eoatex2imxml.py

#!/usr/bin/env python3
# -*- coding: utf-8; mode: python -*-
# Time-stamp: <2018-09-12 11:42:33 (kthoden)>

"""
Converts Latex files into a customized DocBook XML file.

The program depends on the external program tralics for the conversion
as well as xelatex, pdfcrop (part of latex distributions) and
pandoc-citeproc for additional formatting.
"""

# license?
__version__= "1.0"
__author__ = "Klaus Thoden"
__date__="20171205"

# can the job done by BeautifulSoup also be done by lxml.html soupparser?
# as described in http://infohost.nmt.edu/tcc/help/pubs/pylxml/web/soupparser.html
# from lxml.html import soupparser

# imports
import argparse
from lxml import etree
from libeoabibitem import Bibitem
from bs4 import BeautifulSoup
import libeoaconvert
import glob
import os
import re
import string
import shlex
import json
import subprocess
import sys
import shutil
import time
import configparser
import logging
import pickle

# current_directory = os.path.dirname(sys.argv[0])
# is this better?
current_directory = os.path.realpath(__file__)

print("The script is run from {}".format(current_directory))
###############################################################
#  Preperation of certain files and some checks in advance
###############################################################

# Options for the command line: filename / configfile
parser = argparse.ArgumentParser()
parser.add_argument("-c", "--config", help="Name of config file.")
group = parser.add_mutually_exclusive_group()
group.add_argument("-f", "--filename", help="Name of main EOATeX file.")
group.add_argument("-t", "--trash", help="Remove temporary files.")

args = parser.parse_args()

if args.config is not None:
    CONFIG_FILE = os.path.abspath(args.config)
else:
    CONFIG_FILE = os.path.dirname(sys.argv[0]) + os.path.sep.join(["", "config", "eoaconvert.cfg"])

logging.debug("The configfile is %s." % CONFIG_FILE)

# current biber is not compatible with this code
# switch TeX distribution to TeXLive2016,
# run biber_2.1 -O biber2-1n.bbl $INPUT to obtain this file
BIBERFILE = "biber2-1.bbl"

########################
# Constant directories #
########################
CONVERT_DIR = os.getcwd() + os.path.sep + "CONVERT"

##################################
# Reading the configuration file #
##################################
CONFIG = configparser.ConfigParser()
CONFIG.read(CONFIG_FILE)

######################
# Setting up logging #
######################
LOGFILE = CONFIG['General']['logfile']
LOGLEVEL = CONFIG['General']['loglevel']

# numeric_level = getattr(logging, LOGLEVEL.upper(), None)
# if not isinstance(numeric_level, int):
#     raise ValueError('Invalid log level: %s' % loglevel)
logging.basicConfig(filename=LOGFILE, level=LOGLEVEL, format='%(asctime)s - %(levelname)s - %(message)s')

########################
# Paths to executables #
########################
GM_PATH = CONFIG['Executables']['graphicsmagic']
TL_PATH = CONFIG['Executables']['texlive']
TEXBIN_PATH = CONFIG['Executables']['texbin']
TRALICS_PATH_EXEC = CONFIG['Executables']['tralics_path_exec']

############################
# Paths to auxiliary files #
############################
TRALICS_PATH_LIB = CONFIG['Auxiliaries']['TRALICS_PATH_LIB']
TEMPLATE_PATH = CONFIG['Auxiliaries']['template_path']
SUPPORT_PATH = CONFIG['Auxiliaries']['support_path']
# AUX_TeX_FILES_PATH = CONFIG['Auxiliaries']['aux_tex_files_path']

# interimResult = ""

########################################
# Certain functions for specific tasks #
########################################

def getchildren(xmlElement):
    """Include all subelements"""
    1 + 1
    return xmlElement
# def getchildren ends here

def TeX2PNG(LaTeXCode, Type, Chapter, Number):
    """Function to render LaTeX-Code into PNG-Files, returns PNG-Filename (epub & django)"""
    # Dictionary contains Type:begin/end
    Types = {
    "EOAineq" : ["$", "$"],
    "EOAequation" : ["\\begin{equation*}", "\\end{equation*}"],
    "EOAequationnonumber" : ["\\begin{equation*}", "\\end{equation*}"],
    "EOAequationarray" : ["\\begin{align*}", "\\end{align*}"],
    "EOAequationarraynonumber" : ["\\begin{align*}", "\\end{align*}"]
    }
    LaTeXCode = Types[Type][0] + LaTeXCode + Types[Type][1]
    dictRebindedCommands = {
    "\|ket\|" : r"\\ket",
    "\|braket\|" : r"\\braket",
    "\|bra\|" : r"\\bra",
    "\|Bra\|" : r"\\Bra",
    "\|Ket\|" : r"\\Ket",
    "\slashed\|" : r"\\slashed"
    }
    for strCommand in dictRebindedCommands.keys():
        LaTeXCode = re.sub(strCommand, dictRebindedCommands[strCommand], LaTeXCode)

    # Open plain LaTeX-Template
    tmp = open(TEMPLATE_PATH + "formula.tex", "r")
    Template = tmp.read()
    tmp.close()
    # Get tmp-directory for this user account
    # tmpDir = os.getenv("TMPDIR")
    # use local tmpdir
    formula_tmp_dir = os.getcwd() + "/tmp_files/formulas2png/"

    # Make directory items if it doesn't already exist
    if not os.path.exists(os.getcwd() + "/items"):
        os.mkdir(os.getcwd() + "/items")
    s = string.Template(Template)
    e = s.substitute(DERINHALT=LaTeXCode)
    tmpFile = formula_tmp_dir + Type + "_" + str(Chapter) + "_" + str(Number) + ".tex"
    tmp = open(tmpFile, "w")
    tmp.write(e)
    tmp.close()
    Kommando = TEXBIN_PATH + "xelatex --halt-on-error " + tmpFile
    Argumente = shlex.split(Kommando)
    # Redirecting stderr to save XeLaTeX-Output
    Datei = open('tmp_files/xelatex-run.log', 'w')
    Ergebnis = subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
    if Ergebnis == 0:
        print("Successfully converted formula " + Type + str(Chapter) + "_" + str(Number))
    if Ergebnis == 1:
        print("[ERROR]: Failed to convert formula " + Type + str(Chapter) + "_" + str(Number))
    Kommando = TL_PATH + "texmf-dist/scripts/pdfcrop/pdfcrop.pl " + formula_tmp_dir + Type + "_" + str(Chapter) + "_" + str(Number) + ".pdf " + formula_tmp_dir + Type + "_" + str(Chapter) + "_" + str(Number) + "a.pdf"
    Argumente = shlex.split(Kommando)
    subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
    Kommando = GM_PATH + " convert -density 144 " + formula_tmp_dir + Type + "_" + str(Chapter) + "_" + str(Number) + "a.pdf " + os.getenv("PWD") + "/items/" + Type + "_" + str(Chapter) + "_" + str(Number) + ".png"
    Argumente = shlex.split(Kommando)
    subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)

    return LaTeXCode
# def TeX2PNG ends here

def make_bibchecker(bib_database, set_citations):
    """Construct a separate latex file with bibliography.

    The HTML bibliography is still not perfectly formatted like the
    LaTeX version. To check both files, a separate file is made that and
    which is then also converted in the various formats.
    """

    tmp_latex = open(TEMPLATE_PATH + "largebib.tex", "r")
    largebib_template = tmp_latex.read()
    tmp_latex.close()

    tmp_xml = open(TEMPLATE_PATH + "largebib-xml.tex", "r")
    largebib_xml_template = tmp_xml.read()
    tmp_xml.close()

    string_citations = ", ".join(set_citations)

    largebib_template_string = string.Template(largebib_template)
    largebib_replacement = largebib_template_string.substitute(INSERT_BIB_DATABASE = bib_database, INSERT_CITEKEYS = string_citations)

    largebib_template_string_xml = string.Template(largebib_xml_template)
    largebib_replacement_xml = largebib_template_string_xml.substitute(INSERT_BIB_DATABASE = bib_database, INSERT_CITEKEYS = string_citations)

    tmp_latex_file = "%s/debug/debug_onlybib.tex" % (os.getcwd())
    tmp_latex = open(tmp_latex_file, "w")
    tmp_latex.write(largebib_replacement)
    tmp_latex.close()

    tmp_xml_file = "%s/debug/debug_onlybib-xml.tex" % (os.getcwd())
    tmp_xml = open(tmp_xml_file, "w")
    tmp_xml.write(largebib_replacement_xml)
    tmp_xml.close()
# def make_bibchecker ends here

def sanitize_bibentry(bibEntry):
    """Some additional cleanup actions"""

    bibEntry = bibEntry.replace(". , ", ", ")
    bibEntry = bibEntry.replace("vols..", "vols.")

