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NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path' #69

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peterjc opened this Issue Jul 21, 2015 · 7 comments

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peterjc commented Jul 21, 2015

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.

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peterjc Jul 21, 2015

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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')}"?

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peterjc commented Jul 21, 2015

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')}"?

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peterjc Jul 21, 2015

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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.

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peterjc commented Jul 21, 2015

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.

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peterjc Jul 21, 2015

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(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?

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peterjc commented Jul 21, 2015

(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?

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jmchilton Jul 21, 2015

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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...

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jmchilton commented Jul 21, 2015

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 referenced this issue Jul 21, 2015

Replace extra_files_path with files_path.
Bjoen: As far as I know, that is now the recommended way. And
extra_files_path seems to be broken in conjunction with the
object store.

Peter: Confirmed with @jmchilton on pull request #44 discussion
that this is now the preferred way to do this.
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peterjc Jul 21, 2015

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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.

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peterjc commented Jul 21, 2015

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 added a commit that referenced this issue Jul 21, 2015

Fix regression with databases from history.
See GitHub issue #69, must still use .extra_files_path
for input composite datatypes.

peterjc added a commit that referenced this issue Jul 21, 2015

Document history bug fix in version history.
Once released to the Tool Shed, this should close issue #69 on GitHub.
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bgruening Jul 22, 2015

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

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bgruening commented Jul 22, 2015

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

@peterjc peterjc closed this Jul 22, 2015

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