Preparations for release 4.7.0 (#275)

Author: gfrn

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','4.6.0');
+INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.7.0');
 /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */;
@@ -278,7 +278,16 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
 (306,'2025_02_25_AdminVar_bump_version.sql','DONE','2025-02-25 15:51:30'),
 (307,'2025_02_27_ExperimentType_atlas.sql','DONE','2025-03-06 11:58:07'),
 (308,'2025_03_05_Dewar_dewarRegistryId.sql','DONE','2025-03-06 11:58:07'),
-(309,'2025_03_06_AdminVar_bump_version.sql','DONE','2025-03-06 11:58:07');
+(309,'2025_03_06_AdminVar_bump_version.sql','DONE','2025-03-06 11:58:07'),
+(310,'2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql','DONE','2025-05-09 15:21:06'),
+(311,'2025_04_11_Position_blSampleId_positionType.sql','DONE','2025-05-09 15:21:06'),
+(312,'2025_04_16_labContacts_fk_on_delete_set_null.sql','DONE','2025-05-09 15:21:06'),
+(313,'2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql','DONE','2025-05-09 15:21:06'),
+(314,'2025_04_30_Shipping_fk_personId_on_delete_set_null.sql','DONE','2025-05-09 15:21:06'),
+(315,'2025_05_01_BLSamplePosition.sql','DONE','2025-05-09 15:21:06'),
+(316,'2025_05_01_XrayCentringResult_fk_blSampleId.sql','DONE','2025-05-09 15:21:06'),
+(317,'2025_05_02_BLSamplePosition_rename_column.sql','DONE','2025-05-09 15:21:06'),
+(318,'2025_05_12_AdminVar_bump_version.sql','DONE','2025-05-09 15:21:06');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;

schemas/ispyb/routines.sql

@@ -7456,30 +7456,61 @@ BEGIN
     DECLARE row_beamlineLocation varchar(20) DEFAULT NULL;
     DECLARE row_sampleChangerLocation varchar(20) DEFAULT NULL;
     DECLARE row_proposalId int(10) unsigned DEFAULT NULL;
+    DECLARE row_proposalCode varchar(45) DEFAULT NULL;
+    DECLARE row_proposalNumber varchar(45) DEFAULT NULL;
     DECLARE row_queuedCount int(11) unsigned DEFAULT NULL;
+    DECLARE row_samples varchar(255) DEFAULT NULL;
+
+    IF p_beamline IS NULL THEN
+      SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_beamline is NULL';
+    END IF;
 
     IF NOT (p_registry_barcode IS NULL) THEN
         START TRANSACTION;
 
-        SELECT c.containerId, c.containerStatus, c.dewarId, c.beamlineLocation, c.sampleChangerLocation, s.proposalId, count(cq.containerQueueId)
-          INTO row_containerId, row_containerStatus, row_dewarId, row_beamlineLocation, row_sampleChangerLocation, row_proposalId, row_queuedCount
+        SELECT c.containerId,
+          c.containerStatus,
+          c.dewarId,
+          c.beamlineLocation,
+          c.sampleChangerLocation,
+          p.proposalId,
+          p.proposalCode,
+          p.proposalNumber,
+          count(cq.containerQueueId)
+        INTO row_containerId,
+          row_containerStatus,
+          row_dewarId,
+          row_beamlineLocation,
+          row_sampleChangerLocation,
+          row_proposalId,
+          row_proposalCode,
+          row_proposalNumber,
+          row_queuedCount
         FROM Container c
             INNER JOIN ContainerRegistry cr ON c.containerRegistryId = cr.containerRegistryId
             INNER JOIN Dewar d ON d.dewarId = c.dewarId
             INNER JOIN Shipping s ON s.shippingId = d.shippingId
+            INNER JOIN Proposal p ON p.proposalId = s.proposalId
             LEFT OUTER JOIN ContainerQueue cq ON cq.containerId = c.containerId
         WHERE cr.barcode = p_registry_barcode
-        GROUP BY c.containerId, c.containerStatus, c.dewarId, c.beamlineLocation, c.sampleChangerLocation, s.proposalId
+        GROUP BY c.containerId,
+          c.containerStatus,
+          c.dewarId,
+          c.beamlineLocation,
+          c.sampleChangerLocation,
+          p.proposalId,
+          p.proposalCode,
+          p.proposalNumber
         ORDER BY c.containerId DESC
         LIMIT 1;
 
