_clem_and_fib.sql','DONE','2025-11-20 15:47:48'),
+(334,'2025_11_20_AdminVar_bump_version.sql','DONE','2025-11-20 15:47:48');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;
@@ -419,7 +423,9 @@ INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `activ
 (41,'SSX-Chip','mx',1),
 (42,'SSX-Jet','mx',1),
 (43,'Metal ID','mx',1),
-(44,'Atlas','em',1);
+(44,'Atlas','em',1),
+(45,'CLEM','em',1),
+(46,'FIB','em',1);
 /*!40000 ALTER TABLE `ExperimentType` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `InspectionType` DISABLE KEYS */;
@@ -849,63 +855,63 @@ INSERT INTO `Permission` (`permissionId`, `type`, `description`) VALUES (1,'mx_a
 
 /*!40000 ALTER TABLE `UserGroup_has_Permission` DISABLE KEYS */;
 INSERT INTO `UserGroup_has_Permission` (`userGroupId`, `permissionId`) VALUES (1,1),
-(1,7),
-(1,8),
-(1,9),
-(1,10),
-(1,11),
-(1,18),
-(1,20),
-(1,23),
-(1,49),
 (2,1),
-(2,6),
-(2,23),
-(2,80),
-(3,7),
-(3,23),
-(4,20),
-(5,10),
-(6,8),
-(6,23),
 (8,1),
+(9,1),
+(14,1),
+(24,1),
 (8,2),
 (8,4),
+(2,6),
 (8,6),
+(9,6),
+(1,7),
+(3,7),
 (8,7),
+(1,8),
+(6,8),
 (8,8),
+(1,9),
 (8,9),
+(1,10),
+(5,10),
 (8,10),
+(1,11),
 (8,11),
-(8,18),
-(8,20),
-(8,23),
-(8,26),
-(8,29),
-(8,37),
-(8,49),
-(9,1),
-(9,6),
 (10,12),
-(10,77),
 (11,13),
 (11,15),
 (11,16),
 (11,17),
-(11,32),
-(11,43),
-(11,55),
-(11,58),
-(11,64),
+(1,18),
+(8,18),
 (12,18),
-(14,1),
+(1,20),
+(4,20),
+(8,20),
+(1,23),
+(2,23),
+(3,23),
+(6,23),
+(8,23),
+(28,23),
+(8,26),
 (17,26),
+(8,29),
 (20,29),
-(24,1),
-(28,23),
+(11,32),
+(8,37),
 (28,37),
+(11,43),
+(1,49),
+(8,49),
 (34,49),
-(39,69);
+(11,55),
+(11,58),
+(11,64),
+(39,69),
+(10,77),
+(2,80);
 /*!40000 ALTER TABLE `UserGroup_has_Permission` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ScanParametersService` DISABLE KEYS */;

schemas/ispyb/tables.sql

@@ -2210,6 +2210,39 @@ CREATE TABLE `Laboratory` (
   PRIMARY KEY (`laboratoryId`)
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci;
 /*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `LaserParameters`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8mb4 */;
+CREATE TABLE `LaserParameters` (
+  `laserParametersId` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  `robotActionId` int(11) unsigned DEFAULT NULL,
+  `laserRepetitionRate` float DEFAULT NULL COMMENT 'Laser repetition rate, in kHz',
+  `scanheadMoveSpeed` float DEFAULT NULL COMMENT 'Scanhead move speed, in m/s',
+  `laserTransmission` float DEFAULT NULL COMMENT 'Laser transmission, in %',
+  `numberOfPasses` int(10) unsigned DEFAULT NULL,
+  `gonioRotationSpeed` int(10) DEFAULT NULL COMMENT 'Goniometer rotation speed, in deg/s',
+  `totalMarkingTime` float DEFAULT NULL COMMENT 'Total marking time, in s',
+  PRIMARY KEY (`laserParametersId`),
+  KEY `LaserParameters_fk_robotActionId` (`robotActionId`),
+  CONSTRAINT `LaserParameters_fk_robotActionId` FOREIGN KEY (`robotActionId`) REFERENCES `RobotAction` (`robotActionId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_ai_ci COMMENT='Laser parameters';
+/*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `LaserPoint`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8mb4 */;
+CREATE TABLE `LaserPoint` (
+  `laserPointId` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  `laserParametersId` int(11) unsigned DEFAULT NULL,
+  `x` int(10) unsigned NOT NULL COMMENT 'X coordinate of point, in microns',
+  `y` int(10) unsigned NOT NULL COMMENT 'Y coordinate of point, in microns',
+  `pointIndex` int(10) NOT NULL COMMENT 'Index of point, expresses ordinality',
+  `radius` int(10) unsigned DEFAULT NULL COMMENT 'Radius of point, in microns',
+  `laserOn` tinyint(1) DEFAULT 0,
+  PRIMARY KEY (`laserPointId`),
+  KEY `LaserPoint_fk_laserParametersId` (`laserParametersId`),
+  CONSTRAINT `LaserPoint_fk_laserParametersId` FOREIGN KEY (`laserParametersId`) REFERENCES `LaserParameters` (`laserParametersId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_ai_ci COMMENT='Laser points';
+/*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `Ligand`;
 /*!40101 SET @saved_cs_client     = @@character_set_client */;
 /*!40101 SET character_set_client = utf8mb4 */;
@@ -3057,7 +3090,7 @@ CREATE TABLE `RobotAction` (
   `robotActionId` int(11) unsigned NOT NULL AUTO_INCREMENT,
   `blsessionId` int(11) unsigned NOT NULL,
   `blsampleId` int(11) unsigned DEFAULT NULL,
-  `actionType` enum('LOAD','UNLOAD','DISPOSE','STORE','WASH','ANNEAL','MOSAIC') DEFAULT NULL,
+  `actionType` enum('LOAD','UNLOAD','DISPOSE','STORE','WASH','ANNEAL','MOSAIC','LASER') DEFAULT NULL,
   `startTimestamp` timestamp NOT NULL DEFAULT current_timestamp() ON UPDATE current_timestamp(),
   `endTimestamp` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00',
   `status` enum('SUCCESS','ERROR','CRITICAL','WARNING','EPICSFAIL','COMMANDNOTSENT') DEFAULT NULL,

schemas/ispyb/updates/2025_11_20_AdminVar_bump_version.sql

@@ -0,0 +1,5 @@
+INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_11_20_AdminVar_bump_version.sql', 'ONGOING');
+
+UPDATE AdminVar SET `value` = '4.10.0' WHERE `name` = 'schemaVersion';
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_11_20_AdminVar_bump_version.sql';