Mercurial > repos > miller-lab > genome_diversity
changeset 32:03c22b722882
remove BeautifulSoup dependency
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Fri, 20 Sep 2013 13:54:23 -0400 |
| parents | a631c2f6d913 |
| children | 5064f618ec1c |
| files | BeautifulSoup.py pca.xml population_structure.xml tool_dependencies.xml |
| diffstat | 4 files changed, 2023 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BeautifulSoup.py Fri Sep 20 13:54:23 2013 -0400 @@ -0,0 +1,2017 @@ +"""Beautiful Soup +Elixir and Tonic +"The Screen-Scraper's Friend" +http://www.crummy.com/software/BeautifulSoup/ + +Beautiful Soup parses a (possibly invalid) XML or HTML document into a +tree representation. It provides methods and Pythonic idioms that make +it easy to navigate, search, and modify the tree. + +A well-formed XML/HTML document yields a well-formed data +structure. An ill-formed XML/HTML document yields a correspondingly +ill-formed data structure. If your document is only locally +well-formed, you can use this library to find and process the +well-formed part of it. + +Beautiful Soup works with Python 2.2 and up. It has no external +dependencies, but you'll have more success at converting data to UTF-8 +if you also install these three packages: + +* chardet, for auto-detecting character encodings + http://chardet.feedparser.org/ +* cjkcodecs and iconv_codec, which add more encodings to the ones supported + by stock Python. + http://cjkpython.i18n.org/ + +Beautiful Soup defines classes for two main parsing strategies: + + * BeautifulStoneSoup, for parsing XML, SGML, or your domain-specific + language that kind of looks like XML. + + * BeautifulSoup, for parsing run-of-the-mill HTML code, be it valid + or invalid. This class has web browser-like heuristics for + obtaining a sensible parse tree in the face of common HTML errors. + +Beautiful Soup also defines a class (UnicodeDammit) for autodetecting +the encoding of an HTML or XML document, and converting it to +Unicode. Much of this code is taken from Mark Pilgrim's Universal Feed Parser. + +For more than you ever wanted to know about Beautiful Soup, see the +documentation: +http://www.crummy.com/software/BeautifulSoup/documentation.html + +Here, have some legalese: + +Copyright (c) 2004-2010, Leonard Richardson + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + + * Neither the name of the the Beautiful Soup Consortium and All + Night Kosher Bakery nor the names of its contributors may be + used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR +CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE, DAMMIT. + +""" +from __future__ import generators + +__author__ = "Leonard Richardson (leonardr@segfault.org)" +__version__ = "3.2.1" +__copyright__ = "Copyright (c) 2004-2012 Leonard Richardson" +__license__ = "New-style BSD" + +from sgmllib import SGMLParser, SGMLParseError +import codecs +import markupbase +import types +import re +import sgmllib +try: + from htmlentitydefs import name2codepoint +except ImportError: + name2codepoint = {} +try: + set +except NameError: + from sets import Set as set + +#These hacks make Beautiful Soup able to parse XML with namespaces +sgmllib.tagfind = re.compile('[a-zA-Z][-_.:a-zA-Z0-9]*') +markupbase._declname_match = re.compile(r'[a-zA-Z][-_.:a-zA-Z0-9]*\s*').match + +DEFAULT_OUTPUT_ENCODING = "utf-8" + +def _match_css_class(str): + """Build a RE to match the given CSS class.""" + return re.compile(r"(^|.*\s)%s($|\s)" % str) + +# First, the classes that represent markup elements. + +class PageElement(object): + """Contains the navigational information for some part of the page + (either a tag or a piece of text)""" + + def _invert(h): + "Cheap function to invert a hash." + i = {} + for k,v in h.items(): + i[v] = k + return i + + XML_ENTITIES_TO_SPECIAL_CHARS = { "apos" : "'", + "quot" : '"', + "amp" : "&", + "lt" : "<", + "gt" : ">" } + + XML_SPECIAL_CHARS_TO_ENTITIES = _invert(XML_ENTITIES_TO_SPECIAL_CHARS) + + def setup(self, parent=None, previous=None): + """Sets up the initial relations between this element and + other elements.""" + self.parent = parent + self.previous = previous + self.next = None + self.previousSibling = None + self.nextSibling = None + if self.parent and self.parent.contents: + self.previousSibling = self.parent.contents[-1] + self.previousSibling.nextSibling = self + + def replaceWith(self, replaceWith): + oldParent = self.parent + myIndex = self.parent.index(self) + if hasattr(replaceWith, "parent")\ + and replaceWith.parent is self.parent: + # We're replacing this element with one of its siblings. + index = replaceWith.parent.index(replaceWith) + if index and index < myIndex: + # Furthermore, it comes before this element. That + # means that when we extract it, the index of this + # element will change. + myIndex = myIndex - 1 + self.extract() + oldParent.insert(myIndex, replaceWith) + + def replaceWithChildren(self): + myParent = self.parent + myIndex = self.parent.index(self) + self.extract() + reversedChildren = list(self.contents) + reversedChildren.reverse() + for child in reversedChildren: + myParent.insert(myIndex, child) + + def extract(self): + """Destructively rips this element out of the tree.""" + if self.parent: + try: + del self.parent.contents[self.parent.index(self)] + except ValueError: + pass + + #Find the two elements that would be next to each other if + #this element (and any children) hadn't been parsed. Connect + #the two. + lastChild = self._lastRecursiveChild() + nextElement = lastChild.next + + if self.previous: + self.previous.next = nextElement + if nextElement: + nextElement.previous = self.previous + self.previous = None + lastChild.next = None + + self.parent = None + if self.previousSibling: + self.previousSibling.nextSibling = self.nextSibling + if self.nextSibling: + self.nextSibling.previousSibling = self.previousSibling + self.previousSibling = self.nextSibling = None + return self + + def _lastRecursiveChild(self): + "Finds the last element beneath this object to be parsed." + lastChild = self + while hasattr(lastChild, 'contents') and lastChild.contents: + lastChild = lastChild.contents[-1] + return lastChild + + def insert(self, position, newChild): + if isinstance(newChild, basestring) \ + and not isinstance(newChild, NavigableString): + newChild = NavigableString(newChild) + + position = min(position, len(self.contents)) + if hasattr(newChild, 'parent') and newChild.parent is not None: + # We're 'inserting' an element that's already one + # of this object's children. + if newChild.parent is self: + index = self.index(newChild) + if index > position: + # Furthermore we're moving it further down the + # list of this object's children. That means that + # when we extract this element, our target index + # will jump down one. + position = position - 1 + newChild.extract() + + newChild.parent = self + previousChild = None + if position == 0: + newChild.previousSibling = None + newChild.previous = self + else: + previousChild = self.contents[position-1] + newChild.previousSibling = previousChild + newChild.previousSibling.nextSibling = newChild + newChild.previous = previousChild._lastRecursiveChild() + if newChild.previous: + newChild.previous.next = newChild + + newChildsLastElement = newChild._lastRecursiveChild() + + if position >= len(self.contents): + newChild.nextSibling = None + + parent = self + parentsNextSibling = None + while not parentsNextSibling: + parentsNextSibling = parent.nextSibling + parent = parent.parent + if not parent: # This is the last element in the document. + break + if parentsNextSibling: + newChildsLastElement.next = parentsNextSibling + else: + newChildsLastElement.next = None + else: + nextChild = self.contents[position] + newChild.nextSibling = nextChild + if newChild.nextSibling: + newChild.nextSibling.previousSibling = newChild + newChildsLastElement.next = nextChild + + if newChildsLastElement.next: + newChildsLastElement.next.previous = newChildsLastElement + self.contents.insert(position, newChild) + + def append(self, tag): + """Appends the given tag to the contents of this tag.""" + self.insert(len(self.contents), tag) + + def findNext(self, name=None, attrs={}, text=None, **kwargs): + """Returns