def test_create(self):
"""
BarePaper.create checks its arguments are non-empty
"""
names = [
BareName.create('Peter', 'Johnstone'),
BareName.create('Xing', 'Li')
]
pubdate = datetime.date(year=2014, month=9, day=4)
# No title
self.assertRaises(ValueError, BarePaper.create, '', names, pubdate)
# No authors
self.assertRaises(ValueError, BarePaper.create, 'Excellent title', [],
pubdate)
# No publication date
self.assertRaises(ValueError, BarePaper.create, 'Excellent title',
names, None)
# Invalid visibility
self.assertRaises(ValueError,
BarePaper.create,
'Excellent title',
names,
pubdate,
visible="something")
# Not enough affiliations
self.assertRaises(ValueError,
BarePaper.create,
'Excellent title',
names,
pubdate,
affiliations=['ENS'])
def convert_authors(self, authors, orcids):
names = [BareName.create_bare(first, last) for first, last in authors]
names_and_orcids = zip(names, orcids)
filtered = [(n, o) for n, o in names_and_orcids if n is not None]
final_names = [n for n, o in filtered]
final_orcids = [o for n, o in filtered]
return final_names, final_orcids
def get_oai_authors(self, metadata):
"""
Get the authors names out of a metadata record
"""
parsed = list(map(parse_comma_name, metadata['creator']))
names = [BareName.create_bare(fst, lst) for fst, lst in parsed]
return names
def get_oai_authors(self, metadata):
"""
Get the authors names out of a metadata record
"""
parsed = list(map(parse_comma_name, metadata['creator']))
names = [BareName.create_bare(fst, lst) for fst, lst in parsed]
return names
def test_merge(self):
# Get a paper with CrossRef metadata
p = Paper.create_by_doi('10.1111/j.1744-6570.1953.tb01038.x')
p = Paper.from_bare(p)
# Create a copy with slight variations
names = [BareName.create_bare(f, l) for (f, l) in
[('M. H.', 'Jones'), ('R. H.', 'Haase'), ('S. F.', 'Hulbert')]]
p2 = Paper.get_or_create(
'A Survey of the Literature on Technical Positions', names,
date(year=2011, month=0o1, day=0o1))
# The two are not merged because of the difference in the title
self.assertNotEqual(p, p2)
# Fix the title of the second one
p2.title = 'A Survey of the Literature on Job Analysis of Technical Positions'
p2.save()
# Check that the new fingerprint is equal to that of the first paper
self.assertEqual(p2.new_fingerprint(), p.fingerprint)
# and that the new fingerprint and the current differ
self.assertNotEqual(p2.new_fingerprint(), p2.fingerprint)
# and that the first paper matches its own shit
self.assertEqual(Paper.objects.filter(
fingerprint=p.fingerprint).first(), p)
# The two papers should hence be merged together
new_paper = p2.recompute_fingerprint_and_merge_if_needed()
self.assertEqual(new_paper.pk, p.pk)
def test_update_authors(self):
for old_author_names, new_author_names, final in [
([('G.', 'Bodenhausen')],
[('Geoffrey', 'Bodenhausen')],
[('Geoffrey', 'Bodenhausen')]),
([('L. F.', 'Jullien'), ('A.', 'Amarilli')],
[('Ludovic', 'Jullien'), ('R.', 'Pérand'), ('Antoine', 'Amarilli')],
[('Ludovic F.', 'Jullien'), ('R.', 'Pérand'), ('Antoine', 'Amarilli')]),
]:
paper = Paper.get_or_create('This is a test paper',
[BareName.create_bare(f, l) for (
f, l) in old_author_names],
datetime.date(year=2015, month=0o4, day=0o5))
new_authors = [BareAuthor(name=BareName.create_bare(f, l))
for (f, l) in new_author_names]
paper.update_authors(new_authors)
self.assertEqual(paper.bare_author_names(), final)
def test_paper_with_empty_slug(self):
"""
Papers may have titles with characters that
are all ignored by slugify.
