Tool Shed test framework breaking where run_functional_tests.sh works
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right
yet):
...
This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail: Tests that failed *Tool id:* seq_rename *Tool version:* seq_rename *Test:*test_tool_000000 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 ) *Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. *Tool id:* seq_rename *Tool version:* seq_rename *Test:*test_tool_000001 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 ) *Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. Both tests fail with the following assertion: AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. Both tests pass on my development machine run via: $ ./run_functional_tests.sh -id seq_rename The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant: <tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests> I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html Peter
On Thu, May 9, 2013 at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet):
...
This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail:
...
Both tests fail with the following assertion:
AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests pass on my development machine run via:
$ ./run_functional_tests.sh -id seq_rename
The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant:
<tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests>
I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.htm
Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass). Peter
Peter, I have duplicated this discrepancy in my local environment, and will be looking into the cause. I hope to have it resolved in short order. --Dave B. On 5/9/13 06:06:16.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet):
...
This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail:
...
Both tests fail with the following assertion:
AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests pass on my development machine run via:
$ ./run_functional_tests.sh -id seq_rename
The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant:
<tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests>
I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.htm
Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass).
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/
Peter, As of my latest commit, the automated test results should now match that of run_functional_tests.sh. --Dave B. On 5/9/13 06:06:16.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet):
...
This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail:
...
Both tests fail with the following assertion:
AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests pass on my development machine run via:
$ ./run_functional_tests.sh -id seq_rename
The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant:
<tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests>
I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.htm
Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass).
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/
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of my latest commit, the automated test results should now match that of run_functional_tests.sh.
--Dave B.
Thanks Dave, Presumably once the Test Tool Shed is updated, all the old tests will be re-run, and so I should see the revised results for this tool then? Peter
That is correct, the tests are run nightly, some time after midnight eastern US time, unless I manually initiate the testing process. --Dave B. On 5/10/13 05:36:41.000, Peter Cock wrote:
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of my latest commit, the automated test results should now match that of run_functional_tests.sh.
--Dave B.
Thanks Dave,
Presumably once the Test Tool Shed is updated, all the old tests will be re-run, and so I should see the revised results for this tool then?
Peter
Is there a more optimal time to initiate this testing process to better accommodate those in other time zones? If anyone is waiting for the nightly test results, we should tweak cron so no waiting is necessary (if possible). On May 10, 2013, at 8:53 AM, Dave Bouvier wrote:
That is correct, the tests are run nightly, some time after midnight eastern US time, unless I manually initiate the testing process.
--Dave B.
On 5/10/13 05:36:41.000, Peter Cock wrote:
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of my latest commit, the automated test results should now match that of run_functional_tests.sh.
--Dave B.
Thanks Dave,
Presumably once the Test Tool Shed is updated, all the old tests will be re-run, and so I should see the revised results for this tool then?
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/
Buildbot can be triggered here http://buildbot.g2.bx.psu.edu/builders/central-py2.7-linux-x86_64-postgres manually I think. On Fri, May 10, 2013 at 10:56 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Is there a more optimal time to initiate this testing process to better accommodate those in other time zones? If anyone is waiting for the nightly test results, we should tweak cron so no waiting is necessary (if possible).
On May 10, 2013, at 8:53 AM, Dave Bouvier wrote:
That is correct, the tests are run nightly, some time after midnight eastern US time, unless I manually initiate the testing process.
--Dave B.
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of my latest commit, the automated test results should now match
On 5/10/13 05:36:41.000, Peter Cock wrote: that of
run_functional_tests.sh.
--Dave B.
Thanks Dave,
Presumably once the Test Tool Shed is updated, all the old tests will be re-run, and so I should see the revised results for this tool then?
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of my latest commit, the automated test results should now match that of run_functional_tests.sh.
--Dave B.
Hi Dave, This problem seems to have returned since then (unless this time instead of missing test output I'm seeing stale test output?): http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9<http://testtoolshed.g2.bx.psu.edu/repository/view_changelog?id=cd0d8ada19d98f27> --> http://testtoolshed.g2.bx.psu.edu/repository?repository_id=cd0d8ada19d98f27&changeset_revision=16a1a5ae98e9 Peter Tool test results Automated test environment *Time tested:* ~ 7 hours ago*System:* Linux 3.5.0-21-generic*Architecture:* x86_64*Python version:* 2.7.3*Galaxy revision:* 9754:311cf2ae1623*Galaxy database version:* 115*Tool shed revision:* 9753:53d3c967d373*Tool shed database version:* 19*Tool shed mercurial version:* 2.2.3 Tests that failed *Tool id:* seq_rename*Tool version:* seq_rename*Test:* test_tool_000000 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 )*Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1337, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1286, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.*Tool id:* seq_rename*Tool version:* seq_rename*Test:* test_tool_000001 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 )*Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1337, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1286, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Peter, That test output does look wrong, but wrong in a way that suggests a new issue has been uncovered. I'll work on tracking it down as soon as I can. --Dave B. On 5/16/13 11:05:56.000, Peter Cock wrote:
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier <dave@bx.psu.edu <mailto:dave@bx.psu.edu>> wrote:
Peter,
As of my latest commit, the automated test results should now match that of run_functional_tests.sh.
