I have an empty posgresql database:
psql -c "create database galaxy;"
I'm trying to launch run.sh from the latest version of galaxy-dist. Migration proceeds normally up to this point:
######### galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 Migration script to add the cleanup_event* tables. galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 Migrating 105 -> 106... galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 Traceback (most recent call last): File "/opt/galaxy/web/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/galaxy/web/lib/galaxy/app.py", line 45, in __init__ self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) File "/opt/galaxy/web/lib/galaxy/config.py", line 629, in _configure_models create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self ) File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 73, in create_or_verify_database migrate() File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 57, in migrate migrate_to_current_version( engine, db_schema ) File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 131, in migrate_to_current_version schema.runchange( ver, change, changeset.step ) File "/opt/galaxy/web/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 89, in runchange (self.version, startver)) InvalidVersionError: 103 is not 105 #########
I re-run run.sh and get:
######### migrate.versioning.repository DEBUG 2014-05-16 19:12:22,132 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2014-05-16 19:12:22,132 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.model.migrate.check DEBUG 2014-05-16 19:12:22,136 psycopg2 egg successfully loaded for postgres dialect /opt/galaxy/web/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname> Traceback (most recent call last): File "/opt/galaxy/web/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/galaxy/web/lib/galaxy/app.py", line 45, in __init__ self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) File "/opt/galaxy/web/lib/galaxy/config.py", line 629, in _configure_models create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self ) File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 111, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '103' but this code expects version '120'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. #########
I manually run manage_db.sh upgrade. This step passes, and then I run run.sh a third time and galaxy finally starts properly.
My question is: why can't the manage_db.sh upgrade step be included automatically when the initial DB build fails?
This is the first time a DB is being built, so it should be dead simple....
Cheers,
-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu