Re: [galaxy-dev] Tool Shed Tests failing with sniffer/ftype problem
Retitling thread to focus on a regression in the (Tool Shed) test framework to do with input file types and sniffers. On Thu, Aug 1, 2013 at 11:47 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
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.
Hi Dave,
The seq_rename test results (apparently) from last night are still failing, http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
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.
Same issue here?,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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.
And another case which looks the same, http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120 AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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. Note that for the nlstradamus and effectivet3 tests this is using an empty FASTA file with no sequences in it, so the sniffer will not be able guess this is a FASTA file - which is why the tool text gives the ftype explicitly. I originally used a literally empty fasta file (0 bytes) but as I recall the (non-Tool Shed) framework at the time didn't like me doing that in the test framework, so this empty.fasta file just has a couple of blank lines in it. I am testing with empty FASTA files deliberately - they can often occur in gene/protein selection pipelines where an early part of the pipeline is stringent enough to reject all the sequences. However, the seq_rename sniffer problem is not to do with an 'empty' fasta file - it uses a non-empty tabular file. My guess is somewhere in the test framework the ftype attribute is being lost. This is still working locally, $ ./run_functional_tests.sh -id seq_rename $ ./run_functional_tests.sh -id nlstradamus $ ./run_functional_tests.sh -id effectiveT3 Regards, Peter
Peter, I have been able to duplicate the error on nlstradamus, and hope to have a fix out soon. --Dave B. On 8/1/13 07:21:17.000, Peter Cock wrote:
Retitling thread to focus on a regression in the (Tool Shed) test framework to do with input file types and sniffers.
On Thu, Aug 1, 2013 at 11:47 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
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.
Hi Dave,
The seq_rename test results (apparently) from last night are still failing, http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
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.
Same issue here?,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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.
And another case which looks the same,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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.
Note that for the nlstradamus and effectivet3 tests this is using an empty FASTA file with no sequences in it, so the sniffer will not be able guess this is a FASTA file - which is why the tool text gives the ftype explicitly.
I originally used a literally empty fasta file (0 bytes) but as I recall the (non-Tool Shed) framework at the time didn't like me doing that in the test framework, so this empty.fasta file just has a couple of blank lines in it.
I am testing with empty FASTA files deliberately - they can often occur in gene/protein selection pipelines where an early part of the pipeline is stringent enough to reject all the sequences.
However, the seq_rename sniffer problem is not to do with an 'empty' fasta file - it uses a non-empty tabular file.
My guess is somewhere in the test framework the ftype attribute is being lost. This is still working locally,
$ ./run_functional_tests.sh -id seq_rename $ ./run_functional_tests.sh -id nlstradamus $ ./run_functional_tests.sh -id effectiveT3
Regards,
Peter
Peter, As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results. As for seq_rename, it looks like the columns in four_human_proteins.rename.tabular are not being detected correctly, even though they are tab separated. I'll continue to investigate, and let you know what I discover. --Dave B. On 8/1/13 12:52:01.000, Dave Bouvier wrote:
Peter,
I have been able to duplicate the error on nlstradamus, and hope to have a fix out soon.
--Dave B.
On 8/1/13 07:21:17.000, Peter Cock wrote:
Retitling thread to focus on a regression in the (Tool Shed) test framework to do with input file types and sniffers.
On Thu, Aug 1, 2013 at 11:47 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
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.
Hi Dave,
The seq_rename test results (apparently) from last night are still failing, http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
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.
Same issue here?,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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.
And another case which looks the same,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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.
Note that for the nlstradamus and effectivet3 tests this is using an empty FASTA file with no sequences in it, so the sniffer will not be able guess this is a FASTA file - which is why the tool text gives the ftype explicitly.
I originally used a literally empty fasta file (0 bytes) but as I recall the (non-Tool Shed) framework at the time didn't like me doing that in the test framework, so this empty.fasta file just has a couple of blank lines in it.
I am testing with empty FASTA files deliberately - they can often occur in gene/protein selection pipelines where an early part of the pipeline is stringent enough to reject all the sequences.
However, the seq_rename sniffer problem is not to do with an 'empty' fasta file - it uses a non-empty tabular file.
My guess is somewhere in the test framework the ftype attribute is being lost. This is still working locally,
$ ./run_functional_tests.sh -id seq_rename $ ./run_functional_tests.sh -id nlstradamus $ ./run_functional_tests.sh -id effectiveT3
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/
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results.
Great - so this was a sniffer bug for the twobit format going wrong, https://bitbucket.org/galaxy/galaxy-central/commits/d34d6d1da813bfa6e318b0ce...
As for seq_rename, it looks like the columns in four_human_proteins.rename.tabular are not being detected correctly, even though they are tab separated. I'll continue to investigate, and let you know what I discover.
--Dave B.
I was assuming (wrongly perhaps) that if the tool XML for the test defined an ftype this would be used as the datatype - overriding any sniffer guess (or even skipping the sniffer tests). (You can think of this a like testing the process where a user has uploaded a given file and manually overridden the datatype.) i.e. It is good that this issue has apparently uncovered some sniffer bugs, but that doesn't seem to be the root issue. Thanks, Peter
Peter, As it turns out, the automated testing framework was not correctly handling the situation where dataset metadata is set externally. I've committed a fix for that in 10295:59243394031a, and this should result in seq_rename now being correctly tested. When it comes to the sniffer situation, I've created a trello card for that issue, where you can track the status: https://trello.com/c/eCRFKVkt/1024-when-a-file-is-uploaded-upload-py-runs-it... --Dave B. On 8/2/13 05:14:54.000, Peter Cock wrote:
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results.
