value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

Peter Cock
Hi Dave,

The following looks like a regression on the Test Tool Shed, the tests
pass locally (using a recent revision), and on TravisCI using the current
galaxy dev branch on GitHub:
https://travis-ci.org/peterjc/pico_galaxy/builds/54870500

Problem tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs

This may be unrelated, but by chance this is the first time I have
uploaded a tool to the Tool Shed which uses the new functionality
to test the stdout/stderr strings, and more importantly it includes a
test expected to fail via <test expect_failure="true" expect_exit_code="1">

Revision on my development repository:
https://github.com/peterjc/pico_galaxy/commit/55ebb308b911b4acef912cc3b03f4371f4c6dfe6

Test Tool Shed output from last night:

Automated test environment
Time tested: 2015-03-18 02:46:55
System: Linux 3.13.0-36-generic
Architecture: x86_64
Python version: 2.7.6
Galaxy revision: 17050:6395e7035143
Galaxy database version: 128
Tool shed revision: 16867:0468d285f89c
Tool shed database version: 25
Tool shed mercurial version: 3.2.4
Tests that failed
Tool id: sample_seqs
Tool version: sample_seqs
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 37, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 38, in stage_data_in_history
    upload_wait()
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 279, in wait
    while not self.__history_ready( history_id ):
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 297, in __history_ready
    return self._state_ready( state, error_msg="History in error state." )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 356, in _state_ready
    raise Exception( error_msg )
Exception: History in error state.
Traceback (most recent call last):
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/__init__.py",
line 158, in prepare_job
    job_wrapper.prepare()
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/__init__.py",
line 828, in prepare
    tool_evaluator.set_compute_environment( compute_environment,
get_special=get_special )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/evaluation.py",
line 53, in set_compute_environment
    incoming = self.tool.params_from_strings( incoming, self.app )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/__init__.py",
line 1873, in params_from_strings
    return params_from_strings( self.inputs, params, app, ignore_errors )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/__init__.py",
line 103, in params_from_strings
    value = params[key].value_from_basic( value, app, ignore_errors )
  File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/grouping.py",
line 512, in value_from_basic
    raise e
KeyError: 'base_name'
requests.packages.urllib3.connectionpool: DEBUG: "GET
/api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
connection (1): 127.0.0.1
galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files
requests.packages.urllib3.connectionpool: DEBUG: "GET
/api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
connection (1): 127.0.0.1
requests.packages.urllib3.connectionpool: DEBUG: "GET
/api/histories/c33ffb67c9176a6c/contents?key=ae52a59b996b793c4c06a11fc3c33481
HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
connection (1): 127.0.0.1
requests.packages.urllib3.connectionpool: DEBUG: "GET
/api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9?key=ae52a59b996b793c4c06a11fc3c33481
HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
connection (1): 127.0.0.1
requests.packages.urllib3.connectionpool: DEBUG: "GET
/api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9/provenance?key=ae52a59b996b793c4c06a11fc3c33481
HTTP/1.1" 200 None

(All the tests for this tool seem to have failed the same way)

Regards,

Peter



On Wed, Mar 18, 2015 at 1:46 PM, Dave Bouvier <[hidden email]> wrote:

> Gentlemen,
>
> The issue with the nightly testing was due to a stalled test run blocking
> subsequent tests. I've cleared out that blockage and a manual test run
> appears to have completed successfully, as should future automated test
> runs. As always, feel free to let us know if you encounter any additional
> inexplicable behavior.
>
>    --Dave B.
>
> On 03/18/2015 07:00 AM, Peter Cock wrote:
>>
>> ... I can also confirm that the Test Tool Shed example I
>> gave was tested overnight, although it looks like a novel failure:
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

Peter Cock
Hi Dave,

Now that you've fixed some of the test back log, the bad
news is this issue I reported last week appears to be a major
regression affecting multiple tools on the Test Tool Shed:

https://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
...
https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
...
https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
...
https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id

These are all recent test runs from 2015-03-18. Note that
some tool tests from the same date are passing, e.g.

https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition
https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer

I have not yet spotted any pattern in this division.

(However this is clearly not linked to the test expect_failure
test I'd added to the sample_seqs tool, as I speculated last
week.)

