fixed a bug when accessing the variant details page as read only or s…

…tandard user
GC-HBOC · Jan 10, 2024 · 79bc5ca · 79bc5ca
1 parent ce80a09
commit 79bc5ca
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Showing 4 changed files with 80 additions and 71 deletions.
diff --git a/resources/backups/database_dumper/dump_database.sh b/resources/backups/database_dumper/dump_database.sh
@@ -31,6 +31,8 @@ echo $DATE > most_recent_dump.txt
 # information after init_db.py
 ##mysqldump --quick -h sql.img.med.uni-tuebingen.de -P 3306 -u ahdoebm1 -p --column-statistics=0 --no-tablespaces --no-create-info -r /mnt/storage2/users/ahdoebm1/HerediVar/resources/backups/database_dumper/init_db/init_transcripts.sql HerediVar_ahdoebm1  gene gene_alias transcript exon
 
+##mysqldump --quick -h sql.img.med.uni-tuebingen.de -P 3306 -u ahdoebm1 -p --column-statistics=0 --no-tablespaces -r /mnt/storage2/users/ahdoebm1/HerediVar/resources/backups/database_dumper/init_db/task_force_protein_domains.sql HerediVar_ahdoebm1 task_force_protein_domains
+
 
 #mysqldump --quick -h SRV011.img.med.uni-tuebingen.de -P 3306 -u ahdoebm1 -p --column-statistics=0 --no-tablespaces --no-create-info -r /mnt/storage2/users/ahdoebm1/HerediVar/resources/backups/database_dumper/init_db/init.sql HerediVar_ahdoebm1 annotation_type classification_criterium classification_criterium_strength classification_scheme mutually_exclusive_criteria gene gene_alias pfam_id_mapping pfam_legacy task_force_protein_domains transcript 
 

diff --git a/resources/backups/database_dumper/update_database_3.sql b/resources/backups/database_dumper/update_database_3.sql
@@ -178,74 +178,78 @@
 -- ;
 