    return(bibEntry.strip())
# def sanitize_bibentry ends here

def createBibEntryAuthorYear(bibEntry, boolSameAuthor):
    """Function to create a complete Entry of a publication (epub & django) for author-year citation"""
    strBibEntry = ""
    if bibEntry.entrytype() not in libeoaconvert.allowed_bibentry_types:
        print("[ERROR]: You cannot use the entry type %s in entry %s. Allowed entry types are: %s.\n" % (bibEntry.entrytype(), bibEntry.citekey() , ", ".join(libeoaconvert.allowed_bibentry_types)))
        sys.exit()

    bool_edited_book = False
    book_without_author = False
    editor_postfix = bibEntry.fullauthorlastfirst()[1]
    if boolSameAuthor == False:
        if len(editor_postfix) != 0:
            if editor_postfix == "no_author_only_title":
                book_without_author = True
                strAuthor = bibEntry.title()
            else:
                bool_edited_book = True
                strAuthor = bibEntry.fullauthorlastfirst()[0] + ", " + editor_postfix
        else:
            strAuthor = bibEntry.fullauthorlastfirst()[0]
    if boolSameAuthor == True:
        # if there is no author, but a publisher, the localized
        # postfix is returned from the function together with the name in a tuple
        if len(editor_postfix) != 0:
            bool_edited_book = True
            strAuthor = "– " + editor_postfix
        else:
            strAuthor = "–"
    # Next line good for debugging
    # print(bibEntry.citekey(), strAuthor)
    if bibEntry.entrytype() == "book":
        if bool_edited_book == True:
            strBibEntry = strAuthor + " (" + str(bibEntry.labelyear()) + str(bibEntry.labelyearsuffix()) + "). <i>" + str(bibEntry.title()) + "</i> " +  bibEntry.edition() + bibEntry.volumenumeric() + bibEntry.seriesnumber() + bibEntry.note() + str(bibEntry.location()) + bibEntry.pages() + ". " + bibEntry.url()
        elif book_without_author == True:
            strBibEntry =  "<i>" + str(bibEntry.title()) + "</i> " + " (" + str(bibEntry.labelyear()) + str(bibEntry.labelyearsuffix()) + ")." +  bibEntry.edition() + bibEntry.volumenumeric() + bibEntry.seriesnumber() + bibEntry.note()  + str(bibEntry.location()) + bibEntry.pages() + ". " + bibEntry.url()
        else:
            strBibEntry = strAuthor + " (" + str(bibEntry.labelyear()) + str(bibEntry.labelyearsuffix()) + "). <i>" + str(bibEntry.title()) + "</i> " +  bibEntry.editor() + bibEntry.edition() + bibEntry.volumenumeric() + bibEntry.seriesnumber() + bibEntry.note() + str(bibEntry.location()) + bibEntry.pages() + ". " + bibEntry.url()
    if bibEntry.entrytype() == "booklet":
        strBibEntry = strAuthor + " (" + str(bibEntry.labelyear()) + str(bibEntry.labelyearsuffix()) + "). <i>" + str(bibEntry.title()) + "</i>" + str(bibEntry.location()) + bibEntry.howpublished() + "."
    if bibEntry.entrytype() == "report":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + "). <i>" + bibEntry.title() + "</i>"
    if bibEntry.entrytype() == "thesis":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + "). <i>" + bibEntry.title() + "</i>" + bibEntry.thesistype() + bibEntry.institution() + "." + bibEntry.url()
    if bibEntry.entrytype() == "misc":
        strBibEntry = strAuthor + " (" + str(bibEntry.labelyear()) + str(bibEntry.labelyearsuffix()) + "). <i>" + str(bibEntry.title()) + "</i> " + bibEntry.howpublished() + ". " + bibEntry.note() + bibEntry.location() + bibEntry.thesistype() + "." + bibEntry.url()
    if bibEntry.entrytype() == "incollection":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + "). " + bibEntry.title() + bibEntry.booktitle() + ". " + bibEntry.editor() + bibEntry.edition() + bibEntry.volumenumeric() + bibEntry.seriesnumber() + bibEntry.note() + bibEntry.location() + bibEntry.pages() + "." + bibEntry.url()
    if bibEntry.entrytype() == "inproceedings":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + "). " + bibEntry.title() + bibEntry.booktitle() + bibEntry.editor() + bibEntry.series() + bibEntry.location() + bibEntry.pages()
    if bibEntry.entrytype() == "article":
        strBibEntry = strAuthor + " (" + str(bibEntry.labelyear()) + str(bibEntry.labelyearsuffix()) + "). " + str(bibEntry.title()) + str(bibEntry.journaltitle()) + bibEntry.volumenumberpages() + ". " + bibEntry.note() + bibEntry.url()
    if bibEntry.entrytype() == "newspaper":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + "). <i>" + bibEntry.title() + "</i>"

    # print(strBibEntry)

    return sanitize_bibentry(strBibEntry)
# def createBibEntryAuthorYear ends here

def createBibEntryNumeric(bibEntry):
    """Function to create a complete Entry of a publication (epub & django) for numeric citation"""

    strBibEntry = ""
    if bibEntry.entrytype() not in libeoaconvert.allowed_bibentry_types:
        print("[ERROR]: You cannot use the entry type %s in entry %s. Allowed entry types are: %s.\n" % (bibEntry.entrytype(), bibEntry.citekey() , ", ".join(libeoaconvert.allowed_bibentry_types)))
        sys.exit()

    strAuthor = bibEntry.fullauthorfirstlast()
    if bibEntry.entrytype() == "book":
        strBibEntry = strAuthor + ". <i>" + bibEntry.title() + "</i>." + bibEntry.location() + ", " + bibEntry.year()
    if bibEntry.entrytype() == "booklet":
        strBibEntry = strAuthor + ". <i>" + bibEntry.title() + "</i>. " + bibEntry.howpublished() + ". " + bibEntry.location() + ", " + bibEntry.year()
    if bibEntry.entrytype() == "report":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + ") <i>" + bibEntry.title() + "</i>."
    if bibEntry.entrytype() == "thesis":
        strBibEntry = strAuthor + ". <i>" + bibEntry.title() + "</i>. " + bibEntry.thesistype() + bibEntry.institution() + ", " + bibEntry.year()
    if bibEntry.entrytype() == "misc":
        strBibEntry = strAuthor + ". " + bibEntry.title() + ". " + bibEntry.booktitle() + ". "
    if bibEntry.entrytype() == "incollection":
        strBibEntry = strAuthor + ". " + bibEntry.title() + ". " + bibEntry.booktitle() + bibEntry.editor() + ". " + bibEntry.location() + ", " + bibEntry.year() + ". " + bibEntry.pages() + "."
    if bibEntry.entrytype() == "inproceedings":
        strBibEntry = strAuthor + ". " + bibEntry.title() + ". " + bibEntry.booktitle() + ". " + bibEntry.volumenumeric() + bibEntry.year() + ". " + bibEntry.pages() + "."
    if bibEntry.entrytype() == "article":
        strBibEntry = strAuthor + ". " + bibEntry.title() + "<i>" + bibEntry.journaltitle() + "</i> " + bibEntry.volumenumberpages() + " (" + bibEntry.year() + "):" + bibEntry.pages() + "."
    if bibEntry.entrytype() == "newspaper":
        strBibEntry = strAuthor + " (" + bibEntry.labelyear() + bibEntry.labelyearsuffix() + ") <i>" + bibEntry.title() + "</i>."

    return strBibEntry
# def createBibEntryNumeric ends here

def pdf_burst(input_file, tmpDir):
    """Split PDF file into single pages"""
    from PyPDF2 import PdfFileWriter, PdfFileReader

    input1 = PdfFileReader(open(tmpDir + input_file, "rb"))
    logging.debug("Input is %s and has %d pages." % (input_file, input1.getNumPages()))

    for pageno in range(input1.getNumPages()):
        output = PdfFileWriter()
        output.addPage(input1.getPage(pageno))

        output_filename = tmpDir + "EOAformulas_%d.pdf" % (pageno + 1)
        output_stream = open(output_filename, 'wb')
        output.write(output_stream)
        output_stream.close()
        logging.debug("Wrote %s." % output_filename)

        pageno += 1
# def pdf_burst ends here

def progress(count, total, status=''):
    """Progress bar for command line. Taken from
    https://gist.github.com/vladignatyev/06860ec2040cb497f0f3"""

    bar_len = 60
    filled_len = int(round(bar_len * count / float(total)))

    percents = round(100.0 * count / float(total), 1)
    bar = '#' * filled_len + '-' * (bar_len - filled_len)

    sys.stdout.write('[%s] %s%s ... %s\r' % (bar, percents, '%', status))
    sys.stdout.flush()
# def progress ends here

def cleanup():
    """Remove support files"""
    try:
        os.remove((os.getcwd() + "/classes.dtd"))
        os.remove((os.getcwd() + "/mathml2-qname-1.mod"))
        os.remove((os.getcwd() + "/mathml2.dtd"))
        shutil.rmtree((os.getcwd() + "/html"))
        shutil.rmtree((os.getcwd() + "/iso8879"))
        shutil.rmtree((os.getcwd() + "/iso9573-13"))
        shutil.rmtree((os.getcwd() + "/mathml"))
        # shutil.rmtree((os.getcwd() + "/mathml2"))
        logging.debug("Removed support files.")

    except:
        print("No temporary files were found.")
# def cleanup ends here

# Remove temporary files, neccessary for troubleshooting
if args.trash == "temp":
    cleanup()
    sys.exit()

#################################################
# Checking for existance of tools and libraries #
#################################################
if not os.path.exists(TRALICS_PATH_LIB):
    print("Cannot find the Tralics configuration at %s. Exiting." % TRALICS_PATH_LIB)
    sys.exit()

##################################
# Setting up various directories #
##################################

if not os.path.exists("tmp_files"):
    os.mkdir(os.path.expanduser("tmp_files"))
if not os.path.exists("tmp_files/formulas2png/"):
    os.mkdir(os.path.expanduser("tmp_files/formulas2png/"))
if not os.path.exists(os.getcwd() + "/debug"):
    os.mkdir(os.getcwd() + "/debug")

# Check for folder and necessary files
if not os.path.exists(CONVERT_DIR):
    print("The directory CONVERT has not been created yet. Creating it for you")
    time.sleep(1)
    os.makedirs(CONVERT_DIR)
if not os.path.exists(CONVERT_DIR + os.path.sep + "publication.cfg"):
    print("The publication.cfg file is missing in CONVERT directory.")
    if os.path.exists(os.getcwd() + os.path.sep + "publication.cfg"):
        shutil.copy("publication.cfg", CONVERT_DIR)
        print("Copied from current directory.")
    else:
        print("Found no publication.cfg. Exiting")
        sys.exit()
if not os.path.exists(CONVERT_DIR + os.path.sep + "cover.jpg"):
    print("The file Cover.jpg in CONVERT directory is missing.")
    if os.path.exists(os.getcwd() + os.path.sep + "Cover.jpg"):
        shutil.copy("Cover.jpg", CONVERT_DIR + os.path.sep + "cover.jpg")
        print("Copied from current directory.")
    else:
        print("No coverfile found. You can create a temporary one with the mkimage.py script")
        sys.exit()
# if os.path.exists(os.getcwd() + "/pre_xml.tex") == False:
#     print ("pre_xml fehlt")
#     sys.exit()