the first item that matches the given criteria and + appears after this Tag in the document.""" + return self._findOne(self.findAllNext, name, attrs, text, **kwargs) + + def findAllNext(self, name=None, attrs={}, text=None, limit=None, + **kwargs): + """Returns all items that match the given criteria and appear + after this Tag in the document.""" + return self._findAll(name, attrs, text, limit, self.nextGenerator, + **kwargs) + + def findNextSibling(self, name=None, attrs={}, text=None, **kwargs): + """Returns the closest sibling to this Tag that matches the + given criteria and appears after this Tag in the document.""" + return self._findOne(self.findNextSiblings, name, attrs, text, + **kwargs) + + def findNextSiblings(self, name=None, attrs={}, text=None, limit=None, + **kwargs): + """Returns the siblings of this Tag that match the given + criteria and appear after this Tag in the document.""" + return self._findAll(name, attrs, text, limit, + self.nextSiblingGenerator, **kwargs) + fetchNextSiblings = findNextSiblings # Compatibility with pre-3.x + + def findPrevious(self, name=None, attrs={}, text=None, **kwargs): + """Returns the first item that matches the given criteria and + appears before this Tag in the document.""" + return self._findOne(self.findAllPrevious, name, attrs, text, **kwargs) + + def findAllPrevious(self, name=None, attrs={}, text=None, limit=None, + **kwargs): + """Returns all items that match the given criteria and appear + before this Tag in the document.""" + return self._findAll(name, attrs, text, limit, self.previousGenerator, + **kwargs) + fetchPrevious = findAllPrevious # Compatibility with pre-3.x + + def findPreviousSibling(self, name=None, attrs={}, text=None, **kwargs): + """Returns the closest sibling to this Tag that matches the + given criteria and appears before this Tag in the document.""" + return self._findOne(self.findPreviousSiblings, name, attrs, text, + **kwargs) + + def findPreviousSiblings(self, name=None, attrs={}, text=None, + limit=None, **kwargs): + """Returns the siblings of this Tag that match the given + criteria and appear before this Tag in the document.""" + return self._findAll(name, attrs, text, limit, + self.previousSiblingGenerator, **kwargs) + fetchPreviousSiblings = findPreviousSiblings # Compatibility with pre-3.x + + def findParent(self, name=None, attrs={}, **kwargs): + """Returns the closest parent of this Tag that matches the given + criteria.""" + # NOTE: We can't use _findOne because findParents takes a different + # set of arguments. + r = None + l = self.findParents(name, attrs, 1) + if l: + r = l[0] + return r + + def findParents(self, name=None, attrs={}, limit=None, **kwargs): + """Returns the parents of this Tag that match the given + criteria.""" + + return self._findAll(name, attrs, None, limit, self.parentGenerator, + **kwargs) + fetchParents = findParents # Compatibility with pre-3.x + + #These methods do the real heavy lifting. + + def _findOne(self, method, name, attrs, text, **kwargs): + r = None + l = method(name, attrs, text, 1, **kwargs) + if l: + r = l[0] + return r + + def _findAll(self, name, attrs, text, limit, generator, **kwargs): + "Iterates over a generator looking for things that match." + + if isinstance(name, SoupStrainer): + strainer = name + # (Possibly) special case some findAll*(...) searches + elif text is None and not limit and not attrs and not kwargs: + # findAll*(True) + if name is True: + return [element for element in generator() + if isinstance(element, Tag)] + # findAll*('tag-name') + elif isinstance(name, basestring): + return [element for element in generator() + if isinstance(element, Tag) and + element.name == name] + else: + strainer = SoupStrainer(name, attrs, text, **kwargs) + # Build a SoupStrainer + else: + strainer = SoupStrainer(name, attrs, text, **kwargs) + results = ResultSet(strainer) + g = generator() + while True: + try: + i = g.next() + except StopIteration: + break + if i: + found = strainer.search(i) + if found: + results.append(found) + if limit and len(results) >= limit: + break + return results + + #These Generators can be used to navigate starting from both + #NavigableStrings and Tags. + def nextGenerator(self): + i = self + while i is not None: + i = i.next + yield i + + def nextSiblingGenerator(self): + i = self + while i is not None: + i = i.nextSibling + yield i + + def previousGenerator(self): + i = self + while i is not None: + i = i.previous + yield i + + def previousSiblingGenerator(self): + i = self + while i is not None: + i = i.previousSibling + yield i + + def parentGenerator(self): + i = self + while i is not None: + i = i.parent + yield i + + # Utility methods + def substituteEncoding(self, str, encoding=None): + encoding = encoding or "utf-8" + return str.replace("%SOUP-ENCODING%", encoding) + + def toEncoding(self, s, encoding=None): + """Encodes an object to a string in some encoding, or to Unicode. + .""" + if isinstance(s, unicode): + if encoding: + s = s.encode(encoding) + elif isinstance(s, str): + if encoding: + s = s.encode(encoding) + else: + s = unicode(s) + else: + if encoding: + s = self.toEncoding(str(s), encoding) + else: + s = unicode(s) + return s + + BARE_AMPERSAND_OR_BRACKET = re.compile("([<>]|" + + "&(?!#\d+;|#x[0-9a-fA-F]+;|\w+;)" + + ")") + + def _sub_entity(self, x): + """Used with a regular expression to substitute the + appropriate XML entity for an XML special character.""" + return "&" + self.XML_SPECIAL_CHARS_TO_ENTITIES[x.group(0)[0]] + ";" + + +class NavigableString(unicode, PageElement): + + def __new__(cls, value): + """Create a new NavigableString. + + When unpickling a NavigableString, this method is called with + the string in DEFAULT_OUTPUT_ENCODING. That encoding needs to be + passed in to the superclass's __new__ or the superclass won't know + how to handle non-ASCII characters. + """ + if isinstance(value, unicode): + return unicode.__new__(cls, value) + return unicode.__new__(cls, value, DEFAULT_OUTPUT_ENCODING) + + def __getnewargs__(self): + return (NavigableString.__str__(self),) + + def __getattr__(self, attr): + """text.string gives you text. This is for backwards + compatibility for Navigable*String, but for CData* it lets you + get the string without the CData wrapper.""" + if attr == 'string': + return self + else: + raise AttributeError, "'%s' object has no attribute '%s'" % (self.__class__.__name__, attr) + + def __unicode__(self): + return str(self).decode(DEFAULT_OUTPUT_ENCODING) + + def __str__(self, encoding=DEFAULT_OUTPUT_ENCODING): + # Substitute outgoing XML entities. + data = self.BARE_AMPERSAND_OR_BRACKET.sub(self._sub_entity, self) + if encoding: + return data.encode(encoding) + else: + return data + +class CData(NavigableString): + + def __str__(self, encoding=DEFAULT_OUTPUT_ENCODING): + return "<![CDATA[%s]]>" % NavigableString.__str__(self, encoding) + +class ProcessingInstruction(NavigableString): + def __str__(self, encoding=DEFAULT_OUTPUT_ENCODING): + output = self + if "%SOUP-ENCODING%" in output: + output = self.substituteEncoding(output, encoding) + return "<?%s?>" % self.toEncoding(output, encoding) + +class Comment(NavigableString): + def __str__(self, encoding=DEFAULT_OUTPUT_ENCODING): + return "<!--%s-->" % NavigableString.__str__(self, encoding) + +class Declaration(NavigableString): + def __str__(self, encoding=DEFAULT_OUTPUT_ENCODING): + return "<!%s>" % NavigableString.__str__(self, encoding) + +class Tag(PageElement): + + """Represents a found HTML tag with its attributes and contents.""" + + def _convertEntities(self, match): + """Used in a call to re.sub to replace HTML, XML, and numeric + entities with the appropriate Unicode characters. If HTML + entities are being converted, any unrecognized entities are + escaped.""" + x = match.group(1) + if self.convertHTMLEntities and x in name2codepoint: + return unichr(name2codepoint[x]) + elif x in self.XML_ENTITIES_TO_SPECIAL_CHARS: + if self.convertXMLEntities: + return self.XML_ENTITIES_TO_SPECIAL_CHARS[x] + else: + return u'&%s;' % x + elif len(x) > 0 and x[0] == '#': + # Handle numeric entities + if len(x) > 1 and x[1] == 'x': + return unichr(int(x[2:], 16)) + else: + return unichr(int(x[1:])) + + elif self.escapeUnrecognizedEntities: + return u'&%s;' % x + else: + return u'&%s;' % x + + def __init__(self, parser, name, attrs=None, parent=None, + previous=None): + "Basic constructor." + + # We don't actually store the parser object: that lets extracted + # chunks be garbage-collected + self.parserClass = parser.