Regards,

Peter

On Wed, Mar 18, 2015 at 2:14 PM, Peter Cock <[hidden email]> wrote:

> Hi Dave,
>
> The following looks like a regression on the Test Tool Shed, the tests
> pass locally (using a recent revision), and on TravisCI using the current
> galaxy dev branch on GitHub:
> https://travis-ci.org/peterjc/pico_galaxy/builds/54870500
>
> Problem tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>
> This may be unrelated, but by chance this is the first time I have
> uploaded a tool to the Tool Shed which uses the new functionality
> to test the stdout/stderr strings, and more importantly it includes a
> test expected to fail via <test expect_failure="true" expect_exit_code="1">
>
> Revision on my development repository:
> https://github.com/peterjc/pico_galaxy/commit/55ebb308b911b4acef912cc3b03f4371f4c6dfe6
>
> Test Tool Shed output from last night:
>
> Automated test environment
> Time tested: 2015-03-18 02:46:55
> System: Linux 3.13.0-36-generic
> Architecture: x86_64
> Python version: 2.7.6
> Galaxy revision: 17050:6395e7035143
> Galaxy database version: 128
> Tool shed revision: 16867:0468d285f89c
> Tool shed database version: 25
> Tool shed mercurial version: 3.2.4
> Tests that failed
> Tool id: sample_seqs
> Tool version: sample_seqs
> Test: test_tool_000000
> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1)
> Stderr:
> Traceback:
> Traceback (most recent call last):
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 268, in test_tool
>     self.do_it( td )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 37, in do_it
>     stage_data_in_history( galaxy_interactor, testdef.test_data(),
> test_history, shed_tool_id )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 38, in stage_data_in_history
>     upload_wait()
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 279, in wait
>     while not self.__history_ready( history_id ):
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 297, in __history_ready
>     return self._state_ready( state, error_msg="History in error state." )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 356, in _state_ready
>     raise Exception( error_msg )
> Exception: History in error state.
> Traceback (most recent call last):
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/__init__.py",
> line 158, in prepare_job
>     job_wrapper.prepare()
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/__init__.py",
> line 828, in prepare
>     tool_evaluator.set_compute_environment( compute_environment,
> get_special=get_special )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/evaluation.py",
> line 53, in set_compute_environment
>     incoming = self.tool.params_from_strings( incoming, self.app )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/__init__.py",
> line 1873, in params_from_strings
>     return params_from_strings( self.inputs, params, app, ignore_errors )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/__init__.py",
> line 103, in params_from_strings
>     value = params[key].value_from_basic( value, app, ignore_errors )
>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/grouping.py",
> line 512, in value_from_basic
>     raise e
> KeyError: 'base_name'
> requests.packages.urllib3.connectionpool: DEBUG: "GET
> /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
> HTTP/1.1" 200 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files
> requests.packages.urllib3.connectionpool: DEBUG: "GET
> /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
> HTTP/1.1" 200 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> requests.packages.urllib3.connectionpool: DEBUG: "GET
> /api/histories/c33ffb67c9176a6c/contents?key=ae52a59b996b793c4c06a11fc3c33481
> HTTP/1.1" 200 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> requests.packages.urllib3.connectionpool: DEBUG: "GET
> /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9?key=ae52a59b996b793c4c06a11fc3c33481
> HTTP/1.1" 200 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> requests.packages.urllib3.connectionpool: DEBUG: "GET
> /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9/provenance?key=ae52a59b996b793c4c06a11fc3c33481
> HTTP/1.1" 200 None
>
> (All the tests for this tool seem to have failed the same way)
>
> Regards,
>
> Peter
>
>
>
> On Wed, Mar 18, 2015 at 1:46 PM, Dave Bouvier <[hidden email]> wrote:
>> Gentlemen,
>>
>> The issue with the nightly testing was due to a stalled test run blocking
>> subsequent tests. I've cleared out that blockage and a manual test run
>> appears to have completed successfully, as should future automated test
>> runs. As always, feel free to let us know if you encounter any additional
>> inexplicable behavior.
>>
>>    --Dave B.
>>
>> On 03/18/2015 07:00 AM, Peter Cock wrote:
>>>
>>> ... I can also confirm that the Test Tool Shed example I
>>> gave was tested overnight, although it looks like a novel failure:
>>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>>>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

John Chilton-4
It seems to be happening during upload - so it is not unsurprising
that this error would affect multiple tools. I have checked out the
exact revision registered in the tests and the uploads seem fine to
me.

I am having trouble imagining a deployment problem short of an invalid
upload tool that might result in this error. Dave B, is it possible
that a problematic datatype is being installed by some repository and
affecting unrelated tools?

-John


On Mon, Mar 23, 2015 at 8:27 AM, Peter Cock <[hidden email]> wrote:

