Source code for scopus.scopus_search

import warnings
from collections import namedtuple

from scopus.classes import Search
from scopus.utils import listify

[docs]class ScopusSearch(Search): @property def EIDS(self): """Outdated property, will be removed in a future release. Please use get_eids() instead. For details see """ text = "Outdated property, will be removed in a future release. "\ "Please use get_eids() instead. For details see "\ ""\ "migration-guide-to-0-x-to-1-x." warnings.warn(text, DeprecationWarning) return self.get_eids() @property 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, 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['eid'], fund_acr=item.get('fund-acr'), pubmed_id=item.get('pubmed-id')) out.append(new) return out or None def __init__(self, query, refresh=False, subscriber=True, view=None, download=True, **kwds): """Class to perform a query against the Scopus Search API. Parameters ---------- query : str A string of the query. refresh : bool (optional, default=False) Whether to refresh the cached file if it exists or not. subscriber : bool (optional, default=True) Whether the user accesses Scopus with a subscription or not. For subscribers, Scopus's cursor navigation will be used. Sets the number of entries in each query iteration to the maximum number allowed by the corresponding view. view : str (optional, default=None) Which view to use for the query, see Allowed values: STANDARD, COMPLETE. If None, defaults to COMPLETE if subscriber=True and to STANDARD if subscriber=False. cursor : bool (optional, default=True) Whether to use Scopus's cursor navigation to obtain results. Using the cursor allows to download an unlimited results set. Non-subscribers should set this to False. download : bool (optional, default=True) Whether to download results (if they have not been cached). kwds : key-value parings, optional Keywords passed on as query parameters. Must contain fields and values listed mentioned in the API specification (, such as "field" or "date". Raises ------ ScopusQueryError For non-subscribers, if the number of search results exceeds 5000. ValueError If the view parameter is not one of the allowed ones. Notes ----- Json results are cached in ~/.scopus/scopus_search/{fname}, where fname is the md5-hashed version of query. """ # Checks allowed_views = ('STANDARD', 'COMPLETE') if view and view not in allowed_views: raise ValueError('view parameter must be one of ' + ', '.join(allowed_views)) # Parameters if not view: if subscriber: view = "COMPLETE" else: view = "STANDARD" count = 25 if view == "STANDARD" and subscriber: count = 200 # Query self.query = query Search.__init__(self, query=query, api='ScopusSearch', refresh=refresh, count=count, cursor=subscriber, view=view, download_results=download, **kwds) def __str__(self): eids = self.get_eids() s = """Search {} yielded {} document(s):\n {}""" return s.format(self.query, len(eids), '\n '.join(eids))
[docs] def get_eids(self): """EIDs of retrieved documents.""" return [d['eid'] for d in self._json]
def _deduplicate(lst): """Auxiliary function to deduplicate lst.""" out = [] for i in lst: if i not in out: out.append(i) return out def _join(lst, key, sep=";"): """Auxiliary function to join same elements of a list of dictionaries if the elements are not None. """ return sep.join([d[key] for d in lst if d[key]]) def _replace_none(lst, repl=""): """Auxiliary function to replace None's with another value.""" return ['' if v is None else v for v in lst]