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