Nightly testing status on the (Test) Tool Shed

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Nightly testing status on the (Test) Tool Shed

Peter Cock
Hi all,

Are both the main and test Tool Sheds currently meant to be running
nightly tests again?

I've not really got back into Galaxy tool testing since Christmas.
Most of my tools'
test results look sensible, but there seem to be some issues still, e.g.

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Not tested since 2014-01-04

http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-29 missing blast_datatypes dependency (why?)
2014-01-28 showing failed tests for sambamba_filter (wrong tool)

Regards,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hi Peter,


On Jan 29, 2014, at 12:55 PM, Peter Cock <[hidden email]> wrote:

> Hi all,
>
> Are both the main and test Tool Sheds currently meant to be running
> nightly tests again?
>

Yes

> I've not really got back into Galaxy tool testing since Christmas.
> Most of my tools'
> test results look sensible, but there seem to be some issues still, e.g.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
> Not tested since 2014-01-04

I've reset the do_not_test column on the record above ( it was set to not allow testing ), so it should now be tested.


>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> 2014-01-29 missing blast_datatypes dependency (why?)
> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>

I'll have to take a look at the above issue.  I'm completely swamped though, so it will be a while.


> Regards,
>
> Peter
> ___________________________________________________________
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hi Peter,

On Jan 29, 2014, at 1:18 PM, Greg Von Kuster <[hidden email]> wrote:

> Hi Peter,
>
>
>>
>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>> 2014-01-29 missing blast_datatypes dependency (why?)
>> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>>
>
> I'll have to take a look at the above issue.  I'm completely swamped though, so it will be a while.

I believe I have the above issue resolved in 12331:fd4936ae8219 ( at least I took a step in the right direction ).  We'll have to wait for tonight's test run to make sure everything is handled correctly.

Thanks for letting me know about this.

Greg Von Kuster

>
>
>> Regards,
>>
>> Peter
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster <[hidden email]> wrote:

> Hi Peter,
>
> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster <[hidden email]> wrote:
>
>> Hi Peter,
>>
>>
>>>
>>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>>> 2014-01-29 missing blast_datatypes dependency (why?)
>>> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>>>
>>
>> I'll have to take a look at the above issue.  I'm completely
>> swamped though, so it will be a while.
>
> I believe I have the above issue resolved in 12331:fd4936ae8219
> ( at least I took a step in the right direction ).  We'll have to wait for
> tonight's test run to make sure everything is handled correctly.
>
> Thanks for letting me know about this.
>
> Greg Von Kuster

Fingers crossed :)

Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
In reply to this post by Greg Von Kuster
On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster <[hidden email]> wrote:

> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster <[hidden email]> wrote:
>> Peter wrote:
>>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>>> 2014-01-29 missing blast_datatypes dependency (why?)
>>> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>>
>> I'll have to take a look at the above issue.  I'm completely swamped
>> though, so it will be a while.
>
> I believe I have the above issue resolved in 12331:fd4936ae8219
> ( at least I took a step in the right direction ).  We'll have to wait for
> tonight's test run to make sure everything is handled correctly.

Hi again Greg,

That one is still weird - was that fix deployed to the main toolshed?

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

Moreover there is a similar problem with the matching repository
on the Test Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-04 showing failed tests for proteomics_search_tandem_1
2013-12-20 showing failed tests for proteomics_search_tandem_1
2013-12-18 tests for blastxml_to_top_descr passed
2013-12-17 tests for blastxml_to_top_descr passed

--

Returning to the MIRA4 problem, I got a meaningful test
failure which I fixed (I hadn't set an environment variable
in the install script), but I now get only partial test output:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Not datestamped (a glitch if there is only one test entry?):

Automated tool test results
Automated test environment
Time tested: 2014-02-03 16:25:08
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12332:d9f6f3f24671
Tool shed database version: 22
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.

That's all fine, but where are the test results for mira_bait which
I would expect to pass?

Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hi Peter,

I've created the following Trello card for this.  I know what the problems are, but I won't have time to get fixes for them for a while.  Please continue to reposrt issues you discover and I'll make sure to get fixes as soon as I get time.

https://trello.com/c/M1rwVWhI/143-nightly-test-runs-1

Thanks

Greg Von Kuster


On Feb 3, 2014, at 7:01 PM, Peter Cock <[hidden email]> wrote:

> On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster <[hidden email]> wrote:
>> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster <[hidden email]> wrote:
>>> Peter wrote:
>>>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>>>> 2014-01-29 missing blast_datatypes dependency (why?)
>>>> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>>>
>>> I'll have to take a look at the above issue.  I'm completely swamped
>>> though, so it will be a while.
>>
>> I believe I have the above issue resolved in 12331:fd4936ae8219
>> ( at least I took a step in the right direction ).  We'll have to wait for
>> tonight's test run to make sure everything is handled correctly.
>
> Hi again Greg,
>
> That one is still weird - was that fix deployed to the main toolshed?
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>
> Moreover there is a similar problem with the matching repository
> on the Test Tool Shed,
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> 2014-01-04 showing failed tests for proteomics_search_tandem_1
> 2013-12-20 showing failed tests for proteomics_search_tandem_1
> 2013-12-18 tests for blastxml_to_top_descr passed
> 2013-12-17 tests for blastxml_to_top_descr passed
>
> --
>
> Returning to the MIRA4 problem, I got a meaningful test
> failure which I fixed (I hadn't set an environment variable
> in the install script), but I now get only partial test output:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
> Not datestamped (a glitch if there is only one test entry?):
>
> Automated tool test results
> Automated test environment
> Time tested: 2014-02-03 16:25:08
> System:
> Architecture:
> Python version:
> Galaxy revision:
> Galaxy database version:
> Tool shed revision: 12332:d9f6f3f24671
> Tool shed database version: 22
> 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.
>
> That's all fine, but where are the test results for mira_bait which
> I would expect to pass?
>
> Thanks,
>
> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/


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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
In reply to this post by Peter Cock
Hi Peter,

I've created the following Trello card for this.  I know what the problems are, but I won't have time to get fixes for them for a while.  Please continue to reposrt issues you discover and I'll make sure to get fixes as soon as I get time.

https://trello.com/c/M1rwVWhI/143-nightly-test-runs-1

Thanks

Greg Von Kuster


On Feb 3, 2014, at 7:01 PM, Peter Cock <[hidden email]> wrote:

> On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster <[hidden email]> wrote:
>> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster <[hidden email]> wrote:
>>> Peter wrote:
>>>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>>>> 2014-01-29 missing blast_datatypes dependency (why?)
>>>> 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
>>>
>>> I'll have to take a look at the above issue.  I'm completely swamped
>>> though, so it will be a while.
>>
>> I believe I have the above issue resolved in 12331:fd4936ae8219
>> ( at least I took a step in the right direction ).  We'll have to wait for
>> tonight's test run to make sure everything is handled correctly.
>
> Hi again Greg,
>
> That one is still weird - was that fix deployed to the main toolshed?
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
>
> Moreover there is a similar problem with the matching repository
> on the Test Tool Shed,
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> 2014-01-04 showing failed tests for proteomics_search_tandem_1
> 2013-12-20 showing failed tests for proteomics_search_tandem_1
> 2013-12-18 tests for blastxml_to_top_descr passed
> 2013-12-17 tests for blastxml_to_top_descr passed
>
> --
>
> Returning to the MIRA4 problem, I got a meaningful test
> failure which I fixed (I hadn't set an environment variable
> in the install script), but I now get only partial test output:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
> Not datestamped (a glitch if there is only one test entry?):
>
> Automated tool test results
> Automated test environment
> Time tested: 2014-02-03 16:25:08
> System:
> Architecture:
> Python version:
> Galaxy revision:
> Galaxy database version:
> Tool shed revision: 12332:d9f6f3f24671
> Tool shed database version: 22
> 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.
>
> That's all fine, but where are the test results for mira_bait which
> I would expect to pass?
>
> Thanks,
>
> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
In reply to this post by Greg Von Kuster
Hi Peter,



On Jan 29, 2014, at 12:55 PM, Peter Cock <[hidden email]> wrote:


http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-29 missing blast_datatypes dependency (why?)
2014-01-28 showing failed tests for sambamba_filter (wrong tool)



I'll be taking a look at the remaining issues on the following Trello card next.


