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Merged
KarlLevik merged 2 commits into from
Jun 27, 2025
Merged

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

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b171190
Use 'if not exists' when creating role
KarlLevik Jun 27, 2025
fee2848
Refresh schema files
KarlLevik Jun 27, 2025
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2 changes: 1 addition & 1 deletion grants/ispyb_expeye.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down
11 changes: 9 additions & 2 deletions schemas/ispyb/lookups.sql
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Expand Up @@ -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 */;
Expand Down Expand Up @@ -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 */;
Expand Down
118 changes: 113 additions & 5 deletions schemas/ispyb/routines.sql
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Expand Up @@ -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;

Expand Down Expand Up @@ -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 */ ;
Expand Down
49 changes: 47 additions & 2 deletions schemas/ispyb/tables.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -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 */;
Expand Down Expand Up @@ -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 */;
Expand Down Expand Up @@ -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`),
Expand Down Expand Up @@ -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`),
Expand Down Expand Up @@ -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 */;
Expand Down Expand Up @@ -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
Expand Down