__class__ + self.isSelfClosing = parser.isSelfClosingTag(name) + self.name = name + if attrs is None: + attrs = [] + elif isinstance(attrs, dict): + attrs = attrs.items() + self.attrs = attrs + self.contents = [] + self.setup(parent, previous) + self.hidden = False + self.containsSubstitutions = False + self.convertHTMLEntities = parser.convertHTMLEntities + self.convertXMLEntities = parser.convertXMLEntities + self.escapeUnrecognizedEntities = parser.escapeUnrecognizedEntities + + # Convert any HTML, XML, or numeric entities in the attribute values. + convert = lambda(k, val): (k, + re.sub("&(#\d+|#x[0-9a-fA-F]+|\w+);", + self._convertEntities, + val)) + self.attrs = map(convert, self.attrs) + + def getString(self): + if (len(self.contents) == 1 + and isinstance(self.contents[0], NavigableString)): + return self.contents[0] + + def setString(self, string): + """Replace the contents of the tag with a string""" + self.clear() + self.append(string) + + string = property(getString, setString) + + def getText(self, separator=u""): + if not len(self.contents): + return u"" + stopNode = self._lastRecursiveChild().next + strings = [] + current = self.contents[0] + while current is not stopNode: + if isinstance(current, NavigableString): + strings.append(current.strip()) + current = current.next + return separator.join(strings) + + text = property(getText) + + def get(self, key, default=None): + """Returns the value of the 'key' attribute for the tag, or + the value given for 'default' if it doesn't have that + attribute.""" + return self._getAttrMap().get(key, default) + + def clear(self): + """Extract all children.""" + for child in self.contents[:]: + child.extract() + + def index(self, element): + for i, child in enumerate(self.contents): + if child is element: + return i + raise ValueError("Tag.index: element not in tag") + + def has_key(self, key): + return self._getAttrMap().has_key(key) + + def __getitem__(self, key): + """tag[key] returns the value of the 'key' attribute for the tag, + and throws an exception if it's not there.""" + return self._getAttrMap()[key] + + def __iter__(self): + "Iterating over a tag iterates over its contents." + return iter(self.contents) + + def __len__(self): + "The length of a tag is the length of its list of contents." + return len(self.contents) + + def __contains__(self, x): + return x in self.contents + + def __nonzero__(self): + "A tag is non-None even if it has no contents." + return True + + def __setitem__(self, key, value): + """Setting tag[key] sets the value of the 'key' attribute for the + tag.""" + self._getAttrMap() + self.attrMap[key] = value + found = False + for i in range(0, len(self.attrs)): + if self.attrs[i][0] == key: + self.attrs[i] = (key, value) + found = True + if not found: + self.attrs.append((key, value)) + self._getAttrMap()[key] = value + + def __delitem__(self, key): + "Deleting tag[key] deletes all 'key' attributes for the tag." + for item in self.attrs: + if item[0] == key: + self.attrs.remove(item) + #We don't break because bad HTML can define the same + #attribute multiple times. + self._getAttrMap() + if self.attrMap.has_key(key): + del self.attrMap[key] + + def __call__(self, *args, **kwargs): + """Calling a tag like a function is the same as calling its + findAll() method. Eg. tag('a') returns a list of all the A tags + found within this tag.""" + return apply(self.findAll, args, kwargs) + + def __getattr__(self, tag): + #print "Getattr %s.%s" % (self.__class__, tag) + if len(tag) > 3 and tag.rfind('Tag') == len(tag)-3: + return self.find(tag[:-3]) + elif tag.find('__') != 0: + return self.find(tag) + raise AttributeError, "'%s' object has no attribute '%s'" % (self.__class__, tag) + + def __eq__(self, other): + """Returns true iff this tag has the same name, the same attributes, + and the same contents (recursively) as the given tag. + + NOTE: right now this will return false if two tags have the + same attributes in a different order. Should this be fixed?""" + if other is self: + return True + if not hasattr(other, 'name') or not hasattr(other, 'attrs') or not hasattr(other, 'contents') or self.name != other.name or self.attrs != other.attrs or len(self) != len(other): + return False + for i in range(0, len(self.contents)): + if self.contents[i] != other.contents[i]: + return False + return True + + def __ne__(self, other): + """Returns true iff this tag is not identical to the other tag, + as defined in __eq__.""" + return not self == other + + def __repr__(self, encoding=DEFAULT_OUTPUT_ENCODING): + """Renders this tag as a string.""" + return self.__str__(encoding) + + def __unicode__(self): + return self.__str__(None) + + def __str__(self, encoding=DEFAULT_OUTPUT_ENCODING, + prettyPrint=False, indentLevel=0): + """Returns a string or Unicode representation of this tag and + its contents. To get Unicode, pass None for encoding. + + NOTE: since Python's HTML parser consumes whitespace, this + method is not certain to reproduce the whitespace present in + the original string.""" + + encodedName = self.toEncoding(self.name, encoding) + + attrs = [] + if self.attrs: + for key, val in self.attrs: + fmt = '%s="%s"' + if isinstance(val, basestring): + if self.containsSubstitutions and '%SOUP-ENCODING%' in val: + val = self.substituteEncoding(val, encoding) + + # The attribute value either: + # + # * Contains no embedded double quotes or single quotes. + # No problem: we enclose it in double quotes. + # * Contains embedded single quotes. No problem: + # double quotes work here too. + # * Contains embedded double quotes. No problem: + # we enclose it in single quotes. + # * Embeds both single _and_ double quotes. This + # can't happen naturally, but it can happen if + # you modify an attribute value after parsing + # the document. Now we have a bit of a + # problem. We solve it by enclosing the + # attribute in single quotes, and escaping any + # embedded single quotes to XML entities. + if '"' in val: + fmt = "%s='%s'" + if "'" in val: + # TODO: replace with apos when + # appropriate. + val = val.replace("'", "&squot;") + + # Now we're okay w/r/t quotes. But the attribute + # value might also contain angle brackets, or + # ampersands that aren't part of entities. We need + # to escape those to XML entities too. + val = self.BARE_AMPERSAND_OR_BRACKET.sub(self._sub_entity, val) + + attrs.append(fmt % (self.toEncoding(key, encoding), + self.toEncoding(val, encoding))) + close = '' + closeTag = '' + if self.isSelfClosing: + close = ' /' + else: + closeTag = '</%s>' % encodedName + + indentTag, indentContents = 0, 0 + if prettyPrint: + indentTag = indentLevel + space = (' ' * (indentTag-1)) + indentContents = indentTag + 1 + contents = self.renderContents(encoding, prettyPrint, indentContents) + if self.hidden: + s = contents + else: + s = [] + attributeString = '' + if attrs: + attributeString = ' ' + ' '.join(attrs) + if prettyPrint: + s.append(space) + s.append('<%s%s%s>' % (encodedName, attributeString, close)) + if prettyPrint: + s.append("\n") + s.append(contents) + if prettyPrint and contents and contents[-1] != "\n": + s.append("\n") + if prettyPrint and closeTag: + s.append(space) + s.append(closeTag) + if prettyPrint and closeTag and self.nextSibling: + s.append("\n") + s = ''.join(s) + return s + + def decompose(self): + """Recursively destroys the contents of this tree.""" + self.extract() + if len(self.contents) == 0: + return + current = self.contents[0] + while current is not None: + next = current.next + if isinstance(current, Tag): + del current.contents[:] + current.parent = None + current.previous = None + current.previousSibling = None + current.next = None + current.nextSibling = None + current = next + + def prettify(self, encoding=DEFAULT_OUTPUT_ENCODING): + return self.