def get_pubmed_from_doi(doi):
'try to get pubmed dict for this DOI, or None if not found'
import pubmed
xml = pubmed.search_pubmed(doi, retmax='1', field='LID')
try:
d, root = pubmed.dict_from_xml(xml, pubmedID='!Id')
except KeyError: # some DOI not properly indexed in pubmed?!?!
xml = pubmed.search_pubmed(doi, retmax='1')
try:
d, root = pubmed.dict_from_xml(xml, pubmedID='!Id')
except KeyError:
pass
else: # have to check whether title matches
pubmedDict = pubmed.get_pubmed_dict(d['pubmedID'])
if pubmedDict.get('title')[:50].lower() == \
doiDict.get('title')[:50].lower():
return pubmedDict
else:
return pubmed.get_pubmed_dict(d['pubmedID'])
def doi_dict_from_xml(xml, title='title', year='publication_date.year',
volume='journal_volume.volume',
source_url='doi_data.resource', **kwargs):
import pubmed
d, root = pubmed.dict_from_xml(xml, title=title, year=year, volume=volume,
source_url=source_url, **kwargs)
authorNames = [] # extract list of author names
for o in root.findall('.//person_name'):
authorNames.append(safe_text(o, 'given_name') + ' ' +
safe_text(o, 'surname'))
d['authorNames'] = authorNames
return d