Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Nov 28, 2013 at 7:34 PM, Greg Von Kuster  wrote:
> Hi Peter,
>
>> But its not all good news - another test is now listed as failing, but with
>> missing test results:
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
>
> The bad data shoud now be eliminated, and there are 3 test runs displaying
> for this one.  Do these look crrect to you?  The oldest test run has a data
> of 'unknown' because I had not implemented the date deature at that point.

Most of the tests passed (as expected), but a couple of times there
was some kind of time out error, e.g.

> Traceback (most recent call last):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 101, in test_tool
> self.do_it( td )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 31, in do_it
> self.__verify_outputs( testdef, test_history, shed_tool_id, data_list,
> galaxy_interactor )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 64, in __verify_outputs
> galaxy_interactor.verify_output( history, output_data, outfile,
> attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 303, in verify_output
> self.twill_test_case.verify_dataset_correctness( outfile, hid=hid,
> attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 814, in verify_dataset_correctness
> self.wait( maxseconds=maxseconds )  # wait for job to finish
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 1425, in wait
> return self.wait_for(lambda: self.get_running_datasets(), **kwds)
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> line 1440, in wait_for
> assert slept < maxseconds
> AssertionError:

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hi Peter,


On Nov 28, 2013, at 12:56 PM, Peter Cock  wrote:

> On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock  wrote:
>> 
>> Thank you - that alerted me to a missing set of out output files for a
>> recently added test, hopefully addressed in this revision:
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
>> 
>> But its not all good news - another test is now listed as failing, but with
>> missing test results:
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
>> 
> 
> Another little oddity, the three test results for mira_bait.xml are missing
> (although it correctly tells me mira_4_0_mapping and mira_4_0_de_novo
> have no tests):
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler/302d13490b23

Here is what I am seeing for the missing tests.  Is this information ot 
correct?  If not, what is incorrect?


Automated tool test results

Test runs
2013-11-28 13:02:42
Automated test environment
Time tested: 2013-11-28 13:02:42
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tools missing tests or test data
Tool id: mira_4_0_mapping
Tool version: 0.0.2
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2
Missing components: 
Functional test definitions missing for mira_4_0_mapping.
Tool id: mira_4_0_de_novo
Tool version: 0.0.2
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2
Missing components: 
Functional test definitions missing for mira_4_0_de_novo.
2013-11-28 11:29:49
Automated test environment
Time tested: 2013-11-28 11:29:49
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tools missing tests or test data
Tool id: mira_4_0_mapping
Tool version: 0.0.2
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2
Missing components: 
Functional test definitions missing for mira_4_0_mapping.
Tool id: mira_4_0_de_novo
Tool version: 0.0.2
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2
Missing components: 
Functional test definitions missing for mira_4_0_de_novo.


> 
> Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock  wrote:
>
> Thank you - that alerted me to a missing set of out output files for a
> recently added test, hopefully addressed in this revision:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
>
> But its not all good news - another test is now listed as failing, but with
> missing test results:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
>

Another little oddity, the three test results for mira_bait.xml are missing
(although it correctly tells me mira_4_0_mapping and mira_4_0_de_novo
have no tests):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler/302d13490b23

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Nov 28, 2013 at 5:16 PM, Greg Von Kuster  wrote:

> Hello Peter,
>
> On Nov 28, 2013, at 4:56 AM, Peter Cock  wrote:
>
> Hi Greg,
>
> Things look much better today on the Test Tool Shed, with
> most of my tools under "Latest revision: all tool tests pass"
> again - or as expected a few under "Latest revision: missing
> tool tests" due to not yet having full test coverage.
>
> I've only spotted one glitch so far, missing test results for:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
>
>
> The above repository was not displaying the missing test components due to
> a problem in the previous test runs which I fixed yesterday.  The problem
> resulted in test result data that could not be displayed.
>


Perhaps a fall back error message would be useful here (e.g. "Test failed
but unable to display data"), which would be better than the "missing" test
results?



> When I introduced the new feature for stroing and displaying multiple test
> runs, I decided to not eliminate the bad data, but just to let enough test
> runs proceed that the bad data would eventually be eliminated.  I forced
> new test runs, and now things should be displaying as expected.  Here is
> the display for the above repository for the latest run this morning:
>
>

Thank you - that alerted me to a missing set of out output files for a
recently added test, hopefully addressed in this revision:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045

But its not all good news - another test is now listed as failing, but with
missing test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hello Peter,

On Nov 28, 2013, at 4:56 AM, Peter Cock  wrote:

> On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster  wrote:
>> 
>> Hello Peter,
>> 
>> I've done a significant amount of re-engineering of the
>> Tool Shed's install and test framework over the past 2
>> weeks, so the results you are seeing are probably a
>> reflection of some broken peices during the time frame
>> in which I was making changes.  I believe I have most
>> of the things ironed out in 11545:32205f911e74 which
>> is now running on the test tool shed.
>> 
>> We will be performing some test runs of thie new
>> framework over the long weekend, so more correct
>> test results should hopefully be showing up for yours
>> and other repositories.
>> 
> 
> Hi Greg,
> 
> Things look much better today on the Test Tool Shed, with
> most of my tools under "Latest revision: all tool tests pass"
> again - or as expected a few under "Latest revision: missing
> tool tests" due to not yet having full test coverage.
> 
> I've only spotted one glitch so far, missing test results for:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4

The above repository was not displaying the missing test components due to a 
problem in the previous test runs which I fixed yesterday.  The problem 
resulted in test result data that could not be displayed.  When I introduced 
the new feature for stroing and displaying multiple test runs, I decided to not 
eliminate the bad data, but just to let enough test runs proceed that the bad 
data would eventually be eliminated.  I forced new test runs, and now things 
should be displaying as expected.  Here is the display for the above repository 
for the latest run this morning:

Automated tool test results

Automated test environment  
Time tested: 2013-11-28 11:29:38
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tools missing tests or test data  
Tool id: ncbi_rpstblastn_wrapper
Tool version: 0.0.22
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.0.22
Missing components: 
Functional test definitions missing for ncbi_rpstblastn_wrapper.
Tool id: ncbi_blastdbcmd_info
Tool version: 0.0.22
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_info/0.0.22
Missing components: 
Functional test definitions missing for ncbi_blastdbcmd_info.
Tool id: ncbi_makeblastdb
Tool version: 0.0.22
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_makeblastdb/0.0.22
Missing components: 
One or more test files are missing for tool ncbi_makeblastdb: 
four_human_proteins.fasta.log
Tool id: ncbi_blastdbcmd_wrapper
Tool version: 0.0.22
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.0.22
Missing components: 
Functional test definitions missing for ncbi_blastdbcmd_wrapper.
Tool id: ncbi_rpsblast_wrapper
Tool version: 0.0.22
Tool guid: 
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.0.22
Missing components: 
Functional test definitions missing for ncbi_rpsblast_wrapper.


> 
> I saw a recent commit on galaxy-central addressing a test
> time display - that may have explained why yesterday
> the Test Tool Shed was claiming the test results were
> from four days ago.

Yes, there is a flag that can be set for testing a repository that eliminates 
it from being tested by the install and test framework.  This flag had been 
inappropriately set on many repositories, including the one to which you are 
referring.  That problem has been corrected, so testing should be more stable.

> 
>> I've also enhanced the "Tool test results" components to store a
>> configurable number of test runs instead of just 1.  The test tool
>> shed is configured to store 5 test runs.  So from here on you'll
>> begin to see multiple containers in the Tool test results container
>> - something like this:
> 
> That sounds useful when the framework itself is changing
> rapidly, or if there is anything stochastic in a test failure.
> 
> Presumably this shows the last 5 tests against the current
> tool revision?

It displays the last 5 test runs against any installable revision that is 
tested.  We are currently restricting testing to the latest installable 
revision, so the 5 test runs will be displayed for that revision only.


> 
> Thank Greg, and enjoy Thanksgiving,

Thanks Peter, your too!

> 
> Peter

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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster  wrote:
>
> Hello Peter,
>
> I've done a significant amount of re-engineering of the
> Tool Shed's install and test framework over the past 2
> weeks, so the results you are seeing are probably a
> reflection of some broken peices during the time frame
> in which I was making changes.  I believe I have most
> of the things ironed out in 11545:32205f911e74 which
> is now running on the test tool shed.
>
> We will be performing some test runs of thie new
> framework over the long weekend, so more correct
> test results should hopefully be showing up for yours
> and other repositories.
>

Hi Greg,

Things look much better today on the Test Tool Shed, with
most of my tools under "Latest revision: all tool tests pass"
again - or as expected a few under "Latest revision: missing
tool tests" due to not yet having full test coverage.

I've only spotted one glitch so far, missing test results for:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4

I saw a recent commit on galaxy-central addressing a test
time display - that may have explained why yesterday
the Test Tool Shed was claiming the test results were
from four days ago.

> I've also enhanced the "Tool test results" components to store a
> configurable number of test runs instead of just 1.  The test tool
> shed is configured to store 5 test runs.  So from here on you'll
> begin to see multiple containers in the Tool test results container
> - something like this:

That sounds useful when the framework itself is changing
rapidly, or if there is anything stochastic in a test failure.

Presumably this shows the last 5 tests against the current
tool revision?

Thank Greg, and enjoy Thanksgiving,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hello Peter,

I've done a significant amount of re-engineering of the Tool Shed's install and 
test framework over the past 2 weeks, so the results you are seeing are 
probably a reflection of some broken peices during the time frame in which I 
was making changes.  I believe I have most of the things ironed out in 
11545:32205f911e74 which is now running on the test tool shed.  

We will be performing some test runs of thie new framework over the long 
weekend, so more correct test results should hopefully be showing up for yours 
and other repositories.  

I've also enhanced the "Tool test results" components to store a configurable 
number of test runs instead of just 1.  The test tool shed is configured to 
store 5 test runs.  So from here on you'll begin to see multiple containers in 
the Tool test results container - something like this:

Automated tool test results

2013-11-27 15:49:51  
Automated test environment  
Tests that passed successfully  
2013-11-27 15:17:57  
Automated test environment  
Tests that passed successfully  
2013-11-27 14:53:46  
Automated test environment  
Tests that passed successfully  
2013-11-27 14:50:30  
Automated test environment  
Tests that passed successfully  

We'll keep on top of things that need fixing as we proceed with this new 
framework.

