Merge pull request #98 from DiamondLightSource/pp_sprocs_v2

New versions of upsert sprocs for particle picker and particle classifiation
DiamondLightSource · Jul 26, 2021 · 4cd3f1f · 4cd3f1f
2 parents 2dab246 + e9a49f6
commit 4cd3f1f
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -5,6 +5,16 @@ History
 Unreleased / master
 -------------------
 
+1.25.0 (2021-07-26)
+-------------------
+
+New versions of stored procedures:
+
+* ``upsert_particle_picker_v2`` - new parameter ``p_summaryImageFullPath``
+* ``upsert_particle_classification_v2`` - new parameter ``p_classDistribution``
+
+
+
 1.24.0 (2021-07-23)
 -------------------
 

diff --git a/grants/ispyb_processing.sql b/grants/ispyb_processing.sql
@@ -136,5 +136,8 @@ GRANT EXECUTE ON PROCEDURE insert_phasing_analysis_results TO 'ispyb_processing'
 
 GRANT EXECUTE ON PROCEDURE insert_cryoem_initial_model TO 'ispyb_processing';
 GRANT EXECUTE ON PROCEDURE upsert_particle_classification TO 'ispyb_processing';
+GRANT EXECUTE ON PROCEDURE upsert_particle_classification_v2 TO 'ispyb_processing';
 GRANT EXECUTE ON PROCEDURE upsert_particle_classification_group TO 'ispyb_processing';
 GRANT EXECUTE ON PROCEDURE upsert_particle_picker TO 'ispyb_processing';
+GRANT EXECUTE ON PROCEDURE upsert_particle_picker_v2 TO 'ispyb_processing';
+
diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql
diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql
@@ -9657,6 +9657,64 @@ 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 `upsert_particle_classification_v2` */;
+/*!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 `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
+ )
+ MODIFIES SQL DATA
+ COMMENT 'Inserts or updates info about a particle classification (p_id).\nMandatory columns:\nFor insert: p_particleClassificationGroupId\nFor update: p_id \nReturns: Record ID in p_id.'
+BEGIN
+ IF p_id IS NOT NULL OR p_particleClassificationGroupId IS NOT NULL THEN
+ INSERT INTO ParticleClassification (particleClassificationId, 
+ particleClassificationGroupId, classNumber, classImageFullPath, 
+ particlesPerClass, classDistribution, rotationAccuracy, 
+ translationAccuracy, estimatedResolution, overallFourierCompleteness)
+ VALUES (p_id, p_particleClassificationGroupId, p_classNumber, 
+ p_classImageFullPath, 
+ p_particlesPerClass, p_classDistribution, p_rotationAccuracy, 
+ p_translationAccuracy, p_estimatedResolution, 
+ p_overallFourierCompleteness)
+ ON DUPLICATE KEY UPDATE
+ particleClassificationGroupId = IFNULL(p_particleClassificationGroupId, particleClassificationGroupId),
+ classNumber = IFNULL(p_classNumber, classNumber),
+ classImageFullPath = IFNULL(p_classImageFullPath, classImageFullPath),
+ particlesPerClass = IFNULL(p_particlesPerClass, particlesPerClass),
+ classDistribution = IFNULL(p_classDistribution, classDistribution),
+ rotationAccuracy = IFNULL(p_rotationAccuracy, rotationAccuracy),
+ translationAccuracy = IFNULL(p_translationAccuracy, translationAccuracy),
+ estimatedResolution = IFNULL(p_estimatedResolution, estimatedResolution),
+ overallFourierCompleteness = IFNULL(p_overallFourierCompleteness, overallFourierCompleteness);
+
+ IF p_id IS NULL THEN
+ SET p_id = LAST_INSERT_ID();
+ END IF;
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument(s) are NULL: p_id OR p_particleClassificationGroupId must be non-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 `upsert_particle_picker` */;
 /*!50003 SET @saved_cs_client = @@character_set_client */ ;
 /*!50003 SET @saved_cs_results = @@character_set_results */ ;
@@ -9700,6 +9758,51 @@ 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 `upsert_particle_picker_v2` */;
+/*!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 `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)
+ )
+ MODIFIES SQL DATA
+ COMMENT 'Inserts or updates info about a particle picker (p_id).\nMandatory columns:\nFor insert: p_firstMotionCorrectionId\nFor update: p_id \nReturns: Record ID in p_id.'
