Preparations for release 4.11.0

Author: gfrn

RELEASE.md

@@ -6,6 +6,6 @@ This procedure requires write permission to the repository and a valid `.github-
 2. Run `./build.sh`: This will create a clean development database using the schema files in `schemas/ispyb/` and then import any `updates/` files not yet imported.
 3. Manually import any stored programs committed since the previous release.
 4. Create a backup: `cd bin && ./backup.sh /tmp/`.
-5. Copy `/tmp/lookups.sh` to `schemas/ispyb/`. If other changes have been made since the previous release, then you might need to copy other files to the same folder: If any changes to the tables or views, then also copy `/tmp/tables.sql`. If any changes to the stored programs, then also copy `/tmp/routines.sql`. If any changes to the test data, then also copy `/tmp/data.sql`.
+5. Copy `/tmp/lookups.sql` to `schemas/ispyb/`. If other changes have been made since the previous release, then you might need to copy other files to the same folder: If any changes to the tables or views, then also copy `/tmp/tables.sql`. If any changes to the stored programs, then also copy `/tmp/routines.sql`. If any changes to the test data, then also copy `/tmp/data.sql`.
 6. Commit and push your changes to master.
 7. Finally, run the `release.sh` script to create a tag and create a Github release against that tag. The new release should then become available on the project's Github page.

schemas/ispyb/data.sql

@@ -950,11 +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 (6988,55167),
-(7227,55168),
-(474,339525),
+INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (474,339525),
 (477,339528),
-(480,339531);
+(480,339531),
+(6988,55167),
+(7227,55168);
 /*!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','4.10.0');
+INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.11.0');
 /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */;
@@ -303,7 +303,10 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
 (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');
+(334,'2025_11_20_AdminVar_bump_version.sql','DONE','2025-11-20 15:47:48'),
+(335,'2026_01_05_GridSquare_Atlas_channels.sql ','DONE','2026-01-13 15:16:00'),
+(336,'2026_01_12_CTF_iceRingDensity.sql','DONE','2026-01-13 15:16:00'),
+(337,'2026_01_13_AdminVar_bump_version.sql','DONE','2026-01-13 15:16:00');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;
@@ -855,63 +858,63 @@ 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),
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+(2,23),
+(2,80),
+(3,7),
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+(9,1),
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-(2,80);
+(12,18),
+(14,1),
+(17,26),
+(20,29),
+(24,1),
+(28,23),
+(28,37),
+(34,49),
+(39,69);
 /*!40000 ALTER TABLE `UserGroup_has_Permission` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ScanParametersService` DISABLE KEYS */;

schemas/ispyb/tables.sql

@@ -54,6 +54,14 @@ CREATE TABLE `Atlas` (
   `atlasImage` varchar(255) NOT NULL COMMENT 'path to atlas image',
   `pixelSize` float NOT NULL COMMENT 'pixel size of atlas image',
   `cassetteSlot` int(10) unsigned DEFAULT NULL,
+  `hasRed` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has red channel',
+  `hasBlue` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has blue channel',
+  `hasGreen` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has green channel',
+  `hasYellow` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has yellow channel',
+  `hasCyan` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has cyan channel',
+  `hasMagenta` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has magenta channel',
+  `hasGrey` tinyint(1) DEFAULT 0 COMMENT 'Whether atlas has grey channel',
+  `mode` enum('Bright Field and Fluorescent','Bright Field','Fluorescent','Tomography','Single Particle') DEFAULT NULL COMMENT 'Collection mode',
   PRIMARY KEY (`atlasId`),
   KEY `Atlas_fk_dataCollectionGroupId` (`dataCollectionGroupId`),
   CONSTRAINT `Atlas_fk_dataCollectionGroupId` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) ON UPDATE CASCADE
@@ -950,6 +958,7 @@ CREATE TABLE `CTF` (
   `ccValue` float DEFAULT NULL COMMENT 'Correlation value',
   `fftTheoreticalFullPath` varchar(255) DEFAULT NULL COMMENT 'Full path to the jpg image of the simulated FFT',
   `comments` varchar(255) DEFAULT NULL,
+  `iceRingDensity` float DEFAULT NULL COMMENT 'Summed intensity of ice ring in fourier space',
   PRIMARY KEY (`ctfId`),
   KEY `CTF_ibfk1` (`motionCorrectionId`),
   KEY `CTF_ibfk2` (`autoProcProgramId`),
@@ -2040,6 +2049,14 @@ CREATE TABLE `GridSquare` (
   `stageLocationY` float DEFAULT NULL COMMENT 'y stage position (microns)',
   `qualityIndicator` float DEFAULT NULL COMMENT 'metric for determining quality of grid square',
   `pixelSize` float DEFAULT NULL COMMENT 'pixel size of grid square image',
+  `hasRed` tinyint(1) DEFAULT 0 COMMENT 'Whether region has red channel',
+  `hasBlue` tinyint(1) DEFAULT 0 COMMENT 'Whether region has blue channel',
+  `hasGreen` tinyint(1) DEFAULT 0 COMMENT 'Whether region has green channel',
+  `hasYellow` tinyint(1) DEFAULT 0 COMMENT 'Whether region has yellow channel',
+  `hasCyan` tinyint(1) DEFAULT 0 COMMENT 'Whether region has cyan channel',
+  `hasMagenta` tinyint(1) DEFAULT 0 COMMENT 'Whether region has magenta channel',
+  `hasGrey` tinyint(1) DEFAULT 0 COMMENT 'Whether region has grey channel',
+  `mode` enum('Bright Field and Fluorescent','Bright Field','Fluorescent','Tomography','Single Particle') DEFAULT NULL COMMENT 'Collection mode',
   PRIMARY KEY (`gridSquareId`),
   KEY `GridSquare_fk_atlasId` (`atlasId`),
   CONSTRAINT `GridSquare_fk_atlasId` FOREIGN KEY (`atlasId`) REFERENCES `Atlas` (`atlasId`) ON UPDATE CASCADE

schemas/ispyb/updates/2026_01_13_AdminVar_bump_version.sql

@@ -0,0 +1,5 @@
+INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2026_01_13_AdminVar_bump_version.sql', 'ONGOING');
+
+UPDATE AdminVar SET `value` = '4.11.0' WHERE `name` = 'schemaVersion';
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2026_01_13_AdminVar_bump_version.sql';