Thanks,

Greg Von Kuster


On Nov 27, 2013, at 5:44 AM, Peter Cock  wrote:

> On Thu, Nov 21, 2013 at 2:47 PM, Peter Cock  wrote:
>> On Thu, Nov 21, 2013 at 2:38 PM, Dave Bouvier  wrote:
>>> Peter,
>>> 
>>> About three weeks ago, we began to focus a higher priority on fixing the
>>> nightly functional test runs.
>> 
>> And we're starting to see the dividends of this time investment now :)
>> 
> 
> Hi Dave,
> 
> For a while almost all my tools were showing as passing their tests,
> but sadly something seems to have broken - has the Test Tool Shed
> really not run any tests for the last three days? Even if so, the display
> is still missing the last test results.
> 
> Test Tool Shed, "Latest revision: installation errors", no individual test
> results, but says the tests were run ~4 days ago:
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/63eb4456bf71
> 
> Test Tool Shed, "Latest revision: installation errors", but no test results
> section at all:
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/42bca649ec44
> 
> Actual test failure shown, again time tested listed as 4 days ago, but
> apparently a framework issue:
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/324893f5751e
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/61cec46f6be5
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/bedfe8f3d3fb
> (BrowserStateError: cannot go to 'http://None:29009')
> 
> Regards,
> 
> Peter

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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Nov 21, 2013 at 2:47 PM, Peter Cock  wrote:
> On Thu, Nov 21, 2013 at 2:38 PM, Dave Bouvier  wrote:
>> Peter,
>>
>> About three weeks ago, we began to focus a higher priority on fixing the
>> nightly functional test runs.
>
> And we're starting to see the dividends of this time investment now :)
>

Hi Dave,

For a while almost all my tools were showing as passing their tests,
but sadly something seems to have broken - has the Test Tool Shed
really not run any tests for the last three days? Even if so, the display
is still missing the last test results.

Test Tool Shed, "Latest revision: installation errors", no individual test
results, but says the tests were run ~4 days ago:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/63eb4456bf71

Test Tool Shed, "Latest revision: installation errors", but no test results
section at all:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/42bca649ec44

Actual test failure shown, again time tested listed as 4 days ago, but
apparently a framework issue:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/324893f5751e
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/61cec46f6be5
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/bedfe8f3d3fb
(BrowserStateError: cannot go to 'http://None:29009')

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Nov 21, 2013 at 10:02 AM, Peter Cock  wrote:
> Similarly over on the Main Tool Shed (where I have not yet
> updated these two tools).

I currently have three tool repositories on the Main Tool Shed
listed under "Latest revision: failing tool tests" yet with no
test results:

* http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/5208c15805ec
Known dependency mis-configuration, updated version on Test Tool Shed.
I would expect this revision to fail (saying Biopython not installed).

* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/ee5acea162a7
Known dependency mis-configuration, updated version on Test Tool Shed.
I would expect this revision to fail (saying Biopython not installed).

* http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/d4412c04d7b1
Should be identical to the working version on the Test Tool Shed, i.e.
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/93b8db68dde4
I would expect this revision to pass.

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, Nov 4, 2013 at 10:33 AM, Peter Cock  wrote:
>
> More "missing test results", yet listed under "Latest revision:
> failing tool tests":
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
>
> The common feature is they all depend on Biopython - perhaps that
> failed to install, and the tests were skipped?

I updated all three of these tools (and others) on the Test Tool
Shed yesterday to address my misconfigured dependencies
(thanks Greg!), e.g.
https://github.com/peterjc/pico_galaxy/commit/399111894d1ea9432a4c24ed0413698b9a2a1f94

(Note that other tools with the same broken dependency setup
did not suffer from the "missing test output" problem - they
were showing the tool's test failures)

The good news is that seq_select_by_id has gone from an
apparent failure with missing test output, to a passing test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/bedfe8f3d3fb

The bad news is there are still 2 apparently failing tests with
missing test output:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/42bca649ec44

Similarly over on the Main Tool Shed (where I have not yet
updated these two tools).

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, Oct 22, 2013 at 10:43 AM, Peter Cock  wrote:
> On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier  wrote:
>> Peter,
>>
>> Thanks for the information, it uncovered a problem with the testing
>> framework that has been resolved in 10817:6b0c3592dde1. The listed
>> repositories should start showing useful results next time the nightly tests
>> run.
>>
>>--Dave B.
>
>
> Hi Dave,
>
> I must sound like a scratched record (is there a replacement
> phrase now that LPs are a cultural artefact?):
>
> Currently listed under "Latest revision: failing tool tests" but
> missing any test results:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
>
> (I've got a lot of fresh failures pointing at a separate issue,
> email to follow with a new title).
>
> Peter

More "missing test results", yet listed under "Latest revision:
failing tool tests":

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id

The common feature is they all depend on Biopython - perhaps that
failed to install, and the tests were skipped?

Over on the main tool shed, those three are all showing errors
relating to a failed Biopython install.

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Friday, November 1, 2013, Peter Cock wrote:

> On Tue, Oct 22, 2013 at 2:49 PM, Greg Von Kuster 
> >
> wrote:
> > Hi Peter,
> >
> > Here is a new Trello card to track the progress for fixing and
> stabilizing the tool shed install and test framework.  This card will
> evolve over the next few days as items are completed and new issues are
> uncovered that cause problems in the framework.  This work is our top
> priority until it is finished.
> >
> >
> https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes
> >
> > Greg Von Kuster
> >
>
> Hi Greg, Dave,
>
> This is just to comment that there is a (possibly related) oddity in
> the RSS feeds, with lots of entries showning missing test results:
>
> "0 tests passed, 0 tests failed, 0 tests missing test components."
>
> Strangely this is reporting multiple revisions of each tool (not in
> commit order), and it seems the older revisions show no tests
> (possibly true, or simple a sign of no test data?).
>
> Peter
>
>
Looks like Dave's fixed the multiple RSS entries:
https://bitbucket.org/galaxy/galaxy-central/commits/52df185d7552

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, Oct 22, 2013 at 2:49 PM, Greg Von Kuster  wrote:
> Hi Peter,
>
> Here is a new Trello card to track the progress for fixing and stabilizing 
> the tool shed install and test framework.  This card will evolve over the 
> next few days as items are completed and new issues are uncovered that cause 
> problems in the framework.  This work is our top priority until it is 
> finished.
>
> https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes
>
> Greg Von Kuster
>

Hi Greg, Dave,

This is just to comment that there is a (possibly related) oddity in
the RSS feeds, with lots of entries showning missing test results:

"0 tests passed, 0 tests failed, 0 tests missing test components."

Strangely this is reporting multiple revisions of each tool (not in
commit order), and it seems the older revisions show no tests
(possibly true, or simple a sign of no test data?).

Peter

--

e.g.

http://testtoolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjc&status=all

Revision 66d1ca92fb38 of seq_filter_by_id
31 October 2013 22:03
0 tests passed, 0 tests failed, 0 tests missing test components.

Revision b7ec1c9db38d of seq_filter_by_id
31 October 2013 21:14
0 tests passed, 0 tests failed, 0 tests missing test components.

Revision 21a065d5f0e2 of seq_filter_by_id
31 October 2013 22:24
0 tests passed, 0 tests failed, 0 tests missing test components.

Revision 8a34c565a473 of seq_filter_by_id
1 November 2013 09:23
1 tests passed, 0 tests failed, 0 tests missing test components.

Revision 44891766cf9b of seq_filter_by_id
18 October 2013 23:29
0 tests passed, 0 tests failed, 1 tests missing test components.

Revision 726dcfa94b2c of seq_select_by_id
31 October 2013 22:17
0 tests passed, 0 tests failed, 0 tests missing test components.

Revision 9e9e3b860aa0 of seq_select_by_id
1 November 2013 09:26
0 tests passed, 1 tests failed, 0 tests missing test components.

Revision 694208ea6c34 of seq_select_by_id
31 October 2013 22:24
0 tests passed, 0 tests failed, 0 tests missing test components.

Revision 2b27279adeff of seq_select_by_id
18 October 2013 23:28
0 tests passed, 0 tests failed, 1 tests missing test components.

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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hi Peter,

Here is a new Trello card to track the progress for fixing and stabilizing the 
tool shed install and test framework.  This card will evolve over the next few 
days as items are completed and new issues are uncovered that cause problems in 
the framework.  This work is our top priority until it is finished.

https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes

Greg Von Kuster


On Oct 22, 2013, at 5:43 AM, Peter Cock  wrote:

> On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier  wrote:
>> Peter,
>> 
>> Thanks for the information, it uncovered a problem with the testing
>> framework that has been resolved in 10817:6b0c3592dde1. The listed
>> repositories should start showing useful results next time the nightly tests
>> run.
>> 
>>   --Dave B.
> 
> 
> Hi Dave,
> 
> I must sound like a scratched record (is there a replacement
> phrase now that LPs are a cultural artefact?):
> 
> Currently listed under "Latest revision: failing tool tests" but
> missing any test results:
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
> 
> (I've got a lot of fresh failures pointing at a separate issue,
> email to follow with a new title).
> 
> Peter
> ___
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier  wrote:
> Peter,
>
> Thanks for the information, it uncovered a problem with the testing
> framework that has been resolved in 10817:6b0c3592dde1. The listed
> repositories should start showing useful results next time the nightly tests
> run.
>
>--Dave B.


Hi Dave,

I must sound like a scratched record (is there a replacement
phrase now that LPs are a cultural artefact?):

Currently listed under "Latest revision: failing tool tests" but
missing any test results:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls

(I've got a lot of fresh failures pointing at a separate issue,
email to follow with a new title).

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

Thanks for the information, it uncovered a problem with the testing 
framework that has been resolved in 10817:6b0c3592dde1. The listed 
repositories should start showing useful results next time the nightly 
tests run.


   --Dave B.

On 10/04/2013 06:19 AM, Peter Cock wrote:

On Fri, Oct 4, 2013 at 11:11 AM, Peter Cock  wrote:

On Thu, Sep 26, 2013 at 3:29 PM, Dave Bouvier  wrote:

Ross, Peter,

Unfortunately, there are some issues with the automated testing framework
that I am working on resolving. I've created a Trello card to track my
progress:

https://trello.com/c/x8mx7HRB

--Dave B.



Any joy with that "from fabric.api import env" issue?

Meanwhile the set of tools with missing test failures seems to
change from day to day, right now the following are listed under
"Latest revision: failing tool tests" yet have not test results:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/0d39248a7a9f
(expected to pass)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
(expected to pass)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
(expected to pass)

Peter


There's a similar set on the main Tool Shed, where I should have the
same version of those three tools, which may be interesting for
tracing the problem(s):

http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
(expected to pass)

http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
(expected to pass)

http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
(expected to pass)

Also missing test results:

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
(this revision is expected to fail if Biopython not present, see other thread
about packaging NumPy and its dependencies)

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Fri, Oct 4, 2013 at 11:11 AM, Peter Cock  wrote:
> On Thu, Sep 26, 2013 at 3:29 PM, Dave Bouvier  wrote:
>> Ross, Peter,
>>
>> Unfortunately, there are some issues with the automated testing framework
>> that I am working on resolving. I've created a Trello card to track my
>> progress:
>>
>> https://trello.com/c/x8mx7HRB
>>
>>--Dave B.
>>
>
> Any joy with that "from fabric.api import env" issue?
>
> Meanwhile the set of tools with missing test failures seems to
> change from day to day, right now the following are listed under
> "Latest revision: failing tool tests" yet have not test results:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/0d39248a7a9f
> (expected to pass)
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
> (expected to pass)
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
> (expected to pass)
>
> Peter

There's a similar set on the main Tool Shed, where I should have the
same version of those three tools, which may be interesting for
tracing the problem(s):

http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
(expected to pass)

http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
(expected to pass)

http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
(expected to pass)

Also missing test results:

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
(this revision is expected to fail if Biopython not present, see other thread
about packaging NumPy and its dependencies)

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Sep 26, 2013 at 3:29 PM, Dave Bouvier  wrote:
> Ross, Peter,
>
> Unfortunately, there are some issues with the automated testing framework
> that I am working on resolving. I've created a Trello card to track my
> progress:
>
> https://trello.com/c/x8mx7HRB
>
>--Dave B.
>

Any joy with that "from fabric.api import env" issue?

