Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/planemo/linters/xsd.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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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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11 |
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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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18 |
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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 |