def conflict(soup):
conflict_tags = extract_nodes(soup, "fn", attr="fn-type", value="conflict")
conflict_tags += extract_nodes(soup,
"fn",
attr="fn-type",
value="COI-statement")
return conflict_tags
def custom_meta(soup, meta_name=None):
custom_meta_tags = extract_nodes(soup, "custom-meta")
if meta_name is not None:
custom_meta_tags = [
tag for tag in custom_meta_tags if node_contents_str(
first(extract_nodes(tag, "meta-name"))) == meta_name
]
return custom_meta_tags
def fn_group(soup, content_type=None):
if content_type:
return extract_nodes(soup,
"fn-group",
attr="content-type",
value=content_type)
else:
return extract_nodes(soup, "fn-group")
def pub_id(soup, pub_id_type=None):
if pub_id_type:
return extract_nodes(soup,
"pub-id",
attr="pub-id-type",
value=pub_id_type)
else:
return extract_nodes(soup, "pub-id")
def ext_link(soup, ext_link_type=None):
if ext_link_type:
return extract_nodes(soup,
"ext-link",
attr="ext-link-type",
value=ext_link_type)
else:
return extract_nodes(soup, "ext-link")
def abstract(soup, abstract_type=None):
if abstract_type:
return extract_nodes(soup,
"abstract",
attr="abstract-type",
value=abstract_type)
else:
return extract_nodes(soup, "abstract")
def authors(soup, contrib_type="author"):
if contrib_type:
return extract_nodes(soup,
"contrib",
attr="contrib-type",
value=contrib_type)
else:
return extract_nodes(soup, "contrib")
def pub_date(soup, date_type=None, pub_type=None):
if date_type is not None:
return extract_nodes(soup,
"pub-date",
attr="date-type",
value=date_type)
elif pub_type is not None:
return extract_nodes(soup, "pub-date", attr="pub-type", value=pub_type)
else:
return extract_nodes(soup, "pub-date")
def journal_issn(soup, pub_format, pub_type):
if pub_format is None and pub_type is None:
# return the first issn tag found regardless of which type
return first(extract_nodes(soup, "issn"))
elif pub_format is not None:
return first(
extract_nodes(soup,
"issn",
attr="publication-format",
value=pub_format))
elif pub_type is not None:
return first(
extract_nodes(soup, "issn", attr="pub-type", value=pub_type))
def journal_id(soup):
# the first non-nil tag
return firstnn(
extract_nodes(soup,
"journal-id",
attr="journal-id-type",
value="publisher-id"))
def author_keywords(soup):
# A few articles have kwd-group with no kwd-group-type, so account for those
tags = extract_nodes(soup, "kwd-group")
keyword_tags = []
for tag in tags:
if (tag.get("kwd-group-type") == "author-keywords"
or tag.get("kwd-group-type") is None):
keyword_tags += [tag for tag in tag if tag.name == "kwd"]
return keyword_tags
def article_contributors(soup):
article_meta_tag = article_meta(soup)
if article_meta_tag:
contributor_tags = extract_nodes(article_meta_tag,
["contrib", "on-behalf-of"])
return [
tag for tag in contributor_tags
if tag.parent.name == "contrib-group"
]
def research_organism_keywords(soup):
tags = first(
extract_nodes(soup,
"kwd-group",
attr="kwd-group-type",
value="research-organism"))
if not tags:
return None
return [tag for tag in tags if tag.name == "kwd"] or None
def full_subject_area(soup, subject_group_type=None):
subject_group_tags = extract_nodes(soup, "subj-group")
subject_group_tags = [
tag for tag in subject_group_tags
if tag.parent.name == "article-categories"
and tag.parent.parent.name == "article-meta"
]
if subject_group_type:
subject_group_tags = list(
filter(
lambda tag: tag.get("subj-group-type" == subject_group_type)))
return subject_group_tags
def subject_area(soup, subject_group_type=None):
# Supports all subject areas or just particular ones filtered by
subject_area_tags = []
tags = extract_nodes(soup, "subject")
subject_area_tags = [
tag for tag in tags if tag.parent.name == "subj-group"
and tag.parent.parent.name == "article-categories"
and tag.parent.parent.parent.name == "article-meta"
]
if subject_group_type:
subject_area_tags = [
tag for tag in tags
if tag.parent.get("subj-group-type") == subject_group_type
]
return subject_area_tags
def fig_group(soup):
return extract_nodes(soup, "fig-group")
def string_name(soup):
return extract_nodes(soup, "string-name")
def principal_award_recipient(soup):
return extract_nodes(soup, "principal-award-recipient")
def award_group(soup):
return extract_nodes(soup, "award-group")
def funding_group(soup):
return extract_nodes(soup, "funding-group")
def journal_title(soup):
return first(extract_nodes(soup, "journal-title"))
def article_type(soup):
# returns raw data, just that the data doesn't contain any BS nodes
return first(extract_nodes(soup, "article")).get("article-type")
def article_meta(soup):
return first(extract_nodes(soup, "article-meta"))
def fig(soup):
return extract_nodes(soup, "fig")
def math(soup):
return extract_nodes(soup, "math")
def disp_formula(soup):
return extract_nodes(soup, "disp-formula")
def publisher(soup):
return first(extract_nodes(soup, "publisher-name"))
def list(soup): # Redefining `list` could be problematic
return extract_nodes(soup, "list")
def boxed_text(soup):
return extract_nodes(soup, "boxed-text")
def list_item(soup):
return extract_nodes(soup, "list-item")