Meanwhile the set of tools with missing test failures seems to
change from day to day, right now the following are listed under
"Latest revision: failing tool tests" yet have not test results:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/0d39248a7a9f
(expected to pass)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
(expected to pass)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
(expected to pass)

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Ross, Peter,

Unfortunately, there are some issues with the automated testing 
framework that I am working on resolving. I've created a Trello card to 
track my progress:


https://trello.com/c/x8mx7HRB

   --Dave B.

On 09/26/2013 06:47 AM, Ross wrote:

+1

I think it's been a problem with some of my repos for a while on test so
possible not related to blast_datatypes - I sent this privately about 2
weeks ago:

Ross mailto:ross.laza...@gmail.com>>


Sep 13 (13 days ago)

to Dave, Greg

Hey Dave - any thoughts on how to fix
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so the
test results appear?
AFAIK the test works but there's no test results section in the manage
repository sections I can see.


On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock mailto:p.j.a.c...@googlemail.com>> wrote:

On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier mailto:d...@bx.psu.edu>> wrote:
 > Peter,
 >
 > The one on the main tool shed is due to an issue Greg and I are
in the
 > process of resolving. As soon as we've tested the fix, I'll
schedule a
 > re-test of that repository and update you on the status.
 >
 >--Dave B.

Looks to be spreading, or linked to the blast_datatypes dependency?
Listed under "Latest revision: failing tool tests"

http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
- missing test results


http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552
- missing test results

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
- failed as expected (missing Biopython dependency,
   see separate thread about the ALTAS dependency problem)

http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
- failing as expected (missing R dependency)

And over on the Test Tool Shed (which was offline but recently came
back up), listed under "Latest revision: failing tool tests":

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
- missing test results

http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
- missing test results

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Ross]

Great! Thanks!
Don't you ever sleep? It must be some un-allah-ly hour where you are.


On Thu, Sep 26, 2013 at 8:55 PM, Greg Von Kuster  wrote:

> There seems to be issues with some repositories which we'll need to track
> down.  However, I fixed some issues yesterday with styles in the tool shed
> that kep the tool tests from displaing, and now test results are displaying
> at least for this repository:
>
>
> Repository revision
>  31:5b6af671d985 28:c4ee2e69d691 3:fe5c828dee80  *repository tip*
> Select a revision to inspect and download versions of Galaxy utilities
> from this repository.
>
> Repository 'differential_count_models'
> Sharable link to this repository:
> http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models
> Clone this repository:hg clone
> http://testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models
> Name:differential_count_models
> Repository type:Unrestricted
> Synopsis:edgeR, DESeq2 and voom in one tool
> Detailed description:edgeR, DESeq2 and voom for replicate RNA seq data.
>
> 1) TURN OFF HTML SANITIZATION in universe_wsgi.xml or your outputs will lack 
> proper style sheets and look awful
>
> 2) This packages dependencies include R and bioconductor so expect your proxy 
> to time out during the installation - be patient - it takes 10 to 30 minutes 
> to download and compile everything, depending on the velocity of your machine 
> and the interwebs - about 20 minutes on my laptop.
>
> 3) make sure you have a $TMP set in your environment or ghostscript gets 
> unhappy - you'll see a warning every time you run this tool if you've 
> forgotten.
> Revision:31:5b6af671d985
> Owner:fubar
> Times downloaded:15
> Dependencies of this repository
>
> Repository dependencies* - installation of these additional repositories
> is 
> required*
>
> Tool dependencies* - repository tools require handling of these
> dependencies*
>
> Contents of this repository
>
> Valid tools* - click the name to preview the tool and use the pop-up menu
> to inspect all 
> metadata*
>
> Automated tool test results
>
> Tool test 
> results
> Automated test 
> environment
> Tests that 
> failed
> *Tool id:* rgDifferentialCount*Tool version:* rgDifferentialCount*Test:* 
> test_tool_00
> (functional.test_toolbox.TestForTool_testtoolshed.g2.
> bx.psu.edu/repos/fubar/differential_count_models/rgDifferentialCount/0.21)
> *Stderr:*
> *Traceback:*
> Traceback (most recent call last):
>
>   File 
> "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-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/buildslaves/buildslave-ec2-1/buildbot-install-test-test-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/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
>  line 855, in verify_dataset_correctness
> raise AssertionError( errmsg )
>
> AssertionError: History item 4 different than expected, difference (using 
> diff):
>
> ( 
> /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsubztFQ/testtoolshed.g2.
> bx.psu.edu/repos/fubar/differential_count_models/5b6af671d985/differential_count_models/differential_count_models/test-data/edgeRtest1out.xls
>  v. 
> /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpFGK1x1/tmpCzIKTPedgeRtest1out.xls
>  )
> --- local_file
> +++ history_data
> @@ -1,1142 +0,0 @@
> -ID logFC AveExpr t P.Value adj.P.Val B NReads URL
> -Mir192 6.94888256843679 14.6763802609023 42.7229535356942
> 2.30119906424271e-16 2.62566813230094e-13 27.2664713266936 2325567 Mir192
> -Mir208a -11.0150177152075 3.93955375669227 -23.2524066836307
> 1.11893807599952e-12 6.38354172357727e-10 17.2086622097974 4638  >Mir208a
> -Mir122a 10.4261254701779 8.16986409392255 21.7229119192922

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Ross]

+1

I think it's been a problem with some of my repos for a while on test so
possible not related to blast_datatypes - I sent this privately about 2
weeks ago:

Ross 
Sep 13 (13 days ago)
to Dave, Greg
Hey Dave - any thoughts on how to fix
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so
the test results appear?
AFAIK the test works but there's no test results section in the manage
repository sections I can see.


On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock wrote:

> On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier  wrote:
> > Peter,
> >
> > The one on the main tool shed is due to an issue Greg and I are in the
> > process of resolving. As soon as we've tested the fix, I'll schedule a
> > re-test of that repository and update you on the status.
> >
> >--Dave B.
>
> Looks to be spreading, or linked to the blast_datatypes dependency?
> Listed under "Latest revision: failing tool tests"
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
> - missing test results
>
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552
> - missing test results
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
> - failed as expected (missing Biopython dependency,
>   see separate thread about the ALTAS dependency problem)
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
> - failing as expected (missing R dependency)
>
> And over on the Test Tool Shed (which was offline but recently came
> back up), listed under "Latest revision: failing tool tests":
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
> - missing test results
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
> - missing test results
>
> Regards,
>
> Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier  wrote:
> Peter,
>
> The one on the main tool shed is due to an issue Greg and I are in the
> process of resolving. As soon as we've tested the fix, I'll schedule a
> re-test of that repository and update you on the status.
>
>--Dave B.

Looks to be spreading, or linked to the blast_datatypes dependency?
Listed under "Latest revision: failing tool tests"

http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
- missing test results

http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552
- missing test results

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
- failed as expected (missing Biopython dependency,
  see separate thread about the ALTAS dependency problem)

http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
- failing as expected (missing R dependency)

And over on the Test Tool Shed (which was offline but recently came
back up), listed under "Latest revision: failing tool tests":

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
- missing test results

http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
- missing test results

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

The one on the main tool shed is due to an issue Greg and I are in the 
process of resolving. As soon as we've tested the fix, I'll schedule a 
re-test of that repository and update you on the status.


   --Dave B.

On 09/24/2013 05:53 AM, Peter Cock wrote:

Thanks Dave,

Looks like the same thing happened again last night, but as this
is on the Main Tool Shed your fix wouldn't be included anyway:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552

Any clues about the installation failure would be useful, this is
working nicely on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/d8de5b627c88

Additionally, another repository I updated yesterday is missing test
results and this time there are no external dependencies:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls

Regards,

Peter

On Mon, Sep 23, 2013 at 5:27 PM, Dave Bouvier  wrote:

Peter,

Thank you for reporting this. I've been able to determine that there was an
installation error that should have been recorded, but was not. I hope to
have a fix committed shortly.

--Dave B.


On 09/23/2013 05:59 AM, Peter Cock wrote:


Hello again,

I've not have any missing test results for a while, on the main
or test Tool Shed, so this was a bit of a surprise:


http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552

This is listed under "Latest revision: failing tool tests", but
I see no test results at all :(

Regards,

Peter




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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

Thanks Dave,

Looks like the same thing happened again last night, but as this
is on the Main Tool Shed your fix wouldn't be included anyway:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552

Any clues about the installation failure would be useful, this is
working nicely on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/d8de5b627c88

Additionally, another repository I updated yesterday is missing test
results and this time there are no external dependencies:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls

Regards,

Peter

On Mon, Sep 23, 2013 at 5:27 PM, Dave Bouvier  wrote:
> Peter,
>
> Thank you for reporting this. I've been able to determine that there was an
> installation error that should have been recorded, but was not. I hope to
> have a fix committed shortly.
>
>--Dave B.
>
>
> On 09/23/2013 05:59 AM, Peter Cock wrote:
>>
>> Hello again,
>>
>> I've not have any missing test results for a while, on the main
>> or test Tool Shed, so this was a bit of a surprise:
>>
>>
>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552
>>
>> This is listed under "Latest revision: failing tool tests", but
>> I see no test results at all :(
>>
>> Regards,
>>
>> Peter
>>
>
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

Thank you for reporting this. I've been able to determine that there was 
an installation error that should have been recorded, but was not. I 
hope to have a fix committed shortly.


   --Dave B.

On 09/23/2013 05:59 AM, Peter Cock wrote:

Hello again,

I've not have any missing test results for a while, on the main
or test Tool Shed, so this was a bit of a surprise:

http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552

This is listed under "Latest revision: failing tool tests", but
I see no test results at all :(

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

Hello again,

I've not have any missing test results for a while, on the main
or test Tool Shed, so this was a bit of a surprise:

http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552

This is listed under "Latest revision: failing tool tests", but
I see no test results at all :(

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

Hi Dave,

Progress: I can now see the test failures which suggest that the
underlying binaries did not get installed properly. I guess this
either means:

(a) the dependency install failed but the Tool Shed doesn't say
this (my hunch as recently the NCBI BLAST+ tools had stopped
compiling on the Test Tool Shed due to a BOOST system library
change).

Or,

(b) the dependency installed didn't raise any errors but failed
in some way such as not setting the path (unlikely as the
tool_dependencies.xml content has not changed - it has
just been moved to a dependency package repository)

Or,

(c) there is something amiss with the dependency chain meaning
that the BLAST dependencies are not being added to the PATH.
This looks OK but it is the only thing I have changed recently.

