Dannon & John,

Thank you for your feedback.  I agree that documentation is a good start.

I’m still in the process of figuring out what actually happens to the database schema.  It may be completely fine with no referential integrity constraints, which I’m okay with to some degree (we’re still in the infancy stages with Galaxy).  I find it odd that these referential integrity errors popped up “all of a sudden” because I don’t recall noticing these errors when I first installed galaxy/initialized the database.  I did move the database to the new version of MySQL, where InnoDB is the default and referencing primary keys on a MyISAM table caused the problem.

As a side note, I would be interested to know your reasons for avoiding a hardcoded mysql engine.  If galaxy depends on referential integrity (not that I am assuming it does), then setting the MySQL engine to Memory or MyISAM would be disastrous.  Also, do you see any distinct advantages to using MyISAM for galaxy?

Regards,

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.Kandalaft@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: Dannon Baker [mailto:dannon.baker@gmail.com]
Sent: Wednesday, June 11, 2014 10:23 AM
To: John Chilton
Cc: Kandalaft, Iyad; galaxy-dev@bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy updated botched?

Hey Iyad,

I just want to second (and add slightly) to what John said here.  I had also failed to reproduce this locally, but that makes perfect sense now -- I'm glad you figured it out, and thanks for looking into this so closely and reporting back.

Like John said, I wouldn't modify the migrations to force or assume a particular engine, but if you wanted to make a contribution to the code base it would probably be worth improving the detection and reporting of this particular error condition to help anyone else who might run into the issue -- if you wanted to take a stab at that.

On Wed, Jun 11, 2014 at 10:08 AM, John Chilton <jmchilton@gmail.com> wrote:

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.Kandalaft@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.Kandalaft@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-dev@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.Kandalaft@agr.gc.ca
>
> Telephone | Téléphone 613- 759-1228
>
> Facsimile | Télécopieur 613-759-1701
>
> Government of Canada | Gouvernement du Canada
>
>
>
>

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