__str__(encoding, True) + + def renderContents(self, encoding=DEFAULT_OUTPUT_ENCODING, + prettyPrint=False, indentLevel=0): + """Renders the contents of this tag as a string in the given + encoding. If encoding is None, returns a Unicode string..""" + s=[] + for c in self: + text = None + if isinstance(c, NavigableString): + text = c.__str__(encoding) + elif isinstance(c, Tag): + s.append(c.__str__(encoding, prettyPrint, indentLevel)) + if text and prettyPrint: + text = text.strip() + if text: + if prettyPrint: + s.append(" " * (indentLevel-1)) + s.append(text) + if prettyPrint: + s.append("\n") + return ''.join(s) + + #Soup methods + + def find(self, name=None, attrs={}, recursive=True, text=None, + **kwargs): + """Return only the first child of this Tag matching the given + criteria.""" + r = None + l = self.findAll(name, attrs, recursive, text, 1, **kwargs) + if l: + r = l[0] + return r + findChild = find + + def findAll(self, name=None, attrs={}, recursive=True, text=None, + limit=None, **kwargs): + """Extracts a list of Tag objects that match the given + criteria. You can specify the name of the Tag and any + attributes you want the Tag to have. + + The value of a key-value pair in the 'attrs' map can be a + string, a list of strings, a regular expression object, or a + callable that takes a string and returns whether or not the + string matches for some custom definition of 'matches'. The + same is true of the tag name.""" + generator = self.recursiveChildGenerator + if not recursive: + generator = self.childGenerator + return self._findAll(name, attrs, text, limit, generator, **kwargs) + findChildren = findAll + + # Pre-3.x compatibility methods + first = find + fetch = findAll + + def fetchText(self, text=None, recursive=True, limit=None): + return self.findAll(text=text, recursive=recursive, limit=limit) + + def firstText(self, text=None, recursive=True): + return self.find(text=text, recursive=recursive) + + #Private methods + + def _getAttrMap(self): + """Initializes a map representation of this tag's attributes, + if not already initialized.""" + if not getattr(self, 'attrMap'): + self.attrMap = {} + for (key, value) in self.attrs: + self.attrMap[key] = value + return self.attrMap + + #Generator methods + def childGenerator(self): + # Just use the iterator from the contents + return iter(self.contents) + + def recursiveChildGenerator(self): + if not len(self.contents): + raise StopIteration + stopNode = self._lastRecursiveChild().next + current = self.contents[0] + while current is not stopNode: + yield current + current = current.next + + +# Next, a couple classes to represent queries and their results. +class SoupStrainer: + """Encapsulates a number of ways of matching a markup element (tag or + text).""" + + def __init__(self, name=None, attrs={}, text=None, **kwargs): + self.name = name + if isinstance(attrs, basestring): + kwargs['class'] = _match_css_class(attrs) + attrs = None + if kwargs: + if attrs: + attrs = attrs.copy() + attrs.update(kwargs) + else: + attrs = kwargs + self.attrs = attrs + self.text = text + + def __str__(self): + if self.text: + return self.text + else: + return "%s|%s" % (self.name, self.attrs) + + def searchTag(self, markupName=None, markupAttrs={}): + found = None + markup = None + if isinstance(markupName, Tag): + markup = markupName + markupAttrs = markup + callFunctionWithTagData = callable(self.name) \ + and not isinstance(markupName, Tag) + + if (not self.name) \ + or callFunctionWithTagData \ + or (markup and self._matches(markup, self.name)) \ + or (not markup and self._matches(markupName, self.name)): + if callFunctionWithTagData: + match = self.name(markupName, markupAttrs) + else: + match = True + markupAttrMap = None + for attr, matchAgainst in self.attrs.items(): + if not markupAttrMap: + if hasattr(markupAttrs, 'get'): + markupAttrMap = markupAttrs + else: + markupAttrMap = {} + for k,v in markupAttrs: + markupAttrMap[k] = v + attrValue = markupAttrMap.get(attr) + if not self._matches(attrValue, matchAgainst): + match = False + break + if match: + if markup: + found = markup + else: + found = markupName + return found + + def search(self, markup): + #print 'looking for %s in %s' % (self, markup) + found = None + # If given a list of items, scan it for a text element that + # matches. + if hasattr(markup, "__iter__") \ + and not isinstance(markup, Tag): + for element in markup: + if isinstance(element, NavigableString) \ + and self.search(element): + found = element + break + # If it's a Tag, make sure its name or attributes match. + # Don't bother with Tags if we're searching for text. + elif isinstance(markup, Tag): + if not self.text: + found = self.searchTag(markup) + # If it's text, make sure the text matches. + elif isinstance(markup, NavigableString) or \ + isinstance(markup, basestring): + if self._matches(markup, self.text): + found = markup + else: + raise Exception, "I don't know how to match against a %s" \ + % markup.__class__ + return found + + def _matches(self, markup, matchAgainst): + #print "Matching %s against %s" % (markup, matchAgainst) + result = False + if matchAgainst is True: + result = markup is not None + elif callable(matchAgainst): + result = matchAgainst(markup) + else: + #Custom match methods take the tag as an argument, but all + #other ways of matching match the tag name as a string. + if isinstance(markup, Tag): + markup = markup.name + if markup and not isinstance(markup, basestring): + markup = unicode(markup) + #Now we know that chunk is either a string, or None. + if hasattr(matchAgainst, 'match'): + # It's a regexp object. + result = markup and matchAgainst.search(markup) + elif hasattr(matchAgainst, '__iter__'): # list-like + result = markup in matchAgainst + elif hasattr(matchAgainst, 'items'): + result = markup.has_key(matchAgainst) + elif matchAgainst and isinstance(markup, basestring): + if isinstance(markup, unicode): + matchAgainst = unicode(matchAgainst) + else: + matchAgainst = str(matchAgainst) + + if not result: + result = matchAgainst == markup + return result + +class ResultSet(list): + """A ResultSet is just a list that keeps track of the SoupStrainer + that created it.""" + def __init__(self, source): + list.__init__([]) + self.source = source + +# Now, some helper functions. + +def buildTagMap(default, *args): + """Turns a list of maps, lists, or scalars into a single map. + Used to build the SELF_CLOSING_TAGS, NESTABLE_TAGS, and + NESTING_RESET_TAGS maps out of lists and partial maps.""" + built = {} + for portion in args: + if hasattr(portion, 'items'): + #It's a map. Merge it. + for k,v in portion.items(): + built[k] = v + elif hasattr(portion, '__iter__'): # is a list + #It's a list. Map each item to the default. + for k in portion: + built[k] = default + else: + #It's a scalar. Map it to the default. + built[portion] = default + return built + +# Now, the parser classes. + +class BeautifulStoneSoup(Tag, SGMLParser): + + """This class contains the basic parser and search code. It defines + a parser that knows nothing about tag behavior except for the + following: + + You can't close a tag without closing all the tags it encloses. + That is, "<foo><bar></foo>" actually means + "<foo><bar></bar></foo>". + + [Another possible explanation is "<foo><bar /></foo>", but since + this class defines no SELF_CLOSING_TAGS, it will never use that + explanation.] + + This class is useful for parsing XML or made-up markup languages, + or when BeautifulSoup makes an assumption counter to what you were + expecting.""" + + SELF_CLOSING_TAGS = {} + NESTABLE_TAGS = {} + RESET_NESTING_TAGS = {} + QUOTE_TAGS = {} + PRESERVE_WHITESPACE_TAGS = [] + + MARKUP_MASSAGE = [(re.compile('(<[^<>]*)/>'), + lambda x: x.group(1) + ' />'), + (re.compile('<!