# Copy Support-Files from /Library/MPIWG to current directory
shutil.copy(SUPPORT_PATH + "classes.dtd", os.getcwd())
shutil.copy(SUPPORT_PATH + "mathml2-qname-1.mod", os.getcwd())
shutil.copy(SUPPORT_PATH + "mathml2.dtd", os.getcwd())
shutil.copytree(SUPPORT_PATH + "html", (os.getcwd() + "/html"))
shutil.copytree(SUPPORT_PATH + "iso8879", (os.getcwd() + "/iso8879"))
shutil.copytree(SUPPORT_PATH + "iso9573-13", (os.getcwd() + "/iso9573-13"))
shutil.copytree(SUPPORT_PATH + "mathml", (os.getcwd() + "/mathml"))
# shutil.copytree(SUPPORT_PATH + "mathml2", (os.getcwd() + "/mathml2"))

##############################################################
#                  Preparing the main document               #
##############################################################

# Convert TeX to XML via Tralics
Kommando = "%s -log_file %s -confdir %s/tralics_conf -config %s/tralics.tcf -utf8 -utf8output %s.tex" % (TRALICS_PATH_EXEC, args.filename + "-tralics.log", TRALICS_PATH_LIB, TRALICS_PATH_LIB, args.filename)
Argumente = shlex.split(Kommando)
Prozess = subprocess.call(Argumente)

# Fix underscore und fix EOAtranscripted
tmpFile = open ((args.filename) + ".xml", "r")
tmpText = tmpFile.read()
tmpFile.close()

tmpText = re.sub(r"<error n='_' l='(.*?)' c='Missing dollar'/>", "_", tmpText)
tmpText = re.sub(r"<error n='\\par' l='(.*?)' c='Invalid \\par command: paragraph not started'/>", "", tmpText)
tmpFile = open ((args.filename) + ".xml", "w")
tmpFile.write(tmpText)
tmpFile.close()

# Complete XML-Document in xmlTree
xmlParser = etree.XMLParser(no_network=False,load_dtd=True) #resolve_entities=False
xmlTree = etree.parse((args.filename + ".xml"), xmlParser)
xmlChapters = xmlTree.findall("//div1")

# Cleanup of not needed tags in advance. To be cleaned: <error>
etree.strip_elements(xmlTree, with_tail=False, *['error'])

print("-----------------------------------------------------")
print("Move EOAlanguage from <head> into attribute of EOAchapter")
intChapterNumber = 1
for xmlChapter in xmlChapters:
    xmlLanguage = xmlChapter.find(".//EOAlanguage")
    if xmlLanguage is not None:
        strLanguage = xmlLanguage.text or "english"
        xmlChapter.set("language", strLanguage)
        xmlLanguage.text = None
        print("The language of Chapter %d is %s." % (intChapterNumber, strLanguage))
    xmlChapter = etree.strip_tags(xmlChapter, "EOAlanguage")
    intChapterNumber += 1

##############################################################
#      Numbering and Typesetting various Elements            #
##############################################################

# Figure out how to number (like essay or regular)
try:
    strSerie = xmlTree.find(".//EOAseries").text or "regular"
except AttributeError:
    print("\n\nYou are most probably using the preamble for the PDF output. Exiting.")
    sys.exit()

if strSerie == "Essay":
    strNumberingType = "essay"
else:
    strNumberingType = "regular"

# Dictionaries containing UIDs and Numbers
dictChapters = {}
dictFigures = {}
dictEquations = {}
dictSections = {}
dictFootnotes = {}
dictPagelabels = {}
dictTables = {}
dictLists = {}
dictTheorems = {}

set_citations = set()

print("-----------------------------------------------------")
print("Numbering Chapters")
Chapternumber = 1
for xmlChapter in xmlChapters:
    if xmlChapter.get('rend') != "nonumber":
        Chapteruid = xmlChapter.get('id')
        dictChapters[Chapteruid] = str(Chapternumber)
        Chapternumber += 1

# EOAequation, EOAsubequation and EOAequationarray Numbering per Chapter
intChapterNumber = 1
print("-----------------------------------------------------")
print("Processing .//EOAequation | .//EOAequationarray | .//EOAsubequations")
for xmlChapter in xmlChapters:
    intEquationnumber = 1
    xmlDinge = xmlChapter.xpath(".//EOAequation | .//EOAequationarray | .//EOAsubequations")
    print("Working on Chapter %d which contains %d formulæ." % (intChapterNumber, len(xmlDinge)))
    for xmlDing in xmlDinge:
        if xmlDing.tag == "EOAequationarray":
            # tmpNumberinArray is only being used for filename
            tmpNumberinArray = intEquationnumber
            # tmpDictNumberLabel used to insert the attribute value into <EOAequation>
            tmpDictNumberLabel = {}
            # Numbering is being done by <mtr>-Tags
            xmlMathmlrows = xmlDing.findall(".//{http://www.w3.org/1998/Math/MathML}mtr")
            for xmlMathmlrow in xmlMathmlrows:
                if "Label" in xmlMathmlrow.attrib:
                    # Label dem Dictionary für die Euqations hinzufügen
                    if xmlChapter.get("rend") != "nonumber":
                        dictEquations[xmlMathmlrow.get("Label")] = str(dictChapters[xmlChapter.get('id')]) + "." + str(intEquationnumber)
                        tmpDictNumberLabel[str(dictChapters[xmlChapter.get('id')]) + "." + str(intEquationnumber)] = xmlMathmlrow.get("Label")
                    if xmlChapter.get("rend") == "nonumber":
                        dictEquations[xmlMathmlrow.get("Label")] = str(intEquationnumber)
                        tmpDictNumberLabel[str(intEquationnumber)] = xmlMathmlrow.get("Label")
                intEquationnumber += 1
            xmlRohTeX = xmlDing.find(".//texmath")
            xmlNew = etree.Element('EOAequationarray')
            # Blank lines need to be removed otherwise TeX won't work
            textSourcecode = os.linesep.join([s for s in xmlRohTeX.text.splitlines() if s])
            # \rowattributeunknown has to be deleted, its an artefact
            textSourcecode = re.sub("\\\\rowattributeunknown", "", textSourcecode)
            # Push Down loop to parse the raw code
            textFormel = ""
            boolBackslash = False
            for Buchstabe in textSourcecode:
                if Buchstabe == "\n":
                    continue
                if Buchstabe == "\\":
                    if boolBackslash == False:
                        textFormel += Buchstabe
                        boolBackslash = True
                        continue
                    if boolBackslash == True:
                        textFormel += Buchstabe
                        str_latexcode = TeX2PNG(textFormel, "EOAequationarray", str(intChapterNumber), str(tmpNumberinArray))
                        if xmlChapter.get("rend") != "nonumber":
                            tmpXML = etree.Element("EOAequation", filename=("EOAequationarray" + "_" + str(intChapterNumber) + "_" + str(tmpNumberinArray) + ".png"), number=(str(dictChapters[xmlChapter.get('id')]) + "." + str(tmpNumberinArray)))
                        if xmlChapter.get("rend") == "nonumber":
                            tmpXML = etree.Element("EOAequation", filename=("EOAequationarray" + "_" + str(intChapterNumber) + "_" + str(tmpNumberinArray) + ".png"), number=(str(tmpNumberinArray)))
                        tmpXML.set("TeX", str_latexcode)
                        # Put Label into EOAequation
                        if xmlChapter.get("rend") != "nonumber":
                            strTempKey = str(dictChapters[xmlChapter.get('id')]) + "." + str(tmpNumberinArray)
                        if xmlChapter.get("rend") == "nonumber":
                            strTempKey = str(tmpNumberinArray)
                        if strTempKey in tmpDictNumberLabel:
                            #tmpXML.set("label", tmpDictNumberLabel[(str(dictChapters[xmlChapter.get('id')]) + "." + str(tmpNumberinArray))])
                            tmpXML.set("label", tmpDictNumberLabel[strTempKey])
                        xmlNew.append(tmpXML)
                        textFormel = ""
                        boolBackslash = False
                        tmpNumberinArray += 1
                        continue
                if Buchstabe != "\\":
                    textFormel += Buchstabe
                    boolBackslash = False
            # Typeset last equation
            str_latexcode = TeX2PNG(textFormel, "EOAequationarray", str(intChapterNumber), str(tmpNumberinArray))
            if xmlChapter.get("rend") != "nonumber":
                tmpXML = etree.Element("EOAequation", filename=("EOAequationarray" + "_" + str(intChapterNumber) + "_" + str(tmpNumberinArray) + ".png"), number=(dictChapters[xmlChapter.get('id')] + "." + str(tmpNumberinArray)))
            if xmlChapter.get("rend") == "nonumber":
                tmpXML = etree.Element("EOAequation", filename=("EOAequationarray" + "_" + str(intChapterNumber) + "_" + str(tmpNumberinArray) + ".png"), number=(str(tmpNumberinArray)))
            tmpXML.set("TeX", str_latexcode)
            # Put Label into EOAequation
            if xmlChapter.get("rend") != "nonumber":
                strTempKey = str(dictChapters[xmlChapter.get('id')]) + "." + str(tmpNumberinArray)
            if xmlChapter.get("rend") == "nonumber":
                strTempKey = str(tmpNumberinArray)
            if strTempKey in tmpDictNumberLabel:
                print(strTempKey)
                print(tmpDictNumberLabel)
                print(dictChapters)
                tmpXML.set("label", tmpDictNumberLabel[strTempKey])
            xmlNew.append(tmpXML)
            xmlDing.getparent().replace(xmlDing, xmlNew)
            # enclosing <p>-Tag of the Subequations is not wanted, transformed to <temp> to be deleted later on
            #xmlNew.getparent().tag = "temp"
            continue
        if xmlDing.tag == "EOAsubequations":
            # Enclosing <p>-Tag of the EOAsubequations needs to be removed
            xmlDing.getparent().tag = "temp"
            xmlSubequations = xmlDing.findall('.//EOAequation')
            listCharacters = ['a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z']
            tmpI = 0
            # Insert Number of this Subequation into dictEquations
            xmlAnchor = xmlDing.find(".//anchor")
            print(xmlAnchor)
            if xmlChapter.get("rend") != "nonumber":
                dictEquations[xmlAnchor.get('id')] = dictChapters[xmlChapter.get('id')] + "." + str(intEquationnumber)
            if xmlChapter.get("rend") == "nonumber":
                dictEquations[xmlAnchor.get('id')] = str(intEquationnumber)
            # Delete anchor
            xmlAnchor.getparent().remove(xmlAnchor)
            for xmlSubequation in xmlSubequations:
                # Enclosing <p>-Tag of the EOAsubequation needs to be removed
                #xmlSubequation.getparent().tag = "temp"
                # Numbering Subequations with characters
                strSubequationNumber = str(intEquationnumber) + listCharacters[tmpI]
                tmpI += 1
                textSourcecode = xmlSubequation.find('.//texmath').text
                # Blank lines need to be removed otherwise TeX won't work
                textSourcecode = os.linesep.join([s for s in textSourcecode.splitlines() if s])
                str_latexcode = TeX2PNG(textSourcecode, "EOAequation", str(intChapterNumber), strSubequationNumber)
                xmlAnchor = xmlSubequation.find(".//anchor")
                # Clear Equation
                xmlSubequation.clear()
                if xmlChapter.get("rend") != "nonumber":
                    xmlSubequation.set("filename", "EOAequation" + "_" + str(intChapterNumber) + "_" + strSubequationNumber + ".png")
                    xmlSubequation.set("number", dictChapters[xmlChapter.get('id')] + "." + strSubequationNumber)
                    xmlSubequation.set("uid", xmlAnchor.get('id'))
                if xmlChapter.get("rend") == "nonumber":
                    xmlSubequation.set("filename", "EOAequation" + "_" + str(intChapterNumber) + "_" + strSubequationNumber + ".png")
                    xmlSubequation.set("number", strSubequationNumber)
                    xmlSubequation.set("uid", xmlAnchor.get('id'))
                xmlSubequation.set("id", xmlAnchor.get('id'))
                xmlSubequation.set("TeX", str_latexcode)
                # Insert Number of this Equation into dictEquations
                if strNumberingType == "regular":
                    dictEquations[xmlAnchor.get('id')] = str(dictChapters[xmlChapter.get('id')]) + "." + strSubequationNumber
                if strNumberingType == "essay":
                    dictEquations[xmlAnchor.get('id')] = strSubequationNumber
            # TODO: Anchor direkt unter Subequation aufheben, und der ersten Equation zuordnen, so dass auf 8.16 bei 8.16a und 8.16b verlinkt werden kann
            xmlDing.tag = "temp"
            # enclosing <p>-Tag of the Subequations is not wanted, transformed to <temp> to be deleted later on
            #xmlDing.getparent().tag = "temp"
            intEquationnumber += 1
            continue
        if xmlDing.tag == "EOAequation":
            # Check, if Equation has already been found in a Subeqation
            xmlAnchor = xmlDing.find("anchor")
            if xmlAnchor == None:
                continue
            if xmlAnchor.get('id') in dictEquations:
                continue
            if xmlDing.find('.//texmath') is not None:
                textSourcecode = xmlDing.find('.//texmath').text
            else:
                textSourcecode = xmlDing.text
            # Blank lines need to be removed otherwise TeX won't work
            textSourcecode = os.linesep.join([s for s in textSourcecode.splitlines() if s])
            str_latexcode = TeX2PNG(textSourcecode, "EOAequation", intChapterNumber, intEquationnumber)
            #print ("Got:")
            #print (str_latexcode)
            if xmlChapter.get("rend") != "nonumber":
                xmlDing.set("filename", "EOAequation" + "_" + str(intChapterNumber) + "_" + str(intEquationnumber) + ".png")
                xmlDing.set("number", dictChapters[xmlChapter.get('id')] + "." + str(intEquationnumber))
                xmlDing.set("uid", xmlAnchor.get('id'))
            if xmlChapter.get("rend") == "nonumber":
                xmlDing.set("filename", "EOAequation" + "_" + str(intChapterNumber) + "_" + str(intEquationnumber) + ".png")
                xmlDing.set("number", str(intEquationnumber))
                xmlDing.set("uid", xmlAnchor.get('id'))
            xmlDing.set("id", xmlAnchor.get('id'))
            xmlDing.set("TeX", str_latexcode)
            #xmlDing.getparent().replace(xmlDing, xmlNew)
            # Insert Number of this Equation into dictEquations
            if strNumberingType == "regular":
                dictEquations[xmlAnchor.get('id')] = \
                    str(dictChapters[xmlChapter.get('id')]) + "." + str(intEquationnumber)
            if strNumberingType == "essay":
                dictEquations[xmlAnchor.get('id')] = str(intEquationnumber)
            intEquationnumber += 1
            continue
    intChapterNumber += 1

