liftOver functional tests failed

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liftOver functional tests failed

Anne Pajon-2
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>



And here are the results:

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
[hidden email] | +44 (0)1223 769 631


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Re: liftOver functional tests failed

John Chilton-4
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/b27e79133a6b2e467b17f502b05faf5af11127f5) 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 <[hidden email]> 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>



And here are the results:

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
[hidden email] | <a href="tel:%2B44%20%280%291223%20769%20631" value="+441223769631" target="_blank">+44 (0)1223 769 631


___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: liftOver functional tests failed

Anne Pajon-2
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 <[hidden email]> 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/b27e79133a6b2e467b17f502b05faf5af11127f5) 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 <[hidden email]> 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
> [hidden email] | +44 (0)1223 769 631
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>

--
Dr Anne Pajon - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
[hidden email] | +44 (0)1223 769 631

___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/