Refresh schema files and fix minor bug in grants file (#288)

* Use 'if not exists' when creating role

* Refresh schema files

Author: KarlLevik

grants/ispyb_expeye.sql

@@ -8,7 +8,7 @@ CREATE ROLE IF NOT EXISTS ispyb_expeye_core_role;
 
 GRANT ispyb_propagation TO ispyb_expeye_core_role;
 
-CREATE ROLE ispyb_expeye_acquisition_role;
+CREATE ROLE IF NOT EXISTS ispyb_expeye_acquisition_role;
 
 GRANT SELECT, INSERT, UPDATE, DELETE ON Proposal TO ispyb_expeye_acquisition_role;
 GRANT SELECT, INSERT, UPDATE, DELETE ON BLSession TO ispyb_expeye_acquisition_role;

schemas/ispyb/lookups.sql

@@ -287,7 +287,13 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
 (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');
+(318,'2025_05_12_AdminVar_bump_version.sql','DONE','2025-05-09 15:21:06'),
+(319,'2025_05_14_BLSamplePosition_recordTimeStamp_default.sql','DONE','2025-06-27 16:04:05'),
+(320,'2025_05_23_Ligand_and_junction_tables.sql','DONE','2025-06-27 16:04:05'),
+(321,'2025_05_28_BLSession_icatId.sql','DONE','2025-06-27 16:04:05'),
+(322,'2025_06_02_DewarRegistry_type.sql','DONE','2025-06-27 16:04:05'),
+(323,'2025_06_26_ContainerType_cryoem_puck.sql','DONE','2025-06-27 16:04:05'),
+(324,'2025_06_27_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:04:05');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;
@@ -358,7 +364,8 @@ INSERT INTO `ContainerType` (`containerTypeId`, `name`, `proposalType`, `active`
 (34,'I22_Grid_81','saxs',1,81,9,1,1,1,1,0,0,-1),
 (35,'I22_Capillary_Rack_25','saxs',1,25,25,1,1,1,1,0,0,-1),
 (36,'VMXm-Cartridge','mx',1,5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),
-(37,'VMXm-GridBox','mx',1,4,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
+(37,'VMXm-GridBox','mx',1,4,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),
+(38,'Cryo-EM Puck','mx',1,12,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
 /*!40000 ALTER TABLE `ContainerType` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ExperimentType` DISABLE KEYS */;

schemas/ispyb/routines.sql

@@ -4190,25 +4190,27 @@ BEGIN
             SELECT
                 d.dewarId "id", d.shippingId "shippingId", d.code "name", d.comments "comments", d.storageLocation "storageLocation",
                 d.dewarStatus "status", d.isStorageDewar "isStorageDewar", d.barCode "barCode", d.firstExperimentId "firstSessionId",
-				d.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode"
+				        dr.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode"
             FROM Dewar d
+                LEFT JOIN DewarRegistry dr ON dr.facilityCode = d.facilityCode
                 INNER JOIN Shipping s ON s.shippingId = d.shippingId
-		        INNER JOIN Proposal p ON p.proposalId = s.proposalId
+		            INNER JOIN Proposal p ON p.proposalId = s.proposalId
                 INNER JOIN BLSession bs ON bs.proposalId = s.proposalId
                 INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId
                 INNER JOIN Person per ON per.personId = shp.personId
             WHERE per.login = p_authLogin AND p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber
             GROUP BY d.dewarId, d.shippingId, d.code, d.comments, d.storageLocation,
                 d.dewarStatus, d.isStorageDewar, d.barCode, d.firstExperimentId,
-				d.type, d.facilityCode, d.weight, d.deliveryAgent_barcode;
+				        dr.type, d.facilityCode, d.weight, d.deliveryAgent_barcode;
         ELSE
             SELECT
                 d.dewarId "id", d.shippingId "shippingId", d.code "name", d.comments "comments", d.storageLocation "storageLocation",
                 d.dewarStatus "status", d.isStorageDewar "isStorageDewar", d.barCode "barCode", d.firstExperimentId "firstSessionId",
-				d.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode"
+				        dr.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode"
             FROM Dewar d
+                LEFT JOIN DewarRegistry dr ON dr.facilityCode = d.facilityCode
                 INNER JOIN Shipping s ON s.shippingId = d.shippingId
-		        INNER JOIN Proposal p ON p.proposalId = s.proposalId
+		            INNER JOIN Proposal p ON p.proposalId = s.proposalId
             WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber;
         END IF;
 
