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resources/backups/database_dumper/update_database.sql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,128 +1,147 @@ | ||
| ALTER TABLE `HerediVar`.`classification_criterium` | ||
| CHANGE COLUMN `relevant_info` `relevant_info` TEXT NOT NULL DEFAULT '' ; | ||
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| DROP TABLE IF EXISTS `HerediVar`.`import_variant_queue`; | ||
| CREATE TABLE `HerediVar`.`import_variant_queue` ( | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium` | ||
| -- CHANGE COLUMN `relevant_info` `relevant_info` TEXT NOT NULL DEFAULT '' ; | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- DROP TABLE IF EXISTS `HerediVar`.`import_variant_queue`; | ||
| -- CREATE TABLE `HerediVar`.`import_variant_queue` ( | ||
| -- `id` int(10) unsigned NOT NULL AUTO_INCREMENT, | ||
| -- `import_queue_id` int(10) unsigned DEFAULT NULL, | ||
| -- `status` enum('pending','success','error','progress','deleted','update','retry') NOT NULL DEFAULT 'pending', | ||
| -- `requested_at` datetime NOT NULL DEFAULT current_timestamp(), | ||
| -- `finished_at` datetime DEFAULT NULL, | ||
| -- `message` text DEFAULT '', | ||
| -- `celery_task_id` varchar(45) DEFAULT NULL, | ||
| -- `vid` text NOT NULL, | ||
| -- PRIMARY KEY (`id`), | ||
| -- UNIQUE KEY `id_UNIQUE` (`id`), | ||
| -- KEY `fk_import_variant_queue_import_queue_idx` (`import_queue_id`), | ||
| -- CONSTRAINT `fk_import_variant_queue_import_queue` FOREIGN KEY (`import_queue_id`) REFERENCES `import_queue` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION | ||
| -- ) ENGINE=InnoDB AUTO_INCREMENT=42036 DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`variant` | ||
| -- ADD COLUMN `is_hidden` TINYINT(1) NOT NULL DEFAULT 0 AFTER `orig_alt`; | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- CREATE TABLE `HerediVar`.`variant_heredicare_annotation` ( | ||
| -- `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, | ||
| -- `variant_id` INT UNSIGNED NOT NULL, | ||
| -- `vid` VARCHAR(45) NOT NULL, | ||
| -- `n_fam` INT NOT NULL DEFAULT 0 COMMENT 'consensus class: 1:pathogen, 2: vus, 3: polymorphismus/neutral, 11: class1, 12: class2, 32: class3-, 13: class3, 34: class3+, 14: class4, 15: class5, 20: artefakt, 21: nicht klassifiziert, 4: unbekannt', | ||
| -- `n_pat` INT NOT NULL DEFAULT 0, | ||
| -- `consensus_class` ENUM('1', '2', '3', '11', '12', '32', '13', '34', '14', '15', '20', '21', '4') NOT NULL, | ||
| -- `comment` TEXT NOT NULL, | ||
| -- PRIMARY KEY (`id`), | ||
| -- UNIQUE INDEX `id_UNIQUE` (`id` ASC)); | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`variant_heredicare_annotation` | ||
| -- ADD COLUMN `date` DATE NULL AFTER `comment`; | ||
| -- | ||
| -- | ||
| -- GRANT INSERT, DELETE ON HerediVar.variant_heredicare_annotation TO 'HerediVar_annotation'; | ||
| -- GRANT SELECT ON HerediVar.variant_heredicare_annotation TO 'HerediVar_annotation'; | ||
| -- GRANT SELECT ON HerediVar.variant_heredicare_annotation TO 'HerediVar_superuser'; | ||
| -- GRANT SELECT ON HerediVar.variant_heredicare_annotation TO 'HerediVar_read_only'; | ||
| -- GRANT SELECT ON HerediVar.variant_ids TO 'HerediVar_annotation'; | ||
| -- | ||
| -- | ||
| -- | ||
| -- | ||
| -- DELETE FROM `HerediVar`.`annotation_type` WHERE (`id` = '34'); | ||
