Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Thu, Apr 25, 2013 at 4:25 PM, Dave Bouvier  wrote:
> Peter,
>
> Your point is well taken about the utility of the testing framework in the
> tool development process. The framework has been modified as of
> 9520:41d8cdde4729 to only flag a changeset revision not to be tested if no
> valid tests have been found in that revision. If one or more tools have
> functional tests, and there is test data for one or more of those tests, the
> repository will now be installed and tested.
>
> I will be re-running the testing framework on the test tool shed shortly.
>
>--Dave B.

Excellent :)

I have to say since having had a nightly buildbot running unit tests,
and then TravisCI doing continuous integration (testing when a
fresh set of commits is pushed to the repository) for Biopython,
I've come to value unit tests even more. Having something like this
on the Galaxy Tool Shed is a really good move :)

Thanks,

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Dave Bouvier]

Peter,

Your point is well taken about the utility of the testing framework in 
the tool development process. The framework has been modified as of 
9520:41d8cdde4729 to only flag a changeset revision not to be tested if 
no valid tests have been found in that revision. If one or more tools 
have functional tests, and there is test data for one or more of those 
tests, the repository will now be installed and tested.


I will be re-running the testing framework on the test tool shed shortly.

   --Dave B.

On 4/25/13 09:58:39.000, Peter Cock wrote:

Hi Dave,

On Thu, Apr 25, 2013 at 2:27 PM, Dave Bouvier  wrote:

Peter,

That is the intended behavior, but I've added a trello card
(https://trello.com/c/O9YmzUT4) for revisiting that decision at some point.


Is that the right Trello card? Is seems to be all about multiple tool shed
repository revisions rather than what I'm asking about.


We are definitely willing to be flexible about the testing conditions, but
the primary goal of the automated testing framework was to verify functional
correctness of an entire repository, to simplify the approval process for
the category of "tools contained within the repository".

--Dave B.


Well as you can tell, I disagree with that design choice: If there are tools
with tests within a repository I think those tests should be run. It seems
far more pragmatic than the current all-or-nothing approach (for which
I can't see any real justification).

This is especially frustrating when there are still obstacles from the
test framework itself which block writing tests for all my tools. e.g.
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014280.html

Given "the primary goal of the automated testing framework was to
verify functional correctness of an entire repository", not running any
tests if just one tool is missing tests seems very bizarre. Right now I
can run those tests locally, but I have no way to know if they would
work on the Tool Shed tests - until I reach full test coverage for the
repository. If all the tests provided were actually run, I can fix any
failures now, rather than waiting until issues blocking adding any
missing tests are resolved.

I hope this aspect of the design can be revisited sooner rather than later.

Thanks,

Peter


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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

Hi Dave,

On Thu, Apr 25, 2013 at 2:27 PM, Dave Bouvier  wrote:
> Peter,
>
> That is the intended behavior, but I've added a trello card
> (https://trello.com/c/O9YmzUT4) for revisiting that decision at some point.

Is that the right Trello card? Is seems to be all about multiple tool shed
repository revisions rather than what I'm asking about.

> We are definitely willing to be flexible about the testing conditions, but
> the primary goal of the automated testing framework was to verify functional
> correctness of an entire repository, to simplify the approval process for
> the category of "tools contained within the repository".
>
>--Dave B.

Well as you can tell, I disagree with that design choice: If there are tools
with tests within a repository I think those tests should be run. It seems
far more pragmatic than the current all-or-nothing approach (for which
I can't see any real justification).

This is especially frustrating when there are still obstacles from the
test framework itself which block writing tests for all my tools. e.g.
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014280.html

Given "the primary goal of the automated testing framework was to
verify functional correctness of an entire repository", not running any
tests if just one tool is missing tests seems very bizarre. Right now I
can run those tests locally, but I have no way to know if they would
work on the Tool Shed tests - until I reach full test coverage for the
repository. If all the tests provided were actually run, I can fix any
failures now, rather than waiting until issues blocking adding any
missing tests are resolved.

