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script.py
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script.py
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# Import the local scripts
import dateutil.parser
from spacy.lang.en import English
from asyncore import write
from collections import OrderedDict
import os
import re
import spacy
import pandas as pd
import numpy as np
import click
import json
import importmonkey
importmonkey.add_path('assets/scripts/')
from convert import convert2vec, convert_text2vec
import rdf
import const
import upload
import writer
nlp_allowed_types = ['PERSON', "ORG", "LOC"]
nlp = spacy.load('en_core_web_lg')
regex_date = re.compile(const.regex_date)
def clean_footnotes(footnotes):
dict_footnotes = {}
for page_footnotes in footnotes:
for footnote in page_footnotes:
try:
footnote_index = re.findall(const.regex_footnote, footnote)[0]
full_text = re.sub(const.regex_footnote, "",
footnote).lower().replace(")\t", "").strip()
# Create footnote
dict_footnotes[footnote_index] = {
const.footnote_fulltext: full_text
}
# If contains href
href_matches = re.findall(const.regex_href, full_text)
if href_matches:
# Save the links in href attribute
permalinks = [href[1] for href in href_matches]
dict_footnotes[footnote_index][const.footnote_permalinks] = permalinks
# If text contains Biblioteca Berenson
if "biblioteca berenson" in full_text:
dict_footnotes[footnote_index][const.footnote_type] = "Book"
else:
dict_footnotes[footnote_index][const.footnote_type] = "Person"
else:
dict_footnotes[footnote_index][const.footnote_type] = "Notes"
except IndexError as ex:
print(ex)
continue
return dict_footnotes
"""_summary_
Parse the pages of the diary and return a dictionary with the following structure:
{page_number: {text: <text>, content: [{text: <text>, type: <type>}, ... ]}
"""
def parse_pages(paragraphs, diary, l=-1):
# check if text is an header, starting with const.key_header
def _is_day(str):
return str.startswith(const.key_note_header)
def _create_container(text):
# Check if text is encalpsulated in <b> tags
if _is_day(text):
t = const.key_header
text = text.replace(const.key_note_header, '')
else:
t = const.key_paragraph
return {
const.key_text: text.strip(),
const.key_type: t
}
page_start_regex = r'\[p\d+[^\]]*\]'
regex_digit = re.compile(r'\d+')
residual_text = ''
pages = OrderedDict()
page_body = []
# Start from the last paragraph to the first
paragraphs.reverse()
for p in paragraphs:
# Clear the paragraph using specific rules
#p = _clean_text(p)
# Do only non empty strings
if p:
# Check if the paragraph contains the page notation
if re.search(page_start_regex, p, flags=re.MULTILINE):
"""
# Check if the page notation is enclosed in text
split_p = re.split(page_start_regex, p)
if len(split_p) > 1 and (split_p[0] or split_p[1]):
residual_text = split_p[0]
page_body.append(_create_container(split_p[1]))
"""
