On Aug 21, 2014, at 3:48 PM, Michael Ta <m...@pacificdx.com> wrote:
> 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?
Hi Michael,
The documentation should say to back up, but a restore is not necessary unless
you encounter some problem during the migration. Could you point me at the
documentation in question so I can update it?
Could you check that your backup included the sequences and that when you
restored the database, you restored the sequences? It looks like the sequence
in question (tool_version_association_id_seq) is not actually set to the
max(id) on the tool_version_association table, which means that the nextval
selected from that sequence would conflict with an id already in the table.
--nate
>
> Thanks,
> --
> Michael Ta
>
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