def get_user_public_profile(self, user):
session = requests.Session()
key, secret = self.get_key_and_secret()
api = orcid.PublicAPI(key, secret, sandbox=False)
# Get token
res = session.post(self.ACCESS_TOKEN_URL,
data={
'client_id': key,
'client_secret': secret,
'scope': '/read-public',
'grant_type': 'client_credentials'
},
headers={'Accept': 'application/json'})
res.raise_for_status()
access_token = res.json().get('access_token')
uid = user.social_auth.get(provider=self.name).uid
res = session.get(
'https://pub.orcid.org/v1.2/{0}/orcid-profile/'.format(uid),
headers={
'Content-Type': 'application/orcid+json',
'Authorization': 'Bearer ' + access_token
})
res.raise_for_status()
return res.json()
def get_works(user_token, orcid_id):
api = orcid.PublicAPI(config.get("DEFAULT", "ORCID_CLIENT_ID"),
config.get("DEFAULT", "ORCID_SECRET"))
summary = api.read_record_public(orcid_id, "works", user_token)
metadata = []
for work in summary["group"]:
work_summary = work["work-summary"][0]
work_metadata = dict()
work_metadata["id"] = work_summary["put-code"]
work_metadata["title"] = work_summary["title"]["title"]["value"]
work_metadata["last-modified-date"] = work_summary[
"last-modified-date"]["value"]
work_metadata["type"] = work_summary["type"]
work_metadata["publication-year"] = work_summary["publication-date"][
"year"]["value"]
work_metadata["owner"] = orcid_id
for ext_id in work_summary["external-ids"]["external-id"]:
if ext_id["external-id-type"] == "doi":
work_metadata["doi"] = ext_id["external-id-value"]
if ext_id["external-id-type"] == "pmid":
work_metadata["pmid"] = ext_id["external-id-value"]
if ext_id["external-id-type"] == "pmc":
work_metadata["pmcid"] = ext_id["external-id-value"]
metadata.append(work_metadata)
return metadata
def get_orcid_record(orcid_id, token, request_type=''):
"""Get ORCID record details.
It returns a dictionary with the following structure:
.. code-block:: python
{
'orcid-identifier': {
'path': '0000-0000-0000-0000',
},
'person': {
'name': {
'given-names': {
'value': 'John'
},
'family-name': {
'value': 'Doe'
},
},
'emails': {
'email': [{
'email': '*****@*****.**',
}],
},
...
},
...
}
:param orcid_id: (str) ORCID identifier.
:param token: (str) Access token for querying API.
:param request_type: (str) Request type for retreiving a specific section
of the record.
:returns: (dict|None) Dictionary of the Orcid record or none if something
goes wrong
"""
credentials = current_app.config.get('ORCID_APP_CREDENTIALS')
api = orcid.PublicAPI(
credentials['consumer_key'],
credentials['consumer_secret'],
sandbox=(current_app.config.get('ORCID_DOMAIN').startswith('sandbox'))
)
try:
return api.read_record_public(orcid_id, request_type, token)
except RequestException:
return None
from requests import RequestException
import orcid
api = orcid.PublicAPI('APP-H43S7S70C6QGG5GY',
'67c4ec09-c890-494a-b64b-7428e9edee90',
sandbox=True)
token = api.get_token_from_authorization_code(authorization_code, redirect_uri)
#search_results = api.search_public('text:English')
# Get the summary
#token = api.get_token('APP-H43S7S70C6QGG5GY', '67c4ec09-c890-494a-b64b-7428e9edee90', redirect_uri)
#summary = api.read_record_public('0000-0002-3117-5116', 'activities', token)
#summary = api.read_record_public('0000-0002-3117-5116', 'record', token)
def get_dois_from_orcid_api_v2_1(orcid_id, get_titles=False, low_level=True):
"""new api v 2.1 parsing of works"""
if not orcid_id:
return []
works = None
if low_level:
token = CFG_OAUTH2_CONFIGURATIONS['orcid'].get('search_token', '')