Greg Von Kuster



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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
In reply to this post by Peter Cock
Hi Peter,

On Feb 3, 2014, at 7:01 PM, Peter Cock <[hidden email]> wrote:


Moreover there is a similar problem with the matching repository
on the Test Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-04 showing failed tests for proteomics_search_tandem_1
2013-12-20 showing failed tests for proteomics_search_tandem_1
2013-12-18 tests for blastxml_to_top_descr passed
2013-12-17 tests for blastxml_to_top_descr passed

Like the same repository on the main tool shed, the above issue were fixed for the blastxml_to_top_descr on the test tool shed in https://bitbucket.org/galaxy/galaxy-central/commits/e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211


--

Returning to the MIRA4 problem, I got a meaningful test
failure which I fixed (I hadn't set an environment variable
in the install script), but I now get only partial test output:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Not datestamped (a glitch if there is only one test entry?):

Automated tool test results
Automated test environment
Time tested: 2014-02-03 16:25:08
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12332:d9f6f3f24671
Tool shed database version: 22
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.

That's all fine, but where are the test results for mira_bait which
I would expect to pass?


It looks lie the mira_bait tests results are being populated, bu the tests are failing, not passing.  This doesn't look like an issue with the Tool Shed's install and test framework.


Tool id: mira_4_0_bait
Tool version: mira_4_0_bait
Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/a6a56440567c/mirabait'
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: mira_4_0_bait
Tool version: mira_4_0_bait
Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/a6a56440567c/mirabait'
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: mira_4_0_bait
Tool version: mira_4_0_bait
Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/a6a56440567c/mirabait'
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error



Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock



On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster <[hidden email]> wrote:
Hi Peter,

On Feb 3, 2014, at 7:01 PM, Peter Cock <[hidden email]> wrote:


Moreover there is a similar problem with the matching repository
on the Test Tool Shed,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
2014-01-04 showing failed tests for proteomics_search_tandem_1
2013-12-20 showing failed tests for proteomics_search_tandem_1
2013-12-18 tests for blastxml_to_top_descr passed
2013-12-17 tests for blastxml_to_top_descr passed

Like the same repository on the main tool shed, the above issue were fixed for the blastxml_to_top_descr on the test tool shed in https://bitbucket.org/galaxy/galaxy-central/commits/e3a4d4d813fdb8a34cfd6d596e0f4bbdb2d9e211



Great, thanks.
 

--

Returning to the MIRA4 problem, I got a meaningful test
failure which I fixed (I hadn't set an environment variable
in the install script), but I now get only partial test output:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
...
That's all fine, but where are the test results for mira_bait which
I would expect to pass?


It looks lie the mira_bait tests results are being populated, bu 
the tests are failing, not passing.  This doesn't look like an 
issue with the Tool Shed's install and test framework.


Confirmed - the Tool Shed issue where only partial test output
was shown is fixed (did you work out why the test output was
missing?).

I was hoping to see a passing test, but I can now see a failing
test (still something not quite right with my dependency
installation script - I'll look at this next week hopefully).

Thanks,

Peter


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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock <[hidden email]> wrote:

> On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster <[hidden email]> wrote:
>> On Feb 3, 2014, at 7:01 PM, Peter Cock <[hidden email]> wrote:
>>>
>>> Returning to the MIRA4 problem, I got a meaningful test
>>> failure which I fixed (I hadn't set an environment variable
>>> in the install script), but I now get only partial test output:
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>>> ...
>>>
>>> That's all fine, but where are the test results for mira_bait which
>>> I would expect to pass?
>>>
>>
>> It looks lie the mira_bait tests results are being populated, but
>> the tests are failing, not passing.  This doesn't look like an
>> issue with the Tool Shed's install and test framework.
>
> Confirmed - the Tool Shed issue where only partial test output
> was shown is fixed (did you work out why the test output was
> missing?).
>
> I was hoping to see a passing test, but I can now see a failing
> test (still something not quite right with my dependency
> installation script - I'll look at this next week hopefully).

Hi Greg,

I added a little more debug information to the mirabait test,
which confirms a problem in the tool_dependencies.xml file:

Missing mirabait under $MIRA4,
'/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/mirabait'
Folder contained: env.sh

i.e. $MIRA4 was set to $INSTALL_DIR which is the folder
/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/
and (surprisingly) it only contains one file, env.sh

Greg: Could you confirm that on the server? i.e. what does this give?

$ ls -l /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/
...

Upon downloading mira_4.0_linux-gnu_x86_64_static.tar.bz2
and decompressing it, the tool shed should have changed into
the main folder mira_4.0_linux-gnu_x86_64_static and then
moved the contents of the bin folder into the $INSTALL_DIR,

                    <action
type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2</action>
                    <action type="move_directory_files">
                        <source_directory>bin</source_directory>

<destination_directory>$INSTALL_DIR</destination_directory>
                    </action>

i.e. Move files mira, mirabait, miraconvert and miramem
into $INSTALL_DIR

I am somewhat puzzled - other tools like the BLAST+
installers use a very similar setup and work fine (although
there I used $PATH instead).

Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hi Peter,

It looks like you made some changes to your tool dependency recipe since the last test run.  Dave B and I followed the latest revision of your recipe and manually installed it using https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2 and it looked ok.  Let's see what the restults of tonight's test run is for this repository and if there are still problems after your latest changes we'll track them down.

Thanks,

Greg Von Kuster

On Feb 17, 2014, at 6:15 AM, Peter Cock <[hidden email]> wrote:

> On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock <[hidden email]> wrote:
>> On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster <[hidden email]> wrote:
>>> On Feb 3, 2014, at 7:01 PM, Peter Cock <[hidden email]> wrote:
>>>>
>>>> Returning to the MIRA4 problem, I got a meaningful test
>>>> failure which I fixed (I hadn't set an environment variable
>>>> in the install script), but I now get only partial test output:
>>>>
>>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>>>> ...
>>>>
>>>> That's all fine, but where are the test results for mira_bait which
>>>> I would expect to pass?
>>>>
>>>
>>> It looks lie the mira_bait tests results are being populated, but
>>> the tests are failing, not passing.  This doesn't look like an
>>> issue with the Tool Shed's install and test framework.
>>
>> Confirmed - the Tool Shed issue where only partial test output
>> was shown is fixed (did you work out why the test output was
>> missing?).
>>
>> I was hoping to see a passing test, but I can now see a failing
>> test (still something not quite right with my dependency
>> installation script - I'll look at this next week hopefully).
>
> Hi Greg,
>
> I added a little more debug information to the mirabait test,
> which confirms a problem in the tool_dependencies.xml file:
>
> Missing mirabait under $MIRA4,
> '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/mirabait'
> Folder contained: env.sh
>
> i.e. $MIRA4 was set to $INSTALL_DIR which is the folder
> /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/
> and (surprisingly) it only contains one file, env.sh
>
> Greg: Could you confirm that on the server? i.e. what does this give?
>
> $ ls -l /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/
> ...
>
> Upon downloading mira_4.0_linux-gnu_x86_64_static.tar.bz2
> and decompressing it, the tool shed should have changed into
> the main folder mira_4.0_linux-gnu_x86_64_static and then
> moved the contents of the bin folder into the $INSTALL_DIR,
>
>                    <action
> type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2</action>
>                    <action type="move_directory_files">
>                        <source_directory>bin</source_directory>
>
> <destination_directory>$INSTALL_DIR</destination_directory>
>                    </action>
>
> i.e. Move files mira, mirabait, miraconvert and miramem
> into $INSTALL_DIR
>
> I am somewhat puzzled - other tools like the BLAST+
> installers use a very similar setup and work fine (although
> there I used $PATH instead).
>
> Thanks,
>
> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster <[hidden email]> wrote:
> Hi Peter,
>
> It looks like you made some changes to your tool dependency
> recipe since the last test run.

Yeah, the mira de novo test was missing the test-data input files.
But I didn't touch mirabait or the install XML instructions.

>  Dave B and I followed the latest revision of your recipe and manually
> installed it using https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2
> and it looked ok.

If you mean you installed it via the Tool Shed, and it worked - that's good :)

(Or did you mean manually by running wget, tar, etc, by hand?)

> Let's see what the restults of tonight's test run is for this repository
> and if there are still problems after your latest changes we'll track
> them down.

Sure - fingers crossed,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
On Mon, Feb 17, 2014 at 3:08 PM, Peter Cock <[hidden email]> wrote:

> On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster <[hidden email]> wrote:
>> Hi Peter,
>>
>> It looks like you made some changes to your tool dependency
>> recipe since the last test run.
>
> Yeah, the mira de novo test was missing the test-data input files.
> But I didn't touch mirabait or the install XML instructions.
>
>>  Dave B and I followed the latest revision of your recipe and manually
>> installed it using https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2
>> and it looked ok.
>
> If you mean you installed it via the Tool Shed, and it worked - that's good :)
>
> (Or did you mean manually by running wget, tar, etc, by hand?)
>
>> Let's see what the restults of tonight's test run is for this repository
>> and if there are still problems after your latest changes we'll track
>> them down.
>
> Sure - fingers crossed,