# Transform page id in page index: from [019] to 19.
page_index = re.sub(const.regex_brackets, '',
re.findall(page_start_regex, p)[0].strip())
# Set the index as int
page_index = regex_digit.findall(page_index)[0]
page_index = int(page_index.strip())
# Reverse again the body
page_body.reverse()
# Page complete
pages[page_index] = {
const.key_text: '\n'.join([p[const.key_text] for p in page_body]),
const.key_paragraphs: [p for p in page_body]
}
pages[page_index][const.key_paragraphs] = list(
filter(None, pages[page_index][const.key_paragraphs]))
page_body = []
# If, after splitting a paragraph, there is still text
# Add it to the next page body
if residual_text:
page_body.append(_create_container(residual_text))
residual_text = ''
# If not, add the paragraph to the page
else:
page_body.append(_create_container(p))
pages = OrderedDict(reversed(list(pages.items())))
# If limit is set, return only the first l pages
if l != -1:
pages = {k: pages[k] for k in list(pages)[:l]}
return pages
def parse_note_1903_serialize_type(type):
if type == 'organization / group':
return 'organization'
elif type == 'visual art' or type == 'visual arts':
return 'visual_art'
else:
return type
def parse_note_1903(row, pages):
regex_page = re.compile(r'[\d]{3,}')
# Parse pages
entiy_page = row[const.note_header_page]
entity_value = row[const.note_header_entity]
entity_number = row[const.note_header_number]
entity_type = row[const.note_header_type]
authority = row[const.note_header_authority]
note1 = row[const.note_header_descriptor]
note2 = row[const.note_header_context]
disambiguation1 = row[const.note_header_disambiguation1]
disambiguation2 = row[const.note_header_disambiguation2]
disambiguation3 = row[const.note_header_disambiguation3]
disambiguations = [disambiguation1, disambiguation2, disambiguation3]
text = entity_value if entity_value else note1
if entiy_page:
page_number = int(regex_page.findall(entiy_page)[-1])
if page_number in pages:
current_page = pages[page_number]
for p in current_page[const.key_paragraphs]:
if entity_value in p:
return (entity_number, {
const.key_footnote_header_page: page_number,
const.footnote_type: parse_note_1903_serialize_type(entity_type),
const.footnote_fulltext: text,
const.footnote_permalinks: disambiguations,
const.footnote_index: current_page[const.key_paragraphs].index(p)+1,
const.footnote_start: p.index(entity_value),
const.footnote_end: p.index(
entity_value) + len(entity_value)
})
return None
def parse_note_generic(index, row, pages):
entity_page = int(
row[const.diaries['1891'][const.key_footnote_header_page]])
entity_value = row[const.diaries['1891'][const.key_footnote_header_value]]
entity_type = row[const.diaries['1891'][const.key_footnote_header_type]]
try:
entity_annotator = row[const.key_footnote_header_annotator]
except Exception:
entity_annotator = 'admin'
note = None
if entity_type == 'art':
# Get the current page
if entity_page in pages:
current_page = pages[entity_page]
# Check in each paragraph if it contains the entity
for p in current_page[const.key_paragraphs]:
start_index = p[const.key_text].lower().find(
entity_value.lower())
if start_index != -1:
note = (index, {
const.key_footnote_header_page: entity_page,
const.footnote_type: entity_type,
const.footnote_fulltext: entity_value,
const.footnote_permalinks: [],
const.footnote_index: current_page[const.key_paragraphs].index(p)+1,
const.footnote_start: start_index,
const.footnote_end: start_index + len(entity_value),
const.footnote_annotator: entity_annotator.lower()
})
break
return note
def parse_note_1891(index, row, pages):
entity_page = int(
row[const.diaries['1891'][const.key_footnote_header_page]])
entity_value = row[const.diaries['1891'][const.key_footnote_header_value]]
entity_type = row[const.diaries['1891'][const.key_footnote_header_type]]
entity_wikidata = row[const.diaries['1891']
[const.key_footnote_header_permalinks]]
entity_annotator = row[const.diaries['1891']
[const.key_footnote_header_annotator]]
permalinks = [
f'https://www.wikidata.org/wiki/{entity_wikidata}'] if entity_wikidata else []
if entity_page in pages:
current_page = pages[entity_page]
for p in current_page[const.key_paragraphs]:
if entity_value in p:
return (index, {
const.key_footnote_header_page: entity_page,
const.footnote_type: entity_type,
const.footnote_fulltext: entity_value,
const.footnote_annotator: entity_annotator.lower(),
const.footnote_permalinks: permalinks,
const.footnote_index: current_page[const.key_paragraphs].index(p)+1,
const.footnote_start: p.index(entity_value),
const.footnote_end: p.index(
entity_value) + len(entity_value)
})
return None
def parse_notes(pages, diary_notes, diary, limit=-1):
parsed_notes = {}
# Check if note file exists
if os.path.exists(diary_notes):
df_diary_notes = pd.read_csv(diary_notes)
df_diary_notes.sort_values(
by=const.diaries[diary][const.key_footnote_header_page], ascending=True, inplace=True)
df_diary_notes.reset_index(drop=True, inplace=True)
df_diary_notes.fillna('', inplace=True)
for index, row in df_diary_notes.iterrows():
if limit != -1 and index >= limit:
break
note_parsed = parse_note_generic(index, row, pages)
try:
note_parsed_id = note_parsed[0]
note_parsed_body = note_parsed[1]
parsed_notes[note_parsed_id] = note_parsed_body
except Exception as e:
print(e)
continue
# Execute NER if needed
else:
print('No notes file found. NER should be executed...')
