Re: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh
Thanks for your answers !
I will try ./run_tests.sh -installed and see if it can solve the 2
first points. By the way, I didn't know this option (not displayed with
run_tests.sh --help) or documented on the wiki if I'm not mistaken.
For point 3, I'll try the new planemo shed_test subcommand. The
subcommand planemo test uses the run_tests.sh script, isn't it ? Does
the planemo shed_test subcommand use all or any part of the Tool Shed
Install and Test Framework
(https://wiki.galaxyproject.org/AutomatedToolTests) or is it completely
different ?
Is there any way to launch the tool tests against an external server
(point 4) with Planemo ?
Loraine
Le 02/06/2015 15:16, John Chilton a écrit :
On Tue, Jun 2, 2015 at 4:14 AM, Loraine Guéguen
loraine.gueg...@sb-roscoff.fr wrote:
Hi,
I have investigated the testing possibilities within a Galaxy local instance
and within a toolshed. I met some difficulties and I have 4 questions listed
below.
1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
It seems that it is only possible to test the tools that have been manually
installed (run_test.sh -id ...), not the tools that have been installed
through a toolshed. Is that true ? When I try to launch the tests of a
toolshed installed tool, I have the following error message :
#
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
==
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
--
Traceback (most recent call last):
File
/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py,
line 39, in runTest
raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger
--
Ran 1 test in 0.002s
FAILED (errors=1)
./run_tests.sh -installed runs the tests of all installed tool shed
tools. It might be possible to combine that with -id - for a specific
tool but I am not sure. It may be possible to construct that test even
if -id doesn't work - but it is probably pretty hacky. Let me know if
-installed works for you but not when combined with -id and we can
work out the details.
#
2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
Is it possible to test tools which have repository or tool dependencies ? I
have a tool (manually installed in galaxy-dist/tools/) with a dependence to
a datatype installed from a toolshed. The datatype (no_unzip.zip) is defined
in the param input tag (in test) with attribute ftype. When running
run_tests.sh, it seems that the dataype is not known :
#
==
ERROR: test_tool_01 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger ) Test-2
--
Traceback (most recent call last):
File
/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, line
268, in test_tool
self.do_it( td )
File
/w/galaxy/galaxy4loraine/galaxy-dist/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 /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
36, in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': uAn
invalid option was selected for file_type, u'no_unzip.zip', please verify.,
u'files_metadata': [uAn invalid option was selected for file_type,
u'no_unzip.zip', please verify.]}}}
#
It is possible it is the case that tool shed datatypes are not loaded
unless running with the -installed flag. I would either setup the
tests to run locally (manually add datatypes and tools) or run
installed tools with -installed.
3- Toolshed Install and Test framework (
install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if
I don't explicitely defined the dbkey attribute to unknown (dbkey=?) in
the param input tag (in test). The default dbkey value seems to be
hg17 (whereas hg17 is not defined on the server running my toolshed). So I
have the following error message if I don't add dbkey=? in test :
#
==
ERROR: test_tool_01
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR (
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
Test-2
Re: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh
Hi,
I am relatively new to Galaxy so if you get a difference answer from a core
developer consider that one.
Personally I never got the run_test.sh -id ...) to run but I did use
planemo
http://planemo.readthedocs.org/en/latest/readme.html
With success. It is much easier, does not need the tool to be installed in a
local galaxy to test.
It does require the tool xml config file
See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
And depends on their being a tests section.
See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Christian
University of Manchester
PS. I am not a developer of Planemo just a user so please keep all question on
this mailing list
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Loraine Guéguen [loraine.gueg...@sb-roscoff.fr]
Sent: Tuesday, June 02, 2015 9:14 AM
To: Galaxy Dev List
Subject: [galaxy-dev] errors and questions with run_tests.sh and
install_and_test_tool_shed_repositories.sh
Hi,
I have investigated the testing possibilities within a Galaxy local instance
and within a toolshed. I met some difficulties and I have 4 questions listed
below.