Hi Greg, Dave,

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

Same as before, although now both the mirabait and mira de novo
tests are attempted:

Missing mirabait under $MIRA4,
'/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait'
Folder contained: env.sh

Missing mira under $MIRA4,
'/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mira'
Folder contained: env.sh

My Python wrapper checks the $MIRA4 environment variable,
which should be the $INSTALL_DIR location which should hold
the MIRA binaries (mira, mirabait, etc). According to the Python
wrapper, the $MIRA variable was set to:

/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/

However, the Python wrapper reports this folder only contains
one file, env.sh - which leads me to suspect a glitch in my
tool_dependencies.xml and/or the installation framework.

Regards,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hi Peter,

We'll try to get some time to look at your tool_dependencies.xml recipe as soon as possible.

Greg Von Kuster


On Feb 18, 2014, at 5:47 AM, Peter Cock <[hidden email]> wrote:

>
> Hi Greg, Dave,
>
> RE: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>
> Same as before, although now both the mirabait and mira de novo
> tests are attempted:
>
> Missing mirabait under $MIRA4,
> '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait'
> Folder contained: env.sh
>
> Missing mira under $MIRA4,
> '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mira'
> Folder contained: env.sh
>
> My Python wrapper checks the $MIRA4 environment variable,
> which should be the $INSTALL_DIR location which should hold
> the MIRA binaries (mira, mirabait, etc). According to the Python
> wrapper, the $MIRA variable was set to:
>
> /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/
>
> However, the Python wrapper reports this folder only contains
> one file, env.sh - which leads me to suspect a glitch in my
> tool_dependencies.xml and/or the installation framework.
>
> Regards,
>
> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster <[hidden email]> wrote:
> Hi Peter,
>
> We'll try to get some time to look at your tool_dependencies.xml recipe as soon as possible.
>
> Greg Von Kuster

Great.

Re: https://trello.com/c/HVGrShnC/60-tool-shed-should-test-installation-of-packages

Additional actions like asserting a file or folder exists would be good,
e.g. here I would like to add something like this to the install XML script:

assert file exists $MIRA4/mira
assert file exists $MIRA4/mirabait

Should I file a new Trello card for this and similar post-install checks
like the Biopython example:

python -c "import Bio; assert Bio.__version__=='1.62'"

Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
In reply to this post by Greg Von Kuster
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster <[hidden email]> wrote:
> Hi Peter,
>
> We'll try to get some time to look at your tool_dependencies.xml recipe as soon as possible.
>
> Greg Von Kuster
>
>

Hi Greg,

Overnight this has gone back to the previously observed missing
data problem (e.g. email of 4th Feb) - no test results at all:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

Test runs
2014-02-18 16:15:52
Automated test environment
Time tested: 2014-02-18 16:15:52
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12485:64e6873c8825
Tool shed database version: 22
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.

i.e. No test successes or failures reported. Collapsing the sections a bit:

Test runs
 * 2014-02-18 16:15:52
   *Automated test environment

This was on Firefox (logged in, or logged out of the Tool Shed).
Oddly, switching to Safari (not logged into the Tool Shed) on the
same machine, or Chrome on a second machine, I also see an
older test run's information where there is test output:

Test runs
 * 2014-02-18 16:15:52
    *Automated test environment
   * Tools missing tests or test data
 * 2014-02-18 03:40:12
   * Automated test environment
   * Tests that failed
   * Tools missing tests or test data
   * Successful installation

Might some strange cache or Firefox issue be hiding data?

Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hello Peter,
 Please see below…

On Feb 19, 2014, at 4:41 AM, Peter Cock <[hidden email]> wrote:

Hi Greg,

Overnight this has gone back to the previously observed missing
data problem (e.g. email of 4th Feb) - no test results at all:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler

Test runs
2014-02-18 16:15:52
Automated test environment
Time tested: 2014-02-18 16:15:52
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12485:64e6873c8825
Tool shed database version: 22
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.

i.e. No test successes or failures reported. Collapsing the sections a bit:

Test runs
* 2014-02-18 16:15:52
  *Automated test environment

This was on Firefox (logged in, or logged out of the Tool Shed).
Oddly, switching to Safari (not logged into the Tool Shed) on the
same machine, or Chrome on a second machine, I also see an
older test run's information where there is test output:

Test runs
* 2014-02-18 16:15:52
   *Automated test environment
  * Tools missing tests or test data
* 2014-02-18 03:40:12
  * Automated test environment
  * Tests that failed
  * Tools missing tests or test data
  * Successful installation

Might some strange cache or Firefox issue be hiding data?