Great - so this was a sniffer bug for the twobit format going wrong, https://bitbucket.org/galaxy/galaxy-central/commits/d34d6d1da813bfa6e318b0ce...
As for seq_rename, it looks like the columns in four_human_proteins.rename.tabular are not being detected correctly, even though they are tab separated. I'll continue to investigate, and let you know what I discover.
--Dave B.
I was assuming (wrongly perhaps) that if the tool XML for the test defined an ftype this would be used as the datatype - overriding any sniffer guess (or even skipping the sniffer tests).
(You can think of this a like testing the process where a user has uploaded a given file and manually overridden the datatype.)
i.e. It is good that this issue has apparently uncovered some sniffer bugs, but that doesn't seem to be the root issue.
Thanks,
Peter
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results. As for seq_rename, ...
--Dave B.
Hi Dave, That fix is on galaxy-central and the Test Tool Shed, and my tests have been passing there :) However, the tests are currently still failing on the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 The commit for your fix is on the galaxy-central default branch, https://bitbucket.org/galaxy/galaxy-dist/commits/d34d6d1da813 https://bitbucket.org/galaxy/galaxy-dist/src/default/lib/galaxy/datatypes/bi... The fix is not on the stable branch: https://bitbucket.org/galaxy/galaxy-dist/src/stable/lib/galaxy/datatypes/bin... Nor is the fix on the next-stable branch, https://bitbucket.org/galaxy/galaxy-dist/src/next-stable/lib/galaxy/datatype... I'm not quite sure how fixes like this are propagated from galaxy-central to the stable branches on galaxy-dist, but has this been forgotten about? Thanks, Peter
On Fri, Oct 11, 2013 at 10:01 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results. As for seq_rename, ...
--Dave B.
Hi Dave,
That fix is on galaxy-central and the Test Tool Shed, and my tests have been passing there :)
However, the tests are currently still failing on the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
The commit for your fix is on the galaxy-central default branch, https://bitbucket.org/galaxy/galaxy-dist/commits/d34d6d1da813 https://bitbucket.org/galaxy/galaxy-dist/src/default/lib/galaxy/datatypes/bi...
The fix is not on the stable branch: https://bitbucket.org/galaxy/galaxy-dist/src/stable/lib/galaxy/datatypes/bin...
Nor is the fix on the next-stable branch, https://bitbucket.org/galaxy/galaxy-dist/src/next-stable/lib/galaxy/datatype...
I'm not quite sure how fixes like this are propagated from galaxy-central to the stable branches on galaxy-dist, but has this been forgotten about?
Thanks,
Peter
It does appear to have been forgotten about - now that the main Tool Shed is running next-stable in preparation for tentative 4 Nov release, I am seeing these sniffer related test failures once again :( http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus Tool test results Automated test environment Tests that passed successfully Tool id: nlstradamus Tool version: nlstradamus Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8) Tests that failed Tool id: nlstradamus Tool version: nlstradamus Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-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-main-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-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1327, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 Tool test results Automated test environment Tests that passed successfully Tool id: effectiveT3 Tool version: effectiveT3 Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12) Tests that failed Tool id: effectiveT3 Tool version: effectiveT3 Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-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-main-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-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1327, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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. Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1193, in submit_form for value in kwd[ control.name ]: KeyError: 'restrict|type' base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: (That looks like an extra Twill debug logging line as well) Regards, Peter
Peter, The testing framework was running the stable branch for the main tool shed when those repositories were tested. I've updated it to use next-stable until stable is updated. --Dave B. On 10/24/2013 09:34 AM, Peter Cock wrote:
On Fri, Oct 11, 2013 at 10:01 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results. As for seq_rename, ...
--Dave B.
Hi Dave,
That fix is on galaxy-central and the Test Tool Shed, and my tests have been passing there :)
However, the tests are currently still failing on the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
The commit for your fix is on the galaxy-central default branch, https://bitbucket.org/galaxy/galaxy-dist/commits/d34d6d1da813 https://bitbucket.org/galaxy/galaxy-dist/src/default/lib/galaxy/datatypes/bi...
The fix is not on the stable branch: https://bitbucket.org/galaxy/galaxy-dist/src/stable/lib/galaxy/datatypes/bin...
Nor is the fix on the next-stable branch, https://bitbucket.org/galaxy/galaxy-dist/src/next-stable/lib/galaxy/datatype...
I'm not quite sure how fixes like this are propagated from galaxy-central to the stable branches on galaxy-dist, but has this been forgotten about?
Thanks,
Peter
It does appear to have been forgotten about - now that the main Tool Shed is running next-stable in preparation for tentative 4 Nov release, I am seeing these sniffer related test failures once again :(
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
Tool test results Automated test environment Tests that passed successfully Tool id: nlstradamus Tool version: nlstradamus Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8) Tests that failed Tool id: nlstradamus Tool version: nlstradamus Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-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-main-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-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1327, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
Tool test results Automated test environment Tests that passed successfully Tool id: effectiveT3 Tool version: effectiveT3 Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12) Tests that failed Tool id: effectiveT3 Tool version: effectiveT3 Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12) Stderr: Traceback: Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-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-main-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-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1327, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'fasta_file' to value '['empty.fasta']' in form 'tool_form' threw exception: cannot find value/label "empty.fasta" in list control control: <SelectControl(fasta_file=[])> 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. Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1193, in submit_form for value in kwd[ control.name ]: KeyError: 'restrict|type' base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG: base.twilltestcase: DEBUG:
(That looks like an extra Twill debug logging line as well)
Regards,
Peter
participants (2)
-
Dave Bouvier -
Peter Cock