Update HISTORY.md and refresh schema files/doc

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)
 -------------------
 

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).
  Mandatory columns:
  For insert: login

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

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