I hope this aspect of the design can be revisited sooner rather than later.

Thanks,

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Dave Bouvier]

Peter,

That is the intended behavior, but I've added a trello card 
(https://trello.com/c/O9YmzUT4) for revisiting that decision at some 
point. We are definitely willing to be flexible about the testing 
conditions, but the primary goal of the automated testing framework was 
to verify functional correctness of an entire repository, to simplify 
the approval process for the category of "tools contained within the 
repository".



   --Dave B.

On 4/25/13 04:55:50.000, Peter Cock wrote:

On Wed, Apr 24, 2013 at 10:12 AM, Peter Cock  wrote:


..., I've still finding some other cases where despite having
tests defined, nothing shows up on the Tool Shed test results page.

Here's an example where I see that two tools (promoter2 and
wolf_psort) have no tests, but the results of all the other tools
in this suite are not mentioned (some expected to fail/be skipped
due to missing dependencies):

http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Revision 13:dc958c2a963a

Equivalently:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Revision: 14:0d8b1d20ce9c



Here's another example where based on what happens locally,
I am expecting a failure:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename
Revision: 1:6ce8634e2035

This is failing for me locally, but again I suspect this is due to an
issue in the framework - much like the blastxml_to_top_descr
test is failing due to the datatypes not being updated, here there
seems to be something similar going wrong regarding the
second uploaded input file (which is used for to provide the
potential column parameters). See this thread:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003867.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014261.html

Regards,

Peter


Hi Dave,

Yet another case,

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Revision: 8:1f546099212f

and,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
Revision: 5:d42346e675c4

These list five or six invalid tools which do not define any unit
tests, yet there is no mention of the tools present which do have
tests (and if they passed or not).

Even if ncbi_blastdbcmd_wrapper doesn't (yet) have a test,
I still want to know if the ncbi_blastp_wrapper tests pass ;)

Are this further symptoms of whatever was solved here?
https://trello.com/card/toolshed-automated-functional-test-bug/506338ce32ae458f6d15e4b3/793

Or does would a new Trello issue be best?

Thanks,

Peter


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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Wed, Apr 24, 2013 at 10:12 AM, Peter Cock  wrote:
>
> ..., I've still finding some other cases where despite having
> tests defined, nothing shows up on the Tool Shed test results page.
>
> Here's an example where I see that two tools (promoter2 and
> wolf_psort) have no tests, but the results of all the other tools
> in this suite are not mentioned (some expected to fail/be skipped
> due to missing dependencies):
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> Revision 13:dc958c2a963a
>
> Equivalently:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> Revision: 14:0d8b1d20ce9c
>
> 
>
> Here's another example where based on what happens locally,
> I am expecting a failure:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename
> Revision: 1:6ce8634e2035
>
> This is failing for me locally, but again I suspect this is due to an
> issue in the framework - much like the blastxml_to_top_descr
> test is failing due to the datatypes not being updated, here there
> seems to be something similar going wrong regarding the
> second uploaded input file (which is used for to provide the
> potential column parameters). See this thread:
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003867.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014261.html
>
> Regards,
>
> Peter

Hi Dave,

Yet another case,

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Revision: 8:1f546099212f

and,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
Revision: 5:d42346e675c4

These list five or six invalid tools which do not define any unit
tests, yet there is no mention of the tools present which do have
tests (and if they passed or not).

Even if ncbi_blastdbcmd_wrapper doesn't (yet) have a test,
I still want to know if the ncbi_blastp_wrapper tests pass ;)

Are this further symptoms of whatever was solved here?
https://trello.com/card/toolshed-automated-functional-test-bug/506338ce32ae458f6d15e4b3/793

Or does would a new Trello issue be best?

