def authorgroup(self) -> Optional[List[NamedTuple]]:
"""A list of namedtuples representing the article's authors organized
by affiliation, in the form (affiliation_id, dptid, organization,
city, postalcode, addresspart, country, collaboration, auid, orcid,
indexed_name, surname, given_name).
If "given_name" is not present, fall back to initials.
Note: Affiliation information might be missing or mal-assigned even
when it looks correct in the web view. In this case please request
a correction. It is generally missing for collaborations.
"""
# Information can be one of three forms:
# 1. A dict with one key (author) or two keys (affiliation and author)
# 2. A list of dicts with as in 1, one for each affiliation (incl. missing)
# 3. A list of two dicts with one key each (author and collaboration)
# Initialization
fields = 'affiliation_id dptid organization city postalcode '\
'addresspart country collaboration auid orcid indexed_name '\
'surname given_name'
auth = namedtuple('Author', fields)
items = listify(self._head.get('author-group', []))
index_path = ['preferred-name', 'ce:indexed-name']
# Check for collaboration
keys = [k for x in items for k in list(x.keys())]
if "collaboration" in keys:
collaboration = items.pop(-1)['collaboration']
else:
collaboration = {'ce:indexed-name': None}
# Iterate through each author-affiliation combination
out = []
for item in items:
if not item:
continue
# Affiliation information
aff = item.get('affiliation', {})
aff_id = make_int_if_possible(aff.get("@afid"))
dep_id = make_int_if_possible(aff.get("@dptid"))
org = _get_org(aff)
# Author information (might relate to collaborations)
authors = listify(item.get('author', item.get('collaboration',
[])))
for au in authors:
try:
given = au.get('ce:given-name', au['ce:initials'])
except KeyError: # Collaboration
given = au.get('ce:text')
new = auth(affiliation_id=aff_id,
organization=org,
city=aff.get('city'),
dptid=dep_id,
postalcode=aff.get('postal-code'),
addresspart=aff.get('address-part'),
country=aff.get('country'),
collaboration=collaboration.get('ce:indexed-name'),
auid=int(au['@auid']),
orcid=au.get('@orcid'),
surname=au.get('ce:surname'),
given_name=given,
indexed_name=chained_get(au, index_path))
out.append(new)
return out or None
def sequencebank(self):
"""List of namedtuples representing biological entities defined or
mentioned in the text, in the form (name, sequence_number, type).
"""
path = ['enhancement', 'sequencebanks', 'sequencebank']
items = listify(chained_get(self._head, path, []))
bank = namedtuple('Sequencebank', 'name sequence_number type')
out = []
for item in items:
numbers = listify(item['sequence-number'])
for number in numbers:
new = bank(name=item['@name'], sequence_number=number['$'],
type=number['@type'])
out.append(new)
return out or None
def authorgroup(self):
"""A list of namedtuples representing the article's authors organized
by affiliation, in the form (affiliation_id, dptid, organization,
city, postalcode, addresspart, country, auid, indexed_name,
surname, given_name).
If "given_name" is not present, fall back to initials.
Note: Affiliation information might be missing or mal-assigned even
when it lookes correct in the web view. In this case please request
a correction.
"""
out = []
fields = 'affiliation_id dptid organization city postalcode '\
'addresspart country auid indexed_name surname given_name'
auth = namedtuple('Author', fields)
items = listify(self._head.get('author-group', []))
index_path = ['preferred-name', 'ce:indexed-name']
for item in items:
if not item:
continue
# Affiliation information
aff = item.get('affiliation', {})
try:
aff_ids = listify(aff['affiliation-id'])
aff_id = ", ".join([a["@afid"] for a in aff_ids])
except KeyError:
aff_id = aff.get("@afid")
org = _get_org(aff)
# Author information (might relate to collaborations)
authors = listify(item.get('author', item.get('collaboration',
[])))
for au in authors:
try:
given = au.get('ce:given-name', au['ce:initials'])
except KeyError: # Collaboration
given = au.get('ce:text')
new = auth(affiliation_id=aff_id,
organization=org,
city=aff.get('city'),
dptid=aff.get("@dptid"),
postalcode=aff.get('postal-code'),
addresspart=aff.get('address-part'),
country=aff.get('country'),
auid=au.get('@auid'),
surname=au.get('ce:surname'),
given_name=given,
indexed_name=chained_get(au, index_path))
out.append(new)
return out or None
def correspondence(self):
"""List of namedtuples representing the authors to whom correspondence
should be addressed, in the form (surname, initials, organization,
country, city_group). Multiple organziations are joined on semicolon.