--Dave B.
Hi Dave,
This problem seems to have returned since then (unless this time instead of missing test output I'm seeing stale test output?):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 <http://testtoolshed.g2.bx.psu.edu/repository/view_changelog?id=cd0d8ada19d98f27>
-->
Peter
Tool test results Automated test environment *Time tested:* ~ 7 hours ago *System:* Linux 3.5.0-21-generic *Architecture:* x86_64 *Python version:* 2.7.3 *Galaxy revision:* 9754:311cf2ae1623 *Galaxy database version:* 115 *Tool shed revision:* 9753:53d3c967d373 *Tool shed database version:* 19 *Tool shed mercurial version:* 2.2.3
Tests that failed *Tool id:* seq_rename *Tool version:* seq_rename *Test:* test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 <http://functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3>)
*Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id <http://testdef.tool.id>, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1337, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1286, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
*Tool id:* seq_rename *Tool version:* seq_rename *Test:* test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 <http://functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3>)
*Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id <http://testdef.tool.id>, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1337, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1286, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Hi, I also have that error in the latest toolshed: AssertionError: Attempting to set field 'topology' to value '['-c']' in form 'tool_form' threw exception: multiple matches to value/label "c" in list control control: <SelectControl(topology=[-c, -l])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. http://testtoolshed.g2.bx.psu.edu/view/bgruening/trna_prediction Any hint on how to resolve that, or is it a recent regression? Cheers, Björn
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite
right yet):
...
This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via
run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail:
Tests that failed Tool id: seq_rename Tool version: seq_rename Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3) Stderr:
Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. Tool id: seq_rename Tool version: seq_rename Test: test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3) Stderr:
Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests fail with the following assertion:
AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests pass on my development machine run via:
$ ./run_functional_tests.sh -id seq_rename
The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant:
<tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests>
I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html
Peter
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Hi Dave, Did a Trello card get filled for this problem of failing tests on the Tool Shed? Thanks, Peter On Tue, Jun 11, 2013 at 9:04 AM, Björn Grüning <bjoern@gruenings.eu> wrote:
Hi,
I also have that error in the latest toolshed:
AssertionError: Attempting to set field 'topology' to value '['-c']' in form 'tool_form' threw exception: multiple matches to value/label "c" in list control control: <SelectControl(topology=[-c, -l])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
http://testtoolshed.g2.bx.psu.edu/view/bgruening/trna_prediction
Any hint on how to resolve that, or is it a recent regression?
Cheers, Björn
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Here's the output from the (Test) Tool Shed where the tests fail:
Tests that failed Tool id: seq_rename Tool version: seq_rename Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3) Stderr:
Traceback: Traceback (most recent call last): File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set. Tool id: seq_rename Tool version: seq_rename Test: test_tool_000001
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3) Stderr:
Traceback: Traceback (most recent call last): File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests fail with the following assertion:
AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: <SelectControl(new_column=[1])> If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.
Both tests pass on my development machine run via:
$ ./run_functional_tests.sh -id seq_rename
The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant:
<tests> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="1" /> <param name="new_column" value="2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> <test> <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> <param name="old_column" value="c1" /> <param name="new_column" value="c2" /> <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> </test> </tests>
I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html
Peter
On Mon, Jul 29, 2013 at 2:49 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
Did a Trello card get filled for this problem of failing tests on the Tool Shed?
Thanks,
Peter
For anyone following this issue, on another thread Dave just replied:
Peter,
The issue with seq_rename incorrectly failing functional tests has been resolved in 10266:fe04978dadac, and the test results will be corrected the next time the automated testing framework runs. I'm still looking into the other issues you reported.
--Dave B.
https://bitbucket.org/galaxy/galaxy-central/commits/fe04978dadac9974ab1954ab... Thank you, Peter
participants (5)
-
Björn Grüning -
Dave Bouvier -
Greg Von Kuster -
Peter Cock -
Ross