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-newcloud_imagecloud_instancecloud_providercloud_snapshot cloud_storecloud_ucicloud_user_credentialsdatasetdataset_permissions dataset_tag_associationdefault_history_permissionsdefault_user_permissions eventform_definitionform_definition_currentform_valuesgalaxy_group galaxy_sessiongalaxy_session_to_historygalaxy_usergroup_role_association historyhistory_annotation_associationhistory_dataset_association history_dataset_association_annotation_association history_dataset_association_display_at_authorizati... history_dataset_association_tag_associationhistory_tag_association history_user_share_associationimplicitly_converted_dataset_associationjob job_external_output_metadatajob_parameterjob_to_input_dataset job_to_output_datasetjob_to_output_library_datasetlibrarylibrary_dataset library_dataset_dataset_association library_dataset_dataset_association_permissions library_dataset_dataset_info_associationlibrary_dataset_permissions library_folderlibrary_folder_info_associationlibrary_folder_permissions library_info_associationlibrary_permissionsmetadata_filemigrate_versionpage page_revisionpage_tag_associationpage_user_share_associationrequest request_eventrequest_typerolesamplesample_eventsample_statestored_workflow stored_workflow_annotation_associationstored_workflow_menu_entry stored_workflow_tag_associationstored_workflow_user_share_connectiontag user_actionuser_addressuser_group_associationuser_preference user_role_associationvalidation_errorvisualizationvisualization_revision workflowworkflow_stepworkflow_step_annotation_association workflow_step_connectionworkflow_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> 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-ma...
Thanks, --nate
-- Roy Weckiewicz Texas A&M University
-- Roy Weckiewicz Texas A&M University
-- Roy Weckiewicz Texas A&M University