"""
fields = 'surname initials organization country city_group'
auth = namedtuple('Correspondence', fields)
items = listify(self._head.get('correspondence', []))
out = []
for item in items:
aff = item.get('affiliation', {})
try:
org = aff['organization']
try:
org = org['$']
except TypeError: # Multiple names given
org = "; ".join([d['$'] for d in org])
except KeyError:
org = None
new = auth(surname=item.get('person', {}).get('ce:surname'),
initials=item.get('person', {}).get('ce:initials'),
organization=org,
country=aff.get('country'),
city_group=aff.get('city-group'))
out.append(new)
return out or None
def __init__(self, author_id, refresh=False):
"""Class to represent a Scopus Author query by the scopus-id.
Parameters
----------
author_id : str or int
The ID of the author to search for. Optionally expressed
as an Elsevier EID (i.e., in the form 9-s2.0-nnnnnnnn).
refresh : bool (optional, default=False)
Whether to refresh the cached file (if it exists) or not.
Notes
-----
The files are cached in ~/.scopus/author_retrieval/ENHANCED/{author_id}
(without eventually leading '9-s2.0-').
"""
# Load json
view = "ENHANCED" # In case Scopus adds different views in future
self._id = str(int(str(author_id).split('-')[-1]))
Retrieval.__init__(self, identifier=self._id, api='AuthorRetrieval',
refresh=refresh, view=view)
self._json = self._json['author-retrieval-response']
# Checks
try:
self._json = self._json[0]
except KeyError: # Incomplete forward
alias_json = listify(self._json['alias']['prism:url'])
alias = ', '.join([d['$'].split(':')[-1] for d in alias_json])
text = 'Author profile with ID {} has been merged and the main '\
'profile is now one of {}. Please update your records '\
'manually. Functionality of this object is '\
'reduced.'.format(author_id, alias)
warn(text, UserWarning)
def authors(self):
"""A list of namedtuples representing the article's authors, in the
form (auid, indexed_name, surname, given_name, affiliation_id,
affiliation, city, country).
Note: The affiliation referred to here is what Scopus' algorithm
determined as the main affiliation. Property `authorgroup` provides
all affiliations.
"""
out = []
fields = 'auid indexed_name surname given_name affiliation'
auth = namedtuple('Author', fields)
for item in chained_get(self._json, ['authors', 'author'], []):
affs = [a for a in listify(item.get('affiliation')) if a]
if affs:
aff = [aff.get('@id') for aff in affs]
else:
aff = None
new = auth(auid=item['@auid'],
surname=item.get('ce:surname'),
indexed_name=item.get('ce:indexed-name'),
affiliation=aff,
given_name=chained_get(
item, ['preferred-name', 'ce:given-name']))
out.append(new)
return out or None
def funding(self) -> Optional[List[NamedTuple]]:
"""List of namedtuples parsed funding information in the form
(agency, agency_id, string, funding_id, acronym, country).
"""
def _get_funding_id(f_dict: dict) -> list:
funding_get = f_dict.get('xocs:funding-id', [])
try:
return [v['$']
for v in funding_get] or None # multiple or empty
except TypeError:
return [funding_get] # single
path = ['item', 'xocs:meta', 'xocs:funding-list', 'xocs:funding']
funds = listify(chained_get(self._json, path, []))
out = []
fields = 'agency agency_id string funding_id acronym country'
fund = namedtuple('Funding', fields)
for item in funds:
new = fund(agency=item.get('xocs:funding-agency'),
agency_id=item.get('xocs:funding-agency-id'),
string=item.get('xocs:funding-agency-matched-string'),
funding_id=_get_funding_id(item),
acronym=item.get('xocs:funding-agency-acronym'),
country=item.get('xocs:funding-agency-country'))
out.append(new)
return out or None
def classificationgroup(self):
"""List with (subject group ID, number of documents)-tuples."""
path = ['author-profile', 'classificationgroup', 'classifications',
'classification']
out = [(item['$'], item['@frequency']) for item in
listify(chained_get(self._json, path, []))]
return out or None
def authors(self) -> Optional[List[NamedTuple]]:
"""A list of namedtuples representing the article's authors, in the
form (auid, indexed_name, surname, given_name, affiliation). In case
multiple affiliation IDs are given, they are joined on ";".
