def classificationgroup(self):
"""List with (subject group ID, number of documents)-tuples."""
path = ['author-profile', 'classificationgroup', 'classifications',
'classification']
out = [(item['$'], item['@frequency']) for item in
listify(chained_get(self._json, path, []))]
return out or None
def isbn(self):
"""ISBNs belonging to publicationName as tuple of variying length,
(e.g. ISBN-10 or ISBN-13)."""
isbns = listify(chained_get(self._head, ['source', 'isbn'], []))
if len(isbns) == 0:
return None
else:
return tuple((i['$'] for i in isbns))
def confsponsor(self):
"""Sponsor(s) of the conference the abstract belongs to."""
sponsors = chained_get(self._confevent, ['confsponsors', 'confsponsor'], [])
if len(sponsors) == 0:
return None
if isinstance(sponsors, list):
return [s['$'] for s in sponsors]
return sponsors
def name_variants(self):
"""A list of namedtuples representing variants of the affiliation name
with number of documents referring to this variant.
"""
out = []
variant = namedtuple('Variant', 'name doc_count')
for var in chained_get(self._json, ['name-variants', 'name-variant'], []):
new = variant(name=var['$'], doc_count=var.get('@doc-count'))
out.append(new)
return out
def subject_areas(self):
"""List of named tuples of subject areas in the form
(area, abbreviation, code) of author's publication.
"""
path = ['subject-areas', 'subject-area']
area = namedtuple('Subjectarea', 'area abbreviation code')
areas = [area(area=item['$'], code=item['@code'],
abbreviation=item['@abbrev'])
for item in chained_get(self._json, path, [])]
return areas or None
def subject_areas(self):
"""List of namedtuples containing subject areas of the article
in the form ().
Note: Requires the FULL view of the article.
"""
area = namedtuple('Area', 'area abbreviation code')
path = ['subject-areas', 'subject-area']
out = [area(area=item['$'], abbreviation=item['@abbrev'],
code=item['@code'])
for item in listify(chained_get(self._json, path, []))]
return out or None
def publisher(self):
"""Name of the publisher of the abstract.
Note: Information provided in the FULL view of the article might be
more complete.
"""
# Return information from FULL view, fall back to other views
full = chained_get(self._head, ['source', 'publisher', 'publishername'])
if full is None:
return self._json['coredata'].get('dc:publisher')
else:
return full
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['sourcetitle'], issn=pub.get('issn'),
abbreviation=pub.get('sourcetitle-abbrev'),
type=pub['@type'])
for pub in listify(chained_get(self._json, path, []))]
return hist 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)
path = ['author-profile', 'name-variant']
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(chained_get(self._json, path, []))]
return out or None
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 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['$'],
type=number['@type'])
out.append(new)
return out or None
def contributor_group(self):
"""List of namedtuples representing contributors compiled by Scopus,
in the form (given_name, initials, surname, indexed_name, role).
"""
items = listify(chained_get(self._head, ['source', 'contributor-group'], []))
out = []
fields = 'given_name initials surname indexed_name role'
pers = namedtuple('Contributor', fields)
for item in items:
entry = item.get('contributor', {})
new = pers(indexed_name=entry.get('ce:indexed-name'),
role=entry.get('@role'), surname=entry.get('ce:surname'),
given_name=entry.get('ce:given-name'),
initials=entry.get('ce:initials'))
out.append(new)
return out or None
def funding(self):
"""List of namedtuples parsed funding information in the form
(agency string id acronym country).
"""
path = ['item', 'xocs:meta', 'xocs:funding-list', 'xocs:funding']
funds = listify(chained_get(self._json, path, []))
out = []
fund = namedtuple('Funding', 'agency string id acronym country')
for item in funds:
new = fund(agency=item.get('xocs:funding-agency'),
string=item.get('xocs:funding-agency-matched-string'),
id=item.get('xocs:funding-agency-id'),
acronym=item.get('xocs:funding-agency-acronym'),
country=item.get('xocs:funding-agency-country'))
out.append(new)
return out or None
def chemicals(self):
"""List of namedtuples representing chemical entities in the form
(source, chemical_name, cas_registry_number). In case multiple
numbers given, they are joined on ";".
"""
path = ['enhancement', 'chemicalgroup', 'chemicals']
items = listify(chained_get(self._head, path, []))
chemical = namedtuple('Chemical', 'source chemical_name cas_registry_number')
out = []
for item in items:
for chem in listify(item['chemical']):
number = chem.get('cas-registry-number')
try: # Multiple numbers given
num = ";".join([n['$'] 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 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', []))
for item in items:
# 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, ['preferred-name', 'ce:indexed-name']))
out.append(new)
return out or None
def state(self):
"""The state (country's administrative sububunit) of the affiliation."""
path = ['institution-profile', 'address', 'state']
return chained_get(self._json, path)
def refcount(self):
"""Number of references of an article.