intChapterNumber = 1
print("-----------------------------------------------------")
print("Processing .//EOAequationnonumber | .//EOAequationarraynonumber")
for xmlChapter in xmlChapters:
    tempImagenumber = 1
    xmlDinge = xmlChapter.xpath(".//EOAequationnonumber | .//EOAequationarraynonumber")
    print("Working on Chapter %d which contains %d formulæ." % (intChapterNumber, len(xmlDinge)))
    # print ("Working on Chapter " + str(intChapterNumber))
    # print ("Es wurden " + str(len(xmlDinge)) + " Formeln gefunden")
    for xmlDing in xmlDinge:
        if xmlDing.tag == "EOAequationarraynonumber":
            if xmlDing.find(".//texmath") is not None:
                textSourcecode = xmlDing.find(".//texmath").text
            else:
                textSourcecode = xmlDing.text
            xmlNew = etree.Element('EOAequationarraynonumber')
            # Blank lines need to be removed otherwise TeX won't work
            textSourcecode = os.linesep.join([s for s in textSourcecode.splitlines() if s])
            # \rowattributeunknown has to be deleted, its an artefact
            textSourcecode = re.sub("\\\\rowattributeunknown", "", textSourcecode)
            # TODO: HIer überprüfen, ob und inwiefern es ausreichend ist, EOAequationarraynonumber in eine Grafik zu packen
            str_latexcode = TeX2PNG(textSourcecode, "EOAequationarraynonumber", str(intChapterNumber), str(tempImagenumber))
            xmlNew = etree.Element("EOAequationnonumber", filename=("EOAequationarraynonumber" + "_" + str(intChapterNumber) + "_" + str(tempImagenumber) + ".png"))
            xmlNew.set("TeX", str_latexcode)
            xmlDing.getparent().replace(xmlDing, xmlNew)
            tempImagenumber += 1
            continue
            # Push Down loop to parse the raw code (Wird vorerst nicht ausgeführt)
            textFormel = ""
            boolBackslash = False
            for Buchstabe in textSourcecode:
                if Buchstabe == "\n":
                    continue
                if Buchstabe == "\\":
                    if boolBackslash == False:
                        textFormel += Buchstabe
                        boolBackslash = True
                        continue
                    if boolBackslash == True:
                        textFormel += Buchstabe
                        str_latexcode = TeX2PNG(textFormel, "EOAequationarraynonumber", str(intChapterNumber), str(tempImagenumber))
                        tmpXML = etree.Element("EOAequationnonumber", filename=("EOAequationarraynonumber" + "_" + str(intChapterNumber) + "_" + str(tempImagenumber) + ".png"))
                        tmpXML.set("TeX", str_latexcode)
                        xmlNew.append(tmpXML)
                        textFormel = ""
                        boolBackslash = False
                        tempImagenumber += 1
                        continue
                if Buchstabe != "\\":
                    textFormel += Buchstabe
                    boolBackslash = False
            # Typeset last equation
            str_latexcode = TeX2PNG(textFormel, "EOAequationarraynonumber", str(intChapterNumber), str(tempImagenumber))
            tmpXML = etree.Element("EOAequationnonumber", filename=("EOAequationarraynonumber" + "_" + str(intChapterNumber) + "_" + str(tempImagenumber) + ".png"))
            tmpXML.set("TeX", str_latexcode)
            xmlNew.append(tmpXML)
            xmlDing.getparent().replace(xmlDing, xmlNew)
            continue
        if xmlDing.tag == "EOAequationnonumber":
            textSourcecode = xmlDing.find('.//texmath').text
            # Blank lines need to be removed otherwise TeX won't work
            textSourcecode = os.linesep.join([s for s in textSourcecode.splitlines() if s])
            str_latexcode = TeX2PNG(textSourcecode, "EOAequationnonumber", str(intChapterNumber), tempImagenumber)
            # TODO: HTML-Code für das fertige Bild einfügen (Ist dieser ToDo noch aktuell?)
            xmlNew = etree.Element("EOAequationnonumber", filename=("EOAequationnonumber" + "_" + str(intChapterNumber) + "_" + str(tempImagenumber) + ".png"))

            xmlNew.set("TeX", str_latexcode)

            xmlDing.getparent().replace(xmlDing, xmlNew)
            tempImagenumber += 1
            continue
    intChapterNumber += 1

print("-----------------------------------------------------")
print("Converting EOAineq")
intChapterNumber = 1
intEOAineqRunningOrder = 1
dictEOAineqs = {}
strTeXEquations = ""
all_ineq = xmlTree.findall(".//EOAineq")
# if all_ineq is not None:
if len(all_ineq) > 0:
    print("Found " + str(len(all_ineq)) + " formulas")

    for xmlChapter in xmlChapters:
        print("Chapter " + str(intChapterNumber))
        xmlEOAineqs = xmlChapter.findall(".//EOAineq")
        intEOAineqnumber = 1
        for xmlEOAineq in xmlEOAineqs:

            if xmlEOAineq.find('.//texmath') is not None:
                strSourceCode = xmlEOAineq.find('.//texmath').text
            else:
                strSourceCode = xmlEOAineq.text

            progress(intEOAineqnumber, len(xmlEOAineqs),"Processing EOAineq %s of %s." % (intEOAineqnumber, len(xmlEOAineqs)))

            strSourceCode = os.linesep.join([s for s in strSourceCode.splitlines() if s])

