Well it looks like the migration file has these columns listed in a
different order than the mapping Galaxy uses - and the order yours
appeared in were the ones from Galaxy's mapping file. So somehow
Galaxy is automatically creating those tables prior to running the
migration based on the code in Galaxy proper. That is odd.

Ultimately though - I don't think it is harmful that the order is
wrong since Galaxy always references the columns by name instead of
order. I would be more concerned that you aren't getting the right
indices / foreign keys - but it looks like you are still on MyISAM so
you aren't going to get a ton of forced integrity anyway (and maybe
this is why these errors have been okay in the past?).

-John

On Tue, Aug 26, 2014 at 8:52 AM, Kandalaft, Iyad
<iyad.kandal...@agr.gc.ca> wrote:
> I've ran into other mysql problems but never anything like that.
>
> This is just a hunch and not based on anything concrete, but using an 
> outdated version of sqlalchemy is probably not helping things.  We're talking 
> 2 migrations.  Are they even implementing fixes for 0.7 anymore?  It is odd 
> you would ever get "Table already exists" since the ORM's job is to ensure 
> the model consistency in the database.  Why it would try to create the table 
> before it checks for its existence is beyond me.
>
> You might want to make sure that the database user account has the ability to 
> drop and alter tables.  It may be that it tried to revert a failed upgrade 
> and it wasn't able to.
>
> Iyad Kandalaft
>
>
>
> -----Original Message-----
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hans-Rudolf Hotz
> Sent: Tuesday, August 26, 2014 5:22 AM
> To: <galaxy-...@bx.psu.edu>
> Subject: [galaxy-dev] problems with database migration 119 -> 120
>
> Hi all
>
> I am in the process of updating our galaxy servers (from "release_2014.04.14" 
> to "latest_2014.08.11").
>
>
> when I execute
>
> ~/lib/galaxy/model/migrate/versions/0120_dataset_collections.py
>
> as part of the 'manage_db.sh upgrade' I run into a bizarre error:
>
> First, it produces 10 "Mysql 1050 Error 'Table already exists' ", I have
> encountered this before, and usually everything is fine. The table gets
> created and for whatever reason, the command get's executed a second
> time - no big deal.
>
> However, this time for two of those ten table the situation has been
> different. As usual, I have checked all the tables (where I got the
> errors) with the MySQL command describe <table>.
>
> For two tables:
>
> history_dataset_collection_association
>
> library_dataset_collection_association
>
> the order of the columns was wrong (ie did not correspond to the order
> in the create statement) - see below for example.
>
> I have dropped the tables and executed the create statements manually,
> everything seems fine, eg
>
>
>
> mysql> describe library_dataset_collection_association;
> +---------------+--------------+------+-----+---------+----------------+
> | Field         | Type         | Null | Key | Default | Extra          |
> +---------------+--------------+------+-----+---------+----------------+
> | id            | int(11)      | NO   | PRI | NULL    | auto_increment |
> | collection_id | int(11)      | YES  | MUL | NULL    |                |
> | folder_id     | int(11)      | YES  | MUL | NULL    |                |
> | name          | varchar(255) | YES  |     | NULL    |                |
> | deleted       | tinyint(1)   | YES  |     | NULL    |                |
> +---------------+--------------+------+-----+---------+----------------+
> 5 rows in set (0.00 sec)
>
> mysql> drop table library_dataset_collection_association;
> Query OK, 0 rows affected (0.02 sec)
>
> mysql> CREATE TABLE library_dataset_collection_association (
>      ->     id INTEGER NOT NULL AUTO_INCREMENT,
>      ->     collection_id INTEGER,
>      ->     name VARCHAR(255),
>      ->     deleted BOOL,
>      ->     folder_id INTEGER,
>      ->     PRIMARY KEY (id),
>      ->     FOREIGN KEY(collection_id) REFERENCES dataset_collection (id),
>      ->     CHECK (deleted IN (0, 1)),
>      ->     FOREIGN KEY(folder_id) REFERENCES library_folder (id)
>      ->     );
> Query OK, 0 rows affected (0.01 sec)
>
> mysql> describe library_dataset_collection_association;
> +---------------+--------------+------+-----+---------+----------------+
> | Field         | Type         | Null | Key | Default | Extra          |
> +---------------+--------------+------+-----+---------+----------------+
> | id            | int(11)      | NO   | PRI | NULL    | auto_increment |
> | collection_id | int(11)      | YES  | MUL | NULL    |                |
> | name          | varchar(255) | YES  |     | NULL    |                |
> | deleted       | tinyint(1)   | YES  |     | NULL    |                |
> | folder_id     | int(11)      | YES  | MUL | NULL    |                |
> +---------------+--------------+------+-----+---------+----------------+
> 5 rows in set (0.00 sec)
>
> mysql>
>
>
>
> Has anyone else (among those few who are still using MySQL) seen
> something similar?
>
>
> Regards, Hans-Rudolf
>
>
> PS: Please don't make any comments about the fact, that I should change
>      to PostgreSQL. I am more than aware of that, and eventually, I will
>      do it.   ;)
>
>
>
>
> --
>
>
>
> Hans-Rudolf Hotz, PhD
> Bioinformatics Support
>
> Friedrich Miescher Institute for Biomedical Research
> Maulbeerstrasse 66
> 4058 Basel/Switzerland
> ___________________________________________________________
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