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Commit d6e9ce97 authored by Christian Boulanger's avatar Christian Boulanger
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Update documentation

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%% Cell type:markdown id:4c77ab592c98dfd tags: %% Cell type:markdown id:4c77ab592c98dfd tags:
# Convert AnyStyle to TEI-bibl data # Convert AnyStyle to TEI-bibl data
References: References:
- https://www.tei-c.org/release/doc/tei-p5-doc/en/html/CO.html#COBI (Overview) - https://www.tei-c.org/release/doc/tei-p5-doc/en/html/CO.html#COBI (Overview)
- https://www.tei-c.org/release/doc/tei-p5-doc/en/html/CO.html#COBIOT (Mapping to other bibliographic formats)
- https://www.tei-c.org/release/doc/tei-p5-doc/en/html/ref-bibl.html (`<bibl>`) - https://www.tei-c.org/release/doc/tei-p5-doc/en/html/ref-bibl.html (`<bibl>`)
- https://www.tei-c.org/release/doc/tei-p5-doc/en/html/ref-biblStruct.html (`biblStruct`) - https://www.tei-c.org/release/doc/tei-p5-doc/en/html/ref-biblStruct.html (`biblStruct`)
- https://epidoc.stoa.org/gl/latest/supp-bibliography.html (Examples) - https://epidoc.stoa.org/gl/latest/supp-bibliography.html (Examples)
- https://grobid.readthedocs.io/en/latest/training/Bibliographical-references/ (Grobid examples using `<bibl>`) - https://grobid.readthedocs.io/en/latest/training/Bibliographical-references/ (Grobid examples using `<bibl>`)
We use `<bibl>` here for marking up the citation data. These annotations can then be further processed: We use `<bibl>` here for marking up the citation data. These annotations can then be further processed:
- [to Gold Standard based on `<biblStruct>`](tei-to-biblstruct-gs.ipynb) - [to Gold Standard based on `<biblStruct>`](tei-to-biblstruct-gs.ipynb)
- [to bibliographic data formats](tei-to-bibformats.ipynb) - [to bibliographic data formats](tei-to-bibformats.ipynb)
- [to the prodigy annotation format](tei-to-prodigy.ipynb) - [to the prodigy annotation format](tei-to-prodigy.ipynb)
Code was written with assistance by ChatGPT 4. Code was written with assistance by ChatGPT 4.
%% Cell type:markdown id:dd3645db958007fe tags: %% Cell type:markdown id:dd3645db958007fe tags:
## Collect metadata on TEI `<bibl>` tags ## Collect metadata on TEI `<bibl>` tags
%% Cell type:markdown id:c4ebd32b98166eb tags: %% Cell type:markdown id:c4ebd32b98166eb tags:
Cache XML schema for offline use Cache XML schema for offline use
%% Cell type:code id:ff140f40df428a8f tags: %% Cell type:code id:ff140f40df428a8f tags:
``` python ``` python
import xmlschema import xmlschema
import os import os
if not os.path.isdir("schema/tei"): if not os.path.isdir("schema/tei"):
schema = xmlschema.XMLSchema("https://www.tei-c.org/release/xml/tei/custom/schema/xsd/tei_all.xsd") schema = xmlschema.XMLSchema("https://www.tei-c.org/release/xml/tei/custom/schema/xsd/tei_all.xsd")
schema.export(target='schema/tei', save_remote=True) schema.export(target='schema/tei', save_remote=True)
``` ```
%% Cell type:markdown id:3019ff70c4b769cd tags: %% Cell type:markdown id:3019ff70c4b769cd tags:
This generates JSON data with information on the tags used, extracting from the schema and from the documentation pages This generates JSON data with information on the tags used, extracting from the schema and from the documentation pages.
%% Cell type:code id:572f566fc9784238 tags: %% Cell type:code id:572f566fc9784238 tags:
``` python ``` python
import os import os
import xmlschema import xmlschema
import xml.etree.ElementTree as ET import xml.etree.ElementTree as ET
import pandas as pd import pandas as pd
import requests import requests
from bs4 import BeautifulSoup from bs4 import BeautifulSoup
import re import re
from tqdm.notebook import tqdm from tqdm.notebook import tqdm
def extract_headings_and_links(tag, doc_heading, doc_base_url): def extract_headings_and_links(tag, doc_heading, doc_base_url):
# Extract heading numbers from the document # Extract heading numbers from the document
heading_numbers = re.findall(r'\d+(?:\.\d+)*', doc_heading) heading_numbers = re.findall(r'\d+(?:\.\d+)*', doc_heading)
# Download the HTML page # Download the HTML page
url = f"{doc_base_url}/ref-{tag}.html" url = f"{doc_base_url}/ref-{tag}.html"
response = requests.get(url) response = requests.get(url)
soup = BeautifulSoup(response.content, 'html.parser') soup = BeautifulSoup(response.content, 'html.parser')
# Extract the links associated with each heading number # Extract the links associated with each heading number
links = {} links = {}
for link in soup.find_all('a', class_='link_ptr'): for link in soup.find_all('a', class_='link_ptr'):
heading_value = link.find('span', class_='headingNumber').text.strip() heading_value = link.find('span', class_='headingNumber').text.strip()
link_url = link.get('href') link_url = link.get('href')
links[heading_value] = f"{doc_base_url}/{link_url}" links[heading_value] = f"{doc_base_url}/{link_url}"
return {heading: link_url for heading, link_url in zip(heading_numbers, links.values()) if return {heading: link_url for heading, link_url in zip(heading_numbers, links.values()) if
heading in heading_numbers} heading in heading_numbers}
def generate_tag_docs(xsd_path): def generate_tag_docs(xsd_path):
namespaces = {'xs': 'http://www.w3.org/2001/XMLSchema'} namespaces = {'xs': 'http://www.w3.org/2001/XMLSchema'}
doc_base_url = "https://www.tei-c.org/release/doc/tei-p5-doc/en/html" doc_base_url = "https://www.tei-c.org/release/doc/tei-p5-doc/en/html"
tree = ET.parse('schema/tei/tei_all.xsd') tree = ET.parse('schema/tei/tei_all.xsd')
root = tree.getroot() root = tree.getroot()
schema = xmlschema.XMLSchema(xsd_path) schema = xmlschema.XMLSchema(xsd_path)
bibl_schema = schema.find("tei:bibl") bibl_schema = schema.find("tei:bibl")
data_list = [] data_list = []
#names = [child_element.local_name for child_element in bibl_schema.iterchildren()] #names = [child_element.local_name for child_element in bibl_schema.iterchildren()]
names = ['author', 'biblScope', 'citedRange', 'date', 'edition', 'editor', 'idno', 'issue', 'location', 'note', 'orgName', 'ptr', 'pubPlace', 'publisher', 'ref', 'seg', 'series', 'title', 'volume', 'xr'] names = ['author', 'biblScope', 'citedRange', 'date', 'edition', 'editor', 'idno', 'issue', 'location', 'note', 'orgName', 'ptr', 'pubPlace', 'publisher', 'ref', 'seg', 'series', 'title', 'volume', 'xr']
for name in tqdm(names, desc="Processing TEI tags"): for name in tqdm(names, desc="Processing TEI tags"):
doc_node = root.find(f".//xs:element[@name='{name}']/xs:annotation/xs:documentation", namespaces=namespaces) doc_node = root.find(f".//xs:element[@name='{name}']/xs:annotation/xs:documentation", namespaces=namespaces)
if doc_node is not None: if doc_node is not None:
matches = re.search(r'^(.*)\[(.*)]$', doc_node.text) matches = re.search(r'^(.*)\[(.*)]$', doc_node.text)
if matches is None: continue if matches is None: continue
description = matches.group(1) description = matches.group(1)
doc_heading = matches.group(2) doc_heading = matches.group(2)
doc_urls = extract_headings_and_links(name, doc_heading, doc_base_url) doc_urls = extract_headings_and_links(name, doc_heading, doc_base_url)
data_list.append({'name': name, 'description': description, 'documentation': doc_heading, 'urls': doc_urls}) data_list.append({'name': name, 'description': description, 'documentation': doc_heading, 'urls': doc_urls})
return pd.DataFrame(data_list) return pd.DataFrame(data_list)
cache_file = "schema/tei/tei-tags-documentation.json" cache_file = "schema/tei/tei-tags-documentation.json"
if not os.path.isfile(cache_file): if not os.path.isfile(cache_file):
df = generate_tag_docs("schema/tei/tei_all.xsd") df = generate_tag_docs("schema/tei/tei_all.xsd")
json_str = df.to_json(index=False, orient='records', indent=4).replace(r"\/", "/") json_str = df.to_json(index=False, orient='records', indent=4).replace(r"\/", "/")
with open(cache_file, "w", encoding='utf-8') as f: with open(cache_file, "w", encoding='utf-8') as f:
f.write(json_str) f.write(json_str)
else: else:
df = pd.read_json(cache_file) df = pd.read_json(cache_file)
df df
``` ```
%% Output %% Output
name description \ name description \
0 author (author) in a bibliographic reference, contain... 0 author (author) in a bibliographic reference, contain...
1 biblScope (scope of bibliographic reference) defines the... 1 biblScope (scope of bibliographic reference) defines the...
2 citedRange (cited range) defines the range of cited conte... 2 citedRange (cited range) defines the range of cited conte...
3 date (date) contains a date in any format. 3 date (date) contains a date in any format.
4 edition (edition) describes the particularities of one... 4 edition (edition) describes the particularities of one...
5 editor contains a secondary statement of responsibili... 5 editor contains a secondary statement of responsibili...
6 idno (identifier) supplies any form of identifier u... 6 idno (identifier) supplies any form of identifier u...