| -- DELETE FROM `HerediVar`.`annotation_type` WHERE (`id` = '35'); | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`import_queue` | ||
| -- CHANGE COLUMN `status` `status` ENUM('pending', 'progress', 'success', 'error', 'retry') NOT NULL DEFAULT 'pending' ; | ||
| -- | ||
| -- | ||
| -- | ||
| -- GRANT DELETE ON HerediVar.variant_ids TO 'HerediVar_superuser'; | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`variant_consequence` | ||
| -- CHANGE COLUMN `exon_nr` `exon_nr` VARCHAR(45) NULL DEFAULT NULL , | ||
| -- CHANGE COLUMN `intron_nr` `intron_nr` VARCHAR(45) NULL DEFAULT NULL ; | ||
| -- | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`consensus_classification` | ||
| -- CHANGE COLUMN `classification` `classification` ENUM('1', '2', '3', '4', '5', '3+', '3-', 'M') NOT NULL ; | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`user_classification` | ||
| -- CHANGE COLUMN `classification` `classification` ENUM('1', '2', '3', '4', '5', '3-', '3+', 'M') NOT NULL ; | ||
| -- | ||
| -- | ||
| -- GRANT INSERT,UPDATE ON HerediVar.classification_scheme TO 'HerediVar_superuser'; | ||
| -- GRANT INSERT,UPDATE,DELETE ON HerediVar.classification_criterium TO 'HerediVar_superuser'; | ||
| -- GRANT INSERT,UPDATE,DELETE ON HerediVar.classification_criterium_strength TO 'HerediVar_superuser'; | ||
| -- GRANT INSERT,UPDATE,DELETE ON HerediVar.mutually_exclusive_criteria TO 'HerediVar_superuser'; | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| -- CHANGE COLUMN `name` `name` VARCHAR(32) NOT NULL; | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| -- ADD UNIQUE INDEX `UNIQUE_strength_key` (`classification_criterium_id` ASC, `name` ASC); | ||
| -- ALTER TABLE `HerediVar`.`mutually_exclusive_criteria` | ||
| -- ADD UNIQUE INDEX `UNIQUE_mutually_exclusive` (`source` ASC, `target` ASC); | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium` | ||
| -- DROP INDEX `UNIQUE_scheme_id_name` ; | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium` | ||
| -- ADD UNIQUE INDEX `UNIQUE_classification_criterium` (`classification_scheme_id` ASC, `name` ASC); | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| -- DROP FOREIGN KEY `FK_criterium_strength_classification_criterium`; | ||
| -- ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| -- ADD CONSTRAINT `FK_criterium_strength_classification_criterium` | ||
| -- FOREIGN KEY (`classification_criterium_id`) | ||
| -- REFERENCES `HerediVar`.`classification_criterium` (`id`) | ||
| -- ON DELETE CASCADE | ||
| -- ON UPDATE NO ACTION; | ||
| -- | ||
| -- | ||
| -- ALTER TABLE `HerediVar`.`mutually_exclusive_criteria` | ||
| -- DROP FOREIGN KEY `FK_mutually_exclusive_criteria_classification_criteria_1`, | ||
| -- DROP FOREIGN KEY `FK_mutually_exclusive_criteria_classification_criterium`; | ||
| -- ALTER TABLE `HerediVar`.`mutually_exclusive_criteria` | ||
| -- ADD CONSTRAINT `FK_mutually_exclusive_criteria_classification_criteria_1` | ||
| -- FOREIGN KEY (`source`) | ||
| -- REFERENCES `HerediVar`.`classification_criterium` (`id`) | ||
| -- ON DELETE CASCADE | ||
| -- ON UPDATE NO ACTION, | ||
| -- ADD CONSTRAINT `FK_mutually_exclusive_criteria_classification_criterium` | ||
| -- FOREIGN KEY (`target`) | ||
| -- REFERENCES `HerediVar`.`classification_criterium` (`id`) | ||
| -- ON DELETE CASCADE | ||
| -- ON UPDATE NO ACTION; | ||
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| DROP TABLE IF EXISTS `HerediVar`.`import_queue`; | ||
