def test_to_paper(self, container_title, title, citeproc):
p = self.test_class.to_paper(citeproc)
# Ensure that paper is in database (i.e. created)
assert p.pk >= 1
# Check paper fields
for author_p, author_c in zip(p.authors_list, citeproc['author']):
assert author_p['name']['first'] == author_c['given']
assert author_p['name']['last'] == author_c['family']
assert author_p['affiliation'] == author_c['affiliation'][0][
'name']
assert author_p['orcid'] == author_c['ORCID']
assert p.pubdate == date(*citeproc['issued']['date-parts'][0])
assert p.title == title
# Ensure that oairecord is in database (i.e. created)
r = OaiRecord.objects.get(about=p)
# Check oairecord fields
assert r.doi == citeproc['DOI']
assert r.identifier == doi_to_crossref_identifier(citeproc['DOI'])
assert r.issue == citeproc['issue']
assert r.journal_title == container_title
assert r.pages == citeproc['page']
assert r.pubdate == date(*citeproc['issued']['date-parts'][0])
assert r.publisher_name == citeproc['publisher']
assert r.source == OaiSource.objects.get(identifier='crossref')
assert r.splash_url == doi_to_url(citeproc['DOI'])
assert r.volume == citeproc['volume']
def redirect_by_doi(request, doi):
"""
This view is inherited from doai.io, migrated to this code base
to preserve the existing behaviour. We could instead
redirect to unpaywall, but that would not include ResearchGate urls.
"""
doi = unquote(doi)
doi = to_doi(doi)
if not doi:
raise Http404(_("Invalid DOI."))
paper = Paper.get_by_doi(doi)
if paper and paper.pdf_url:
return HttpResponsePermanentRedirect(paper.pdf_url)
return HttpResponsePermanentRedirect(doi_to_url(doi))
def create_oairecord(self, record):
"""
Given one line of the dump (represented as a dict),
add it to the corresponding paper (if it exists)
"""
doi = to_doi(record['doi'])
if not doi:
return
prefix = doi.split('/')[0]
if prefix in free_doi_prefixes:
return
paper = Paper.get_by_doi(doi)
if not paper:
try:
paper = Paper.create_by_doi(doi)
except (MetadataSourceException, ValueError):
return
if not paper:
print('no such paper for doi {doi}'.format(doi=doi))
return
url = record['url']
# just to speed things up a bit...
if paper.pdf_url == url:
return
identifier = 'oadoi:' + url
source = self.oadoi_source
if record['host_type'] == 'publisher':
url = doi_to_url(doi)
identifier = doi_to_crossref_identifier(doi)
source = self.crossref_source
record = BareOaiRecord(paper=paper,
doi=doi,
pubtype=paper.doctype,
source=source,
identifier=identifier,
splash_url=url,
pdf_url=record['url'])
try:
paper.add_oairecord(record)
paper.update_availability()
# TODO re-enable this
#paper.update_index()
except (DataError, ValueError):
print('Record does not fit in the DB')
def redirect_by_doi(request, doi):
"""
This view is inherited from doai.io, migrated to this code base
to preserve the existing behaviour. We could instead
redirect to unpaywall, but that would not include ResearchGate urls.
"""
doi = unquote(doi)
doi = to_doi(doi)
if not doi:
raise Http404(_("Invalid DOI."))
paper = Paper.get_by_doi(doi)
if paper and paper.pdf_url:
return HttpResponsePermanentRedirect(paper.pdf_url)
return HttpResponsePermanentRedirect(doi_to_url(doi))
def citation_dict(self):
"""
Dictionary representation of the paper, for citation purposes, based on
the internal model used by Python-bibtexparser.