"""
p = Paper.get_or_create('!@#$%^*()',
[BareName.create('Jean', 'Saisrien')],
datetime.date(2016, 7, 2))
self.assertEqual(p.slug, '')
self.checkPage('paper', args=[p.pk, p.slug])
def test_add_author(self):
"""
p.add_author adds the author at the right place
"""
names = [BareName.create('Peter', 'Johnstone'),
BareName.create('Xing', 'Li'),
BareName.create('John', 'Dubuc')]
p = BarePaper.create('The title', [names[0]],
datetime.date(year=2012, month=1, day=9))
p.add_author(BareAuthor(name=names[2]))
self.assertEqual(len(p.authors), 2)
p.add_author(BareAuthor(name=names[1]), position=1)
self.assertListEqual(p.author_names(), names)
self.assertRaises(ValueError, p.add_author,
BareAuthor(name=BareName.create(
'Cantor', 'Bernstein')),
position=8)
def test_update_authors(self):
for old_author_names, new_author_names, final in [
([('G.', 'Bodenhausen')], [('Geoffrey', 'Bodenhausen')],
[('Geoffrey', 'Bodenhausen')]),
([('L. F.', 'Jullien'), ('A.', 'Amarilli')
], [('Ludovic', 'Jullien'), ('R.', 'Pérand'),
('Antoine', 'Amarilli')], [('Ludovic F.', 'Jullien'),
('R.', 'Pérand'),
('Antoine', 'Amarilli')]),
]:
paper = Paper.get_or_create(
'This is a test paper',
[BareName.create_bare(f, l) for (f, l) in old_author_names],
datetime.date(year=2015, month=0o4, day=0o5))
new_authors = [
BareAuthor(name=BareName.create_bare(f, l))
for (f, l) in new_author_names
]
paper.update_authors(new_authors)
self.assertEqual(paper.bare_author_names(), final)
def test_paper_with_empty_slug(self, db, check_page):
"""
Papers may have titles with characters that
are all ignored by slugify.
"""
p = Paper.get_or_create('!@#$%^*()',
[BareName.create('Jean', 'Saisrien')],
datetime.date(2016, 7, 2))
p.visible = True # Force paper to be visible even if it an orphan
p.save()
assert p.slug == ''
check_page(200, 'paper', args=[p.pk, p.slug])
def test_create(self):
"""
BarePaper.create checks its arguments are non-empty
"""
names = [BareName.create('Peter', 'Johnstone'),
BareName.create('Xing', 'Li')]
pubdate = datetime.date(year=2014, month=9, day=4)
# No title
self.assertRaises(ValueError, BarePaper.create,
'', names, pubdate)
# No authors
self.assertRaises(ValueError, BarePaper.create,
'Excellent title', [], pubdate)
# No publication date
self.assertRaises(ValueError, BarePaper.create,
'Excellent title', names, None)
# Invalid visibility
self.assertRaises(ValueError, BarePaper.create,
'Excellent title', names, pubdate, visible="something")
# Not enough affiliations
self.assertRaises(ValueError, BarePaper.create,
'Excellent title', names, pubdate, affiliations=['ENS'])
def test_paper_with_empty_slug(self):
"""
Papers may have titles with characters that
are all ignored by slugify.