 
-ALTER TABLE `HerediVar`.`classification_scheme` 
-ADD COLUMN `version` VARCHAR(45) NOT NULL DEFAULT 'v1.0.0' AFTER `name`;
-UPDATE classification_scheme SET version = "v1.4.0" WHERE name = "enigma-tp53";
-UPDATE classification_scheme SET version = "v1.1.0" WHERE name = "enigma-ATM";
-
-ALTER TABLE `HerediVar`.`classification_scheme` 
-CHANGE COLUMN `name` `name` VARCHAR(45) NOT NULL ;
-
-
-ALTER TABLE `HerediVar`.`classification_scheme` 
-ADD UNIQUE INDEX `UNIQUE_classification_scheme` (`name` ASC, `version` ASC);
-;
-
-
-ALTER TABLE `HerediVar`.`mutually_inclusive_criteria` 
-DROP FOREIGN KEY `FK_mutually_inclusive_criteria_source`,
-DROP FOREIGN KEY `FK_mutually_inlusive_criteria_target`;
-ALTER TABLE `HerediVar`.`mutually_inclusive_criteria` 
-ADD CONSTRAINT `FK_mutually_inclusive_criteria_source`
-  FOREIGN KEY (`source`)
-  REFERENCES `HerediVar`.`classification_criterium` (`id`)
-  ON DELETE CASCADE
-  ON UPDATE NO ACTION,
-ADD CONSTRAINT `FK_mutually_inlusive_criteria_target`
-  FOREIGN KEY (`target`)
-  REFERENCES `HerediVar`.`classification_criterium` (`id`)
-  ON DELETE CASCADE
-  ON UPDATE NO ACTION;
-
-
-CREATE TABLE `HerediVar`.`classification_scheme_alias` (
-  `id` INT UNSIGNED NOT NULL AUTO_INCREMENT,
-  `classification_scheme_id` INT UNSIGNED NOT NULL,
-  `alias` VARCHAR(45) NOT NULL,
-  PRIMARY KEY (`id`))
-ENGINE = InnoDB
-DEFAULT CHARACTER SET = utf8;
-
-
-ALTER TABLE `HerediVar`.`classification_scheme_alias` 
-ADD INDEX `FK_classification_scheme_alias_classification_scheme_idx` (`classification_scheme_id` ASC);
-;
-ALTER TABLE `HerediVar`.`classification_scheme_alias` 
-ADD CONSTRAINT `FK_classification_scheme_alias_classification_scheme`
-  FOREIGN KEY (`classification_scheme_id`)
-  REFERENCES `HerediVar`.`classification_scheme` (`id`)
-  ON DELETE NO ACTION
-  ON UPDATE NO ACTION;
-
-
-GRANT SELECT ON HerediVar.classification_scheme_alias TO 'HerediVar_annotation';
-GRANT SELECT ON HerediVar.classification_scheme TO 'HerediVar_annotation';
-GRANT SELECT,INSERT,UPDATE,DELETE ON HerediVar.classification_scheme_alias TO 'HerediVar_superuser';
-
-
-
-ALTER TABLE `HerediVar`.`automatic_classification` 
-DROP COLUMN `scheme_name`;
-
-ALTER TABLE `HerediVar`.`automatic_classification` 
-ADD COLUMN `classification_scheme_id` INT UNSIGNED NOT NULL AFTER `variant_id`;
+-- ALTER TABLE `HerediVar`.`classification_scheme` 
+-- ADD COLUMN `version` VARCHAR(45) NOT NULL DEFAULT 'v1.0.0' AFTER `name`;
+-- UPDATE classification_scheme SET version = "v1.4.0" WHERE name = "enigma-tp53";
+-- UPDATE classification_scheme SET version = "v1.1.0" WHERE name = "enigma-ATM";
+-- 
+-- ALTER TABLE `HerediVar`.`classification_scheme` 
+-- CHANGE COLUMN `name` `name` VARCHAR(45) NOT NULL ;
+-- 
+-- 
+-- ALTER TABLE `HerediVar`.`classification_scheme` 
+-- ADD UNIQUE INDEX `UNIQUE_classification_scheme` (`name` ASC, `version` ASC);
+-- ;
+-- 
+-- 
+-- ALTER TABLE `HerediVar`.`mutually_inclusive_criteria` 
+-- DROP FOREIGN KEY `FK_mutually_inclusive_criteria_source`,
+-- DROP FOREIGN KEY `FK_mutually_inlusive_criteria_target`;
+-- ALTER TABLE `HerediVar`.`mutually_inclusive_criteria` 
+-- ADD CONSTRAINT `FK_mutually_inclusive_criteria_source`
+--   FOREIGN KEY (`source`)
+--   REFERENCES `HerediVar`.`classification_criterium` (`id`)
+--   ON DELETE CASCADE
+--   ON UPDATE NO ACTION,
+-- ADD CONSTRAINT `FK_mutually_inlusive_criteria_target`
+--   FOREIGN KEY (`target`)
+--   REFERENCES `HerediVar`.`classification_criterium` (`id`)
+--   ON DELETE CASCADE
+--   ON UPDATE NO ACTION;
+-- 
+-- 
+-- CREATE TABLE `HerediVar`.`classification_scheme_alias` (
+--   `id` INT UNSIGNED NOT NULL AUTO_INCREMENT,
+--   `classification_scheme_id` INT UNSIGNED NOT NULL,
+--   `alias` VARCHAR(45) NOT NULL,
+--   PRIMARY KEY (`id`))
+-- ENGINE = InnoDB
+-- DEFAULT CHARACTER SET = utf8;
+-- 
+-- 
+-- ALTER TABLE `HerediVar`.`classification_scheme_alias` 
+-- ADD INDEX `FK_classification_scheme_alias_classification_scheme_idx` (`classification_scheme_id` ASC);
+-- ;
+-- ALTER TABLE `HerediVar`.`classification_scheme_alias` 
+-- ADD CONSTRAINT `FK_classification_scheme_alias_classification_scheme`
+--   FOREIGN KEY (`classification_scheme_id`)
+--   REFERENCES `HerediVar`.`classification_scheme` (`id`)
+--   ON DELETE NO ACTION
+--   ON UPDATE NO ACTION;
+-- 
+-- 
+-- GRANT SELECT ON HerediVar.classification_scheme_alias TO 'HerediVar_annotation';
+-- GRANT SELECT ON HerediVar.classification_scheme TO 'HerediVar_annotation';
+-- GRANT SELECT,INSERT,UPDATE,DELETE ON HerediVar.classification_scheme_alias TO 'HerediVar_superuser';
+-- 
+-- 
+-- 
+-- ALTER TABLE `HerediVar`.`automatic_classification` 
+-- DROP COLUMN `scheme_name`;
+-- 
+-- ALTER TABLE `HerediVar`.`automatic_classification` 
+-- ADD COLUMN `classification_scheme_id` INT UNSIGNED NOT NULL AFTER `variant_id`;
+-- 
+-- ALTER TABLE `HerediVar`.`automatic_classification` 
+-- ADD INDEX `FK_autoclass_classification_scheme_idx` (`classification_scheme_id` ASC);
+-- ;
+-- ALTER TABLE `HerediVar`.`automatic_classification` 
+-- ADD CONSTRAINT `FK_autoclass_classification_scheme`
+--   FOREIGN KEY (`classification_scheme_id`)
+--   REFERENCES `HerediVar`.`classification_scheme` (`id`)
+--   ON DELETE NO ACTION
+--   ON UPDATE NO ACTION;
+-- 
 