return parsed_notes
def check_cleaned(output_path):
return os.path.exists(os.path.join(output_path, 'footnotes_cleaned.tsv'))
def parse_footnotes(pages, footnotes):
elements = []
# Link footnotes
for key, page in pages.items():
text = page[const.key_text]
try:
# Search if there are footnotes in pages
for match in re.findall(const.regex_footnote_id, text):
identifier = match.replace("----", "")
before = text.split(match)[0]
nlp_tokenizer = English()
# Create a Tokenizer with the default settings for English
# including punctuation rules and exceptions
tokenizer = nlp_tokenizer.tokenizer
tokens = tokenizer(before)
if const.footnote_permalinks in footnotes[identifier]:
element = [key, identifier, tokens[-4:], footnotes[identifier][const.footnote_fulltext],
footnotes[identifier][const.footnote_type], ', '.join(footnotes[identifier][const.footnote_permalinks])]
else:
element = [key, identifier, tokens[-4:], footnotes[identifier]
[const.footnote_fulltext], footnotes[identifier][const.footnote_type], '']
elements.append(element)
except Exception as ex:
print(ex)
return elements
def parse_footnotes_cleaned(pages, footnotes):
elements = {}
for footnote_id, row in footnotes.iterrows():
try:
page_number = row[const.key_footnote_header_page]
page = pages[page_number]
text = row[const.key_footnote_header_before]
paragraphs = page[const.key_paragraphs]
footnote_id_complete = f'----{footnote_id}----'
# get page and offset
index = [idx for idx, s in enumerate(
paragraphs) if footnote_id_complete in s][0]
match = re.search(text.lower(), paragraphs[index].lower())
elements[footnote_id] = {
const.key_footnote_header_page: page_number,
const.footnote_index: index,
const.footnote_start: match.start(),
const.footnote_end: match.end(),
const.footnote_fulltext: paragraphs[index][match.start():match.end()],
const.footnote_type: row[const.key_footnote_header_type],
const.footnote_permalinks: row[const.key_footnote_header_permalinks].split(
', ')
}
except Exception as ex:
print(f'Error with {footnote_id}: {ex}')
continue
# Remove footnote to handle subsequent offsets
finally:
re.sub(footnote_id_complete, '', paragraphs[index])
return elements
def is_type_allowed(t):
return t in nlp_allowed_types
def normalize_type(t):
new_t = ""
if t == "PERSON":
new_t = "person"
if t == "ORG" or t == "NORP":
new_t = "organization"
if t == "FAC" or t == "GPE" or t == "LOC":
new_t = "location"
if t == "DATE":
new_t = "date"
return new_t
def execute_ner(pages, name):
data = {}
i = 1
for page_number, page in pages.items():
ps = page["paragraphs"]
for p in ps:
doc = nlp(p)
for ent in doc.ents:
if is_type_allowed(ent.label_):
data[i] = {
const.key_footnote_header_page: page_number,
const.footnote_fulltext: ent.text,
const.footnote_index: ps.index(p)+1,
const.footnote_start: ent.start_char,
const.footnote_end: ent.end_char,
const.footnote_type: normalize_Type(ent.label_),
const.footnote_permalinks: []
}
i += 1
return data
def parse_days(df):
# get days
days = df['text'].str.contains(',[0-9]{4}$', na=False)
df_out = df[days].copy()
df_out['image_link'] = 'https://iiif.lib.harvard.edu/manifests/view/drs:493343177$' + \
df_out["page"].astype(str) + 'i'
df_out = df_out.rename(columns={'text': 'day_title'})
df_out.to_csv(os.path.join(output_path, 'csv', 'metadata.csv'), columns=[
'day', 'day_title', 'page', 'image_link'], index=False)
def parse_people(df):
print(df.head())
people = df['type'].str.fullmatch('PERSON')
df_out = df[people].copy()
df_out.to_csv(os.path.join(output_path, 'csv', 'people_extracted.csv'), columns=[