Note: The affiliation referred to here is what Scopus' algorithm
determined as the main affiliation. Property `authorgroup` provides
all affiliations.
"""
out = []
fields = 'auid indexed_name surname given_name affiliation'
auth = namedtuple('Author', fields)
for item in chained_get(self._json, ['authors', 'author'], []):
affs = [a for a in listify(item.get('affiliation')) if a] or None
try:
aff = ";".join([aff.get('@id') for aff in affs])
except TypeError:
aff = None
new = auth(auid=int(item['@auid']),
surname=item.get('ce:surname'),
indexed_name=item.get('ce:indexed-name'),
affiliation=aff,
given_name=chained_get(
item, ['preferred-name', 'ce:given-name']))
out.append(new)
return out or None
def contributor_group(self):
"""List of namedtuples representing contributors compiled by Scopus,
in the form (given_name, initials, surname, indexed_name, role).
"""
path = ['source', 'contributor-group']
items = listify(chained_get(self._head, path, []))
out = []
fields = 'given_name initials surname indexed_name role'
pers = namedtuple('Contributor', fields)
for item in items:
try:
entry = item.get('contributor', {})
new = pers(indexed_name=entry.get('ce:indexed-name'),
role=entry.get('@role'),
surname=entry.get('ce:surname'),
given_name=entry.get('ce:given-name'),
initials=entry.get('ce:initials'))
out.append(new)
except AttributeError:
for i in entry:
e = i.get('contributor', {})
new = pers(indexed_name=e.get('ce:indexed-name'),
role=e.get('@role'),
surname=e.get('ce:surname'),
given_name=e.get('ce:given-name'),
initials=e.get('ce:initials'))
out.append(new)
return out or None
def isbn(self):
"""ISBNs belonging to publicationName as tuple of variying length,
(e.g. ISBN-10 or ISBN-13)."""
isbns = listify(chained_get(self._head, ['source', 'isbn'], []))
if len(isbns) == 0:
return None
else:
return tuple((i['$'] for i in isbns))
def __init__(self, author_id, refresh=False, view="ENHANCED"):
"""Interaction with the Author Retrieval API.
Parameters
----------
author_id : str or int
The ID of the author to search for. Optionally expressed
as an Elsevier EID (i.e., in the form 9-s2.0-nnnnnnnn).
refresh : bool or int (optional, default=False)
Whether to refresh the cached file if it exists or not. If int
is passed, cached file will be refreshed if the number of days
since last modification exceeds that value.
view : str (optional, default=META_ABS)
The view of the file that should be downloaded. Allowed values:
METRICS, LIGHT, STANDARD, ENHANCED, where STANDARD includes all
information of LIGHT view and ENHANCED includes all information of
any view. For details see
https://dev.elsevier.com/sc_author_retrieval_views.html.
Note: Neither the BASIC nor the DOCUMENTS view are not active,
although documented.
Examples
--------
See https://pybliometrics.readthedocs.io/en/stable/examples/AuthorRetrieval.html.
Notes
-----
The directory for cached results is `{path}/ENHANCED/{author_id}`,
where `path` is specified in `~/.scopus/config.ini` and `author_id`
is stripped of an eventually leading `'9-s2.0-'`.
"""
# Checks
allowed_views = ('METRICS', 'LIGHT', 'STANDARD', 'ENHANCED')
check_parameter_value(view, allowed_views, "view")
# Load json
self._id = str(int(str(author_id).split('-')[-1]))
Retrieval.__init__(self, identifier=self._id, api='AuthorRetrieval',
refresh=refresh, view=view)
self._json = self._json['author-retrieval-response']
try:
self._json = self._json[0]
except KeyError: # Incomplete forward
alias_json = listify(self._json['alias']['prism:url'])
self._alias = [d['$'].split(':')[-1] for d in alias_json]
alias_str = ', '.join(self._alias)
text = f'Author profile with ID {author_id} has been merged and '\
f'the main profile is now one of {alias_str}. Please update '\
'your records manually. Functionality of this object is '\
'reduced.'
warn(text, UserWarning)
else:
self._alias = None
self._profile = self._json.get("author-profile", {})
def subject_areas(self):
"""List of namedtuples containing subject areas of the article
in the form (area abbreviation code).