7 location (location) defines the location of a place as ... 7 location (location) defines the location of a place as ...
8 note (note) contains a note or annotation. 8 note (note) contains a note or annotation.
9 orgName (organization name) contains an organizational... 9 orgName (organization name) contains an organizational...
10 publisher (publisher) provides the name of the organizat... 10 publisher (publisher) provides the name of the organizat...
11 pubPlace (publication place) contains the name of the p... 11 pubPlace (publication place) contains the name of the p...
12 ptr (pointer) defines a pointer to another location. 12 ptr (pointer) defines a pointer to another location.
13 seg (arbitrary segment) represents any segmentatio... 13 seg (arbitrary segment) represents any segmentatio...
14 series (series information) contains information abou... 14 series (series information) contains information abou...
15 title (title) contains a title for any kind of work. 15 title (title) contains a title for any kind of work.
documentation \ documentation \
0 3.12.2.2. Titles, Authors, and Editors 2.2.1. ... 0 3.12.2.2. Titles, Authors, and Editors 2.2.1. ...
1 3.12.2.5. Scopes and Ranges in Bibliographic C... 1 3.12.2.5. Scopes and Ranges in Bibliographic C...
2 3.12.2.5. Scopes and Ranges in Bibliographic C... 2 3.12.2.5. Scopes and Ranges in Bibliographic C...
3 3.6.4. Dates and Times 2.2.4. Publication, Dis... 3 3.6.4. Dates and Times 2.2.4. Publication, Dis...
4 2.2.2. The Edition Statement 4 2.2.2. The Edition Statement
5 3.12.2.2. Titles, Authors, and Editors 5 3.12.2.2. Titles, Authors, and Editors
6 14.3.1. Basic Principles 2.2.4. Publication, D... 6 14.3.1. Basic Principles 2.2.4. Publication, D...
7 14.3.4. Places 7 14.3.4. Places
8 3.9.1. Notes and Simple Annotation 2.2.6. The ... 8 3.9.1. Notes and Simple Annotation 2.2.6. The ...
9 14.2.2. Organizational Names 9 14.2.2. Organizational Names
10 3.12.2.4. Imprint, Size of a Document, and Rep... 10 3.12.2.4. Imprint, Size of a Document, and Rep...
11 3.12.2.4. Imprint, Size of a Document, and Rep... 11 3.12.2.4. Imprint, Size of a Document, and Rep...
12 3.7. Simple Links and Cross-References 17.1. L... 12 3.7. Simple Links and Cross-References 17.1. L...
13 17.3. Blocks, Segments, and Anchors 6.2. Compo... 13 17.3. Blocks, Segments, and Anchors 6.2. Compo...
14 3.12.2.1. Analytic, Monographic, and Series Le... 14 3.12.2.1. Analytic, Monographic, and Series Le...
15 3.12.2.2. Titles, Authors, and Editors 2.2.1. ... 15 3.12.2.2. Titles, Authors, and Editors 2.2.1. ...
urls urls
0 {'3.12.2.2': 'https://www.tei-c.org/release/do... 0 {'3.12.2.2': 'https://www.tei-c.org/release/do...
1 {'3.12.2.5': 'https://www.tei-c.org/release/do... 1 {'3.12.2.5': 'https://www.tei-c.org/release/do...
2 {'3.12.2.5': 'https://www.tei-c.org/release/do... 2 {'3.12.2.5': 'https://www.tei-c.org/release/do...
3 {'3.6.4': 'https://www.tei-c.org/release/doc/t... 3 {'3.6.4': 'https://www.tei-c.org/release/doc/t...
4 {'2.2.2': 'https://www.tei-c.org/release/doc/t... 4 {'2.2.2': 'https://www.tei-c.org/release/doc/t...
5 {'3.12.2.2': 'https://www.tei-c.org/release/do... 5 {'3.12.2.2': 'https://www.tei-c.org/release/do...
6 {'14.3.1': 'https://www.tei-c.org/release/doc/... 6 {'14.3.1': 'https://www.tei-c.org/release/doc/...
7 {'14.3.4': 'https://www.tei-c.org/release/doc/... 7 {'14.3.4': 'https://www.tei-c.org/release/doc/...
8 {'3.9.1': 'https://www.tei-c.org/release/doc/t... 8 {'3.9.1': 'https://www.tei-c.org/release/doc/t...
9 {'14.2.2': 'https://www.tei-c.org/release/doc/... 9 {'14.2.2': 'https://www.tei-c.org/release/doc/...
10 {'3.12.2.4': 'https://www.tei-c.org/release/do... 10 {'3.12.2.4': 'https://www.tei-c.org/release/do...
11 {'3.12.2.4': 'https://www.tei-c.org/release/do... 11 {'3.12.2.4': 'https://www.tei-c.org/release/do...
12 {'3.7': 'https://www.tei-c.org/release/doc/tei... 12 {'3.7': 'https://www.tei-c.org/release/doc/tei...
13 {'17.3': 'https://www.tei-c.org/release/doc/te... 13 {'17.3': 'https://www.tei-c.org/release/doc/te...
14 {'3.12.2.1': 'https://www.tei-c.org/release/do... 14 {'3.12.2.1': 'https://www.tei-c.org/release/do...
15 {'3.12.2.2': 'https://www.tei-c.org/release/do... 15 {'3.12.2.2': 'https://www.tei-c.org/release/do...
%% Cell type:markdown id:aaf43ee43bb6d4d tags: %% Cell type:markdown id:aaf43ee43bb6d4d tags:
## Convert AnyStyle Gold Standard to TEI ## Convert AnyStyle Gold Standard to TEI
This converts the AnyStyle XML data to TEI, translating from the flat schema to the nested TEI `<bibl>` structure. This converts the AnyStyle XML data to TEI, translating from the flat schema to the nested TEI `<bibl>` structure.
%% Cell type:code id:b3ee84984b88f24a tags: %% Cell type:code id:b3ee84984b88f24a tags:
``` python ``` python
import xml.etree.ElementTree as ET import xml.etree.ElementTree as ET
import regex as re import regex as re
import glob import glob
import os import os
import xml.dom.minidom import xml.dom.minidom
import json import json
import xmlschema import xmlschema
from nameparser import HumanName from nameparser import HumanName
def even_num_brackets(string: str): def even_num_brackets(string: str):
""" """
Simple heuristic to determine if string contains an even number of round and square brackets, Simple heuristic to determine if string contains an even number of round and square brackets,
so that if not, trailing or leading brackets will be removed. so that if not, trailing or leading brackets will be removed.
""" """
return ((string.endswith(")") and string.count(")") == string.count("(")) return ((string.endswith(")") and string.count(")") == string.count("("))
or (string.endswith("]") and string.count("]") == string.count("["))) or (string.endswith("]") and string.count("]") == string.count("[")))
def remove_punctuation(text, keep_trailing_chars="?!"): def remove_punctuation(text, keep_trailing_chars="?!"):
"""This removes leading and trailing punctuation using very simple rules for German and English""" """This removes leading and trailing punctuation using very simple rules for German and English"""
start, end = 0, len(text) start, end = 0, len(text)
while start < len(text) and re.match("\p{P}", text[start]) and text[end - 1]: while start < len(text) and re.match("\p{P}", text[start]) and text[end - 1]:
start += 1 start += 1
while end > start and re.match("\p{P}", text[end - 1]) and not even_num_brackets(text[start:end]) and text[end - 1] not in keep_trailing_chars: while end > start and re.match("\p{P}", text[end - 1]) and not even_num_brackets(text[start:end]) and text[end - 1] not in keep_trailing_chars:
end -= 1 end -= 1
return text[start:end].strip() return text[start:end].strip()
def remove_punctuation2(text): def remove_punctuation2(text):
"""same as remove_punctuation, but keep trailing periods.""" """same as remove_punctuation, but keep trailing periods."""
return remove_punctuation(text, "?!.") return remove_punctuation(text, "?!.")