            # this occurred once in sources 11
            strSourceCode = strSourceCode.replace(r"\@root", r"\root")

            strTeXEquations = strTeXEquations + "$" + strSourceCode + "$\n\\newpage\n"
            # Add intEOAineqRunningOrder : Filename to dictionary
            strFilename = "EOAineq_" + str(intChapterNumber) + "_" + str(intEOAineqnumber)
            dictEOAineqs[intEOAineqRunningOrder] = strFilename
            # Prepare XML
            tmpTail = xmlEOAineq.tail
            xmlEOAineq.clear()
            xmlEOAineq.tail = tmpTail
            xmlEOAineq.set("src", strFilename + ".png")
            xmlEOAineq.set("TeX", strSourceCode)
            # increment integers
            intEOAineqRunningOrder += 1
            intEOAineqnumber +=1
        intChapterNumber += 1

    dictRebindedCommands = {
        "\|ket\|" : r"\\ket",
        "\|braket\|" : r"\\braket",
        "\|bra\|" : r"\\bra",
        "\|Bra\|" : r"\\Bra",
        "\|Ket\|" : r"\\Ket",
        "\slashed\|" : r"\\slashed"
    }
    for strCommand in dictRebindedCommands.keys():
        strTeXEquations = re.sub(strCommand, dictRebindedCommands[strCommand], strTeXEquations)

    tmp = open(TEMPLATE_PATH + "formula.tex", "r")
    Template = tmp.read()
    tmp.close()
    # Get tmp-directory for this user account
    # tmpDir = os.getenv("TMPDIR")
    # use local tmpdir
    formula_tmp_dir = os.getcwd() + "/tmp_files/formulas2png/"

    # Make directory items if it doesn't already exist
    if not os.path.exists(os.getcwd() + "/items"):
        os.mkdir(os.getcwd() + "/items")
    s = string.Template(Template)
    e = s.substitute(DERINHALT=strTeXEquations)
    tmpFile = formula_tmp_dir + "EOAinline.tex"
    tmp = open(tmpFile, "w")
    tmp.write(e)
    tmp.close()
    print("Typesetting all Inline Equations")
    Kommando = TEXBIN_PATH + "xelatex --halt-on-error " + tmpFile
    Argumente = shlex.split(Kommando)
    Datei = open('tmp_files/xelatex-run.log', 'w')
    Ergebnis = subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
    print("Splitting all Inline Equations")
    pdf_burst("EOAinline.pdf", formula_tmp_dir)
    print("Converting %s split pages into PNG-Images" % len(dictEOAineqs.keys()))
    counter_dictEOAineqs = 1
    for intRunningOrder in dictEOAineqs.keys():
        # provide more status information here in output!
        progress(counter_dictEOAineqs, len(dictEOAineqs.keys()),"Splitting all inline equations, image %s of %s" % (counter_dictEOAineqs, len(dictEOAineqs.keys())))
        Kommando = TL_PATH + "texmf-dist/scripts/pdfcrop/pdfcrop.pl " + formula_tmp_dir + "EOAformulas_" + str(intRunningOrder) + ".pdf " + formula_tmp_dir + dictEOAineqs[intRunningOrder] + ".pdf"
        Argumente = shlex.split(Kommando)
        subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
        Kommando = GM_PATH + " convert -density 144 " + formula_tmp_dir + dictEOAineqs[intRunningOrder] + ".pdf " + os.getenv("PWD") + "/items/" + dictEOAineqs[intRunningOrder] + ".png"
        Argumente = shlex.split(Kommando)
        subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
        counter_dictEOAineqs += 1

else:
    print("Found no EOAineq. Continuing")


###########
# Formula #
###########
print("-----------------------------------------------------")
print("Converting EOAchem")
intChapterNumber = 1
int_EOAchem_running_order = 1
dictEOAchems = {}
str_tex_chem = ""
all_chem = xmlTree.findall(".//EOAchem")
# if all_chem is not None:
if len(all_chem) > 0:
    print("Found " + str(len(all_chem)) + " chemical formulas")

    for xmlChapter in xmlChapters:
        print("Chapter " + str(intChapterNumber))
        xmlEOAchems = xmlChapter.findall(".//EOAchem")
        int_EOAchem_number = 1
        for xml_EOAchem in xmlEOAchems:

            str_chem_text = xml_EOAchem.text

            progress(int_EOAchem_number, len(xmlEOAchems),"Processing EOAchem %s of %s." % (int_EOAchem_number, len(xmlEOAchems)))

            str_chem_text = os.linesep.join([s for s in str_chem_text.splitlines() if s])
            str_tex_chem = str_tex_chem + "\ce{" + str_chem_text + "}\n\\newpage\n"
            # Add int_EOAchem_running_order : Filename to dictionary
            strFilename = "EOAchem_" + str(intChapterNumber) + "_" + str(int_EOAchem_number)
            dictEOAchems[int_EOAchem_running_order] = strFilename
            # Prepare XML
            tmpTail = xml_EOAchem.tail
            xml_EOAchem.clear()
            xml_EOAchem.tail = tmpTail
            xml_EOAchem.set("src", strFilename + ".png")
            xml_EOAchem.set("TeX", str_chem_text)
            # increment integers
            int_EOAchem_running_order += 1
            int_EOAchem_number +=1
        intChapterNumber += 1

    tmp = open(TEMPLATE_PATH + "formula.tex", "r")
    Template = tmp.read()
    tmp.close()
    # Get tmp-directory for this user account
    # tmpDir = os.getenv("TMPDIR")
    # use local tmpdir
    formula_tmp_dir = os.getcwd() + "/tmp_files/formulas2png/"

    # Make directory items if it doesn't already exist
    if not os.path.exists(os.getcwd() + "/items"):
        os.mkdir(os.getcwd() + "/items")
    s = string.Template(Template)
    e = s.substitute(DERINHALT=str_tex_chem)
    tmpFile = formula_tmp_dir + "EOAchem.tex"
    tmp = open(tmpFile, "w")
    tmp.write(e)
    tmp.close()
    print("Typesetting all inline Chemical formulas")
    Kommando = TEXBIN_PATH + "xelatex --halt-on-error " + tmpFile
    Argumente = shlex.split(Kommando)
    Datei = open('tmp_files/xelatex-run.log', 'w')
    Ergebnis = subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
    print("Splitting all Inline Chemical formulas")
    pdf_burst("EOAchem.pdf", formula_tmp_dir)
    print("Converting %s split pages into PNG-Images" % len(dictEOAchems.keys()))
    counter_dictEOAchems = 1
    for intRunningOrder in dictEOAchems.keys():
        # provide more status information here in output!
        progress(counter_dictEOAchems, len(dictEOAchems.keys()),"Splitting all inline equations, image %s of %s" % (counter_dictEOAchems, len(dictEOAchems.keys())))
        Kommando = TL_PATH + "texmf-dist/scripts/pdfcrop/pdfcrop.pl " + formula_tmp_dir + "EOAformulas_" + str(intRunningOrder) + ".pdf " + formula_tmp_dir + dictEOAchems[intRunningOrder] + ".pdf"
        Argumente = shlex.split(Kommando)
        subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
        Kommando = GM_PATH + " convert -density 144 " + formula_tmp_dir + dictEOAchems[intRunningOrder] + ".pdf " + os.getenv("PWD") + "/items/" + dictEOAchems[intRunningOrder] + ".png"
        Argumente = shlex.split(Kommando)
        subprocess.call(Argumente,cwd=formula_tmp_dir,stdout=Datei)
        counter_dictEOAchems += 1

else:
    print("Found no EOAchem. Continuing")

###############
# Formula end #
###############

print("-----------------------------------------------------")
print("EOAFigure Numbering per Chapter")
for xmlChapter in xmlChapters:
    Figurenumber = 1
    xmlFigures = xmlChapter.xpath(".//EOAfigure | .//EOAlsfigure")
    for xmlFigure in xmlFigures:
        xmlAnchor = xmlFigure.find("anchor")
        # Check if Figure is in a numbered Chapter
        # Otherwise just put the Number of the figure
        if xmlChapter.get('id'):
            dictFigures[xmlAnchor.get('id')] = \
                str(dictChapters[xmlChapter.get('id')]) + "." + str(Figurenumber)
        else:
            dictFigures[xmlAnchor.get('id')] = str(Figurenumber)
        xmlFigure.set("id", xmlAnchor.get("id"))
        Figurenumber += 1

print("-----------------------------------------------------")
print("Numbering Theorems")
for xmlChapter in xmlChapters:
    xmlTheorems = xmlChapter.findall(".//theorem")
    for xmlTheorem in xmlTheorems:
        strUID = xmlTheorem.get("id")
        strNumber = xmlTheorem.get("id-text")
        dictTheorems[strUID] = strNumber

print("-----------------------------------------------------")
print("Section, Subsection,... Numbering per Chapter")
intChapterNumber = 1
for xmlChapter in xmlChapters:
    strUID = xmlChapter.get("id")
    #dictChapters[strUID] = str(intChapterNumber)
    xmlSections = xmlChapter.findall("div2")
    intSectionNumber = 1
    for xmlSection in xmlSections:
        if xmlSection.get("rend") == "nonumber":
            continue
        strUID = xmlSection.get("id")
        if xmlChapter.get("rend") != "nonumber":
            dictSections[strUID] = str(intChapterNumber) + "." + str(intSectionNumber)
        if xmlChapter.get("rend") == "nonumber":
            dictSections[strUID] = str(intSectionNumber)
        xmlSubsections = xmlSection.findall("div3")
        intSubsectionNumber = 1
        for xmlSubsection in xmlSubsections:
            if xmlSubsection.get("rend") == "nonumber":
                continue
            strUID = xmlSubsection.get("id")
            if xmlChapter.get("rend") != "nonumber":
                dictSections[strUID] = str(intChapterNumber) + "." + str(intSectionNumber) + "." + str(intSubsectionNumber)
            if xmlChapter.get("rend") == "nonumber":
                dictSections[strUID] = str(intSectionNumber) + "." + str(intSubsectionNumber)
            intSubsectionNumber += 1
        intSectionNumber += 1
    if xmlChapter.get("rend") != "nonumber":
        intChapterNumber += 1

print("-----------------------------------------------------")
print("Numbering of Footnotes per Chapter")
intChapterNumber = 1
for xmlChapter in xmlChapters:
    intNoteNumber = 1
    xmlFootnotes = xmlChapter.findall(".//note")
    for xmlFootnote in xmlFootnotes:
        strUID = xmlFootnote.get("id")
        dictFootnotes[strUID] = str(intNoteNumber)
        intNoteNumber += 1

