def test_insertion(self):
self.assertEqual(unify_name_lists(
[('Jean', 'Dupont'), ('Marie', 'Dupré'), ('Alphonse', 'de Lamartine')],
[('J.', 'Dupont'), ('M.', 'Dupré'), ('A.', 'de Lamartine'), ('R.', 'Badinter')]),
[(('Jean', 'Dupont'), (0, 0)), (('Marie', 'Dupré'), (1, 1)),
(('Alphonse', 'de Lamartine'), (2, 2)), (('R.', 'Badinter'), (None, 3))])
self.assertEqual(unify_name_lists(
[('Élise', 'Chaumont'), ('Jean', 'Dupont'),
('Marie', 'Dupré'), ('Alphonse', 'de Lamartine')],
[('J.', 'Dupont'), ('M.', 'Dupré'), ('A.', 'de Lamartine')]),
[(('Élise', 'Chaumont'), (0, None)), (('Jean', 'Dupont'), (1, 0)), (('Marie', 'Dupré'), (2, 1)), (('Alphonse', 'de Lamartine'), (3, 2))])
def test_same_last_name(self):
self.assertTrue(unify_name_lists(
[('Jean', 'Dupont'), ('Marie', 'Dupont')],
[('M.', 'Dupont'), ('J. P.', 'Dupont')]) in
[
[(('Jean P.', 'Dupont'), (0, 1)), (('Marie', 'Dupont'), (1, 0))],
[(('Marie', 'Dupont'), (1, 0)), (('Jean P.', 'Dupont'), (0, 1))]
])
def test_insertion(self):
self.assertEqual(
unify_name_lists([('Jean', 'Dupont'), ('Marie', 'Dupré'),
('Alphonse', 'de Lamartine')],
[('J.', 'Dupont'), ('M.', 'Dupré'),
('A.', 'de Lamartine'), ('R.', 'Badinter')]),
[(('Jean', 'Dupont'), (0, 0)), (('Marie', 'Dupré'), (1, 1)),
(('Alphonse', 'de Lamartine'), (2, 2)),
(('R.', 'Badinter'), (None, 3))])
self.assertEqual(
unify_name_lists([('Élise', 'Chaumont'), ('Jean', 'Dupont'),
('Marie', 'Dupré'),
('Alphonse', 'de Lamartine')],
[('J.', 'Dupont'), ('M.', 'Dupré'),
('A.', 'de Lamartine')]),
[(('Élise', 'Chaumont'), (0, None)), (('Jean', 'Dupont'), (1, 0)),
(('Marie', 'Dupré'), (2, 1)),
(('Alphonse', 'de Lamartine'), (3, 2))])
def test_same_last_name(self):
self.assertTrue(
unify_name_lists([('Jean', 'Dupont'), ('Marie', 'Dupont')], [(
'M.', 'Dupont'), (
'J. P.',
'Dupont')]) in [[(('Jean P.', 'Dupont'),
(0, 1)), (('Marie', 'Dupont'), (1, 0))],
[(('Marie', 'Dupont'),
(1, 0)), (('Jean P.', 'Dupont'), (0,
1))]])
def test_inverted(self):
# in the wild:
# https://doi.org/10.1371/journal.pone.0156198
# http://hdl.handle.net/11573/870611
self.assertEqual(
len([
x for x in unify_name_lists([
('Sarnelli', 'Giovanni'),
("d'Alessandro", 'Alessandra'),
], [
('Giovanni', 'Sarnelli'),
('Giovanni', 'Domenico de Palma'),
('Alessandra', "D'Alessandro"),
]) if x[0] != None
]), 3)
def test_inverted(self):
# in the wild:
# https://doi.org/10.1371/journal.pone.0156198
# http://hdl.handle.net/11573/870611
self.assertEqual(len([x for x in unify_name_lists(
[
('Sarnelli', 'Giovanni'),
("d'Alessandro", 'Alessandra'),
],
[
('Giovanni', 'Sarnelli'),
('Giovanni', 'Domenico de Palma'),
('Alessandra', "D'Alessandro"),
]) if x[0] != None]),
3)
def test_simple(self):
self.assertEqual(unify_name_lists([], []), [])
self.assertEqual(
unify_name_lists([('Jean', 'Dupont')], [('Jean', 'Dupont')]),
[(('Jean', 'Dupont'), (0, 0))])
self.assertEqual(
unify_name_lists([('Jean', 'Dupont')], [('J.', 'Dupont')]),
[(('Jean', 'Dupont'), (0, 0))])
self.assertEqual(
unify_name_lists([('Jean', 'Dupont')], [('J. F.', 'Dupont')]),
[(('Jean F.', 'Dupont'), (0, 0))])
self.assertEqual(
unify_name_lists([('Jean', 'Dupont'), ('Marie', 'Dupré'),
('Alphonse', 'de Lamartine')],
[('J.', 'Dupont'), ('M.', 'Dupré'),
('A.', 'de Lamartine')]),
[(('Jean', 'Dupont'), (0, 0)), (('Marie', 'Dupré'), (1, 1)),
(('Alphonse', 'de Lamartine'), (2, 2))])
