NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path'

[peterjc]

Reported by email on the galaxy-dev list, see
https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-July/022459.html
http://dev.list.galaxyproject.org/quot-Failure-when-preparing-job-quot-on-blastp-tc4667584.html

Hi there

I'm trying to use the blastp tools from the ncbi_blast_tools, but every time I try and run a job I get the following error:

Traceback (most recent call last):
  File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py", line 163, in prepare_job
    job_wrapper.prepare()
  File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/__init__.py", line 859, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/tools/evaluation.py", line 422, in build
    raise e
NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path'

This is happening when expanding the tool template. The BLAST db in in the history (thus the reference to histdb) but why can it not find this attribute?

Peter

Given 2bbbf7f my guess was that since this used to be .extra_files_path perhaps the Galaxy was too old for .files_path to work? However, this is a recent Galaxy:

This is release_15.07 (last commit listed is 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b. So no, its not an old Galaxy.

Pinging @bgruening and @jmchilton to comment.

[peterjc]

Is is worth asking Peter van Heusden to try editing ncbi_macros.xml to switch "${os.path.join($db_opts.histdb.files_path,'blastdb')}" to "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"?

[peterjc]

I've asked him to try the previous Tool Shed release (revision 2fe07f50a41e aka v0.1.01) which used the alternative form $db_opts.histdb.extra_files_path rather than the current $db_opts.histdb.files_path which appears to be failing.

[peterjc]

(The other) Peter confirmed by email that the previous Tool Shed release works, so it seems we may need to use .extra_files_path after all?

[jmchilton]

I feel like this is some sort of odd regression - no one should retreat back to extra_files_path - I feel like I unilaterally decided files_path was the "one correct answer" :).

Checking it out now...

[peterjc]

Thanks John - it looks like Galaxy needs some work on using extra_files_path with input files, but for now we'll go back to using files_path here and get an update to the Tool Shed.

Sadly we don't yet have any unit tests which would have caught this, see #3.

[peterjc]

TravisCI tests green, pushed v0.1.04 update to tool sheds:

• https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/188d2aca045b
• https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/b5f1f599d1fb

[bgruening]

Great! Thanks Peter, and sorry to be so silent was travelling and on workshops.