def clean_editor(text): def clean_editor(text):
text = re.sub(r'^in(:| )', '', remove_punctuation(text), flags=re.IGNORECASE) text = re.sub(r'^in(:| )', '', remove_punctuation(text), flags=re.IGNORECASE)
text = re.sub(r'\(?(hrsg\. v\.|hg\. v|hrsg\.|ed\.|eds\.)\)?', '', text, flags=re.IGNORECASE) text = re.sub(r'\(?(hrsg\. v\.|hg\. v|hrsg\.|ed\.|eds\.)\)?', '', text, flags=re.IGNORECASE)
return text.strip() return text.strip()
def clean_container(text): def clean_container(text):
return remove_punctuation(re.sub(r'^(in|aus|from)(:| )', '', text.strip(), flags=re.IGNORECASE)) return remove_punctuation(re.sub(r'^(in|aus|from)(:| )', '', text.strip(), flags=re.IGNORECASE))
def extract_page_range(text): def extract_page_range(text):
match = re.match(r'(\p{Alnum}+)(?: *\p{Pd} *(\p{Alnum}+))?', text) match = re.match(r'(\p{Alnum}+)(?: *\p{Pd} *(\p{Alnum}+))?', text)
attributes = {"unit": "page"} attributes = {"unit": "page"}
if match: if match:
from_page = match.group(1) from_page = match.group(1)
to_page = match.group(2) to_page = match.group(2)
attributes.update({"from": from_page}) attributes.update({"from": from_page})
if to_page is not None: if to_page is not None:
attributes.update({"to": to_page}) attributes.update({"to": to_page})
return attributes return attributes
def process_range(text): def process_range(text):
text = re.sub(r'^(S\.|p\.|pp\.)', '', text.strip(), flags=re.IGNORECASE) text = re.sub(r'^(S\.|p\.|pp\.)', '', text.strip(), flags=re.IGNORECASE)
text = re.sub(r'(ff?\.|seqq?\.)$', '', text.strip(), flags=re.IGNORECASE) text = re.sub(r'(ff?\.|seqq?\.)$', '', text.strip(), flags=re.IGNORECASE)
text = remove_punctuation(text) text = remove_punctuation(text)
attributes = extract_page_range(text) attributes = extract_page_range(text)
return (text, attributes) return (text, attributes)
def handle_pages(text, bibl, tag, preserve): def handle_pages(text, bibl, tag, preserve):
if text == "": return if text == "": return
# split by comma or semicolon along with any trailing spaces # split by comma or semicolon along with any trailing spaces
ranges = re.split(r'([,;] *)', text) ranges = re.split(r'([,;] *)', text)
# initialize an empty list to store results # initialize an empty list to store results
page_locators = [] page_locators = []
# loop through indices with a step of 2 # loop through indices with a step of 2
for i in range(0, len(ranges) - 1, 2): for i in range(0, len(ranges) - 1, 2):
# combine current element with the next one (which is a separator), and append to the list # combine current element with the next one (which is a separator), and append to the list
page_locators.append(ranges[i] + ranges[i+1]) page_locators.append(ranges[i] + ranges[i+1])
# if the input text doesn't end with a separator, add the last element # if the input text doesn't end with a separator, add the last element
if text[-1] not in [',', ';']: if text[-1] not in [',', ';']:
page_locators.append(ranges[-1]) page_locators.append(ranges[-1])
for page_locator in page_locators: for page_locator in page_locators:
add_node(bibl, tag, page_locator, clean_func=process_range, preserve=preserve) add_node(bibl, tag, page_locator, clean_func=process_range, preserve=preserve)
def clean_volume(text): def clean_volume(text):
text = re.sub(r'(vol\.|bd\.)', '', text.strip(), flags=re.IGNORECASE) text = re.sub(r'(vol\.|bd\.)', '', text.strip(), flags=re.IGNORECASE)
text = re.sub(r'(issue\.|heft\.)$', '', text.strip(), flags=re.IGNORECASE) text = re.sub(r'(issue\.|heft\.)$', '', text.strip(), flags=re.IGNORECASE)
text = remove_punctuation(text) text = remove_punctuation(text)
return text, {"from": text, "to": text} return text, {"from": text, "to": text}
def extract_text_in_parentheses(text): def extract_text_in_parentheses(text):
match = re.search(r'(.*?)\s*(\(.*?\))', text) match = re.search(r'(.*?)\s*(\(.*?\))', text)
if match: if match:
return match.group(1), match.group(2) return match.group(1), match.group(2)
else: else:
return text, None return text, None
def extract_year(text): def extract_year(text):
m = re.search( r'[12][0-9]{3}', text) m = re.search( r'[12][0-9]{3}', text)
return m.group(0) if m else None return m.group(0) if m else None
def find_string(string, container): def find_string(string, container):
start = container.find(string) start = container.find(string)
if start > -1: if start > -1:
end = start + len(string) end = start + len(string)
return start, end return start, end
raise ValueError(f"Could not find '{string}' in '{container}'") raise ValueError(f"Could not find '{string}' in '{container}'")
def add_node(parent, tag, text="", attributes=None, clean_func=None, preserve=False): def add_node(parent, tag, text="", attributes=None, clean_func=None, preserve=False):
""" """
Adds a child node to the parent, optionally adding text and attributes. Adds a child node to the parent, optionally adding text and attributes.
If a clean_func is passed, the text is set after applying the function to it. If a clean_func is passed, the text is set after applying the function to it.
If the `preserve` flag is True, the removed preceding or trailing text is preserved in the xml, outside of the node content If the `preserve` flag is True, the removed preceding or trailing text is preserved in the xml, outside of the node content
""" """
node = ET.SubElement(parent, tag, (attributes or {})) node = ET.SubElement(parent, tag, (attributes or {}))
if clean_func: if clean_func:
cleaned_text = clean_func(text) cleaned_text = clean_func(text)
if type(cleaned_text) is tuple: if type(cleaned_text) is tuple:
# in a tuple result, the first element is the text and the second node attributes # in a tuple result, the first element is the text and the second node attributes
for key,value in cleaned_text[1].items(): for key,value in cleaned_text[1].items():
node.set(key, value) node.set(key, value)
cleaned_text = cleaned_text[0] cleaned_text = cleaned_text[0]
if preserve: if preserve:
start, end = find_string(cleaned_text, text) start, end = find_string(cleaned_text, text)
prefix, suffix = text[:start], text[end:] prefix, suffix = text[:start], text[end:]
if prefix !="" and len(parent) > 1: if prefix !="" and len(parent) > 1:
prev_sibling = parent[-2] prev_sibling = parent[-2]
prev_tail = (prev_sibling.tail or '') prev_tail = (prev_sibling.tail or '')
new_prev_tail = f'{prev_tail} {prefix}'.strip() new_prev_tail = f'{prev_tail} {prefix}'.strip()
prev_sibling.tail = new_prev_tail prev_sibling.tail = new_prev_tail
node.text = cleaned_text node.text = cleaned_text
if suffix != "": if suffix != "":
node.tail = suffix node.tail = suffix
else: else:
node.text = text node.text = text
return node return node
def create_tei_root(): def create_tei_root():
return ET.Element('TEI', { return ET.Element('TEI', {
'xmlns': "http://www.tei-c.org/ns/1.0" 'xmlns': "http://www.tei-c.org/ns/1.0"
}) })
def create_tei_header(tei_root, title): def create_tei_header(tei_root, title):
tei_header = add_node(tei_root, 'teiHeader') tei_header = add_node(tei_root, 'teiHeader')
file_desc = add_node(tei_header, 'fileDesc') file_desc = add_node(tei_header, 'fileDesc')
title_stmt = add_node(file_desc, 'titleStmt') title_stmt = add_node(file_desc, 'titleStmt')
add_node(title_stmt, 'title', title) add_node(title_stmt, 'title', title)
publication_stmt = add_node(file_desc, 'publicationStmt') publication_stmt = add_node(file_desc, 'publicationStmt')
add_node(publication_stmt, 'publisher', 'mpilhlt') add_node(publication_stmt, 'publisher', 'mpilhlt')
source_desc = add_node(file_desc, 'sourceDesc') source_desc = add_node(file_desc, 'sourceDesc')
add_node(source_desc, 'p', title) add_node(source_desc, 'p', title)
return tei_header return tei_header
def create_body(text_root): def create_body(text_root):
body = ET.SubElement(text_root, 'body') body = ET.SubElement(text_root, 'body')
add_node(body, 'p', 'The article text is not part of this document') add_node(body, 'p', 'The article text is not part of this document')
return body return body
def prettify(xml_string, indentation=" "): def prettify(xml_string, indentation=" "):
"""Return a pretty-printed XML string""" """Return a pretty-printed XML string"""
return xml.dom.minidom.parseString(xml_string).toprettyxml(indent=indentation) return xml.dom.minidom.parseString(xml_string).toprettyxml(indent=indentation)
def split_creators(text:str, bibl, tag, clean_func, preserve): def split_creators(text:str, bibl, tag, clean_func, preserve):
sep_regex = r'[;&/]| and | und ' sep_regex = r'[;&/]| and | und '
creators = re.split(sep_regex, text) creators = re.split(sep_regex, text)
seperators = re.findall(sep_regex, text) seperators = re.findall(sep_regex, text)
for creator in creators: for creator in creators:
# <author>/<editor> # <author>/<editor>
creator_node = add_node(bibl, tag, creator, clean_func=clean_func, preserve=preserve) creator_node = add_node(bibl, tag, creator, clean_func=clean_func, preserve=preserve)
# <persName> # <persName>
name = HumanName(creator_node.text) name = HumanName(creator_node.text)
creator_node.text = '' creator_node.text = ''
pers_name = add_node(creator_node, 'persName') pers_name = add_node(creator_node, 'persName')
inv_map = {v: k for k, v in name.as_dict(False).items()} inv_map = {v: k for k, v in name.as_dict(False).items()}
if len(name) == 1: if len(name) == 1:
add_node(pers_name, 'surname', list(name)[0]) add_node(pers_name, 'surname', list(name)[0])
else: else:
for elem in list(name): for elem in list(name):
match inv_map[elem]: match inv_map[elem]:
case 'last': case 'last':
# <surname> # <surname>
add_node(pers_name, 'surname', elem) add_node(pers_name, 'surname', elem)
case 'first' | 'middle': case 'first' | 'middle':
# <forename> # <forename>
add_node(pers_name, 'forename', elem) add_node(pers_name, 'forename', elem)
if len(seperators): if len(seperators):
creator_node.tail = seperators.pop(0).strip() creator_node.tail = seperators.pop(0).strip()