         SELECT row_containerStatus INTO currentContainerStatus;
 
-
+        
         IF NOT row_containerId IS NULL THEN
           IF (NOT row_containerStatus <=> 'processing') OR (row_beamlineLocation = p_beamline AND row_sampleChangerLocation = p_position) THEN
 
-
+            
             UPDATE Container c
               INNER JOIN Dewar d ON d.dewarId = c.dewarId
               INNER JOIN Shipping s ON s.shippingId = d.shippingId
@@ -7496,8 +7527,8 @@ BEGIN
             SELECT IF(row_containerStatus<=>'processing', 'at facility', 'processing') INTO currentContainerStatus;
 
             IF NOT row_containerStatus <=> 'processing' THEN
-
-
+              
+              
               UPDATE Container c
                 INNER JOIN Dewar d ON d.dewarId = c.dewarId
                 INNER JOIN Shipping s ON s.shippingId = d.shippingId
@@ -7506,12 +7537,12 @@ BEGIN
               WHERE s.proposalId = row_proposalId AND c.beamlineLocation = p_beamline AND
                 c.sampleChangerLocation = p_position AND c.containerId <> row_containerId;
 
-
+              
               INSERT INTO DewarTransportHistory (dewarId, dewarStatus, storageLocation, arrivalDate)
                 VALUES (row_dewarId, 'processing', p_beamline, NOW());
             END IF;
 
-
+            
             INSERT INTO ContainerHistory (containerId, location, status, beamlineName, currentDewarId)
               SELECT row_containerId, p_position, IF(row_containerStatus<=>'processing', 'at facility', 'processing'), p_beamline, currentDewarId
               FROM Container
@@ -7525,9 +7556,19 @@ BEGIN
     ELSE
         SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_registry_barcode is NULL';
     END IF;
+
+    SELECT group_concat(location ORDER BY cast(location AS integer) SEPARATOR ',')
+      INTO row_samples
+    FROM BLSample
+    WHERE containerId = row_containerId
+    GROUP BY containerId;
+
     SELECT row_containerId as "containerId",
       currentContainerStatus as "containerStatus",
-      row_queuedCount as "queuedCount";
+      row_proposalCode as "proposalCode",
+      row_proposalNumber as "proposalNumber",
+      row_queuedCount as "queuedCount",
+      row_samples as "samples";
 END ;;
 DELIMITER ;
 /*!50003 SET sql_mode              = @saved_sql_mode */ ;