\s+([^<>]*)>'), + lambda x: '<!' + x.group(1) + '>') + ] + + ROOT_TAG_NAME = u'[document]' + + HTML_ENTITIES = "html" + XML_ENTITIES = "xml" + XHTML_ENTITIES = "xhtml" + # TODO: This only exists for backwards-compatibility + ALL_ENTITIES = XHTML_ENTITIES + + # Used when determining whether a text node is all whitespace and + # can be replaced with a single space. A text node that contains + # fancy Unicode spaces (usually non-breaking) should be left + # alone. + STRIP_ASCII_SPACES = { 9: None, 10: None, 12: None, 13: None, 32: None, } + + def __init__(self, markup="", parseOnlyThese=None, fromEncoding=None, + markupMassage=True, smartQuotesTo=XML_ENTITIES, + convertEntities=None, selfClosingTags=None, isHTML=False): + """The Soup object is initialized as the 'root tag', and the + provided markup (which can be a string or a file-like object) + is fed into the underlying parser. + + sgmllib will process most bad HTML, and the BeautifulSoup + class has some tricks for dealing with some HTML that kills + sgmllib, but Beautiful Soup can nonetheless choke or lose data + if your data uses self-closing tags or declarations + incorrectly. + + By default, Beautiful Soup uses regexes to sanitize input, + avoiding the vast majority of these problems. If the problems + don't apply to you, pass in False for markupMassage, and + you'll get better performance. + + The default parser massage techniques fix the two most common + instances of invalid HTML that choke sgmllib: + + <br/> (No space between name of closing tag and tag close) + <! --Comment--> (Extraneous whitespace in declaration) + + You can pass in a custom list of (RE object, replace method) + tuples to get Beautiful Soup to scrub your input the way you + want.""" + + self.parseOnlyThese = parseOnlyThese + self.fromEncoding = fromEncoding + self.smartQuotesTo = smartQuotesTo + self.convertEntities = convertEntities + # Set the rules for how we'll deal with the entities we + # encounter + if self.convertEntities: + # It doesn't make sense to convert encoded characters to + # entities even while you're converting entities to Unicode. + # Just convert it all to Unicode. + self.smartQuotesTo = None + if convertEntities == self.HTML_ENTITIES: + self.convertXMLEntities = False + self.convertHTMLEntities = True + self.escapeUnrecognizedEntities = True + elif convertEntities == self.XHTML_ENTITIES: + self.convertXMLEntities = True + self.convertHTMLEntities = True + self.escapeUnrecognizedEntities = False + elif convertEntities == self.XML_ENTITIES: + self.convertXMLEntities = True + self.convertHTMLEntities = False + self.escapeUnrecognizedEntities = False + else: + self.convertXMLEntities = False + self.convertHTMLEntities = False + self.escapeUnrecognizedEntities = False + + self.instanceSelfClosingTags = buildTagMap(None, selfClosingTags) + SGMLParser.__init__(self) + + if hasattr(markup, 'read'): # It's a file-type object. + markup = markup.read() + self.markup = markup + self.markupMassage = markupMassage + try: + self._feed(isHTML=isHTML) + except StopParsing: + pass + self.markup = None # The markup can now be GCed + + def convert_charref(self, name): + """This method fixes a bug in Python's SGMLParser.""" + try: + n = int(name) + except ValueError: + return + if not 0 <= n <= 127 : # ASCII ends at 127, not 255 + return + return self.convert_codepoint(n) + + def _feed(self, inDocumentEncoding=None, isHTML=False): + # Convert the document to Unicode. + markup = self.markup + if isinstance(markup, unicode): + if not hasattr(self, 'originalEncoding'): + self.originalEncoding = None + else: + dammit = UnicodeDammit\ + (markup, [self.fromEncoding, inDocumentEncoding], + smartQuotesTo=self.smartQuotesTo, isHTML=isHTML) + markup = dammit.unicode + self.originalEncoding = dammit.originalEncoding + self.declaredHTMLEncoding = dammit.declaredHTMLEncoding + if markup: + if self.markupMassage: + if not hasattr(self.markupMassage, "__iter__"): + self.markupMassage = self.MARKUP_MASSAGE + for fix, m in self.markupMassage: + markup = fix.sub(m, markup) + # TODO: We get rid of markupMassage so that the + # soup object can be deepcopied later on. Some + # Python installations can't copy regexes. If anyone + # was relying on the existence of markupMassage, this + # might cause problems. + del(self.markupMassage) + self.reset() + + SGMLParser.feed(self, markup) + # Close out any unfinished strings and close all the open tags. + self.endData() + while self.currentTag.name != self.ROOT_TAG_NAME: + self.popTag() + + def __getattr__(self, methodName): + """This method routes method call requests to either the SGMLParser + superclass or the Tag superclass, depending on the method name.""" + #print "__getattr__ called on %s.%s" % (self.__class__, methodName) + + if methodName.startswith('start_') or methodName.startswith('end_') \ + or methodName.startswith('do_'): + return SGMLParser.__getattr__(self, methodName) + elif not methodName.startswith('__'): + return Tag.__getattr__(self, methodName) + else: + raise AttributeError + + def isSelfClosingTag(self, name): + """Returns true iff the given string is the name of a + self-closing tag according to this parser.""" + return self.SELF_CLOSING_TAGS.has_key(name) \ + or self.instanceSelfClosingTags.has_key(name) + + def reset(self): + Tag.__init__(self, self, self.ROOT_TAG_NAME) + self.hidden = 1 + SGMLParser.reset(self) + self.currentData = [] + self.currentTag = None + self.tagStack = [] + self.quoteStack = [] + self.pushTag(self) + + def popTag(self): + tag = self.tagStack.pop() + + #print "Pop", tag.name + if self.tagStack: + self.currentTag = self.tagStack[-1] + return self.currentTag + + def pushTag(self, tag): + #print "Push", tag.name + if self.currentTag: + self.currentTag.contents.append(tag) + self.tagStack.append(tag) + self.currentTag = self.tagStack[-1] + + def endData(self, containerClass=NavigableString): + if self.currentData: + currentData = u''.join(self.currentData) + if (currentData.translate(self.STRIP_ASCII_SPACES) == '' and + not set([tag.name for tag in self.tagStack]).intersection( + self.PRESERVE_WHITESPACE_TAGS)): + if '\n' in currentData: + currentData = '\n' + else: + currentData = ' ' + self.currentData = [] + if self.parseOnlyThese and len(self.tagStack) <= 1 and \ + (not self.parseOnlyThese.text or \ + not self.parseOnlyThese.search(currentData)): + return + o = containerClass(currentData) + o.setup(self.currentTag, self.previous) + if self.previous: + self.previous.next = o + self.previous = o + self.currentTag.contents.append(o) + + + def _popToTag(self, name, inclusivePop=True): + """Pops the tag stack up to and including the most recent + instance of the given tag. If inclusivePop is false, pops the tag + stack up to but *not* including the most recent instqance of + the given tag.""" + #print "Popping to %s" % name + if name == self.ROOT_TAG_NAME: + return + + numPops = 0 + mostRecentTag = None + for i in range(len(self.tagStack)-1, 0, -1): + if name == self.tagStack[i].name: + numPops = len(self.tagStack)-i + break + if not inclusivePop: + numPops = numPops - 1 + + for i in range(0, numPops): + mostRecentTag = self.popTag() + return mostRecentTag + + def _smartPop(self, name): + + """We need to pop up to the previous tag of this type, unless + one of this tag's nesting reset triggers comes between this + tag and the previous tag of this type, OR unless this tag is a + generic nesting trigger and another generic nesting trigger + comes between this tag and the previous tag of this type. + + Examples: + <p>Foo<b>Bar *<p>* should pop to 'p', not 'b'. + <p>Foo<table>Bar *<p>* should pop to 'table', not 'p'. + <p>Foo<table><tr>Bar *<p>* should pop to 'tr', not 'p'. + + <li><ul><li> *<li>* should pop to 'ul', not the first 'li'. + <tr><table><tr> *<tr>* should pop to 'table', not the first 'tr' + <td><tr><td> *<td>* should pop to 'tr', not the first 'td' + """ + + nestingResetTriggers = self.NESTABLE_TAGS.get(name) + isNestable = nestingResetTriggers != None + isResetNesting = self.RESET_NESTING_TAGS.has_key(name) + popTo = None + inclusive = True + for i in range(len(self.tagStack)-1, 0, -1): + p = self.tagStack[i] + if (not p or p.name == name) and not isNestable: + #Non-nestable tags get popped to the top or to their + #last occurance. + popTo = name + break + if (nestingResetTriggers is not None + and p.name in nestingResetTriggers) \ + or (nestingResetTriggers is None and isResetNesting + and self.RESET_NESTING_TAGS.has_key(p.name)): + + #If we encounter one of the nesting reset triggers + #peculiar to this tag, or we encounter another tag + #that causes nesting to reset, pop up to but not + #including that tag. + popTo = p.name + inclusive = False + break + p = p.parent + if popTo: + self._popToTag(popTo, inclusive) + + def