I pushed a fix to the nglims fork on bitbucket which should resolve this
errors. Apologies, the nglims error is a mistake on my part. The way
Galaxy handles version updates changed a bit on the infrastructure side
and I hadn't coded correctly to handle all the cases.
You shouldn't need to restart and lose all your data. I think you're
nearly there with the upgrade. More details below and thanks for all the
> 114 -> 115...
> OperationalError: (OperationalError) there is already another table or
> index with this name: migration_tmp u'ALTER TABLE galaxy_user R
> ENAME TO migration_tmp' ()
This is the same error as before, so needs the same hack to work around:
$ sqlite3 database/universe.sqlite
sqlite> drop table migration_tmp;
Sorry about that one, not sure exactly how to fix this more cleanly.
> 115 -> 116...
> Tables for a next generation sequencing lims tied to requests.
> sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already
> defined for this MetaData instance. Specify 'extend_existin
> g=True' to redefine options and columns on an existing Table
This is my bug mentioned above, so should work with an updated checkout
of the code.
Hope this gets you there. Fingers crossed,
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