def extract_refs(dois, urls, pmids):
results = {}
def gen_error(id):
return {'message': 'No references found for {}.'.format(id)}
if dois:
for doi in dois:
results[doi] = []
try:
r = get_scopus_references(doi)
refs = r.get('references', None)
if not refs:
results[doi] = gen_error(doi)
else:
for ref in refs:
results[doi].append(getPubMedID(ref))
except HTTPException:
results[doi] = gen_error(doi)
if urls:
for url in urls:
results[url] = []
try:
r = get_scopus_references(url)
refs = r.get('references', None)
if not refs:
results[url] = gen_error(url)
else:
for ref in refs:
results[url].append(getPubMedID(ref))
except HTTPException:
results[url] = gen_error(url)
if pmids:
for pmid in pmids:
results[pmid] = []
try:
r = getReferenceInfo(getRefID(pmid))
if not r:
results[pmid] = gen_error(pmid)
else:
for ref in r:
results[pmid].append(ref)
except HTTPException:
results[pmid] = gen_error(pmid)
return results
def wrapper(*args, **kwargs):
result = func(*args, **kwargs)
ret_dict = {'length': 0, 'result': []}
if type(result) == list:
for r in result:
ret_dict['result'].append(getPubMedID(r))
ret_dict['length'] = len(ret_dict['result'])
else:
ret_dict['result'].append(getPubMedID(result))
ret_dict['length'] = 1
return ret_dict
def deferred_search(citations, cr_only=False, md_only=False):
results = multi_search(citations, cr_only, md_only)
final = []
for res in results:
final.append(getPubMedID(res))
return final
def post(self):
data = self.parser.parse_args()
query = data.get('query', None)
get_all = data.get('chkbox', False)
if not query:
return self.get()
result = integrated_lookup(query.strip(), return_all=get_all)
ret_dict = {'length': 0, 'result': []}
if get_all:
for r in result:
ret_dict['result'].append(getPubMedID(r))
ret_dict['length'] = len(ret_dict['result'])
else:
ret_dict['result'].append(getPubMedID(result))
ret_dict['length'] = 1
return ret_dict
def batch_lookup(refl):
"""
Mendeley & Crossref integrated lookup. This one receives a list of references and resolves them based on the
integrated lookup, returning only the best result of each citation with it's respective pubmedI lookpu result
:param refl: List of references to resolve
:return: List of reference lookup results
"""
results = []
for ref in refl:
res = integrated_lookup(ref, return_all=False, return_empty=True)
res = getPubMedID(res)
results.append(res)
return results
def lookup_and_extract(citation_list):
results = []
for citation in citation_list:
ref = getPubMedID(single_search(citation))
doi = ref.get('ids', {}).get('doi', None)
pmid = ref.get('ids', {}).get('pubmed', None)
url = ref.get('ids', {}).get('scopus', None)
dois = [doi] if doi else []
pmids = [pmid] if pmid else []
urls = [url] if url else []
extracted_refs = extract_refs(dois, urls, pmids)
ref['references'] = extracted_refs
results.append(ref)
return results
def deferred_extract_references(doi):
res = get_scopus_references(doi)
results = []
for r in res:
results.append(getPubMedID(r))
return results