"""
entry = {
'ENTRYTYPE': PAPER_TYPE_TO_BIBTEX.get(self.doctype, 'misc'),
'ID': (
'%s%s' % (
self.authors[0].name.last,
self.pubdate.year
)
),
'title': self.title,
'author': ' and '.join([
'%s, %s' % (a.name.last, a.name.first)
for a in self.authors
])
}
for publi in self.publications[:3]:
if publi.volume:
entry['volume'] = publi.volume
if publi.pages:
entry['pages'] = publi.pages
if publi.journal:
entry['journal'] = publi.journal.title
elif publi.journal_title:
entry['journal'] = publi.journal_title
if self.pubdate:
entry['month'] = self.pubdate.strftime('%b').lower()
entry['year'] = self.pubdate.strftime('%Y')
if self.abstract:
entry['abstract'] = self.abstract
doi = self.get_doi()
if self.pdf_url:
entry['url'] = self.pdf_url
if doi:
entry['doi'] = doi
if not self.pdf_url:
entry['url'] = doi_to_url(doi)
return entry
def test_get_oairecord_data(self, db, monkeypatch, container_title, issn,
citeproc, journal):
"""
We do some assertions on the results, but relatively lax, as we test the called functions, too
"""
monkeypatch.setattr(Journal, 'find', lambda issn, title: journal)
r = self.test_class._get_oairecord_data(citeproc)
assert r['doi'] == citeproc['DOI']
assert r['description'] == citeproc['abstract']
assert r['identifier'] == doi_to_crossref_identifier(citeproc['DOI'])
assert r['issn'] == issn
assert r['issue'] == citeproc['issue']
assert r['journal'] == journal
assert r['journal_title'] == container_title
assert r['pages'] == citeproc['page']
assert r['pdf_url'] == '' # Is not OA
assert r['pubdate'] == date(*citeproc['issued']['date-parts'][0])
assert r['publisher_name'] == citeproc['publisher']
assert r['pubtype'] == citeproc['type']
assert r['source'] == OaiSource.objects.get(identifier='crossref')
assert r['splash_url'] == doi_to_url(citeproc['DOI'])
assert r['volume'] == citeproc['volume']
def _get_oairecord_data(cls, data):
"""
:param data: citeproc metadata
:returns: Returns a dict, ready to passed to a BarePaper instance
:raises: CiteprocError
"""
doi = cls._get_doi(data)
splash_url = doi_to_url(doi)
licenses = data.get('licenses', [])
pdf_url = cls._get_pdf_url(doi, licenses, splash_url)
journal_title = cls._get_container(data)
issn = cls._get_issn(data)
journal = Journal.find(issn=issn, title=journal_title)
publisher_name = data.get('publisher', '')[:512]
publisher = cls._get_publisher(publisher_name, journal)
bare_oairecord_data = {
'doi': doi,
'description': cls._get_abstract(data),
'identifier': doi_to_crossref_identifier(doi),
'issn': issn,
'issue': data.get('issue', ''),
'journal': journal,
'journal_title': journal_title,
'pages': data.get('page', ''),
'pdf_url': pdf_url,
'pubdate': cls._get_pubdate(data),
'publisher': publisher,
'publisher_name': publisher_name,
'pubtype': cls._get_pubtype(data),
'source': OaiSource.objects.get(identifier='crossref'),
'splash_url': splash_url,
'volume': data.get('volume', ''),
}
return bare_oairecord_data
def test_fallback(self):
self.checkPermanentRedirect('paper-redirect-doi', kwargs={'doi': '10.1385/1592597998'},
url=doi_to_url('10.1385/1592597998'))
def test_fallback(self, check_permanent_redirect):
check_permanent_redirect('paper-redirect-doi',
kwargs={'doi': '10.1385/1592597998'},
url=doi_to_url('10.1385/1592597998'))
def _create_publication(paper, metadata):
if not metadata:
return
if not metadata.get('container-title'):
return
doi = to_doi(metadata.get('DOI', None))
title = metadata['container-title']
if isinstance(title, list):
title = title[0]
title = title[:512]