1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) : It
seems that it is only possible to test the tools that have been manually
installed (run_test.sh -id ...), not the tools that have been installed through
a toolshed. Is that true ? When I try to launch the tests of a toolshed
installed tool, I have the following error message :
#
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
==
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
--
Traceback (most recent call last):
File
/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py,
line 39, in runTest
raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger
--
Ran 1 test in 0.002s
FAILED (errors=1)
#
2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) : Is
it possible to test tools which have repository or tool dependencies ? I have a
tool (manually installed in galaxy-dist/tools/) with a dependence to a datatype
installed from a toolshed. The datatype (no_unzip.zip) is defined in the
param input tag (in test) with attribute ftype. When running
run_tests.sh, it seems that the dataype is not known :
#
==
ERROR: test_tool_01 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger ) Test-2
--
Traceback (most recent call last):
File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py,
line 268, in test_tool
self.do_it( td )
File /w/galaxy/galaxy4loraine/galaxy-dist/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 /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line 36,
in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': uAn
invalid option was selected for file_type, u'no_unzip.zip', please verify.,
u'files_metadata': [uAn invalid option was selected for file_type,
u'no_unzip.zip', please verify.]}}}
#
3- Toolshed Install and Test framework (
install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if I
don't explicitely defined the dbkey attribute to unknown (dbkey=?) in the
param input tag (in test). The default dbkey value seems to be hg17
(whereas hg17 is not defined on the server running my toolshed). So I have the
following error message if I don't add dbkey=? in test :
#
==
ERROR: test_tool_01
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR (
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
Test-2
--
Traceback (most recent call last):
File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py,
line 268, in test_tool
self.do_it( td )
File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py,
line 37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
Re: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh
On Tue, Jun 2, 2015 at 4:14 AM, Loraine Guéguen
loraine.gueg...@sb-roscoff.fr wrote:
Hi,
I have investigated the testing possibilities within a Galaxy local instance
and within a toolshed. I met some difficulties and I have 4 questions listed
below.
1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
It seems that it is only possible to test the tools that have been manually
installed (run_test.sh -id ...), not the tools that have been installed
through a toolshed. Is that true ? When I try to launch the tests of a
toolshed installed tool, I have the following error message :
#
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
==
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
--
Traceback (most recent call last):
File
/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py,
line 39, in runTest
raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger
--
Ran 1 test in 0.002s
FAILED (errors=1)
./run_tests.sh -installed runs the tests of all installed tool shed
tools. It might be possible to combine that with -id - for a specific
tool but I am not sure. It may be possible to construct that test even
if -id doesn't work - but it is probably pretty hacky. Let me know if
-installed works for you but not when combined with -id and we can
work out the details.
#
2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
Is it possible to test tools which have repository or tool dependencies ? I
have a tool (manually installed in galaxy-dist/tools/) with a dependence to
a datatype installed from a toolshed. The datatype (no_unzip.zip) is defined
in the param input tag (in test) with attribute ftype. When running
run_tests.sh, it seems that the dataype is not known :
#
==
ERROR: test_tool_01 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger ) Test-2
--
Traceback (most recent call last):
File
/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, line
268, in test_tool
self.do_it( td )
File
/w/galaxy/galaxy4loraine/galaxy-dist/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 /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
36, in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': uAn
invalid option was selected for file_type, u'no_unzip.zip', please verify.,
u'files_metadata': [uAn invalid option was selected for file_type,
u'no_unzip.zip', please verify.]}}}
#
It is possible it is the case that tool shed datatypes are not loaded
unless running with the -installed flag. I would either setup the
tests to run locally (manually add datatypes and tools) or run
installed tools with -installed.
3- Toolshed Install and Test framework (
install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if
I don't explicitely defined the dbkey attribute to unknown (dbkey=?) in
the param input tag (in test). The default dbkey value seems to be
hg17 (whereas hg17 is not defined on the server running my toolshed). So I
have the following error message if I don't add dbkey=? in test :
#
==
ERROR: test_tool_01
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR (
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
Test-2
--
Traceback (most recent call last):
File
/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, line
268, in test_tool
self.do_it( td )
File
/w/galaxy/galaxy4loraine/galaxy-dist/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 /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line
36, in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
File
