def test_mismatch(self):
self.assertAlmostEqual(
shallower_name_similarity(('Robin K.', 'Ryder'),
('Robin J.', 'Ryder')), 0)
self.assertAlmostEqual(
shallower_name_similarity(('Robin', 'Ryder'), ('Robin', 'Rider')),
0)
def test_symmetric(self):
pairs = [
(('Robin', 'Ryder'), ('Robin', 'Ryder')),
(('Robin', 'Ryder'), ('R.', 'Ryder')),
(('R.', 'Ryder'), ('R.', 'Ryder')),
(('Robin J.', 'Ryder'), ('R.', 'Ryder')),
(('Robin J.', 'Ryder'), ('R. J.', 'Ryder')),
(('R. J.', 'Ryder'), ('J.', 'Ryder')),
(('Robin', 'Ryder'), ('Robin J.', 'Ryder')),
(('W. Timothy', 'Gowers'), ('Timothy', 'Gowers')),
(('Robin K.', 'Ryder'), ('Robin J.', 'Ryder')),
(('Claire', 'Mathieu'), ('Claire', 'Kenyon-Mathieu')),
]
for a, b in pairs:
self.assertAlmostEqual(shallower_name_similarity(
a, b), shallower_name_similarity(b, a))
def test_symmetric(self):
pairs = [
(('Robin', 'Ryder'), ('Robin', 'Ryder')),
(('Robin', 'Ryder'), ('R.', 'Ryder')),
(('R.', 'Ryder'), ('R.', 'Ryder')),
(('Robin J.', 'Ryder'), ('R.', 'Ryder')),
(('Robin J.', 'Ryder'), ('R. J.', 'Ryder')),
(('R. J.', 'Ryder'), ('J.', 'Ryder')),
(('Robin', 'Ryder'), ('Robin J.', 'Ryder')),
(('W. Timothy', 'Gowers'), ('Timothy', 'Gowers')),
(('Robin K.', 'Ryder'), ('Robin J.', 'Ryder')),
(('Claire', 'Mathieu'), ('Claire', 'Kenyon-Mathieu')),
]
for a, b in pairs:
self.assertAlmostEqual(shallower_name_similarity(a, b),
shallower_name_similarity(b, a))
def affiliate_author_with_orcid(ref_name,
orcid,
authors,
initial_affiliations=None):
"""
Given a reference name and an ORCiD for a researcher, find out which
author in the list is the most likely to be that author. This function
is run on author lists of papers listed in the ORCiD record so we expect
that one of the authors should be the same person as the ORCiD holder.
This just finds the most similar name and returns the appropriate affiliations
list (None everywhere except for the most similar name where it is the ORCiD).
"""
max_sim_idx = None
max_sim = 0.
for idx, name in enumerate(authors):
cur_similarity = shallower_name_similarity(name, ref_name)
if cur_similarity > max_sim:
max_sim_idx = idx
max_sim = cur_similarity
affiliations = [None] * len(authors)
if initial_affiliations and len(initial_affiliations) == len(authors):
affiliations = initial_affiliations
if max_sim_idx is not None:
affiliations[max_sim_idx] = orcid
return affiliations
def test_malformed(self):
inputs = [
((' ', ' '), ('John', 'Doe')),
(('Alfred', 'Kastler'), (' ', ' ')),
('', (None, '')),
]
for a, b in inputs:
self.assertEqual(shallower_name_similarity(a, b), False)
def test_malformed(self):
inputs = [
((' ', ' '), ('John', 'Doe')),
(('Alfred', 'Kastler'), (' ', ' ')),
('', (None, '')),
]
for a, b in inputs:
self.assertEqual(shallower_name_similarity(a, b), False)
def test_matching(self):
self.assertAlmostEqual(
shallower_name_similarity(('Robin', 'Ryder'), ('Robin', 'Ryder')), 1.0)
self.assertGreater(
shallower_name_similarity(('Robin', 'Ryder'), ('R.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('R.', 'Ryder'), ('R.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin J.', 'Ryder'), ('R.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin J.', 'Ryder'), ('R. J.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin', 'Ryder'), ('Robin J.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin', 'Ryder'), ('', 'Ryder')), 0)