Or some other mode of failure I'm not guessed at yet?

Is this something you can diagnose, or do I need to press
ahead with a local Tool Shed to help me work out what is
amiss?

Thanks,

Peter

On Fri, Aug 9, 2013 at 1:58 PM, Dave Bouvier  wrote:
> Peter,
>
> The automated build prior to this email was executed incorrectly. I've
> resolved that status, and the current test results look correct.
>
>--Dave B.
>
>
> On 8/8/13 10:30:37.000, Peter Cock wrote:
>>
>> I've been updating the BLAST+ repository - currently it does
>> show some failures due to missing test, but there seems to be
>> test information missing here - and also I'm expecting the
>> installation to fail with BOOST issues:
>>
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec
>>
>> (The other problems from 1 August look OK now)
>>
>> Thanks,
>>
>> Peter
>>
>
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

The automated build prior to this email was executed incorrectly. I've 
resolved that status, and the current test results look correct.


   --Dave B.

On 8/8/13 10:30:37.000, Peter Cock wrote:

On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock  wrote:


Hi Dave,

The good news is it does seem some of the missing test results I
had on Monday have been resolved. However, there are still
others showing with no test results: :(

No test results here (I expect some to pass and some to fail):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a


I've been updating the BLAST+ repository - currently it does
show some failures due to missing test, but there seems to be
test information missing here - and also I'm expecting the
installation to fail with BOOST issues:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec

(The other problems from 1 August look OK now)

Thanks,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock  wrote:
>
> Hi Dave,
>
> The good news is it does seem some of the missing test results I
> had on Monday have been resolved. However, there are still
> others showing with no test results: :(
>
> No test results here (I expect some to pass and some to fail):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a

I've been updating the BLAST+ repository - currently it does
show some failures due to missing test, but there seems to be
test information missing here - and also I'm expecting the
installation to fail with BOOST issues:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec

(The other problems from 1 August look OK now)

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier  wrote:
> Peter,
>
> I've created a Trello card where you can track this issue:
> https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
>
> Most of these look like display issues, the test results are correctly
> recorded in the database. I hope to have that and the seq_rename and
> tmhmm_and_signalp issues resolved shortly.
>
>--Dave B.

Hi Dave,

The good news is it does seem some of the missing test results I
had on Monday have been resolved. However, there are still
others showing with no test results: :(

No test results here (I expect some to pass and some to fail):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a

No test results here (I expect a failure due to a missing R dependency):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow/41d8f46e0343

No test results here (I expect these to pass):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bc4e7c0dc6e3
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/deb6cb2db22b

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock  wrote:
> On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier  wrote:
>> Peter,
>>
>> The issue with seq_rename incorrectly failing functional tests has been
>> resolved in 10266:fe04978dadac, and the test results will be corrected the
>> next time the automated testing framework runs. I'm still looking into the
>> other issues you reported.
>>
>>--Dave B.
>
> Hi Dave,
>
> The seq_rename test results (apparently) from last night are still failing,
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
>
> AssertionError: Attempting to set field 'new_column' to value '['2']'
> in form 'tool_form' threw exception: cannot find value/label "2" in
> list control control:  If the above
> control is a DataToolparameter whose data type class does not include
> a sniff() method, make sure to include a proper 'ftype' attribute to
> the tag for the control within the  tag set.

Same issue here?,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e

AssertionError: Attempting to set field 'fasta_file' to value
'['empty.fasta']' in form 'tool_form' threw exception: cannot find
value/label "empty.fasta" in list control control:
 If the above control is a
DataToolparameter whose data type class does not include a sniff()
method, make sure to include a proper 'ftype' attribute to the tag for
the control within the  tag set.

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier  wrote:
> Peter,
>
> The issue with seq_rename incorrectly failing functional tests has been
> resolved in 10266:fe04978dadac, and the test results will be corrected the
> next time the automated testing framework runs. I'm still looking into the
> other issues you reported.
>
>--Dave B.

Hi Dave,

The seq_rename test results (apparently) from last night are still failing,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c

AssertionError: Attempting to set field 'new_column' to value '['2']'
in form 'tool_form' threw exception: cannot find value/label "2" in
list control control:  If the above
control is a DataToolparameter whose data type class does not include
a sniff() method, make sure to include a proper 'ftype' attribute to
the tag for the control within the  tag set.

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Monday, July 29, 2013, Dave Bouvier wrote:

> Peter,
>
> From what I've been able to determine, the tmhmm_and_signalp test results
> predate the introduction of the skip tool tests option, and the script to
> check repositories for the presence of functional tests and test data has
> been updating the last test date every day, hence the misleading entry for
> time last tested. I've committed a fix to that script in
> 10267:5ad8db7ff748, which will be included in the next release, at which
> point the main tool shed should correctly display no test results for that
> repository and any others you have specified not to be tested.
>
>--Dave B.
>

Thanks - that probably makes sense for future repositories with similar
issues, I suspect people are going to tick the skip box after getting
unresolvable test failures.

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

From what I've been able to determine, the tmhmm_and_signalp test 
results predate the introduction of the skip tool tests option, and the 
script to check repositories for the presence of functional tests and 
test data has been updating the last test date every day, hence the 
misleading entry for time last tested. I've committed a fix to that 
script in 10267:5ad8db7ff748, which will be included in the next 
release, at which point the main tool shed should correctly display no 
test results for that repository and any others you have specified not 
to be tested.


   --Dave B.

On 7/29/13 12:03:23.000, Dave Bouvier wrote:

Peter,

The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be corrected
the next time the automated testing framework runs. I'm still looking
into the other issues you reported.

--Dave B.

On 7/29/13 10:50:58.000, Peter Cock wrote:

On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier  wrote:

Peter,

I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue


Thanks Dave.


Most of these look like display issues, the test results are correctly
recorded in the database. I hope to have that and the seq_rename and
tmhmm_and_signalp issues resolved shortly.

--Dave B.


Oh good - that sounds less troublesome than a problem running
the tests themselves.

Cheers,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

The issue with seq_rename incorrectly failing functional tests has been 
resolved in 10266:fe04978dadac, and the test results will be corrected 
the next time the automated testing framework runs. I'm still looking 
into the other issues you reported.


   --Dave B.

On 7/29/13 10:50:58.000, Peter Cock wrote:

On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier  wrote:

Peter,

I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue


Thanks Dave.


Most of these look like display issues, the test results are correctly
recorded in the database. I hope to have that and the seq_rename and
tmhmm_and_signalp issues resolved shortly.

--Dave B.


Oh good - that sounds less troublesome than a problem running
the tests themselves.

Cheers,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier  wrote:
> Peter,
>
> I've created a Trello card where you can track this issue:
> https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue

Thanks Dave.

> Most of these look like display issues, the test results are correctly
> recorded in the database. I hope to have that and the seq_rename and
> tmhmm_and_signalp issues resolved shortly.
>
>--Dave B.

Oh good - that sounds less troublesome than a problem running
the tests themselves.

Cheers,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

I've created a Trello card where you can track this issue: 
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue


Most of these look like display issues, the test results are correctly 
recorded in the database. I hope to have that and the seq_rename and 
tmhmm_and_signalp issues resolved shortly.


   --Dave B.

On 7/29/13 09:50:41.000, Peter Cock wrote:

Hello all,

I'm seeing missing test results again on the Test Tool Shed, e.g.
listed under "Latest revision: failing tool tests
"
I have:

http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus

Tool test results
Automated test environment
*Time tested:* ~ 11 hours ago
*System:* Linux 3.8.0-25-generic
*Architecture:* x86_64
*Python version:* 2.7.4
*Galaxy revision:* 10265:e19301cc51b9
*Galaxy database version:* 115
*Tool shed revision:* 10098:adee6fc31991
*Tool shed database version:* 19
*Tool shed mercurial version:* 2.2.3

Tests that passed successfully
*Tool id:* nlstradamus
*Tool version:* nlstradamus
*Test:* test_tool_00
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.7
)


Tests that failed

i.e. The failed test isn't shown

http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 - same problem as
above

http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp - should be
skipping tests (as I expect it to fail)

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename - test framework
regression raised here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-July/015710.html


Thanks,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

Hello all,

I'm seeing missing test results again on the Test Tool Shed, e.g.
listed under "Latest revision: failing tool
tests"
I have:

http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus

   Tool test results
Automated test environment
   *Time tested:* ~ 11 hours ago *System:* Linux 3.8.0-25-generic *
Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy
revision:*10265:e19301cc51b9
*Galaxy database version:* 115 *Tool shed revision:* 10098:adee6fc31991 *Tool
shed database version:* 19 *Tool shed mercurial version:* 2.2.3
 Tests that passed successfully
   *Tool id:* nlstradamus *Tool version:* nlstradamus *Test:*test_tool_00 (
functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.7
)
 Tests that failed

 i.e. The failed test isn't shown

http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3  - same problem as
above

http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp  - should be
skipping tests (as I expect it to fail)

http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename - test framework
regression raised here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-July/015710.html


Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Ross]

I'm not seeing anything other than the test environment report in the
failing tests report for
http://testtoolshed.g2.bx.psu.edu/view/fubar/htseq_bams_to_count_matrix -
if you have time to take a look Dave? I'm having a hard time figuring out
what I've done wrong - it builds, installs and tests fine on my test
machine but I've probably forgotten some dependency that I already have
installed on my laptop...

The result for http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_testmakes
me think that one or more of the test input files is missing but it's
hard to tell.
I wonder if overall we need a more or less complete output data spew for
failing tests to make the task of tracking them down easier?


On Thu, Jun 27, 2013 at 8:58 AM, Peter Cock 
wrote:
>
> On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier  wrote:
> > Peter,
> >
> > The empty failed tests folder issue has been resolved in
10171:eaa5112fefcd,
> > and the test tool shed has been updated to that revision.
> >
> >--Dave B.
>
> Great - currently all the missing test failures have been resolved :)
> The bad news is there seems to be a new sniffer bug.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
> Can see test failures (tool configuration problem).
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
> One test pass, on test failure. The failure is a bit odd and
> is likely a new sniffer related bug.
>
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
> Tests pass.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
> Can see test failure, good.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
> One pass, one failure - same new failure as effectiveT3 above.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
> Can see a failure, also seems to be sniffer related (but
> using a different datatype).
>
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b
> As before, no test results as there are marked as skip - yet
> this is still listed under "Latest revision: failing tool tests".
> The filter for this needs to exclude repositories marked as
> skip testing.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
> Can see test failure, good (missing undeclared dependency)
>
> Thanks,
>
> Peter
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4J
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier  wrote:
> Peter,
>
> The empty failed tests folder issue has been resolved in 10171:eaa5112fefcd,
> and the test tool shed has been updated to that revision.
>
>--Dave B.

Great - currently all the missing test failures have been resolved :)
The bad news is there seems to be a new sniffer bug.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
Can see test failures (tool configuration problem).

