def add_citations(warehouse_home, server_name, cache_dir,
resume=False, password=None, online=True):
"""
Add citation string to Article nodes
Parameters
----------
warehouse_home
server_name
cache_dir
resume
password
Returns
-------
"""
session = get_session(warehouse_home, server_name, password=password)
if resume:
query = """
MATCH (a:Article)
WHERE a.citation is NULL
RETURN a.doi as doi"""
else:
query = """
MATCH (a:Article)
RETURN a.doi as doi"""
records = session.run(query)
try:
records.peek()
except ResultError:
log.info('no Article nodes without citation property')
return
# The reason to use pickleshare is that it uses a separate pickle file
# for each key (i.e. doi), so if the process crashes, at least most of the
# looked up citations/metadata is saved to file
cache_path = Path(cache_dir)
cache_path.dirname().makedirs_p()
log.info('reading cached citations from ' + cache_path)
cache = pickleshare.PickleShareDB(cache_dir)
for rec in records:
doi = rec['doi']
citation = get_citation(doi, cache, online=online)
if citation:
session.run("""
MATCH (a:Article)
WHERE a.doi = {doi}
SET a.citation = {citation}
""", {'doi': doi, 'citation': citation})
log.info('added citation for DOI ' + doi)
def add_metadata(warehouse_home, server_name, cache_dir,
resume=False, password=None, online=True):
"""
Add article metadata to Article nodes
Parameters
----------
warehouse_home
server_name
cache_dir
resume
password
Returns
-------
"""
session = get_session(warehouse_home, server_name, password=password)
if resume:
query = """
MATCH (a:Article)
WHERE ( a.title is NULL OR
a.journal is NULL OR
a.publisher is NULL OR
a.year is NULL OR
a.ISSN is NULL )
RETURN a.doi as doi"""
else:
query = """
MATCH (a:Article)
RETURN a.doi as doi"""
records = session.run(query)
try:
records.peek()
except ResultError:
log.info('no Article nodes without title property')
return
cache_path = Path(cache_dir)
cache_path.dirname().makedirs_p()
log.info('reading cached metadata from ' + cache_path)
cache = pickleshare.PickleShareDB(cache_dir)
for rec in records:
doi = rec['doi']
metadata = get_all_metadata(doi, cache, online)
session.run("""
MATCH (a:Article)
WHERE a.doi = {doi}
SET a.title = {title},
a.journal = {journal},
a.year = {year},
a.month = {month},
a.day = {day},
a.ISSN = {ISSN},
a.publisher = {publisher}
""", metadata)
log.info('added metadata for DOI ' + doi)
