From 3cb031a857b7ebef0c8b1c4ae95edf454d91f3a9 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Tue, 31 Aug 2021 16:35:16 +0100 Subject: [PATCH] Update HISTORY.md and refresh schema files/doc --- HISTORY.rst | 18 +++++++++++++++++- docs/list_of_procs.rst | 10 ++++++++++ schemas/ispyb/lookups.sql | 8 ++++---- schemas/ispyb/routines.sql | 38 ++++++++++++++++++++++++++++++++++++-- schemas/ispyb/tables.sql | 3 ++- 5 files changed, 69 insertions(+), 8 deletions(-) diff --git a/HISTORY.rst b/HISTORY.rst index 1ea20ad2..65e840b3 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,23 @@ History Unreleased / master ------------------- +1.26.0 (2021-08-31) +------------------- + +Column changes: + +* Add a source column to the PDB table + +Stored procedure changes: + +* New stored procedure ``update_dewar_comments_json_merge`` to JSON merge the Dewar comments with a parameter +* Add 'plan' prefix to new DCPlan column aliases in ``retrieve_scm_sample*`` stored procedures (bug) + +Lookup table data changes: + +* Fill in some missing properties for container types + + 1.25.1 (2021-07-28) ------------------- @@ -23,7 +40,6 @@ New versions of stored procedures: * ``upsert_particle_classification_v2`` - new parameter ``p_classDistribution`` - 1.24.0 (2021-07-23) ------------------- diff --git a/docs/list_of_procs.rst b/docs/list_of_procs.rst index 2e884cf0..95e6acd3 100644 --- a/docs/list_of_procs.rst +++ b/docs/list_of_procs.rst @@ -208,11 +208,21 @@ For insert: p_particlePickerId For update: p_id Returns: Record ID in p_id." + "**upsert_particle_classification_v2**", "INOUT p_id int unsigned, p_particleClassificationGroupId int unsigned, p_classNumber int unsigned, p_classImageFullPath varchar(255), p_particlesPerClass int unsigned, p_classDistribution float, p_rotationAccuracy float, p_translationAccuracy float, p_estimatedResolution float, p_overallFourierCompleteness float", "Inserts or updates info about a particle classification (p_id). + Mandatory columns: + For insert: p_particleClassificationGroupId + For update: p_id + Returns: Record ID in p_id." "**upsert_particle_picker**", "INOUT p_id int(11) unsigned, p_firstMotionCorrectionId int(11) unsigned, p_programId int(11) unsigned, p_particlePickingTemplate varchar(255), p_particleDiameter float, p_numberOfParticles int unsigned", "Inserts or updates info about a particle picker (p_id). Mandatory columns: For insert: p_firstMotionCorrectionId For update: p_id Returns: Record ID in p_id." + "**upsert_particle_picker_v2**", "INOUT p_id int(11) unsigned, p_firstMotionCorrectionId int(11) unsigned, p_programId int(11) unsigned, p_particlePickingTemplate varchar(255), p_particleDiameter float, p_numberOfParticles int unsigned, p_summaryImageFullPath varchar(255)", "Inserts or updates info about a particle picker (p_id). + Mandatory columns: + For insert: p_firstMotionCorrectionId + For update: p_id + Returns: Record ID in p_id." "**upsert_person**", "INOUT p_id int(10) unsigned, p_laboratoryId int(10) unsigned, p_familyName varchar(100), p_givenName varchar(45), p_title varchar(45), p_emailAddress varchar(60), p_phoneNumber varchar(45), p_login varchar(45), p_externalPkId int(11) unsigned, p_externalPkUUID varchar(32)", "Inserts or updates info about a person (p_id). 