Hi John
Thanks for the insights
Hi Iyad
Yes, the user account has the ability to drop and alter tables.
Hans-Rudolf
On 08/26/2014 03:08 PM, John Chilton wrote:
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This is just a hunch and not based on anything concrete, but using an outdated version of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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