@@ -9996,6 +9998,112 @@ DELIMITER ;
 /*!50003 SET character_set_results = @saved_cs_results */ ;
 /*!50003 SET collation_connection  = @saved_col_connection */ ;
 /*!50003 SET @saved_sql_mode       = @@sql_mode */ ;
+/*!50003 SET sql_mode              = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+/*!50003 DROP PROCEDURE IF EXISTS `upsert_dewar_v3` */;
+/*!50003 SET @saved_cs_client      = @@character_set_client */ ;
+/*!50003 SET @saved_cs_results     = @@character_set_results */ ;
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client  = utf8mb3 */ ;
+/*!50003 SET character_set_results = utf8mb3 */ ;
+/*!50003 SET collation_connection  = utf8mb3_general_ci */ ;
+DELIMITER ;;
+CREATE PROCEDURE `upsert_dewar_v3`(
+
+	 INOUT p_id int(10) unsigned,
+	 p_authLogin varchar(45),
+	 p_shippingId int(10) unsigned,
+	 p_name varchar(45),
+	 p_comments tinytext,
+	 p_storageLocation varchar(45),
+	 p_status varchar(45),
+	 p_isStorageDewar tinyint(1),
+	 p_barcode varchar(45),
+	 p_firstSessionId int(10) unsigned,
+	 p_customsValue int(11) unsigned,
+	 p_transportValue int(11) unsigned,
+	 p_trackingNumberToSynchrotron varchar(30),
+	 p_trackingNumberFromSynchrotron varchar(30),
+	 p_facilityCode varchar(20),
+	 p_weight float,
+	 p_deliveryAgentBarcode varchar(30)
+ )
+    MODIFIES SQL DATA
+    COMMENT 'Inserts or updates info about a dewar/parcel (p_id).\nMandatory columns:\nFor insert: none\nFor update: p_id \nReturns: Record ID in p_id.'
+BEGIN
+	DECLARE row_storageLocation varchar(45) DEFAULT NULL;
+	DECLARE row_dewarStatus varchar(45) DEFAULT NULL;
+  DECLARE row_count int unsigned DEFAULT 0;
+
+	IF p_storageLocation IS NULL THEN
+		SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_storageLocation is NULL';
+	END IF;
+
+  IF p_authLogin IS NOT NULL AND p_shippingId IS NOT NULL THEN
+
+    
+    
+    SELECT count(*) INTO row_count
+    FROM Shipping s
+      INNER JOIN BLSession bs ON bs.proposalId = s.proposalId
+      INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId
+      INNER JOIN Person p ON p.personId = shp.personId
+    WHERE p.login = p_authLogin AND s.shippingId = p_shippingId;
+
+    IF row_count = 0 THEN
+        SIGNAL SQLSTATE '02000'
+            SET MYSQL_ERRNO=1643, MESSAGE_TEXT = 'Dewar not in a shipping belonging to one of the p_authLogin Person sessions';
+    END IF;
+  END IF;
+
+  IF p_id IS NULL THEN
+    INSERT INTO Dewar(dewarId,shippingId,code,comments,storageLocation,dewarStatus,isStorageDewar,barCode,firstExperimentId,customsValue,transportValue,