self.assertEqual(
unify_name_lists([('Antonin', 'Delpeuch'), ('Anne', 'Preller')],
[('Antonin', 'Delpeuch'), ('Anne', 'Preller')]),
[(('Antonin', 'Delpeuch'), (0, 0)), (('Anne', 'Preller'), (1, 1))])
def test_simple(self):
self.assertEqual(unify_name_lists([], []), [])
self.assertEqual(unify_name_lists(
[('Jean', 'Dupont')],
[('Jean', 'Dupont')]),
[(('Jean', 'Dupont'), (0, 0))])
self.assertEqual(unify_name_lists(
[('Jean', 'Dupont')],
[('J.', 'Dupont')]),
[(('Jean', 'Dupont'), (0, 0))])
self.assertEqual(unify_name_lists(
[('Jean', 'Dupont')],
[('J. F.', 'Dupont')]),
[(('Jean F.', 'Dupont'), (0, 0))])
self.assertEqual(unify_name_lists(
[('Jean', 'Dupont'), ('Marie', 'Dupré'), ('Alphonse', 'de Lamartine')],
[('J.', 'Dupont'), ('M.', 'Dupré'), ('A.', 'de Lamartine')]),
[(('Jean', 'Dupont'), (0, 0)), (('Marie', 'Dupré'), (1, 1)), (('Alphonse', 'de Lamartine'), (2, 2))])
self.assertEqual(unify_name_lists(
[('Antonin', 'Delpeuch'), ('Anne', 'Preller')],
[('Antonin', 'Delpeuch'), ('Anne', 'Preller')]),
[(('Antonin', 'Delpeuch'), (0, 0)), (('Anne', 'Preller'), (1, 1))])
def update_author_names(self, new_author_names, new_affiliations=None):
"""
Improves the current list of authors by considering a new list of author names.
Missing authors are added, and names are unified.
If affiliations are provided, they will replace the old ones if they are
more informative.
:param new_author_names: list of Name instances (the order matters)
:param new_affiliations: (optional) list of affiliation strings for the new author names.
"""
if new_affiliations is None:
new_affiliations = [None] * len(new_author_names)
assert len(new_author_names) == len(new_affiliations)
if hasattr(self, 'authors'):
del self.authors
old_authors = list(self.authors)
# Invalidate cached properties
if hasattr(self, 'interesting_authors'):
del self.interesting_authors
old_names = map(lambda a: (a.name.first, a.name.last), old_authors)
unified_names = unify_name_lists(old_names, new_author_names)
seen_old_names = set()
for i, (new_name, (idx, new_idx)) in enumerate(unified_names):
if idx is not None: # Updating the name of an existing author
seen_old_names.add(idx)
author = old_authors[idx]
if new_name is None:
# Delete that author, it was pruned because it already
# appears elsewhere
if author.id is not None:
author.delete()
continue
fields = []
if idx != i:
author.position = i
fields.append('position')
if new_name != (author.name.first, author.name.last):
name = Name.lookup_name(new_name)
name.save()
author.name = name
fields.append('name')
if new_idx is not None and affiliation_is_greater(
new_affiliations[new_idx], author.affiliation):
author.affiliation = new_affiliations[new_idx]
fields.append('affiliation')
author.update_name_variants_if_needed()
if fields:
author.name.save_if_not_saved()
author.save()
elif new_name is not None: # Creating a new author
name = Name.lookup_name(new_name)
name.save()
author = Author(paper=self,
name=name,
position=i,
affiliation=new_affiliations[new_idx])
author.save()
# Just in case unify_name_lists pruned authors without telling us…
for idx, author in enumerate(old_authors):
if idx not in seen_old_names:
print("** Deleting author %d **" % author.pk)
author.delete()
# Invalidate our local cache
if hasattr(self, 'authors'):
del self.authors
