Hi John,
Many thanks for coming back to me on this issue. Unfortunately adding the full path into the test did not solve the issue for me, e.g.
<param name="to_dbkey" value="/data/galaxy/genomes/hg18/liftOver/hg18ToPanTro2.over.chain" />
So for the time being I will comment these out. Many thanks again.
Kind regards, Anne.
On 24 Feb 2015, at 04:02, John Chilton jmchilton@gmail.com wrote:
Yes, indeed liftOver's tests are broken :(. Thanks for the bug report.
The way liftOver's loc file is being handled is problematic - it uses full paths as parameter "value"s. Fixing that (https://github.com/jmchilton/galaxy/commit/b27e79133a6b2e467b17f502b05faf5af...) fixes the test cases and would make liftOver more robust - a seeming win-win. Unfortunately I don't think I can fix liftOver in -dist because it would break everyone's tool re-runs and workflows (but if I were running my own new Galaxy I would definitely apply that commit now).
Back to the functional test - the testing framework can no longer handle this case for some fairly technical and uninteresting reasons. I could fix it but it would be a substantial amount of work and the corner case is sufficiently corner-y that I imagine only liftOver is affected by the bug - so I would prefer to just say the test framework cannot do this anymore and comment out the liftOver tests until we bite the bullet on the loc file structure.
If you want the tests and you want them to pass without the above commit - you can replace the test values that look like:
<param name="to_dbkey" value="panTro2" />
with full paths to the .over.chain file, e.g.
<param name="to_dbkey" value="/path/to/hg18ToPanTro2.over.chain" />
I would expect to see these tests all just commented out in the next release though :(.
Hope this helps and thanks again for the bug report,
-John
On Mon, Feb 16, 2015 at 1:34 PM, Anne Pajon Anne.Pajon@cruk.cam.ac.uk wrote: Dear All,
I am still trying to migrate my production server to new hardware and would like to have all functional tests pass before turning off my old server.
I am facing an issue with liftOver functional tests, they failed when running 'sh run_tests.sh -id liftOver1' on the command line with these errors:
====================================================================== ERROR: test_tool_000000 (functional.test_toolbox.TestForTool_liftOver1) Convert genome coordinates ( liftOver1 ) > Test-1
Traceback (most recent call last): File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it data_list, jobs = galaxy_interactor.run_tool( testdef, test_history ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool raise Exception( datasets_object[ 'message' ] ) Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}} -------------------- >> begin captured logging << --------------------
====================================================================== ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_liftOver1) Convert genome coordinates ( liftOver1 ) > Test-2
Traceback (most recent call last): File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it data_list, jobs = galaxy_interactor.run_tool( testdef, test_history ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool raise Exception( datasets_object[ 'message' ] ) Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}} -------------------- >> begin captured logging << --------------------
====================================================================== ERROR: test_tool_000002 (functional.test_toolbox.TestForTool_liftOver1) Convert genome coordinates ( liftOver1 ) > Test-3
Traceback (most recent call last): File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it data_list, jobs = galaxy_interactor.run_tool( testdef, test_history ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool raise Exception( datasets_object[ 'message' ] ) Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}} -------------------- >> begin captured logging << --------------------
====================================================================== ERROR: test_tool_000003 (functional.test_toolbox.TestForTool_liftOver1) Convert genome coordinates ( liftOver1 ) > Test-4
Traceback (most recent call last): File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 122, in test_tool self.do_it( td ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 37, in do_it data_list, jobs = galaxy_interactor.run_tool( testdef, test_history ) File "/mnt/nfs/data/galaxy/galaxy-dist/test/base/interactor.py", line 218, in run_tool raise Exception( datasets_object[ 'message' ] ) Exception: {u'type': u'error', u'data': {u'to_dbkey': u'An invalid option was selected, please verify'}} -------------------- >> begin captured logging << --------------------
But when tested using the GUI, they did pass.
I have configured the alignseq.loc and liftOver.loc, they both contained TAB delimited data and file locations have been checked. I’ve downloaded 5.bed into the GUI, used for testing liftOver, and configure the parameters according to those set in the test: <test> <param name="input" value="5.bed" dbkey="hg18" ftype="bed" /> <param name="to_dbkey" value="panTro2" /> <param name="minMatch" value="0.95" /> <param name="choice" value="0" /> <output name="out_file1" file="5_liftover_mapped.bed"/> <output name="out_file2" file="5_liftover_unmapped.bed"/> </test>
<Screen Shot 2015-02-16 at 18.29.38.png>
<Screen Shot 2015-02-16 at 18.30.57.png>
And here are the results: <Screen Shot 2015-02-16 at 18.31.39.png>
Any ideas of what could be that the functional tests on the command line failed? Any help to where to look would be greatly appreciated. Many thanks in advance. Best wishes, Anne.
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
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-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631