def __write_list_publications_md(self, global_index, filtered_bibkeys,
string_rules):
html_format = bibtexformatter.HTML_Formatter(string_rules)
dict_pubs = {}
for bib_key in filtered_bibkeys:
bib_key = bib_key.lower()
try:
html_bibkey, year, pub_type, pub_details = self.__append_publication_md(
global_index, bib_key, html_format)
pub_details = pub_details.replace('_', ' ').strip()
dict_pubs[bib_key] = {}
dict_pubs[bib_key]['html'] = html_bibkey
dict_pubs[bib_key]['year'] = int(year)
dict_pubs[bib_key]['pub_type'] = pub_type
dict_pubs[bib_key]['pub_details'] = pub_details
if pub_type.lower() == '@phdthesis':
dict_pubs[bib_key]['author_name'] = global_index[
bib_key].entry['author']
dict_pubs[bib_key]['title_thesis'] = global_index[
bib_key].entry['title']
# TODO this is a hardcode capital first letter of bibkey
dict_pubs[bib_key]['coverpng'] = bib_key[0].title(
) + bib_key[1:] + '.png'
except:
print(
f"Failed writing html for publication list for {bib_key}, skipping this entry."
)
print(traceback.format_exc())
return dict_pubs
def write_list_publications_md(global_index, filtered_publications, out_dir,
string_rules):
html_format = bibtexformatter.HTML_Formatter(string_rules)
md_format = 'title: Publications\n\n'
md_format += '<ul>\n'
for bib_key in filtered_publications:
md_format += append_publication_md(global_index,
bib_key,
html_format,
go_parent_dir=False)
md_format += '</ul>\n'
# publications.md
out_path = out_dir + '.md'
write_md_pass(out_path, md_format)
def write_author_publications_md(global_index, author_index, list_researchers,
out_dir, string_rules):
list_bibs_error = []
html_format = bibtexformatter.HTML_Formatter(string_rules)
for researcher_names in list_researchers:
full_name = "-".join(researcher_names)
title_md = " ".join(researcher_names).title() # camel case
md_format = 'title: Publications of ' + title_md + '\n'
md_format += 'template: publications-author\n'
md_format += 'author: ' + "-".join(researcher_names) + '\n'
md_format += 'author_name: ' + title_md + '\n'
list_pubs_author = []
for author_name in author_index.keys():
if researcher_names[-1] == author_name.lower():
for bib_key in author_index[author_name]:
list_pubs_author.append(bib_key)
md_format += 'bibkeys: ' + ','.join(list_pubs_author)
out_path = os.path.join(out_dir, full_name + '.md')
write_md_pass(out_path, md_format)
def write_list_publications_md(global_index, filtered_publications, out_dir,
string_rules):
html_format = bibtexformatter.HTML_Formatter(string_rules)
dict_pubs = {}
for bib_key in filtered_publications:
bib_key = bib_key.lower()
html_bibkey, year, pub_type, pub_details = append_publication_md(
global_index, bib_key, html_format, go_parent_dir=False)
dict_pubs[bib_key] = {}
dict_pubs[bib_key]['html'] = html_bibkey
dict_pubs[bib_key]['year'] = int(year)
dict_pubs[bib_key]['pub_type'] = pub_type
dict_pubs[bib_key]['pub_details'] = pub_details
if pub_type.lower() == '@phdthesis':
dict_pubs[bib_key]['author_name'] = global_index[bib_key].entry[
'author']
dict_pubs[bib_key]['title_thesis'] = global_index[bib_key].entry[
'title']
# TODO this is a hardcode capital first letter of bibkey
dict_pubs[bib_key]['coverpng'] = bib_key[0].title(
) + bib_key[1:] + '.png'
return dict_pubs
def write_author_publications_md(global_index, author_index, list_researchers,
out_dir, string_rules):
list_bibs_error = []
html_format = bibtexformatter.HTML_Formatter(string_rules)
for researcher_names in list_researchers:
full_name = "-".join(researcher_names)
title_md = " ".join(researcher_names).title() # camel case
md_format = 'title: Publications of ' + title_md + '\n'
md_format += 'template: publication-list\n\n'
