a collection of monkeypatch methods that helps handle better the ET.Element instances from Uniprot XML files

ET_uniprot_monkeypatch.py

__description__ = """
This is a collection of methods that helps handle better the ET.Element instances from Uniprot XML files.
They are monkeypatched to the class object itself.
The Element can be monkeypached by importing xmlschema, as opposed to using the __builtin__ workaround.
Basically, I am piggybacking my monkeypatch on it, meaning that I don't need to copypaste from SO.

* `ET.Element.ns_strip()`  #returns the tag with the {namespace}
* `ET.Element.is_tag(value)` # boolean fx to check if tag == value
* `ET.Element.describe()` # prints the content of the elemtn for debugging, similarly to dump but better.
* `ET.Element.is_human()` # boolean fx to check if human or dancer
* `ET.Element.has_attr(key, opt_value)` # boolean fx to check if it has key and optionally it key has the given value
    """
#### Expanding element tree element...
class ElementalExpansion:
    def ns_strip(self, ns='{http://uniprot.org/uniprot}'):
        return self.tag.replace(ns, '').replace('ns0', '').replace('{', '').replace('}', '')

    def is_tag(self, tag):
        if self.ns_strip() == tag:
            return True
        else:
            return False

    def describe(self):
        print('*' * 10)
        print('element', self)
        print('tag', self.tag)
        print('text', self.text)
        print('tail', self.tail)
        print('attr', self.attrib)
        print([child for child in self])
        print('*' * 10)

    def is_human(self):
        for elem in self:
            if elem.is_tag('organism'):
                for organism_el in list(elem):
                    if organism_el.text == 'Human':
                        return True
        else:
            return False

    def has_attr(self, key, value=None):
        if key in self.attrib:
            if not value:
                return True
            elif self.attrib[key] == value:
                return True
        return False

#### monkeypatching
# Only the Python XML Element can be monkeypatched, the C-implemented one cannot.
# eg. ET.parse or ET.fromstring will return the original.
# this is the hack from xmlschema.
import sys, importlib
sys.modules.pop('xml.etree.ElementTree', None)
sys.modules['_elementtree'] = None
ET = importlib.import_module('xml.etree.ElementTree')
########

ET.Element.ns_strip = ElementalExpansion.ns_strip
ET.Element.is_tag = ElementalExpansion.is_tag
ET.Element.describe = ElementalExpansion.describe
ET.Element.is_human = ElementalExpansion.is_human
ET.Element.has_attr = ElementalExpansion.has_attr