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: