Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo/linters/xsd.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/planemo/linters/xsd.py Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,28 @@ +"""Tool linting module that lints Galaxy tool against experimental XSD.""" +import copy +import os +import tempfile + +import galaxy.tool_util + +import planemo.lint + +TOOL_XSD = os.path.join(os.path.dirname(galaxy.tool_util.__file__), 'xsd', "galaxy.xsd") + + +def lint_tool_xsd(tool_xml, lint_ctx): + """Write a temp file out and lint it.""" + with tempfile.NamedTemporaryFile() as tf: + _clean_root(tool_xml).write(tf.name) + planemo.lint.lint_xsd(lint_ctx, TOOL_XSD, tf.name) + + +def _clean_root(tool_xml): + """XSD assumes macros have been expanded, so remove them.""" + clean_tool_xml = copy.deepcopy(tool_xml) + to_remove = [] + for macros_el in clean_tool_xml.getroot().findall("macros"): + to_remove.append(macros_el) + for macros_el in to_remove: + clean_tool_xml.getroot().remove(macros_el) + return clean_tool_xml