"""
p = Paper.get_or_create(
'!@#$%^*()',
[BareName.create('Jean', 'Saisrien')],
datetime.date(2016, 7, 2))
p.visible = True # Force paper to be visible even if it an orphan
p.save()
self.assertEqual(p.slug, '')
self.checkPage('paper', args=[p.pk, p.slug])
def test_add_author(self):
"""
p.add_author adds the author at the right place
"""
names = [
BareName.create('Peter', 'Johnstone'),
BareName.create('Xing', 'Li'),
BareName.create('John', 'Dubuc')
]
p = BarePaper.create('The title', [names[0]],
datetime.date(year=2012, month=1, day=9))
p.add_author(BareAuthor(name=names[2]))
self.assertEqual(len(p.authors), 2)
p.add_author(BareAuthor(name=names[1]), position=1)
self.assertListEqual(p.author_names(), names)
self.assertRaises(
ValueError,
p.add_author,
BareAuthor(name=BareName.create('Cantor', 'Bernstein')),
position=8)
def test_deposit_on_behalf_of(self):
paper = Paper.create_by_doi('10.1007/978-3-662-47666-6_5')
prefs = self.proto.get_preferences(self.user)
prefs.on_behalf_of = 'mweg3' # sample user id on the sandbox
# with name "Jean Saisrien"
paper.add_author(BareAuthor(name=BareName.create_bare('Jean', 'Saisrien')))
paper.save()
request = self.dry_deposit(
paper,
license='58fd62fcda3e2400012ca5d3',
abstract='Salagadoola menchicka boola bibbidi-bobbidi-boo.',
subjects=['59552884da3e240081ba32de'],
tags='Pumpkin, Mouse, Godmother')
self.assertEqualOrLog(request.status, 'published')
def test_deposit_on_behalf_of(self):
paper = Paper.create_by_doi('10.1007/978-3-662-47666-6_5')
prefs = self.proto.get_preferences(self.user)
prefs.on_behalf_of = 'mweg3' # sample user id on the sandbox
# with name "Jean Saisrien"
paper.add_author(
BareAuthor(name=BareName.create_bare('Jean', 'Saisrien')))
paper.save()
request = self.dry_deposit(
paper,
license='58fd62fcda3e2400012ca5d3',
abstract='Salagadoola menchicka boola bibbidi-bobbidi-boo.',
subjects=['59552884da3e240081ba32de'],
tags='Pumpkin, Mouse, Godmother')
self.assertEqualOrLog(request.status, 'published')
def authors_and_orcids(self):
"""
:returns: two lists of equal length, the first with BareName objects
representing authors, the second with ORCID ids (or None) for
each of these authors
"""
authors = self.authors
orcids = affiliate_author_with_orcid(self.profile.name, self.id,
authors)
names = [
BareName.create_bare(first, last) for first, last in self.authors
]
names_and_orcids = zip(names, orcids)
filtered = [(n, o) for n, o in names_and_orcids if n is not None]
final_names = [n for n, o in filtered]
final_orcids = [o for n, o in filtered]
return final_names, final_orcids
def _get_authors(cls, data):
"""
:param data: citeproc metadata
:returns: List of barenames
:raises: CiteprocAuthorError
"""
authors = data.get('author')
if not isinstance(authors, list):
raise CiteprocAuthorError('No list of authors in metadata')
name_pairs = list(map(cls._convert_to_name_pair, authors))
if None in name_pairs:
raise CiteprocAuthorError('Author list compromised')
authors = [
BareName.create_bare(first, last) for first, last in name_pairs
]
if not authors:
raise CiteprocAuthorError('No list of authors in metadata')
return authors
def api_paper_query(request):
try:
fields = json.loads(request.body.decode('utf-8'))
except (ValueError, UnicodeDecodeError):
raise BadRequest('Invalid JSON payload')
doi = fields.get('doi')
if doi:
p = None
try:
p = Paper.get_by_doi(doi)
if not p:
p = Paper.create_by_doi(doi)
except MetadataSourceException:
pass
if p is None:
raise BadRequest('Could not find a paper with this DOI')
return {'status': 'ok', 'paper': p.json()}
title = fields.get('title')
if not isinstance(title, str) or not title or len(title) > 512:
raise BadRequest(
'Invalid title, has to be a non-empty string shorter than 512 characters')
date = fields.get('date')
if not isinstance(date, str):
raise BadRequest('A date is required')
try:
date = tolerant_datestamp_to_datetime(date)
except ValueError as e:
raise BadRequest(str(e))
authors = fields.get('authors')
if not isinstance(authors, list):
raise BadRequest('A list of authors is expected')
parsed_authors = []
for a in authors:
author = None
if not isinstance(a, dict):
raise BadRequest('Invalid author')
if 'first' in a and 'last' in a:
if not isinstance(a['first'], str) or not isinstance(a['last'], str) or not a['last']:
raise BadRequest('Invalid (first,last) name provided')
else:
author = (a['first'], a['last'])
elif 'plain' in a:
if not isinstance(a['plain'], str) or not a['plain']:
raise BadRequest('Invalid plain name provided')
else:
author = parse_comma_name(a['plain'])
if author is None:
raise BadRequest('Invalid author')
parsed_authors.append(BareName.create(author[0], author[1]))
if not authors:
raise BadRequest('No authors provided')
try:
