JJ, Arg this is a mess. I am very sorry about this - I still don't understand extra_files_path versus files_path myself. There are open questions on Peter's blast repo and no one ever followed up on my object store questions about this with Bjoern's issues a couple release cycles ago. We need to get these to work - write documetation explicitly declaring best practices we can all agree on and then write some tests to ensure things don't break in the future.
When you say your tools broke recently - can you say for certain which release broke these - the August14, October14, something older? I'll try to do some more research and get back to you. -John On Tue, Oct 14, 2014 at 6:04 AM, Jim Johnson <johns...@umn.edu> wrote: > Andrew, > > Thanks for investigating this. I changed the subject and sent to the galaxy > dev list. > > I've had a number of tools quit working recently. Particularly tools that > inspect the extra_files_path when setting metadata, Defuse, Rsem, SnpEff. > > I think there was a change in the galaxy framework: > The extra_files_path when referenced from an input or output in the cheetah > template sections of the tool config xml will be relative to the job working > directly rather than the files location. > I've just changed a few of my tools on my server yesterday > from: <param_name>.extra_files_path > to: <param_name>.dataset.extra_files_path > and they now work again. > > Dan or John, is that the right way to handle this? > Thanks, > > JJ > > > > On 10/13/14, 9:29 PM, Andrew Lonie wrote: >> >> Hi Jim. I am probably going about this the wrong way, but I am not >> clear on how to report tool errors (if in fact this is a tool error!) >> >> I've been trialling your snpeff wrapper from the test toolshed and >> getting a consistent error with the SnpEff Download and SnpEff sub >> tools (the SnpSift dbNSFP works fine). The problem seems to be with an >> attribute declaration and manifests during database download as: >> >> Traceback (most recent call last): >> File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py", >> line 564, in finish_job >> job_state.job_wrapper.finish( stdout, stderr, exit_code ) >> File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/__init__.py", line >> 1107, in finish >> dataset.datatype.set_meta( dataset, overwrite=False ) # call >> datatype.set_meta directly for the initial set_meta call during >> dataset creation >> File >> "/mnt/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/snpeff/1938721334b3/snpeff/lib/galaxy/datatypes/snpeff.py", >> line 21, in set_meta >> data_dir = dataset.files_path >> AttributeError: 'HistoryDatasetAssociation' object has no attribute >> 'files_path' >> >> >> We fiddled around with the wrapper, eventually replacing >> 'dataset.files_path' with 'dataset.extra_files_path' in snpeff.py, >> which fixed the download bug, but then SnpEff subtool itself threw a >> similar error when I tried to use that database from the history. >> >> I chased up a bit more but cannot understand the various posts on >> files_path vs extra_files_path >> >> I've shared a history with both of these errors here: >> http://130.56.251.62/galaxy/u/alonie/h/unnamed-history >> >> Maybe this is a problem with our Galaxy image? >> >> Any help appreciated! >> >> Andrew >> >> >> >> >> A/Prof Andrew Lonie >> University of Melbourne > > > > -- > James E. Johnson Minnesota Supercomputing Institute University of Minnesota > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