Note: Requires the FULL view of the article.
"""
path = ['item', 'bibrecord', 'tail', 'bibliography', '@refcount']
return chained_get(self._json, path)
def publisheraddress(self):
"""Name of the publisher of the abstract."""
return chained_get(self._head, ['source', 'publisher', 'publisheraddress'])
def surname(self):
"""Author's preferred surname."""
path = ['author-profile', 'preferred-name', 'surname']
return chained_get(self._json, path)
def status(self):
"""The status of the author profile."""
return chained_get(self._json, ["author-profile", "status"])
def indexed_name(self):
"""Author's name as indexed by Scopus."""
path = ['author-profile', 'preferred-name', 'indexed-name']
return chained_get(self._json, path)
def given_name(self):
"""Author's preferred given name."""
path = ['author-profile', 'preferred-name', 'given-name']
return chained_get(self._json, path)
def website(self):
"""Website of publisher."""
return chained_get(self._head, ['source', 'website', 'ce:e-address', '$'])
def funding_text(self):
"""The raw text from which Scopus derives funding information."""
path = ['item', 'xocs:meta', 'xocs:funding-list', 'xocs:funding-text']
return chained_get(self._json, path)
def references(self):
"""List of namedtuples representing references listed in the abstract,
in the form (position, id, doi, title, authors, authors_auid,
authors_affiliationid, sourcetitle, publicationyear, volume, issue, first,
last, citedbycount, text, fulltext).
`position` is the number at which the reference appears in the
document, `id` is the Scopus ID of the referenced abstract (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, `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 of the article. Might
be empty even if refcount is positive. Specific fields can be empty.
Author lists (authors, authors_auid, authors_affiliationid) may contain
duplicates but have been filtered of None's.
"""
out = []
fields = 'position id doi title authors authors_auid '\
'authors_affiliationid sourcetitle publicationyear volume '\
'issue first last citedbycount text fulltext'
ref = namedtuple('Reference', fields)
path = ['item', 'bibrecord', 'tail', 'bibliography', 'reference']
items = listify(chained_get(self._json, path,
self._json.get('references', {}).get('reference', [])))
for item in items:
info = item.get('ref-info', item)
volisspag = info.get('volisspag', {}) or {}
if isinstance(volisspag, list):
volisspag = volisspag[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
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])
# Parse IDs
try:
ids = listify(info['refd-itemidlist']['itemid'])
except KeyError:
ids = []
try:
doi = _select_by_idtype(ids, 'DOI')[0]
except IndexError:
doi = info.get('ce:doi')
try:
scopus_id = _select_by_idtype(ids, 'SGR')[0]
except IndexError:
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=volisspag.get('voliss', {}).get('@volume'),
issue=volisspag.get('voliss', {}).get('@issue'),
first=volisspag.get('pagerange', {}).get('@first'),
last=volisspag.get('pagerange', {}).get('@last'),
citedbycount=info.get('citedby-count'),
text=info.get('ref-text'),
fulltext=item.get('ref-fulltext'))
out.append(new)
return out or None
def refcount(self):
"""Number of references of an article.
Note: Requires the FULL view of the article.
"""
path = ['item', 'bibrecord', 'tail', 'bibliography', '@refcount']
return chained_get(self._json, path)
def postal_code(self):
"""The postal code of the affiliation."""
path = ['institution-profile', 'address', 'postal-code']
return chained_get(self._json, path)
def references(self):
"""List of namedtuples representing references listed in the abstract,
in the form (position, id, doi, title, authors, authors_auid,
authors_affiliationid, sourcetitle, publicationyear, volume, issue, first,
last, citedbycount, text, fulltext).
`position` is the number at which the reference appears in the
document, `id` is the Scopus ID of the referenced abstract (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, `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 of the article. Might
be empty even if refcount is positive. Specific fields can be empty.
Author lists (authors, authors_auid, authors_affiliationid) may contain
duplicates but have been filtered of None's.