+BEGIN
+ IF p_id IS NOT NULL OR p_firstMotionCorrectionId IS NOT NULL THEN
+ INSERT INTO ParticlePicker (particlePickerId, firstMotionCorrectionId, programId, particlePickingTemplate, particleDiameter, numberOfParticles, summaryImageFullPath)
+ VALUES (p_id, p_firstMotionCorrectionId, p_programId, p_particlePickingTemplate, p_particleDiameter, p_numberOfParticles, p_summaryImageFullPath)
+ ON DUPLICATE KEY UPDATE
+ firstMotionCorrectionId = IFNULL(p_firstMotionCorrectionId, firstMotionCorrectionId),
+ programId = IFNULL(p_programId, programId),
+ particlePickingTemplate = IFNULL(p_particlePickingTemplate, particlePickingTemplate),
+ particleDiameter = IFNULL(p_particleDiameter, particleDiameter),
+ numberOfParticles = IFNULL(p_numberOfParticles, numberOfParticles),
+ summaryImageFullPath = IFNULL(p_summaryImageFullPath, summaryImageFullPath);
+
+ IF p_id IS NULL THEN
+ SET p_id = LAST_INSERT_ID();
+ END IF;
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument(s) are NULL: p_id OR p_firstMotionCorrectionId must be non-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 `upsert_person` */;
 /*!50003 SET @saved_cs_client = @@character_set_client */ ;
 /*!50003 SET @saved_cs_results = @@character_set_results */ ;
@@ -11027,7 +11130,7 @@ DELIMITER ;
 /*!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 2021-07-26 11:38:57
 -- MariaDB dump 10.19 Distrib 10.5.10-MariaDB, for Linux (x86_64)
 --
 -- Host: 10.88.0.5 Database: ispyb_build
@@ -11074,4 +11177,4 @@ DELIMITER ;
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2021-07-23 18:38:11
+-- Dump completed on 2021-07-26 11:38:57
diff --git a/schemas/ispyb/stored_programs/sp_upsert_particle_classification_v2.sql b/schemas/ispyb/stored_programs/sp_upsert_particle_classification_v2.sql
@@ -0,0 +1,64 @@
+-- Example calls:
+--
+-- First create a Movie, a MotionCorrection, a ParticlePicker and a ParticleClassificationGroup:
+
+/*
+SET @mid := NULL;
+SET @mcid := NULL;
+CALL upsert_movie(@mid, 6017405, NULL, NULL, NULL, NULL, NULL, NULL);
+CALL upsert_motion_correction(@mcid, @mid, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
+SET @ppid := NULL;
+CALL upsert_particle_picker_v2(@ppid, @mcid, NULL, 'pp template 1', 8.1, 151, '/xyzls/bl101/data/2021/bi23456-1/processed/kl_1_summary.jpg');
+SET @pcgid := NULL;
+CALL upsert_particle_classification_group(@pcgid, @ppid, NULL, '2D', 1, 1300, 2, 'P222');
+
+-- Then call this procedure:
+SET @pcid := NULL;
+CALL upsert_particle_classification_v2(@pcid, @pcgid, 1, '/absolute/path/to/image/file', 1200, 0.91, 2, 3.5, 2.8, 92);
+*/
+
+DELIMITER ;;
+CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `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
+ )
+ MODIFIES SQL DATA
+ COMMENT 'Inserts or updates info about a particle classification (p_id).\nMandatory columns:\nFor insert: p_particleClassificationGroupId\nFor update: p_id \nReturns: Record ID in p_id.'
