Hi Linda,

> 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:

that is really strange. Can you show us what the output of hg tip is?
Do you mind to start with a fresh checkout and that particular change?

Thanks,
Björn 

>   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' ()
> 
> 
> 
> 
> Inactive hide details for Dannon Baker ---06/05/2013 11:40:32 AM---Hi
> Linda, The decorator issue should be resolved in galaxy-cDannon 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 <lc...@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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> 
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