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update scripts
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@marinadamato
marinadamato committed Jan 25, 2024
1 parent 45e3e7e commit af05191
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199 changes: 101 additions & 98 deletions scripts/automatic_update/get_biblatex.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,10 @@


class GetBiblatex:
def __init__(self, doi, diag_bib):
def __init__(self, doi, ss_id, diag_bib):
self.doi = doi
self.diag_bib = diag_bib
self.ss_id = ss_id
self.accent_mappings = accent_mappings

def _get_doi_csl(self):
Expand Down Expand Up @@ -118,104 +119,106 @@ def _clean_author_abbreviation(auth_abr, year, bib_file):
return auth_abr

def get_bib_text(self):
try:
response_json = self._get_doi_csl()
abstract = self._get_doi_abstract()
abstract = self._convert_to_biblatex_format(author_name=abstract)

if 'proceedings-article' in response_json['type']:
kind = 'inproceedings'
journal = response_json['container-title']
elif 'journal-article' in response_json['type']:
kind = 'article'
journal = response_json['container-title']
elif 'article' in response_json['type']:
kind = 'article'

# Convert doi to arXiv journal format "arXiv:xxxx.xxxxx"
index = self.doi.find('arXiv')
arxiv_id = self.doi[index:]
journal = arxiv_id.replace('.', ':', 1)
elif 'book-chapter' in response_json['type']:
kind = 'book'
journal = response_json['container-title']

elif 'posted-content' in response_json['type']:
kind = 'article'
journal = 'Preprint'





author_string = "{"
for index, author in enumerate(response_json["author"]):
if index == len(response_json["author"])-1:
if 'name' in author: # Add research groups. For example COPD Investigators
author_string = author_string + f"{author['name']}" + "}"
continue
if 'given' in author:
author_string = author_string + f"{author['family']}, {author['given']}" + "}"
else:
author_string = author_string + f"{author['family']}" + "}"

#try:
response_json = self._get_doi_csl()
abstract = self._get_doi_abstract()
abstract = self._convert_to_biblatex_format(author_name=abstract)

if 'proceedings-article' in response_json['type']:
kind = 'inproceedings'
journal = response_json['container-title']
elif 'journal-article' in response_json['type']:
kind = 'article'
journal = response_json['container-title']
elif 'article' in response_json['type']:
kind = 'article'

# Convert doi to arXiv journal format "arXiv:xxxx.xxxxx"
index = self.doi.find('arXiv')
arxiv_id = self.doi[index:]
journal = arxiv_id.replace('.', ':', 1)
elif 'book-chapter' in response_json['type']:
kind = 'book'
journal = response_json['container-title']

elif 'posted-content' in response_json['type']:
kind = 'article'
journal = 'Preprint'





author_string = "{"
for index, author in enumerate(response_json["author"]):
if index == len(response_json["author"])-1:
if 'name' in author: # Add research groups. For example COPD Investigators
author_string = author_string + f"{author['name']}" + "}"
continue
if 'given' in author:
author_string = author_string + f"{author['family']}, {author['given']}" + "}"
else:
if 'name' in author:
author_string = author_string + f"{author['name']} and "
continue
if 'given' in author:
author_string = author_string + f"{author['family']}, {author['given']} and "
else:
author_string = author_string + f"{author['family']} and "
author_string = self._convert_to_biblatex_format(author_name=author_string)
newline = '\n'
tab = '\t'
author_abbreviation = response_json['author'][0]['family'].rsplit(' ')[-1]
author_abbreviation = author_abbreviation.replace("'", "").lower().capitalize()[:4]

published = response_json.get("published")
if published is None:
published = response_json.get("issued")
year_short = str(published.get('date-parts')[0][0])[2:]
year = str(published.get('date-parts')[0][0])
# year = str(response_json["published"]["date-parts"][0][0])[2:]
author_abbreviation = self._clean_author_abbreviation(author_abbreviation, year_short, self.diag_bib)
title = response_json["title"]
title = self._convert_to_biblatex_format(author_name=title)
optnote = "DIAG, RADIOLOGY"

biblatex = f"@{kind}{{{author_abbreviation}, {newline}" \
f"{tab}author = {author_string}, {newline} " \
f"{tab}title = {{{title}}}, {newline}" \
f"{tab}doi = {{{response_json['DOI']}}}, {newline}" \
f"{tab}year = {{{year}}}, {newline}" \
f"{tab}abstract = {{{abstract}}}, {newline}" \
f"{tab}url = {{{response_json['URL']}}}, {newline}" \
f"{tab}file = {{{author_abbreviation}.pdf:pdf\\\\{author_abbreviation}.pdf:PDF}}, {newline}" \
f"{tab}optnote = {{{optnote}}}, {newline}" \
f"{tab}journal = {{{journal}}}, {newline}" \
f"{tab}automatic = {{yes}}, {newline}" \
# f"{tab}citation-count = {{{response_json['is-referenced-by-count']}}}, {newline}" \
# f"}}{newline}"

if 'is-referenced-by-count' in response_json.keys():
biblatex = biblatex + f"{tab}citation-count = {{{response_json['is-referenced-by-count']}}}, {newline}"

if 'page' in response_json.keys() and 'volume' in response_json.keys():
biblatex = biblatex + f"{tab}pages = {{{response_json['page']}}},{newline}" + f"{tab}volume = {{{response_json['volume']}}}, {newline}" + f"}}{newline}"
elif 'page' in response_json.keys():
biblatex = biblatex + f"{tab}pages = {{{response_json['page']}}},{newline}" + f"}}{newline}"
elif 'volume' in response_json.keys():
biblatex = biblatex + f"{tab}volume = {{{response_json['volume']}}}, {newline}" + f"}}{newline}"
author_string = author_string + f"{author['family']}" + "}"
else:
biblatex = biblatex + f"}}{newline}"