def test_shallower_similarity(self):
self.assertEqual(
unify_name_lists([('Clement F.', 'Pit Claudel')],
[('Clément', 'Pit-Claudel')])[0][1], (0, 0))
def test_duplicates(self):
self.assertEqual(
unify_name_lists([('Jérémie', 'Boutier'), ('Jérémie', 'Boutier')],
[('J.', 'Boutier')]),
[(('Jérémie', 'Boutier'), (0, 0)), (None, (1, None))])
def test_dirty_input(self):
self.assertEqual(
unify_name_lists([('Jérémie', 'Boutier'), ('Alphonse', 'Viger')],
[('J{é}r{é}mie', 'Boutier'), ('A.', 'Viger')]),
[(('Jérémie', 'Boutier'), (0, 0)),
(('Alphonse', 'Viger'), (1, 1))])
def test_shallower_similarity(self):
self.assertEqual(unify_name_lists(
[('Clement F.', 'Pit Claudel')],
[('Clément', 'Pit-Claudel')])[0][1],
(0,0))
def test_duplicates(self):
self.assertEqual(unify_name_lists(
[('Jérémie', 'Boutier'), ('Jérémie', 'Boutier')],
[('J.', 'Boutier')]),
[(('Jérémie', 'Boutier'), (0, 0)), (None, (1, None))])
def test_dirty_input(self):
self.assertEqual(unify_name_lists(
[('Jérémie', 'Boutier'), ('Alphonse', 'Viger')],
[('J{é}r{é}mie', 'Boutier'), ('A.', 'Viger')]),
[(('Jérémie', 'Boutier'), (0, 0)), (('Alphonse', 'Viger'), (1, 1))])
def update_author_names(self, new_author_names, new_affiliations=None):
"""
Improves the current list of authors by considering a new list of author names.
Missing authors are added, and names are unified.
If affiliations are provided, they will replace the old ones if they are
more informative.
:param new_author_names: list of Name instances (the order matters)
:param new_affiliations: (optional) list of affiliation strings for the new author names.
"""
if new_affiliations is None:
new_affiliations = [None]*len(new_author_names)
assert len(new_author_names) == len(new_affiliations)
if hasattr(self, 'authors'):
del self.authors
old_authors = list(self.authors)
# Invalidate cached properties
if hasattr(self, 'interesting_authors'):
del self.interesting_authors
old_names = map(lambda a: (a.name.first,a.name.last), old_authors)
unified_names = unify_name_lists(old_names, new_author_names)
seen_old_names = set()
for i, (new_name, (idx,new_idx)) in enumerate(unified_names):
if idx is not None: # Updating the name of an existing author
seen_old_names.add(idx)
author = old_authors[idx]
if new_name is None:
# Delete that author, it was pruned because it already
# appears elsewhere
if author.id is not None:
author.delete()
continue
fields = []
if idx != i:
author.position = i
fields.append('position')
if new_name != (author.name.first,author.name.last):
name = Name.lookup_name(new_name)
name.save()
author.name = name
fields.append('name')
if new_idx is not None and affiliation_is_greater(new_affiliations[new_idx], author.affiliation):
author.affiliation = new_affiliations[new_idx]
fields.append('affiliation')
author.update_name_variants_if_needed()
if fields:
author.name.save_if_not_saved()
author.save()
elif new_name is not None: # Creating a new author
name = Name.lookup_name(new_name)
name.save()
author = Author(paper=self,name=name,position=i,affiliation=new_affiliations[new_idx])
author.save()
# Just in case unify_name_lists pruned authors without telling us…
for idx, author in enumerate(old_authors):
if idx not in seen_old_names:
print("** Deleting author %d **" % author.pk)
author.delete()
# Invalidate our local cache
if hasattr(self, 'authors'):
del self.authors