unknown_starttag(self, name, attrs, selfClosing=0): + #print "Start tag %s: %s" % (name, attrs) + if self.quoteStack: + #This is not a real tag. + #print "<%s> is not real!" % name + attrs = ''.join([' %s="%s"' % (x, y) for x, y in attrs]) + self.handle_data('<%s%s>' % (name, attrs)) + return + self.endData() + + if not self.isSelfClosingTag(name) and not selfClosing: + self._smartPop(name) + + if self.parseOnlyThese and len(self.tagStack) <= 1 \ + and (self.parseOnlyThese.text or not self.parseOnlyThese.searchTag(name, attrs)): + return + + tag = Tag(self, name, attrs, self.currentTag, self.previous) + if self.previous: + self.previous.next = tag + self.previous = tag + self.pushTag(tag) + if selfClosing or self.isSelfClosingTag(name): + self.popTag() + if name in self.QUOTE_TAGS: + #print "Beginning quote (%s)" % name + self.quoteStack.append(name) + self.literal = 1 + return tag + + def unknown_endtag(self, name): + #print "End tag %s" % name + if self.quoteStack and self.quoteStack[-1] != name: + #This is not a real end tag. + #print "</%s> is not real!" % name + self.handle_data('</%s>' % name) + return + self.endData() + self._popToTag(name) + if self.quoteStack and self.quoteStack[-1] == name: + self.quoteStack.pop() + self.literal = (len(self.quoteStack) > 0) + + def handle_data(self, data): + self.currentData.append(data) + + def _toStringSubclass(self, text, subclass): + """Adds a certain piece of text to the tree as a NavigableString + subclass.""" + self.endData() + self.handle_data(text) + self.endData(subclass) + + def handle_pi(self, text): + """Handle a processing instruction as a ProcessingInstruction + object, possibly one with a %SOUP-ENCODING% slot into which an + encoding will be plugged later.""" + if text[:3] == "xml": + text = u"xml version='1.0' encoding='%SOUP-ENCODING%'" + self._toStringSubclass(text, ProcessingInstruction) + + def handle_comment(self, text): + "Handle comments as Comment objects." + self._toStringSubclass(text, Comment) + + def handle_charref(self, ref): + "Handle character references as data." + if self.convertEntities: + data = unichr(int(ref)) + else: + data = '&#%s;' % ref + self.handle_data(data) + + def handle_entityref(self, ref): + """Handle entity references as data, possibly converting known + HTML and/or XML entity references to the corresponding Unicode + characters.""" + data = None + if self.convertHTMLEntities: + try: + data = unichr(name2codepoint[ref]) + except KeyError: + pass + + if not data and self.convertXMLEntities: + data = self.XML_ENTITIES_TO_SPECIAL_CHARS.get(ref) + + if not data and self.convertHTMLEntities and \ + not self.XML_ENTITIES_TO_SPECIAL_CHARS.get(ref): + # TODO: We've got a problem here. We're told this is + # an entity reference, but it's not an XML entity + # reference or an HTML entity reference. Nonetheless, + # the logical thing to do is to pass it through as an + # unrecognized entity reference. + # + # Except: when the input is "&carol;" this function + # will be called with input "carol". When the input is + # "AT&T", this function will be called with input + # "T". We have no way of knowing whether a semicolon + # was present originally, so we don't know whether + # this is an unknown entity or just a misplaced + # ampersand. + # + # The more common case is a misplaced ampersand, so I + # escape the ampersand and omit the trailing semicolon. + data = "&%s" % ref + if not data: + # This case is different from the one above, because we + # haven't already gone through a supposedly comprehensive + # mapping of entities to Unicode characters. We might not + # have gone through any mapping at all. So the chances are + # very high that this is a real entity, and not a + # misplaced ampersand. + data = "&%s;" % ref + self.handle_data(data) + + def handle_decl(self, data): + "Handle DOCTYPEs and the like as Declaration objects." + self._toStringSubclass(data, Declaration) + + def parse_declaration(self, i): + """Treat a bogus SGML declaration as raw data. Treat a CDATA + declaration as a CData object.""" + j = None + if self.rawdata[i:i+9] == '<![CDATA[': + k = self.rawdata.find(']]>', i) + if k == -1: + k = len(self.rawdata) + data = self.rawdata[i+9:k] + j = k+3 + self._toStringSubclass(data, CData) + else: + try: + j = SGMLParser.parse_declaration(self, i) + except SGMLParseError: + toHandle = self.rawdata[i:] + self.handle_data(toHandle) + j = i + len(toHandle) + return j + +class BeautifulSoup(BeautifulStoneSoup): + + """This parser knows the following facts about HTML: + + * Some tags have no closing tag and should be interpreted as being + closed as soon as they are encountered. + + * The text inside some tags (ie. 'script') may contain tags which + are not really part of the document and which should be parsed + as text, not tags. If you want to parse the text as tags, you can + always fetch it and parse it explicitly. + + * Tag nesting rules: + + Most tags can't be nested at all. For instance, the occurance of + a <p> tag should implicitly close the previous <p> tag. + + <p>Para1<p>Para2 + should be transformed into: + <p>Para1</p><p>Para2 + + Some tags can be nested arbitrarily. For instance, the occurance + of a <blockquote> tag should _not_ implicitly close the previous + <blockquote> tag. + + Alice said: <blockquote>Bob said: <blockquote>Blah + should NOT be transformed into: + Alice said: <blockquote>Bob said: </blockquote><blockquote>Blah + + Some tags can be nested, but the nesting is reset by the + interposition of other tags. For instance, a <tr> tag should + implicitly close the previous <tr> tag within the same <table>, + but not close a <tr> tag in another table. + + <table><tr>Blah<tr>Blah + should be transformed into: + <table><tr>Blah</tr><tr>Blah + but, + <tr>Blah<table><tr>Blah + should NOT be transformed into + <tr>Blah<table></tr><tr>Blah + + Differing assumptions about tag nesting rules are a major source + of problems with the BeautifulSoup class. If BeautifulSoup is not + treating as nestable a tag your page author treats as nestable, + try ICantBelieveItsBeautifulSoup, MinimalSoup, or + BeautifulStoneSoup before writing your own subclass.""" + + def __init__(self, *args, **kwargs): + if not kwargs.has_key('smartQuotesTo'): + kwargs['smartQuotesTo'] = self.HTML_ENTITIES + kwargs['isHTML'] = True + BeautifulStoneSoup.__init__(self, *args, **kwargs) + + SELF_CLOSING_TAGS = buildTagMap(None, + ('br' , 'hr', 'input', 'img', 'meta', + 'spacer', 'link', 'frame', 'base', 'col')) + + PRESERVE_WHITESPACE_TAGS = set(['pre', 'textarea']) + + QUOTE_TAGS = {'script' : None, 'textarea' : None} + + #According to the HTML standard, each of these inline tags can + #contain another tag of the same type. Furthermore, it's common + #to actually use these tags this way. + NESTABLE_INLINE_TAGS = ('span', 'font', 'q', 'object', 'bdo', 'sub', 'sup', + 'center') + + #According to the HTML standard, these block tags can contain + #another tag of the same type. Furthermore, it's common + #to actually use these tags this way. + NESTABLE_BLOCK_TAGS = ('blockquote', 'div', 'fieldset', 'ins', 'del') + + #Lists can contain other lists, but there are restrictions. + NESTABLE_LIST_TAGS = { 'ol' : [], + 'ul' : [], + 'li' : ['ul', 'ol'], + 'dl' : [], + 'dd' : ['dl'], + 'dt' : ['dl'] } + + #Tables can contain other tables, but there are restrictions. + NESTABLE_TABLE_TAGS = {'table' : [], + 'tr' : ['table', 'tbody', 'tfoot', 'thead'], + 'td' : ['tr'], + 'th' : ['tr'], + 'thead' : ['table'], + 'tbody' : ['table'], + 'tfoot' : ['table'], + } + + NON_NESTABLE_BLOCK_TAGS = ('address', 'form', 'p', 'pre') + + #If one of these tags is encountered, all tags up to the next tag of + #this type are popped. + RESET_NESTING_TAGS = buildTagMap(None, NESTABLE_BLOCK_TAGS, 'noscript', + NON_NESTABLE_BLOCK_TAGS, + NESTABLE_LIST_TAGS, + NESTABLE_TABLE_TAGS) + + NESTABLE_TAGS = buildTagMap([], NESTABLE_INLINE_TAGS, NESTABLE_BLOCK_TAGS, + NESTABLE_LIST_TAGS, NESTABLE_TABLE_TAGS) + + # Used to detect the charset in a META tag; see start_meta + CHARSET_RE = re.compile("((^|;)\s*charset=)([^;]*)", re.M) + + def start_meta(self, attrs): + """Beautiful Soup can detect a charset included in a META tag, + try to convert the document to that charset, and re-parse