Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/lxml/ElementInclude.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/lxml/ElementInclude.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,244 @@ +# +# ElementTree +# $Id: ElementInclude.py 1862 2004-06-18 07:31:02Z Fredrik $ +# +# limited xinclude support for element trees +# +# history: +# 2003-08-15 fl created +# 2003-11-14 fl fixed default loader +# +# Copyright (c) 2003-2004 by Fredrik Lundh. All rights reserved. +# +# fredrik@pythonware.com +# http://www.pythonware.com +# +# -------------------------------------------------------------------- +# The ElementTree toolkit is +# +# Copyright (c) 1999-2004 by Fredrik Lundh +# +# By obtaining, using, and/or copying this software and/or its +# associated documentation, you agree that you have read, understood, +# and will comply with the following terms and conditions: +# +# Permission to use, copy, modify, and distribute this software and +# its associated documentation for any purpose and without fee is +# hereby granted, provided that the above copyright notice appears in +# all copies, and that both that copyright notice and this permission +# notice appear in supporting documentation, and that the name of +# Secret Labs AB or the author not be used in advertising or publicity +# pertaining to distribution of the software without specific, written +# prior permission. +# +# SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD +# TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANT- +# ABILITY AND FITNESS. IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR +# BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY +# DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, +# WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS +# ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE +# OF THIS SOFTWARE. +# -------------------------------------------------------------------- + +""" +Limited XInclude support for the ElementTree package. + +While lxml.etree has full support for XInclude (see +`etree.ElementTree.xinclude()`), this module provides a simpler, pure +Python, ElementTree compatible implementation that supports a simple +form of custom URL resolvers. +""" + +from lxml import etree +try: + from urlparse import urljoin + from urllib2 import urlopen +except ImportError: + # Python 3 + from urllib.parse import urljoin + from urllib.request import urlopen + +XINCLUDE = "{http://www.w3.org/2001/XInclude}" + +XINCLUDE_INCLUDE = XINCLUDE + "include" +XINCLUDE_FALLBACK = XINCLUDE + "fallback" +XINCLUDE_ITER_TAG = XINCLUDE + "*" + +# For security reasons, the inclusion depth is limited to this read-only value by default. +DEFAULT_MAX_INCLUSION_DEPTH = 6 + + +## +# Fatal include error. + +class FatalIncludeError(etree.LxmlSyntaxError): + pass + + +class LimitedRecursiveIncludeError(FatalIncludeError): + pass + + +## +# ET compatible default loader. +# This loader reads an included resource from disk. +# +# @param href Resource reference. +# @param parse Parse mode. Either "xml" or "text". +# @param encoding Optional text encoding. +# @return The expanded resource. If the parse mode is "xml", this +# is an ElementTree instance. If the parse mode is "text", this +# is a Unicode string. If the loader fails, it can return None +# or raise an IOError exception. +# @throws IOError If the loader fails to load the resource. + +def default_loader(href, parse, encoding=None): + file = open(href, 'rb') + if parse == "xml": + data = etree.parse(file).getroot() + else: + data = file.read() + if not encoding: + encoding = 'utf-8' + data = data.decode(encoding) + file.close() + return data + + +## +# Default loader used by lxml.etree - handles custom resolvers properly +# + +def _lxml_default_loader(href, parse, encoding=None, parser=None): + if parse == "xml": + data = etree.parse(href, parser).getroot() + else: + if "://" in href: + f = urlopen(href) + else: + f = open(href, 'rb') + data = f.read() + f.close() + if not encoding: + encoding = 'utf-8' + data = data.decode(encoding) + return data + + +## +# Wrapper for ET compatibility - drops the parser + +def _wrap_et_loader(loader): + def load(href, parse, encoding=None, parser=None): + return loader(href, parse, encoding) + return load + + +## +# Expand XInclude directives. +# +# @param elem Root element. +# @param loader Optional resource loader. If omitted, it defaults +# to {@link default_loader}. If given, it should be a callable +# that implements the same interface as <b>default_loader</b>. +# @param base_url The base URL of the original file, to resolve +# relative include file references. +# @param max_depth The maximum number of recursive inclusions. +# Limited to reduce the risk of malicious content explosion. +# Pass None to disable the limitation. +# @throws LimitedRecursiveIncludeError If the {@link max_depth} was exceeded. +# @throws FatalIncludeError If the function fails to include a given +# resource, or if the tree contains malformed XInclude elements. +# @throws IOError If the function fails to load a given resource. +# @returns the node or its replacement if it was an XInclude node + +def include(elem, loader=None, base_url=None, + max_depth=DEFAULT_MAX_INCLUSION_DEPTH): + if max_depth is None: + max_depth = -1 + elif max_depth < 0: + raise ValueError("expected non-negative depth or None for 'max_depth', got %r" % max_depth) + + if base_url is None: + if hasattr(elem, 'getroot'): + tree = elem + elem = elem.getroot() + else: + tree = elem.getroottree() + if hasattr(tree, 'docinfo'): + base_url = tree.docinfo.URL + elif hasattr(elem, 'getroot'): + elem = elem.getroot() + _include(elem, loader, base_url, max_depth) + + +def _include(elem, loader=None, base_url=None, + max_depth=DEFAULT_MAX_INCLUSION_DEPTH, _parent_hrefs=None): + if loader is not None: + load_include = _wrap_et_loader(loader) + else: + load_include = _lxml_default_loader + + if _parent_hrefs is None: + _parent_hrefs = set() + + parser = elem.getroottree().parser + + include_elements = list( + elem.iter(XINCLUDE_ITER_TAG)) + + for e in include_elements: + if e.tag == XINCLUDE_INCLUDE: + # process xinclude directive + href = urljoin(base_url, e.get("href")) + parse = e.get("parse", "xml") + parent = e.getparent() + if parse == "xml": + if href in _parent_hrefs: + raise FatalIncludeError( + "recursive include of %r detected" % href + ) + if max_depth == 0: + raise LimitedRecursiveIncludeError( + "maximum xinclude depth reached when including file %s" % href) + node = load_include(href, parse, parser=parser) + if node is None: + raise FatalIncludeError( + "cannot load %r as %r" % (href, parse) + ) + node = _include(node, loader, href, max_depth - 1, {href} | _parent_hrefs) + if e.tail: + node.tail = (node.tail or "") + e.tail + if parent is None: + return node # replaced the root node! + parent.replace(e, node) + elif parse == "text": + text = load_include(href, parse, encoding=e.get("encoding")) + if text is None: + raise FatalIncludeError( + "cannot load %r as %r" % (href, parse) + ) + predecessor = e.getprevious() + if predecessor is not None: + predecessor.tail = (predecessor.tail or "") + text + elif parent is None: + return text # replaced the root node! + else: + parent.text = (parent.text or "") + text + (e.tail or "") + parent.remove(e) + else: + raise FatalIncludeError( + "unknown parse type in xi:include tag (%r)" % parse + ) + elif e.tag == XINCLUDE_FALLBACK: + parent = e.getparent() + if parent is not None and parent.tag != XINCLUDE_INCLUDE: + raise FatalIncludeError( + "xi:fallback tag must be child of xi:include (%r)" % e.tag + ) + else: + raise FatalIncludeError( + "Invalid element found in XInclude namespace (%r)" % e.tag + ) + return elem