# here was OU's footnote code, now in libeoaconvert
# def get_bigfoot_data(chapter)

# bigfoot needs to be integrated into
# 'fndict': {'uid11': '2', 'uid12': '3', 'uid9': '1'},

# the new-style footnotes that use LaTeX bigfoot show up in the following order:
footnote_groups = ["decimal", "lower-latin"]


print("-----------------------------------------------------")
print("Numbering of Lists per Chapter")
for xmlChapter in xmlChapters:
    xmlListitems = xmlChapter.findall(".//item")
    for xmlListitem in xmlListitems:
        strUID = xmlListitem.get("id")
        strItemNumber = xmlListitem.get("id-text")
        dictLists[strUID] = strItemNumber

print("-----------------------------------------------------")
print("Working on Page Numbers for References")
listAuxFiles = glob.glob(os.getcwd() + "/*.aux")
if len(listAuxFiles) == 0:
    print("No aux file found. Exiting")
    sys.exit(1)
else:
    for strFile in listAuxFiles:
        tmpFile = open(strFile, "r")
        lines = tmpFile.readlines()
        tmpFile.close()
        for line in lines:
            # hyperref makes the lines much much longer
            # \newlabel{BL}{{1.1}{4}{Forschungsüberblick zur Literatur über Alvarus Thomas}{section.1.1}{}}
            # \newlabel{BL}{{1.1}{4}}
            matched_label = re.match(r'\\newlabel\{(.*?)\}\{\{(.*?)\}\{(.*?)\}', line)
            # matchObjectLabel = re.match(r'\newlabel\{(.*?)\}', line)
            if matched_label:
                # matchObjectPage = re.match(r'(.*?)\}\{(\d{1,})\}\}$', line)
                # if matchObjectPage:
                dictPagelabels[matched_label.group(1)] = matched_label.group(3)
            # parsing out information on cite works
            matched_citation = re.match(r'\\abx@aux@cite{(.*?)}', line)
            if matched_citation is not None:
                set_citations.add(matched_citation.group(1))

print(dictPagelabels)
print(set_citations)

print("-----------------------------------------------------")
print("Numbering of Tables per Chapter")
intChapterNumber = 1
for xmlChapter in xmlChapters:
    intTableNumber = 1
    xmlTables = xmlChapter.findall(".//EOAtable")
    for xmlTable in xmlTables:
        xmlTableLabel = xmlTable.find(".//EOAtablelabel")
        strTableCaption = xmlTable.find(".//EOAtablecaption").text
        if strTableCaption == "nonumber":
            continue
        if not xmlTableLabel.text or xmlTableLabel.text == "":
            xmlTableLabel.text = "table" + str(intChapterNumber) + str(intTableNumber)
        strUID = xmlTableLabel.text
        print(strUID)
        if xmlChapter.get("rend") != "nonumber":
            dictTables[strUID] = dictChapters[xmlChapter.get('id')] + "." + str(intTableNumber)
        if xmlChapter.get("rend") == "nonumber":
            dictTables[strUID] = str(intTableNumber)
        intTableNumber += 1
        print(dictTables)
    intChapterNumber += 1

##############################################################
#                  Preparing the Bibliography                #
##############################################################
if xmlTree.find(".//EOAbibliographydatabase") is not None:
    bib_database = xmlTree.find(".//EOAbibliographydatabase").text
    HAS_BIBLIOGRAPHY = True
else:
    print("No database found.")
    HAS_BIBLIOGRAPHY = False
    input()

bib_type = xmlTree.find(".//EOAbibliographytype").text
if bib_type not in ["monograph", "anthology", "monograph-numeric", "anthology-numeric"]:
    print("The bibtype must be one of ", ",".join[bib_type] + ". Exiting")
    sys.exit()

# the new solution: pandoc-citeproc
interim_bib_json_file = (args.filename) + "-bib.json"
citeproc_command = "pandoc-citeproc --bib2json  %s" % bib_database + ".bib"
logging.debug(citeproc_command)
citeproc_arguments = shlex.split(citeproc_command)
citeproc_process = subprocess.Popen(citeproc_arguments, stdout=subprocess.PIPE)
citeproc_json = citeproc_process.stdout.read()
citations_json = json.loads(citeproc_json)
# for x in citations_json:
#     print(x["title"])

# with open(interim_bib_json_file, 'w') as ibjf:
#     json.dump(citeproc_json.decode('utf-8'), ibjf)



####################
# the old solution #
####################
# # Copy interim .bbl-File to interim bib.tex file
# interim_bibtex_file = (args.filename) + "bib.tex"
# try:
#     shutil.copy(BIBERFILE, interim_bibtex_file)
# except FileNotFoundError:
#     print("%s has not been created yet. Switch TeX distribution to TeXLive2016, run biber_2.1 -O biber2-1.bbl %s to obtain this file" % (BIBERFILE, args.filename))
# # Read all lines of Bibliographic TeX
# tmpFile = open(interim_bibtex_file, "r")
# tmpLines = tmpFile.readlines()
# tmpFile.close()

# # First line should link to Bibliographic Praeambel
# tmpLines[0] = "\\include{%spre_bib}\n" % TEMPLATE_PATH
# # Remove unwanted lines
# for i in range(18,0,-1):
#     del tmpLines[i]
# # Save changes
# tmpFile = open(interim_bibtex_file, "w")
# tmpFile.writelines(tmpLines)
# tmpFile.close()
# # TeX has been sanitized, now tralics to make it intermediate XML
# print("TeX has been sanitized, now tralics to make it intermediate XML")
# Kommando = "%s -log_file %s -confdir %s/tralics_conf -config %s/tralics.tcf -utf8 -utf8output -entnames=false %sbib.tex" % (TRALICS_PATH_EXEC, args.filename + "-bib-tralics.log", TRALICS_PATH_LIB, TRALICS_PATH_LIB, args.filename)
# Argumente = shlex.split(Kommando)
# Prozess = subprocess.call(Argumente)
# # Sanitize XML to make it useable
# tmpFile = open((args.filename) + "bib.xml", "r")
# tmpContent = tmpFile.read()
# tmpFile.close()
# listReplace = [ r"<math mode='display' xmlns='http://www.w3.org/1998/Math/MathML'>",
# r"<formula textype='displaymath' type='display'>",
# r"<mi>",
# r"</mi>",
# r"<mn>",
# r"<mn>",
# r"<mo>",
# r"</mo>",
# r"<mn>",
# r"</mn>",
# r"<mrow/>",
# r"<msup>",
# r"</msup>",
# r"</math>",
# r"</formula>",
# r"<formula type='inline'>",
# r"<math xmlns='http://www.w3.org/1998/Math/MathML'>",
# r"<formula textype='math' type='inline'>",
# r"<mrow>uniquename=(.*?),hash=(.*?)</mrow>",
# r"<mrow>hash=(.*?)</mrow>",
# ]
# for strReplace in listReplace:
#     tmpContent = re.sub(strReplace, "", tmpContent)

# # Put Back Underscore _
# tmpContent = re.sub(r"<error n='_' l='(.*?)' c='Missing dollar'/>", "_", tmpContent)

# # Remove empty Lines
# tmpContent = re.sub(r"\n\n", "\n", tmpContent)

# # Put back Ampersand
# tmpContent = re.sub(r"&", "&amp;", tmpContent)
# tmpFile = open((args.filename) + "bib.xml", "w")
# tmpFile.write(tmpContent)
# tmpFile.close()

# # TeXML has been sanitized, now load xml-Tree
# xmlParser2 = etree.XMLParser(no_network=False,load_dtd=False)
# xmlBibTree = etree.parse((args.filename + "bib.xml"), xmlParser2)
# xml_bib_entries = xmlBibTree.findall(".//entry")

###########################
# end of the old solution #
###########################

make_bibchecker(bib_database, set_citations)

# If Bibliography-Type is monograph search for EOAbibliography and make it all
if bib_type == "monograph":

    if xmlTree.find(".//EOAprintbibliography") is not None:
        xmlBibliography = xmlTree.find(".//EOAprintbibliography")
        xmlBibliography.clear()
        xmlBibliography.tag = "div"

        bib_parent = xmlBibliography.getparent()
        bib_parent.tag = "div"

        xmlBibliographyDiv = etree.Element("div")
        xmlBibliography.addnext(xmlBibliographyDiv)
        ###############
        # new version #
        ###############
        tmp_citation_filename = "used_citations-monograph"
        formatted_references = libeoaconvert.format_citations(set_citations, bib_database + ".bib", strLanguage, tmp_citation_filename)[0]

        fixed_entries = libeoaconvert.fix_bib_entries(formatted_references)
        for entry in fixed_entries:
            xmlBibliographyDiv.append(entry)
        ######################
        # end of new version #
        ######################

        ###############
        # old version #
        ###############
        # xml_bib_entries = xmlBibTree.findall(".//entry")
        # intNumberOfEntry = 0
        # for xmlEntry in xml_bib_entries:
        #     if intNumberOfEntry == 0:
        #         # Don't check for previous author if first entry of the Bibliography
        #         bibEntry = Bibitem(xmlEntry)
        #         strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=False) + "</p>"
        #     else:
        #         bibEntry = Bibitem(xmlEntry)
        #         # Check if author of previous Entry is the same
        #         bibEntryPrevious = Bibitem(xml_bib_entries[intNumberOfEntry - 1])
        #         if bibEntry.fullauthorlastfirst()[0] == bibEntryPrevious.fullauthorlastfirst()[0]:
        #             strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=True) + "</p>"
        #         elif bibEntryPrevious.fullauthorlastfirst()[0] == bibEntry.fullauthorlastfirst()[0]:
        #             strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=True) + "</p>"
        #         elif bibEntry.fullauthorlastfirst()[0] == bibEntryPrevious.fullauthorlastfirst()[0]:
        #             strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=True) + "</p>"
        #         else:
        #             strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=False) + "</p>"

        #     xmlNew = etree.fromstring(strNewentry)
            # next one writes the bibliography into the document
            # xmlBibliography.append(xmlNew)

            # intNumberOfEntry += 1
        ######################
        # end of old version #
        ######################


# If Bibliography-Type is anthology search for EOAbibliography and make one per chapter
if bib_type == "anthology":
    print("bib type is anthology")
    intChapterNumber = 1
    for xmlChapter in xmlChapters:
        tmp_citation_filename = "used_citations-anthology-chapter_{:02d}".format(intChapterNumber)
        if xmlChapter.find(".//EOAprintbibliography") is not None:
            xmlBibliography = xmlChapter.find(".//EOAprintbibliography")
            xmlBibliography.getparent().tag = "div"
            xmlBibliographyDiv = etree.Element("div")
            xmlBibliography.addnext(xmlBibliographyDiv)

            citekeys = xmlChapter.xpath(".//citekey/text()")
            set_citations = set(citekeys)

            formatted_references = libeoaconvert.format_citations(set_citations, bib_database + ".bib", strLanguage, tmp_citation_filename)[0]

            fixed_entries = libeoaconvert.fix_bib_entries(formatted_references)
            for entry in fixed_entries:
                xmlBibliographyDiv.append(entry)
        else:
            # create an empty file
            open("tmp_files" + os.path.sep + tmp_citation_filename + "_nocites", 'a').close()

