def get_plos_journal(article_file, caps_fixed=True):
"""
For an individual PLOS article, get the journal it was published in.
:param article_file: individual local PLOS XML article
:param caps_fixed: whether to render the journal name correctly or as-is
:return: PLOS journal at specified xpath location
"""
try:
journal = get_article_xml(article_file=article_file,
tag_path_elements=[
"/", "article", "front", "journal-meta",
"journal-title-group", "journal-title"
])
journal = journal[0].text
except IndexError:
# Need to file ticket for this
journal_meta = get_article_xml(
article_file='allofplos_xml/journal.pone.0047704.xml',
tag_path_elements=["/", "article", "front", "journal-meta"])
for journal_child in journal_meta[0]:
if journal_child.attrib['journal-id-type'] == 'nlm-ta':
journal = journal_child.text
break
if caps_fixed:
journal = journal.split()
if journal[0].lower() == 'plos':
journal[0] = "PLOS"
journal = (' ').join(journal)
return journal
def get_article_dates(article_file, string_=False):
"""
For an individual article, get all of its dates
:param article_file: file path/DOI of the article
:return: tuple of dict of date types mapped to datetime objects for that article, dict for date strings if wrong order
"""
dates = {}
tag_path_1 = ["/", "article", "front", "article-meta", "pub-date"]
raw_xml_1 = get_article_xml(article_file=article_file,
tag_path_elements=tag_path_1)
for element in raw_xml_1:
pub_type = element.get('pub-type')
try:
date = parse_article_date(element)
except ValueError:
print('Error getting pubdate for {}'.format(article_file))
date = ''
dates[pub_type] = date
tag_path_2 = ["/", "article", "front", "article-meta", "history"]
raw_xml_2 = get_article_xml(article_file=article_file,
tag_path_elements=tag_path_2)
for element in raw_xml_2:
for part in element:
date_type = part.get('date-type')
try:
date = parse_article_date(part)
except ValueError:
print(
'Error getting history dates for {}'.format(article_file))
date = ''
dates[date_type] = date
if dates.get('received', '') and dates.get('accepted', '') in dates:
if not dates['received'] <= dates['accepted'] <= dates['epub']:
wrong_date_strings = {
date_type: date.strftime('%Y-%m-%d')
for date_type, date in dates.items()
}
wrong_date_strings['doi'] = filename_to_doi(article_file)
# print('Dates not in correct order: {}'.format(date_strings))
else:
wrong_date_strings = ''
else:
wrong_date_strings = ''
if string_:
for key, value in dates.items():
if value:
dates[key] = value.strftime('%Y-%m-%d')
return dates, wrong_date_strings
def get_article_abstract(article_file):
"""
For an individual article in the PLOS corpus, create a tuple of a set of metadata fields sbout that corpus.
Make it small, medium, or large depending on number of fields desired.
:param article_file: individual local PLOS XML article
:return: plain-text string of content in abstract
"""
abstract = get_article_xml(article_file,
tag_path_elements=[
"/", "article", "front", "article-meta",
"abstract"
])
try:
abstract_text = et.tostring(abstract[0],
encoding='unicode',
method='text')
except IndexError:
if check_article_type(article_file) == 'research-article' and \
get_plos_article_type(article_file) == 'Research Article':
print('No abstract found for research article {}'.format(
filename_to_doi(article_file)))
abstract_text = ''
# clean up text: rem white space, new line marks, blank lines
abstract_text = abstract_text.strip().replace(' ', '')
abstract_text = os.linesep.join(
[s for s in abstract_text.splitlines() if s])
return abstract_text
def get_article_doi(article_file):
raw_xml = get_article_xml(article_file=article_file,
tag_path_elements=[
"/", "article", "front", "article-meta",
"article-id"
])
for x in raw_xml:
for name, value in x.items():
if value == 'doi':
doi = x.text
break
return doi
def get_article_title(article_file):
"""
For an individual PLOS article, get its title.
:param article_file: individual local PLOS XML article
:return: string of article title at specified xpath location
"""
title = get_article_xml(article_file=article_file,
tag_path_elements=[
"/", "article", "front", "article-meta",
"title-group", "article-title"
])
title_text = et.tostring(title[0], encoding='unicode', method='text')
return title_text
def get_article_body_word_count(article_file):
"""
For an article, get how many words are in the body
:param article_file: individual local PLOS XML article
:return: count of words in the body of the PLOS article
"""
body = get_article_xml(article_file,
tag_path_elements=["/", "article", "body"])
try:
body_text = et.tostring(body[0], encoding='unicode', method='text')
body_word_count = len(body_text.split(" "))
except IndexError:
print("Error parsing article body: {}".format(article_file))
body_word_count = 0
return body_word_count
def get_article_dtd(article_file):
"""
For more information on these DTD tagsets, see https://jats.nlm.nih.gov/1.1d3/ and https://dtd.nlm.nih.gov/3.0/
"""
try:
dtd = get_article_xml(article_file=article_file,
tag_path_elements=["/", "article"])
dtd = dtd[0].attrib['dtd-version']
if str(dtd) == '3.0':
dtd = 'NLM 3.0'
elif dtd == '1.1d3':
dtd = 'JATS 1.1d3'
except KeyError:
print('Error parsing DTD from', article_file)
dtd = 'N/A'
return dtd
def get_plos_article_type(article_file):
article_categories = get_article_xml(article_file=article_file,
tag_path_elements=[
"/", "article", "front",
"article-meta",
"article-categories"
])
subject_list = article_categories[0].getchildren()
for i, subject in enumerate(subject_list):
if subject.get('subj-group-type') == "heading":
subject_instance = subject_list[i][0]
s = ''
for text in subject_instance.itertext():
s = s + text
PLOS_article_type = s
return PLOS_article_type
def get_article_counts(article_file):
"""
For a single article, return a dictionary of the several counts functions that are available
(figures: fig-count, pages: page-count, tables: table-count)
:param article_file: file path/DOI of the article
:return: counts dictionary
"""
counts = {}
tag_path = ["/", "article", "front", "article-meta", "counts"]
raw_xml = get_article_xml(article_file=article_file,
tag_path_elements=tag_path)
for element in raw_xml:
for count_item in element:
count = count_item.get('count')
count_type = count_item.tag
counts[count_type] = count
if len(counts) > 3:
print(counts)
return counts