+	    trackingNumberToSynchrotron,trackingNumberFromSynchrotron,FACILITYCODE,weight,deliveryAgent_barcode)
+	    VALUES (p_id, p_shippingId, p_name, p_comments, p_storageLocation, p_status, p_isStorageDewar, p_barcode, p_firstSessionId, p_customsValue, p_transportValue,
+		    p_trackingNumberToSynchrotron, p_trackingNumberFromSynchrotron, p_facilityCode, p_weight, p_deliveryAgentBarcode);
+	  SET p_id = LAST_INSERT_ID();
+	ELSE
+
+    SELECT storageLocation, dewarStatus INTO row_storageLocation, row_dewarStatus FROM Dewar WHERE dewarId = p_id;
+
+		UPDATE Dewar
+			SET shippingId = IFNULL(p_shippingId, shippingId),
+			code = IFNULL(p_name, code),
+			comments = IFNULL(p_comments, comments),
+			storageLocation = IFNULL(p_storageLocation, storageLocation),
+			dewarStatus = IFNULL(p_status, dewarStatus),
+			isStorageDewar = IFNULL(p_isStorageDewar, isStorageDewar),
+			barCode = IFNULL(p_barcode, barCode),
+			firstExperimentId = IFNULL(p_firstSessionId, firstExperimentId),
+			customsValue = IFNULL(p_customsValue, customsValue),
+			transportValue = IFNULL(p_transportValue, transportValue),
+			trackingNumberToSynchrotron = IFNULL(p_trackingNumberToSynchrotron, trackingNumberToSynchrotron),
+			trackingNumberFromSynchrotron = IFNULL(p_trackingNumberFromSynchrotron, trackingNumberFromSynchrotron),
+			FACILITYCODE = IFNULL(p_facilityCode, FACILITYCODE),
+			weight = IFNULL(p_weight, weight),
+			deliveryAgent_barcode = IFNULL(p_deliveryAgentBarcode, deliveryAgent_barcode)
+		WHERE dewarId = p_id;
+
+		
+    IF row_storageLocation <> p_storageLocation OR row_dewarStatus <> p_status THEN
+      INSERT INTO DewarTransportHistory (dewarId, dewarStatus, storageLocation, arrivalDate)
+				VALUES (p_id, p_status, p_storageLocation, NOW());
+    END IF;
+
+		
+		IF row_storageLocation <> p_storageLocation THEN
+			
+      UPDATE Container
+			SET sampleChangerLocation = '', containerStatus = 'at facility'
+			WHERE dewarId = p_id;
+		END IF;
+	END IF;
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode              = @saved_sql_mode */ ;
+/*!50003 SET character_set_client  = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection  = @saved_col_connection */ ;
+/*!50003 SET @saved_sql_mode       = @@sql_mode */ ;
 /*!50003 SET sql_mode              = '' */ ;
 /*!50003 DROP PROCEDURE IF EXISTS `upsert_energy_scan` */;
 /*!50003 SET @saved_cs_client      = @@character_set_client */ ;

