Python: Accessing files inside folders in a zipfile

I would like to access files(xml files) in a zip file in order to do some filtering on them. But how can I go far into the folders in the zip file to access files? My problem is that I can not access files by zip_file.namelist If they are in some folders, here is my code:

import sys, getopt
from lxml import etree
from io import StringIO
import zipfile

def main(argv):

    inputfile = ''
    outputfile = ''
    try:
       opts, args = getopt.getopt(argv,"hi:o:",["ifile=","ofile="])
    except getopt.GetoptError:
       print 'test.py -i <inputfile> -o <outputfile>'
       sys.exit(2)
    for opt, arg in opts:
       if opt == '-h':
          print 'test.py -i <inputfile> -o <outputfile>'
          sys.exit()
       elif opt in ("-i", "--ifile"):
          inputfile = arg
       elif opt in ("-o", "--ofile"):
          outputfile = arg

    archive = zipfile.ZipFile(inputfile, 'r')

    with archive as zip_file:
      for file in zip_file.namelist():
          try:

              print("Process the file")
              xslt_root = etree.XML('''\
                <xsl:stylesheet version="1.0"
                xmlns:xsl="http://ift.tt/tCZ8VR"> 

                <xsl:template match="node() | @*">
                  <xsl:copy>
                      <xsl:apply-templates select="node() | @*"/>
                  </xsl:copy>
                </xsl:template>


                <xsl:template match="TimeStamp"/>
                <xsl:template match="@timeStamp"/>
                <xsl:template match="TimeStamps"/>
                <xsl:template match="Signature"/>

                </xsl:stylesheet>
                ''')

              transform = etree.XSLT(xslt_root)

              doc = etree.parse(file)
              result_tree = transform(doc)

              resultfile = StringIO(unicode(str(result_tree)))
              zip_file.write(resultfile)


          finally:
              zip_file.close()

if __name__=='__main__':
     main(sys.argv[1:])

Exception: It can not read "ex4_linktime/" as this is a folder and not a file!

 File "parser.pxi", line 1110, in lxml.etree._BaseParser._parseDocFromFile     (src\lxml\lxml.etree.c:96832)
 File "parser.pxi", line 582, in lxml.etree._ParserContext._handleParseResultDoc (src\lxml\lxml.etree.c:91290)
 File "parser.pxi", line 683, in lxml.etree._handleParseResult (src\lxml\lxml.etree.c:92476)
 File "parser.pxi", line 620, in lxml.etree._raiseParseError (src\lxml\lxml.etree.c:91737)
 IOError: Error reading file 'ex4_linktime/': failed to load external entity "ex4_linktime/"