def anystyle_to_tei(input_xml_path, id, preserve=False): def anystyle_to_tei(input_xml_path, id, preserve=False):
anystyle_root = ET.parse(input_xml_path).getroot() anystyle_root = ET.parse(input_xml_path).getroot()
tei_root = create_tei_root() tei_root = create_tei_root()
create_tei_header(tei_root, title=id) create_tei_header(tei_root, title=id)
text_root = add_node(tei_root, 'text') text_root = add_node(tei_root, 'text')
body = create_body(text_root) body = create_body(text_root)
# <listBibl> element for <bibl> elements that are not in footnotes, such as a bibliography # <listBibl> element for <bibl> elements that are not in footnotes, such as a bibliography
listBibl = add_node(body, 'listBibl') listBibl = add_node(body, 'listBibl')
# iterate over all sequences (=footnotes) and translate into TEI equivalents # iterate over all sequences (=footnotes) and translate into TEI equivalents
for sequence in anystyle_root.findall('sequence'): for sequence in anystyle_root.findall('sequence'):
# if the sequence contains a citation-number, create a new <note> to add <bibl> elements to # if the sequence contains a citation-number, create a new <note> to add <bibl> elements to
if (cn:= sequence.findall('citation-number')): if (cn:= sequence.findall('citation-number')):
footnote_number = cn[0].text footnote_number = cn[0].text
attributes = { attributes = {
'n': footnote_number, 'n': footnote_number,
'type': 'footnote', 'type': 'footnote',
'place': 'bottom' 'place': 'bottom'
} }
node = add_node(body, 'note', attributes=attributes, clean_func=remove_punctuation, preserve=preserve) node = add_node(body, 'note', attributes=attributes, clean_func=remove_punctuation, preserve=preserve)
else: else:
# otherwise add to <listBibl> element # otherwise add to <listBibl> element
node = listBibl node = listBibl
bibl = None bibl = None
for child in sequence: for child in sequence:
tag = child.tag tag = child.tag
text = child.text text = child.text
if tag == "citation-number": continue # this has already been taken care of if tag == "citation-number": continue # this has already been taken care of
if (bibl is None # if we do not have a bibl element yet if (bibl is None # if we do not have a bibl element yet
or (bibl.find(tag) and tag != "note") # or tag already exists in the current element or (bibl.find(tag) and tag != "note") # or tag already exists in the current element
or tag in ['signal', 'legal-ref'] # or tag belongs to a specific groups that signal a separate reference or tag in ['signal', 'legal-ref'] # or tag belongs to a specific groups that signal a separate reference
or (tag in ["author", "editor", "authority"] and bibl.find('date'))): # or specific tags follow a date field or (tag in ["author", "editor", "authority"] and bibl.find('date'))): # or specific tags follow a date field
# then create a new bibl element # then create a new bibl element
bibl = ET.SubElement(node, 'bibl') bibl = ET.SubElement(node, 'bibl')
match tag.lower(): match tag.lower():
case 'author': case 'author':
split_creators(text, bibl, 'author', clean_func=remove_punctuation, preserve=preserve) split_creators(text, bibl, 'author', clean_func=remove_punctuation, preserve=preserve)
case 'authority': case 'authority':
split_creators(text, bibl, 'publisher', clean_func=remove_punctuation, preserve=preserve) split_creators(text, bibl, 'publisher', clean_func=remove_punctuation, preserve=preserve)
case 'backref': case 'backref':
add_node(bibl, 'ref', text, clean_func=remove_punctuation2, preserve=preserve) add_node(bibl, 'ref', text, clean_func=remove_punctuation2, preserve=preserve)
case 'container-title': case 'container-title':
add_node(bibl, 'title', text, {'level': 'm'}, clean_func= clean_container, preserve=preserve) add_node(bibl, 'title', text, {'level': 'm'}, clean_func= clean_container, preserve=preserve)
case 'collection-title': case 'collection-title':
add_node(bibl, 'title', text, {'level': 's'}, clean_func= clean_container, preserve=preserve) add_node(bibl, 'title', text, {'level': 's'}, clean_func= clean_container, preserve=preserve)
case 'date': case 'date':
add_node(bibl, 'date', text, clean_func= extract_year, preserve=preserve) add_node(bibl, 'date', text, clean_func= extract_year, preserve=preserve)
case 'doi': case 'doi':
add_node(bibl, 'idno', text, {'type':'DOI'}) add_node(bibl, 'idno', text, {'type':'DOI'})
case 'edition': case 'edition':
add_node(bibl, 'edition', text, clean_func=remove_punctuation2, preserve=preserve) add_node(bibl, 'edition', text, clean_func=remove_punctuation2, preserve=preserve)
case 'editor': case 'editor':
split_creators(text, bibl, 'editor', clean_func=clean_editor, preserve=preserve) split_creators(text, bibl, 'editor', clean_func=clean_editor, preserve=preserve)
case 'location': case 'location':
add_node(bibl, 'pubPlace', text, clean_func=remove_punctuation, preserve=preserve) add_node(bibl, 'pubPlace', text, clean_func=remove_punctuation, preserve=preserve)
case 'note': case 'note':
add_node(bibl, 'seg', text, {'type': 'comment'}, clean_func=remove_punctuation, preserve=preserve) add_node(bibl, 'seg', text, {'type': 'comment'}, clean_func=remove_punctuation, preserve=preserve)
case 'journal': case 'journal':
add_node(bibl, 'title', text, {'level': 'j'}, clean_func= clean_container, preserve=preserve) add_node(bibl, 'title', text, {'level': 'j'}, clean_func= clean_container, preserve=preserve)
case 'legal-ref': case 'legal-ref':
add_node(bibl, 'idno', text, {'type': 'caseNumber'}, clean_func = remove_punctuation, preserve=preserve) add_node(bibl, 'idno', text, {'type': 'caseNumber'}, clean_func = remove_punctuation, preserve=preserve)
case 'pages': case 'pages':
if bibl[-1].tag == "xr": if bibl[-1].tag == "xr":
handle_pages(text, bibl, 'citedRange', preserve=preserve) handle_pages(text, bibl, 'citedRange', preserve=preserve)
else: else:
pages, cited_range = extract_text_in_parentheses(text) pages, cited_range = extract_text_in_parentheses(text)
handle_pages(pages, bibl, 'biblScope', preserve=preserve) handle_pages(pages, bibl, 'biblScope', preserve=preserve)
if cited_range: if cited_range:
handle_pages(cited_range, bibl, 'citedRange', preserve=preserve) handle_pages(cited_range, bibl, 'citedRange', preserve=preserve)
case 'signal': case 'signal':
add_node(bibl, 'seg', text, {'type': 'signal'}) add_node(bibl, 'seg', text, {'type': 'signal'})
case 'title': case 'title':
add_node(bibl, 'title', text, {'level': 'a'}, clean_func=remove_punctuation2, preserve=preserve) add_node(bibl, 'title', text, {'level': 'a'}, clean_func=remove_punctuation2, preserve=preserve)
case 'url': case 'url':
add_node(bibl, 'ptr', text, {'type':'web'}, clean_func=remove_punctuation, preserve=preserve) add_node(bibl, 'ptr', text, {'type':'web'}, clean_func=remove_punctuation, preserve=preserve)
case 'volume': case 'volume':
volume, issue = extract_text_in_parentheses(text) volume, issue = extract_text_in_parentheses(text)
add_node(bibl, 'biblScope', volume, {'unit': 'volume'}, clean_func = clean_volume, preserve=preserve) add_node(bibl, 'biblScope', volume, {'unit': 'volume'}, clean_func = clean_volume, preserve=preserve)
if issue: if issue:
add_node(bibl, 'biblScope', issue, {'unit': 'issue'}, clean_func = clean_volume, preserve=preserve) add_node(bibl, 'biblScope', issue, {'unit': 'issue'}, clean_func = clean_volume, preserve=preserve)
if len(bibl) == 0: if len(bibl) == 0:
node.remove(bibl) node.remove(bibl)
if len(listBibl) == 0: if len(listBibl) == 0:
body.remove(listBibl) body.remove(listBibl)
return ET.tostring(tei_root, 'unicode') return ET.tostring(tei_root, 'unicode')
def tei_to_json(tei_xml, schema): def tei_to_json(tei_xml, schema):
dict_obj = xmlschema.to_dict(tei_xml, schema=schema, converter=xmlschema.JsonMLConverter) dict_obj = xmlschema.to_dict(tei_xml, schema=schema, converter=xmlschema.JsonMLConverter)
return json.dumps(dict_obj, default=str) return json.dumps(dict_obj, default=str)
# main # main
print("Converting AnyStyle XML into TEI/bibl elements") print("Converting AnyStyle XML into TEI/bibl elements")
for input_path in glob.glob('anystyle/*.xml'): for input_path in glob.glob('anystyle/*.xml'):
base_name = os.path.basename(input_path) base_name = os.path.basename(input_path)
id = os.path.splitext(base_name)[0] id = os.path.splitext(base_name)[0]
print(f' - {base_name}') print(f' - {base_name}')
output_xml = anystyle_to_tei(input_path, id, preserve=True) output_xml = anystyle_to_tei(input_path, id, preserve=True)
# output_json = tei_to_json(output_xml, schema) # output_json = tei_to_json(output_xml, schema)
with open(f'tei-bibl/{id}.xml', 'w', encoding='utf-8') as f: with open(f'tei-bibl/{id}.xml', 'w', encoding='utf-8') as f:
f.write(prettify(output_xml)) f.write(prettify(output_xml))
``` ```
%% Output %% Output
Converting AnyStyle XML into TEI/bibl elements Converting AnyStyle XML into TEI/bibl elements
- 10.1111_1467-6478.00057.xml - 10.1111_1467-6478.00057.xml
- 10.1111_1467-6478.00080.xml - 10.1111_1467-6478.00080.xml
- 10.1515_zfrs-1980-0103.xml - 10.1515_zfrs-1980-0103.xml
- 10.1515_zfrs-1980-0104.xml - 10.1515_zfrs-1980-0104.xml
%% Cell type:markdown id:8c8b2d820086d461 tags: %% Cell type:markdown id:8c8b2d820086d461 tags:
%% Cell type:markdown id:bb9da323c357ca4c tags: %% Cell type:markdown id:bb9da323c357ca4c tags:
## Recreate input data from TEI/bibl and compare with AnyStyle input data ## Recreate input data from TEI/bibl and compare with AnyStyle input data
To see how much information is lost or which errors are introduced in the translation of Anystyle to TEI, we compare the input data generated from the (lossless) anystyle markup with that "reverse-engineered" from the TEI and save a character-level diff in the `html` directory. To see how much information is lost or which errors are introduced in the translation of Anystyle to TEI, we compare the input data generated from the (lossless) anystyle markup with that "reverse-engineered" from the TEI and save a character-level diff in the `html` directory.