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
One test pass, on test failure. The failure is a bit odd and
is likely a new sniffer related bug.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
Tests pass.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
Can see test failure, good.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
One pass, one failure - same new failure as effectiveT3 above.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
Can see a failure, also seems to be sniffer related (but
using a different datatype).

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b
As before, no test results as there are marked as skip - yet
this is still listed under "Latest revision: failing tool tests".
The filter for this needs to exclude repositories marked as
skip testing.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
Can see test failure, good (missing undeclared dependency)

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

The empty failed tests folder issue has been resolved in 
10171:eaa5112fefcd, and the test tool shed has been updated to that 
revision.


   --Dave B.

On 6/26/13 11:34:38.000, Dave Bouvier wrote:

Peter,

It looks like the failed tests container is being populated, but there
is some odd behavior with displaying it. As soon as we've tracked down
the issue, I'll update you.

--Dave B.

On 6/26/13 02:00:30.000, Peter Cock wrote:

On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier  wrote:

Peter,

It turns out that the automated functional testing framework was not
actually running. I suggest having a look in the morning, and if
there are
still any missing test results, I'll get them resolved then.

--Dave B.


Thanks Dave,

That has made a difference but there are still a couple of
issues here - at least in my current browser (Safari):


Here is the current list of my failing repositories from the Test
Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
- can see test failure, good.


No change, good.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
- shows one passing test (which is odd, where is the failure?)


Improved, says there are test failures, but the arrow section fails
to expand with any details. Could this just be a slow connection
issue?


http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040

- no test results visible


Tests have passed now :)


http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658

- can see test failure, good.


No change, good.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
- some test results visible, but no failures


No change, bad. As above, the arrow/section for the failing test
does not expand.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
- no test results visible


Can see test failures, good.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b

- no test results visible (strange, should be skipping the tests, so
 why is this listed as failing?)


No change, bad.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
- can see test failure, good.


No change, good.

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

It looks like the failed tests container is being populated, but there 
is some odd behavior with displaying it. As soon as we've tracked down 
the issue, I'll update you.


   --Dave B.

On 6/26/13 02:00:30.000, Peter Cock wrote:

On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier  wrote:

Peter,

It turns out that the automated functional testing framework was not
actually running. I suggest having a look in the morning, and if there are
still any missing test results, I'll get them resolved then.

--Dave B.


Thanks Dave,

That has made a difference but there are still a couple of
issues here - at least in my current browser (Safari):


Here is the current list of my failing repositories from the Test
Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
- can see test failure, good.


No change, good.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
- shows one passing test (which is odd, where is the failure?)


Improved, says there are test failures, but the arrow section fails
to expand with any details. Could this just be a slow connection
issue?


http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
- no test results visible


Tests have passed now :)


http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
- can see test failure, good.


No change, good.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
- some test results visible, but no failures


No change, bad. As above, the arrow/section for the failing test
does not expand.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
- no test results visible


Can see test failures, good.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b
- no test results visible (strange, should be skipping the tests, so
 why is this listed as failing?)


No change, bad.


http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
- can see test failure, good.


No change, good.

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier  wrote:
> Peter,
>
> It turns out that the automated functional testing framework was not
> actually running. I suggest having a look in the morning, and if there are
> still any missing test results, I'll get them resolved then.
>
>--Dave B.

Thanks Dave,

That has made a difference but there are still a couple of
issues here - at least in my current browser (Safari):

>> Here is the current list of my failing repositories from the Test
>> Tool Shed,
>>
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
>> - can see test failure, good.

No change, good.

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
>> - shows one passing test (which is odd, where is the failure?)

Improved, says there are test failures, but the arrow section fails
to expand with any details. Could this just be a slow connection
issue?

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
>> - no test results visible

Tests have passed now :)

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
>> - can see test failure, good.

No change, good.

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
>> - some test results visible, but no failures

No change, bad. As above, the arrow/section for the failing test
does not expand.

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
>> - no test results visible

Can see test failures, good.

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b
>> - no test results visible (strange, should be skipping the tests, so
>> why is this listed as failing?)

No change, bad.

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
>> - can see test failure, good.

No change, good.

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

It turns out that the automated functional testing framework was not 
actually running. I suggest having a look in the morning, and if there 
are still any missing test results, I'll get them resolved then.


   --Dave B.

On 6/25/13 02:10:10.000, Peter Cock wrote:

Hi again Dave,

Have you worked out any possible causes for missing test results?
I do suspect some sort of caching issue is to blame...

Here is the current list of my failing repositories from the Test
Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
- can see test failure, good.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
- shows one passing test (which is odd, where is the failure?)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
- no test results visible

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
- can see test failure, good.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
- some test results visible, but no failures

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
- no test results visible

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b
- no test results visible (strange, should be skipping the tests, so
why is this listed as failing?)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
- can see test failure, good.

Note that for get_orfs_or_cdss and seq_rename, I am trying to
use an automatically installed dependency on Biopython - so
perhaps there is a silent dependency failure which means the
tests are not being run?

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

Hi again Dave,

Have you worked out any possible causes for missing test results?
I do suspect some sort of caching issue is to blame...

Here is the current list of my failing repositories from the Test
Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
- can see test failure, good.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
- shows one passing test (which is odd, where is the failure?)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
- no test results visible

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
- can see test failure, good.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
- some test results visible, but no failures

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
- no test results visible

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5590b
- no test results visible (strange, should be skipping the tests, so
   why is this listed as failing?)

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
- can see test failure, good.

Note that for get_orfs_or_cdss and seq_rename, I am trying to
use an automatically installed dependency on Biopython - so
perhaps there is a silent dependency failure which means the
tests are not being run?

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Wed, May 22, 2013 at 8:05 PM, Peter Cock 
wrote:
> On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier  wrote:
>> Peter,
>>
>> I have implemented a system that will explicitly exclude a defined list
of
>> repositories from the testing framework, so your repositories' tests
should
>> now be running.
>>
>>--Dave B.
>
> Looks good - and now I have some more errors to sort out :)
>

Hi Dave,

I'm guessing you need to black-list a few more repositories as I'm
again seeing missing test results, e.g.

--

On the test Tool Shed page for this revision I see nothing at all
about the tests for clinod:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/04aed2f80910
Functional test results for changeset revision 04aed2f80910 of clinod
0 tests passed, 0 tests failed, 0 tests missing test components.

The RSS entry is cryptic - either tests didn't run at all (due to something
timing out elsewhere in the test suite), or there was an installation error
perhaps?

-

This one is different - there is a minimal test result output but with
no test results or install failures shown:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr



 Automated tool test results

   Tool test results
Automated test environment
   *Time tested:* ~ 13 hours ago *System:* Linux 3.0.0-1-amd64 *
Architecture:* x86_64 *Python version:* 2.7.2+ *Galaxy revision:* *Galaxy
database version:* *Tool shed revision:* 9872:31714646a7b4 *Tool shed
database version:* 19 *Tool shed mercurial version:* 2.2.3




Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier  wrote:
> Peter,
>
> I have implemented a system that will explicitly exclude a defined list of
> repositories from the testing framework, so your repositories' tests should
> now be running.
>
>--Dave B.

Looks good - and now I have some more errors to sort out :)

Thank you,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

I have implemented a system that will explicitly exclude a defined list 
of repositories from the testing framework, so your repositories' tests 
should now be running.


   --Dave B.

On 5/21/13 06:26:56.000, Peter Cock wrote:

On Mon, May 13, 2013 at 11:09 AM, Peter Cock  wrote:


I remain puzzled why I am seeing seemingly stochastic missing test
results.



Hi Dave,

This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
repositories reported as failing but I can't see the error (and so
can't do much about fixing it):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss 

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
When previously visible this was due to a test framework
limitation testing with composite output files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html

Given I suspect a cache issue hiding the test failures, it might
help if rather than the current text like "Time tested: ~ 8 hours ago"
this could also state the date and time of the test (in UTC/GMT to
avoid locale confusion).

Thanks,

Peter



Other repositories failing with a clear error message:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Missing dependencies, should have been skipped, see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler   
Limitation of test framework, Trello issue open for this,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename   
Limitation of test framework, issue raised,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list
Missing an R/Bioconductor dependency, best practise for handling
this has yet to be agreed.


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

The most likely cause of this is that there is an issue with some 
preceding repositories that hang on installation, causing the build 
process to time out and not test later repositories in the list. I am in 
the process of working out a solution for that situation.


   --Dave B.

On 5/21/13 06:26:56.000, Peter Cock wrote:

On Mon, May 13, 2013 at 11:09 AM, Peter Cock  wrote:


I remain puzzled why I am seeing seemingly stochastic missing test
results.



Hi Dave,

This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
repositories reported as failing but I can't see the error (and so
can't do much about fixing it):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss 

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
When previously visible this was due to a test framework
limitation testing with composite output files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html

Given I suspect a cache issue hiding the test failures, it might
help if rather than the current text like "Time tested: ~ 8 hours ago"
this could also state the date and time of the test (in UTC/GMT to
avoid locale confusion).

Thanks,

Peter



Other repositories failing with a clear error message:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Missing dependencies, should have been skipped, see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler   
Limitation of test framework, Trello issue open for this,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename   
Limitation of test framework, issue raised,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list
Missing an R/Bioconductor dependency, best practise for handling
this has yet to be agreed.


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, May 13, 2013 at 11:09 AM, Peter Cock  wrote:
>
> I remain puzzled why I am seeing seemingly stochastic missing test
> results.
>

Hi Dave,

This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
repositories reported as failing but I can't see the error (and so
can't do much about fixing it):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss 

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
When previously visible this was due to a test framework
limitation testing with composite output files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html

Given I suspect a cache issue hiding the test failures, it might
help if rather than the current text like "Time tested: ~ 8 hours ago"
this could also state the date and time of the test (in UTC/GMT to
avoid locale confusion).

Thanks,

Peter



Other repositories failing with a clear error message:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Missing dependencies, should have been skipped, see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler   
Limitation of test framework, Trello issue open for this,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename   
Limitation of test framework, issue raised,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list
Missing an R/Bioconductor dependency, best practise for handling
this has yet to be agreed.
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, May 13, 2013 at 10:08 AM, Peter Cock  wrote:

 http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
 Functional test results for changeset revision c70df461aae5 of effectivet3
 0 tests passed, 0 tests failed, 0 tests missing test components.
 7:38 AM (2 hours ago)
>
> Failures still showing (good), I've not uploaded the suggested changes
> Dave made on Friday yet:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014619.html

I uploaded a minor change which should still fail but with a more helpful
error when running the tests (which confirmed the install script is failing
to create an expected directory):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/b863c4bec840

Using my default browser Firefox (on two machines) the tests are missing,
just:

Tool test results
Automated test environment
Time tested: 28 minutes ago
System: Linux 3.5.0-21-generic
Architecture: x86_64
Python version: 2.7.3
Galaxy revision: 9701:65a81aead95e
Galaxy database version: 115
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:

However, switching to Safari and Chrome I can see the failures here.
I remain puzzled why I am seeing seemingly stochastic missing test
results.

