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ensembl-gh-mirror
ensembl
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543dea1a
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543dea1a
authored
14 years ago
by
Andreas Kusalananda Kähäri
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Added README for the scripts here.
Currently does not cover populate_analysis_description.pl
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misc-scripts/production_database/scripts/README
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543dea1a
========================================================================
== About the scripts here ==
========================================================================
update_database_list.pl
- Purpose
Updates the 'db' table in the production database on ens-staging1
with new databases found on the staging servers. It will discover
new databases and will set the 'is_current' flag for all found
databases to 1 (true). It will also notice when databases goes away
from one reason or another.
- Who runs this and when?
The release coordinator runs this script whenever a new database or
a set of new databases has been copied onto the staging servers.
This means that this script may be run many times during the release
process.
- How to run it?
In the simplest case, this is how it's done (release NN):
./update_database_list.pl -r NN -wp PASSWORD
Run the script with no options to see a short usage info text. Run
with -a to get a description of the script.
- What to look out for?
Running this script with the wrong release will mark all databases
of the current release as "not current". Just running it again,
specifying the correct release, will sort this out.
Running it twice will have no adverse effects.
populate_production_db_tables.pl
- Purpose
Takes the data from the four views 'attrib_type', 'external_db',
'misc_set', and 'unmapped_reason' in the production database and
copies them to one or several other databases.
- Who runs this and when?
This script may be used by the genebuilders to populate a new
database with the data of these four tables, but the release
coordinator may also use it during the release process, before the
handover to the web-team, to synchronise them over all Core-like
databases on the staging servers.
- How to run it?
To insert the four tables into one single database:
populate_production_db_tables.pl -h HOST \
-u USER -p PASSWORD -d DATABASE
To only pick the 'external_db' table:
populate_production_db_tables.pl -h HOST \
-u USER -p PASSWORD -d DATABASE -t external_db
To update all database on a server with all four tables (release
NN):
populate_production_db_tables.pl -h HOST \
-u USER -p PASSWORD --core=NN
- What to look out for?
The script creates a backup of the tables that it replaces. These
backups should be deleted. This is done simply like this (for all
Core-like databases on a server):
populate_production_db_tables.pl -h HOST \
-u USER -p PASSWORD --core=NN --cleanup
Running the script twice will make it complain about already
existing backup tables. These may be automatically dropped by using
the -D flag, but you need to be sure you actually want to drop all
backups.
The script will notify you of any new or deleted entries (compared
to the entries in the backed up tables) and will give you an SQL
statement that may be use to study these.
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