issn = metadata.get('ISSN', None)
if issn and isinstance(issn, list):
issn = issn[0] # TODO pass all the ISSN to the RoMEO interface
volume = metadata.get('volume', None)
pages = metadata.get('page', None)
issue = metadata.get('issue', None)
date_dict = metadata.get('issued', dict())
pubdate = None
if 'date-parts' in date_dict:
dateparts = date_dict.get('date-parts')[0]
pubdate = date_from_dateparts(dateparts)
# for instance it outputs dates like 2014-2-3
publisher_name = metadata.get('publisher', None)
if publisher_name:
publisher_name = publisher_name[:512]
pubtype = metadata.get('type', 'unknown')
pubtype = CROSSREF_PUBTYPE_ALIASES.get(pubtype, pubtype)
splash_url = doi_to_url(doi)
# PDF availability
pdf_url = None
licenses = set([(license or {}).get('URL')
for license in metadata.get('license', [])])
doi_prefix = doi.split('/')[0]
if doi_prefix in free_doi_prefixes or any(map(is_oa_license, licenses)):
pdf_url = splash_url
# Lookup journal
search_terms = {'jtitle': title}
if issn:
search_terms['issn'] = issn
journal = fetch_journal(search_terms)
publisher = None
if journal:
publisher = journal.publisher
AliasPublisher.increment(publisher_name, journal.publisher)
else:
publisher = fetch_publisher(publisher_name)
barepub = BareOaiRecord(
paper=paper,
journal_title=title,
issue=issue,
volume=volume,
pubdate=pubdate,
pages=pages,
doi=doi,
pubtype=pubtype,
publisher_name=publisher_name,
journal=journal,
publisher=publisher,
pdf_url=pdf_url,
splash_url=splash_url,
source=OaiSource.objects.get(identifier='crossref'),
identifier=doi_to_crossref_identifier(doi))
rec = paper.add_oairecord(barepub)
paper.update_availability()
return paper, rec
def test_doi_to_url(self):
self.assertEqual(doi_to_url('10.1093/jhmas/xxxi.4.480'),
'https://doi.org/10.1093/jhmas/xxxi.4.480')
def _create_publication(paper, metadata):
if not metadata:
return
if not metadata.get('container-title'):
return
doi = to_doi(metadata.get('DOI', None))
title = metadata['container-title']
if isinstance(title, list):
title = title[0]
title = title[:512]
issn = metadata.get('ISSN', None)
if issn and isinstance(issn, list):
issn = issn[0] # TODO pass all the ISSN to the RoMEO interface
volume = metadata.get('volume', None)
pages = metadata.get('page', None)
issue = metadata.get('issue', None)
date_dict = metadata.get('issued', dict())
pubdate = None
if 'date-parts' in date_dict:
dateparts = date_dict.get('date-parts')[0]
pubdate = date_from_dateparts(dateparts)
# for instance it outputs dates like 2014-2-3
publisher_name = metadata.get('publisher', None)
if publisher_name:
publisher_name = publisher_name[:512]
pubtype = metadata.get('type', 'unknown')
pubtype = CROSSREF_PUBTYPE_ALIASES.get(pubtype, pubtype)
splash_url = doi_to_url(doi)
# PDF availability
pdf_url = None
licenses = set([(license or {}).get('URL')
for license in metadata.get('license', [])])
doi_prefix = doi.split('/')[0]
if doi_prefix in free_doi_prefixes or any(map(is_oa_license, licenses)):
pdf_url = splash_url
# Lookup journal
journal = Journal.find(issn=issn, title=title)
publisher = None
if journal:
publisher = journal.publisher
AliasPublisher.increment(publisher_name, journal.publisher)
else:
publisher = Publisher.find(publisher_name)
barepub = BareOaiRecord(
paper=paper,
journal_title=title,
issue=issue,
volume=volume,
pubdate=pubdate,
pages=pages,
doi=doi,
pubtype=pubtype,
publisher_name=publisher_name,
journal=journal,
publisher=publisher,
pdf_url=pdf_url,
splash_url=splash_url,
source=OaiSource.objects.get(identifier='crossref'),
identifier=doi_to_crossref_identifier(doi))
rec = paper.add_oairecord(barepub)
paper.update_availability()
return paper, rec
def _create_publication(paper, metadata):
if not metadata:
return
if not 'container-title' in metadata or not metadata['container-title']:
return
doi = to_doi(metadata.get('DOI',None))
title = metadata['container-title']
if type(title) == type([]):
title = title[0]
title = title[:512]
issn = metadata.get('ISSN',None)
if issn and type(issn) == type([]):
issn = issn[0] # TODO pass all the ISSN to the RoMEO interface
volume = metadata.get('volume',None)
pages = metadata.get('page',None)
issue = metadata.get('issue',None)
date_dict = metadata.get('issued',dict())
pubdate = None
if 'date-parts' in date_dict:
dateparts = date_dict.get('date-parts')[0]
pubdate = date_from_dateparts(dateparts)
# for instance it outputs dates like 2014-2-3
publisher_name = metadata.get('publisher', None)
if publisher_name:
publisher_name = publisher_name[:512]
pubtype = metadata.get('type','unknown')
pubtype = CROSSREF_PUBTYPE_ALIASES.get(pubtype, pubtype)
# PDF availability
pdf_url = None
licenses = set([(license or {}).get('URL') for license in metadata.get('license', [])])
if any(map(is_oa_license, licenses)):
pdf_url = doi_to_url(doi)
splash_url = doi_to_url(doi)
# Lookup journal
search_terms = {'jtitle':title}
if issn:
search_terms['issn'] = issn
journal = fetch_journal(search_terms)
publisher = None
if journal:
publisher = journal.publisher
AliasPublisher.increment(publisher_name, journal.publisher)
else:
publisher = fetch_publisher(publisher_name)
barepub = BareOaiRecord(
paper=paper,
journal_title=title,
issue=issue,
volume=volume,
pubdate=pubdate,
pages=pages,
doi=doi,
pubtype=pubtype,
publisher_name=publisher_name,
journal=journal,
publisher=publisher,
pdf_url=pdf_url,
splash_url=splash_url,
source=crossref_oai_source,
identifier=doi_to_crossref_identifier(doi))
rec = paper.add_oairecord(barepub)
paper.update_availability()
return paper, rec
def create_oairecord(self, record, update_index=True, create_missing_dois=True):
"""
Given one line of the dump (represented as a dict),
add it to the corresponding paper (if it exists)
"""
doi = to_doi(record['doi'])
if not doi:
return
prefix = doi.split('/')[0]
if prefix in free_doi_prefixes:
return
if not record.get('oa_locations'):
return
paper = Paper.get_by_doi(doi)
if not paper:
if not create_missing_dois:
return
try:
paper = Paper.create_by_doi(doi)
except (MetadataSourceException, ValueError):
return
if not paper:
logger.info('no such paper for doi {doi}'.format(doi=doi))
return
logger.info(doi)
paper.cache_oairecords()
for oa_location in record.get('oa_locations') or []:
url = oa_location['url']
# just to speed things up a bit...
if paper.pdf_url == url:
return
identifier='oadoi:'+url
source = self.oadoi_source
if oa_location['host_type'] == 'publisher':
url = doi_to_url(doi)
identifier = doi_to_crossref_identifier(doi)
source = self.crossref_source
record = BareOaiRecord(
paper=paper,
doi=doi,
pubtype=paper.doctype,
source=source,
identifier=identifier,
splash_url=url,
pdf_url=oa_location['url'])
try:
# We disable checks by DOI since we know the paper has been looked up by DOI already.
old_pdf_url = paper.pdf_url
paper.add_oairecord(record, check_by_doi=False)
super(Paper, paper).update_availability()
if old_pdf_url != paper.pdf_url:
paper.save()
if update_index:
paper.update_index()
except (DataError, ValueError):
logger.warning('Record does not fit in the DB')
