Spent a couple hours yesterday trying to track down this - I was not
getting anywhere though and I see why now.
Well this definitely an unfortunate situation - but I think
documentation improvements are the right fix not enforcing the engine
type in sqlalchemy migrations. For one, I don't think we can assume a
particular engine type because different deployers may already going
to have both kinds out there right?
I think it would be better to update the wiki to encourage InnoDB for
all new installations and warn this can happen for MySQL upgrades.
Is this okay?
Sorry about this.
-John
On Wed, Jun 11, 2014 at 8:48 AM, Kandalaft, Iyad
<iyad.kandal...@agr.gc.ca> wrote:
> This is a follow up for those that are interested with regards to my failed
> schema upgrade.
>
>
>
> I believe I have determined why all the tables are set to use the MyISAM
> engine. When I initialized galaxy on our enterprise servers, they were
> running a dated version of CentOS. Hence, the OS defaults to a dated MySQL
> version. MySQL only switched to using InnoDB (over MyISAM) as the default
> engine in version 5.5. If I’m not mistaken, I initialized galaxy in MySQL
> 5.1 without changing the default engine to InnoDB (big mistake). Due to my
> ignorance, I will now have to try to compare v118 of our database with a new
> install of galaxy running schema v118. Then, I will try “migrating” to the
> true schema state without destroying the data.
>
>
>
> I do feel that I should still modify the galaxy schema to set the MySQL
> engine to InnoDB to thwart problems like this for other unsuspecting users.
> If anyone can point me at some documentation about how Galaxy schema changes
> should occur in this case, that would be great.
>
> As per my previous comment, I’m not certain whether I would edit all schema
> versions to ensure table definitions include the mysql_engine=InnoDB
> attribute or whether using a DDL event in SQLAlchemy. I suspect that
> setting this option globally would mean that future developers don’t need to
> remember to define mysql_engine on every new table.
>
>
>
>
>
> Iyad Kandalaft
>
> Microbial Biodiversity Bioinformatics
>
> Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
> 960 Carling Ave.| 960 Ave. Carling
>
> Ottawa, ON| Ottawa (ON) K1A 0C6
>
> E-mail Address / Adresse courriel iyad.kandal...@agr.gc.ca
> Telephone | Téléphone 613-759-1228
> Facsimile | Télécopieur 613-759-1701
> Teletypewriter | Téléimprimeur 613-773-2600
>
> Government of Canada | Gouvernement du Canada
>
>
>
>
>
>
>
> From: Kandalaft, Iyad
> Sent: Tuesday, June 10, 2014 1:39 PM
> To: 'galaxy-...@bx.psu.edu'
> Subject: Re: Galaxy updated botched?
>
>
>
> Hi Everyone,
>
>
>
> This is follow-up information/questions to the issue I ran into with the
> galaxy June 2nd, 2014 update. I hope to receive feedback on how to proceed.
>
>
>
> Background:
>
> - Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end
>
> - When updating galaxy to the june 2nd release, the v120 DB schema
> has referential integrity constraints, which produced errors during the
> upgrade.
>
> - Completed two galaxy updates in the past 4 months without
> encountering this before (schema changes included)
>
>
>
> Discussion:
>
> In the past, referential integrity in the DB schema was never an issue. I
> checked backups and the current database to find that the database tables
> are using the MyISAM engine. MyISAM = no referential integrity support, no
> transactions.
>
> I reviewed galaxy’s SQLAlchemy templates and determined that
> mysql_engine='InnoDB' isn’t set on tables. This explains why all tables
> were created with the MyISAM engine. If the mysql_engine is not innodb, SQL
> Alchemy is supposed to drop any referential integrity constraints defined in
> the schema. What I don’t understand is why SQL Alchemy is no longer
> ignoring the referential integrity constraints.
>
>
>
> Going forward, can anyone propose how I can salvage the database or continue
> ignoring referential integrity for now?
>
> Assuming that my limited understanding of SQLAlchemy holds water, I was
> looking at fixing the galaxy code base but I need some clarification on the
> DB schema versioning. Do I edit schema v1 and add the appropriate table
> args to make every table an innodb engine table or do I add a new schema and
> modify all tables to use the innodb engine? Alternatively, I can use DDL
> events
>
> def after_create(target, connection, **kw):
>
> connection.execute("ALTER TABLE %s ENGINE=InnoDB;
>
> (target.name, target.name))
>
>
>
> Thank you for your help.
>
>
>
> Regards,
>
> Iyad Kandalaft
>
>
>
> Bioinformatics Application Developer
>
> Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
>
> KW Neatby Bldg | éd. KW Neatby
>
> 960 Carling Ave| 960, avenue Carling
>
> Ottawa, ON | Ottawa (ON) K1A 0C6
>
> E-mail Address / Adresse courriel: iyad.kandal...@agr.gc.ca
>
> Telephone | Téléphone 613- 759-1228
>
> Facsimile | Télécopieur 613-759-1701
>
> Government of Canada | Gouvernement du Canada
>
>
>
>
> ___________________________________________________________
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