        """
  <div2 rend="nonumber">
    <head>References</head>
    <div>
      <EOAprintbibliography/>
      <div>
        <p class="bibliography">Abril Castelló, Vidal (1987). Las Casas contra Vitoria, 1550–1552: La revolución de la duodécima réplica. Causas y consecuencias. <i>Revista de Indias</i> 47(179):83–101.</p>
        <p class="bibliography">Agrawal, Arun (1995). Dismantling the Divide Between Indigenous and Scientific Knowledge. <i>Development and Change</i> 26:413–439.</p>
      </div>
    </div>
  </div2>
        """


            ###############
            # old version #
            ###############
            # xmlRefsections = xmlBibTree.findall(".//refsection")
            # for xmlRefsection in xmlRefsections:
            #     if xmlRefsection.find(".//number").text == str(intChapterNumber):
            #         break
            # xml_bib_entries = xmlRefsection.findall(".//entry")
            # intNumberOfEntry = 0
            # for xmlEntry in xml_bib_entries:
            #     if intNumberOfEntry == 0:
            #         # Don't check for previous author if first entry of the Bibliography
            #         bibEntry = Bibitem(xmlEntry)
            #         strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=False) + "</p>"
            #         xmlNew = etree.fromstring(strNewentry)
            #         xmlBibliographyDiv.append(xmlNew)
            #     else:
            #         bibEntry = Bibitem(xmlEntry)
            #         # Check if author of previous Entry is the same
            #         bibEntryPrevious = Bibitem(xml_bib_entries[intNumberOfEntry - 1])
            #         if bibEntry.fullauthorlastfirst() == bibEntryPrevious.fullauthorlastfirst():
            #             print(bibEntry.citekey())
            #             strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=True) + "</p>"
            #             xmlNew = etree.fromstring(strNewentry)
            #             xmlBibliographyDiv.append(xmlNew)
            #         else:
            #             print(bibEntry.citekey())
            #             strNewentry = "<p class=\"bibliography\">" + createBibEntryAuthorYear(bibEntry, boolSameAuthor=False) + "</p>"
            #             xmlNew = etree.fromstring(strNewentry)
            #             xmlBibliographyDiv.append(xmlNew)
            #     intNumberOfEntry += 1

        ######################
        # end of old version #
        ######################

        intChapterNumber += 1
# for the time being
strCitation = ""

# Bibliographies are done, now for the citations
if bib_type == "anthology" or bib_type == "monograph":
    intChapterNumber = 1

    if bib_type == "monograph":
        tmp_citation_filename = "used_citations-monograph"
        tmp_path_html = "tmp_files" + os.path.sep + tmp_citation_filename + ".html"
        with open(tmp_path_html, "r") as formatted_citations:
            form_cit = BeautifulSoup(formatted_citations, "html.parser")

    for xmlChapter in xmlChapters:
        print("-----------------------------------------------------")
        print("Processing References for Chapter " + str(intChapterNumber))
        xmlCitations = xmlChapter.xpath(".//EOAciteauthoryear | .//EOAciteyear | .//EOAcitemanual")

        if bib_type == "anthology":
            tmp_citation_filename = "used_citations-anthology-chapter_{:02d}".format(intChapterNumber)
            tmp_path_html = "tmp_files" + os.path.sep + tmp_citation_filename + ".html"
            no_cite_path = "tmp_files" + os.path.sep + tmp_citation_filename + "_nocites"
            if os.path.exists(tmp_path_html):
                with open(tmp_path_html, "r") as formatted_citations:
                    form_cit = BeautifulSoup(formatted_citations, "html.parser")
            elif os.path.exists(no_cite_path):
                print("no cites in this chapter")
                intChapterNumber += 1
                continue

        counter_citations = 1

        for xmlCitation in xmlCitations:
            string_citekey = xmlCitation.find("./citekey").text
            progress(counter_citations, len(xmlCitations),"Processing reference %s of %s: %s" % (counter_citations, len(xmlCitations), string_citekey))
            # If Bibliography-Type is anthology find Refsection for this Chapter
            ###############
            # old version #
            ###############
            # if bib_type == "anthology":
            #     print("Yes, it's anthology time!")
                # xmlRefsections = xmlBibTree.findall(".//refsection")
                # for xmlRefsection in xmlRefsections:
                #     if xmlRefsection.find(".//number").text == str(intChapterNumber):
                #         break
                # xml_bib_entries = xmlRefsection.findall(".//entry")

                ###################
                # end old version #
                ###################
            # If Bibliography-Type is monograph find all entries, forget about refsection

            ###############
            # old version #
            ###############
            """
            if bib_type == "monograph":
                xml_bib_entries = xmlBibTree.findall(".//entry")
            for xmlEntry in xml_bib_entries:
                bibEntry = Bibitem(xmlEntry)
                if bibEntry.citekey() == xmlCitation.find("./citekey").text:
                    if xmlCitation.tag == "EOAciteauthoryear":
                        strCitation = bibEntry.shortauthor() + " " + bibEntry.labelyear()
                        if bibEntry.labelyearsuffix() is not None:
                            strCitation = strCitation + bibEntry.labelyearsuffix()
                        strTitle = bibEntry.title()
                    if xmlCitation.tag == "EOAciteyear":
                        strCitation = bibEntry.labelyear()
                        if bibEntry.labelyearsuffix() is not None:
                            strCitation = strCitation + bibEntry.labelyearsuffix()
                        strTitle = bibEntry.title()
                    if xmlCitation.tag == "EOAcitemanual":
                        cite_text = xmlCitation.find("citetext")
                        if cite_text.getchildren():
                            tmp_string = xmlCitation.find("citetext")
                            tmp_string = cite_text.getchildren()[0]
                            strCitation = etree.tostring(tmp_string)
                            # BAUSTELLE!!!!!
                            # tmp_string2 = etree.tostring(tmp_string)
                            # tmp_string3 = tmp_string2.decode()
                            # strCitation = tmp_string3.replace("&lt;", "<")
                        else:
                            strCitation = xmlCitation.find("citetext").text
                        strTitle = bibEntry.title()
            if xmlCitation.find("./page") is not None and xmlCitation.find("./page").text is not None:
                strCitation = strCitation + ", " + xmlCitation.find("./page").text
            """
            ######################
            # end of old version #
            ######################

            ###############
            # new version #
            ###############

            # string_citekey = xmlCitation.find("./citekey").text
            for entry in citations_json:
                if entry["id"] == string_citekey:
                    current_citation = entry
                    strTitle = current_citation["title"]

            # [1:-1] to remove parentheses around citations
            try:
                citeauthoryear_value = form_cit.select("#citeauthoryear ~ p > span[data-cites='%s']" % string_citekey)[0].text[1:-1]
            except IndexError:
                print("Could not find {}. Exiting.".format(string_citekey))
                sys.exit()
            data_title_value = citeauthoryear_value
            if xmlCitation.tag == "EOAciteauthoryear":
                strCitation = citeauthoryear_value
            elif xmlCitation.tag == "EOAciteyear":
                strCitation = form_cit.select("#citeyear ~ p > span[data-cites='%s']" % string_citekey)[0].text[1:-1]
            elif xmlCitation.tag == "EOAcitemanual":
                cite_text = xmlCitation.find("citetext")
                if cite_text.getchildren():
                    tmp_string = xmlCitation.find("citetext")
                    tmp_string = cite_text.getchildren()[0]
                    strCitation = etree.tostring(tmp_string)
                    # BAUSTELLE!!!!!
                    # tmp_string2 = etree.tostring(tmp_string)
                    # tmp_string3 = tmp_string2.decode()
                    # strCitation = tmp_string3.replace("&lt;", "<")
                else:
                    strCitation = xmlCitation.find("citetext").text

            if xmlCitation.find("./page") is not None and xmlCitation.find("./page").text is not None:
                pages_text = libeoaconvert.gettext(xmlCitation.find("./page"))
                strCitation = strCitation + ", " + pages_text
                data_title_value = data_title_value + ", " + pages_text
                # strCitation = strCitation + ", " + xmlCitation.find("./page").text

            ######################
            # end of new version #
            ######################

            # Hier den XML-Tag durch die Quellenangabe ersetzen
            tmpTail = xmlCitation.tail
            xmlCitation.clear()
            xmlCitation.tag = "span"
            xmlCitation.set("rel", "popover")
            xmlCitation.set("class", "citation")
            xmlCitation.set("citekey", string_citekey)
            xmlCitation.text = strCitation
            xmlCitation.tail = tmpTail
            # Create Link to be used for website in a popover
            xmlCitation.set("data-toggle", "popover")
            xmlCitation.set("html", "true")
            xmlCitation.set("data-placement", "bottom")
            xmlCitation.set("data-title", data_title_value)
            try:
                xmlCitation.set("data-content", strTitle)
            except:
                xmlCitation.set("data-content", "missing")
            counter_citations += 1
        intChapterNumber += 1

