def get_tr_metadata(ev_tr_dict):
cord_by_doi, cord_by_pmid = get_cord_info()
# If has DOI, look up in CORD19
title, authors, journal, date = (None, None, None, None)
if ev_tr_dict.get('DOI'):
doi = ev_tr_dict['DOI']
cord_entry = cord_by_doi.get(doi)
if cord_entry:
return (cord_entry['title'], cord_entry['authors'],
cord_entry['journal'], cord_entry['publish_time'].year)
# Article not in CORD-19 corpus, get metadata from Crossref
print("Querying crossref")
cr_entry = crossref_client.get_metadata(doi)
if cr_entry:
try:
author_str = '; '.join([
f"{auth['family']}, {auth.get('given', '')}"
for auth in cr_entry['author']
])
except KeyError:
try:
author_str = '; '.join(
[f"{auth['name']}" for auth in cr_entry['author']])
except KeyError:
author_str = ''
title_list = cr_entry['title']
if title_list:
title = title_list[0]
container_list = cr_entry['container-title']
if container_list:
journal = container_list[0]
return (title, author_str, journal,
cr_entry['issued']['date-parts'][0][0])
# If we got here, then we haven't found the metadata yet, try by PMID
if ev_tr_dict.get('PMID'):
pmid = ev_tr_dict['PMID']
cord_entry = cord_by_pmid.get(pmid)
if cord_entry:
return (cord_entry['title'], cord_entry['authors'],
cord_entry['journal'], cord_entry['publish_time'].year)
print("Querying Pubmed")
pm_entry = pubmed_client.get_metadata_for_ids([pmid])
if pm_entry:
pm_md = pm_entry[pmid]
author_str = '; '.join(pm_md['authors'])
return (pm_md['title'], author_str, pm_md.get('journal_title', ''),
pm_md['publication_date']['year'])
# No luck, return empty strings
return ('', '', '', '')
def _get_doi_title(doi):
m = crossref_client.get_metadata(doi)
if m:
title = m.get('title')
if title:
return title[0]
def test_get_metadata():
metadata = crossref_client.get_metadata(test_doi)
assert (metadata['DOI'] == test_doi)
assert unicode_strs(metadata)
metadata = crossref_client.get_metadata('xyz')
assert (metadata is None)
def test_get_metadata():
metadata = crossref_client.get_metadata(test_doi)
assert metadata['DOI'] == test_doi
assert unicode_strs(metadata)
metadata = crossref_client.get_metadata('xyz')
assert metadata is None