md_format += '<ul>\n'
for author_name in author_index.keys():
if researcher_names[-1] == author_name.lower():
for bib_key in author_index[author_name]:
md_format += append_publication_md(global_index,
bib_key,
html_format,
go_parent_dir=True)
md_format += '</ul>\n'
out_path = os.path.join(out_dir, full_name + '.md')
write_md_pass(out_path, md_format)
def __write_single_publication_md(self, global_index, string_rules,
filtered_bibkeys, out_dir):
html_format = bibtexformatter.HTML_Formatter(string_rules)
list_bibs_error = []
for bibkey in filtered_bibkeys:
try:
md_format = ''
if 'author' not in global_index[
bibkey].entry or 'title' not in global_index[
bibkey].entry:
# It skips bibkeys either without authors or title
continue
global_index = self.__cleanup_global_index(
global_index, bibkey)
authors_format = bibtexformatter.authors_to_string(
global_index[bibkey].author)
title = codecs.decode(global_index[bibkey].entry['title'],
"ulatex")
md_format += 'title: ' + title + '\n'
md_format += 'authors: ' + authors_format + '\n'
pub_type = global_index[bibkey].entry_type
has_pdf = 'file' in global_index[bibkey].entry
md_format += 'has_pdf: ' + str(has_pdf) + '\n'
if pub_type.lower() == '@phdthesis':
md_format += 'template: publication-thesis\n'
# TODO this is a hardcode capital first letter of bibkey
md_format += 'coverpng: ' + bibkey[0].title(
) + bibkey[1:] + '.png\n'
for k in 'promotor', 'copromotor', 'school', 'optmonth', 'year':
if k in global_index[bibkey].entry:
md_format += k + ': ' + global_index[bibkey].entry[
k] + '\n'
if 'url' in global_index[bibkey].entry:
url_pub = global_index[bibkey].entry['url']
md_format += 'urlweb: ' + url_pub + '\n'
else:
md_format += 'template: publication\n'
md_format += 'bibkey: ' + bibkey + '\n'
if 'booktitle' in global_index[
bibkey].entry or 'journal' in global_index[
bibkey].entry:
event_type = 'journal' if 'journal' in global_index[
bibkey].entry else 'booktitle'
if global_index[bibkey].entry[
event_type] in string_rules:
event_name = string_rules[
global_index[bibkey].entry[event_type]]
else:
event_name = global_index[bibkey].entry[event_type]
event_name = event_name.replace('_', ' ').strip()
md_format += 'published_in: ' + event_name + '\n'
_, pub_details = html_format.apply(
global_index[bibkey])
pub_details = pub_details.replace('_', ' ').strip()
md_format += 'pub_details: ' + pub_details + '\n'
md_format_bibitem, is_preprint = self.__format_bibitem(
global_index[bibkey], is_html_format=False)
md_format += md_format_bibitem
if 'abstract' in global_index[bibkey].entry:
md_format += global_index[bibkey].entry['abstract'] + '\n\n'
# if 'file' in global_index[bibitem].entry:
# TODO: Disabled for now as we don't have a version of the PDFs on the new website
# md_format += 'A <b>pdf file</b> of this publication is available for personal use.'
# md_format += 'Enter your e-mail address in the box below and press the button. '
# md_format += 'You will receive an e-mail message with a link to the pdf file.\n'
#
# md_format += '<form action=\"sender.php\">' # TODO implement sender.php
# md_format += ' <input type=\"text\" name=\"email\">'
# md_format += ' <input type=\"submit\" value=\"Send ' + global_index[bibitem].entry[
# 'file'] + ' by e-mail\">'
# md_format += '</form>'
md_format = md_format.replace('{', '').replace('}', '')
out_path = os.path.join(out_dir, bibkey + '.md')
file = open(out_path, 'w')
try: # This is ugly but necessary for now to avoid UnicodeEncodeError
file.write(md_format)
file.close()
except UnicodeEncodeError:
list_bibs_error.append(bibkey)
except Exception as exc:
print(f"Failed writing bib entry {bibkey} to markdown file.")