The comparison is done with a copy of the files stored in `./tei-bibl-corrected` so that they are not overwritten when running the previous cell, and so that they can be manually corrected to fit the original data. The comparison is done with a copy of the files stored in `./tei-bibl-corrected` so that they are not overwritten when running the previous cell, and so that they can be manually corrected to fit the original data.
For better viewing, the result is published on gitlab pages (see links in the output). For better viewing, the result is published on gitlab pages (see links in the output).
%% Cell type:code id:4c19609699dc79c tags: %% Cell type:code id:4c19609699dc79c tags:
``` python ``` python
from lxml import etree from lxml import etree
import glob import glob
import os import os
import json import json
import regex as re import regex as re
from lib.string import remove_whitespace from lib.string import remove_whitespace
from difflib import HtmlDiff from difflib import HtmlDiff
from IPython.display import display, Markdown from IPython.display import display, Markdown
def tei_to_ground_truth_input(tei_xml_doc): def tei_to_ground_truth_input(tei_xml_doc):
""" """
Extract the original footnote strings from the <note> elements in a given TEI document and return a list of strings Extract the original footnote strings from the <note> elements in a given TEI document and return a list of strings
""" """
root = etree.fromstring(tei_xml_doc) root = etree.fromstring(tei_xml_doc)
ground_truth_list = [] ground_truth_list = []
ns = {"tei": "http://www.tei-c.org/ns/1.0"} ns = {"tei": "http://www.tei-c.org/ns/1.0"}
# iterate over the <note type="footnote"> elements # iterate over the <note type="footnote"> elements
for note in root.findall('.//tei:note[@type="footnote"]', ns): for note in root.findall('.//tei:note[@type="footnote"]', ns):
footnote_elements = [note.attrib['n']] footnote_elements = [note.attrib['n']]
# iterate over the <bibl> elements # iterate over the <bibl> elements
for bibl in note.findall('tei:bibl', ns): for bibl in note.findall('tei:bibl', ns):
# extract the text without xml tags, still contains all (collapsed) whitespace # extract the text without xml tags, still contains all (collapsed) whitespace
text = etree.tostring(bibl, method="text", encoding='utf-8').decode() text = etree.tostring(bibl, method="text", encoding='utf-8').decode()
text = remove_whitespace(text) text = remove_whitespace(text)
footnote_elements.append(text) footnote_elements.append(text)
ground_truth_list.append(" ".join(footnote_elements)) ground_truth_list.append(" ".join(footnote_elements))
return ground_truth_list return ground_truth_list
for input_path in glob.glob('tei-bibl-corrected/*.xml'): for input_path in glob.glob('tei-bibl-corrected/*.xml'):
base_name = os.path.basename(input_path) base_name = os.path.basename(input_path)
id = os.path.splitext(base_name)[0] id = os.path.splitext(base_name)[0]
with open(input_path, 'r', encoding='utf-8') as f: with open(input_path, 'r', encoding='utf-8') as f:
tei_input_data = tei_to_ground_truth_input(f.read()) tei_input_data = tei_to_ground_truth_input(f.read())
anystyle_input_path = f'refs/{id}.txt' anystyle_input_path = f'refs/{id}.txt'
with open(anystyle_input_path, 'r', encoding='utf-8') as f: with open(anystyle_input_path, 'r', encoding='utf-8') as f:
anystyle_input_data = f.read().splitlines() anystyle_input_data = f.read().splitlines()
# create files showing the diff between the reverse engineering of the input data from the TEI and the original raw strings # create files showing the diff between the reverse engineering of the input data from the TEI and the original raw strings
html_diff = HtmlDiff().make_file(anystyle_input_data, tei_input_data) html_diff = HtmlDiff().make_file(anystyle_input_data, tei_input_data)
with open(f"../public/convert-anystyle-data/diffs/{id}.diff.html", "w", encoding="utf-8") as f: with open(f"../public/convert-anystyle-data/diffs/{id}.diff.html", "w", encoding="utf-8") as f:
f.write(html_diff) f.write(html_diff)
display(Markdown(f'Extracted and compared input data for {id} ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/{id}.diff.html))')) display(Markdown(f'Extracted and compared input data for {id} ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/{id}.diff.html))'))
``` ```
%% Output %% Output
Extracted and compared input data for 10.1111_1467-6478.00057 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1111_1467-6478.00057.diff.html)) Extracted and compared input data for 10.1111_1467-6478.00057 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1111_1467-6478.00057.diff.html))
Extracted and compared input data for 10.1111_1467-6478.00080 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1111_1467-6478.00080.diff.html)) Extracted and compared input data for 10.1111_1467-6478.00080 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1111_1467-6478.00080.diff.html))
Extracted and compared input data for 10.1515_zfrs-1980-0103 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1515_zfrs-1980-0103.diff.html)) Extracted and compared input data for 10.1515_zfrs-1980-0103 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1515_zfrs-1980-0103.diff.html))
Extracted and compared input data for 10.1515_zfrs-1980-0104 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1515_zfrs-1980-0104.diff.html)) Extracted and compared input data for 10.1515_zfrs-1980-0104 ([See diff](https://experiments-boulanger-27b5c1c5c975b0350675064f0f85580e618945eef.pages.gwdg.de/convert-anystyle-data/diffs/10.1515_zfrs-1980-0104.diff.html))
......
%% Cell type:code id:initial_id tags: %% Cell type:markdown id:1d998503d27b0be9 tags:
``` python
# Convert AnyStyle GT back to original strings # Convert AnyStyle GT back to original strings
```
The AnyStyle format is easily converted to the original raw reference string by simply stripping all XML tags.
%% Cell type:code id:d8ff3eba78b2d0d8 tags: %% Cell type:code id:d8ff3eba78b2d0d8 tags:
``` python ``` python
import xml.etree.ElementTree as ET import xml.etree.ElementTree as ET
import glob import glob
import os import os
import json import json
import re import re
for input_path in glob.glob('anystyle/*.xml'): for input_path in glob.glob('anystyle/*.xml'):
base_name = os.path.basename(input_path) base_name = os.path.basename(input_path)
id = os.path.splitext(base_name)[0] id = os.path.splitext(base_name)[0]
print(f'Extracting GT input data from {base_name} ...') print(f'Extracting GT input data from {base_name} ...')
root = ET.parse(input_path) root = ET.parse(input_path)
refs = [] refs = []
for sequence in root.findall('.//sequence'): for sequence in root.findall('.//sequence'):
ref = " ".join(element.text.strip() if element.text else '' for element in sequence) ref = " ".join(element.text.strip() if element.text else '' for element in sequence)
ref = re.sub(r'\n *', ' ', ref) ref = re.sub(r'\n *', ' ', ref)
refs.append(ref) refs.append(ref)
with open(f'refs/{base_name.replace(".xml",".txt")}', 'w', encoding='utf-8') as f: with open(f'refs/{base_name.replace(".xml",".txt")}', 'w', encoding='utf-8') as f:
f.write('\n'.join(refs)) f.write('\n'.join(refs))
``` ```
%% Output %% Output
Extracting GT input data from 10.1111_1467-6478.00057.xml ... Extracting GT input data from 10.1111_1467-6478.00057.xml ...
Extracting GT input data from 10.1111_1467-6478.00080.xml ... Extracting GT input data from 10.1111_1467-6478.00080.xml ...
Extracting GT input data from 10.1515_zfrs-1980-0103.xml ... Extracting GT input data from 10.1515_zfrs-1980-0103.xml ...
Extracting GT input data from 10.1515_zfrs-1980-0104.xml ... Extracting GT input data from 10.1515_zfrs-1980-0104.xml ...
%% Cell type:code id:f55d360989a07f5d tags: %% Cell type:code id:f55d360989a07f5d tags:
``` python ``` python
``` ```
......