| CREATE TABLE `import_queue` ( | ||
| `id` int(10) unsigned NOT NULL AUTO_INCREMENT, | ||
| `import_queue_id` int(10) unsigned DEFAULT NULL, | ||
| `status` enum('pending','success','error','progress','deleted','update','retry') NOT NULL DEFAULT 'pending', | ||
| `user_id` int(10) unsigned NOT NULL, | ||
| `requested_at` datetime NOT NULL DEFAULT current_timestamp(), | ||
| `status` enum('pending','progress','success','error','retry') NOT NULL DEFAULT 'pending', | ||
| `finished_at` datetime DEFAULT NULL, | ||
| `message` text DEFAULT '', | ||
| `celery_task_id` varchar(45) DEFAULT NULL, | ||
| `vid` text NOT NULL, | ||
| `celery_task_id` text DEFAULT NULL, | ||
| PRIMARY KEY (`id`), | ||
| UNIQUE KEY `id_UNIQUE` (`id`), | ||
| KEY `fk_import_variant_queue_import_queue_idx` (`import_queue_id`), | ||
| CONSTRAINT `fk_import_variant_queue_import_queue` FOREIGN KEY (`import_queue_id`) REFERENCES `import_queue` (`id`) ON DELETE CASCADE ON UPDATE NO ACTION | ||
| ) ENGINE=InnoDB AUTO_INCREMENT=42036 DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; | ||
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| ALTER TABLE `HerediVar`.`variant` | ||
| ADD COLUMN `is_hidden` TINYINT(1) NOT NULL DEFAULT 0 AFTER `orig_alt`; | ||
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| CREATE TABLE `HerediVar`.`variant_heredicare_annotation` ( | ||
| `id` INT UNSIGNED NOT NULL AUTO_INCREMENT, | ||
| `variant_id` INT UNSIGNED NOT NULL, | ||
| `vid` VARCHAR(45) NOT NULL, | ||
| `n_fam` INT NOT NULL DEFAULT 0 COMMENT 'consensus class: 1:pathogen, 2: vus, 3: polymorphismus/neutral, 11: class1, 12: class2, 32: class3-, 13: class3, 34: class3+, 14: class4, 15: class5, 20: artefakt, 21: nicht klassifiziert, 4: unbekannt', | ||
| `n_pat` INT NOT NULL DEFAULT 0, | ||
| `consensus_class` ENUM('1', '2', '3', '11', '12', '32', '13', '34', '14', '15', '20', '21', '4') NOT NULL, | ||
| `comment` TEXT NOT NULL, | ||
| PRIMARY KEY (`id`), | ||
| UNIQUE INDEX `id_UNIQUE` (`id` ASC)); | ||
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| ALTER TABLE `HerediVar`.`variant_heredicare_annotation` | ||
| ADD COLUMN `date` DATE NULL AFTER `comment`; | ||
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| GRANT INSERT, DELETE ON HerediVar.variant_heredicare_annotation TO 'HerediVar_annotation'; | ||
| GRANT SELECT ON HerediVar.variant_heredicare_annotation TO 'HerediVar_annotation'; | ||
| GRANT SELECT ON HerediVar.variant_heredicare_annotation TO 'HerediVar_superuser'; | ||
| GRANT SELECT ON HerediVar.variant_heredicare_annotation TO 'HerediVar_read_only'; | ||
| GRANT SELECT ON HerediVar.variant_ids TO 'HerediVar_annotation'; | ||
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| DELETE FROM `HerediVar`.`annotation_type` WHERE (`id` = '34'); | ||
| DELETE FROM `HerediVar`.`annotation_type` WHERE (`id` = '35'); | ||
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| ALTER TABLE `HerediVar`.`import_queue` | ||
| CHANGE COLUMN `status` `status` ENUM('pending', 'progress', 'success', 'error', 'retry') NOT NULL DEFAULT 'pending' ; | ||
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| GRANT DELETE ON HerediVar.variant_ids TO 'HerediVar_superuser'; | ||
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| ALTER TABLE `HerediVar`.`variant_consequence` | ||
| CHANGE COLUMN `exon_nr` `exon_nr` VARCHAR(45) NULL DEFAULT NULL , | ||