def test_matching(self):
self.assertAlmostEqual(
shallower_name_similarity(('Robin', 'Ryder'), ('Robin', 'Ryder')),
1.0)
self.assertGreater(
shallower_name_similarity(('Robin', 'Ryder'), ('R.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('R.', 'Ryder'), ('R.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin J.', 'Ryder'), ('R.', 'Ryder')),
0)
self.assertGreater(
shallower_name_similarity(('Robin J.', 'Ryder'),
('R. J.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin', 'Ryder'),
('Robin J.', 'Ryder')), 0)
self.assertGreater(
shallower_name_similarity(('Robin', 'Ryder'), ('', 'Ryder')), 0)
def affiliate_author_with_orcid(ref_name, orcid, authors, initial_affiliations=None):
"""
Given a reference name and an ORCiD for a researcher, find out which
author in the list is the most likely to be that author. This function
is run on author lists of papers listed in the ORCiD record so we expect
that one of the authors should be the same person as the ORCiD holder.
This just finds the most similar name and returns the appropriate affiliations
list (None everywhere except for the most similar name where it is the ORCiD).
"""
max_sim_idx = None
max_sim = 0.
for idx, name in enumerate(authors):
cur_similarity = shallower_name_similarity(name, ref_name)
if cur_similarity > max_sim:
max_sim_idx = idx
max_sim = cur_similarity
affiliations = [None]*len(authors)
if initial_affiliations and len(initial_affiliations) == len(authors):
affiliations = initial_affiliations
if max_sim_idx is not None:
affiliations[max_sim_idx] = orcid
return affiliations
def test_multiple(self):
self.assertAlmostEqual(
shallower_name_similarity(('Juan Pablo', 'Corella'), ('J. Pablo', 'Corella')), 1.0)
def test_unicode(self):
self.assertGreater(
shallower_name_similarity(('Cl\u0102\u0160ment', 'Pit-Claudel'), ('Clément', 'Pit-Claudel')), 0)
def test_reverse(self):
self.assertGreater(
shallower_name_similarity(('W. Timothy', 'Gowers'),
('Timothy', 'Gowers')), 0)
def test_unicode(self):
self.assertGreater(
shallower_name_similarity(('Cl\u0102\u0160ment', 'Pit-Claudel'),
('Clément', 'Pit-Claudel')), 0)
def test_multiple(self):
self.assertAlmostEqual(
shallower_name_similarity(('Juan Pablo', 'Corella'),
('J. Pablo', 'Corella')), 1.0)
def test_hyphen(self):
self.assertGreater(
shallower_name_similarity(('Clement F.', 'Pit Claudel'),
('Clément', 'Pit-Claudel')), 0)
def test_hyphen(self):
self.assertGreater(
shallower_name_similarity(('Clement F.', 'Pit Claudel'),
('Clément', 'Pit-Claudel')),
0)
def test_reverse(self):
self.assertGreater(
shallower_name_similarity(('W. Timothy', 'Gowers'), ('Timothy', 'Gowers')), 0)
def test_mismatch(self):
self.assertAlmostEqual(
shallower_name_similarity(('Robin K.', 'Ryder'), ('Robin J.', 'Ryder')), 0)
self.assertAlmostEqual(
shallower_name_similarity(('Robin', 'Ryder'), ('Robin', 'Rider')), 0)
def search_by_name(first, last, instance=settings.ORCID_BASE_DOMAIN):
"""
Searches for an ORCID profile matching this (first,last) name.
Returns a list of such ORCID profiles.
