Hi Peter, I just wanted to chime in and say that I have been able to reproduce this issue locally (on a different tool), and I’d consider it a pretty significant bug for reproducibility, etc.
Thanks, Dan On Mar 31, 2015, at 12:33 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Tue, Mar 31, 2015 at 12:04 PM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock <p.j.a.c...@googlemail.com> >> wrote: >>> ... >>> >>> Summary: Workflow requesting key entry "xxx" from example.loc >>> (a) example.loc empty, gets empty path, fails cleanly. >>> (b) example.loc contains xxx, gets correct path, works. >>> (c) example.loc non empty but lacks xxx, runs with WRONG path. >>> >>> Peter >> > > I've started adding debug logging to traces this, focusing on > lib/galaxy/tools/parameters/dynamic_options.py > > At the "workflow preview", the BLAST database is still "nr" > (and has not yet been validated). At this point class > DynamicOptions method get_fields and get_options have > been called, so the mismatch could be spotted... > > After clicking "run workflow", by the time the DynamicOptions > methods get_fields_by_value and get_field_by_name_for_value > are called "nr" has been replaced with the first entry in the > loc file. > > I might need a few more clues to make any headway here. > The code in lib/galaxy/workflow/run.py is not yet clear to me... > > Peter > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