| CHANGE COLUMN `intron_nr` `intron_nr` VARCHAR(45) NULL DEFAULT NULL ; | ||
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| ALTER TABLE `HerediVar`.`consensus_classification` | ||
| CHANGE COLUMN `classification` `classification` ENUM('1', '2', '3', '4', '5', '3+', '3-', 'M') NOT NULL ; | ||
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| ALTER TABLE `HerediVar`.`user_classification` | ||
| CHANGE COLUMN `classification` `classification` ENUM('1', '2', '3', '4', '5', '3-', '3+', 'M') NOT NULL ; | ||
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| GRANT INSERT,UPDATE ON HerediVar.classification_scheme TO 'HerediVar_superuser'; | ||
| GRANT INSERT,UPDATE,DELETE ON HerediVar.classification_criterium TO 'HerediVar_superuser'; | ||
| GRANT INSERT,UPDATE,DELETE ON HerediVar.classification_criterium_strength TO 'HerediVar_superuser'; | ||
| GRANT INSERT,UPDATE,DELETE ON HerediVar.mutually_exclusive_criteria TO 'HerediVar_superuser'; | ||
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| ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| CHANGE COLUMN `name` `name` VARCHAR(32) NOT NULL; | ||
| ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| ADD UNIQUE INDEX `UNIQUE_strength_key` (`classification_criterium_id` ASC, `name` ASC); | ||
| ALTER TABLE `HerediVar`.`mutually_exclusive_criteria` | ||
| ADD UNIQUE INDEX `UNIQUE_mutually_exclusive` (`source` ASC, `target` ASC); | ||
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| ALTER TABLE `HerediVar`.`classification_criterium` | ||
| DROP INDEX `UNIQUE_scheme_id_name` ; | ||
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| ALTER TABLE `HerediVar`.`classification_criterium` | ||
| ADD UNIQUE INDEX `UNIQUE_classification_criterium` (`classification_scheme_id` ASC, `name` ASC); | ||
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| ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| DROP FOREIGN KEY `FK_criterium_strength_classification_criterium`; | ||
| ALTER TABLE `HerediVar`.`classification_criterium_strength` | ||
| ADD CONSTRAINT `FK_criterium_strength_classification_criterium` | ||
| FOREIGN KEY (`classification_criterium_id`) | ||
| REFERENCES `HerediVar`.`classification_criterium` (`id`) | ||
| ON DELETE CASCADE | ||
| ON UPDATE NO ACTION; | ||
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| ALTER TABLE `HerediVar`.`mutually_exclusive_criteria` | ||
| DROP FOREIGN KEY `FK_mutually_exclusive_criteria_classification_criteria_1`, | ||
| DROP FOREIGN KEY `FK_mutually_exclusive_criteria_classification_criterium`; | ||
| ALTER TABLE `HerediVar`.`mutually_exclusive_criteria` | ||
| ADD CONSTRAINT `FK_mutually_exclusive_criteria_classification_criteria_1` | ||
| FOREIGN KEY (`source`) | ||
| REFERENCES `HerediVar`.`classification_criterium` (`id`) | ||
| ON DELETE CASCADE | ||
| ON UPDATE NO ACTION, | ||
| ADD CONSTRAINT `FK_mutually_exclusive_criteria_classification_criterium` | ||
| FOREIGN KEY (`target`) | ||
| REFERENCES `HerediVar`.`classification_criterium` (`id`) | ||
| ON DELETE CASCADE | ||
| ON UPDATE NO ACTION; | ||
| KEY `FK_import_queue_user_id_idx` (`user_id`), | ||
| CONSTRAINT `FK_import_queue_user_id` FOREIGN KEY (`user_id`) REFERENCES `user` (`id`) ON DELETE NO ACTION ON UPDATE NO ACTION | ||
| ) ENGINE=InnoDB AUTO_INCREMENT=281 DEFAULT CHARSET=utf8 COLLATE=utf8_general_ci; |