schemas/ispyb/tables.sql

@@ -605,6 +605,22 @@ CREATE TABLE `BLSampleImage_has_Positioner` (
   CONSTRAINT `BLSampleImageHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`)
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Allows a BLSampleImage to store motor positions along with the image';
 /*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `BLSamplePosition`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8mb4 */;
+CREATE TABLE `BLSamplePosition` (
+  `blSamplePositionId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)',
+  `blSampleId` int(11) unsigned NOT NULL COMMENT 'FK, references parent sample',
+  `posX` double DEFAULT NULL,
+  `posY` double DEFAULT NULL,
+  `posZ` double DEFAULT NULL,
+  `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time',
+  `positionType` enum('dispensing') DEFAULT NULL COMMENT 'Type of marked position (e.g.: dispensing location)',
+  PRIMARY KEY (`blSamplePositionId`),
+  KEY `BLSamplePosition_fk_blSampleId` (`blSampleId`),
+  CONSTRAINT `BLSamplePosition_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
+/*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `BLSampleType`;
 /*!40101 SET @saved_cs_client     = @@character_set_client */;
 /*!40101 SET character_set_client = utf8mb4 */;
@@ -1687,7 +1703,7 @@ CREATE TABLE `DewarRegistry_has_Proposal` (
   CONSTRAINT `DewarRegistry_has_Proposal_ibfk1` FOREIGN KEY (`dewarRegistryId`) REFERENCES `DewarRegistry` (`dewarRegistryId`),
   CONSTRAINT `DewarRegistry_has_Proposal_ibfk2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`),
   CONSTRAINT `DewarRegistry_has_Proposal_ibfk3` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`),
-  CONSTRAINT `DewarRegistry_has_Proposal_ibfk4` FOREIGN KEY (`labContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE NO ACTION ON UPDATE CASCADE
+  CONSTRAINT `DewarRegistry_has_Proposal_ibfk4` FOREIGN KEY (`labContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `DewarReport`;
@@ -2396,6 +2412,8 @@ CREATE TABLE `ParticleClassification` (
   `bFactorFitIntercept` float DEFAULT NULL COMMENT 'Intercept of quadratic fit to refinement resolution against the logarithm of the number of particles',
   `bFactorFitLinear` float DEFAULT NULL COMMENT 'Linear coefficient of quadratic fit to refinement resolution against the logarithm of the number of particles, equal to half of the B factor',
   `bFactorFitQuadratic` float DEFAULT NULL COMMENT 'Quadratic coefficient of quadratic fit to refinement resolution against the logarithm of the number of particles',
+  `angularEfficiency` double DEFAULT NULL COMMENT 'Variation in resolution across different angles, 1-2sig/mean',
+  `suggestedTilt` double DEFAULT NULL COMMENT 'Suggested stage tilt angle to improve angular efficiency. Unit: degrees',
   PRIMARY KEY (`particleClassificationId`),
   KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`),
   CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE
@@ -3456,9 +3474,9 @@ CREATE TABLE `Shipping` (
   KEY `Shipping_FKIndexStatus` (`shippingStatus`),
   KEY `Shipping_ibfk_4` (`deliveryAgent_flightCodePersonId`),
   CONSTRAINT `Shipping_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE,
-  CONSTRAINT `Shipping_ibfk_2` FOREIGN KEY (`sendingLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE CASCADE ON UPDATE CASCADE,
-  CONSTRAINT `Shipping_ibfk_3` FOREIGN KEY (`returnLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE CASCADE ON UPDATE CASCADE,
-  CONSTRAINT `Shipping_ibfk_4` FOREIGN KEY (`deliveryAgent_flightCodePersonId`) REFERENCES `Person` (`personId`)
+  CONSTRAINT `Shipping_ibfk_2` FOREIGN KEY (`sendingLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE,
+  CONSTRAINT `Shipping_ibfk_3` FOREIGN KEY (`returnLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE,
+  CONSTRAINT `Shipping_ibfk_4` FOREIGN KEY (`deliveryAgent_flightCodePersonId`) REFERENCES `Person` (`personId`) ON DELETE SET NULL ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `ShippingHasSession`;
@@ -3762,8 +3780,11 @@ CREATE TABLE `XrayCentringResult` (
   `boundingBoxMaxZ` float DEFAULT NULL COMMENT 'Maximum z-coordinate of the bounding box containing the crystal (in voxels)',
   `status` enum('success','failure','pending') DEFAULT NULL COMMENT 'to be removed',
   `gridInfoId` int(11) unsigned DEFAULT NULL COMMENT 'to be removed',
+  `blSampleId` int(11) unsigned DEFAULT NULL COMMENT 'The BLSample attributed for this x-ray centring result, i.e. the actual sample even for multi-pins',
   PRIMARY KEY (`xrayCentringResultId`),
   KEY `xrayCentringId` (`xrayCentringId`),
+  KEY `XrayCentringResult_fk_blSampleId` (`blSampleId`),
+  CONSTRAINT `XrayCentringResult_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE SET NULL ON UPDATE CASCADE,
   CONSTRAINT `XrayCentringResult_ibfk_1` FOREIGN KEY (`xrayCentringId`) REFERENCES `XrayCentring` (`xrayCentringId`) ON DELETE CASCADE ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Xray Centring result.';
 /*!40101 SET character_set_client = @saved_cs_client */;

schemas/ispyb/updates/2025_05_12_AdminVar_bump_version.sql

@@ -0,0 +1,5 @@
+INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_12_AdminVar_bump_version.sql', 'ONGOING');
+
+UPDATE AdminVar SET `value` = '4.7.0' WHERE `name` = 'schemaVersion';
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_12_AdminVar_bump_version.sql';