'day', 'text', 'description', 'page', 'p', 'start', 'end'], index=False)
def update_days(df):
df['day'] = df['text'].str.contains(',[0-9]{4}$', na=False).cumsum()
return df
def parse_metadata(pages, diary, limit=-1):
# Search for headers stored in page paragraphs
for index, page in pages.items():
page_metadata = []
for paragraph in page[const.key_paragraphs]:
if paragraph[const.key_type] == 'h3':
try:
page_metadata.append({
const.key_object: dateutil.parser.parse(paragraph[const.key_text], fuzzy=True).strftime('%Y-%m-%d'),
const.key_predicate: const.key_note_header
})
except dateutil.parser.ParserError as ex:
print(ex)
continue
if len(page_metadata) > 0 and const.key_metadata not in page[const.key_paragraphs]:
page[const.key_metadata] = page_metadata
return pages
def ner(output_path):
txt_path = os.path.join(output_path, 'txt')
csv_path = os.path.join(output_path, 'csv')
xlsx_path = os.path.join(output_path, 'xslx')
ner_body = []
for txt_file in os.listdir(txt_path):
name_file = txt_file.replace('.txt', '')
with open(os.path.join(txt_path, txt_file), 'r') as f:
ner_body_curr = execute_ner(f.read(), name_file)
ner_body.append(ner_body_curr)
writer.write_csv(os.path.join(
csv_path, f'{name_file}.csv'), ner_body_curr)
writer.write_xlsx(os.path.join(
xlsx_path, f'{name_file}.xlsx'), ner_body_curr)
@click.command()
@click.option('-d', 'diaries', required=True, multiple=True, help="Diaries to iterate. -d 1933 [-d 1933]")
@click.option('-u', 'exec_upload', is_flag=True, help="Execute the upload", default=False)
@click.option('-c', 'config', help="Type of connection in config.ini to use", default="localhost")
@click.option('-t', 'title', help="Name of the diary", default=None)
@click.option('-i', 'index', help="Index of the diary", default=None)
@click.option('-iiif', 'iiif_manifest', help="URL of the IIIF Manifest", default=None)
def exec(diaries, exec_upload, config, title, index, iiif_manifest):
cur_path = os.path.dirname(os.path.realpath(__file__))
for diary in diaries:
print(f'### Executing year {diary} ###')
# Update default paths with specific
input_path = os.path.join(cur_path, 'assets', 'input', diary)
output_path = os.path.join(cur_path, 'assets', 'output', diary)
manifest = json.load(
open(os.path.join(input_path, f'{diary}.json')))
# Check if output_path exists
writer.create_dir(output_path)
# Get text and footnote from a docx document
#vec = convert2vec(os.path.join(input_path, f'{diary}.docx'))
# get text from txt document
vec = convert_text2vec(os.path.join(input_path, f'{diary}.txt'))
# Parse and write page
pages = parse_pages(vec[const.key_document], diary)
writer.write_json(os.path.join(output_path, 'pages.json'), pages)
writer.write_pages(output_path, pages)
writer.write_pages_html(output_path, pages, diary, app_path='/Users/gspinaci/projects/mb_diaries/apps/MB_Diaries-app')
# Create RDF Graphs for the diary
diary_graphs = rdf.diary2graphs(diary, manifest, title, index, iiif_manifest)
rdf.write_graphs(output_path, diary_graphs, 'diary')
# Create RDF Graphs for the pages including metadata if any
pages = parse_metadata(pages, diary)
pages_graphs = rdf.pages2graphs(diary, manifest, pages, output_path)
rdf.write_graphs(output_path, pages_graphs, 'document')
# diary_notes = os.path.join(input_path, const.key_notes_dir, f'{diary}.csv')
# notes_parsed = parse_notes(pages, diary_notes, diary)
# notes = rdf.footnotes2graphs(diary, notes_parsed)
# rdf.write_graphs(output_path, notes, 'annotation')
# Upload RDF graphs
if exec_upload:
upload.upload(output_path, diary, config)
if __name__ == '__main__':
exec()