Merge pull request #68 from DiamondLightSource/cryoem_v2.0

WIP: Proposed new tables for CryoEM

schemas/ispyb/updates/2021_03_03_cryoEMv2_0_tables.sql

@@ -0,0 +1,78 @@
+INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2021_03_03_cryoEMv2_0_tables.sql', 'ONGOING');
+
+CREATE TABLE ParticlePicker (
+ particlePickerId int unsigned auto_increment PRIMARY KEY,
+ particlePickerProgramId int unsigned,
+ particleClassificationProgramId int unsigned,
+ firstMotionCorrectionId int unsigned,
+ particlePickingTemplate varchar(255) COMMENT 'Cryolo model',
+ particleDiameter float COMMENT 'Unit: nm',
+ numberOfParticles int unsigned,
+ CONSTRAINT `ParticlePicker_fk_particlePickerProgramId`
+ FOREIGN KEY (`particlePickerProgramId`)
+ REFERENCES `AutoProcProgram` (`autoProcProgramId`)
+ ON DELETE NO ACTION ON UPDATE CASCADE,
+ CONSTRAINT `ParticlePicker_fk_particleClassificationProgramId`
+ FOREIGN KEY (`particleClassificationProgramId`)
+ REFERENCES `AutoProcProgram` (`autoProcProgramId`)
+ ON DELETE NO ACTION ON UPDATE CASCADE,
+ CONSTRAINT `ParticlePicker_fk_motionCorrectionId`
+ FOREIGN KEY (`firstMotionCorrectionId`)
+ REFERENCES `MotionCorrection` (`motionCorrectionId`)
+ ON DELETE NO ACTION ON UPDATE CASCADE
+)
+COMMENT 'An instance of a particle picker program that was run';
+
+-- 2D and 3D particle classification fields are almost the same, so using
+-- the same tables seems to make sense:
+CREATE TABLE ParticleClassification (
+ particleClassificationId int unsigned auto_increment PRIMARY KEY,
+ particlePickerId int unsigned,
+ type enum('2D', '3D') COMMENT 'Indicates the type of particle classification',
+ batchNumber int unsigned COMMENT 'Corresponding to batch number',
+ classNumber int unsigned COMMENT 'Identified of the class. A unique ID given by Relion',
+ classImageFullPath varchar(255) COMMENT 'The PNG of the class',
+ numberOfParticlesPerBatch int unsigned COMMENT 'total number of particles per batch (a large integer)',
+ numberOfClassesPerBatch int unsigned,
+ particlesPerClass int unsigned COMMENT 'Number of particles within the selected class, can then be used together with the total number above to calculate the percentage', -- is this just numberOfParticlesPerBatch * numberOfClassesPerBatch ? If so, this column is unnecessary.
+ rotationAccuracy int unsigned COMMENT '???', -- or "accuracyRotations" as in spreadsheet? float?
+ translationAccuracy float COMMENT 'Unit: Angstroms', 
+ estimatedResolution float COMMENT '???, Unit: Angstroms',
+ overallFourierCompleteness float,
+ symmetry varchar(20),
+ -- classRepresentativePreview ?,
+ CONSTRAINT `ParticleClassification_fk_particlePickerId`
+ FOREIGN KEY (`particlePickerId`)
+ REFERENCES `ParticlePicker` (`particlePickerId`)
+ ON DELETE CASCADE ON UPDATE CASCADE
+)
+COMMENT 'Results of 2D or 2D classification';
+
+-- Are we creating a "final" model later? If so, should they 
+-- go into the same table?
+-- Also, the ispyb schema has a couple of other "model" tables, so this should
+-- probably have some kind of prefix to make clear it's for EM.
+CREATE TABLE CryoemInitialModel (
+ cryoemInitialModelId int unsigned auto_increment PRIMARY KEY,
+ resolution float COMMENT 'Unit: Angstroms',
+ numberOfParticles int unsigned
+)
+COMMENT 'Initial cryo-EM model generation results';
+
+-- n:m relationship between ParticleClassification and InitialModel:
+CREATE TABLE ParticleClassification_has_CryoemInitialModel (
+ particleClassificationId int unsigned,
+ cryoemInitialModelId int unsigned,
+ PRIMARY KEY (particleClassificationId, cryoemInitialModelId),
+ CONSTRAINT `ParticleClassification_has_CryoemInitialModel_fk1`
+ FOREIGN KEY (`particleClassificationId`)
+ REFERENCES `ParticleClassification` (`particleClassificationId`)
+ ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT `ParticleClassification_has_InitialModel_fk2`
+ FOREIGN KEY (`cryoemInitialModelId`)
+ REFERENCES `CryoemInitialModel` (`cryoemInitialModelId`)
+ ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2021_03_03_cryoEMv2_0_tables.sql';