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annotate env/lib/python3.7/site-packages/planemo/linters/xsd.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 """Tool linting module that lints Galaxy tool against experimental XSD."""
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2 import copy
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3 import os
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4 import tempfile
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5
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6 import galaxy.tool_util
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7
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8 import planemo.lint
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9
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10 TOOL_XSD = os.path.join(os.path.dirname(galaxy.tool_util.__file__), 'xsd', "galaxy.xsd")
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12
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13 def lint_tool_xsd(tool_xml, lint_ctx):
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14 """Write a temp file out and lint it."""
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15 with tempfile.NamedTemporaryFile() as tf:
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16 _clean_root(tool_xml).write(tf.name)
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17 planemo.lint.lint_xsd(lint_ctx, TOOL_XSD, tf.name)
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19
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20 def _clean_root(tool_xml):
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21 """XSD assumes macros have been expanded, so remove them."""
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22 clean_tool_xml = copy.deepcopy(tool_xml)
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23 to_remove = []
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24 for macros_el in clean_tool_xml.getroot().findall("macros"):
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25 to_remove.append(macros_el)
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26 for macros_el in to_remove:
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27 clean_tool_xml.getroot().remove(macros_el)
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28 return clean_tool_xml