Re: [galaxy-dev] database migration error 79->80 (NameError: name 'BigInteger' is not defined)
Edward Kirton wrote: > hi, we are getting the following error migrating from 79 to 80. > curiously, my own galaxy didn't have this problem, but another > developer here was getting this error. i moved him from sqlite to > postgres but that didn't help. > thanks for any assistance, > ed Hi Ed, Is this with the current galaxy-dist version? --nate > > Migrating 79 -> 80... > galaxy.model.migrate.check INFO 2011-08-31 13:15:31,446 > Traceback (most recent call last): > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/web/buildapp.py", > line 82, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/app.py", > line 32, in __init__ > create_or_verify_database( db_url, kwargs.get( 'global_conf', {} > ).get( '__file__', None ), self.config.database_engine_options ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", > line 67, in create_or_verify_database > migrate_to_current_version( engine, db_schema ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", > line 125, in migrate_to_current_version > schema.runchange( ver, change, changeset.step ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", > line 184, in runchange > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 100, in run > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 112, in _func > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 108, in module > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 65, in verify_module > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/util/importpath.py", > line 12, in import_path > File "lib/galaxy/model/migrate/versions/0080_quota_tables.py", line > 29, in > Column( "bytes", BigInteger ), > NameError: name 'BigInteger' is not defined > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] database migration error 79->80 (NameError: name 'BigInteger' is not defined)
please disregard my previous message, it was the developer's error; he accidentally had deleted or reverted something in the libs folder. On Wed, Aug 31, 2011 at 3:36 PM, Edward Kirton wrote: > hi, we are getting the following error migrating from 79 to 80. > curiously, my own galaxy didn't have this problem, but another > developer here was getting this error. i moved him from sqlite to > postgres but that didn't help. > thanks for any assistance, > ed > > Migrating 79 -> 80... > galaxy.model.migrate.check INFO 2011-08-31 13:15:31,446 > Traceback (most recent call last): > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/web/buildapp.py", > line 82, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/app.py", > line 32, in __init__ > create_or_verify_database( db_url, kwargs.get( 'global_conf', {} > ).get( '__file__', None ), self.config.database_engine_options ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", > line 67, in create_or_verify_database > migrate_to_current_version( engine, db_schema ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", > line 125, in migrate_to_current_version > schema.runchange( ver, change, changeset.step ) > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", > line 184, in runchange > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 100, in run > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 112, in _func > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 108, in module > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", > line 65, in verify_module > File > "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/util/importpath.py", > line 12, in import_path > File "lib/galaxy/model/migrate/versions/0080_quota_tables.py", line > 29, in > Column( "bytes", BigInteger ), > NameError: name 'BigInteger' is not defined > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] database migration error 79->80 (NameError: name 'BigInteger' is not defined)
hi, we are getting the following error migrating from 79 to 80. curiously, my own galaxy didn't have this problem, but another developer here was getting this error. i moved him from sqlite to postgres but that didn't help. thanks for any assistance, ed Migrating 79 -> 80... galaxy.model.migrate.check INFO 2011-08-31 13:15:31,446 Traceback (most recent call last): File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", line 67, in create_or_verify_database migrate_to_current_version( engine, db_schema ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", line 125, in migrate_to_current_version schema.runchange( ver, change, changeset.step ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 100, in run File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 112, in _func File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 108, in module File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 65, in verify_module File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/util/importpath.py", line 12, in import_path File "lib/galaxy/model/migrate/versions/0080_quota_tables.py", line 29, in Column( "bytes", BigInteger ), NameError: name 'BigInteger' is not defined ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/