"""
# Validate arguments
if not last:
return
# Perform query
base_base_pub = "https://pub." + instance + "/"
baseurl = base_base_pub + 'v1.2/search/orcid-bio/'
dct = {
'rows': 10,
'start': 0,
'q': 'family-name:%s given-names:%s' % (last, first),
}
url = baseurl + '?' + urlencode(dct)
try:
r = requests.get(url)
# the namespace is the same for both the production and the
# sandbox versions.
ns = {'ns': 'http://www.orcid.org/ns/orcid'}
xml = etree.fromstring(r.text.encode('utf-8'))
for elem in xml.xpath('//ns:orcid-search-result', namespaces=ns):
candidateFirst = None
candidateLast = None
# Get name
pers_details = elem.xpath('.//ns:personal-details',
namespaces=ns)
if not pers_details:
continue
for item in pers_details[0]:
if item.tag.endswith('given-names'):
candidateFirst = item.text
elif item.tag.endswith('family-name'):
candidateLast = item.text
if not candidateFirst or not candidateLast:
continue
# Check that the names are compatible
if shallower_name_similarity(
(first, last), (candidateFirst, candidateLast)) == 0:
continue
# Get ORCID iD
orcid_elem = elem.xpath(
'./ns:orcid-profile/ns:orcid-identifier/ns:path',
namespaces=ns)
if not orcid_elem:
continue
orcid = orcid_elem[0].text
# Add other things
lst = elem.xpath(
'./ns:orcid-profile/ns:orcid-bio/ns:researcher-urls/ns:researcher-url/ns:url/text()',
namespaces=ns)
homepage = None
for url in lst:
homepage = urlize(url)
break
keywords = elem.xpath(
'./ns:orcid-profile/ns:orcid-bio/ns:keywords/ns:keyword/text()',
namespaces=ns)
yield {
'first': candidateFirst,
'last': candidateLast,
'orcid': orcid,
'homepage': homepage,
'keywords': keywords,
}
except etree.XMLSyntaxError as e:
print e
except requests.exceptions.RequestException as e:
print e
def search_by_name(first, last):
"""
Searches for an ORCID profile matching this (first,last) name.
Returns a list of such ORCID profiles.
"""
# Validate arguments
if not last:
return
# Perform query
baseurl = 'http://pub.orcid.org/v1.2/search/orcid-bio/'
dct = {
'rows':10,
'start':0,
'q':'family-name:%s given-names:%s' % (last,first),
}
url = baseurl+'?'+urlencode(dct)
try:
r = requests.get(url)
ns = {'ns':'http://www.orcid.org/ns/orcid' }
xml = etree.fromstring(r.text.encode('utf-8'))
for elem in xml.xpath('//ns:orcid-search-result', namespaces=ns):
candidateFirst = None
candidateLast = None
# Get name
pers_details = elem.xpath('.//ns:personal-details', namespaces=ns)
if not pers_details:
continue
for item in pers_details[0]:
if item.tag.endswith('given-names'):
candidateFirst = item.text
elif item.tag.endswith('family-name'):
candidateLast = item.text
if not candidateFirst or not candidateLast:
continue
# Check that the names are compatible
if shallower_name_similarity((first,last),(candidateFirst,candidateLast)) == 0:
continue
# Get ORCID iD
orcid_elem = elem.xpath('./ns:orcid-profile/ns:orcid-identifier/ns:path', namespaces=ns)
if not orcid_elem:
continue
orcid = orcid_elem[0].text
# Add other things
lst = elem.xpath('./ns:orcid-profile/ns:orcid-bio/ns:researcher-urls/ns:researcher-url/ns:url/text()', namespaces=ns)
homepage = None
for url in lst:
homepage = urlize(url)
break
keywords = elem.xpath('./ns:orcid-profile/ns:orcid-bio/ns:keywords/ns:keyword/text()', namespaces=ns)
yield {
'first':candidateFirst,
'last':candidateLast,
'orcid':orcid,
'homepage':homepage,
'keywords':keywords,
}
except etree.XMLSyntaxError as e:
print e
except requests.exceptions.RequestException as e:
print e
