Hi all,
I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed).
This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097
Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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 108, 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 35, 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 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, 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 53, in verify_output self.wait_for_history( history_id, maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 2453, in wait_for result = func() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in <lambda> self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 257, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state.
Is a more detailed log available which might help debug this?
Thanks,
Peter
As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests?
Peter,
I believe part of the problem is that the install and test framework is unable to resolve the dependency on blast+ 2.2.29 because it is defined as a repository dependency, not a tool dependency. I would recommend replacing the repository dependency in the blast_rbh repository with a tool dependency definition that references package_blast_plus_2_2_29.
--Dave B. On 07/30/2014 05:27 AM, Peter Cock wrote:
Hi all,
I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed).
This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097
Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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 108, 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 35, 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 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, 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 53, in verify_output self.wait_for_history( history_id, maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 2453, in wait_for result = func() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in <lambda> self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 257, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state.
Is a more detailed log available which might help debug this?
Thanks,
Peter
As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests? ___________________________________________________________ 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/
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml and repository_dependencies.xml *again*. Evidentially my mental model does not match Greg's here:
(*) I need to define a tool installation recipe for something not in the Tool Shed --> write an install script called tool_dependencies.xml
(*) I need to depend on a Python package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
(*) I need to depend on a datatype package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
(*) I need to depend on a binary package by pointing at another repository in the Tool Shed --> repository_dependencies.xml ? No. You need tool_dependencies.xml for this too.
But that aside, the test framework error here is completely unhelpful.
Why is there no error message about missing a dependency? Was there an error from running my tool which was not shown?
Thanks,
Peter
On Wed, Jul 30, 2014 at 6:07 PM, Dave Bouvier dave@bx.psu.edu wrote:
Peter,
I believe part of the problem is that the install and test framework is unable to resolve the dependency on blast+ 2.2.29 because it is defined as a repository dependency, not a tool dependency. I would recommend replacing the repository dependency in the blast_rbh repository with a tool dependency definition that references package_blast_plus_2_2_29.
--Dave B.
On 07/30/2014 05:27 AM, Peter Cock wrote:
Hi all,
I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed).
This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097
Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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 108, 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 35, 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 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, 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 53, in verify_output self.wait_for_history( history_id, maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 2453, in wait_for result = func() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in <lambda> self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 257, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state.
Is a more detailed log available which might help debug this?
Thanks,
Peter
As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests? ___________________________________________________________ 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/
Hi Peter,
2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.cock@googlemail.com:
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml and repository_dependencies.xml *again*. Evidentially my mental model does not match Greg's here:
(*) I need to define a tool installation recipe for something not in the Tool Shed --> write an install script called tool_dependencies.xml
(*) I need to depend on a Python package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
I might be wrong, but I think that also goes to tool_dependencies.xml
(*) I need to depend on a datatype package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
(*) I need to depend on a binary package by pointing at another repository in the Tool Shed --> repository_dependencies.xml ? No. You need tool_dependencies.xml for this too
As far as I understood, everything that is referenced in the tool.xml under the requirement section, needs to be in a tool_dependencies.xml file. Any other dependency are from the repository (data_types, data_manager, workflows ...).
Ciao, Bjoern
But that aside, the test framework error here is completely unhelpful.
Why is there no error message about missing a dependency? Was there an error from running my tool which was not shown?
Thanks,
Peter
On Wed, Jul 30, 2014 at 6:07 PM, Dave Bouvier dave@bx.psu.edu wrote:
Peter,
I believe part of the problem is that the install and test framework is unable to resolve the dependency on blast+ 2.2.29 because it is defined
as a
repository dependency, not a tool dependency. I would recommend replacing the repository dependency in the blast_rbh repository with a tool
dependency
definition that references package_blast_plus_2_2_29.
--Dave B.
On 07/30/2014 05:27 AM, Peter Cock wrote:
Hi all,
I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed).
This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097
Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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 108, 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 35, 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 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, 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 53, in verify_output self.wait_for_history( history_id, maxseconds ) File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 2453, in wait_for result = func() File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 107, in <lambda> self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 257, in __history_ready return self._state_ready( state, error_msg="History in error
state."
) File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state.
Is a more detailed log available which might help debug this?
Thanks,
Peter
As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests? ___________________________________________________________ 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 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/
On Thu, Jul 31, 2014 at 5:21 PM, bjoern.gruening@googlemail.com bjoern.gruening@gmail.com wrote:
Hi Peter,
2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.cock@googlemail.com:
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml and repository_dependencies.xml *again*. Evidentially my mental model does not match Greg's here:
(*) I need to define a tool installation recipe for something not in the Tool Shed --> write an install script called tool_dependencies.xml
(*) I need to depend on a Python package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
I might be wrong, but I think that also goes to tool_dependencies.xml
Correct, e.g. https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id
Thanks!
(*) I need to depend on a datatype package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
(*) I need to depend on a binary package by pointing at another repository in the Tool Shed --> repository_dependencies.xml ? No. You need tool_dependencies.xml for this too
As far as I understood, everything that is referenced in the tool.xml under the requirement section, needs to be in a tool_dependencies.xml file. Any other dependency are from the repository (data_types, data_manager, workflows ...).
Ciao, Bjoern
Sure, there is a logic here - but its a definition which I seem to still struggle with :(
But that aside, the test framework error here is completely unhelpful.
Why is there no error message about missing a dependency? Was there an error from running my tool which was not shown?
Thanks,
Peter
I'd still like to get a more explicit error from the test suite than "History in error state" though ;)
Regards,
Peter
On Thu, Jul 31, 2014 at 12:29 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Jul 31, 2014 at 5:21 PM, bjoern.gruening@googlemail.com bjoern.gruening@gmail.com wrote:
Hi Peter,
2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.cock@googlemail.com:
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml and repository_dependencies.xml *again*. Evidentially my mental model does not match Greg's here:
(*) I need to define a tool installation recipe for something not in the Tool Shed --> write an install script called tool_dependencies.xml
(*) I need to depend on a Python package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
I might be wrong, but I think that also goes to tool_dependencies.xml
Correct, e.g. https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id
Thanks!
(*) I need to depend on a datatype package by pointing at another repository in the Tool Shed --> repository_dependencies.xml
(*) I need to depend on a binary package by pointing at another repository in the Tool Shed --> repository_dependencies.xml ? No. You need tool_dependencies.xml for this too
As far as I understood, everything that is referenced in the tool.xml under the requirement section, needs to be in a tool_dependencies.xml file. Any other dependency are from the repository (data_types, data_manager, workflows ...).
Ciao, Bjoern
Sure, there is a logic here - but its a definition which I seem to still struggle with :(
But that aside, the test framework error here is completely unhelpful.
Why is there no error message about missing a dependency? Was there an error from running my tool which was not shown?
Thanks,
Peter
I'd still like to get a more explicit error from the test suite than "History in error state" though ;)
Yes - that is problematic.
Dave B - can we set GALAXY_TEST_VERBOSE_ERRORS to "True" in the environment of the install and test framework? I disabled it by default because it causes to sqlite to fallover rather frequently - but if install and test framework is backed by a postgres database this is probably not a problem.
-John
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/
galaxy-dev@lists.galaxyproject.org
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bjoern.gruening＠googlemail.com -
Dave Bouvier -
John Chilton -
Peter Cock