Note: Requires the FULL view of the article.
"""
area = namedtuple('Area', 'area abbreviation code')
path = ['subject-areas', 'subject-area']
out = [area(area=item['$'], abbreviation=item['@abbrev'],
code=item['@code'])
for item in listify(chained_get(self._json, path, []))]
return out or None
def name_variants(self):
"""List of named tuples containing variants of the author name with
number of documents published with that variant.
"""
fields = 'indexed_name initials surname given_name doc_count'
variant = namedtuple('Variant', fields)
out = [variant(indexed_name=var['indexed-name'], surname=var['surname'],
doc_count=var.get('@doc-count'), initials=var['initials'],
given_name=var.get('given-name'))
for var in listify(self._profile.get('name-variant', []))]
return out or None
def journal_history(self):
"""List of named tuples of authored publications in the form
(sourcetitle, abbreviation, type, issn). issn is only given
for journals. abbreviation and issn may be None.
"""
jour = namedtuple('Journal', 'sourcetitle abbreviation type issn')
path = ['author-profile', 'journal-history', 'journal']
hist = [jour(sourcetitle=pub.get('sourcetitle'), issn=pub.get('issn'),
abbreviation=pub.get('sourcetitle-abbrev'),
type=pub.get('@type'))
for pub in listify(chained_get(self._json, path, []))]
return hist or None
def idxterms(self):
"""List of index terms (these are just one category of those
Scopus provides in the web version)
."""
try:
terms = listify(self._json.get("idxterms", {}).get('mainterm', []))
except AttributeError: # idxterms is empty
return None
try:
return [d['$'] for d in terms] or None
except AttributeError:
return None
def chemicals(self):
"""List of namedtuples representing chemical entities in the form
(source, chemical_name, cas_registry_number). In case multiple
numbers given, they are joined on ";".
"""
path = ['enhancement', 'chemicalgroup', 'chemicals']
items = listify(chained_get(self._head, path, []))
fields = 'source chemical_name cas_registry_number'
chemical = namedtuple('Chemical', fields)
out = []
for item in items:
for chem in listify(item['chemical']):
number = chem.get('cas-registry-number')
try: # Multiple numbers given
num = ";".join([n['$'] for n in number])
except TypeError:
num = number
new = chemical(source=item['@source'], cas_registry_number=num,
chemical_name=chem['chemical-name'])
out.append(new)
return out or None
def isbn(self):
"""ISBNs belonging to publicationName as tuple of variying length,
(e.g. ISBN-10 or ISBN-13)."""
isbns = listify(chained_get(self._head, ['source', 'isbn'], []))
try:
if len(isbns) == 0:
return None
elif isinstance(isbns, str):
return tuple((isbns, ))
else:
return tuple((i['$'] for i in isbns))
except TypeError:
return tuple((isbns, ))
def affiliation(self):
"""A list of namedtuples representing listed affiliations in
the form (id, name, city, country).
Note: Might be empty.
"""
out = []
aff = namedtuple('Affiliation', 'id name city country')
affs = listify(self._json.get('affiliation', []))
for item in affs:
new = aff(id=item.get('@id'), name=item.get('affilname'),
city=item.get('affiliation-city'),
country=item.get('affiliation-country'))
out.append(new)
return out or None
def affiliation(self) -> Optional[List[NamedTuple]]:
"""A list of namedtuples representing listed affiliations in
the form (id, name, city, country).
"""
out = []
aff = namedtuple('Affiliation', 'id name city country')
affs = listify(self._json.get('affiliation', []))
for item in affs:
new = aff(id=int(item['@id']),
name=item.get('affilname'),
city=item.get('affiliation-city'),
country=item.get('affiliation-country'))
out.append(new)
return out or None
def authors(self) -> Optional[List[NamedTuple]]:
"""A list of namedtuples storing author information,
where each namedtuple corresponds to one author.
The information in each namedtuple is (eid orcid surname initials givenname
documents affiliation affiliation_id city country areas).
All entries are strings or None. Areas combines abbreviated subject
areas followed by the number of documents in this subject.
Raises
------
ValueError
If the elements provided in integrity_fields do not match the
actual field names (listed above).