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Fri, May 10, 2013 at 2:30 PM, Peter Cock  wrote:
> On Fri, May 10, 2013 at 1:51 PM, Dave Bouvier  wrote:
>> Peter,
>>
>> The automated testing framework consists of a series of scripts that run in
>> a certain order, so between one script and the next, there may sometimes be
>> unexpected results displayed. I've had a look at the repositories you
>> listed, and the results all seem to be in order now. The RSS feed also seems
>> to be displaying the same results as the web interface.
>
> There seems to be some kind of caching problem for me:
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
>>> Functional test results for changeset revision 20e44218fa63 of clinod
>>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>>> 7:38 AM (2 hours ago)
>>>
>>> --> No test results shown (positive or negative), yet it is
>>>   listed under "Latest revision: failing tool tests"
>
> That URL redirects to here, still no test results shown in my main
> browser (Firefox v20.0 on Mac):
> http://testtoolshed.g2.bx.psu.edu/repository?repository_id=27e2bf03e13aae5d&changeset_revision=20e44218fa63
>
> However, switching to Safari or Firefox on Windows I see the failing
> test (Error: Unable to access jarfile ...).

Today all those browsers show no test results for clinod :(

Tool test results
Automated test environment
Time tested: ~ 4 hours ago
System: Linux 3.0.0-1-amd64
Architecture: x86_64
Python version: 2.7.2+
Galaxy revision:
Galaxy database version:
Tool shed revision: 9701:65a81aead95e
Tool shed database version: 18
Tool shed mercurial version: 2.2.3

>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
>>> Functional test results for changeset revision c70df461aae5 of effectivet3
>>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>>> 7:38 AM (2 hours ago)

Failures still showing (good), I've not uploaded the suggested changes
Dave made on Friday yet:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014619.html

But in addition to clinod (above), here are some more repositories where
the test results are currently missing (tested in three browsers over two
machines):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/58359ce5bde9
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/88f002677c63
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/06e6112091aa

Might there be a timing issue here? Is it possible that when I check
in the morning UK time, the test results haven't yet all been recorded
in the database so the Tool Shed only has partial information - then
when you check in the afternoon UK time (morning in USA) things are
working (although I don't always see this if there is also a cache problem).

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Fri, May 10, 2013 at 1:51 PM, Dave Bouvier  wrote:
> Peter,
>
> The automated testing framework consists of a series of scripts that run in
> a certain order, so between one script and the next, there may sometimes be
> unexpected results displayed. I've had a look at the repositories you
> listed, and the results all seem to be in order now. The RSS feed also seems
> to be displaying the same results as the web interface.

There seems to be some kind of caching problem for me:

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
>> Functional test results for changeset revision 20e44218fa63 of clinod
>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>> 7:38 AM (2 hours ago)
>>
>> --> No test results shown (positive or negative), yet it is
>>   listed under "Latest revision: failing tool tests"

That URL redirects to here, still no test results shown in my main
browser (Firefox v20.0 on Mac):
http://testtoolshed.g2.bx.psu.edu/repository?repository_id=27e2bf03e13aae5d&changeset_revision=20e44218fa63

However, switching to Safari or Firefox on Windows I see the failing
test (Error: Unable to access jarfile ...).

>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
>> Functional test results for changeset revision c70df461aae5 of effectivet3
>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>> 7:38 AM (2 hours ago)
>>
>> --> No test results shown (positive or negative), yet it is
>>  listed under "Latest revision: failing tool tests"

That URL redirects to here, still no test results in my main browser
(Firefox v20.0 on Mac):
http://testtoolshed.g2.bx.psu.edu/repository?repository_id=26f26c7aa084d325&changeset_revision=c70df461aae5

Again, switching to Safari or Firefox on Windows I see two failing tests
(Effective T3 model JAR file not found ...).

This suggest some caching problem - but restarting Firefox didn't
solve it, nor did deleting the cache files in Firefox. Puzzling.

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

The automated testing framework consists of a series of scripts that run 
in a certain order, so between one script and the next, there may 
sometimes be unexpected results displayed. I've had a look at the 
repositories you listed, and the results all seem to be in order now. 
The RSS feed also seems to be displaying the same results as the web 
interface.


A repository is set not to be tested only in a few cases, among those is 
when there is a more recent installable changeset revision, and the 
revision currently being tested has missing components or does not pass 
the tests.


   --Dave B.

On 5/10/13 05:34:59.000, Peter Cock wrote:

On Thu, May 9, 2013 at 10:49 AM, Peter Cock  wrote:

On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier  wrote:

Peter,

A technical issue prevented the tests from automatically running. I've
resolved the issue and started a manual run, you should be seeing test
results within 2-3 hours.

--Dave B.


Hi Dave,

As you hoped, these test now shows up on the tool page (as expected
they are test failures - apparently my install script isn't quite right yet):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Functional test results for changeset revision a66a914c39b5 of clinod
0 tests passed, 1 tests failed, 0 tests missing test components.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965
Functional test results for changeset revision 5644c28cf965 of effectivet3
0 tests passed, 2 tests failed, 0 tests missing test components.

This one is more interesting, and appears to be a problem with the
test framework (both tests pass locally via run_functional_tests.sh):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
0 tests passed, 2 tests failed, 0 tests missing test components.

I'll raise that on a new thread,

Peter


Hi again Dave,

There is something breaking intermittently - my overnight RSS feed:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
Functional test results for changeset revision 20e44218fa63 of clinod
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)

--> No test results shown (positive or negative), yet it is
  listed under "Latest revision: failing tool tests"

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/6e7694a0ae00
Functional test results for changeset revision 6e7694a0ae00 of blast2go
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)

--> Actually one failure due to dependency on main Tool Shed,
 correctly listed under "Latest revision: failing tool tests"

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
Functional test results for changeset revision c70df461aae5 of effectivet3
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)

--> No test results shown (positive or negative), yet it is
 listed under "Latest revision: failing tool tests"

These were the only three feed entries overnight from:
http://testtoolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjc&status=all

Presumably then other tools were not tested - which makes
sense to save resources if neither the tool nor the tool shed
was updated since the last time a tool was tested.

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Thu, May 9, 2013 at 10:49 AM, Peter Cock  wrote:
> On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier  wrote:
>> Peter,
>>
>> A technical issue prevented the tests from automatically running. I've
>> resolved the issue and started a manual run, you should be seeing test
>> results within 2-3 hours.
>>
>>--Dave B.
>
> Hi Dave,
>
> As you hoped, these test now shows up on the tool page (as expected
> they are test failures - apparently my install script isn't quite right yet):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
> Functional test results for changeset revision a66a914c39b5 of clinod
> 0 tests passed, 1 tests failed, 0 tests missing test components.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965
> Functional test results for changeset revision 5644c28cf965 of effectivet3
> 0 tests passed, 2 tests failed, 0 tests missing test components.
>
> This one is more interesting, and appears to be a problem with the
> test framework (both tests pass locally via run_functional_tests.sh):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
> Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
> 0 tests passed, 2 tests failed, 0 tests missing test components.
>
> I'll raise that on a new thread,
>
> Peter

Hi again Dave,

There is something breaking intermittently - my overnight RSS feed:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
Functional test results for changeset revision 20e44218fa63 of clinod
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)

--> No test results shown (positive or negative), yet it is
 listed under "Latest revision: failing tool tests"

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/6e7694a0ae00
Functional test results for changeset revision 6e7694a0ae00 of blast2go
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)

--> Actually one failure due to dependency on main Tool Shed,
correctly listed under "Latest revision: failing tool tests"

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
Functional test results for changeset revision c70df461aae5 of effectivet3
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)

--> No test results shown (positive or negative), yet it is
listed under "Latest revision: failing tool tests"

These were the only three feed entries overnight from:
http://testtoolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owner=peterjc&status=all

Presumably then other tools were not tested - which makes
sense to save resources if neither the tool nor the tool shed
was updated since the last time a tool was tested.

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier  wrote:
> Peter,
>
> A technical issue prevented the tests from automatically running. I've
> resolved the issue and started a manual run, you should be seeing test
> results within 2-3 hours.
>
>--Dave B.

Hi Dave,

As you hoped, these test now shows up on the tool page (as expected
they are test failures - apparently my install script isn't quite right yet):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Functional test results for changeset revision a66a914c39b5 of clinod
0 tests passed, 1 tests failed, 0 tests missing test components.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965
Functional test results for changeset revision 5644c28cf965 of effectivet3
0 tests passed, 2 tests failed, 0 tests missing test components.

This one is more interesting, and appears to be a problem with the
test framework (both tests pass locally via run_functional_tests.sh):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
0 tests passed, 2 tests failed, 0 tests missing test components.

I'll raise that on a new thread,

Peter

(Sorry for resending this Dave, I left off the mailing list the first time)
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Wed, May 8, 2013 at 3:28 PM, Greg Von Kuster  wrote:
> Hi Peter,
>
> On May 8, 2013, at 6:45 AM, Peter Cock wrote:
>
>> On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster  wrote:
>>> Hi Peter,
>>>
>>> Missing test components implies a tool config that does not define a
>>> test (i.e, a missing test definition) or a tool config that defines a test,
>>> but the test's input or output files are missing from the repository.
>>
>> This seems to be our point of confusion: I don't understand combining
>> these two categories - it seems unhelpful to me.
>
> I feel this is just a difference of opinion.  Combining missing tests and
> missing test data into a single category is certainly justifiable.  Any
> repository that falls into this category clearly states to the owner what
> is missing, and the owner can easily know that work is needed to
> prepare the repository contents for testing, whether that work falls
> into the category of adding a missing test or adding missing test data.

Speaking as a tool author, these are two rather different categories
which should not be merged. I personally would put "tools with defined
tests but missing input/output files" under "failing tests" not under
"missing tests".

>> Tools missing a test definition clearly can't be tested - but since we'd
>> like every tool to have tests having this as an easily view listing is
>> useful both for authors and reviewers.
>
> But is is an easily viewed listing.  It is currently very easy to determine
> if a tool is missing a defined test, is missing test data, or both.

No it isn't easily viewable - it is easy to get a combined listing of
repositories with (a) missing tests and/or (b) tests with missing files,
and then very tedious to look at these repositories one by one to see
which it is.

>> It highlights tools which need
>> some work - or in some cases work on the Galaxy test framework itself.
>> They are neither passing nor failing tests - and it makes sense to list
>> them separately.
>>
>> Tools with a test definition should be tested
>
> This is where I disagree. ... 
> Installing a testing repositories that have tools with defined tests
> but missing test data is potentially costly from a time perspective.
> 

I wasn't meaning to suggest you do that though - you're already
able to short cut these cases and mark the test as failed. These
are the quickest possible tests to run - they fail at the first hurdle.

>> - if they are missing an input or output
>> file this is just a special case of a test failure (and can
>> be spotted without actually attempting to run the tool).
>
> Yes, but this is what we are doing now.  We are spotting
> this scenario without installing the repository or running
> any defined tests by running the tool.

Yes, and that is fine - I'm merely talking about how this information
is presented to the Tool Shed viewer.

