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
e...@msi.umn.edu
boll0...@umn.edu
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