diff --git a/resources/backups/database_dumper/update_database_2.sql b/resources/backups/database_dumper/update_database_2.sql index 17b6b4c2..123ff022 100644 --- a/resources/backups/database_dumper/update_database_2.sql +++ b/resources/backups/database_dumper/update_database_2.sql @@ -103,4 +103,69 @@ UPDATE annotation_type SET group_name = "ID" WHERE title = 'rsid' -INSERT INTO `HerediVar_ahdoebm1`.`annotation_type` (`title`, `display_title`, `description`, `value_type`, `version`, `version_date`, `group_name`, `is_transcript_specific`) VALUES ('clinvar', 'ClinVar variation ID', 'The Variation ID from ClinVar', 'int', '-', '2023-02-26', 'None', '0'); +INSERT INTO `HerediVar_ahdoebm1`.`annotation_type` (`title`, `display_title`, `description`, `value_type`, `version`, `version_date`, `group_name`, `is_transcript_specific`) VALUES ('clinvar', 'ClinVar variation ID', 'The Variation ID from ClinVar', 'int', '-', '2023-02-26', 'ID', '0'); + + + + + +SET FOREIGN_KEY_CHECKS = 0; +TRUNCATE table gene_alias; +SET FOREIGN_KEY_CHECKS = 1; + +SET FOREIGN_KEY_CHECKS = 0; +TRUNCATE table gene; +SET FOREIGN_KEY_CHECKS = 1; + +SET FOREIGN_KEY_CHECKS = 0; +TRUNCATE table transcript; +SET FOREIGN_KEY_CHECKS = 1; + + +ALTER TABLE `HerediVar_ahdoebm1`.`transcript` +ADD COLUMN `start` INT NOT NULL AFTER `length`, +ADD COLUMN `end` INT NOT NULL AFTER `start`; + + +ALTER TABLE `HerediVar_ahdoebm1`.`transcript` +ADD COLUMN `chrom` ENUM('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrMT') NOT NULL AFTER `length`; + + +ALTER TABLE `HerediVar_ahdoebm1`.`transcript` +ADD COLUMN `orientation` ENUM('+', '-') NOT NULL AFTER `end`; + + +CREATE TABLE `HerediVar_ahdoebm1`.`new_table` ( + `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, + `transcript_id` INT UNSIGNED NOT NULL, + `start` INT NOT NULL, + `end` INT NOT NULL, + `cdna_start` INT NULL, + `cdna_end` INT NULL, + `is_cds` TINYINT(1) NOT NULL DEFAULT 0, + PRIMARY KEY (`id`)); + +ALTER TABLE `HerediVar_ahdoebm1`.`new_table` +RENAME TO `HerediVar_ahdoebm1`.`exon` ; + +ALTER TABLE `HerediVar_ahdoebm1`.`exon` +ADD INDEX `FK_exon_transcript_idx` (`transcript_id` ASC); +; +ALTER TABLE `HerediVar_ahdoebm1`.`exon` +ADD CONSTRAINT `FK_exon_transcript` + FOREIGN KEY (`transcript_id`) + REFERENCES `HerediVar_ahdoebm1`.`transcript` (`id`) + ON DELETE NO ACTION + ON UPDATE NO ACTION; + +ALTER TABLE `HerediVar_ahdoebm1`.`exon` +DROP FOREIGN KEY `FK_exon_transcript`; +ALTER TABLE `HerediVar_ahdoebm1`.`exon` +ADD CONSTRAINT `FK_exon_transcript` + FOREIGN KEY (`transcript_id`) + REFERENCES `HerediVar_ahdoebm1`.`transcript` (`id`) + ON DELETE CASCADE + ON UPDATE NO ACTION; + + +INSERT INTO `HerediVar_ahdoebm1`.`annotation_type` (`title`, `display_title`, `description`, `value_type`, `version`, `version_date`, `group_name`, `is_transcript_specific`) VALUES ('gnomad_popmax_AC', 'popmax AC', 'The allele count from the popmax population from GnomAD', 'int', 'v3.1.2', '2021-10-22', 'gnomAD', '0');