"""
# Initiate namedtuple with ordered list of fields
fields = 'eid orcid surname initials givenname affiliation documents '\
'affiliation_id city country areas'
auth = namedtuple('Author', fields)
check_field_consistency(self._integrity, fields)
# Parse elements one-by-one
out = []
for item in self._json:
name = item.get('preferred-name', {})
aff = item.get('affiliation-current', {})
fields = item.get('subject-area', [{
'@abbrev': '',
'@frequency': ''
}])
areas = [
f"{d.get('@abbrev', '')} ({d.get('@frequency', '')})"
for d in listify(fields)
]
new = auth(eid=item.get('eid'),
orcid=item.get('orcid'),
initials=name.get('initials'),
surname=name.get('surname'),
areas="; ".join(areas),
givenname=name.get('given-name'),
documents=int(item['document-count']),
affiliation=aff.get('affiliation-name'),
affiliation_id=aff.get('affiliation-id'),
city=aff.get('affiliation-city'),
country=aff.get('affiliation-country'))
out.append(new)
# Finalize
check_integrity(out, self._integrity, self._action)
return out or None
def funding(self):
"""List of namedtuples parsed funding information in the form
(agency string id acronym country).
"""
path = ['item', 'xocs:meta', 'xocs:funding-list', 'xocs:funding']
funds = listify(chained_get(self._json, path, []))
out = []
fund = namedtuple('Funding', 'agency string id acronym country')
for item in funds:
new = fund(agency=item.get('xocs:funding-agency'),
string=item.get('xocs:funding-agency-matched-string'),
id=item.get('xocs:funding-agency-id'),
acronym=item.get('xocs:funding-agency-acronym'),
country=item.get('xocs:funding-agency-country'))
out.append(new)
return out or None
def __init__(self, author_id, refresh=False):
"""Interaction with the Author Retrieval API.
Parameters
----------
author_id : str or int
The ID of the author to search for. Optionally expressed
as an Elsevier EID (i.e., in the form 9-s2.0-nnnnnnnn).
refresh : bool or int (optional, default=False)
Whether to refresh the cached file if it exists or not. If int
is passed, cached file will be refreshed if the number of days
since last modification exceeds that value.
Examples
--------
See https://pybliometrics.readthedocs.io/en/stable/examples/AuthorRetrieval.html
Notes
-----
The directory for cached results is `{path}/ENHANCED/{author_id}`,
where `path` is specified in `~/.scopus/config.ini` and `author_id`
is stripped of an eventually leading `'9-s2.0-'`.
"""
# Load json
view = "ENHANCED" # In case Scopus adds different views in future
self._id = str(int(str(author_id).split('-')[-1]))
Retrieval.__init__(self,
identifier=self._id,
api='AuthorRetrieval',
refresh=refresh,
view=view)
self._json = self._json['author-retrieval-response']
# Checks
try:
self._json = self._json[0]
except KeyError: # Incomplete forward
alias_json = listify(self._json['alias']['prism:url'])
self._alias = [d['$'].split(':')[-1] for d in alias_json]
alias_str = ', '.join(self._alias)
text = f'Author profile with ID {author_id} has been merged and '\
f'the main profile is now one of {alias_str}. Please update '\
'your records manually. Functionality of this object is '\
'reduced.'
warn(text, UserWarning)
else:
self._alias = None
def references(self):
"""List of namedtuples representing references listed in the document,
in the form (position, id, doi, title, authors, authors_auid,
authors_affiliationid, sourcetitle, publicationyear, volume, issue,
first, last, citedbycount, type, text, fulltext).
`position` is the number at which the reference appears in the
document, `id` is the Scopus ID of the referenced document (EID
without the "2-s2.0-"), `authors` is a string of the names of the
authors in the format "Surname1, Initials1; Surname2, Initials2",
`authors_auid` is a string of the author IDs joined on "; ",
`authors_affiliationid` is a string of the authors' affiliation IDs
joined on "; ", `sourcetitle` is the name of the source (e.g. the
journal), `publicationyear` is the year of the publication as a string,
`volume` and `issue`, are strings referring to the volume and issue,
`first` and `last` refer to the page range, `citedbycount` is a string
for the total number of citations of the cited item, `type` describes
the parsing status of the reference (resolved or not), `text` is
Scopus-provided information on the publication, `fulltext` is the text
the authors used for the reference.
Note: Requires either the FULL view or REF view.
Might be empty even if refcount is positive. Specific fields can
be empty.
Author lists (authors, authors_auid, authors_affiliationid) may contain
duplicates but None's have been filtered out.
