Hi Dannon,

Thanks.  I tried to do the hg pull and update and hg tip but I do not see the changes in my working directory.  So I added the one liner eggs.require( "decorator" ) to scripts/manage_db.py.
Ran the sh manage_db.sh upgrade and get this error:

  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute
  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, "Duplicate column name 'slug'") '\nALTER TABLE history ADD slug TEXT' ()

So I thought maybe I should remove the column that was added before.

ALTER TABLE history DROP COLUMN slug;

Ran the sh manage_db.sh upgrade again, but now it gives back the original error:

  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1170, "BLOB/TEXT column 'slug' used in key specification without a key length") 'CREATE INDEX ix_history_slug ON history (slug)' ()

Interesting to note that if I ran the sh manage_db.sh again after the CREATE INDEX error above, I get back this error now:
  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, "Duplicate column name 'slug'") '\nALTER TABLE history ADD slug TEXT' ()




Dannon Baker ---06/05/2013 11:40:32 AM---Hi Linda, The decorator issue should be resolved in galaxy-central now.  I'm setting

Hi Linda,

The decorator issue should be resolved in galaxy-central now.  I'm setting up a test environment to see if I can reproduce the mysql issue now, and will let you know what I come up with.

Thanks!

-Dannon


On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham <lcham@us.ibm.com> wrote:

Hi.   I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64.

On a newly installed OS node, using the hg clone command (hg clone https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh:
  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute
    self.errorhandler(self, exc, value)
  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler
    raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, "BLOB/TEXT column 'slug' used in key specification without a key length") 'CREATE INDEX ix_history_slug ON history (slug)' ()

Reading the forum, someone stated it can be bypass by running the CREATE INDEX.

mysql> CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0  Duplicates: 0  Warnings: 0

When trying to run.sh again after the CREATE INDEX, will get this error:
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
    create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self )
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py", line 107, in create_or_verify_database
    % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '29' but this code expects version '115'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.

So try to run the "sh manage_db.sh upgrade' now will get this error:
$ sh manage_db.sh upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 13, in <module>
    from migrate.versioning.shell import main
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 12, in <module>
    from migrate.versioning import api
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 33, in <module>
    from migrate.versioning import (repository, schema, version,
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 13, in <module>
    from migrate.versioning import version, pathed, cfgparse
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 10, in <module>
    from migrate.versioning import pathed, script
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py", line 11, in <module>
    from migrate.versioning.util import KeyedInstance
  File "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 7, in <module>
    from decorator import decorator
ImportError: No module named decorator

In some searches, there were tips of deleting the eggs directory and rerun run.sh or use a python env.  Neither option worked.
Was not able to find anything meaningful about the decorator error.

Note:, I was able to get Galaxy up with MySQL using the Galaxy 788cd3d06541 image on a different node.  So I am thinking maybe it is the new 20130603 image that is giving me issues?

Commands used to get Galaxy up: 

Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1]
python version [2.6.6]

Grant ALL PRIVILEGES galaxy_db.* TO  galaxy_user on localhostname with PWD
Images tested: 

*Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image  Did not run the hg update command. [This worked]  

*hg clone stable of newest image [Failed] 

Update the universe_wsg.ini with the port, host, database_connection to mysql 

Ran run.sh


Thanks. 

Linda

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