Thanks,

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Fri, Apr 19, 2013 at 4:46 PM, Dave Bouvier  wrote:
> Peter,
>
> I've committed a fix for this in 9480:a80175a97194, and re-run the automated
> testing framework. However, as you will see, the test still reports an
> error. This is not due to an issue in your repository, but an problem on the
> Galaxy side, as described in the following trello card:
> https://trello.com/c/KdGX3hkh
>
>--Dave B.

Thanks - once this and the best way forward for defining Python
modules as dependencies are sorted out I should be able to get
more of my tools in the Tool Shed passing their unit tests :)

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Dave Bouvier]

Peter,

I've committed a fix for this in 9480:a80175a97194, and re-run the 
automated testing framework. However, as you will see, the test still 
reports an error. This is not due to an issue in your repository, but an 
problem on the Galaxy side, as described in the following trello card: 
https://trello.com/c/KdGX3hkh


   --Dave B.

On 4/17/13 06:20:39.000, Peter Cock wrote:

On Wed, Apr 17, 2013 at 9:44 AM, Peter Cock mailto:p.j.a.c...@googlemail.com>> wrote:



On Tue, Apr 16, 2013 at 9:42 PM, Greg Von Kuster mailto:g...@bx.psu.edu>> wrote:

Hello Peter,

On Apr 15, 2013, at 11:04 AM, Peter Cock wrote:


The "View tool functional test results" option clearly lists
failed tests,
but it is not obvious if there were any successful tests.
Could that
be indicated somehow (e.g. five tests passed for tool xxx).





Here's a problem case,
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

This has one unit test defined,

 
 
 
 
 
 
 

However, it is not shown via "View tool functional test results":

Tool functional test results
Time tested: ~ 6 hours ago
*Tool Shed environment*

Tool shed version: 9252:da2d6ee29f30
Tool shed database version: 17
Mercurial version: 2.2.3
*Galaxy environment*

Galaxy version: unknown
Galaxy database version: unknown
Architecture: x86_64
Operating system: Linux 3.0.0-1-amd64
Python version: 2.7.2+


i.e. No mention of the fact there was (presumably) one successful test.

Peter


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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Wed, Apr 17, 2013 at 9:44 AM, Peter Cock wrote:

>
>
> On Tue, Apr 16, 2013 at 9:42 PM, Greg Von Kuster  wrote:
>
>> Hello Peter,
>>
>> On Apr 15, 2013, at 11:04 AM, Peter Cock wrote:
>>
>> The "View tool functional test results" option clearly lists failed tests,
>> but it is not obvious if there were any successful tests. Could that
>> be indicated somehow (e.g. five tests passed for tool xxx).
>>
>>
>>

Here's a problem case,
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

This has one unit test defined,









However, it is not shown via "View tool functional test results":

 Tool functional test results
 Time tested: ~ 6 hours ago
 *Tool Shed environment*
 Tool shed version: 9252:da2d6ee29f30
 Tool shed database version: 17
 Mercurial version: 2.2.3
 *Galaxy environment*
 Galaxy version: unknown
 Galaxy database version: unknown
 Architecture: x86_64
 Operating system: Linux 3.0.0-1-amd64
 Python version: 2.7.2+


i.e. No mention of the fact there was (presumably) one successful test.

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Tue, Apr 16, 2013 at 9:42 PM, Greg Von Kuster  wrote:

> Hello Peter,
>
> On Apr 15, 2013, at 11:04 AM, Peter Cock wrote:
>
> The "View tool functional test results" option clearly lists failed tests,
> but it is not obvious if there were any successful tests. Could that
> be indicated somehow (e.g. five tests passed for tool xxx).
>
>
> If I understand your request, I believe we already provide it.  Functional
> test results are displayed for tests that passed or failed.  For example,
> see the functional test results for revision 
> 3:aa76c8dd97e6
>  of jjohnson's pileup_to_vcf
> repository, which displays the following.  Is this what you are asking for?
>
> Thanks!
>
>
> *Tests that failed*
>   Tool id: *pileup_to_vcf* version: *2.0*  *Test id* test_tool_01 (
> functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0
> )  *Status* Test failed  *Stderr*  *Traceback*
> Traceback (most recent call last):
>
>   File 
> "/var/opt/buildbot/slaves/buildbot-install-test-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
>  line 171, in test_tool
> self.do_it( td, shed_tool_id=shed_tool_id )
>
>   File 
> "/var/opt/buildbot/slaves/buildbot-install-test-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
>  line 102, in do_it
>
> self.verify_dataset_correctness( outfile, hid=elem_hid, 
> maxseconds=testdef.maxseconds, attributes=attributes, 
> shed_tool_id=shed_tool_id )
>
>   File 
> "/var/opt/buildbo  line 798, in verify_dataset_correctness
> raise AssertionError( errmsg )
> AssertionError: History item 2 different than expected
>
> No text matching expression 'chr1\t158571283\t.\tA\tC\t.\tPASS\t.*' was found 
> in output file.
>   *Tests that passed successfully*
>   Tool id: *pileup_to_vcf* version: *2.0*  *Test id* test_tool_00 (
> functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0
> )  *Status* Test passed
>
>
>
That does look good - maybe I've been unlucky in the examples I've looked
at due to missing dependencies and/or true results being hidden by this
issue:

https://trello.com/card/toolshed
-automated-functional-test-bug/506338ce32ae458f6d15e4b3/793

Thanks,

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Greg Von Kuster]

Hello Peter,

On Apr 15, 2013, at 11:04 AM, Peter Cock wrote:

> The "View tool functional test results" option clearly lists failed tests,
> but it is not obvious if there were any successful tests. Could that
> be indicated somehow (e.g. five tests passed for tool xxx).
> 

If I understand your request, I believe we already provide it.  Functional test 
results are displayed for tests that passed or failed.  For example, see the 
functional test results for revision 3:aa76c8dd97e6 of jjohnson's pileup_to_vcf 
repository, which displays the following.  Is this what you are asking for?

Thanks!


Tests that failed
Tool id: pileup_to_vcf version: 2.0
Test id test_tool_01 
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0)
Status  Test failed
Stderr  
Traceback   Traceback (most recent call last):
  File 
"/var/opt/buildbot/slaves/buildbot-install-test-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
 line 171, in test_tool
self.do_it( td, shed_tool_id=shed_tool_id )
  File 
"/var/opt/buildbot/slaves/buildbot-install-test-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
 line 102, in do_it
self.verify_dataset_correctness( outfile, hid=elem_hid, 
maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id 
)
  File 
"/var/opt/buildbot/slaves/buildbot-install-test-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
 line 798, in verify_dataset_correctness
raise AssertionError( errmsg )
AssertionError: History item 2 different than expected
No text matching expression 'chr1\t158571283\t.\tA\tC\t.\tPASS\t.*' was found 
in output file.
Tests that passed successfully
Tool id: pileup_to_vcf version: 2.0
Test id test_tool_00 
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0)
Status  Test passed




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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Mon, Apr 15, 2013 at 4:14 PM, Dave Bouvier  wrote:
> That does sound like a useful option, I'll be discussing that and other
> enhancements to the automated testing system with Greg in the near future.
>
> In this specific case, it looks like functional tests were set to not be
> executed, because two of the tools in the repository were missing functional
> test definitions. Our rationale for doing so was that if any tool can't be
> tested due to missing functional tests or test data, then the repository as
> a whole can't be proven functionally correct.
>
>--Dave B.

It would still be useful to the tool author and potential tool users to
know that tools X and Y in a repository work, even if Z fails a test.

Thanks,

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Dave Bouvier]

That does sound like a useful option, I'll be discussing that and other 
enhancements to the automated testing system with Greg in the near future.


In this specific case, it looks like functional tests were set to not be 
executed, because two of the tools in the repository were missing 
functional test definitions. Our rationale for doing so was that if any 
tool can't be tested due to missing functional tests or test data, then 
the repository as a whole can't be proven functionally correct.