"""
out = []
fields = 'position id doi title authors authors_auid '\
'authors_affiliationid sourcetitle publicationyear volume '\
'issue first last citedbycount type text fulltext'
ref = namedtuple('Reference', fields)
items = listify(self._ref.get("reference", []))
for item in items:
info = item.get('ref-info', item)
volisspag = info.get('volisspag', {}) or {}
if isinstance(volisspag, list):
volisspag = volisspag[0]
volis = volisspag.get("voliss", {})
if isinstance(volis, list):
volis = volis[0]
# Parse author information
try: # FULL view parsing
auth = listify(item['ref-info']['ref-authors']['author'])
authors = [', '.join([d['ce:surname'], d['ce:initials']])
for d in auth]
auids = None
affids = None
ids = listify(info['refd-itemidlist']['itemid'])
doi = _select_by_idtype(ids, id_type='DOI')
scopus_id = _select_by_idtype(ids, id_type='SGR')
except KeyError: # REF view parsing
auth = (info.get('author-list') or {}).get('author', [])
authors = [', '.join(filter(None, [d.get('ce:surname'),
d.get('ce:given-name')]))
for d in auth]
auids = "; ".join(filter(None, [d.get('@auid') for d in auth]))
affs = filter(None, [d.get('affiliation') for d in auth])
affids = "; ".join([aff.get('@id') for aff in affs])
doi = info.get('ce:doi')
scopus_id = info.get('scopus-id')
# Combine information
new = ref(position=item.get('@id'), id=scopus_id, doi=doi,
authors="; ".join(authors), authors_auid=auids or None,
authors_affiliationid=affids or None,
title=info.get('ref-title', {}).get('ref-titletext', info.get('title')),
sourcetitle=info.get('ref-sourcetitle', info.get('sourcetitle')),
publicationyear=info.get('ref-publicationyear', {}).get('@first'),
volume=volis.get('@volume'), issue=volis.get('@issue'),
first=volisspag.get('pagerange', {}).get('@first'),
last=volisspag.get('pagerange', {}).get('@last'),
citedbycount=info.get('citedby-count'), type=info.get('type'),
text=info.get('ref-text'),
fulltext=item.get('ref-fulltext'))
out.append(new)
return out or None
def results(self) -> Optional[List[NamedTuple]]:
"""A list of namedtuples in the form (eid doi pii pubmed_id title
subtype subtypeDescription creator afid affilname affiliation_city
affiliation_country author_count author_names author_ids author_afids
coverDate coverDisplayDate publicationName issn source_id eIssn
aggregationType volume issueIdentifier article_number pageRange
description authkeywords citedby_count openaccess freetoread
freetoreadLabel fund_acr fund_no fund_sponsor).
Field definitions correspond to
https://dev.elsevier.com/guides/ScopusSearchViews.htm and return the
values as-is, except for afid, affilname, affiliation_city,
affiliation_country, author_names, author_ids and author_afids: These
information are joined on ";". In case an author has multiple
affiliations, they are joined on "-"
(e.g. Author1Aff;Author2Aff1-Author2Aff2).
Raises
------
ValueError
If the elements provided in integrity_fields do not match the
actual field names (listed above).
Notes
-----
The list of authors and the list of affiliations per author are
deduplicated.