> Hi Dave,
>
> Now that you've fixed some of the test back log, the bad
> news is this issue I reported last week appears to be a major
> regression affecting multiple tools on the Test Tool Shed:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
> ...
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
> ...
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
> ...
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
>
> These are all recent test runs from 2015-03-18. Note that
> some tool tests from the same date are passing, e.g.
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer
>
> I have not yet spotted any pattern in this division.
>
> (However this is clearly not linked to the test expect_failure
> test I'd added to the sample_seqs tool, as I speculated last
> week.)
>
> Regards,
>
> Peter
>
> On Wed, Mar 18, 2015 at 2:14 PM, Peter Cock <[hidden email]> wrote:
>> Hi Dave,
>>
>> The following looks like a regression on the Test Tool Shed, the tests
>> pass locally (using a recent revision), and on TravisCI using the current
>> galaxy dev branch on GitHub:
>> https://travis-ci.org/peterjc/pico_galaxy/builds/54870500
>>
>> Problem tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>>
>> This may be unrelated, but by chance this is the first time I have
>> uploaded a tool to the Tool Shed which uses the new functionality
>> to test the stdout/stderr strings, and more importantly it includes a
>> test expected to fail via <test expect_failure="true" expect_exit_code="1">
>>
>> Revision on my development repository:
>> https://github.com/peterjc/pico_galaxy/commit/55ebb308b911b4acef912cc3b03f4371f4c6dfe6
>>
>> Test Tool Shed output from last night:
>>
>> Automated test environment
>> Time tested: 2015-03-18 02:46:55
>> System: Linux 3.13.0-36-generic
>> Architecture: x86_64
>> Python version: 2.7.6
>> Galaxy revision: 17050:6395e7035143
>> Galaxy database version: 128
>> Tool shed revision: 16867:0468d285f89c
>> Tool shed database version: 25
>> Tool shed mercurial version: 3.2.4
>> Tests that failed
>> Tool id: sample_seqs
>> Tool version: sample_seqs
>> Test: test_tool_000000
>> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1)
>> Stderr:
>> Traceback:
>> Traceback (most recent call last):
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
>> line 268, in test_tool
>>     self.do_it( td )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
>> line 37, in do_it
>>     stage_data_in_history( galaxy_interactor, testdef.test_data(),
>> test_history, shed_tool_id )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 38, in stage_data_in_history
>>     upload_wait()
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 279, in wait
>>     while not self.__history_ready( history_id ):
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 297, in __history_ready
>>     return self._state_ready( state, error_msg="History in error state." )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
>> line 356, in _state_ready
>>     raise Exception( error_msg )
>> Exception: History in error state.
>> Traceback (most recent call last):
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/__init__.py",
>> line 158, in prepare_job
>>     job_wrapper.prepare()
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/__init__.py",
>> line 828, in prepare
>>     tool_evaluator.set_compute_environment( compute_environment,
>> get_special=get_special )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/evaluation.py",
>> line 53, in set_compute_environment
>>     incoming = self.tool.params_from_strings( incoming, self.app )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/__init__.py",
>> line 1873, in params_from_strings
>>     return params_from_strings( self.inputs, params, app, ignore_errors )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/__init__.py",
>> line 103, in params_from_strings
>>     value = params[key].value_from_basic( value, app, ignore_errors )
>>   File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/grouping.py",
>> line 512, in value_from_basic
>>     raise e
>> KeyError: 'base_name'
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c/contents?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
>> connection (1): 127.0.0.1
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9/provenance?key=ae52a59b996b793c4c06a11fc3c33481
>> HTTP/1.1" 200 None
>>
>> (All the tests for this tool seem to have failed the same way)
>>
>> Regards,
>>
>> Peter
>>
>>
>>
>> On Wed, Mar 18, 2015 at 1:46 PM, Dave Bouvier <[hidden email]> wrote:
>>> Gentlemen,
>>>
>>> The issue with the nightly testing was due to a stalled test run blocking
>>> subsequent tests. I've cleared out that blockage and a manual test run
>>> appears to have completed successfully, as should future automated test
>>> runs. As always, feel free to let us know if you encounter any additional
>>> inexplicable behavior.
>>>
>>>    --Dave B.
>>>
>>> On 03/18/2015 07:00 AM, Peter Cock wrote:
>>>>
>>>> ... I can also confirm that the Test Tool Shed example I
>>>> gave was tested overnight, although it looks like a novel failure:
>>>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
>>>>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

Peter Cock
On Mon, Mar 23, 2015 at 1:07 PM, John Chilton <[hidden email]> wrote:
> It seems to be happening during upload - so it is not unsurprising
> that this error would affect multiple tools. I have checked out the
> exact revision registered in the tests and the uploads seem fine to
> me.

You mean during the test-data upload at the start of running a test?

> I am having trouble imagining a deployment problem short of an invalid
> upload tool that might result in this error. Dave B, is it possible
> that a problematic datatype is being installed by some repository and
> affecting unrelated tools?

That sounds like a believable scenario. However, if this was a
problem in a specific datatype (even one not being used, but
referenced via the sniffer configuration), I'm at lost to explain
the division between failures and passes. e.g. these both take
just FASTA input and return just tabular output:

Failed:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus

Passed:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh

I suspect this is specific to select parameters (from the exception)
and my hunch is this is a regression from the recent work on
grouping parameters (again, pointed to by the exception).

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?

Peter Cock
In reply to this post by Peter Cock
On Mon, Mar 23, 2015 at 12:27 PM, Peter Cock <[hidden email]> wrote:
Hi Dave,

These tools do not seem to have been tested on the TestToolShed
since 2015-03-18. Does something need resetting/unblocking again?

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:
  https://lists.galaxyproject.org/

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