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

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