Thanks! I did hg pull -u. For the database, I downgraded to 108 and then
upgraded again but got this error when upgrading. Is it due to the Ubuntu
bug? Or something else? Should I be sticking with a particular Hg version
instead of the latest?
$ sh manage_db.sh upgrade
115 -> 116...
Tables for a next generation sequencing lims tied to requests.
/home/galaxy/bin/chapman-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py:723:
SAWarning: Did not recognize type 'BIGINT' of column 'bytes'
Traceback (most recent call last):
File "./scripts/manage_db.py", line 65, in <module>
main( repository=repo, url=db_url )
File
"/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py",
line 207, in main
ret = command_func(**kwargs)
File
"/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py",
line 186, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File "<string>", line 2, in _migrate
File
"/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py",
line 159, in with_engine
return f(*a, **kw)
File
"/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py",
line 366, in _migrate
schema.runchange(ver, change, changeset.step)
File
"/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py",
line 91, in runchange
change.run(self.engine, step)
File
"/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py",
line 145, in run
script_func(engine)
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 52, in
upgrade
for table in _get_tables(metadata):
File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 34, in
_get_tables
primary_key = True),
File "build/bdist.linux-x86_64/egg/sqlalchemy/schema.py", line 305, in
__new__
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already
defined for this MetaData instance. Specify 'extend_existing=True' to
redefine options and columns on an existing Table object.
On Tue, Jul 2, 2013 at 10:59 AM, Dannon Baker <dannon.ba...@gmail.com>wrote:
> On Mon, Jul 1, 2013 at 8:34 PM, Brad Chapman <chapm...@50mail.com> wrote:
>
>>
>> This was a typo in the downgrade function for one of the patches. I
>> pushed a fix so if you update from bitbucket things should work smoothly
>> again (once we get to problem 2 below).
>>
>> For anyone with galaxy-dist commit privileges, here's the one liner:
>>
>>
>> https://bitbucket.org/chapmanb/galaxy-central/commits/463852762a6eeadcf177312330ad1cd01053263d
>
>
> Thanks Brad, added to stable branch in
> https://bitbucket.org/galaxy/galaxy-central/commits/0a06df7da177a204c7f3800ee39e5b9fd0956d7a
>
>
>
--
Lee Katz, Ph.D.
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