if not token:
return []
headers = {'Content-type': 'application/vnd.orcid+json',
'Authorization type': 'Bearer', 'Access token': token}
url = 'https://pub.orcid.org/v2.1/{0}/works'.format(orcid_id)
@retry(wrap_exception=True,
retry_on_exception=retry_if_timeout_error,
wait_exponential_multiplier=250,
stop_max_attempt_number=3)
def _get_works_from_orcid(url, headers, timeout=16):
res = requests.get(url, headers=headers, timeout=timeout)
if not res.status_code == requests.codes.ok:
res.raise_for_status()
return res
try:
res = _get_works_from_orcid(url, headers)
except RetryError:
register_exception(alert_admin=True)
return []
except Exception:
register_exception(alert_admin=True)
return []
try:
works = res.json()
except ValueError:
register_exception(alert_admin=True)
return []
else:
# requires orcid.py version >= '1.0.0'
import pkg_resources
try:
orcversion = pkg_resources.get_distribution("orcid").version
except Exception:
return []
if orcversion and orcversion.startswith(0):
return []
try:
sandbox = 'sandbox' in CFG_OAUTH2_CONFIGURATIONS['orcid']['member_url']
ap = orcid.PublicAPI(
institution_key=CFG_OAUTH2_CONFIGURATIONS['orcid']['consumer_key'],
institution_secret=CFG_OAUTH2_CONFIGURATIONS['orcid']['consumer_secret'],
sandbox=sandbox,
timeout=60)
token = CFG_OAUTH2_CONFIGURATIONS['orcid'].get('search_token', '')
if not token:
token = ap.get_search_token_from_orcid()
works = ap.read_record_public(orcid_id, 'works', token)
except Exception:
register_exception(alert_admin=True)
if not works:
return []
dois = []
for work in works.get('group', {}):
if get_titles:
wksummary = work.get('work-summary', [])
for summary in wksummary:
title = ''
titles = summary.get('title', {})
if titles is not None:
title = titles.get('title', {}).get('value', '')
eids = summary.get('external-ids', {})
if eids is None:
continue
for eid in eids.get('external-id', []):
if eid.get('external-id-type', '') == 'doi':
doi = get_doi(eid.get('external-id-value', ''))
if not doi:
continue
dois.append((doi, title))
else:
for eid in work.get('external-ids', {}).get('external-id', []):
if eid.get('external-id-type', '') == 'doi':
doi = get_doi(eid.get('external-id-value', ''))
if not doi:
continue
dois.append(doi)
return dois
orcid_ids = [
"0000-0003-3008-253X", # Mark
"0000-0003-1805-8617", # Alessandro
"0000-0001-7078-2720", # Ben Boys
"0000-0002-5248-1219", # Deniz
"0000-0002-0225-5010", # Lawrence
"0000-0002-5984-7295", # Toni
"0000-0001-9690-0887", # Ieva
"0000-0003-0982-6733", # Hussein
"0000-0002-7927-8720", # Kangrui
"0000-0003-1230-3028", # Connor
"0000-0002-7503-2117", # Yannis
"0000-0002-5112-7373", # Jan
]
api = orcid.PublicAPI(os.environ['ORCID_CLIENT_ID'],
os.environ['ORCID_CLIENT_SECRET'])
search_token = api.get_search_token_from_orcid()
pub_list = []
for orcid_id in orcid_ids:
logging.info(f"Downloading publications for ORCID ID: {orcid_id}.")
query_result = api.read_record_public(orcid_id, 'works', search_token)
for orcid_entry in query_result['group']:
put_code = orcid_entry['work-summary'][0]['put-code']
orcid_full_entry = api.read_record_public(orcid_id,
'work',
search_token,
put_code=put_code)
logging.info(orcid_full_entry)
def __init__(self, client_id, client_secret):
""" Set up the ORCID API and retrieve a search token. """
self.api = orcid.PublicAPI(client_id, client_secret, sandbox=False)
self.search_token = self.api.get_search_token_from_orcid()
def connect_api(self):
"""Connects to the orcid api to provide handle for searching"""
self.P_api = orcid.PublicAPI(KEY, SECRET)