def create_orcid(self, orcid, name=None, facts=None):
"""
Creates an ORCID object and populates it with data
(this endpoint will query the API to discover
information about the author; so it is potentially
expensive)
:param: orcid - String, ORCID ID
:param: name - String, name of the author (optional)
:param: facts - dictionary of other facts we want to
know/store (about the author)
:return: AuthorInfo object
"""
name = names.cleanup_name(name)
# retrieve profile from our own orcid microservice
if not name or not facts:
profile = self.harvest_author_info(orcid, name, facts)
name = name or profile.get('name', None)
if not name:
raise IgnorableException(
'Cant find an author name for orcid-id: {}'.format(orcid))
facts = profile
return AuthorInfo(orcidid=orcid,
name=name,
facts=json.dumps(facts),
account_id=facts.get('authorized', None) and 1
or None)
def harvest_author_info(self, orcidid, name=None, facts=None):
"""
Does the hard job of querying public and private
API's for whatever information we want to collect
about the ORCID ID;
At this stage, we want to mainly retrieve author
names (ie. variations of the author name)
:param: orcidid - String
:param: name - String, name of the author (optional)
:param: facts - dict, info about the author
:return: dict with various keys: name, author, author_norm, orcid_name
(if available)
"""
author_data = {}
# first verify the public ORCID profile
j = self.get_public_orcid_profile(orcidid)
if j is None:
self.logger.error(
'We cant verify public profile of: http://orcid.org/%s' %
orcidid)
else:
# no need to check ORCID API version here; this is always fresh and must use current API
# j['person']['name']['family-name']
if 'person' in j and 'name' in j['person'] and \
'family-name' in j['person']['name'] and \
'given-names' in j['person']['name']:
fname = (j['person']['name'].get('family-name', {})
or {}).get('value', None)
gname = (j['person']['name'].get('given-names', {})
or {}).get('value', None)
if fname and gname:
author_data['orcid_name'] = ['%s, %s' % (fname, gname)]
author_data['name'] = author_data['orcid_name'][0]
# search for the orcidid in our database (but only the publisher populated fiels)
# we can't trust other fiels to bootstrap our database
r = requests.get(
'%(endpoint)s?q=%(query)s&fl=author,author_norm,orcid_pub&rows=100&sort=pubdate+desc' % \
{
'endpoint': self._config.get('API_SOLR_QUERY_ENDPOINT'),
'query' : 'orcid_pub:%s' % names.cleanup_orcidid(orcidid),
},
headers={'Authorization': 'Bearer %s' % self._config.get('API_TOKEN')})
if r.status_code != 200:
self.logger.error(
'Failed getting data from our own API! (err: %s)' %
r.status_code)
raise Exception(r.text)
# go through the documents and collect all the names that correspond to the ORCID
master_set = {}
for doc in r.json()['response']['docs']:
for k, v in names.extract_names(orcidid, doc).items():
if v:
master_set.setdefault(k, {})
n = names.cleanup_name(v)
if not master_set[k].has_key(n):
master_set[k][n] = 0
master_set[k][n] += 1
# get ADS data about the user
# 0000-0003-3052-0819 | {"authorizedUser": true, "currentAffiliation": "Australian Astronomical Observatory", "nameVariations": ["Green, Andrew W.", "Green, Andy", "Green, Andy W."]}
r = self.get_ads_orcid_profile(orcidid)
if r:
_author = r
_info = _author.get('info', {}) or {}
if _info.get('authorizedUser', False):
author_data['authorized'] = True
if _info.get('currentAffiliation', False):
author_data['current_affiliation'] = _info[
'currentAffiliation']
_vars = _info.get('nameVariations', None)
if _vars:
master_set.setdefault('author', {})
for x in _vars:
x = names.cleanup_name(x)
v = master_set['author'].get(x, 1)
master_set['author'][x] = v
# elect the most frequent name to become the 'author name'
# TODO: this will choose the normalized names (as that is shorter)
# maybe we should choose the longest (but it is not too important
# because the matcher will be checking all name variants during
# record update)
mx = 0
for k, v in master_set.items():
author_data[k] = sorted(list(v.keys()))
for name, freq in v.items():
if freq > mx:
author_data['name'] = name
# automatically add the short names, because they make us find
# more matches
short_names = set()
for x in ('author', 'orcid_name', 'author_norm'):
if x in author_data and author_data[x]:
for name in author_data[x]:
for variant in names.build_short_forms(name):
short_names.add(variant)
if len(short_names):
author_data['short_name'] = sorted(list(short_names))
# Create the transliterated/ascii form of the name, in case there are accented Unicode characters
asc_names = set()
for x in ('author', 'orcid_name', 'author_norm', 'short_name'):
if x in author_data and author_data[x]:
for name in author_data[x]:
asc_names.add(u2asc(name))
if len(asc_names):
author_data['ascii_name'] = sorted(list(asc_names))
return author_data
def update_record(rec, claim, min_levenshtein):
"""
update the ADS Record; we'll add ORCID information into it
(at the correct position)
:param: rec - JSON structure, it contains metadata; we expect
it to have 'authors' field, and 'claims' field
:param: claim - JSON structure, it contains claim data,
especially:
orcidid
author
author_norm
We use those field to find out which author made the
claim.