the + document from the beginning.""" + httpEquiv = None + contentType = None + contentTypeIndex = None + tagNeedsEncodingSubstitution = False + + for i in range(0, len(attrs)): + key, value = attrs[i] + key = key.lower() + if key == 'http-equiv': + httpEquiv = value + elif key == 'content': + contentType = value + contentTypeIndex = i + + if httpEquiv and contentType: # It's an interesting meta tag. + match = self.CHARSET_RE.search(contentType) + if match: + if (self.declaredHTMLEncoding is not None or + self.originalEncoding == self.fromEncoding): + # An HTML encoding was sniffed while converting + # the document to Unicode, or an HTML encoding was + # sniffed during a previous pass through the + # document, or an encoding was specified + # explicitly and it worked. Rewrite the meta tag. + def rewrite(match): + return match.group(1) + "%SOUP-ENCODING%" + newAttr = self.CHARSET_RE.sub(rewrite, contentType) + attrs[contentTypeIndex] = (attrs[contentTypeIndex][0], + newAttr) + tagNeedsEncodingSubstitution = True + else: + # This is our first pass through the document. + # Go through it again with the encoding information. + newCharset = match.group(3) + if newCharset and newCharset != self.originalEncoding: + self.declaredHTMLEncoding = newCharset + self._feed(self.declaredHTMLEncoding) + raise StopParsing + pass + tag = self.unknown_starttag("meta", attrs) + if tag and tagNeedsEncodingSubstitution: + tag.containsSubstitutions = True + +class StopParsing(Exception): + pass + +class ICantBelieveItsBeautifulSoup(BeautifulSoup): + + """The BeautifulSoup class is oriented towards skipping over + common HTML errors like unclosed tags. However, sometimes it makes + errors of its own. For instance, consider this fragment: + + <b>Foo<b>Bar</b></b> + + This is perfectly valid (if bizarre) HTML. However, the + BeautifulSoup class will implicitly close the first b tag when it + encounters the second 'b'. It will think the author wrote + "<b>Foo<b>Bar", and didn't close the first 'b' tag, because + there's no real-world reason to bold something that's already + bold. When it encounters '</b></b>' it will close two more 'b' + tags, for a grand total of three tags closed instead of two. This + can throw off the rest of your document structure. The same is + true of a number of other tags, listed below. + + It's much more common for someone to forget to close a 'b' tag + than to actually use nested 'b' tags, and the BeautifulSoup class + handles the common case. This class handles the not-co-common + case: where you can't believe someone wrote what they did, but + it's valid HTML and BeautifulSoup screwed up by assuming it + wouldn't be.""" + + I_CANT_BELIEVE_THEYRE_NESTABLE_INLINE_TAGS = \ + ('em', 'big', 'i', 'small', 'tt', 'abbr', 'acronym', 'strong', + 'cite', 'code', 'dfn', 'kbd', 'samp', 'strong', 'var', 'b', + 'big') + + I_CANT_BELIEVE_THEYRE_NESTABLE_BLOCK_TAGS = ('noscript',) + + NESTABLE_TAGS = buildTagMap([], BeautifulSoup.NESTABLE_TAGS, + I_CANT_BELIEVE_THEYRE_NESTABLE_BLOCK_TAGS, + I_CANT_BELIEVE_THEYRE_NESTABLE_INLINE_TAGS) + +class MinimalSoup(BeautifulSoup): + """The MinimalSoup class is for parsing HTML that contains + pathologically bad markup. It makes no assumptions about tag + nesting, but it does know which tags are self-closing, that + <script> tags contain Javascript and should not be parsed, that + META tags may contain encoding information, and so on. + + This also makes it better for subclassing than BeautifulStoneSoup + or BeautifulSoup.""" + + RESET_NESTING_TAGS = buildTagMap('noscript') + NESTABLE_TAGS = {} + +class BeautifulSOAP(BeautifulStoneSoup): + """This class will push a tag with only a single string child into + the tag's parent as an attribute. The attribute's name is the tag + name, and the value is the string child. An example should give + the flavor of the change: + + <foo><bar>baz</bar></foo> + => + <foo bar="baz"><bar>baz</bar></foo> + + You can then access fooTag['bar'] instead of fooTag.barTag.string. + + This is, of course, useful for scraping structures that tend to + use subelements instead of attributes, such as SOAP messages. Note + that it modifies its input, so don't print the modified version + out. + + I'm not sure how many people really want to use this class; let me + know if you do. Mainly I like the name.""" + + def popTag(self): + if len(self.tagStack) > 1: + tag = self.tagStack[-1] + parent = self.tagStack[-2] + parent._getAttrMap() + if (isinstance(tag, Tag) and len(tag.contents) == 1 and + isinstance(tag.contents[0], NavigableString) and + not parent.attrMap.has_key(tag.name)): + parent[tag.name] = tag.contents[0] + BeautifulStoneSoup.popTag(self) + +#Enterprise class names! It has come to our attention that some people +#think the names of the Beautiful Soup parser classes are too silly +#and "unprofessional" for use in enterprise screen-scraping. We feel +#your pain! For such-minded folk, the Beautiful Soup Consortium And +#All-Night Kosher Bakery recommends renaming this file to +#"RobustParser.py" (or, in cases of extreme enterprisiness, +#"RobustParserBeanInterface.class") and using the following +#enterprise-friendly class aliases: +class RobustXMLParser(BeautifulStoneSoup): + pass +class RobustHTMLParser(BeautifulSoup): + pass +class RobustWackAssHTMLParser(ICantBelieveItsBeautifulSoup): + pass +class RobustInsanelyWackAssHTMLParser(MinimalSoup): + pass +class SimplifyingSOAPParser(BeautifulSOAP): + pass + +###################################################### +# +# Bonus library: Unicode, Dammit +# +# This class forces XML data into a standard format (usually to UTF-8 +# or Unicode). It is heavily based on code from Mark Pilgrim's +# Universal Feed Parser. It does not rewrite the XML or HTML to +# reflect a new encoding: that happens in BeautifulStoneSoup.handle_pi +# (XML) and BeautifulSoup.start_meta (HTML). + +# Autodetects character encodings. +# Download from http://chardet.feedparser.org/ +try: + import chardet +# import chardet.constants +# chardet.constants._debug = 1 +except ImportError: + chardet = None + +# cjkcodecs and iconv_codec make Python know about more character encodings. +# Both are available from http://cjkpython.i18n.org/ +# They're built in if you use Python 2.4. +try: + import cjkcodecs.aliases +except ImportError: + pass +try: + import iconv_codec +except ImportError: + pass + +class UnicodeDammit: + """A class for detecting the encoding of a *ML document and + converting it to a Unicode string. If the source encoding is + windows-1252, can replace MS smart quotes with their HTML or XML + equivalents.""" + + # This dictionary maps commonly seen values for "charset" in HTML + # meta tags to the corresponding Python codec names. It only covers + # values that aren't in Python's aliases and can't be determined + # by the heuristics in find_codec. + CHARSET_ALIASES = { "macintosh" : "mac-roman", + "x-sjis" : "shift-jis" } + + def __init__(self, markup, overrideEncodings=[], + smartQuotesTo='xml', isHTML=False): + self.declaredHTMLEncoding = None + self.markup, documentEncoding, sniffedEncoding = \ + self._detectEncoding(markup, isHTML) + self.smartQuotesTo = smartQuotesTo + self.triedEncodings = [] + if markup == '' or isinstance(markup, unicode): + self.originalEncoding = None + self.unicode = unicode(markup) + return + + u = None + for proposedEncoding in overrideEncodings: + u = self._convertFrom(proposedEncoding) + if u: break + if not u: + for proposedEncoding in (documentEncoding, sniffedEncoding): + u = self._convertFrom(proposedEncoding) + if u: break + + # If no luck and we have auto-detection library, try that: + if not u and chardet and not isinstance(self.markup, unicode): + u = self._convertFrom(chardet.detect(self.markup)['encoding']) + + # As a last resort, try utf-8 and windows-1252: + if not u: + for proposed_encoding in ("utf-8", "windows-1252"): + u = self._convertFrom(proposed_encoding) + if u: break + + self.unicode = u + if not u: self.originalEncoding = None + + def _subMSChar(self, orig): + """Changes a MS smart quote character to an XML or HTML + entity.""" + sub = self.MS_CHARS.get(orig) + if isinstance(sub, tuple): + if self.smartQuotesTo == 'xml': + sub = '&#x%s;' % sub[1] + else: + sub = '&%s;' % sub[0] + return sub + + def _convertFrom(self, proposed): + proposed = self.find_codec(proposed) + if not proposed or proposed in self.triedEncodings: + return None + self.triedEncodings.append(proposed) + markup = self.markup + + # Convert smart quotes to HTML if coming from an encoding + # that might have them. + if self.smartQuotesTo and proposed.lower() in("windows-1252", + "iso-8859-1", + "iso-8859-2"): + markup = re.compile("([\x80-\x9f])").sub \ + (lambda(x): self._subMSChar(x.group(1)), + markup) + + try: + # print "Trying to convert document to %s" % proposed + u = self._toUnicode(markup, proposed) + self.markup = u + self.originalEncoding = proposed + except Exception, e: + # print "That didn't work!" + # print e + return None + #print "Correct encoding: %s" % proposed + return self.markup + + def _toUnicode(self, data, encoding): + '''Given a string and its encoding, decodes the string into Unicode. + %encoding is a string recognized by encodings.aliases''' + + # strip Byte Order Mark (if present) + if (len(data) >= 4) and (data[:2] == '\xfe\xff') \ + and (data[2:4] != '\x00\x00'): + encoding = 'utf-16be' + data = data[2:] + elif (len(data) >= 4) and (data[:2] == '\xff\xfe') \ + and (data[2:4] != '\x00\x00'): + encoding = 'utf-16le' + data = data[2:] + elif data[:3] == '\xef\xbb\xbf': + encoding = 'utf-8' + data = data[3:] + elif data[:4] == '\x00\x00\xfe\xff': + encoding = 'utf-32be' + data = data[4:] + elif data[:4] == '\xff\xfe\x00\x00': + encoding = 'utf-32le' + data = data[4:] + newdata = unicode(data, encoding) + return newdata + + def _detectEncoding(self, xml_data, isHTML=False): + """Given a document, tries to detect its XML encoding.""" + xml_encoding = sniffed_xml_encoding = None + try: + if xml_data[:4] == '\x4c\x6f\xa7\x94': + # EBCDIC + xml_data = self._ebcdic_to_ascii(xml_data) + elif xml_data[:4] == '\x00\x3c\x00\x3f': + # UTF-16BE + sniffed_xml_encoding = 'utf-16be' + xml_data = unicode(xml_data, 'utf-16be').encode('utf-8') + elif (len(xml_data) >= 4) and (xml_data[:2] == '\xfe\xff') \ + and (xml_data[2:4] != '\x00\x00'): + # UTF-16BE with BOM + sniffed_xml_encoding = 'utf-16be' + xml_data = unicode(xml_data[2:], 'utf-16be').encode('utf-8') + elif xml_data[:4] == '\x3c\x00\x3f\x00': + # UTF-16LE + sniffed_xml_encoding = 'utf-16le' + xml_data = unicode(xml_data, 'utf-16le').encode('utf-8') + elif (len(xml_data) >= 4) and (xml_data[:2] == '\xff\xfe') and \ + (xml_data[2:4] != '\x00\x00'): + # UTF-16LE with BOM + sniffed_xml_encoding = 'utf-16le' + xml_data = unicode(xml_data[2:], 'utf-16le').encode('utf-8') + elif xml_data[:4] == '\x00\x00\x00\x3c': + # UTF-32BE + sniffed_xml_encoding = 'utf-32be' + xml_data = unicode(xml_data, 'utf-32be').encode('utf-8') + elif xml_data[:4] == '\x3c\x00\x00\x00': + # UTF-32LE + sniffed_xml_encoding = 'utf-32le' + xml_data = unicode(xml_data, 'utf-32le').encode('utf-8') + elif xml_data[:4] == '\x00\x00\xfe\xff': + # UTF-32BE with BOM + sniffed_xml_encoding = 'utf-32be' + xml_data = unicode(xml_data[4:], 'utf-32be').encode('utf-8') + elif xml_data[:4] == '\xff\xfe\x00\x00': + # UTF-32LE with BOM + sniffed_xml_encoding = 'utf-32le' + xml_data = unicode(xml_data[4:], 'utf-32le').encode('utf-8') + elif xml_data[:3] == '\xef\xbb\xbf': + # UTF-8 with BOM + sniffed_xml_encoding = 'utf-8' + xml_data = unicode(xml_data[3:], 'utf-8').encode('utf-8') + else: + sniffed_xml_encoding = 'ascii' + pass + except: + xml_encoding_match = None + xml_encoding_match = re.compile( + '^<\?.*encoding=[\'"](.*?)[\'"].*\?>').match(xml_data) + if not xml_encoding_match and isHTML: + regexp = re.compile('<\s*meta[^>]+charset=([^>]*?)[;\'">]', re.I) + xml_encoding_match = regexp.search(xml_data) + if xml_encoding_match is not None: + xml_encoding = xml_encoding_match.groups()[0].lower() + if isHTML: + self.declaredHTMLEncoding = xml_encoding + if sniffed_xml_encoding and \ + (xml_encoding in ('iso-10646-ucs-2', 'ucs-2', 'csunicode', + 'iso-10646-ucs-4', 'ucs-4', 'csucs4', + 'utf-16', 'utf-32', 'utf_16', 'utf_32', + 'utf16', 'u16')): + xml_encoding = sniffed_xml_encoding + return xml_data, xml_encoding, sniffed_xml_encoding + + + def find_codec(self, charset): + return self._codec(self.CHARSET_ALIASES.get(charset, charset)) \ + or (charset and self._codec(charset.replace("-", ""))) \ + or (charset and self._codec(charset.replace("-", "_"))) \ + or charset + + def _codec(self, charset): + if not charset: return charset + codec = None + try: + codecs.lookup(charset) + codec = charset + except (LookupError, ValueError): + pass + return codec + + EBCDIC_TO_ASCII_MAP = None + def _ebcdic_to_ascii(self, s): + c = self.__class__ + if not c.EBCDIC_TO_ASCII_MAP: + emap = (0,1,2,3,156,9,134,127,151,141,142,11,12,13,14,15, + 16,17,18,19,157,133,8,135,24,25,146,143,28,29,30,31, + 128,129,130,131,132,10,23,27,136,137,138,139,140,5,6,7, + 144,145,22,147,148,149,150,4,152,153,154,155,20,21,158,26, + 32,160,161,162,163,164,165,166,167,168,91,46,60,40,43,33, + 38,169,170,171,172,173,174,175,176,177,93,36,42,41,59,94, + 45,47,178,179,180,181,182,183,184,185,124,44,37,95,62,63, + 186,187,188,189,190,191,192,193,194,96,58,35,64,39,61,34, + 195,97,98,99,100,101,102,103,104,105,196,197,198,199,200, + 201,202,106,107,108,109,110,111,112,113,114,203,204,205, + 206,207,208,209,126,115,116,117,118,119,120,121,122,210, + 211,212,213,214,215,216,217,218,219,220,221,222,223,224, + 225,226,227,228,229,230,231,123,65,66,67,68,69,70,71,72, + 73,232,233,234,235,236,237,125,74,75,76,77,78,79,80,81, + 82,238,239,240,241,242,243,92,159,83,84,85,86,87,88,89, + 90,244,245,246,247,248,249,48,49,50,51,52,53,54,55,56,57, + 250,251,252,253,254,255) + import string + c.EBCDIC_TO_ASCII_MAP = string.maketrans( \ + ''.join(map(chr, range(256))), ''.join(map(chr, emap))) + return s.translate(c.EBCDIC_TO_ASCII_MAP) + + MS_CHARS = { '\x80' : ('euro', '20AC'), + '\x81' : ' ', + '\x82' : ('sbquo', '201A'), + '\x83' : ('fnof', '192'), + '\x84' : ('bdquo', '201E'), + '\x85' : ('hellip', '2026'), + '\x86' : ('dagger', '2020'), + '\x87' : ('Dagger', '2021'), + '\x88' : ('circ', '2C6'), + '\x89' : ('permil', '2030'), + '\x8A' : ('Scaron', '160'), + '\x8B' : ('lsaquo', '2039'), + '\x8C' : ('OElig', '152'), + '\x8D' : '?', + '\x8E' : ('#x17D', '17D'), + '\x8F' : '?', + '\x90' : '?', + '\x91' : ('lsquo', '2018'), + '\x92' : ('rsquo', '2019'), + '\x93' : ('ldquo', '201C'), + '\x94' : ('rdquo', '201D'), + '\x95' : ('bull', '2022'), + '\x96' : ('ndash', '2013'), + '\x97' : ('mdash', '2014'), + '\x98' : ('tilde', '2DC'), + '\x99' : ('trade', '2122'), + '\x9a' : ('scaron', '161'), + '\x9b' : ('rsaquo', '203A'), + '\x9c' : ('oelig', '153'), + '\x9d' : '?', + '\x9e' : ('#x17E', '17E'), + '\x9f' : ('Yuml', ''),} + +####################################################################### + + +#By default, act as an HTML pretty-printer. +if __name__ == '__main__': + import sys + soup = BeautifulSoup(sys.stdin) + print soup.prettify()
--- a/pca.xml Fri Sep 20 13:25:27 2013 -0400 +++ b/pca.xml Fri Sep 20 13:54:23 2013 -0400 @@ -16,7 +16,9 @@ <requirements> <requirement type="package" version="5.0.1">eigensoft</requirement> <requirement type="package" version="0.1">gd_c_tools</requirement> + <!-- <requirement type="package" version="3.2.1">beautifulsoup</requirement> + --> </requirements> <!--
--- a/population_structure.xml Fri Sep 20 13:25:27 2013 -0400 +++ b/population_structure.xml Fri Sep 20 13:54:23 2013 -0400 @@ -14,9 +14,11 @@ <data name="output" format="html" /> </outputs> + <!-- <requirements> <requirement type="package" version="3.2.1">beautifulsoup</requirement> </requirements> + --> <!-- <tests>
--- a/tool_dependencies.xml Fri Sep 20 13:25:27 2013 -0400 +++ b/tool_dependencies.xml Fri Sep 20 13:54:23 2013 -0400 @@ -1,8 +1,10 @@ <?xml version="1.0"?> <tool_dependency> + <!-- <package name="beautifulsoup" version="3.2.1"> <repository prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" owner="miller-lab" name="package_beautifulsoup_3_2_1" changeset_revision="83c21b81ee9d" /> </package> + --> <package name="eigensoft" version="5.0.1"> <repository prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" owner="miller-lab" name="package_eigensoft_5_0_1" changeset_revision="02f04f3579b5" /> </package>