Hi all I am due to give galaxy training tomorrow and the Galaxy server has gone down. Our galaxy admin is travelling and not responding and I appreciate a quick response to this issue. When I run galaxy_restart.sh I get the following error in web0.pid: migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} lib/galaxy/model/migrate galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg successfully loaded for postgresql dialect Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 104, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '124' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. ------ I did then try to do sh manage_db.sh downgrade 115 but I got this error: Traceback (most recent call last): File "./scripts/manage_db.py", line 62, in <module> main( repository=repo, url=db_url ) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 207, in main ret = command_func(**kwargs) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 202, in downgrade return _migrate(url, repository, version, upgrade=False, err=err, **opts) File "<string>", line 2, in _migrate File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 159, in with_engine return f(*a, **kw) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 345, in _migrate changeset = schema.changeset(version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 80, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 225, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 189, in version return self.versions.version(*p, **k) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 140, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(124)> Any help asap will be greatly appreciated. Ali ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
It looks like the Galaxy server was downgraded relative the database. Do you know how this may have happened? It also looks like this instance is probably quite a bit out of date, in any event, so I'd be hesitant to give advice recommending a major upgrade given the current state of things. I'd say you should really get in touch with the Galaxy Admin prior to trying much. Is using a cloud instance for the training an option? On Thu, Oct 29, 2015 at 11:44 AM Ali Al-Shahib <Ali.Al-Shahib@phe.gov.uk> wrote:
Hi all
I am due to give galaxy training tomorrow and the Galaxy server has gone down. Our galaxy admin is travelling and not responding and I appreciate a quick response to this issue.
When I run galaxy_restart.sh I get the following error in web0.pid:
migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
lib/galaxy/model/migrate
galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg successfully loaded for postgresql dialect
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self )
File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 104, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '124' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.
------
I did then try to do sh manage_db.sh downgrade 115 but I got this error:
Traceback (most recent call last):
File "./scripts/manage_db.py", line 62, in <module>
main( repository=repo, url=db_url )
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 207, in main
ret = command_func(**kwargs)
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 202, in downgrade
return _migrate(url, repository, version, upgrade=False, err=err, **opts)
File "<string>", line 2, in _migrate
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 159, in with_engine
return f(*a, **kw)
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 345, in _migrate
changeset = schema.changeset(version)
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 80, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 225, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 189, in version
return self.versions.version(*p, **k)
File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 140, in version
return self.versions[VerNum(vernum)]
KeyError: <VerNum(124)>
Any help asap will be greatly appreciated.
Ali
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ 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: https://lists.galaxyproject.org/
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Not to worry, I was restarting another server. Its fixed now. Thanks ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: 29 October 2015 18:03 To: Ali Al-Shahib; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] URGENT HELP! It looks like the Galaxy server was downgraded relative the database. Do you know how this may have happened? It also looks like this instance is probably quite a bit out of date, in any event, so I'd be hesitant to give advice recommending a major upgrade given the current state of things. I'd say you should really get in touch with the Galaxy Admin prior to trying much. Is using a cloud instance for the training an option? On Thu, Oct 29, 2015 at 11:44 AM Ali Al-Shahib <Ali.Al-Shahib@phe.gov.uk<mailto:Ali.Al-Shahib@phe.gov.uk>> wrote: Hi all I am due to give galaxy training tomorrow and the Galaxy server has gone down. Our galaxy admin is travelling and not responding and I appreciate a quick response to this issue. When I run galaxy_restart.sh I get the following error in web0.pid: migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} lib/galaxy/model/migrate galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg successfully loaded for postgresql dialect Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 104, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '124' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. ------ I did then try to do sh manage_db.sh downgrade 115 but I got this error: Traceback (most recent call last): File "./scripts/manage_db.py", line 62, in <module> main( repository=repo, url=db_url ) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 207, in main ret = command_func(**kwargs) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 202, in downgrade return _migrate(url, repository, version, upgrade=False, err=err, **opts) File "<string>", line 2, in _migrate File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 159, in with_engine return f(*a, **kw) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 345, in _migrate changeset = schema.changeset(version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 80, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 225, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 189, in version return self.versions.version(*p, **k) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 140, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(124)> Any help asap will be greatly appreciated. Ali ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
participants (2)
-
Ali Al-Shahib
-
Dannon Baker