Good news, Roy, Let us know if there's anything more we can do. Thanks, --nate Roy Weckiewicz wrote:

Just created a new database again and tried it -- Seems like it worked ! Complete migration as far as I can tell:

Tables: 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

So far so good !

Rgds,

Roy Weckiewicz.

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

Thanks, --nate

-- Roy Weckiewicz Texas A&M University

-- Roy Weckiewicz Texas A&M University

-- Roy Weckiewicz Texas A&M University

Hi Galaxy team, If I want to run another application (for eg Gbrowse) or put a static site, how can I do that while Galaxy is running at the root? For example, galaxy is located in www.test.com How can I put gbrowse or static page to www.test.com/gbrowse or www.test.com/another_page.html I tried tinkering with Apache but i still cant get it. Im using Fedora 10. Thanks!