print(traceback.format_exc())
print('List of bibkeys returning UnicodeEncodeError')
for bib in list_bibs_error:
print(bib)
def write_single_publication_md(global_index, string_rules,
filtered_publications, out_dir, json_path):
html_format = bibtexformatter.HTML_Formatter(string_rules)
list_bibs_error = []
for bibitem in filtered_publications:
md_format = ''
if 'author' not in global_index[
bibitem].entry or 'title' not in global_index[bibitem].entry:
# It skips bibitems with absence of authors or title
continue
for attr_key in global_index[bibitem].entry:
global_index[bibitem].entry[attr_key] = global_index[
bibitem].entry[attr_key].replace('{', '').replace('}', '')
authors_format = bibtexformatter.authors_to_string(
global_index[bibitem].author)
title = codecs.decode(global_index[bibitem].entry['title'], "ulatex")
md_format += 'title: ' + title + '\n'
md_format += 'authors: ' + authors_format + '\n'
pub_type = global_index[bibitem].entry_type
if pub_type.lower() == '@phdthesis':
md_format += 'template: publication-thesis\n'
# TODO this is a hardcode capital first letter of bibkey
md_format += 'coverpng: ' + bibitem[0].title(
) + bibitem[1:] + '.png\n'
for k in 'promotor', 'copromotor', 'school', 'optmonth', 'year':
if k in global_index[bibitem].entry:
md_format += k + ': ' + global_index[bibitem].entry[
k] + '\n'
else:
md_format += 'template: publication\n'
if 'booktitle' in global_index[
bibitem].entry or 'journal' in global_index[bibitem].entry:
event_type = 'journal' if 'journal' in global_index[
bibitem].entry else 'booktitle'
if global_index[bibitem].entry[event_type] in string_rules:
event_name = string_rules[
global_index[bibitem].entry[event_type]]
event_name = event_name.replace('_', ' ').strip()
else:
event_name = global_index[bibitem].entry[event_type]
md_format += 'published_in: ' + event_name + '\n'
_, pub_details = html_format.apply(global_index[bibitem])
md_format += 'pub_details: ' + pub_details + '\n'
if 'doi' in global_index[bibitem].entry:
md_format += 'doi: ' + 'https://doi.org/' + global_index[
bibitem].entry['doi'] + '\n'
if 'url' in global_index[bibitem].entry and 'arxiv' in global_index[
bibitem].entry['url']:
md_format += 'arxiv: ' + global_index[bibitem].entry[
'url'] + '\n'
if 'pmid' in global_index[bibitem].entry:
url_pmid = 'http://www.ncbi.nlm.nih.gov/pubmed/' + global_index[
bibitem].entry['pmid']
md_format += 'pmid: ' + url_pmid + '\n'
if 'abstract' in global_index[bibitem].entry:
md_format += global_index[bibitem].entry['abstract'] + '\n\n'
# if 'file' in global_index[bibitem].entry:
# TODO: Disabled for now as we don't have a version of the PDFs on the new website
# md_format += 'A <b>pdf file</b> of this publication is available for personal use.'
# md_format += 'Enter your e-mail address in the box below and press the button. '
# md_format += 'You will receive an e-mail message with a link to the pdf file.\n'
#
# md_format += '<form action=\"sender.php\">' # TODO implement sender.php
# md_format += ' <input type=\"text\" name=\"email\">'
# md_format += ' <input type=\"submit\" value=\"Send ' + global_index[bibitem].entry[
# 'file'] + ' by e-mail\">'
# md_format += '</form>'
md_format = md_format.replace('{', '').replace('}', '')
out_path = os.path.join(out_dir, bibitem + '.md')
file = open(out_path, 'w')
try: # This is ugly but necessary for now to avoid UnicodeEncodeError
file.write(md_format)
file.close()
except UnicodeEncodeError:
list_bibs_error.append(bibitem)
print('List of bibkeys returning UnicodeEncodeError')
for bib in list_bibs_error:
print(bib)