# replace any EN DASH with Hyphen
if "–" in biblatex:
biblatex = biblatex.replace("–", "-")

except Exception as e:
print(f'Unable to generate bibtext for {self.doi}')
print(e)
biblatex = 'empty'
if 'name' in author:
author_string = author_string + f"{author['name']} and "
continue
if 'given' in author:
author_string = author_string + f"{author['family']}, {author['given']} and "
else:
author_string = author_string + f"{author['family']} and "
author_string = self._convert_to_biblatex_format(author_name=author_string)
newline = '\n'
tab = '\t'
author_abbreviation = response_json['author'][0]['family'].rsplit(' ')[-1]
author_abbreviation = author_abbreviation.replace("'", "").lower().capitalize()[:4]

published = response_json.get("published")
if published is None:
published = response_json.get("issued")
year_short = str(published.get('date-parts')[0][0])[2:]
year = str(published.get('date-parts')[0][0])
# year = str(response_json["published"]["date-parts"][0][0])[2:]
author_abbreviation = self._clean_author_abbreviation(author_abbreviation, year_short, self.diag_bib)
title = response_json["title"]
title = self._convert_to_biblatex_format(author_name=title)
optnote = "DIAG, RADIOLOGY"
self.ss_id = "['"+self.ss_id+"']"
biblatex = f"@{kind}{{{author_abbreviation}, {newline}" \
f"{tab}author = {author_string}, {newline} " \
f"{tab}title = {{{title}}}, {newline}" \
f"{tab}doi = {{{response_json['DOI']}}}, {newline}" \
f"{tab}year = {{{year}}}, {newline}" \
f"{tab}abstract = {{{abstract}}}, {newline}" \
f"{tab}url = {{{response_json['URL']}}}, {newline}" \
f"{tab}file = {{{author_abbreviation}.pdf:pdf\\\\{author_abbreviation}.pdf:PDF}}, {newline}" \
f"{tab}optnote = {{{optnote}}}, {newline}" \
f"{tab}journal = {{{journal}}}, {newline}" \
f"{tab}automatic = {{yes}}, {newline}" \
f"{tab}all_ss_ids = {{{self.ss_id}}}, {newline}"
# f"{tab}citation-count = {{{response_json['is-referenced-by-count']}}}, {newline}" \
# f"}}{newline}"

if 'is-referenced-by-count' in response_json.keys():
biblatex = biblatex + f"{tab}citation-count = {{{response_json['is-referenced-by-count']}}}, {newline}"

if 'page' in response_json.keys() and 'volume' in response_json.keys():
biblatex = biblatex + f"{tab}pages = {{{response_json['page']}}},{newline}" + f"{tab}volume = {{{response_json['volume']}}}, {newline}" + f"}}{newline}"
elif 'page' in response_json.keys():
biblatex = biblatex + f"{tab}pages = {{{response_json['page']}}},{newline}" + f"}}{newline}"
elif 'volume' in response_json.keys():
biblatex = biblatex + f"{tab}volume = {{{response_json['volume']}}}, {newline}" + f"}}{newline}"
else:
biblatex = biblatex + f"}}{newline}"

# replace any EN DASH with Hyphen
if "–" in biblatex:
biblatex = biblatex.replace("–", "-")

#except Exception as e:
# print(f'Unable to generate bibtext for {self.doi}')
# print(e)
# biblatex = 'empty'

return biblatex
4 changes: 1 addition & 3 deletions scripts/automatic_update/update_bibfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,9 +90,8 @@ def get_bib_info(diag_bib_file, item): #diag_bib_file is the file read in as a s
print('similar doi already exists in bib file, but new item will be added for ', item['ss_doi'], item['ss_id'])

# Get BibLatex information based on DOI if not in the file
reader = GetBiblatex(doi=item['ss_doi'], diag_bib=diag_bib_file)
reader = GetBiblatex(doi=item['ss_doi'], ss_id=item['ss_id'], diag_bib=diag_bib_file)
bibtext = reader.get_bib_text()

# Return the bibtext if it is not 'empty', otherwise return None
return bibtext if bibtext != 'empty' else None

Expand Down Expand Up @@ -246,7 +245,6 @@ def loop_manual_check(manually_checked, diag_bib_orig):
elif "[add new item]" == bib_item['action'].strip():

bib_item_text = get_bib_info(diag_bib_orig, bib_item)

if bib_item_text is not None:
items_to_add += bib_item_text
# if there is a pmid note it to be added afterwards
Expand Down

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