Hi,

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,
-- 
Michael Ta
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