Python 2.6 ElementTree breaks linting SyntaxError: expected path separator ([) #371
Description
Problem found with planemo lint and planemo shed_lint and something in my MIRA wrapper https://github.com/peterjc/galaxy_mira/blob/master/tools/mira3/mira.xml when using Python 2.6.
I can reproduce this on TravisCI (e.g. https://travis-ci.org/peterjc/galaxy_mira/jobs/89677153 with Python 2.6.9), and locally (Python 2.6.6):
$ planemo --version
planemo, version 0.19.1.dev0
$ planemo lint --report_level warn --fail_level error tools/mira3/
Linting tool /mnt/galaxy/repositories/galaxy_mira/tools/mira3/mira.xml
Traceback (most recent call last):
File "/usr/bin/planemo", line 9, in <module>
load_entry_point('planemo==0.19.1.dev0', 'console_scripts', 'planemo')()
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/core.py", line 664, in __call__
return self.main(*args, **kwargs)
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/core.py", line 644, in main
rv = self.invoke(ctx)
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/core.py", line 991, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/core.py", line 837, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/core.py", line 464, in invoke
return callback(*args, **kwargs)
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/decorators.py", line 64, in new_func
return ctx.invoke(f, obj, *args[1:], **kwargs)
File "/usr/lib/python2.6/site-packages/click-4.1-py2.6.egg/click/core.py", line 464, in invoke
return callback(*args, **kwargs)
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo/commands/cmd_lint.py", line 42, in cli
recursive=kwds["recursive"]
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo/tool_lint.py", line 28, in lint_tools_on_path
if not lint_xml(tool_xml, **lint_args):
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo_ext/galaxy/tools/lint.py", line 12, in lint_xml
lint_xml_with(lint_context, tool_xml, extra_modules)
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo_ext/galaxy/tools/lint.py", line 24, in lint_xml_with
lint_context.lint(name, value, tool_xml)
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo_ext/galaxy/tools/lint.py", line 44, in lint
lint_func(lint_target, self)
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo_ext/galaxy/tools/linters/inputs.py", line 38, in lint_inputs
booleans = find_list(conditional, "./param[@type='boolean']")
File "/usr/lib/python2.6/site-packages/planemo-0.19.1.dev0-py2.6.egg/planemo_ext/galaxy/tools/linters/inputs.py", line 30, in find_list
matching = elem.findall(expression)
File "/usr/lib64/python2.6/xml/etree/ElementTree.py", line 355, in findall
return ElementPath.findall(self, path)
File "/usr/lib64/python2.6/xml/etree/ElementPath.py", line 198, in findall
return _compile(path).findall(element)
File "/usr/lib64/python2.6/xml/etree/ElementPath.py", line 176, in _compile
p = Path(path)
File "/usr/lib64/python2.6/xml/etree/ElementPath.py", line 93, in __init__
"expected path separator (%s)" % (op or tag)
SyntaxError: expected path separator ([)
Apparently searching with the [@attribute] syntax is not supported in Python 2.6's ElementTree, possible work around here: http://stackoverflow.com/questions/15753714/elementtree-syntaxerror-expected-path-separator
This suggests 44f16ba triggered this (fix for #194), CC @erasche