%% Cell type:markdown id:2cdf8ba1eefa38e0 tags: %% Cell type:markdown id:2cdf8ba1eefa38e0 tags:
# Convert the generated TEI to bibliographic formats # Convert the generated TEI to bibliographic formats
References:
- https://www.tei-c.org/release/doc/tei-p5-doc/en/html/CO.html#COBIOT (Mapping of TEI to other bibliographic formats)
- https://github.com/OpenArabicPE/convert_tei-to-bibliographic-data (XSLT for conversion of bibl/biblStruct to MODS)
- https://www.loc.gov/standards/mods/mods-conversions.html (XSLT for conversion of MODS to other formats)
%% Cell type:markdown id:db65c4065691c578 tags: %% Cell type:markdown id:db65c4065691c578 tags:
## Download required XSLT documents ## Download required XSLT documents
we use XSLT provided by https://github.com/OpenArabicPE/convert_tei-to-bibliographic-data we use XSLT provided by https://github.com/OpenArabicPE/convert_tei-to-bibliographic-data
%% Cell type:code id:1de7cedbb3514188 tags: %% Cell type:code id:1de7cedbb3514188 tags:
``` python ``` python
import os import os
from urllib.parse import urljoin from urllib.parse import urljoin
import requests import requests
from lxml import etree from lxml import etree
cache = set() cache = set()
def download_xslt(url, target_dir = 'lib/xslt'): def download_xslt(url, target_dir = 'lib/xslt'):
"""written by GPT-4""" """written by GPT-4"""
response = requests.get(url) response = requests.get(url)
response.raise_for_status() response.raise_for_status()
doc = etree.fromstring(response.content) doc = etree.fromstring(response.content)
for elem in doc.xpath('//*[local-name() = "import"]'): for elem in doc.xpath('//*[local-name() = "import"]'):
import_url = urljoin(url, elem.get('href')) import_url = urljoin(url, elem.get('href'))
if import_url not in cache: if import_url not in cache:
cache.add(import_url) cache.add(import_url)
download_xslt(import_url, target_dir) download_xslt(import_url, target_dir)
os.makedirs(target_dir, exist_ok=True) os.makedirs(target_dir, exist_ok=True)
with open(os.path.join(target_dir, os.path.basename(url)), 'wb') as f: with open(os.path.join(target_dir, os.path.basename(url)), 'wb') as f:
f.write(response.content) f.write(response.content)
print(f'Downloaded {os.path.basename(url)} to {target_dir}') print(f'Downloaded {os.path.basename(url)} to {target_dir}')
# TEI -> BiblStruct/MODS # TEI -> BiblStruct/MODS
base_url = 'https://openarabicpe.github.io/convert_tei-to-bibliographic-data/xslt' base_url = 'https://openarabicpe.github.io/convert_tei-to-bibliographic-data/xslt'
xslt_docs = ['convert_tei-to-biblstruct_bibl.xsl', xslt_docs = ['convert_tei-to-biblstruct_bibl.xsl',
'convert_tei-to-mods_bibl.xsl', 'convert_tei-to-mods_bibl.xsl',
'convert_tei-to-zotero-rdf_bibl.xsl'] 'convert_tei-to-zotero-rdf_bibl.xsl']
for xslt_doc in xslt_docs: for xslt_doc in xslt_docs:
download_xslt(f'{base_url}/{xslt_doc}') download_xslt(f'{base_url}/{xslt_doc}')
# MODS -> BIBO-RDF # MODS -> BIBO-RDF
base_url = 'https://www.loc.gov/standards/mods/v3' base_url = 'https://www.loc.gov/standards/mods/v3'
xslt_docs = ['MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl', 'conf/languageCrosswalk.xml'] xslt_docs = ['MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl', 'conf/languageCrosswalk.xml']
for xslt_doc in xslt_docs: for xslt_doc in xslt_docs:
download_xslt(f'{base_url}/{xslt_doc}', target_dir=f'lib/xslt/{os.path.dirname(xslt_doc)}') download_xslt(f'{base_url}/{xslt_doc}', target_dir=f'lib/xslt/{os.path.dirname(xslt_doc)}')
``` ```
%% Output %% Output
Downloaded parameters.xsl to lib/xslt Downloaded parameters.xsl to lib/xslt
Downloaded functions.xsl to lib/xslt Downloaded functions.xsl to lib/xslt
Downloaded convert_tei-to-biblstruct_functions.xsl to lib/xslt Downloaded convert_tei-to-biblstruct_functions.xsl to lib/xslt
Downloaded convert_tei-to-biblstruct_bibl.xsl to lib/xslt Downloaded convert_tei-to-biblstruct_bibl.xsl to lib/xslt
Downloaded date-functions.xsl to lib/xslt Downloaded date-functions.xsl to lib/xslt
Downloaded convert_tei-to-mods_functions.xsl to lib/xslt Downloaded convert_tei-to-mods_functions.xsl to lib/xslt
Downloaded convert_tei-to-mods_bibl.xsl to lib/xslt Downloaded convert_tei-to-mods_bibl.xsl to lib/xslt
Downloaded convert_tei-to-zotero-rdf_bibl.xsl to lib/xslt Downloaded convert_tei-to-zotero-rdf_bibl.xsl to lib/xslt
Downloaded MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl to lib/xslt/ Downloaded MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl to lib/xslt/
Downloaded languageCrosswalk.xml to lib/xslt/conf Downloaded languageCrosswalk.xml to lib/xslt/conf
%% Cell type:markdown id:781d0e0e7a9dd346 tags: %% Cell type:markdown id:781d0e0e7a9dd346 tags:
## Download the Saxon jar ## Download the Saxon jar
As the xslt uses v2.0 features, and there are no native-python xslt-2.0 processors, we need to use the Saxon processor. Possible alternatives (untested): As the xslt uses v2.0 features, and there are no native-python xslt-2.0 processors, we need to use the Saxon processor. Possible alternatives (untested):
- https://pypi.org/project/saxonpy - https://pypi.org/project/saxonpy
- https://github.com/cts2/pyjxslt - https://github.com/cts2/pyjxslt
%% Cell type:code id:72b688e9b2e0d1f2 tags: %% Cell type:code id:72b688e9b2e0d1f2 tags:
``` python ``` python
import requests import requests
import zipfile import zipfile
import io import io
import os import os
url = "https://github.com/Saxonica/Saxon-HE/releases/download/SaxonHE12-5/SaxonHE12-5J.zip" url = "https://github.com/Saxonica/Saxon-HE/releases/download/SaxonHE12-5/SaxonHE12-5J.zip"
target_dir = 'lib/SaxonHE12-5' target_dir = 'lib/SaxonHE12-5'
response = requests.get(url, stream=True) response = requests.get(url, stream=True)
file_zip = zipfile.ZipFile(io.BytesIO(response.content)) file_zip = zipfile.ZipFile(io.BytesIO(response.content))
os.makedirs(target_dir, exist_ok=True) os.makedirs(target_dir, exist_ok=True)
file_zip.extractall(path=target_dir) file_zip.extractall(path=target_dir)
``` ```
%% Cell type:markdown id:ddb489a0e84d0ad6 tags: %% Cell type:markdown id:ddb489a0e84d0ad6 tags:
## Convert TEI-bibl to TEI-biblStruct ## Convert TEI-bibl to TEI-biblStruct
%% Cell type:code id:6228841009ae6c5f tags: %% Cell type:code id:6228841009ae6c5f tags:
``` python ``` python
from lib.xslt import transform from lib.xslt import transform
transform(xslt_path='lib/xslt/convert_tei-to-biblstruct_bibl.xsl', transform(xslt_path='lib/xslt/convert_tei-to-biblstruct_bibl.xsl',
input_path='tei-bibl-corrected', input_path='tei-bibl-corrected',
output_path='tei-biblStruct', output_path='tei-biblStruct',
rename_extension=('-bibl_biblStruct.TEIP5.xml','.biblStruct.xml')) rename_extension=('-bibl_biblStruct.TEIP5.xml','.biblStruct.xml'))
``` ```
%% Output %% Output
--------------------------------------------------------------------------- ---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last) FileNotFoundError Traceback (most recent call last)
Cell In[3], line 2 Cell In[3], line 2
1 from lib.xslt import transform 1 from lib.xslt import transform
----> 2 transform(xslt_path='lib/xslt/convert_tei-to-biblstruct_bibl.xsl', ----> 2 transform(xslt_path='lib/xslt/convert_tei-to-biblstruct_bibl.xsl',
3 input_path='tei-bibl-corrected', 3 input_path='tei-bibl-corrected',
4 output_path='tei-biblStruct', 4 output_path='tei-biblStruct',
5 rename_extension=('-bibl_biblStruct.TEIP5.xml','.biblStruct.xml')) 5 rename_extension=('-bibl_biblStruct.TEIP5.xml','.biblStruct.xml'))
File ~\DataspellProjects\experiments\convert-anystyle-data\lib\xslt.py:12, in transform(xslt_path, input_path, output_path, rename_extension, remove_prefix) File ~\DataspellProjects\experiments\convert-anystyle-data\lib\xslt.py:12, in transform(xslt_path, input_path, output_path, rename_extension, remove_prefix)
8 xslt_path = os.path.normpath(xslt_path) 8 xslt_path = os.path.normpath(xslt_path)
9 cmd = ['java', '-jar', 'lib/SaxonHE12-5J/saxon-he-12.5.jar', 9 cmd = ['java', '-jar', 'lib/SaxonHE12-5J/saxon-he-12.5.jar',
10 f'-s:{input_path}', f'-xsl:{xslt_path}', f'-o:{output_path}/', 10 f'-s:{input_path}', f'-xsl:{xslt_path}', f'-o:{output_path}/',
11 'p_target-language=de', 'p_github-action=true', f'p_output-folder={output_path}/'] 11 'p_target-language=de', 'p_github-action=true', f'p_output-folder={output_path}/']
---> 12 process = subprocess.run(cmd, capture_output=True, text=True) ---> 12 process = subprocess.run(cmd, capture_output=True, text=True)
14 # clean up the output dir 14 # clean up the output dir
15 for file_path in glob(f'{output_path}/*.xml'): 15 for file_path in glob(f'{output_path}/*.xml'):
File ~\AppData\Local\miniconda3\Lib\subprocess.py:548, in run(input, capture_output, timeout, check, *popenargs, **kwargs) File ~\AppData\Local\miniconda3\Lib\subprocess.py:548, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
545 kwargs['stdout'] = PIPE 545 kwargs['stdout'] = PIPE
546 kwargs['stderr'] = PIPE 546 kwargs['stderr'] = PIPE
--> 548 with Popen(*popenargs, **kwargs) as process: --> 548 with Popen(*popenargs, **kwargs) as process:
549 try: 549 try:
550 stdout, stderr = process.communicate(input, timeout=timeout) 550 stdout, stderr = process.communicate(input, timeout=timeout)
File ~\AppData\Local\miniconda3\Lib\subprocess.py:1026, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group) File ~\AppData\Local\miniconda3\Lib\subprocess.py:1026, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize, process_group)
1022 if self.text_mode: 1022 if self.text_mode:
1023 self.stderr = io.TextIOWrapper(self.stderr, 1023 self.stderr = io.TextIOWrapper(self.stderr,
1024 encoding=encoding, errors=errors) 1024 encoding=encoding, errors=errors)
-> 1026 self._execute_child(args, executable, preexec_fn, close_fds, -> 1026 self._execute_child(args, executable, preexec_fn, close_fds,
1027 pass_fds, cwd, env, 1027 pass_fds, cwd, env,
1028 startupinfo, creationflags, shell, 1028 startupinfo, creationflags, shell,
1029 p2cread, p2cwrite, 1029 p2cread, p2cwrite,
1030 c2pread, c2pwrite, 1030 c2pread, c2pwrite,
1031 errread, errwrite, 1031 errread, errwrite,
1032 restore_signals, 1032 restore_signals,
1033 gid, gids, uid, umask, 1033 gid, gids, uid, umask,
1034 start_new_session, process_group) 1034 start_new_session, process_group)
1035 except: 1035 except:
1036 # Cleanup if the child failed starting. 1036 # Cleanup if the child failed starting.
