Tables_in_galaxy-new
cloud_image
cloud_instance
cloud_provider
cloud_snapshot
cloud_store
cloud_uci
cloud_user_credentials
dataset
dataset_permissions
dataset_tag_association
default_history_permissions
default_user_permissions
event
form_definition
form_definition_current
form_values
galaxy_group
galaxy_session
galaxy_session_to_history
galaxy_user
group_role_association
history
history_annotation_association
history_dataset_association
history_dataset_association_annotation_association
history_dataset_association_display_at_authorizati...
history_dataset_association_tag_association
history_tag_association
history_user_share_association
implicitly_converted_dataset_association
job
job_external_output_metadata
job_parameter
job_to_input_dataset
job_to_output_dataset
job_to_output_library_dataset
library
library_dataset
library_dataset_dataset_association
library_dataset_dataset_association_permissions
library_dataset_dataset_info_association
library_dataset_permissions
library_folder
library_folder_info_association
library_folder_permissions
library_info_association
library_permissions
metadata_file
migrate_version
page
page_revision
page_tag_association
page_user_share_association
request
request_event
request_type
role
sample
sample_event
sample_state
stored_workflow
stored_workflow_annotation_association
stored_workflow_menu_entry
stored_workflow_tag_association
stored_workflow_user_share_connection
tag
user_action
user_address
user_group_association
user_preference
user_role_association
validation_error
visualization
visualization_revision
workflow
workflow_step
workflow_step_annotation_association
workflow_step_connection
workflow_step_tag_association
workflow_tag_association

On Fri, Feb 19, 2010 at 1:46 PM, Roy Weckiewicz <roystefan@gmail.com> wrote:

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

--
Roy Weckiewicz
Texas A&M University