# Validate the metadata against our data model,
# and compute the fingerprint to look up the paper in the DB.
# This does NOT create a paper in the database - we do not want
# to create papers for every search query we get!
p = BarePaper.create(title, parsed_authors, date)
except ValueError as e:
raise BadRequest('Invalid paper: {}'.format(e))
try:
model_paper = Paper.objects.get(fingerprint=p.fingerprint)
return {'status': 'ok', 'paper': model_paper.json()}
except Paper.DoesNotExist:
return {'status': 'not found'}, 404
def api_paper_query(request):
try:
fields = json.loads(request.body.decode('utf-8'))
except (ValueError, UnicodeDecodeError):
raise BadRequest('Invalid JSON payload')
doi = fields.get('doi')
if doi:
p = None
try:
p = Paper.get_by_doi(doi)
if not p:
p = Paper.create_by_doi(doi)
except MetadataSourceException:
pass
if p is None:
raise BadRequest('Could not find a paper with this DOI')
return {'status': 'ok', 'paper': p.json()}
title = fields.get('title')
if not isinstance(title, str) or not title or len(title) > 512:
raise BadRequest(
'Invalid title, has to be a non-empty string shorter than 512 characters'
)
date = fields.get('date')
if not isinstance(date, str):
raise BadRequest('A date is required')
try:
date = tolerant_datestamp_to_datetime(date)
except ValueError as e:
raise BadRequest(str(e))
authors = fields.get('authors')
if not isinstance(authors, list):
raise BadRequest('A list of authors is expected')
parsed_authors = []
for a in authors:
author = None
if not isinstance(a, dict):
raise BadRequest('Invalid author')
if 'first' in a and 'last' in a:
if not isinstance(a['first'], str) or not isinstance(
a['last'], str) or not a['last']:
raise BadRequest('Invalid (first,last) name provided')
else:
author = (a['first'], a['last'])
elif 'plain' in a:
if not isinstance(a['plain'], str) or not a['plain']:
raise BadRequest('Invalid plain name provided')
else:
author = parse_comma_name(a['plain'])
if author is None:
raise BadRequest('Invalid author')
parsed_authors.append(BareName.create(author[0], author[1]))
if not authors:
raise BadRequest('No authors provided')
try:
# Validate the metadata against our data model,
# and compute the fingerprint to look up the paper in the DB.
# This does NOT create a paper in the database - we do not want
# to create papers for every search query we get!
p = BarePaper.create(title, parsed_authors, date)
except ValueError as e:
raise BadRequest('Invalid paper: {}'.format(e))
try:
model_paper = Paper.objects.get(fingerprint=p.fingerprint)
return {'status': 'ok', 'paper': model_paper.json()}
except Paper.DoesNotExist:
return {'status': 'not found'}, 404
def api_paper_query(request):
try:
fields = json.loads(request.body.decode('utf-8'))
except (ValueError, UnicodeDecodeError):
raise BadRequest('Invalid JSON payload')
doi = fields.get('doi')
if doi:
p = None
try:
p = Paper.create_by_doi(doi, bare=True)
except MetadataSourceException:
pass
if p is None:
raise BadRequest('Could not find a paper with this DOI')
return {'status': 'ok', 'paper': p.json()}
title = fields.get('title')
if not isinstance(title, unicode) or not title or len(title) > 512:
raise BadRequest(
'Invalid title, has to be a non-empty string shorter than 512 characters'
)
date = fields.get('date')
if not isinstance(date, unicode):
raise BadRequest('A date is required')
try:
date = tolerant_datestamp_to_datetime(date)
except ValueError as e:
raise BadRequest(unicode(e))
authors = fields.get('authors')
if not isinstance(authors, list):
raise BadRequest('A list of authors is expected')
parsed_authors = []
for a in authors:
author = None
if not isinstance(a, dict):
raise BadRequest('Invalid author')
if 'first' in a and 'last' in a:
if not isinstance(a['first'], unicode) or not isinstance(
a['last'], unicode) or not a['last']:
raise BadRequest('Invalid (first,last) name provided')
else:
author = (a['first'], a['last'])
elif 'plain' in a:
if not isinstance(a['plain'], unicode) or not a['plain']:
raise BadRequest('Invalid plain name provided')
else:
author = parse_comma_name(a['plain'])
if author is None:
raise BadRequest('Invalid author')
parsed_authors.append(BareName.create(author[0], author[1]))
if not authors:
raise BadRequest('No authors provided')
try:
p = BarePaper.create(title, parsed_authors, date)
except ValueError:
raise BadRequest('Invalid paper')
return {'status': 'ok', 'paper': p.json()}
def save_doi_metadata(self, metadata, extra_orcids=None):
"""
Given the metadata as Citeproc+JSON or from CrossRef, create the associated paper and publication
:param extra_orcids: an optional orcids list, which will be unified
with the orcids extracted from the metadata. This is useful for the ORCID interface.
:returns: the paper, created if needed
"""
# Normalize metadata
if metadata is None or not isinstance(metadata, dict):
raise ValueError('Invalid metadata format, expecting a dict')
if not metadata.get('author'):
raise ValueError('No author provided')
if not metadata.get('title'):
raise ValueError('No title')
# the upstream function ensures that there is a non-empty title
if not to_doi(metadata.get('DOI')):
raise ValueError("No DOI, skipping")
pubdate = get_publication_date(metadata)
if pubdate is None:
raise ValueError('No pubdate')
title = metadata['title']
# CrossRef metadata stores titles in lists
if isinstance(title, list):
title = title[0]
subtitle = metadata.get('subtitle')
if subtitle:
if isinstance(subtitle, list):
subtitle = subtitle[0]
title += ': '+subtitle
name_pairs = map(convert_to_name_pair, metadata['author'])
if None in name_pairs:
raise ValueError('Invalid author')
authors = [BareName.create_bare(first, last) for first, last in
name_pairs]
def get_affiliation(author_elem):
for dct in author_elem.get('affiliation', []):
if 'name' in dct:
return dct['name']
def get_orcid(author_elem):
orcid = validate_orcid(author_elem.get('ORCID'))
if orcid:
return orcid
new_orcids = map(get_orcid, metadata['author'])
if extra_orcids:
orcids = [new or old for (old, new) in zip(
extra_orcids, new_orcids)]
else:
orcids = new_orcids
affiliations = map(get_affiliation, metadata['author'])
paper = BarePaper.create(title, authors, pubdate,
visible=True, affiliations=affiliations, orcids=orcids)
result = create_publication(paper, metadata)
if result is None: # Creating the publication failed!
# Make sure the paper only appears if it is still associated
# with another source.
paper.update_visible()
else:
paper = result[0]
return paper
def save_doi_metadata(self, metadata, extra_orcids=None):
"""
Given the metadata as Citeproc+JSON or from CrossRef, create the associated paper and publication
:param extra_orcids: an optional orcids list, which will be unified
with the orcids extracted from the metadata. This is useful for the ORCID interface.
