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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