def queryAltmetric(pmid):
"""
Check the altmetric journal percentile score of the publication
"""
a = Altmetric()
try:
resp = a.pmid(pmid)
if resp is None:
logger.debug("PMID %s. Not found" % pmid)
return -1
else:
if 'context' in resp:
metric = resp['context']['journal'][
'pct'] # Percentage attention for this journal
logger.debug("PMID %s. Metric %s" % (pmid, metric))
return metric
logger.debug("PMID %s. Percentage attention not found" % pmid)
return -2
except AltmetricHTTPException as e:
if e.status_code == 403:
logger.error(
"You aren't authorized for this call: {}".format(pmid))
elif e.status_code == 420:
logger.error(
'You are being rate limited, currently {}'.format(pmid))
elif e.status_code == 502:
logger.error(
'The API version you are using is currently down for maintenance.'
)
elif e.status_code == 404:
logger.error('Invalid API function')
logger.error(e.msg)
logger.warn("PMID %s. Exception %s" % (pmid, e.msg))
return -3
def update(self):
rsp = None
a = Altmetric(settings.ALTMETRIC_API_KEY)
ids = self.paper.get_ids()
# Fetch altmetric data based on paper supported id
try:
if 'doi' in ids:
rsp = a.doi(ids.get('doi', ''))
if not rsp and 'arx' in ids:
rsp = a.arxiv(ids.get('arx'))
if not rsp and 'pmi' in ids:
rsp = a.pmid(ids.get('pmi'))
except AltmetricHTTPException:
raise
# Parse json
if rsp:
self.score = rsp.get('score')
self.altmetric_id = rsp.get('altmetric_id')
self.altmetric_jid = rsp.get('altmetric_jid', '')
self.score_1d = rsp.get('history').get('1d')
self.score_2d = rsp.get('history').get('2d')
self.score_3d = rsp.get('history').get('3d')
self.score_4d = rsp.get('history').get('4d')
self.score_5d = rsp.get('history').get('5d')
self.score_6d = rsp.get('history').get('6d')
self.score_1w = rsp.get('history').get('1w')
self.score_1m = rsp.get('history').get('1m')
self.score_3m = rsp.get('history').get('3m')
self.score_6m = rsp.get('history').get('6m')
self.score_1y = rsp.get('history').get('1y')
self.cited_by_posts_count = rsp.get('cited_by_posts_count', 0)
self.cited_by_delicious_count = rsp.get('cited_by_delicious_count',
0)
self.cited_by_fbwalls_count = rsp.get('cited_by_fbwalss_count', 0)
self.cited_by_feeds_count = rsp.get('cited_by_feeds_count', 0)
self.cited_by_forum_count = rsp.get('cited_by_forum_count', 0)
self.cited_by_gplus_count = rsp.get('cited_by_gplus_count', 0)
self.cited_by_linkedin_count = rsp.get('cited_by_linkedin_count',
0)
self.cited_by_msm_count = rsp.get('cited_by_msm_count', 0)
self.cited_by_peer_review_sites_count = rsp.get(
'cited_by_peer_review_sites_count', 0)
self.cited_by_pinners_count = rsp.get('cited_by_pinners_count', 0)
self.cited_by_policies_count = rsp.get('cited_by_policies_count',
0)
self.cited_by_qs_count = rsp.get('cited_by_qs_count', 0)
self.cited_by_rdts_count = rsp.get('cited_by_rdts_count', 0)
self.cited_by_rh_count = rsp.get('cited_by_rh_count', 0)
self.cited_by_tweeters_count = rsp.get('cited_by_tweeters_count',
0)
self.cited_by_videos_count = rsp.get('cited_by_videos_count', 0)
self.cited_by_weibo_count = rsp.get('cited_by_weibo_count', 0)
self.cited_by_wikipedia_count = rsp.get('cited_by_wikipedia_count',
0)
if isinstance(rsp.get('readers'), dict):
self.readers_citeulike = rsp.get('readers').get('citeulike')
self.readers_mendeley = rsp.get('readers').get('mendeley')
self.image = rsp.get('images').get('small')
match = re.findall(r'types=(P?[\w]+)', self.image)
if match:
self.type = match[0]
# save
self.save()
outputFile.write('pmid, score, numReaders, cited (altmetric), scopus\n')
am_metadata = Altmetric()
c = 0
for line in setLinks:
if c > numLines2Skip:
parsedData = line.split('\n')[0].split(',')
pmid = parsedData[2]
if not (pmid in listpmid_alreadyDone):
paperMetadata = am_metadata.pmid(pmid)
if paperMetadata != None:
print('Evaluating pmid ' + pmid)
score = paperMetadata['score']
numReaders = paperMetadata['readers_count']
cited_by = 0
for key in paperMetadata.keys():
if 'cited_by_' in key:
cited_by += paperMetadata[key]
if 'scopus_subjects' in paperMetadata.keys():
scopus_subjects = paperMetadata['scopus_subjects']
now = datetime.now()
try:
resp = paperbuzz.search(doi)
err = None
except Exception as e:
resp = None
err = e
row = [pmid, doi, json.dumps(resp), str(err), str(now)]
csv_writer.writerow(row)
# Query Altmetric API
logging.info('Collecting Altmetric.com metrics for {}'.format(query))
with open(str(output_dir / query / "altmetric.csv"), "w") as f:
csv_writer = csv.writer(f)
csv_writer.writerow(METRICS_COLUMNS)
for pmid, doi in tqdm(zip(input_df.pmid, input_df.doi), total=len(input_df)):
now = datetime.now()
try:
resp = altmetric.pmid(str(pmid))
err = None
except Exception as e:
resp = None
err = e
row = [pmid, doi, json.dumps(resp), str(err), str(now)]
csv_writer.writerow(row)
