Hi Peter, The Amazon EC2 instance ran out of memory in last night's run which resulted in the missing test results for some repositories as well as the issue you've documented below. We're looking into the cause of this and will have it resolved (see Trello card from my previousl email).
Thanks, Greg Von Kuster On Oct 22, 2013, at 5:48 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hi Dave, Greg, > > Based on my tool's overnight test results from the Test Tool Shed, > something seems to have been broken to do with sniffing datatypes > on upload. > > e.g. using blastxml format, > http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr > > Tool test results > Automated test environment > Tests that failed > Tool id: blastxml_to_top_descr > Tool version: blastxml_to_top_descr > Test: test_tool_000000 > (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.0.9) > 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 1327, 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 1276, in submit_form > raise AssertionError( errmsg ) > AssertionError: Attempting to set field 'blastxml_file' to value > '['blastp_four_human_vs_rhodopsin.xml']' in form 'tool_form' threw > exception: cannot find value/label "blastp_four_human..odopsin.xml" in > list control > control: <SelectControl(blastxml_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-test-tool-shed-py27/build/lib/galaxy/jobs/runners/local.py", > line 83, in queue_job > preexec_fn = os.setpgrp ) > File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ > errread, errwrite) > File "/usr/lib/python2.7/subprocess.py", line 1205, in _execute_child > self.pid = os.fork() > OSError: [Errno 12] Cannot allocate memory > base.twilltestcase: DEBUG: > base.twilltestcase: DEBUG: > base.twilltestcase: DEBUG: > base.twilltestcase: DEBUG: > base.twilltestcase: DEBUG: > base.twilltestcase: DEBUG: > > > e.g. just fasta and tabular, > > Tool test results > Automated test environment > Tests that failed > Tool id: seq_primer_clip > Tool version: seq_primer_clip > Test: test_tool_000000 > (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_primer_clip/seq_primer_clip/0.0.10) > 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 1327, 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 1276, in submit_form > raise AssertionError( errmsg ) > AssertionError: Attempting to set field 'primer_fasta' to value > '['dop_primers.fasta']' in form 'tool_form' threw exception: cannot > find value/label "dop_primers.fasta" in list control > control: <SelectControl(primer_fasta=[])> > 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-test-tool-shed-py27/build/lib/galaxy/jobs/runners/local.py", > line 83, in queue_job > preexec_fn = os.setpgrp ) > File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ > errread, errwrite) > File "/usr/lib/python2.7/subprocess.py", line 1205, in _execute_child > self.pid = os.fork() > OSError: [Errno 12] Cannot allocate memory > galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 381 > galaxy.jobs: DEBUG: (381) Working directory for job is: > /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/database/job_working_directory/000/381 > galaxy.jobs.handler: DEBUG: (381) Dispatching to local runner > galaxy.jobs: DEBUG: (381) Persisting job destination (destination id: local) > galaxy.jobs.handler: INFO: (381) Job dispatched > galaxy.tools.deps: DEBUG: Building dependency shell command for > dependency 'samtools' > galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', > ignoring > galaxy.jobs.runners.local: DEBUG: (381) executing: export > GALAXY_SLOTS="1"; python > /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/tools/data_source/upload.py > /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build > /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpDEZCBr/tmpG8dIQ8 > /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpDEZCBr/tmpMD8cHQ > > 404:/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/database/job_working_directory/000/381/dataset_404_files:/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpALDdhE/database/files/000/dataset_404.dat > galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files > galaxy.jobs.runners.local: ERROR: failure running job 381 > Traceback (most recent call last): > File > "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/local.py", > line 83, in queue_job > preexec_fn = os.setpgrp ) > File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ > errread, errwrite) > File "/usr/lib/python2.7/subprocess.py", line 1205, in _execute_child > self.pid = os.fork() > OSError: [Errno 12] Cannot allocate memory > 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: > > (snip - first test only, rest do the same). > > 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/ ___________________________________________________________ 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/