"""
out = []
fields = 'position id doi title authors authors_auid '\
'authors_affiliationid sourcetitle publicationyear volume '\
'issue first last citedbycount text fulltext'
ref = namedtuple('Reference', fields)
path = ['item', 'bibrecord', 'tail', 'bibliography', 'reference']
items = listify(
chained_get(self._json, path,
self._json.get('references', {}).get('reference', [])))
for item in items:
info = item.get('ref-info', item)
volisspag = info.get('volisspag', {}) or {}
if isinstance(volisspag, list):
volisspag = volisspag[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
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])
# Parse IDs
try:
ids = listify(info['refd-itemidlist']['itemid'])
except KeyError:
ids = []
try:
doi = [d['$'] for d in ids if d['@idtype'] == 'DOI'][0]
except IndexError:
doi = info.get('ce:doi')
try:
scopus_id = [d['$'] for d in ids if d['@idtype'] == 'SGR'][0]
except IndexError:
scopus_id = info.get('scopus-id')
# Combine information
new = ref(position=item.get('@id'),
id=scopus_id,
doi=doi,
authors="; ".join(authors),
authors_auid=auids or None,
authors_affiliationid=affids or None,
title=info.get('ref-title',
{}).get('ref-titletext',
info.get('title')),
sourcetitle=info.get('ref-sourcetitle',
info.get('sourcetitle')),
publicationyear=info.get('ref-publicationyear',
{}).get('@first'),
volume=volisspag.get('voliss', {}).get('@volume'),
issue=volisspag.get('voliss', {}).get('@issue'),
first=volisspag.get('pagerange', {}).get('@first'),
last=volisspag.get('pagerange', {}).get('@last'),
citedbycount=info.get('citedby-count'),
text=info.get('ref-text'),
fulltext=item.get('ref-fulltext'))
out.append(new)
return out or None
def initials(self):
"""Author's preferred initials."""
path = ['author-profile', 'preferred-name', 'initials']
return chained_get(self._json, path)
def state(self):
"""The state (country's administrative sububunit) of the affiliation."""
path = ['institution-profile', 'address', 'state']
return chained_get(self._json, path)
def postal_code(self):
"""The postal code of the affiliation."""
path = ['institution-profile', 'address', 'postal-code']
return chained_get(self._json, path)
def funding_text(self):
"""The raw text from which Scopus derives funding information."""
path = ['item', 'xocs:meta', 'xocs:funding-list', 'xocs:funding-text']
return chained_get(self._json, path)
def website(self):
"""Website of publisher."""
return chained_get(self._head,
['source', 'website', 'ce:e-address', '$'])
def publisheraddress(self):
"""Name of the publisher of the abstract."""
return chained_get(self._head,
['source', 'publisher', 'publisheraddress'])
def __init__(self, identifier=None, view='META_ABS', refresh=False,
id_type=None, EID=None):
"""Class to represent the results from a Scopus abstract.
Parameters
----------
identifier : str or int
The identifier of an abstract. Can be the Scoups EID, the Scopus
ID, the PII, the Pubmed-ID or the DOI.
EID : str (deprecated since 1.2)
Deprecated in favor of `identifier`, will be removed in a future
release.
id_type: str (optional, default=None)
The type of used ID. Allowed values: None, 'eid', 'pii',
'scopus_id', 'pubmed_id', 'doi'. If the value is None, the
function tries to infer the ID type itself.
view : str (optional, default=META_ABS)
The view of the file that should be downloaded. Will not take
effect for already cached files. Allowed values: META, META_ABS,
REF, FULL, where FULL includes all information of META_ABS view
and META_ABS includes all information of the META view. See
https://dev.elsevier.com/guides/AbstractRetrievalViews.htm
for details.
refresh : bool (optional, default=False)
Whether to refresh the cached file if it exists or not.
Raises
------
ValueError
If the id_type parameter or the view parameter contains
invalid entries.
Notes
-----
The files are cached in ~/.scopus/abstract_retrieval/{identifier}. In
case a DOI is used as identifier, an underscore replaces the forward
slash in the filename.
"""
# Checks
if identifier is None and EID:
text = "Parameter EID is deprecated in favor of parameter "\
"identifier. Please update your code."
warn(text, UserWarning)
identifier = EID
identifier = str(identifier)
allowed_views = ('META', 'META_ABS', 'REF', 'FULL')
if view not in allowed_views:
raise ValueError('view parameter must be one of ' +
', '.join(allowed_views))
if id_type is None:
id_type = detect_id_type(identifier)
else:
allowed_id_types = ('eid', 'pii', 'scopus_id', 'pubmed_id', 'doi')
if id_type not in allowed_id_types:
raise ValueError('id_type parameter must be one of ' +
', '.join(allowed_id_types))
# Load json
Retrieval.__init__(self, identifier=identifier, id_type=id_type,
api='AbstractRetrieval', refresh=refresh, view=view)
self._json = self._json['abstracts-retrieval-response']
self._head = chained_get(self._json, ["item", "bibrecord", "head"], {})
path = ['source', 'additional-srcinfo', 'conferenceinfo', 'confevent']
self._confevent = chained_get(self._head, path, {})
def language(self):
"""Language of the article."""
return chained_get(self._json, ['language', '@xml:lang'])
def historical_identifier(self):
"""Scopus IDs of previous profiles now compromising this profile."""
hist = chained_get(self._json, ["coredata", 'historical-identifier'], [])
return [d['$'].split(":")[-1] for d in hist] or None
def language(self):
"""Language of the article."""
return chained_get(self._json, ['language', '@xml:lang'])
