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 <module> Column( "bytes", BigInteger ), 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 <eskirton@lbl.gov> 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 <module> Column( "bytes", BigInteger ), 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 <module> Column( "bytes", BigInteger ), NameError: name 'BigInteger' is not defined
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participants (2)
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Edward Kirton -
Nate Coraor