diff options
| -rw-r--r-- | scripts/update-case-attribute-tables-20230818 | 42 |
1 files changed, 39 insertions, 3 deletions
diff --git a/scripts/update-case-attribute-tables-20230818 b/scripts/update-case-attribute-tables-20230818 index 5f21e9c..70e8c1a 100644 --- a/scripts/update-case-attribute-tables-20230818 +++ b/scripts/update-case-attribute-tables-20230818 @@ -1,9 +1,45 @@ #!/usr/bin/env python3 """ -This script is to be run only one time to update the schema for the -case-attributes. The script should probably not be commited to be tracked with -git. +WARNING + This script is to be run only one time to update the schema for the + `CaseAttribute` and the `CaseAttributeXRefNew` tables. + Running the script more than once has no useful purpose, and will just + litter your database schema with `BACKUP_CaseAttribute*` tables. + +DESCRIPTION + The script makes the following schema updates + + For the `CaseAttribute` table: + * Adds `InbredSetId` column: links each case attribute to a population + * Rename `Id` to `CaseAttributeId`: Makes it explicit what the ID is for, + and helps simplify queries with joins against this table + + For the `CaseAttributeXRefNew` table: + * Reorganise order of columns. + + For out of date databases (e.g. small db), the script will also: + * Ppdate the character set for the `InbredSet` and `Strain` tables to + utf8mb4. + * Change the database engine for the `InbredSet` and `Strain` tables to + InnoDB. + +TABLE BACKUPS + The script will backup the `CaseAttribute` and `CaseAttributeXRefNew` tables. + The backup table names take the form: + + BACKUP_<tablename>_<timestr> + + Where <tablename> is one of `CaseAttribute` or `CaseAttributeXRefNew` and + <timestr> is a string indicating the date and time the script was run (in + local timezone for system the script is run on). + +USAGE + python3 update-case-attribute-tables-20230818 SQL_URI + + The `SQL_URI` argument is mandatory and is of the form: + + mysql://<username>:<password>@<host>[:<port>]/<database> """ import os import sys |