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This is just a hunch and not based on anything concrete, but using an outdated 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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