[galaxy-user] upgrade script
Hi,
I'm trying to use the upgrade script given that the current schema is now
version 90.
I get the following error.
Can anyone point me out, maybe there is something to do before upgrading?
thanks in advance.
Victor
trying to start galaxy I get
Traceback (most recent call last):
File /opt/galaxy/galaxy-dist-original/lib/galaxy/web/buildapp.py, line 82,
in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /opt/galaxy/galaxy-dist-original/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 /opt/galaxy/galaxy-dist-original/lib/galaxy/model/migrate/check.py,
line 105, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '90' but this code expects version '79'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
--trying to upgrade
sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
line 150, in main
ret = command_func(**kwargs)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 327, in _migrate
changeset = schema.changeset(version)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py,
line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py,
line 145, in version
return self.versions.version(*p, **k)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py,
line 125, in version
return self.versions[VerNum(vernum)]
KeyError: VerNum(90)
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Re: [galaxy-user] upgrade script
Hello Victor,
The following statement in your log is concerning because it looks like
something in your environment got corrupted in some way.
Exception: Your database has version '90' but this code expects version '79'.
Clean database schema migration upgrades go from smaller to larger numbers
(e.g., 89 - 90, 90 - 91, etc). Your migrate_versions.version database table
column has a value of 90, but your ~/lib/galaxy/model/migrate/versions
sub-directory has scripts only up to 0079... (or so it seems). Not sure how
best to fix the problem...
Greg Von Kuster
On Feb 21, 2012, at 2:21 PM, Victor Ruotti wrote:
Hi,
I'm trying to use the upgrade script given that the current schema is now
version 90.
I get the following error.
Can anyone point me out, maybe there is something to do before upgrading?
thanks in advance.
Victor
trying to start galaxy I get
Traceback (most recent call last):
File /opt/galaxy/galaxy-dist-original/lib/galaxy/web/buildapp.py, line 82,
in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /opt/galaxy/galaxy-dist-original/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 /opt/galaxy/galaxy-dist-original/lib/galaxy/model/migrate/check.py,
line 105, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '90' but this code expects version '79'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
--trying to upgrade
sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
line 150, in main
ret = command_func(**kwargs)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 327, in _migrate
changeset = schema.changeset(version)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py,
line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py,
line 145, in version
return self.versions.version(*p, **k)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py,
line 125, in version
return self.versions[VerNum(vernum)]
KeyError: VerNum(90)
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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please use the interface at:
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___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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Re: [galaxy-user] ftp Server unavailable
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Re: [galaxy-user] about primer/adaptor removal?
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[galaxy-user] Cufflinks related problem
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Re: [galaxy-user] Megablast
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[galaxy-user] merging databases
Hi! Here's a really simple question, but I somehow can't find an easy answer in Galaxy. I want to merge two fastq files (they contain 2 sequencing runs of the same library, and I want to pool them). How do I do that in Galaxy? Thanks! Karel ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
