Upgrade migration scripts

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Upgrade migration scripts

Matthias Bernt
Der galaxy-dev list,

I just updated my 16.10 installation to 17.01 in order to see how
upgrading works.

I followed https://wiki.galaxyproject.org/Admin/Maintenance where point
8 is to run migration scripts.

Also the Admin Course
(https://martenson.github.io/dagobah-training/10-upgrading-release/upgrading.html#9)
refers to tool and DB migration steps that need(?) to be invoked.

I checked the output of run.sh and it seems to me that all migration
scripts are run automatically: eg. there is output like:

migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Loading
script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Script
lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
...

So I was wondering what the admin should do here? Just check for errors
or problems?

Cheers,
Matthias



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Re: Upgrade migration scripts

Martin Čech
Hi Matthias,

DB migrations need only to be run when there is a change in DB schema in between the releases. That is not the case between 16.10 and 17.01 so there is no migration to be run.

When there is a migration to run, the startup process of Galaxy will abort and you will be presented with a message that includes the command to run ($ sh manage_db.sh upgrade).

The tool migrations are even rarer than DB migrations, and there was not a one in past ~2 years I think. It would work similarly to the process above.

In standard cases, the only thing admin is recommended to do is to backup DB before running the upgrade script.

Thank you for using Galaxy and let us know if you have more questions!

Martin

On Wed, Feb 15, 2017 at 10:52 AM Matthias Bernt <[hidden email]> wrote:
Der galaxy-dev list,

I just updated my 16.10 installation to 17.01 in order to see how
upgrading works.

I followed https://wiki.galaxyproject.org/Admin/Maintenance where point
8 is to run migration scripts.

Also the Admin Course
(https://martenson.github.io/dagobah-training/10-upgrading-release/upgrading.html#9)
refers to tool and DB migration steps that need(?) to be invoked.

I checked the output of run.sh and it seems to me that all migration
scripts are run automatically: eg. there is output like:

migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Loading
script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2017-02-15 13:56:53,451 Script
lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
...

So I was wondering what the admin should do here? Just check for errors
or problems?

Cheers,
Matthias


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/