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`dropPerWellX`, `dropPerWellY`, `dropHeight`, `dropWidth`, `dropOffsetX`, `dropOffsetY`, `wellDrop`) VALUES 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3 Drop','mx',1,288,12,3,1,0.5,1,0,0,-1),(19,'MRC Maxi','mx',1,48,6,1,1,1,0.5,0,0,-1),(20,'MRC 2 Drop','mx',1,192,12,1,2,1,0.5,0.5,0,-1),(21,'Griener 1536','mx',1,1536,12,4,4,1,1,0,0,-1),(22,'3 Drop Square','mx',1,288,12,2,2,1,1,0,0,3),(23,'SWISSCI 3 Drop','mx',1,288,12,2,2,1,1,0,0,1),(24,'1 drop','mx',1,96,12,1,1,0.5,0.5,0,0,-1),(25,'LCP Glass','mx',1,96,12,1,1,1,1,0,0,-1),(26,'PCRStrip','saxs',1,9,9,1,1,1,1,0,0,-1),(27,'Basket','mx',0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(28,'Cane','mx',0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(29,'Terasaki72','mx',0,72,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(30,'Puck-16','mx',1,16,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(31,'Block-4','mx',1,16,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(32,'Box','xpdf',1,25,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(33,'Puck-22','xpdf',1,22,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(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); /*!40000 ALTER TABLE `ContainerType` ENABLE KEYS */; -- @@ -248,4 +248,4 @@ INSERT INTO `ScanParametersService` (`scanParametersServiceId`, `name`, `descrip /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-07-28 12:13:38 +-- Dump completed on 2021-08-31 11:30:56 diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index 6208b551..90101a16 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -7608,6 +7608,40 @@ DELIMITER ; /*!50003 SET character_set_client = @saved_cs_client */ ; /*!50003 SET character_set_results = @saved_cs_results */ ; /*!50003 SET collation_connection = @saved_col_connection */ ; +/*!50003 DROP PROCEDURE IF EXISTS `update_dewar_comments_json_merge` */; +/*!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 = utf8 */ ; +/*!50003 SET character_set_results = utf8 */ ; +/*!50003 SET collation_connection = utf8_general_ci */ ; +/*!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' */ ; +DELIMITER ;; +CREATE PROCEDURE `update_dewar_comments_json_merge`( + IN p_id int(10) unsigned, + p_comments JSON +) + MODIFIES SQL DATA + COMMENT 'Merges in additional JSON into the comments column on a dewar/parcel (p_id).\nMandatory columns: p_id \nReturns: Nothing' +BEGIN + IF p_id IS NOT NULL THEN + IF JSON_VALID(p_comments) THEN + UPDATE Dewar + SET comments = JSON_MERGE_PRESERVE(IFNULL(comments, '{}'), p_comments) + WHERE dewarId = p_id; + ELSE + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_comments is invalid JSON'; + END IF; + ELSE + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_id is NULL'; + 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 DROP PROCEDURE IF EXISTS `update_processing_program_for_id_range` */; /*!50003 SET @saved_cs_client = @@character_set_client */ ; /*!50003 SET @saved_cs_results = @@character_set_results */ ; @@ -11166,7 +11200,7 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-07-28 12:13:38 +-- Dump completed on 2021-08-31 16:30:17 -- MariaDB dump 10.19 Distrib 10.5.10-MariaDB, for Linux (x86_64) -- -- Host: 10.88.0.5 Database: ispyb_build @@ -11213,4 +11247,4 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-07-28 12:13:38 +-- Dump completed on 2021-08-31 16:30:17 diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index a69556e8..250b9b9a 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -3150,6 +3150,7 @@ CREATE TABLE `PDB` ( `name` varchar(255) DEFAULT NULL, `contents` mediumtext DEFAULT NULL, `code` varchar(4) DEFAULT NULL, + `source` varchar(30) DEFAULT NULL COMMENT 'Could be e.g. AlphaFold or RoseTTAFold', PRIMARY KEY (`pdbId`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; @@ -6127,4 +6128,4 @@ CREATE TABLE `zc_ZocaloBuffer` ( /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-07-23 18:38:10 +-- Dump completed on 2021-08-31 11:30:55