"""
# Initiate namedtuple with ordered list of fields
fields = 'eid doi pii pubmed_id title subtype subtypeDescription ' \
'creator afid affilname affiliation_city ' \
'affiliation_country author_count author_names author_ids '\
'author_afids coverDate coverDisplayDate publicationName '\
'issn source_id eIssn aggregationType volume '\
'issueIdentifier article_number pageRange description '\
'authkeywords citedby_count openaccess freetoread '\
'freetoreadLabel fund_acr fund_no fund_sponsor'
doc = namedtuple('Document', fields)
check_field_consistency(self._integrity, fields)
# Parse elements one-by-one
out = []
for item in self._json:
info = {}
# Parse affiliations
info["affilname"] = _join(item, 'affilname')
info["afid"] = _join(item, 'afid')
info["aff_city"] = _join(item, 'affiliation-city')
info["aff_country"] = _join(item, 'affiliation-country')
# Parse authors
try:
# Deduplicate list of authors
authors = deduplicate(item['author'])
# Extract information
surnames = _replace_none([d['surname'] for d in authors])
firstnames = _replace_none([d['given-name'] for d in authors])
info["auth_names"] = ";".join([", ".join([t[0], t[1]]) for t in
zip(surnames, firstnames)])
info["auth_ids"] = ";".join([d['authid'] for d in authors])
affs = []
for auth in authors:
aff = listify(deduplicate(auth.get('afid', [])))
affs.append('-'.join([d['$'] for d in aff]))
if [a for a in affs if a]:
info["auth_afid"] = ';'.join(affs)
else:
info["auth_afid"] = None
except KeyError:
pass
date = item.get('prism:coverDate')
if isinstance(date, list):
date = date[0].get('$')
default = [None, {"$": None}]
freetoread = get_freetoread(item, ["freetoread", "value"], default)
freetoreadLabel = get_freetoread(item, ["freetoreadLabel", "value"], default)
new = doc(article_number=item.get('article-number'),
title=item.get('dc:title'), fund_no=item.get('fund-no'),
fund_sponsor=item.get('fund-sponsor'),
subtype=item.get('subtype'), doi=item.get('prism:doi'),
subtypeDescription=item.get('subtypeDescription'),
issn=item.get('prism:issn'), creator=item.get('dc:creator'),
affilname=info.get("affilname"),
author_names=info.get("auth_names"),
coverDate=date, volume=item.get('prism:volume'),
coverDisplayDate=item.get('prism:coverDisplayDate'),
publicationName=item.get('prism:publicationName'),
source_id=item.get('source-id'), author_ids=info.get("auth_ids"),
aggregationType=item.get('prism:aggregationType'),
issueIdentifier=item.get('prism:issueIdentifier'),
pageRange=item.get('prism:pageRange'),
author_afids=info.get("auth_afid"),
affiliation_country=info.get("aff_country"),
citedby_count=int(item['citedby-count']),
openaccess=int(item['openaccess']),
freetoread=freetoread, freetoreadLabel=freetoreadLabel,
eIssn=item.get('prism:eIssn'),
author_count=item.get('author-count', {}).get('$'),
affiliation_city=info.get("aff_city"), afid=info.get("afid"),
description=item.get('dc:description'), pii=item.get('pii'),
authkeywords=item.get('authkeywords'), eid=item.get('eid'),
fund_acr=item.get('fund-acr'), pubmed_id=item.get('pubmed-id'))
out.append(new)
# Finalize
check_integrity(out, self._integrity, self._action)
return out or None
def results(self):
"""A list of namedtuples in the form (eid doi pii pubmed_id title
subtype creator afid affilname affiliation_city affiliation_country
author_count author_names author_ids author_afids coverDate
coverDisplayDate publicationName issn source_id eIssn aggregationType
volume issueIdentifier article_number pageRange description
authkeywords citedby_count openaccess fund_acr fund_no fund_sponsor).
Field definitions correspond to
https://dev.elsevier.com/guides/ScopusSearchViews.htm, except for
afid, affilname, affiliation_city, affiliation_country, author_count,
author_names, author_ids and author_afids: These information are
joined on ";". In case an author has multiple affiliations, they are
joined on "-" (e.g. Author1Aff;Author2Aff1-Author2Aff2).
Notes
-----
The list of authors and the list of affiliations per author are
deduplicated.
