def parse_semantic_scholar_corpus_file(path, database_path="aip.db"):
database = DatabaseManager(location=database_path)
hash, parsed = database.did_parse_file(path)
if parsed:
return True
file_iterator_func = iterload_file_lines_gzip if path.endswith("gz") else iterload_file_lines
# print(corpus_file)
# The json files contain stacked json objects, which is bad practice. It should be wrapped in a JSON array.
# Libraries will throw errors if you attempt to load the file, so now we lazy load each object line by line.
publication_iterator = file_iterator_func(path)
for publication in publication_iterator:
if publication is None: # Corrupt JSON line possibly. Skip it.
continue
if "venue" not in publication: # While parsing we sometimes get KeyError: 'venue'...
continue
# Try to match the publication to a venue we are interested in.
# Wrap in str() as it sometimes is an int (???)
venue_string = str(publication['venue'])
if len(venue_string) == 0:
continue
# Check if any of the venue strings are a substring of the mentioned value, add it to that set.
publication_title = publication['title']
publication_abstract = publication['paperAbstract']
publication_year = publication['year'] if 'year' in publication else -1
publication_journal_volume = publication['journalVolume'].replace(" ",
"_") # Empty for conferences.
# publication_keywords = publication['entities']
publication_id = publication['id']
num_citations = 0
if "inCitations" in publication:
num_citations = len(publication["inCitations"])
publication_doi = publication['doi']
if publication_doi is None or len(publication_doi) == 0:
publication_doi_url = publication['doiUrl']
if "doi.org/" in publication_doi_url:
publication_doi = publication['doiUrl'][
publication['doiUrl'].index("doi.org/") + len("doi.org/"):]
database.update_or_insert_paper(id=publication_id, doi=publication_doi, title=publication_title,
abstract=publication_abstract, raw_venue_string=venue_string,
year=publication_year, volume=publication_journal_volume,
num_citations=num_citations)
# database.flush_missing_venues()
database.add_parsed_file(hash)
database.close()
return True
def parse_aminer_corpus_file(path, database_path="aip", logger_disabled=False):
logger.disabled = logger_disabled
database = DatabaseManager(location=database_path)
hash, parsed = database.did_parse_file(path)
if parsed:
return True
# print(path)
# The json files contain stacked json objects, which is bad practice.
# It should be wrapped in a JSON array.
# Libraries will throw errors if you attempt to load the file, so now we lazy load each object.
file_iterator_func = iterload_file_lines_gzip if path.endswith(
"gz") else iterload_file_lines
publication_iterator = file_iterator_func(path)
for publication in tqdm(publication_iterator):
if publication is None: # Corrupt JSON line possibly. Skip it.
continue
# Try to match the publication to a venue we are interested in.
# Warning: contrary to the documentation, the key is "venue" NOT "venue.raw"!
if 'venue' not in publication:
logger.warning("Skipping line missing venue: %s in %s.",
publication, path)
continue
if 'title' not in publication:
logger.warning("Skipping line missing title: %s in %s.",
publication, path)
continue
venue_string = publication['venue']
# Sometimes the venue string is yet another dict...
if isinstance(venue_string, dict) and "raw" in venue_string:
venue_string = venue_string["raw"]
publication_title = str(publication['title']).rstrip(".")
publication_abstract = publication[
'abstract'] if 'abstract' in publication else ""
publication_year = publication[
'year'] if 'year' in publication else None
publication_journal_volume = publication[
'volume'] if 'volume' in publication else None
# publication_keywords = publication['keywords']
publication_id = publication['id']
# citation_count = int(publication['n_citation']) if "n_citation" in publication else None
publication_doi = publication['doi'] if 'doi' in publication else None
# Sometimes in the urls, a doi link is used. If there is, we attempt to extract the doi from the link.
if publication_doi is None or len(publication_doi) == 0:
publication_doi_urls = publication[
'url'] if 'url' in publication else []
for publication_doi_url in publication_doi_urls:
if "doi.org/" in publication_doi_url:
publication_doi = publication_doi_url[publication_doi_url.
index("doi.org/") +
len("doi.org/"):]
break
database.update_or_insert_paper(id=publication_id,
doi=publication_doi,
title=publication_title,
abstract=publication_abstract,
raw_venue_string=venue_string,
year=publication_year,
volume=publication_journal_volume)
# database.flush_missing_venues()
database.add_parsed_file(hash)
database.close()
return True
def parse(dblp_file, database_path="aip.db"):
database = DatabaseManager(location=database_path)
hash, parsed = database.did_parse_file(dblp_file)
if parsed:
return True
counter = 0 # counter for new keys.
# dtd = etree.DTD(file="/media/lfdversluis/datastore/dblp.dtd")
for event, element in etree.iterparse(dblp_file,
load_dtd=True,
dtd_validation=True):
if element.tag not in ['article', 'inproceedings', 'proceedings']:
continue
if 'key' in element.attrib:
id = str(element.attrib['key'])
else:
id = "id" + str(counter)
counter += 1
title = element.find('title') # type: Optional[str]
if title is not None:
title = str(title.text).rstrip(".")
year = element.find('year') # type: Optional[int]
if year is not None:
try:
year = int(re.search(r'\d+', str(year.text)).group())
if 20 < year < 100: # Weird cases like 92-93
year += 1900
elif year < 20: # weird cases like '12
year += 2000
except:
year = None
volume = element.find('volume') # type: Optional[int]
if volume is not None:
try:
volume = int(volume.text)
except:
volume = None
# authors = element.find('author') # type: Optional[str]
venue = element.find('booktitle') # type: Optional[str]
if venue is None and len(element.findall('journal')) > 0:
venue = element.find('journal')
if venue is not None and venue.text is not None:
venue = str(venue.text)
else:
venue = None
doi = None
for ee in element.findall('ee'):
ee_str = str(ee.text)
if ee is not None and "doi.org" in ee_str:
doi = ee_str[ee_str.index("doi.org/") + len("doi.org/"):]
break
if title is not None and year is not None and venue is not None:
# Clean the title which may have HTML elements
database.update_or_insert_paper(id=id,
doi=doi,
title=title,
abstract="",
raw_venue_string=venue,
year=year,
volume=volume,
num_citations=-1)
# Get the authors for this paper and add them to the database
authors = [] # tuples of ID, orcid
for author_element in element.findall('author'):
orcid = None
if "orcid" in author_element.attrib:
orcid = str(author_element.attrib['orcid'])
authors.append((author_element.text, orcid))
database.add_authors_for_article(authors=authors, article_id=id)
element.clear()
# database.flush_missing_venues()
database.add_parsed_file(hash)
database.close()
return True
