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 This is just a hunch and not based on anything concrete, but using an outdated version of sqlalchemy is probably not helping things.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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Hans-Rudolf Hotz Sent: Tuesday, August 26, 2014 5:22 AM To: <galaxy-dev@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 ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/