"""
out = []
fields = 'eid doi pii pubmed_id title subtype creator afid affilname '\
'affiliation_city affiliation_country author_count '\
'author_names author_ids author_afids coverDate '\
'coverDisplayDate publicationName issn source_id eIssn '\
'aggregationType volume issueIdentifier article_number '\
'pageRange description authkeywords citedby_count '\
'openaccess fund_acr fund_no fund_sponsor'
doc = namedtuple('Document', fields)
for item in self._json:
info = {}
# Parse affiliations
try:
info["affilname"] = _join(item['affiliation'], 'affilname')
info["afid"] = _join(item['affiliation'], 'afid')
info["aff_city"] = _join(item['affiliation'],
'affiliation-city')
info["aff_country"] = _join(item['affiliation'],
'affiliation-country')
except KeyError:
pass
# Parse authors
try:
# Deduplicate list of authors
authors = _deduplicate(item['author'])
# Extract information
surnames = _replace_none([d['surname'] for d in authors])
firstnames = _replace_none([d['given-name'] for d in authors])
info["auth_names"] = ";".join([
", ".join([t[0], t[1]]) for t in zip(surnames, firstnames)
])
info["auth_ids"] = ";".join([d['authid'] for d in authors])
affs = []
for auth in authors:
aff = listify(_deduplicate(auth.get('afid', [])))
affs.append('-'.join([d['$'] for d in aff]))
info["auth_afid"] = (';'.join(affs) or None)
except KeyError:
pass
date = item.get('prism:coverDate')
if isinstance(date, list):
date = date[0].get('$')
new = doc(article_number=item.get('article-number'),
title=item.get('dc:title'),
fund_sponsor=item.get('fund-sponsor'),
subtype=item.get('subtype'),
issn=item.get('prism:issn'),
creator=item.get('dc:creator'),
affilname=info.get("affilname"),
author_names=info.get("auth_names"),
doi=item.get('prism:doi'),
coverDate=date,
volume=item.get('prism:volume'),
coverDisplayDate=item.get('prism:coverDisplayDate'),
publicationName=item.get('prism:publicationName'),
source_id=item.get('source-id'),
author_ids=info.get("auth_ids"),
aggregationType=item.get('prism:aggregationType'),
issueIdentifier=item.get('prism:issueIdentifier'),
pageRange=item.get('prism:pageRange'),
author_afids=info.get("auth_afid"),
fund_no=item.get('fund-no'),
affiliation_country=info.get("aff_country"),
citedby_count=item.get('citedby-count'),
openaccess=item.get('openaccess'),
eIssn=item.get('prism:eIssn'),
author_count=item.get('author-count', {}).get('$'),
affiliation_city=info.get("aff_city"),
afid=info.get("afid"),
description=item.get('dc:description'),
pii=item.get('pii'),
authkeywords=item.get('authkeywords'),
eid=item.get('eid'),
fund_acr=item.get('fund-acr'),
pubmed_id=item.get('pubmed-id'))
out.append(new)
return out or None
def __init__(self,
author_id: Union[int, str],
refresh: Union[bool, int] = False,
view: str = "ENHANCED",
**kwds: str) -> None:
"""Interaction with the Author Retrieval API.
:param author_id: The ID or the EID of the author.
:param refresh: Whether to refresh the cached file if it exists or not.
If int is passed, cached file will be refreshed if the
number of days since last modification exceeds that value.
:param view: The view of the file that should be downloaded. Allowed
values: METRICS, LIGHT, STANDARD, ENHANCED, where STANDARD
includes all information of LIGHT view and ENHANCED
includes all information of any view. For details see
https://dev.elsevier.com/sc_author_retrieval_views.html.
Note: Neither the BASIC nor the DOCUMENTS view are active,
although documented.
:param kwds: Keywords passed on as query parameters. Must contain
fields and values mentioned in the API specification at
https://dev.elsevier.com/documentation/AuthorRetrievalAPI.wadl.
Raises
------
ValueError
If any of the parameters `refresh` or `view` is not
one of the allowed values.
Notes
-----
The directory for cached results is `{path}/ENHANCED/{author_id}`,
where `path` is specified in your configuration file, and `author_id`
is stripped of an eventually leading `'9-s2.0-'`.
"""
# Checks
allowed_views = ('METRICS', 'LIGHT', 'STANDARD', 'ENHANCED')
check_parameter_value(view, allowed_views, "view")
# Load json
self._id = str(author_id).split('-')[-1]
self._view = view
self._refresh = refresh
Retrieval.__init__(self,
identifier=self._id,
api='AuthorRetrieval',
**kwds)
# Parse json
self._json = self._json['author-retrieval-response']
try:
self._json = self._json[0]
except KeyError: # Incomplete forward
alias_json = listify(self._json['alias']['prism:url'])
self._alias = [d['$'].split(':')[-1] for d in alias_json]
alias_str = ', '.join(self._alias)
text = f'Author profile with ID {author_id} has been merged and '\
f'the main profile is now one of {alias_str}. Please update '\
'your records manually. Functionality of this object is '\
'reduced.'
warn(text, UserWarning)
else:
self._alias = None
self._profile = self._json.get("author-profile", {})
def classificationgroup(self) -> Optional[List[Tuple[int, int]]]:
"""List with (subject group ID, number of documents)-tuples."""
path = ['classificationgroup', 'classifications', 'classification']
out = [(int(item['$']), int(item['@frequency']))
for item in listify(chained_get(self._profile, path, []))]
return out or None