1037 for f in filter(None, (self.stdin, self.stdout, self.stderr)): 1037 for f in filter(None, (self.stdin, self.stdout, self.stderr)):
File ~\AppData\Local\miniconda3\Lib\subprocess.py:1538, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_gid, unused_gids, unused_uid, unused_umask, unused_start_new_session, unused_process_group) File ~\AppData\Local\miniconda3\Lib\subprocess.py:1538, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_gid, unused_gids, unused_uid, unused_umask, unused_start_new_session, unused_process_group)
1536 # Start the process 1536 # Start the process
1537 try: 1537 try:
-> 1538 hp, ht, pid, tid = _winapi.CreateProcess(executable, args, -> 1538 hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
1539 # no special security 1539 # no special security
1540 None, None, 1540 None, None,
1541 int(not close_fds), 1541 int(not close_fds),
1542 creationflags, 1542 creationflags,
1543 env, 1543 env,
1544 cwd, 1544 cwd,
1545 startupinfo) 1545 startupinfo)
1546 finally: 1546 finally:
1547 # Child is launched. Close the parent's copy of those pipe 1547 # Child is launched. Close the parent's copy of those pipe
1548 # handles that only the child should have open. You need 1548 # handles that only the child should have open. You need
(...) (...)
1551 # pipe will not close when the child process exits and the 1551 # pipe will not close when the child process exits and the
1552 # ReadFile will hang. 1552 # ReadFile will hang.
1553 self._close_pipe_fds(p2cread, p2cwrite, 1553 self._close_pipe_fds(p2cread, p2cwrite,
1554 c2pread, c2pwrite, 1554 c2pread, c2pwrite,
1555 errread, errwrite) 1555 errread, errwrite)
FileNotFoundError: [WinError 2] Das System kann die angegebene Datei nicht finden FileNotFoundError: [WinError 2] Das System kann die angegebene Datei nicht finden
%% Cell type:markdown id:dcdb762867feb96a tags: %% Cell type:markdown id:dcdb762867feb96a tags:
## Convert TEI-bibl to MODS ## Convert TEI-bibl to MODS
%% Cell type:code id:34087ef2f498ffa6 tags: %% Cell type:code id:34087ef2f498ffa6 tags:
``` python ``` python
from lib.xslt import transform from lib.xslt import transform
transform(xslt_path='lib/xslt/convert_tei-to-mods_bibl.xsl', transform(xslt_path='lib/xslt/convert_tei-to-mods_bibl.xsl',
input_path='tei-bibl-corrected', input_path='tei-bibl-corrected',
output_path='mods', output_path='mods',
rename_extension=('-bibl.MODS.xml','.mods.xml')) rename_extension=('-bibl.MODS.xml','.mods.xml'))
``` ```
%% Output %% Output
Applied lib\xslt\convert_tei-to-mods_bibl.xsl to files in tei-bibl-corrected and saved result in mods. Applied lib\xslt\convert_tei-to-mods_bibl.xsl to files in tei-bibl-corrected and saved result in mods.
CompletedProcess(args=['java', '-jar', 'lib/SaxonHE12-5J/saxon-he-12.5.jar', '-s:tei-bibl-corrected', '-xsl:lib\\xslt\\convert_tei-to-mods_bibl.xsl', '-o:mods/', 'p_target-language=de', 'p_github-action=true', 'p_output-folder=mods/'], returncode=0, stdout='', stderr='') CompletedProcess(args=['java', '-jar', 'lib/SaxonHE12-5J/saxon-he-12.5.jar', '-s:tei-bibl-corrected', '-xsl:lib\\xslt\\convert_tei-to-mods_bibl.xsl', '-o:mods/', 'p_target-language=de', 'p_github-action=true', 'p_output-folder=mods/'], returncode=0, stdout='', stderr='')
%% Cell type:markdown id:5e75488ae4379946 tags: %% Cell type:markdown id:5e75488ae4379946 tags:
## Convert MODS to RIS tagged file format ## Convert MODS to RIS tagged file format
This requires the install the [Bibutils suite of executables](https://sourceforge.net/p/bibutils/home/Bibutils) available in most distros. This requires the install the [Bibutils suite of executables](https://sourceforge.net/p/bibutils/home/Bibutils) available in most distros.
If you are on Windows, you will need to install it to the standard WSL distro. If you are on Windows, you will need to install it to the standard WSL distro.
%% Cell type:code id:fde37a9e4a182bad tags: %% Cell type:code id:fde37a9e4a182bad tags:
``` python ``` python
import subprocess import subprocess
import platform import platform
cmd = ['bash', 'lib/run-bibutils.sh', 'xml2ris'] cmd = ['bash', 'lib/run-bibutils.sh', 'xml2ris']
if platform.system() == 'Windows': if platform.system() == 'Windows':
cmd = ['wsl.exe', '-e'] + cmd cmd = ['wsl.exe', '-e'] + cmd
output = subprocess.check_output(cmd, stderr=subprocess.STDOUT) output = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
print(output.decode()) print(output.decode())
``` ```
%% Output %% Output
Running xml2ris to convert mods/10.1111_1467-6478.00057.mods.xml to ris/10.1111_1467-6478.00057.ris... Running xml2ris to convert mods/10.1111_1467-6478.00057.mods.xml to ris/10.1111_1467-6478.00057.ris...
Running xml2ris to convert mods/10.1111_1467-6478.00080.mods.xml to ris/10.1111_1467-6478.00080.ris... Running xml2ris to convert mods/10.1111_1467-6478.00080.mods.xml to ris/10.1111_1467-6478.00080.ris...
Running xml2ris to convert mods/10.1515_zfrs-1980-0103.mods.xml to ris/10.1515_zfrs-1980-0103.ris... Running xml2ris to convert mods/10.1515_zfrs-1980-0103.mods.xml to ris/10.1515_zfrs-1980-0103.ris...
Running xml2ris to convert mods/10.1515_zfrs-1980-0104.mods.xml to ris/10.1515_zfrs-1980-0104.ris... Running xml2ris to convert mods/10.1515_zfrs-1980-0104.mods.xml to ris/10.1515_zfrs-1980-0104.ris...
%% Cell type:markdown id:61f6cfe7d3de482a tags: %% Cell type:markdown id:61f6cfe7d3de482a tags:
## Convert MODS -> Bibframe RDF -> JSON-LD ## Convert MODS -> Bibframe RDF -> JSON-LD
See: See:
- https://www.loc.gov/standards/mods/modsrdf/mods3-7-bibframe2-0-mapping.html - https://www.loc.gov/standards/mods/modsrdf/mods3-7-bibframe2-0-mapping.html
- https://rdflib.readthedocs.io/ - https://rdflib.readthedocs.io/
%% Cell type:code id:6ba739963096f858 tags: %% Cell type:code id:6ba739963096f858 tags:
``` python ``` python
# MODS -> Bibframe # MODS -> Bibframe
transform(xslt_path='lib/xslt/MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl', transform(xslt_path='lib/xslt/MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl',
input_path='mods', output_path='bibframe', input_path='mods', output_path='bibframe',
rename_extension=('.mods.xml','.bibframe.xml')) rename_extension=('.mods.xml','.bibframe.xml'))
``` ```
%% Output %% Output
Applied lib\xslt\MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl to files in mods and saved result in bibframe. Applied lib\xslt\MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl to files in mods and saved result in bibframe.
CompletedProcess(args=['java', '-jar', 'lib/SaxonHE12-5J/saxon-he-12.5.jar', '-s:mods', '-xsl:lib\\xslt\\MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl', '-o:bibframe', 'p_target-language=de', 'p_github-action=true', 'p_output-folder=bibframe'], returncode=0, stdout='', stderr='') CompletedProcess(args=['java', '-jar', 'lib/SaxonHE12-5J/saxon-he-12.5.jar', '-s:mods', '-xsl:lib\\xslt\\MODS3-7_Bibframe2-0_XSLT2-0_20230505.xsl', '-o:bibframe', 'p_target-language=de', 'p_github-action=true', 'p_output-folder=bibframe'], returncode=0, stdout='', stderr='')
%% Cell type:code id:4cb509fa7f296d1f tags: %% Cell type:code id:4cb509fa7f296d1f tags:
``` python ``` python
from rdflib import Graph from rdflib import Graph
for in_path in glob(f'bibframe/*'): for in_path in glob(f'bibframe/*'):
out_file = os.path.basename(in_path).replace('.bibframe.xml','.json') out_file = os.path.basename(in_path).replace('.bibframe.xml','.json')
g = Graph() g = Graph()
g.parse(in_path) g.parse(in_path)
g.serialize(destination=f'json-ld/{out_file}', format='json-ld') g.serialize(destination=f'json-ld/{out_file}', format='json-ld')
``` ```
%% Cell type:markdown id:8ce07a1a294b5408 tags: %% Cell type:markdown id:8ce07a1a294b5408 tags:
%% Cell type:markdown id:be771aec518bf10a tags: %% Cell type:markdown id:be771aec518bf10a tags:
## Convert MODS -> BibTex -> CSL-JSON ## Convert MODS -> BibTex -> CSL-JSON
This also requires Bibutils and additionally, the [pandoc executable](https://pandoc.org/installing.html). This also requires Bibutils and additionally, the [pandoc executable](https://pandoc.org/installing.html).