:return: tuple(clain_category, position) or None if no record
was updated
"""
assert (isinstance(rec, dict))
assert (isinstance(claim, dict))
assert ('authors' in rec)
assert ('claims' in rec)
assert (isinstance(rec['authors'], list))
claims = rec.get('claims', {})
rec['claims'] = claims
authors = rec.get('authors', [])
# make sure the claims have the necessary structure
fld_name = u'unverified'
if 'account_id' in claim and claim[
'account_id']: # the claim was made by ADS verified user
fld_name = u'verified'
num_authors = len(authors)
if fld_name not in claims or claims[fld_name] is None:
claims[fld_name] = ['-'] * num_authors
elif len(claims[fld_name]) < num_authors: # check the length is correct
claims[fld_name] += ['-'] * (num_authors - len(claims[fld_name]))
elif len(claims[fld_name]) > num_authors:
claims[fld_name] = claims[fld_name][0:num_authors]
# always remove the orcidid
modified = False
orcidid = claim['orcidid']
for v in list(claims.values()):
while orcidid in v:
v[v.index(orcidid)] = '-'
modified = True
variant_keys = ('author', 'orcid_name', 'author_norm', 'short_name',
'ascii_name')
# first check to see if there's an exact name match on the appropriate keys
claims_clean = set()
for key in variant_keys:
for variant in claim.get(key, []):
if bool(variant.strip()):
try:
claims_clean.add(
names.cleanup_name(variant).lower().encode('utf-8'))
except RuntimeError:
# don't add a blank variant to the set
continue
aidx = 0
for author in rec['authors']:
try:
author_clean = names.cleanup_name(author).lower().encode('utf8')
except RuntimeError:
# don't add a blank name to the set
continue
if author_clean in claims_clean:
claims[fld_name][aidx] = claim.get(
'status', 'created') == 'removed' and '-' or orcidid
return (fld_name, aidx)
# also try the transliterated/ascii form of the author name
elif u2asc(author_clean) in claims_clean:
claims[fld_name][aidx] = claim.get(
'status', 'created') == 'removed' and '-' or orcidid
return (fld_name, aidx)
aidx += 1
# if there is no exact match, try on Levenshtein distance, searching using descending priority
for fx in variant_keys:
if fx in claim and claim[fx]:
#c = [x for x in claim[fx] if bool(x.strip())]
assert (isinstance(claim[fx], list))
idx = find_orcid_position(rec['authors'],
claim[fx],
min_levenshtein=min_levenshtein)
if idx > -1:
if idx >= num_authors:
logger.error(
u'Index is beyond list boundary: \n' +
u'Field {fx}, author {author}, len(authors)={la}, len({fx})=lfx'
.format(fx=fx,
author=claim[fx],
la=num_authors,
lfx=len(claim[fx])))
continue
claims[fld_name][idx] = claim.get(
'status', 'created') == 'removed' and '-' or orcidid
return (fld_name, idx)
if modified:
return ('removed', -1)
def find_orcid_position(authors_list, name_variants, min_levenshtein=0.9):
"""
Find the position of ORCID in the list of other strings
:param authors_list - array of names that will be searched
:param name_variants - array of names of a single author
:return list of positions that match
"""
try:
al = [
names.cleanup_name(x).lower().encode('utf8') for x in authors_list
]
except RuntimeError:
logger.error('Blank author present in author list: %s' % authors_list)
return -1
# compute similarity between all authors (and the supplied variants)
# this is not very efficient, however the lists should be small
# and short, so 3000 operations take less than 1s)
res = []
res_asc = []
aidx = vidx = 0
nv = []
for name in name_variants:
try:
variant = names.cleanup_name(name).lower().encode('utf8')
nv.append(variant)
except RuntimeError:
# don't accept a blank name
continue
if bool(variant.strip()):
aidx = 0
for author in al:
res.append((Levenshtein.ratio(author, variant), aidx, vidx))
# check transliterated/ascii form of names in author list if name is different from ascii version
if u2asc(author) != author:
if sys.version_info > (3, ):
res_asc.append((Levenshtein.ratio(
u2asc(author).encode(), variant), aidx, vidx))
else:
res_asc.append(
(Levenshtein.ratio(u2asc(author),
variant), aidx, vidx))
else:
res_asc.append(res[-1])
aidx += 1
vidx += 1
# sort results from the highest match
res = sorted(res, key=lambda x: x[0], reverse=True)
res_asc = sorted(res_asc, key=lambda x: x[0], reverse=True)
if len(res) == 0:
return -1
# if transliterated forms have a higher Lev ratio, accept the transliterated form
if res_asc[0][0] > res[0][0]:
res = res_asc
if res[0][0] < min_levenshtein:
# test submatch (0.6470588235294118, 19, 0) (required:0.69) closest: vernetto, s, variant: vernetto, silvia teresa
author_name = al[res[0][1]]
variant_name = nv[res[0][2]]
if author_name in variant_name or variant_name in author_name:
if sys.version_info < (3, ):
logger.debug(u'Using submatch for: %s (required:%s) closest: %s, variant: %s' \
% (res[0], min_levenshtein,
unicode(author_name, 'utf-8'),
unicode(variant_name, 'utf-8')))
else:
logger.debug('Using submatch for: %s (required:%s) closest: %s, variant: %s' \
% (res[0], min_levenshtein,
author_name,
variant_name))
return res[0][1]
if sys.version_info < (3, ):
logger.debug(u'No match found: the closest is: %s (required:%s) closest: %s, variant: %s' \
% (res[0], min_levenshtein,
unicode(author_name, 'utf-8'),
unicode(variant_name, 'utf-8')))
else:
logger.debug('No match found: the closest is: %s (required:%s) closest: %s, variant: %s' \
% (res[0], min_levenshtein,
author_name,
variant_name))
return -1
logger.debug('Found match: %s (min_levenstein=%s), authors=%s',
authors_list[res[0][1]], min_levenshtein, authors_list)
return res[0][1]