>> This is clearly
>> a broken test and the tool author should be able to fix this easily (by
>> uploading the missing test data file)
>
> Yes, but this is already possible for them to clearly see without
> having to install the repository or run any tests.

Indeed, but it this is a failing test and should (in my view) be
listed under failing tests not under missing tests.

We're just debating where to list such problem tools/repositories
in the Tool Shed's test results interface.

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hi Peter,

On May 8, 2013, at 6:45 AM, Peter Cock wrote:

> On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster  wrote:
>> Hi Peter,
>> 
>> Missing test components implies a tool config that does not define a
>> test (i.e, a missing test definition) or a tool config that defines a test,
>> but the test's input or output files are missing from the repository.
> 
> This seems to be our point of confusion: I don't understand combining
> these two categories - it seems unhelpful to me.

I feel this is just a difference of opinion.  Combining missing tests and 
missing test data into a single category is certainly justifiable.  Any 
repository that falls into this category clearly states to the owner what is 
missing, and the owner can easily know that work is needed to prepare the 
repository contents for testing, whether that work falls into the category of 
adding a missing test or adding missing test data.

> 
> Tools missing a test definition clearly can't be tested - but since we'd
> like every tool to have tests having this as an easily view listing is
> useful both for authors and reviewers.

But is is an easily viewed listing.  It is currently very easy to determine if 
a tool is missing a defined test, is missing test data, or both.

> It highlights tools which need
> some work - or in some cases work on the Galaxy test framework itself.
> They are neither passing nor failing tests - and it makes sense to list
> them separately.
> 
> Tools with a test definition should be tested

This is where I disagree.  It currently takes a few seconds for our check 
repositories for test components to crawl the entire main tool shed and set 
flags for those repositories missing test components.  However, the separate 
script that crawls the main tool shed and installs and tests repositories that 
are not missing test components currently takes hours to run even though less 
than 10% of the repositories are currently tests (due to missing test 
components on most of them).

Installing a testing repositories that have tools with defined tests but 
missing test data is potentially costly from a time perspective.  Let's take a 
simple example:

Repo A has 1 tool that includes a defined test, but is missing required test 
data from the repository.  The tool in repo A defines 2 3rd party tool 
dependencies that must be installed and compiled.  In addition, repo A defines 
a repository dependency whose ultimate chain of repository installations 
results in 4 additional repositories with 16 additional 3rd party tool 
dependencies, with a total installation time of 2 hours.  All of this time is 
taken in order to test the tool in repo A when we already know that it will not 
succeed because it is missing test data.  This is certainly a realistic 
scenario.


> - if they are missing an
> input or output file this is just a special case of a test failure (and can
> be spotted without actually attempting to run the tool).

Yes, but this is what we are doing now.  We are spotting this scenario without 
installing the repository or running any defined tests by running the tool.

> This is clearly
> a broken test and the tool author should be able to fix this easily (by
> uploading the missing test data file)

Yes, but this is already possible for them to clearly see without having to 
install the repository or run any tests.

> 
>> I don't see the benefit of the above where you place tools missing tests
>> into a different category than tools with defined tests, but missing test 
>> data.
>> If any of the test components (test definition or required input or output 
>> files)
>> are missing, then the test cannot be executed, so defining it as a failing
>> test in either case is a bit misleading.  It is actually a tool that is 
>> missing
>> test components that are required for execution which will result in a pass
>> / fail status.
> 
> It is still a failing test (just for the trivial reason of missing a
> test data file).
> 
>> It would be much simpler to change the filter for failing tests to include
>> those that are missing test components so that the list of missing test
>> components is a subset of the list of failing tests.
> 
> What I would like is three lists:
> 
> Latest revision: missing tool tests
> - repositories where at least 1 tool has no test defined
> 
> [The medium term TO-DO list for the Tool Author]
> 
> Latest revision: failing tool tests
> - repositories where at least 1 tool has a failing test (where I include
>  tests missing their input or output test data files)
> 
> [The priority TO-DO list for the Tool Author]
> 
> Latest revision: all tool tests pass
> - repositories where every tool has tests and they all pass
> 
> [The good list, Tool Authors should aim to have everything here]
> 
> Right now http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
> would appear under both "missing tool tests" and "failing tool tests",
> but I hope to fix this and have this under "missing tool tests" only
> (

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

A technical issue prevented the tests from automatically running. I've 
resolved the issue and started a manual run, you should be seeing test 
results within 2-3 hours.


   --Dave B.

On 5/8/13 07:09:28.000, Peter Cock wrote:

On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier  wrote:

Peter,

As you've already noticed, I've tracked down and fixed the main issue that
was causing inaccurate test results. Thank you again for the data you
provided, which was of great help narrowing down the cause of the issue.

--Dave B.


Hi Dave,

I've got another problem set for you, some repositories are listed under
"Latest revision: failing tool tests", yet there are no test results are shown
(positive or negative).

Tool shed revision: 9661:cb0432cfcc8a

My clinod wrapper with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Revision 3:a66a914c39b5

My effective T3 wrapper with two tests:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/4567618bebbd
Revision 5:4567618bebbd

My seq_rename tool with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/b51633a69a92
Revision 2:b51633a69a92

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier  wrote:
> Peter,
>
> As you've already noticed, I've tracked down and fixed the main issue that
> was causing inaccurate test results. Thank you again for the data you
> provided, which was of great help narrowing down the cause of the issue.
>
>--Dave B.

Hi Dave,

I've got another problem set for you, some repositories are listed under
"Latest revision: failing tool tests", yet there are no test results are shown
(positive or negative).

Tool shed revision: 9661:cb0432cfcc8a

My clinod wrapper with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Revision 3:a66a914c39b5

My effective T3 wrapper with two tests:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/4567618bebbd
Revision 5:4567618bebbd

My seq_rename tool with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/b51633a69a92
Revision 2:b51633a69a92

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster  wrote:
> Hi Peter,
>
> Missing test components implies a tool config that does not define a
> test (i.e, a missing test definition) or a tool config that defines a test,
> but the test's input or output files are missing from the repository.

This seems to be our point of confusion: I don't understand combining
these two categories - it seems unhelpful to me.

Tools missing a test definition clearly can't be tested - but since we'd
like every tool to have tests having this as an easily view listing is
useful both for authors and reviewers. It highlights tools which need
some work - or in some cases work on the Galaxy test framework itself.
They are neither passing nor failing tests - and it makes sense to list
them separately.

Tools with a test definition should be tested - if they are missing an
input or output file this is just a special case of a test failure (and can
be spotted without actually attempting to run the tool). This is clearly
a broken test and the tool author should be able to fix this easily (by
uploading the missing test data file)

> I don't see the benefit of the above where you place tools missing tests
> into a different category than tools with defined tests, but missing test 
> data.
> If any of the test components (test definition or required input or output 
> files)
> are missing, then the test cannot be executed, so defining it as a failing
> test in either case is a bit misleading.  It is actually a tool that is 
> missing
> test components that are required for execution which will result in a pass
> / fail status.

It is still a failing test (just for the trivial reason of missing a
test data file).

> It would be much simpler to change the filter for failing tests to include
> those that are missing test components so that the list of missing test
> components is a subset of the list of failing tests.

What I would like is three lists:

Latest revision: missing tool tests
 - repositories where at least 1 tool has no test defined

[The medium term TO-DO list for the Tool Author]

Latest revision: failing tool tests
 - repositories where at least 1 tool has a failing test (where I include
   tests missing their input or output test data files)

[The priority TO-DO list for the Tool Author]

Latest revision: all tool tests pass
 - repositories where every tool has tests and they all pass

[The good list, Tool Authors should aim to have everything here]

Right now http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
would appear under both "missing tool tests" and "failing tool tests",
but I hope to fix this and have this under "missing tool tests" only
(until my current roadblocks with the Galaxy Test Framework are
resolved).

I hope I've managed a clearer explanation this time,

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hi Peter,


On May 7, 2013, at 9:10 AM, Peter Cock wrote:

> On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster  wrote:
>> Hi Peter,
>> 
>> This change would be simple to make, but it would result in the inclusion
>> of all repositories with missing test components to be included in the list
>> of failing tests.  There are currently 2 filters that provide the
>> information to categorize these repositories: missing test components ( True
>> / False ) and tools functionally correct ( True / False ).  I'm not sure it
>> makes sense to add a 3rd filter, but if we can come up with a sensible one,
>> I would be happy to add it.  If not, do you want the list of failing tool
>> tests to include repositories that are missing test components?
> 
> By missing test components do you mean things like missing a test input
> or output file? If so, that would be fine. If I've written a test but
> not included
> the sample data, then to me that is just a special case of a failing test that
> needs fixing (and it should be a trivial fix).


Missing test components implies a tool config that does not define a test (i.e, 
a missing test definition) or a tool config that defines a test, but the test's 
input or output files are missing from the repository.


> 
> Currently (according to the yellow notes on the Test Tool Shed),
> 
> Latest revision: missing tool tests:
> * you are authorized to update them
> * the latest installable revision contains at least 1 tool with no
> defined tests OR:
> * the latest installable revision contains at least 1 tool with a
> test that requires a missing test data file
> 
> Latest revision: failing tool tests:
> * you are authorized to update them
> * the latest installable revision contains at least 1 tool
> * the latest installable revision is not missing any tool test components
> * the latest installable revision has at least 1 tool test that fails
> 
> My suggestion would be to treat missing test data files as a failing
> test, something like this:
> 
> Latest revision: missing tool tests:
> * you are authorized to update them
> * the latest installable revision contains at least 1 tool with no
> defined tests

I don't see the benefit of the above where you place tools missing tests into a 
different category than tools with defined tests, but missing test data.  If 
any of the test components (test definition or required input or output files) 
are missing, then the test cannot be executed, so defining it as a failing test 
in either case is a bit misleading.  It is actually a tool that is missing test 
components that are required for execution which will result in a pass / fail 
status.

It would be much simpler to change the filter for failing tests to include 
those that are missing test components so that the list of missing test 
components is a subset of the list of failing tests.

> 
> Latest revision: failing tool tests:
> * you are authorized to update them
> * the latest installable revision has at least 1 tool test that fails
> OR requires a missing test data file
> 
> Under this scheme, right now on the Test Tool Shed my ncbi_blast_plus
> repository would appear on both lists due to missing tests for tools like
> ncbi_rpsblast_wrapper, and failing tests like ncbi_blastn_wrapper (due
> to a glitch in the dependency installation changes I made).
> 
> Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier  wrote:
> Peter,
>
> As you've already noticed, I've tracked down and fixed the main issue that
> was causing inaccurate test results. Thank you again for the data you
> provided, which was of great help narrowing down the cause of the issue.
>
>--Dave B.

I'm glad that's sorted - I should be able to get back into fixing tests
and adding a few more now that I'm getting nightly feedback again :)

Thanks!

Peter

P.S. Is the idea of running the tests whenever a tool is updated likely to
happen in the near future, or is that still a wish list item?
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

As you've already noticed, I've tracked down and fixed the main issue 
that was causing inaccurate test results. Thank you again for the data 
you provided, which was of great help narrowing down the cause of the 
issue.