   --Dave B.

On 4/15/13 11:04:51.000, Peter Cock wrote:

On Mon, Apr 15, 2013 at 3:56 PM, Dave Bouvier  wrote:

Peter,

I'm unable to duplicate that behavior, the "View tool functional test
results" option shows up on the test tool shed both when I'm logged in and
logged out. My suggestion would be to clear your browser's cookies and
cache, and see if that makes a difference.

--Dave B.


That did it - thanks :)

I also have a feature request now though ;)

The "View tool functional test results" option clearly lists failed tests,
but it is not obvious if there were any successful tests. Could that
be indicated somehow (e.g. five tests passed for tool xxx).

Peter


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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Mon, Apr 15, 2013 at 3:56 PM, Dave Bouvier  wrote:
> Peter,
>
> I'm unable to duplicate that behavior, the "View tool functional test
> results" option shows up on the test tool shed both when I'm logged in and
> logged out. My suggestion would be to clear your browser's cookies and
> cache, and see if that makes a difference.
>
>--Dave B.

That did it - thanks :)

I also have a feature request now though ;)

The "View tool functional test results" option clearly lists failed tests,
but it is not obvious if there were any successful tests. Could that
be indicated somehow (e.g. five tests passed for tool xxx).

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Dave Bouvier]

Peter,

I'm unable to duplicate that behavior, the "View tool functional test 
results" option shows up on the test tool shed both when I'm logged in 
and logged out. My suggestion would be to clear your browser's cookies 
and cache, and see if that makes a difference.


   --Dave B.

On 4/15/13 09:35:40.000, Peter Cock wrote:

On Mon, Apr 15, 2013 at 2:20 PM, Dave Bouvier  wrote:

Peter,

The automated testing framework is also running against the test tool shed.
Could you send me a link to the repository that is behaving oddly?



e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
On the main tool shed, when I am logged in, on this page under
the top right menu "Repository actions" the second entry is
"View tool functional test results".

However, on the test tool shed, that menu item is missing:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

Although the history is different, I believe the same tarball for
v0.2.1 of the suite was uploaded to both the main and test
tool sheds.

Peter


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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

On Mon, Apr 15, 2013 at 2:20 PM, Dave Bouvier  wrote:
> Peter,
>
> The automated testing framework is also running against the test tool shed.
> Could you send me a link to the repository that is behaving oddly?
>

e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
On the main tool shed, when I am logged in, on this page under
the top right menu "Repository actions" the second entry is
"View tool functional test results".

However, on the test tool shed, that menu item is missing:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

Although the history is different, I believe the same tarball for
v0.2.1 of the suite was uploaded to both the main and test
tool sheds.

Peter
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Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)

[Dave Bouvier]

Peter,

The automated testing framework is also running against the test tool 
shed. Could you send me a link to the repository that is behaving oddly?


   --Dave B.

On 4/12/13 06:42:04.000, Peter Cock wrote:

Hi all,

I'd like to be able to experiment with the new automated testing
recently added to the main Tool Shed http://toolshed.g2.bx.psu.edu/
by first trying my updates on the Test Tool Shed (to make sure my
tests will work before making the tool update public).

It appears that the testing features are not available on the
Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/

Is this correct? Is this intentional?

Thanks,

Peter

P.S. This would be less urgent if I could solve this issue which
is blocking my local testing:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014123.html
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[galaxy-dev] TestToolShed out of date? (not running unit tests)

[Peter Cock]

Hi all,

I'd like to be able to experiment with the new automated testing
recently added to the main Tool Shed http://toolshed.g2.bx.psu.edu/
by first trying my updates on the Test Tool Shed (to make sure my
tests will work before making the tool update public).

It appears that the testing features are not available on the
Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/

Is this correct? Is this intentional?

Thanks,

Peter

P.S. This would be less urgent if I could solve this issue which
is blocking my local testing:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014123.html
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