I updated a local Galaxy installation a while back and I followed the steps listed on one of the wiki pages. The update included changes to the database schema and I was careful to backup and restore it according to the directions. However, when I try to install new tools from the tool shed or update a tool to a new revision it does not complete successfully. The following error appears in the log file.
File '/home/galaxy/galaxy-dist/lib/tool_shed/util/tool_util.py', line 761 in handle_tool_versions
context.flush()
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py', line 114 in do
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1718 in flush
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', line 1789 in _flush
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p y', line 331 in execute
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p y', line 475 in execute
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence. py', line 64 in save_obj
File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence. py', line 558 in _emit_insert_statements
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.p y', line 331 in do_execute
IntegrityError: (IntegrityError) duplicate key value violates unique constraint "tool_version_association_pk ey"
DETAIL: Key (id)=(83) already exists.
'INSERT INTO tool_version_association (tool_id, parent_id) VALUES (%(tool_id)s, %(parent_id)s) RETURNING to
ol_version_association.id' {'parent_id': 440, 'tool_id': 439}
A few of the keys appear to be colliding with values already in the database, did I miss something when I updated and restored the database that is causing this?
Thanks,
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