I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post <http://gregvonkuster.org/galaxy-tool-shed-june-2-2014-release/>. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user.
This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (*e.g.* the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno
$ sh ~/galaxy_dist/run_tool_shed.sh -bootstrap_from_tool_shed
testtoolshed.g2.bx.psu.edu
Bootstrapping from tool shed at testtoolshed.g2.bx.psu.edu.
Creating database... done.
Creating user 'bgrande' with email address 'bgra...@sfu.ca'...Traceback (most
recent call last):
File "lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py",
line 152, in <module>
app = BootstrapApplication( config )
File "lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py",
line 46, in __init__
create_tables=False )
File
"/home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/model/mapping.py", line
330, in init
result.shed_counter = shed_statistics.ShedCounter( result )
File
"/home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/util/shed_statistics.py",
line 20, in __init__
self.generate_statistics()
File
"/home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/util/shed_statistics.py",
line 39, in generate_statistics
for repository in self.sa_session.query( self.model.Repository ):
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 2227, in __iter__
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 2242, in _execute_and_instances
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
File
"/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
sqlalchemy.exc.OperationalError: (OperationalError) no such table: repository
u'SELECT repository.id AS repository_id, repository.create_time AS
repository_create_time, repository.update_time AS repository_update_time,
repository.name AS repository_name, repository.type AS repository_type,
repository.description AS repository_description, repository.long_description
AS repository_long_description, repository.user_id AS repository_user_id,
repository.private AS repository_private, repository.deleted AS
repository_deleted, repository.email_alerts AS repository_email_alerts,
repository.times_downloaded AS repository_times_downloaded,
repository.deprecated AS repository_deprecated \nFROM repository' ()
done.
Starting tool shed in order to populate users and categories... done.
Retrieving admin user's API key from http://127.0.0.1:9009... done.
Creating users... done.
Creating categories... done.
Bootstrap complete, shutting down temporary tool shed process. A log has been
saved to tool_shed_bootstrap.log
tool_shed_bootstrap.log
Description: Binary data
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