:returns: the paper, created if needed
"""
# Normalize metadata
if metadata is None or not isinstance(metadata, dict):
raise ValueError('Invalid metadata format, expecting a dict')
if not metadata.get('author'):
raise ValueError('No author provided')
if not metadata.get('title'):
raise ValueError('No title')
# the upstream function ensures that there is a non-empty title
if not to_doi(metadata.get('DOI')):
raise ValueError("No DOI, skipping")
pubdate = get_publication_date(metadata)
if pubdate is None:
raise ValueError('No pubdate')
title = metadata['title']
# CrossRef metadata stores titles in lists
if isinstance(title, list):
title = title[0]
subtitle = metadata.get('subtitle')
if subtitle:
if isinstance(subtitle, list):
subtitle = subtitle[0]
title += ': '+subtitle
name_pairs = list(map(convert_to_name_pair, metadata['author']))
if None in name_pairs:
raise ValueError('Invalid author')
authors = [BareName.create_bare(first, last) for first, last in
name_pairs]
def get_affiliation(author_elem):
for dct in author_elem.get('affiliation', []):
if 'name' in dct:
return dct['name']
def get_orcid(author_elem):
orcid = validate_orcid(author_elem.get('ORCID'))
if orcid:
return orcid
new_orcids = list(map(get_orcid, metadata['author']))
if extra_orcids:
# remove the extra_orcids if they already exist on different authors
set_of_extra_orcids = set(x for x in extra_orcids if x != None)
new_orcids = [(x if x not in set_of_extra_orcids else None)
for x in new_orcids]
# now do the union
orcids = [new or old for (old, new) in zip(
extra_orcids, new_orcids)]
else:
orcids = new_orcids
affiliations = list(map(get_affiliation, metadata['author']))
paper = BarePaper.create(title, authors, pubdate,
visible=True, affiliations=affiliations, orcids=orcids)
result = create_publication(paper, metadata)
if result is None: # Creating the publication failed!
# Make sure the paper only appears if it is still associated
# with another source.
paper.update_visible()
else:
paper = result[0]
return paper
def setUp(self):
self.ist = BarePaper.create('Groundbreaking Results', [
BareName.create('Alfred', 'Kastler'),
BareName.create('John', 'Dubuc')
], datetime.date(year=2015, month=3, day=2))
def api_paper_query(request):
try:
fields = json.loads(request.body.decode('utf-8'))
except (ValueError, UnicodeDecodeError):
raise BadRequest('Invalid JSON payload')
doi = fields.get('doi')
if doi:
p = None
try:
p = Paper.get_by_doi(doi)
if not p:
p = Paper.create_by_doi(doi)
except MetadataSourceException:
pass
if p is None:
raise BadRequest('Could not find a paper with this DOI')
return {'status': 'ok', 'paper': p.json()}
title = fields.get('title')
if not isinstance(title, str) or not title or len(title) > 512:
raise BadRequest(
'Invalid title, has to be a non-empty string shorter than 512 characters')
date = fields.get('date')
if not isinstance(date, str):
raise BadRequest('A date is required')
try:
date = tolerant_datestamp_to_datetime(date)
except ValueError as e:
raise BadRequest(str(e))
authors = fields.get('authors')
if not isinstance(authors, list):
raise BadRequest('A list of authors is expected')
parsed_authors = []
for a in authors:
author = None
if not isinstance(a, dict):
raise BadRequest('Invalid author')
if 'first' in a and 'last' in a:
if not isinstance(a['first'], str) or not isinstance(a['last'], str) or not a['last']:
raise BadRequest('Invalid (first,last) name provided')
else:
author = (a['first'], a['last'])
elif 'plain' in a:
if not isinstance(a['plain'], str) or not a['plain']:
raise BadRequest('Invalid plain name provided')
else:
author = parse_comma_name(a['plain'])
if author is None:
raise BadRequest('Invalid author')
parsed_authors.append(BareName.create(author[0], author[1]))
if not authors:
raise BadRequest('No authors provided')
try:
p = BarePaper.create(title, parsed_authors, date)
except ValueError:
raise BadRequest('Invalid paper')
return {'status': 'ok', 'paper': p.json()}
def setUp(self):
self.ist = BarePaper.create('Groundbreaking Results',
[BareName.create('Alfred', 'Kastler'),
BareName.create('John', 'Dubuc')],
datetime.date(year=2015, month=3, day=2))
