# from sys import argv
# import os
# import re
# import logging
# from bs4 import BeautifulSoup
#
#
# def switch_extension(name, ext):
# """Takes the name of a file (str) and changes the extension to the one provided (str)"""
# return os.path.splitext(name)[0] + ext
#
#
# def convert_xml_to_brat(xml_file_path):
# with open(xml_file_path) as f:
# xml_text = f.read()
#
# xml_text = re.sub(">", ">", xml_text)
# whole_soup = BeautifulSoup(xml_text, features="html.parser")
# abstract_in_tags = whole_soup.find("abstracttext")
# abstract_soup = BeautifulSoup(str(abstract_in_tags), features="html.parser")
#
# # The text of the abstract without any tags
# abstract_text = abstract_soup.get_text()
#
# tags = set([tag.name for tag in abstract_soup.find_all()])
# tags.remove("abstracttext")
#
# infix = "( |<.*?>|)+"
# circumfix = "<.*?>"
#
# all_annotations = []
#
# for tag in tags:
#
# all_for_tag = abstract_soup.find_all(tag)
#
# escaped_patterns = []
# for tagged_item in all_for_tag:
# tag_pattern = re.escape(str(tagged_item))
# if tag_pattern not in escaped_patterns:
# escaped_patterns.append(tag_pattern)
#
# matches_for_tag = []
# for pattern in escaped_patterns:
# iter_matches = re.finditer(pattern, str(abstract_soup))
# for match in iter_matches:
# matches_for_tag.append(match)
#
# # Get all the instances of that tag
# for tagged_item in matches_for_tag:
# # We only want to search up to the end of the match we're looking at
# cap_index = tagged_item.span()[1]
# match_text = tagged_item.string[tagged_item.span()[0]:tagged_item.span()[1]]
# match_soup = BeautifulSoup(match_text, features="html.parser")
# match_tagless = match_soup.get_text()
#
# # Construct the regex pattern to get all instances of the phrase
# # in the xml file (not the tagless version)
# # regardless of whether there are tags in between words
# tagless_escaped = re.escape(match_tagless)
# spaced = re.sub(r"\\ ", infix, tagless_escaped)
# spaced = re.sub(r"\\-", infix + "-" + infix, spaced)
# spaced = re.sub(r"\\,", r"," + infix, spaced)
# spaced = re.sub(r"\\/", infix + r"\\/" + infix, spaced)
# circumfixed = circumfix + spaced + circumfix
#
# # Figure out how many matches come before the instance we're looking at, including itself
# search_text = str(abstract_soup)[:cap_index]
# search_text = re.sub(">", ">", search_text)
# similar_matches = list(re.finditer(circumfixed, search_text))
# specific_instance = len(similar_matches) - 1
# assert specific_instance >= 0, "specific_instance should never be negative"
#
# # Find the same instance of the entity in the txt version
# parallel_matches = list(re.finditer(spaced, abstract_text))
# specific_match = parallel_matches[specific_instance]
#
# new_annotation = {
# "entity": specific_match.string[specific_match.span()[0]:specific_match.span()[1]],
# "entity_type": tag,
# "start_ind": specific_match.span()[0],
# "end_ind": specific_match.span()[1]
# }
#
# all_annotations.append(new_annotation)
#
# all_annotations = sorted(all_annotations, key=lambda x: (x["start_ind"], x["end_ind"]))
#
# brat_text = ""
# t = 1
#
# for d in all_annotations:
# brat_line = "T%i\t%s %i %i\t%s\n" % (t, d["entity_type"], d["start_ind"], d["end_ind"], d["entity"])
# brat_text += brat_line
# t += 1
#
# return brat_text, abstract_text
#
#
# if __name__ == "__main__":
# # Get the input and output directories from the command line.
#
# if len(argv) < 3:
# # Command-line arguments must be provided for the input and output directories.
# raise IOError("Please run the program again, entering the input and output directories as command-line"
# " arguments in that order.")
#
# try:
# input_dir_name = argv[1]
# input_dir = os.listdir(input_dir_name)
# except FileNotFoundError: # dir doesn't exist
# while not os.path.isdir(input_dir_name):
# input_dir_name = input("Input directory not found; please try another directory:")
# input_dir = os.listdir(input_dir_name)
# try:
# output_dir_name = argv[2]
# output_dir = os.listdir(output_dir_name)
# except FileNotFoundError:
# while not os.path.isdir(output_dir_name):
# output_dir_name = input("Output directory not found; please try another directory:")
# output_dir = os.listdir(output_dir_name)
#
# # Create the log
# log_path = os.path.join(output_dir_name, "conversion.log")
# logging.basicConfig(filename=log_path)
#
# # Get only the text files in input_dir
# xml_files = [f for f in input_dir if f.endswith(".xml")]
#
# # Ensure user is aware if there are no files to convert
# if len(xml_files) < 1:
# raise FileNotFoundError("There were no xml files in the input directory.")
#
# for input_file_name in xml_files:
# full_file_path = os.path.join(input_dir_name, input_file_name)
# ann_str, txt_str = convert_xml_to_brat(full_file_path)
#
# output_ann_name = switch_extension(input_file_name, ".ann")
# output_ann_path = os.path.join(output_dir_name, output_ann_name)
# with open(output_ann_path, "a+") as f:
# f.write(ann_str)
#
# output_txt_name = switch_extension(input_file_name, ".txt")
# output_txt_path = os.path.join(output_dir_name, output_txt_name)
# with open(output_txt_path, "a+") as f:
# f.write(txt_str)