%% Cell type:code id:3e95a38e223dae51 tags: %% Cell type:code id:3e95a38e223dae51 tags:
``` python ``` python
# MODS -> BibTeX # MODS -> BibTeX
import subprocess import subprocess
import platform import platform
cmd = ['bash', 'lib/run-bibutils.sh', 'xml2bib'] cmd = ['bash', 'lib/run-bibutils.sh', 'xml2bib']
if platform.system() == 'Windows': if platform.system() == 'Windows':
cmd = ['wsl.exe', '-e'] + cmd cmd = ['wsl.exe', '-e'] + cmd
output = subprocess.check_output(cmd, stderr=subprocess.STDOUT) output = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
print(output.decode()) print(output.decode())
``` ```
%% Output %% Output
Running xml2bib to convert mods/10.1111_1467-6478.00057.mods.xml to bib/10.1111_1467-6478.00057.bib... Running xml2bib to convert mods/10.1111_1467-6478.00057.mods.xml to bib/10.1111_1467-6478.00057.bib...
Running xml2bib to convert mods/10.1111_1467-6478.00080.mods.xml to bib/10.1111_1467-6478.00080.bib... Running xml2bib to convert mods/10.1111_1467-6478.00080.mods.xml to bib/10.1111_1467-6478.00080.bib...
Running xml2bib to convert mods/10.1515_zfrs-1980-0103.mods.xml to bib/10.1515_zfrs-1980-0103.bib... Running xml2bib to convert mods/10.1515_zfrs-1980-0103.mods.xml to bib/10.1515_zfrs-1980-0103.bib...
Running xml2bib to convert mods/10.1515_zfrs-1980-0104.mods.xml to bib/10.1515_zfrs-1980-0104.bib... Running xml2bib to convert mods/10.1515_zfrs-1980-0104.mods.xml to bib/10.1515_zfrs-1980-0104.bib...
%% Cell type:code id:a2cdccaf919c268e tags: %% Cell type:code id:a2cdccaf919c268e tags:
``` python ``` python
# BibTeX to CSL # BibTeX to CSL
cmd = ['bash', 'lib/run-pandoc.sh', 'bibtex', 'csljson'] cmd = ['bash', 'lib/run-pandoc.sh', 'bibtex', 'csljson']
if platform.system() == 'Windows': if platform.system() == 'Windows':
cmd = ['wsl.exe', '-e'] + cmd cmd = ['wsl.exe', '-e'] + cmd
output = subprocess.check_output(cmd, stderr=subprocess.STDOUT) output = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
print(output.decode()) print(output.decode())
``` ```
%% Output %% Output
Running citeproc to convert bib/10.1111_1467-6478.00057.bib to csljson/10.1111_1467-6478.00057.csl.json... Running citeproc to convert bib/10.1111_1467-6478.00057.bib to csljson/10.1111_1467-6478.00057.csl.json...
Running citeproc to convert bib/10.1111_1467-6478.00080.bib to csljson/10.1111_1467-6478.00080.csl.json... Running citeproc to convert bib/10.1111_1467-6478.00080.bib to csljson/10.1111_1467-6478.00080.csl.json...
Running citeproc to convert bib/10.1515_zfrs-1980-0103.bib to csljson/10.1515_zfrs-1980-0103.csl.json... Running citeproc to convert bib/10.1515_zfrs-1980-0103.bib to csljson/10.1515_zfrs-1980-0103.csl.json...
Running citeproc to convert bib/10.1515_zfrs-1980-0104.bib to csljson/10.1515_zfrs-1980-0104.csl.json... Running citeproc to convert bib/10.1515_zfrs-1980-0104.bib to csljson/10.1515_zfrs-1980-0104.csl.json...
%% Cell type:code id:77ff73f83a1db70e tags: %% Cell type:code id:77ff73f83a1db70e tags:
``` python ``` python
``` ```
......
%% Cell type:markdown id:cb631197c03a0768 tags: %% Cell type:markdown id:cb631197c03a0768 tags:
# Convert TEI files to the Prodigy format # Convert TEI files to the Prodigy format
Uses https://github.com/standoff-nlp/standoffconverter and https://spacy.io/ This notebook converts the TEI/bibl annotations to a JSON format which can be imported into prodigy annotation tool.
based on https://github.com/standoff-nlp/standoffconverter/blob/master/examples/tei-spacy-tei.ipynb Resources:
- https://github.com/standoff-nlp/standoffconverter
- https://spacy.io
- https://github.com/standoff-nlp/standoffconverter/blob/master/examples/tei-spacy-tei.ipynb
%% Cell type:code id:29d86dcc18e8ffe4 tags: %% Cell type:code id:29d86dcc18e8ffe4 tags:
``` python ``` python
!pip install standoffconverter !pip install standoffconverter
!pip install spacy !pip install spacy
``` ```
%% Cell type:code id:8cf7971ebda71f27 tags: %% Cell type:code id:8cf7971ebda71f27 tags:
``` python ``` python
from lxml import etree from lxml import etree
from standoffconverter import Standoff, View from standoffconverter import Standoff, View
parser = etree.XMLParser(remove_blank_text=True) parser = etree.XMLParser(remove_blank_text=True)
input_path = 'tei/10.1111_1467-6478.00057.xml' input_path = 'tei/10.1111_1467-6478.00057.xml'
namespaces = {'tei': 'http://www.tei-c.org/ns/1.0'} namespaces = {'tei': 'http://www.tei-c.org/ns/1.0'}
tree = etree.parse(input_path, parser=parser) tree = etree.parse(input_path, parser=parser)
so = Standoff(tree, namespaces=namespaces) so = Standoff(tree, namespaces=namespaces)
so.json so.json
``` ```
%% Output %% Output
'[{"tag": "{http://www.tei-c.org/ns/1.0}text", "attrib": {}, "begin": 0, "end": 21209, "depth": 0}, {"tag": "{http://www.tei-c.org/ns/1.0}body", "attrib": {}, "begin": 0, "end": 21209, "depth": 1}, {"tag": "{http://www.tei-c.org/ns/1.0}p", "attrib": {}, "begin": 0, "end": 45, "depth": 2}, {"tag": "{http://www.tei-c.org/ns/1.0}note", "attrib": {"n": "1", "type": "footnote", "place": "bottom"}, "begin": 45, "end": 259, "depth": 2}, {"tag": "{http://www.tei-c.org/ns/1.0}bibl", "attrib": {}, "begin": 45, "end": 259, "depth": 3}, {"tag": "{http://www.tei-c.org/ns/1.0}author", "attrib": {}, "begin": 45, "end": 55, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}persName", "attrib": {}, "begin": 45, "end": 55, "depth": 5}, {"tag": "{http://www.tei-c.org/ns/1.0}forename", "attrib": {}, "begin": 45, "end": 47, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}surname", "attrib": {}, "begin": 47, "end": 55, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}title", "attrib": {"level": "a"}, "begin": 80, "end": 113, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}title", "attrib": {"level": "m"}, "begin": 139, "end": 150, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}editor", "attrib": {}, "begin": 177, "end": 186, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}persName", "attrib": {}, "begin": 177, "end": 186, "depth": 5}, {"tag": "{http://www.tei-c.org/ns/1.0}forename", "attrib": {}, "begin": 177, "end": 179, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}surname", "attrib": {}, "begin": 179, "end": 186, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}date", "attrib": {}, "begin": 209, "end": 213, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}biblScope", "attrib": {"unit": "page", "from": "77"}, "begin": 236, "end": 238, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}note", "attrib": {"n": "2", "type": "footnote", "place": "bottom"}, "begin": 259, "end": 519, "depth": 2}, {"tag": "{http://www.tei-c.org/ns/1.0}bibl", "attrib": {}, "begin": 259, "end": 519, "depth": 3}, {"tag": "{http://www.tei-c.org/ns/1.0}author", "attrib": {}, "begin": 259, "end": 268, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}persName", "attrib": {}, "begin": 259, "end": 268, "depth": 5}, {"tag": "{http://www.tei-c.org/ns/1.0}forename", "attrib": {}, "begin": 259, "end": 261, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}surname", "attrib": {}, "begin": 261, "end": 268, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}author", "attrib": {}, "begin": 293, "end": 302, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}persName", "attrib": {}, "begin": 293, "end": 302, "depth": 5}, {"tag": "{http://www.tei-c.org/ns/1.0}forename", "attrib": {}, "begin": 293, "end": 295, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}surname", "attrib": {}, "begin": 295, "end": 302, "depth": 6}, {"tag": "{http://www.tei-c.org/ns/1.0}title", "attrib": {"level": "a"}, "begin": 328, "end": 402, "depth": 4}, {"tag": "{http://www.tei-c.org/ns/1.0}date", "attrib": 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%% Cell type:code id:f67a3774493ffd9 tags: %% Cell type:code id:f67a3774493ffd9 tags:
``` python ``` python
``` ```
......
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