On Dec 21, 2011, at 2:49 PM, Iry Witham wrote:

> I have installed a new Galaxy server utilizing the November 18,2011 
> distribution on a SLES 11 VM and cannot get it to launch cleanly.  I am 
> running postgreSQL v. 8.3.9 to create my database.  Once the database is 
> created and running I launch my Galaxy server and within moments all of the 
> PID fail except for the reports_webapp.pid.  When I tail the logs I find the 
> following:
> 
> tail reports_webapp.log - 
> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,179 Enabling 
> 'httpexceptions' middleware
> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,194 Enabling 
> 'recursive' middleware
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11:
>  DeprecationWarning: the md5 module is deprecated; use hashlib instead
>   import md5
> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,272 Enabling 
> 'error' middleware
> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling 'trans 
> logger' middleware
> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling 
> 'config' middleware
> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,294 Enabling 
> 'x-forwarded-host' middleware
> Starting server in PID 20411.
> serving on 0.0.0.0:9001 view at http://127.0.0.1:9001
> 
> tail web0.log - 
> galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,793 psycopg2 egg 
> successfully loaded for postgres dialect
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp.py",
>  line 82, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py", 
> line 39, in __init__
>     create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
> '__file__', None ), self.config.database_engine_options )
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/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 '38' but this code expects version '85'. 
>  Please backup your database and then migrate the schema by running 'sh 
> manage_db.sh -c ./universe_wsgi.webapp.ini upgrade'.
> Removing PID file web0.pid
> 
> tail runner0.log - 
> galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,789 psycopg2 egg 
> successfully loaded for postgres dialect
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp.py",
>  line 82, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py", 
> line 39, in __init__
>     create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
> '__file__', None ), self.config.database_engine_options )
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/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 '38' but this code expects version '85'. 
>  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
> 
> 
> sh manage_db.sh upgrade -
> 
> 38 -> 39... 
> 
> Migration script to add a synopsis column to the library table.
> 
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 63, in <module>
>     main( repository=repo, url=db_url )
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
>  line 150, in main
>     ret = command_func(**kwargs)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/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 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
>  line 349, in _migrate
>     schema.runchange(ver, change, changeset.step)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
>  line 184, in runchange
>     change.run(self.engine, step)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py",
>  line 101, in run
>     func()
>   File 
> "lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py",
>  line 20, in upgrade
>     c.create( Library_table )
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/changeset/schema.py",
>  line 365, in create
>     engine._run_visitor(visitorcallable, self, *args, **kwargs)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 1158, in _run_visitor
>     visitorcallable(self.dialect, conn, **kwargs).traverse(element)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py",
>  line 89, in traverse
>     return traverse(obj, self.__traverse_options__, self._visitor_dict)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py",
>  line 200, in traverse
>     return traverse_using(iterate(obj, opts), obj, visitors)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py",
>  line 194, in traverse_using
>     meth(target)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/changeset/ansisql.py",
>  line 97, in visit_column
>     self.execute()
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 1812, in execute
>     return self.connection.execute(self.buffer.getvalue())
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 824, in execute
>     return Connection.executors[c](self, object, multiparams, params)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 888, in _execute_text
>     return self.__execute_context(context)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 896, in __execute_context
>     self._cursor_execute(context.cursor, context.statement, 
> context.parameters[0], context=context)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 950, in _cursor_execute
>     self._handle_dbapi_exception(e, statement, parameters, cursor, context)
>   File 
> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
>  line 931, in _handle_dbapi_exception
>     raise exc.DBAPIError.instance(statement, parameters, e, 
> connection_invalidated=is_disconnect)
> sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "synopsis" of 
> relation "library" already exists
>  '\nALTER TABLE "library"  ADD synopsis TEXT' {}
> 
> I have dropped the database multiple times and recreated it and intentionally 
> left out steps when creating DB users and roles and the manage_db.sh fails at 
> different spots.  However, I cannot get past 38 -> 39.  Any suggestions?

Hi Iry,

Can you clarify whether you are manually creating any tables?  You only need to 
create the database itself, Galaxy handles all of the tables.

If you're not creating any tables, what is the output of the very first run of 
Galaxy on an empty database?

--nate

> 
> Thanks,
> 
> IRy
> ___________________________________________________________
> 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/

Reply via email to