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' ()






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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