Hi Nate,

Sorry I had an empty database set the first time (which was giving me the revision error):

Part of my problem has been trying to convert the db from sqlite to mysql -- the closest I got using scripts was 40 tables in the database:

dataset
dataset_permissions
default_history_permissions
default_user_permissions
event
form_definition_current
galaxy_group
galaxy_session
galaxy_session_to_history
galaxy_user
group_role_association
history
history_dataset_association
history_user_share_association
implicitly_converted_dataset_association
job
job_external_output_metadata
job_parameter
job_to_input_dataset
job_to_output_dataset
library
library_dataset
library_dataset_dataset_association
library_dataset_dataset_association_permissions
library_dataset_permissions
library_folder
library_folder_permissions
library_permissions
metadata_file
migrate_version
role
stored_workflow
stored_workflow_menu_entry
stored_workflow_user_share_connection
user_group_association
user_role_association
validation_error
workflow
workflow_step
workflow_step_connection

When I try to run it linked to the above database I get the following error:

galaxy.model.migrate.check DEBUG 2010-02-19 13:42:18,987 MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", line 61, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", line 28, in __init__
    create_or_verify_database( db_url, self.config.database_engine_options )
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", line 102, in create_or_verify_database
    % ( db_schema.version, migrate_repository.versions.latest ) )
Exception: Your database has version '22' but this code expects version '39'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.

So when I try to run the manage_db.sh I get: 

22 -> 23... 

Migration script to add columns for tracking whether pages are deleted and
publicly accessible.

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 45, in <module>
    main( repository='lib/galaxy/model/migrate', url=db_url )
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/shell.py", line 150, in main
    ret = command_func(**kwargs)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py", line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py", line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 184, in runchange
    change.run(self.engine, step)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/script/py.py", line 101, in run
    func()
  File "lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py", line 20, in upgrade
    Page_table = Table( "page", metadata, autoload=True )
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 108, in __call__
    return type.__call__(self, name, metadata, *args, **kwargs)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 236, in __init__
    _bind_or_error(metadata).reflecttable(self, include_columns=include_columns)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable
    self.dialect.reflecttable(conn, table, include_columns)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable
    sql = self._show_create_table(connection, table, charset)
  File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table
    raise exc.NoSuchTableError(full_name)
sqlalchemy.exc.NoSuchTableError: page


I guess my problem all along is not having the full table schema for use in mySQL.



Rgds,


Roy Weckiewicz

On Fri, Feb 19, 2010 at 1:33 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Roy Weckiewicz wrote:
Thanks again Nate,

I just tried the one you sent me - it seems I just have a database revision issue:

Traceback (most recent call last):
 File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", line 61, in app_factory
   app = UniverseApplication( global_conf = global_conf, **kwargs )
 File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", line 28, in __init__
   create_or_verify_database( db_url, self.config.database_engine_options )
 File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", line 72, in create_or_verify_database
   raise Exception( "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually" )
Exception: Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually

Hi Roy,

Is this the database you converted from sqlite?  Does it include the 'migrate_version' table?  Could you paste the output of 'SHOW TABLES;'?

Thanks,



Rgds,


Roy Weckiewicz


On Fri, Feb 19, 2010 at 1:28 PM, Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>> wrote:

   Roy Weckiewicz wrote:

       What's strange is that eventhough the file name on the egg is
       MySQL*fat-ucs2.egg the error still reports the file in question
       as MySQL*fat.egg -- I've tried renaming the egg to match the
       original file, but it didn't seem to make a difference.
       Furthermore, when I run.sh, the program will create a directory
       in home called .python-eggs/ containing the _MySQL.so file,
       among other things - Will I have to add a different URL to the
       eggs.ini to keep it from re-downloading the old file?


   Ah, sorry, that egg relies on some uncommitted patches.  I've
   rebuilt it using a clean checkout, could you try this one instead?:

   http://www.bx.psu.edu/~nate/galaxy/MySQL_python-1.2.2_5.0.67_static-py2.5-macosx-10.3-fat.egg

   Thanks,
   --nate




--
Roy Weckiewicz
Texas A&M University




--
Roy Weckiewicz
Texas A&M University