# If Bibliography-Type is monograph-numeric search for EOAbibliography and make it all
if bib_type == "monograph-numeric":
    if xmlTree.find(".//EOAprintbibliography") is not None:
        dictCitekeysNumbers = {}
        dictCitekeysTitles = {}
        xmlBibliography = xmlTree.find(".//EOAprintbibliography")
        xmlBibliography.clear()
        xmlBibliography.tag = "div"
        xmlBibliography.getparent().tag = "div"
        xml_bib_entries = xmlBibTree.findall(".//entry")
        intNumberOfEntry = 1
        for xmlEntry in xml_bib_entries:
            # Go through all entries and assign a number to the citekey
            bibEntry = Bibitem(xmlEntry)
            strCitekey = bibEntry.citekey()
            dictCitekeysNumbers[strCitekey] = str(intNumberOfEntry)
            dictCitekeysTitles[strCitekey] = str(bibEntry.title())
            strNewentry = "<p class=\"bibliography\">[" + str(intNumberOfEntry) + "] " + createBibEntryNumeric(bibEntry) + "</p>"
            xmlNew = etree.fromstring(strNewentry)
            xmlBibliography.append(xmlNew)
            intNumberOfEntry += 1
        # Now for the references via EOAcitenumeric
        xmlCitenumerics = xmlTree.findall(".//EOAcitenumeric")
        for xmlCitenumeric in xmlCitenumerics:
            print(etree.tostring(xmlCitenumeric))
            strPopover = ""
            tmpCitekeys = xmlCitenumeric.find(".//citekey").text
            tmpCitekeys = re.sub(" ", "", tmpCitekeys)
            tmpCitekeys = re.sub("\n", "", tmpCitekeys)
            listCitekeys = re.split("\,", tmpCitekeys)
            listCitenumbers = []
            for strCitekey in listCitekeys:
                listCitenumbers.append(dictCitekeysNumbers[strCitekey])
                # Create Text to be used on the website in a popover
                strPopover = strPopover + "[" + dictCitekeysNumbers[strCitekey] + "] " + dictCitekeysTitles[strCitekey] + " "
            listCitenumbers = sorted(listCitenumbers, key=int)
            strResult = "[" + listCitenumbers[0]
            intNumberOfSequentialCite = 0
            for i in range(1,len(listCitenumbers)):
                intPreviousCitenumber = int(listCitenumbers[i-1])
                intCurrentCitenumber = int(listCitenumbers[i])
                if i == (len(listCitenumbers)-1):
                    if (intPreviousCitenumber + 1) == intCurrentCitenumber:
                        if intNumberOfSequentialCite == 0:
                            strResult = strResult + "," + str(listCitenumbers[i])
                        else:
                            strResult = strResult + "-" + str(listCitenumbers[i])
                            intNumberOfSequentialCite == 0
                    else:
                        strResult = strResult + "," + str(listCitenumbers[i])
                    break
                intNextCitenumber = int(listCitenumbers[i+1])
                if (intCurrentCitenumber + 1) != intNextCitenumber:
                    if intNumberOfSequentialCite != 0:
                        strResult = strResult + "-" + str(intCurrentCitenumber)
                        intNumberOfSequentialCite = 0
                    else:
                        strResult = strResult + "," + str(intCurrentCitenumber)
                    continue
                if (intPreviousCitenumber + 1) == intCurrentCitenumber:
                    intNumberOfSequentialCite += 1
                    continue
                else:
                    strResult = strResult + "," + str(intCurrentCitenumber)
                    intNumberOfSequentialCite = 0
            strResult = strResult + "]"
            xmlCitenumeric.text = strResult
            # Create Link to be used for website
            xmlCitenumeric.set("data-toggle", "popover")
            xmlCitenumeric.set("html", "true")
            xmlCitenumeric.set("data-content", strPopover)
            xmlCitenumeric.set("class","citation")
            xmlCitenumeric.set("data-placement", "bottom")
            xmlCitenumeric.set("data-title", strResult)

# author is missing!
# print("xmlBibliography")
# print(etree.tostring(xmlBibliography))
# input()

# Numeric citations for the individual chapters
if bib_type == "anthology-numeric":
    intChapterNumber = 1
    for xmlChapter in xmlChapters:
        print("Processing Bibliography")
        if xmlChapter.find(".//EOAprintbibliography") is not None:
            dictCitekeysNumbers = {}
            dictCitekeysTitles = {}
            xmlBibliography = xmlChapter.find(".//EOAprintbibliography")
            #xmlBibliography.clear()
            xmlBibliography.tag = "div"
            xmlBibliography.getparent().tag = "div"
            xmlRefsections = xmlBibTree.findall(".//refsection")
            for xmlRefsection in xmlRefsections:
                if xmlRefsection.find(".//number").text == str(intChapterNumber):
                    break
            xml_bib_entries = xmlRefsection.findall(".//entry")
            intNumberOfEntry = 1
            for xmlEntry in xml_bib_entries:
                # Go through all entries and assign a number to the citekey
                bibEntry = Bibitem(xmlEntry)
                strCitekey = bibEntry.citekey()
                dictCitekeysNumbers[strCitekey] = str(intNumberOfEntry)
                dictCitekeysTitles[strCitekey] = str(bibEntry.title())
                strNewentry = "<p class=\"bibliography\">[" + str(intNumberOfEntry) + "] " + createBibEntryNumeric(bibEntry) + "</p>"
                xmlNew = etree.fromstring(strNewentry)
                xmlBibliography.append(xmlNew)
                intNumberOfEntry += 1
            # Now for the references via EOAcitenumeric
            xmlCitenumerics = xmlChapter.xpath(".//EOAcitenumeric | .//EOAciteauthoryear | .//EOAciteyear")
            print("Found numeric citation in chapter " + str(intChapterNumber))
            for xmlCitenumeric in xmlCitenumerics:
                strPopover = ""
                tmpCitekeys = xmlCitenumeric.find(".//citekey").text
                tmpCitekeys = re.sub(" ", "", tmpCitekeys)
                tmpCitekeys = re.sub("\n", "", tmpCitekeys)
                print(tmpCitekeys)
                listCitekeys = re.split("\,", tmpCitekeys)
                listCitenumbers = []
                for strCitekey in listCitekeys:
                    print(strCitekey)
                    listCitenumbers.append(dictCitekeysNumbers[strCitekey])
                    # Create Text to be used on the website in a popover
                    strPopover = strPopover + "[" + dictCitekeysNumbers[strCitekey] + "] " + dictCitekeysTitles[strCitekey] + " "
                listCitenumbers = sorted(listCitenumbers, key=int)
                strResult = "[" + listCitenumbers[0]
                intNumberOfSequentialCite = 0
                for i in range(1,len(listCitenumbers)):
                    intPreviousCitenumber = int(listCitenumbers[i-1])
                    intCurrentCitenumber = int(listCitenumbers[i])
                    if i == (len(listCitenumbers)-1):
                        if (intPreviousCitenumber + 1) == intCurrentCitenumber:
                            if intNumberOfSequentialCite == 0:
                                strResult = strResult + "," + str(listCitenumbers[i])
                            else:
                                strResult = strResult + "-" + str(listCitenumbers[i])
                                intNumberOfSequentialCite == 0
                        else:
                            strResult = strResult + "," + str(listCitenumbers[i])
                        break
                    intNextCitenumber = int(listCitenumbers[i+1])
                    if (intCurrentCitenumber + 1) != intNextCitenumber:
                        if intNumberOfSequentialCite != 0:
                            strResult = strResult + "-" + str(intCurrentCitenumber)
                            intNumberOfSequentialCite = 0
                        else:
                            strResult = strResult + "," + str(intCurrentCitenumber)
                        continue
                    if (intPreviousCitenumber + 1) == intCurrentCitenumber:
                        intNumberOfSequentialCite += 1
                        continue
                    else:
                        strResult = strResult + "," + str(intCurrentCitenumber)
                        intNumberOfSequentialCite = 0
                strResult = strResult + "]"
                xmlCitenumeric.text = strResult
                # Create Link to be used for website in a popover
                xmlCitenumeric.set("data-toggle", "popover")
                xmlCitenumeric.set("data-placement", "bottom")
                xmlCitenumeric.set("data-title", " " + strResult)
                xmlCitenumeric.set("data-content", strPopover)
                xmlCitenumeric.set("class","citation")
        intChapterNumber += 1

# this is somewhat luzzini-specific
bib_parent_element = xmlBibliography.getparent()
upper_div = bib_parent_element.xpath("./ancestor::div1")[0]
previous_div0 = upper_div.getparent()

# possible culprit for not finding the index
# other_content = bib_parent_element.xpath(".//EOAtocentry | .//EOAprintpersonindex | .//EOAprintlocationindex | .//EOAprintindex")
other_content = upper_div.xpath(".//EOAtocentry | .//EOAprintpersonindex | .//EOAprintlocationindex | .//EOAprintindex")
if len(other_content) > 0:
    for element in other_content:
        previous_div0.append(element)

# here followed the conversion to epub and the conversion to django.xml
# both parts were removed and put into separate files.

intermediate_file_pre = "tmp_files/IntermediateXMLFile_pre.xml"
intermediate_file = "tmp_files/IntermediateXMLFile.xml"
ergebnisdatei = open(intermediate_file_pre, "w")
ergebnis = etree.tostring(xmlTree, pretty_print=True, encoding="unicode")
ergebnisdatei.write(ergebnis)
ergebnisdatei.close()

# replacing a milestone element by a closing and opening combination
with open(intermediate_file_pre, 'r') as tmp_file:
  filedata = tmp_file.read()

# add XML declaration
filedata_declaration = "<?xml version='1.0' encoding='UTF-8'?>\n" + filedata

# Replace the target string
filedata_clean = filedata_declaration.replace('<msparbreak/>', '</p><p>')

# Write the file out again
with open(intermediate_file, 'w') as outfile:
  outfile.write(filedata_clean)

# saving some data
data_to_pickle = {'chapterdict' : dictChapters,
                  'eqdict' : dictEquations,
                  'listdict' : dictLists,
                  'theoremdict' : dictTheorems,
                  'figdict' : dictFigures,
                  'secdict' : dictSections,
                  'fndict' : dictFootnotes,
                  'tabdict' : dictTables,
                  'pagelabeldict' : dictPagelabels
                      }

with open('tmp_files/data.pickle', 'wb') as f:
    # Pickle the 'data' dictionary using the highest protocol available.
    pickle.dump(data_to_pickle, f, pickle.HIGHEST_PROTOCOL)

grep_command = "grep -A1 -B2 'argument of \\\EOAfn' %s-tralics.log" % args.filename
grep_command_arguments = shlex.split(grep_command)
grep_result = subprocess.Popen(grep_command_arguments, stdout=subprocess.PIPE)
grep_output = grep_result.stdout.read()
if len(grep_output) > 0:
    print("\n===\nFootnotes with paragraphs were found. They have to be replaced by the \EOAfnpar command.\n")
    print(grep_output.decode("utf-8"))
    print("===\n")

print("Removing temporary files.")
cleanup()
print("Done!")
sys.exit()