On Aug 21, 2014, at 3:48 PM, Michael Ta <mta@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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/