On Tue, Mar 31, 2015 at 12:04 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock <p.j.a.cock@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