+BEGIN
+ IF p_id IS NOT NULL OR p_particleClassificationGroupId IS NOT NULL THEN
+ INSERT INTO ParticleClassification (particleClassificationId, 
+ particleClassificationGroupId, classNumber, classImageFullPath, 
+ particlesPerClass, classDistribution, rotationAccuracy, 
+ translationAccuracy, estimatedResolution, overallFourierCompleteness)
+ VALUES (p_id, p_particleClassificationGroupId, p_classNumber, 
+ p_classImageFullPath, 
+ p_particlesPerClass, p_classDistribution, p_rotationAccuracy, 
+ p_translationAccuracy, p_estimatedResolution, 
+ p_overallFourierCompleteness)
+ ON DUPLICATE KEY UPDATE
+ particleClassificationGroupId = IFNULL(p_particleClassificationGroupId, particleClassificationGroupId),
+ classNumber = IFNULL(p_classNumber, classNumber),
+ classImageFullPath = IFNULL(p_classImageFullPath, classImageFullPath),
+ particlesPerClass = IFNULL(p_particlesPerClass, particlesPerClass),
+ classDistribution = IFNULL(p_classDistribution, classDistribution),
+ rotationAccuracy = IFNULL(p_rotationAccuracy, rotationAccuracy),
+ translationAccuracy = IFNULL(p_translationAccuracy, translationAccuracy),
+ estimatedResolution = IFNULL(p_estimatedResolution, estimatedResolution),
+ overallFourierCompleteness = IFNULL(p_overallFourierCompleteness, overallFourierCompleteness);
+
+ IF p_id IS NULL THEN
+ SET p_id = LAST_INSERT_ID();
+ END IF;
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument(s) are NULL: p_id OR p_particleClassificationGroupId must be non-NULL.';
+ END IF;
+END;;
+DELIMITER ;
diff --git a/schemas/ispyb/stored_programs/sp_upsert_particle_picker_v2.sql b/schemas/ispyb/stored_programs/sp_upsert_particle_picker_v2.sql
@@ -0,0 +1,46 @@
+-- Example calls:
+-- First create a Movie and a MotionCorrection:
+--
+/*
+SET @mid := NULL;
+SET @mcid := NULL;
+CALL upsert_movie(@mid, 6017405, NULL, NULL, NULL, NULL, NULL, NULL);
+CALL upsert_motion_correction(@mcid, @mid, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
+
+-- Then call this procedure:
+SET @ppid := NULL;
+CALL upsert_particle_picker_v2(@ppid, @mcid, NULL, 'pp template 1', 8.1, 151, '/xyzls/bl101/data/2021/bi23456-1/processed/kl_1_summary.jpg');
+*/
+
+DELIMITER ;;
+CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `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)
+ )
+ MODIFIES SQL DATA
+ COMMENT 'Inserts or updates info about a particle picker (p_id).\nMandatory columns:\nFor insert: p_firstMotionCorrectionId\nFor update: p_id \nReturns: Record ID in p_id.'
+BEGIN
+ IF p_id IS NOT NULL OR p_firstMotionCorrectionId IS NOT NULL THEN
+ INSERT INTO ParticlePicker (particlePickerId, firstMotionCorrectionId, programId, particlePickingTemplate, particleDiameter, numberOfParticles, summaryImageFullPath)
+ VALUES (p_id, p_firstMotionCorrectionId, p_programId, p_particlePickingTemplate, p_particleDiameter, p_numberOfParticles, p_summaryImageFullPath)
+ ON DUPLICATE KEY UPDATE
+ firstMotionCorrectionId = IFNULL(p_firstMotionCorrectionId, firstMotionCorrectionId),
+ programId = IFNULL(p_programId, programId),
+ particlePickingTemplate = IFNULL(p_particlePickingTemplate, particlePickingTemplate),
+ particleDiameter = IFNULL(p_particleDiameter, particleDiameter),
+ numberOfParticles = IFNULL(p_numberOfParticles, numberOfParticles),
+ summaryImageFullPath = IFNULL(p_summaryImageFullPath, summaryImageFullPath);
+
+ IF p_id IS NULL THEN
+ SET p_id = LAST_INSERT_ID();
+ END IF;
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument(s) are NULL: p_id OR p_firstMotionCorrectionId must be non-NULL.';
+ END IF;
+END;;
+DELIMITER ;
diff --git a/schemas/ispyb/updates/2021_07_26_AdminVar_bump_version.sql b/schemas/ispyb/updates/2021_07_26_AdminVar_bump_version.sql
@@ -0,0 +1,5 @@
+INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2021_07_26_AdminVar_bump_version.sql', 'ONGOING');
+
+UPDATE AdminVar SET `value` = '1.25.0' WHERE `name` = 'schemaVersion';
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2021_07_26_AdminVar_bump_version.sql';