Yay! Happy New Year for the Galaxy Tool community :) Thank you, Peter On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
After fixing a number of issues, it appears that the tests are now running as they should. I'll keep an eye on the test framework in case any new errors crop up.
--Dave B.
On 12/10/2014 09:19 AM, Peter Cock wrote:
On Wed, Dec 10, 2014 at 2:03 PM, John Chilton <jmchilton@gmail.com> wrote:
On Wed, Dec 10, 2014 at 5:46 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi guys,
The good news is my list of failing tools has shrunk to the following, none of which seem to have been tested yet in December, stuck with "Exception: Job in error state.":
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
Meanwhile, on the main tool, "Exception: Job in error state." and not yet tested in December:
https://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
It would be nice to have a more informative error here...
Ugh - yes it clearly would - very sorry about that.
Have these tools been automatically earmarked not to be retested? Note that some tools have been tested earlier this month:
I also have a legitimate failure for missing tests, run 2014-12-09, https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
Interesting... some tests did run though? Does the framework not report passing tests - seems like it would be hard to know if it working in that case.
The "Latest revision: all tool tests pass" search returns lots of repositories, but I must examine each one-by-one to see when the tests were last run. The sample I just checked on the main Tool Shed were all lasted tested 2014-11-23,
https://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://toolshed.g2.bx.psu.edu/view/peterjc/clinod https://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
However at least some tests have been run in December, e.g. https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Things seem similar on the Test Tool Shed. Presumably you can sort the test results over the entire Tool Shed via a database search? That might help explain any pattern here.
Thanks,
Peter