Your above email arrived in my inbox at 4:42 AM EST, and it looks like your repository in question was not yet tested.  Using Firefox, I see the following resutls for today's test run, the results of which were updated in your Tool Shed repository at 4:50 AM EST.  The nightly Install and Test Framework is finishing at about 8:00 AM EST for hte Test Tool Shed.  The runs finish for the Main Tool Shed at about 5:00 AM EST.


Time tested: 2014-02-19 04:50:21
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 12536:c85f8fb5d63e
Galaxy database version: 118
Tool shed revision: 12485:64e6873c8825
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: mira_4_0_bait
Tool version: mira_4_0_bait
Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait'
Folder contained: env.sh
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: mira_4_0_bait
Tool version: mira_4_0_bait
Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait'
Folder contained: env.sh
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: mira_4_0_bait
Tool version: mira_4_0_bait
Test: test_tool_000002 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_bait/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mirabait'
Folder contained: env.sh
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
Tool id: mira_4_0_de_novo
Tool version: mira_4_0_de_novo
Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2)
Stderr:
Fatal error: Exit code 1 ()
Missing mira under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40/mira'
Folder contained: env.sh
Traceback:
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 106, 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 34, 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 67, 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 312, 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 827, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 641, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
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 shedNameOwnerChangeset revision
testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 54195f1d4b0f
TypeNameVersion
MIRA package 4.0
Installation directory
/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/133b863a8a40
TypeNameVersion
samtools package 0.1.19
Installation directory
/ToolDepsTest/samtools/0.1.19/peterjc/mira4_assembler/133b863a8a40



Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Peter Cock
On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster <[hidden email]> wrote:
>
> Hello Peter,
>  Please see below...
>
> ...
>
> Your above email arrived in my inbox at 4:42 AM EST, and
> it looks like your repository in question was not yet tested.

Ah. That would partly explain things - perhaps coupled with
a cache effect it might even explain why different browsers
seemed to give me different output....

Could Galaxy include the time zone (EST) in the Tool Shed
test time stamps and/or show GMT/UTC? (You have no
easy way of knowing the user's local timezone do you?).

Alternatively,  "Test in progress" would be nice :)

As to the test failure, it seems $INSTALL_DIR or at least
$MIRA4 only contains env.sh (which puzzles me).

Thanks,

Peter
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Re: Nightly testing status on the (Test) Tool Shed

Greg Von Kuster
Hi Peter,

Dave B and I just discovered that issue that causes your tests to fail.  

The problem lies with our current implementation supporting the <move_directory_files> action tag, which is used in your recipe.  This tag ultimately uses Python's os.listdir via shutil.move.

It turns out that certain Python versions produce different results from os.listdir - the order is different.  This is a problem with MIRA because during the instlllation it is moving a directory of files where the directory includes symlinks to other files in the directory.  When the symlinks are moved after the files to which they link, problems occur.  Again, this behavior is intermittent depending on the Pyhton version ( and perhaps the os ).

In any case, we have a fix for out move_directory_files which Dave is now committing.  So your tests should pass with tonight's run - Let's hope!

Thanks Peter!

Greg Von Kuster

On Feb 19, 2014, at 3:49 PM, Peter Cock <[hidden email]> wrote:

> On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster <[hidden email]> wrote:
>>
>> Hello Peter,
>> Please see below...
>>
>> ...
>>
>> Your above email arrived in my inbox at 4:42 AM EST, and
>> it looks like your repository in question was not yet tested.
>
> Ah. That would partly explain things - perhaps coupled with
> a cache effect it might even explain why different browsers
> seemed to give me different output....
>
> Could Galaxy include the time zone (EST) in the Tool Shed
> test time stamps and/or show GMT/UTC? (You have no
> easy way of knowing the user's local timezone do you?).
>
> Alternatively,  "Test in progress" would be nice :)
>
> As to the test failure, it seems $INSTALL_DIR or at least
> $MIRA4 only contains env.sh (which puzzles me).
>
> Thanks,
>
> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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12