schemas/ispyb/tables.sql

@@ -614,12 +614,12 @@ CREATE TABLE `BLSamplePosition` (
   `posX` double DEFAULT NULL,
   `posY` double DEFAULT NULL,
   `posZ` double DEFAULT NULL,
-  `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time',
+  `recordTimeStamp` datetime DEFAULT current_timestamp(),
   `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;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
 /*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `BLSampleType`;
 /*!40101 SET @saved_cs_client     = @@character_set_client */;
@@ -672,6 +672,18 @@ CREATE TABLE `BLSample_has_EnergyScan` (
   CONSTRAINT `BLSample_has_EnergyScan_ibfk_2` FOREIGN KEY (`energyScanId`) REFERENCES `EnergyScan` (`energyScanId`) ON DELETE CASCADE ON UPDATE CASCADE
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `BLSample_has_Ligand`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8mb4 */;
+CREATE TABLE `BLSample_has_Ligand` (
+  `blSampleId` int(10) unsigned NOT NULL,
+  `ligandId` int(11) unsigned NOT NULL,
+  PRIMARY KEY (`blSampleId`,`ligandId`),
+  KEY `BLSample_has_Ligand_fk2` (`ligandId`),
+  CONSTRAINT `BLSample_has_Ligand_fk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT `BLSample_has_Ligand_fk2` FOREIGN KEY (`ligandId`) REFERENCES `Ligand` (`ligandId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Junction table for BLSample and Ligand';
+/*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `BLSample_has_Positioner`;
 /*!40101 SET @saved_cs_client     = @@character_set_client */;
 /*!40101 SET character_set_client = utf8mb4 */;
@@ -709,6 +721,7 @@ CREATE TABLE `BLSession` (
   `archived` tinyint(1) DEFAULT 0 COMMENT 'The data for the session is archived and no longer available on disk',
   `riskRating` enum('Low','Medium','High','Not Permitted') DEFAULT NULL COMMENT 'ERA in user admin system',
   `purgedProcessedData` tinyint(1) DEFAULT 0 COMMENT 'Flag to indicate whether the processed folder in the associated visit directory has been purged',
+  `icatId` int(11) unsigned DEFAULT NULL COMMENT 'The internal ICAT ID for this BLSession',
   PRIMARY KEY (`sessionId`),
   UNIQUE KEY `proposalId` (`proposalId`,`visit_number`),
   KEY `Session_FKIndex2` (`beamLineSetupId`),
@@ -1677,6 +1690,7 @@ CREATE TABLE `DewarRegistry` (
   `purchaseDate` datetime DEFAULT NULL,
   `bltimestamp` datetime NOT NULL DEFAULT current_timestamp(),
   `manufacturerSerialNumber` varchar(15) DEFAULT NULL COMMENT 'Dewar serial number as given by manufacturer. Used to be typically 5 or 6 digits, more likely to be 11 alphanumeric chars in future',
+  `type` enum('Dewar','Toolbox','Thermal Shipper') NOT NULL DEFAULT 'Dewar',
   PRIMARY KEY (`dewarRegistryId`),
   UNIQUE KEY `facilityCode` (`facilityCode`),
   KEY `DewarRegistry_ibfk_1` (`proposalId`),
@@ -2195,6 +2209,35 @@ CREATE TABLE `Laboratory` (
   PRIMARY KEY (`laboratoryId`)
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!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 */;
+CREATE TABLE `Ligand` (
+  `ligandId` int(11) unsigned NOT NULL AUTO_INCREMENT,
+  `proposalId` int(10) unsigned NOT NULL COMMENT 'References Proposal table',
+  `name` varchar(30) NOT NULL COMMENT 'Ligand name',
+  `SMILES` varchar(400) DEFAULT NULL COMMENT 'Chemical structure',
+  `libraryName` varchar(30) DEFAULT NULL COMMENT 'Name of ligand library, to preserve provenance',
+  `libraryBatchNumber` varchar(30) DEFAULT NULL COMMENT 'Batch number of library, to preserve provenance',
+  `plateBarcode` varchar(30) DEFAULT NULL COMMENT 'Specific barcode of the plate it came from, to preserve provenance',
+  `sourceWell` varchar(30) DEFAULT NULL COMMENT 'Location within that plate, to preserve provenance',
+  PRIMARY KEY (`ligandId`),
+  KEY `Ligand_fk_proposalId` (`proposalId`),
+  CONSTRAINT `Ligand_fk_proposalId` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Ligands in biochemistry are substances that bind to biomolecules';
+/*!40101 SET character_set_client = @saved_cs_client */;
+DROP TABLE IF EXISTS `Ligand_has_PDB`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8mb4 */;
+CREATE TABLE `Ligand_has_PDB` (
+  `ligandId` int(11) unsigned NOT NULL,
+  `pdbId` int(11) unsigned NOT NULL,
+  PRIMARY KEY (`ligandId`,`pdbId`),
+  KEY `Ligand_Has_PDB_fk2` (`pdbId`),
+  CONSTRAINT `Ligand_Has_PDB_fk1` FOREIGN KEY (`ligandId`) REFERENCES `Ligand` (`ligandId`) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT `Ligand_Has_PDB_fk2` FOREIGN KEY (`pdbId`) REFERENCES `PDB` (`pdbId`) ON DELETE CASCADE ON UPDATE CASCADE
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Junction table for Ligand and PDB';
+/*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `MXMRRun`;
 /*!40101 SET @saved_cs_client     = @@character_set_client */;
 /*!40101 SET character_set_client = utf8mb4 */;
@@ -2414,6 +2457,8 @@ CREATE TABLE `ParticleClassification` (
   `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',
+  `pixelLocationX` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (x)',
+  `pixelLocationY` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (y)',
   PRIMARY KEY (`particleClassificationId`),
   KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`),
   CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE