diff --git a/resources/backups/database_dumper/update_database_5.sql b/resources/backups/database_dumper/update_database_5.sql index fc75337b..f1a7c884 100644 --- a/resources/backups/database_dumper/update_database_5.sql +++ b/resources/backups/database_dumper/update_database_5.sql @@ -52,71 +52,71 @@ -- -- ALTER TABLE `HerediVar`.`variant_heredicare_annotation` -- CHANGE COLUMN `lr_family` `lr_family` FLOAT NULL DEFAULT NULL ; +-- +-- +-- UPDATE `HerediVar`.`annotation_type` SET is_deleted=1 WHERE title="arup_classification"; +-- +-- +-- +-- +-- CREATE TABLE `HerediVar`.`assay_metadata` ( +-- `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, +-- `assay_id` INT UNSIGNED NOT NULL, +-- `metadata_type` VARCHAR(45) NOT NULL, +-- `value` VARCHAR(45) NULL, +-- PRIMARY KEY (`id`)) +-- ENGINE = InnoDB +-- DEFAULT CHARACTER SET = utf8; +-- +-- +-- CREATE TABLE `HerediVar`.`assay_metadata_type` ( +-- `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, +-- `title` VARCHAR(45) NOT NULL, +-- `display_title` VARCHAR(45) NOT NULL, +-- `assay_type_id` INT NOT NULL, +-- `value_type` ENUM('int', 'float', 'text', 'bool') NOT NULL, +-- PRIMARY KEY (`id`)) +-- ENGINE = InnoDB +-- DEFAULT CHARACTER SET = utf8; +-- +-- ALTER TABLE `HerediVar`.`assay_metadata` +-- CHANGE COLUMN `metadata_type` `metadata_type_id` INT NOT NULL ; +-- +-- +-- ALTER TABLE `HerediVar`.`assay_metadata_type` +-- ADD COLUMN `is_deleted` TINYINT(1) NOT NULL DEFAULT 0 AFTER `value_type`; +-- +-- CREATE TABLE `HerediVar`.`assay_type` ( +-- `id` INT NOT NULL, +-- `title` VARCHAR(45) NOT NULL, +-- PRIMARY KEY (`id`)) +-- ENGINE = InnoDB +-- DEFAULT CHARACTER SET = utf8; +-- +-- ALTER TABLE `HerediVar`.`assay_type` +-- CHANGE COLUMN `id` `id` INT(11) UNSIGNED NOT NULL AUTO_INCREMENT ; +-- +-- INSERT INTO `HerediVar`.`assay_type` (`title`) VALUES ('functional'); +-- INSERT INTO `HerediVar`.`assay_type` (`title`) VALUES ('splicing'); +-- +-- ALTER TABLE `HerediVar`.`assay` +-- ADD COLUMN `paper` TEXT NULL AFTER `filename`, +-- CHANGE COLUMN `report` `report` MEDIUMBLOB NULL , +-- CHANGE COLUMN `filename` `filename` TEXT NULL ; +-- +-- ALTER TABLE `HerediVar`.`assay_metadata_type` +-- CHANGE COLUMN `value_type` `value_type` TEXT NOT NULL ; -UPDATE `HerediVar`.`annotation_type` SET is_deleted=1 WHERE title="arup_classification"; - - - - -CREATE TABLE `HerediVar`.`assay_metadata` ( - `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, - `assay_id` INT UNSIGNED NOT NULL, - `metadata_type` VARCHAR(45) NOT NULL, - `value` VARCHAR(45) NULL, - PRIMARY KEY (`id`)) -ENGINE = InnoDB -DEFAULT CHARACTER SET = utf8; - - -CREATE TABLE `HerediVar`.`assay_metadata_type` ( - `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, - `title` VARCHAR(45) NOT NULL, - `display_title` VARCHAR(45) NOT NULL, - `assay_type_id` INT NOT NULL, - `value_type` ENUM('int', 'float', 'text', 'bool') NOT NULL, - PRIMARY KEY (`id`)) -ENGINE = InnoDB -DEFAULT CHARACTER SET = utf8; - -ALTER TABLE `HerediVar`.`assay_metadata` -CHANGE COLUMN `metadata_type` `metadata_type_id` INT NOT NULL ; - - -ALTER TABLE `HerediVar`.`assay_metadata_type` -ADD COLUMN `is_deleted` TINYINT(1) NOT NULL DEFAULT 0 AFTER `value_type`; - -CREATE TABLE `HerediVar`.`assay_type` ( - `id` INT NOT NULL, - `title` VARCHAR(45) NOT NULL, - PRIMARY KEY (`id`)) -ENGINE = InnoDB -DEFAULT CHARACTER SET = utf8; - -ALTER TABLE `HerediVar`.`assay_type` -CHANGE COLUMN `id` `id` INT(11) UNSIGNED NOT NULL AUTO_INCREMENT ; - -INSERT INTO `HerediVar`.`assay_type` (`title`) VALUES ('functional'); -INSERT INTO `HerediVar`.`assay_type` (`title`) VALUES ('splicing'); - -ALTER TABLE `HerediVar`.`assay` -ADD COLUMN `paper` TEXT NULL AFTER `filename`, -CHANGE COLUMN `report` `report` MEDIUMBLOB NULL , -CHANGE COLUMN `filename` `filename` TEXT NULL ; - -ALTER TABLE `HerediVar`.`assay_metadata_type` -CHANGE COLUMN `value_type` `value_type` TEXT NOT NULL ; - - -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('patient_rna', 'Patient RNA', (SELECT id FROM assay_type WHERE title='splicing'), 'bool'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('minigene', 'Minigene', (SELECT id FROM assay_type WHERE title='splicing'), 'bool'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('allele_specific', 'Allele-Specific', (SELECT id FROM assay_type WHERE title='splicing'), 'ENUM:True,False,Construct'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('comment', 'Comment', (SELECT id FROM assay_type WHERE title='splicing'), 'text'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('score', 'Score', (SELECT id FROM assay_type WHERE title='splicing'), 'float'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('minimal_percentage', 'Percent aberrant transcript', (SELECT id FROM assay_type WHERE title='splicing'), 'float'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('patient_rna', 'Patient RNA', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='splicing'), 'bool'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('minigene', 'Minigene', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='splicing'), 'bool'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('allele_specific', 'Allele-Specific', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='splicing'), 'ENUM:True,False,Construct'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('comment', 'Comment', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='splicing'), 'text'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('score', 'Score', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='splicing'), 'float'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('minimal_percentage', 'Percent aberrant transcript', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='splicing'), 'float'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('functional_category', 'Functional category', (SELECT id FROM assay_type WHERE title='functional'), 'ENUM:Pathogenic,Benign,Ambigous'); -INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('score', 'Score', (SELECT id FROM assay_type WHERE title='functional'), 'float'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('functional_category', 'Functional category', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='functional'), 'ENUM:Pathogenic,Benign,Ambigous'); +INSERT INTO `HerediVar`.`assay_metadata_type` (title, display_title, assay_type_id, value_type) VALUES ('score', 'Score', (SELECT id FROM `HerediVar`.`assay_type` WHERE title='functional'), 'float'); UPDATE `HerediVar`.`assay_metadata_type` SET `is_required` = '0' WHERE (`title` = 'comment'); @@ -127,13 +127,13 @@ UPDATE `HerediVar`.`assay_metadata_type` SET `is_required` = '0' WHERE (`title` ALTER TABLE `HerediVar`.`assay` ADD COLUMN `assay_type_id` INT UNSIGNED NOT NULL AFTER `assay_type`; -UPDATE assay SET assay_type_id = (SELECT id FROM assay_type WHERE title = 'functional') WHERE assay_type = 'functional'; -UPDATE assay SET assay_type_id = (SELECT id FROM assay_type WHERE title = 'splicing') WHERE assay_type = 'splicing'; +UPDATE `HerediVar`.`assay` SET assay_type_id = (SELECT id FROM `HerediVar`.`assay_type` WHERE title = 'functional') WHERE assay_type = 'functional'; +UPDATE `HerediVar`.`assay` SET assay_type_id = (SELECT id FROM `HerediVar`.`assay_type` WHERE title = 'splicing') WHERE assay_type = 'splicing'; ALTER TABLE `HerediVar`.`assay` DROP COLUMN `assay_type`; -INSERT INTO `HerediVar`.`assay_metadata` (assay_id, metadata_type_id, value) SELECT id, (SELECT id FROM assay_metadata_type WHERE assay_metadata_type.title = 'score' AND assay_metadata_type.assay_type_id = assay.assay_type_id), score FROM assay +INSERT INTO `HerediVar`.`assay_metadata` (assay_id, metadata_type_id, value) SELECT id, (SELECT id FROM `HerediVar`.assay_metadata_type WHERE assay_metadata_type.title = 'score' AND assay_metadata_type.assay_type_id = assay.assay_type_id), score FROM assay ALTER TABLE `HerediVar`.`assay` DROP COLUMN `score`;