-ALTER TABLE `HerediVar`.`automatic_classification` 
-ADD INDEX `FK_autoclass_classification_scheme_idx` (`classification_scheme_id` ASC);
-;
-ALTER TABLE `HerediVar`.`automatic_classification` 
-ADD CONSTRAINT `FK_autoclass_classification_scheme`
-  FOREIGN KEY (`classification_scheme_id`)
-  REFERENCES `HerediVar`.`classification_scheme` (`id`)
-  ON DELETE NO ACTION
-  ON UPDATE NO ACTION;
+GRANT INSERT,UPDATE ON HerediVar.heredivar_clinvar_submissions TO 'HerediVar_user';
+GRANT INSERT,UPDATE ON HerediVar.heredivar_clinvar_submissions TO 'HerediVar_read_only';
diff --git a/resources/backups/database_dumper/users/user_privileges.sql b/resources/backups/database_dumper/users/user_privileges.sql
@@ -50,6 +50,7 @@ GRANT SELECT ON HerediVar_ahdoebm1.gene_alias TO 'HerediVar_user';
 GRANT SELECT ON HerediVar_ahdoebm1.variant_heredicare_annotation TO 'HerediVar_user';
 GRANT SELECT ON HerediVar_ahdoebm1.variant_transcript_annotation TO 'HerediVar_user';
 GRANT SELECT ON HerediVar_ahdoebm1.mutually_inclusive_criteria TO 'HerediVar_user';
+GRANT INSERT,UPDATE ON HerediVar_ahdoebm1.heredivar_clinvar_submissions TO 'HerediVar_user';
 
 /* grant priviliges to super user */
 GRANT SELECT, INSERT, UPDATE ON HerediVar_ahdoebm1.user TO 'HerediVar_superuser';
@@ -94,4 +95,5 @@ GRANT INSERT, DELETE ON HerediVar_ahdoebm1.list_variants TO 'HerediVar_read_only
 GRANT INSERT, UPDATE, DELETE ON HerediVar_ahdoebm1.user_variant_lists TO 'HerediVar_read_only';
 GRANT SELECT ON HerediVar_ahdoebm1.gene_alias TO 'HerediVar_read_only';
 GRANT SELECT ON HerediVar_ahdoebm1.variant_heredicare_annotation TO 'HerediVar_read_only';
-GRANT SELECT ON HerediVar_ahdoebm1.variant_transcript_annotation TO 'HerediVar_read_only';
+GRANT SELECT ON HerediVar_ahdoebm1.variant_transcript_annotation TO 'HerediVar_read_only';
+GRANT INSERT,UPDATE ON HerediVar.heredivar_clinvar_submissions TO 'HerediVar_read_only';
diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
@@ -134,6 +134,7 @@ <h4>Changelog</h4>
             <li>Sometimes, the classification scheme was not changeable in consensus classifications</li>
             <li>BRCA1 v1.0.0 PP1 criterium was missing strength selection and PP4 criterium was missing very strong strength</li>
             <li>BRCA2 v1.0.0 PP1 and PP4 criteria were missing very strong strength</li>
+            <li>Fixed a bug when a standard or read only user was accessing the variant details page when a ClinVar submission was unfinished</li>
         </ul>
         Known issues:
         <ul>