   --Dave B.

On 5/7/13 04:50:23.000, Peter Cock wrote:

On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier  wrote:

Peter,

Yes, there are a few issues that are causing some repositories not to be
tested correctly. I've discovered the problem, but the solution will require
a bit of work. My goal is to have this resolved as soon as possible.

--Dave B.


Hi Dave,

Things are looking sensible again on the Test Tool Shed - thanks :)

I have a query which might deserve discussion: Currently my
some of my BLAST+ tools have missing tests and some are
failing (due in part to limitations of the test framework) yet
the repository is only listed under missing tool tests:

Latest revision: missing tool tests - includes ncbi_blast_plus
Latest revision: failing tool tests - omits ncbi_blast_plus
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

As the yellow description makes clear, this is deliberate,
but I would prefer to have ncbi_blast_plus listed in both
places. In this case I know there are missing tests, but
would hope there are no failing tests - yet the Tool Shed
interface is effectively 'hiding' these failures from the
prominent listing.

(Right now the failures are unexpected, it seems my
changes to the automated installation were not successful
- but that's why I'm testing them here to check this)

What does everyone else think?

Thanks,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster  wrote:
> Hi Peter,
>
> This change would be simple to make, but it would result in the inclusion
> of all repositories with missing test components to be included in the list
> of failing tests.  There are currently 2 filters that provide the
> information to categorize these repositories: missing test components ( True
> / False ) and tools functionally correct ( True / False ).  I'm not sure it
> makes sense to add a 3rd filter, but if we can come up with a sensible one,
> I would be happy to add it.  If not, do you want the list of failing tool
> tests to include repositories that are missing test components?

By missing test components do you mean things like missing a test input
or output file? If so, that would be fine. If I've written a test but
not included
the sample data, then to me that is just a special case of a failing test that
needs fixing (and it should be a trivial fix).

Currently (according to the yellow notes on the Test Tool Shed),

Latest revision: missing tool tests:
 * you are authorized to update them
 * the latest installable revision contains at least 1 tool with no
defined tests OR:
 * the latest installable revision contains at least 1 tool with a
test that requires a missing test data file

Latest revision: failing tool tests:
 * you are authorized to update them
 * the latest installable revision contains at least 1 tool
 * the latest installable revision is not missing any tool test components
 * the latest installable revision has at least 1 tool test that fails

My suggestion would be to treat missing test data files as a failing
test, something like this:

Latest revision: missing tool tests:
 * you are authorized to update them
 * the latest installable revision contains at least 1 tool with no
defined tests

Latest revision: failing tool tests:
 * you are authorized to update them
 * the latest installable revision has at least 1 tool test that fails
OR requires a missing test data file

Under this scheme, right now on the Test Tool Shed my ncbi_blast_plus
repository would appear on both lists due to missing tests for tools like
ncbi_rpsblast_wrapper, and failing tests like ncbi_blastn_wrapper (due
to a glitch in the dependency installation changes I made).

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hi Peter,

This change would be simple to make, but it would result in the inclusion of 
all repositories with missing test components to be included in the list of 
failing tests.  There are currently 2 filters that provide the information to 
categorize these repositories: missing test components ( True / False ) and 
tools functionally correct ( True / False ).  I'm not sure it makes sense to 
add a 3rd filter, but if we can come up with a sensible one, I would be happy 
to add it.  If not, do you want the list of failing tool tests to include 
repositories that are missing test components?

Thanks!

Greg

On May 7, 2013, at 4:50 AM, Peter Cock wrote:

> On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier  wrote:
>> Peter,
>> 
>> Yes, there are a few issues that are causing some repositories not to be
>> tested correctly. I've discovered the problem, but the solution will require
>> a bit of work. My goal is to have this resolved as soon as possible.
>> 
>>  --Dave B.
> 
> Hi Dave,
> 
> Things are looking sensible again on the Test Tool Shed - thanks :)
> 
> I have a query which might deserve discussion: Currently my
> some of my BLAST+ tools have missing tests and some are
> failing (due in part to limitations of the test framework) yet
> the repository is only listed under missing tool tests:
> 
> Latest revision: missing tool tests - includes ncbi_blast_plus
> Latest revision: failing tool tests - omits ncbi_blast_plus
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
> 
> As the yellow description makes clear, this is deliberate,
> but I would prefer to have ncbi_blast_plus listed in both
> places. In this case I know there are missing tests, but
> would hope there are no failing tests - yet the Tool Shed
> interface is effectively 'hiding' these failures from the
> prominent listing.
> 
> (Right now the failures are unexpected, it seems my
> changes to the automated installation were not successful
> - but that's why I'm testing them here to check this)
> 
> What does everyone else think?
> 
> Thanks,
> 
> Peter
> ___
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier  wrote:
> Peter,
>
> Yes, there are a few issues that are causing some repositories not to be
> tested correctly. I've discovered the problem, but the solution will require
> a bit of work. My goal is to have this resolved as soon as possible.
>
>--Dave B.

Hi Dave,

Things are looking sensible again on the Test Tool Shed - thanks :)

I have a query which might deserve discussion: Currently my
some of my BLAST+ tools have missing tests and some are
failing (due in part to limitations of the test framework) yet
the repository is only listed under missing tool tests:

Latest revision: missing tool tests - includes ncbi_blast_plus
Latest revision: failing tool tests - omits ncbi_blast_plus
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

As the yellow description makes clear, this is deliberate,
but I would prefer to have ncbi_blast_plus listed in both
places. In this case I know there are missing tests, but
would hope there are no failing tests - yet the Tool Shed
interface is effectively 'hiding' these failures from the
prominent listing.

(Right now the failures are unexpected, it seems my
changes to the automated installation were not successful
- but that's why I'm testing them here to check this)

What does everyone else think?

Thanks,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

Yes, there are a few issues that are causing some repositories not to be 
tested correctly. I've discovered the problem, but the solution will 
require a bit of work. My goal is to have this resolved as soon as possible.


   --Dave B.

On 5/6/13 05:10:57.000, Peter Cock wrote:

On 2013-05-01 08:52, Greg Von Kuster wrote:


Hi Peter,

I created the following Trello card for this and things will be fixed as a
priority.  Thanks for letting us know!


https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823


On Wed, May 1, 2013 at 11:50 PM, Dave Bouvier  wrote:

Peter,

Thanks for the data, I am in the process of tracking down the source of the
issue, and I hope to have a fix ready shortly.

  --Dave B.


Hi Dave,

I see from the Trello card you've made some progress here - but I am
still seeing odd results on the Test Tool Shed (including not seeing
any test results), which has also been reflected in the RSS feed.
e.g. Conflicting RSS entries:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe469503441b
Functional test results for changeset revision fae4084a0bc0 of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 5 tests missing test components.

vs

http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe469503441b
Functional test results for changeset revision fe469503441b of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 0 tests missing test components.

Currently the Test Tool Shed shows me no test information at all
for this example (and sadly many others).

This seems to be part of a larger issue, "Latest revision: failing tool tests"
currently only lists mira_assembler - yet viewing this shows no failure
(or any other results):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658

Last week I had numerous failing tests (mostly due to missing tool
dependencies, some due to issues with the text framework). Many
of the (presumably still problematic) repositories are now listed under
"Latest revision: all tool tests pass" yet on viewing them there are no
test results shown at all, e.g.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/54c3d14e5621
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/af3174637834

Something seems to have gone wrong on Friday or over the weekend,

Regards,

Peter


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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Peter Cock]

> On 2013-05-01 08:52, Greg Von Kuster wrote:
>>
>> Hi Peter,
>>
>> I created the following Trello card for this and things will be fixed as a
>> priority.  Thanks for letting us know!
>>
>>
>> https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823

On Wed, May 1, 2013 at 11:50 PM, Dave Bouvier  wrote:
> Peter,
>
> Thanks for the data, I am in the process of tracking down the source of the
> issue, and I hope to have a fix ready shortly.
>
>  --Dave B.

Hi Dave,

I see from the Trello card you've made some progress here - but I am
still seeing odd results on the Test Tool Shed (including not seeing
any test results), which has also been reflected in the RSS feed.
e.g. Conflicting RSS entries:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe469503441b
Functional test results for changeset revision fae4084a0bc0 of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 5 tests missing test components.

vs

http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe469503441b
Functional test results for changeset revision fe469503441b of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 0 tests missing test components.

Currently the Test Tool Shed shows me no test information at all
for this example (and sadly many others).

This seems to be part of a larger issue, "Latest revision: failing tool tests"
currently only lists mira_assembler - yet viewing this shows no failure
(or any other results):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658

Last week I had numerous failing tests (mostly due to missing tool
dependencies, some due to issues with the text framework). Many
of the (presumably still problematic) repositories are now listed under
"Latest revision: all tool tests pass" yet on viewing them there are no
test results shown at all, e.g.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/54c3d14e5621
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/af3174637834

Something seems to have gone wrong on Friday or over the weekend,

Regards,

Peter
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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Dave Bouvier]

Peter,

Thanks for the data, I am in the process of tracking down the source of 
the issue, and I hope to have a fix ready shortly.


 --Dave B.

On 2013-05-01 08:52, Greg Von Kuster wrote:

Hi Peter,

I created the following Trello card for this and things will be fixed as a 
priority.  Thanks for letting us know!

https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823


On May 1, 2013, at 7:09 AM, Peter Cock wrote:


Hi Greg & Dave,

I really like the new features on the (Test) Tool Shed for searching
my repositories:

* Latest revision missing tool tests
* Latest revision failing tool tests
* Latest revision all tool tests pass

However there are some teething problems. Some of my tools are
listed under "Latest revision failing tool tests", but when I go to look
at them, no test results are shown (passing or failing):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

In some cases there is indeed a failing test, for instance this is
due to a bug in the test framework:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
https://trello.com/c/KdGX3hkh

And here there are missing dependencies (due to restrictive
licensing problems):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
https://trello.com/card/-/506338ce32ae458f6d15e4b3/770

Peter



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Re: [galaxy-dev] Missing test results on (Test) Tool Shed

[Greg Von Kuster]

Hi Peter,

I created the following Trello card for this and things will be fixed as a 
priority.  Thanks for letting us know!

https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823


On May 1, 2013, at 7:09 AM, Peter Cock wrote:

> Hi Greg & Dave,
> 
> I really like the new features on the (Test) Tool Shed for searching
> my repositories:
> 
> * Latest revision missing tool tests
> * Latest revision failing tool tests
> * Latest revision all tool tests pass
> 
> However there are some teething problems. Some of my tools are
> listed under "Latest revision failing tool tests", but when I go to look
> at them, no test results are shown (passing or failing):
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
> 
> In some cases there is indeed a failing test, for instance this is
> due to a bug in the test framework:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
> https://trello.com/c/KdGX3hkh
> 
> And here there are missing dependencies (due to restrictive
> licensing problems):
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> https://trello.com/card/-/506338ce32ae458f6d15e4b3/770
> 
> Peter


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