def test_affiliation_is_greater_partial_order(self):
for a, b in [(None, None), (None, 'Cambridge'), ('0000-0002-8612-8827', 'ENS'),
('University of Oxford, Oxfordshire', '0000-0001-5892-7431')]:
self.assertFalse(affiliation_is_greater(a, b) and
affiliation_is_greater(b, a))
self.assertFalse(affiliation_is_greater(a, a))
self.assertFalse(affiliation_is_greater(b, b))
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_affiliation_is_greater(self):
self.assertEqual(affiliation_is_greater(None, None), False)
self.assertEqual(affiliation_is_greater(None, 'UPenn'), False)
self.assertEqual(affiliation_is_greater('UPenn', None), True)
self.assertEqual(affiliation_is_greater('0000-0001-8633-6098', 'Ecole normale superieure, Paris'), True)
self.assertEqual(affiliation_is_greater('Ecole normale superieure', 'Upenn'), True)
def save_doi_metadata(self,
metadata,
extra_affiliations=None,
allow_unknown_authors=False):
"""
Given the metadata as Citeproc+JSON or from CrossRef, create the associated paper and publication
:param extra_affiliations: an optional affiliations list, which will be unified
with the affiliations extracted from the metadata. This is useful for the ORCID interface.
:param allow_unknown_authors: create the paper even if no author matches our researchers
:returns: the paper, created if needed
"""
# Normalize metadata
if metadata is None or type(metadata) != dict:
if metadata is not None:
print "WARNING: Invalid metadata: type is " + str(
type(metadata))
print "The doi proxy is doing something nasty!"
raise ValueError('Invalid metadata format, expecting a dict')
if not 'author' in metadata:
raise ValueError('No author provided')
if not 'title' in metadata or not metadata['title']:
raise ValueError('No title')
# the upstream function ensures that there is a non-empty title
if not 'DOI' in metadata or not metadata['DOI']:
raise ValueError("No DOI, skipping")
doi = to_doi(metadata['DOI'])
pubdate = get_publication_date(metadata)
if pubdate is None:
raise ValueError('No pubdate')
title = metadata['title']
# CrossRef metadata stores titles in lists
if type(title) == list:
title = title[0]
subtitle = metadata.get('subtitle')
if subtitle:
if type(subtitle) == list:
subtitle = subtitle[0]
title += ': ' + subtitle
authors = map(name_lookup_cache.lookup,
map(convert_to_name_pair, metadata['author']))
authors = filter(lambda x: x != None, authors)
if (not allow_unknown_authors
and all(not elem.is_known
for elem in authors)) or authors == []:
raise ValueError('No known author')
def get_affiliation(author_elem):
# First, look for an ORCID id
orcid = validate_orcid(author_elem.get('ORCID'))
if orcid:
return orcid
# Otherwise return the plain affiliation, if any
for dct in author_elem.get('affiliation', []):
if 'name' in dct:
return dct['name']
affiliations = map(get_affiliation, metadata['author'])
if extra_affiliations and len(affiliations) == len(extra_affiliations):
for i in range(len(affiliations)):
if affiliation_is_greater(extra_affiliations[i],
affiliations[i]):
affiliations[i] = extra_affiliations[i]
paper = BarePaper.create(title, authors, pubdate, 'VISIBLE',
affiliations)
result = create_publication(paper, metadata)
if result is None: # Creating the publication failed!
paper.update_visibility()
# Make sure the paper only appears if it is still associated
# with another source.
# TODO add unit test for this
else:
paper = result[0]
return paper
def save_doi_metadata(self, metadata, extra_affiliations=None, allow_unknown_authors=False):
"""
Given the metadata as Citeproc+JSON or from CrossRef, create the associated paper and publication
:param extra_affiliations: an optional affiliations list, which will be unified
with the affiliations extracted from the metadata. This is useful for the ORCID interface.
:param allow_unknown_authors: create the paper even if no author matches our researchers
:returns: the paper, created if needed
"""
# Normalize metadata
if metadata is None or type(metadata) != dict:
if metadata is not None:
print "WARNING: Invalid metadata: type is "+str(type(metadata))
print "The doi proxy is doing something nasty!"
raise ValueError('Invalid metadata format, expecting a dict')
if not 'author' in metadata:
raise ValueError('No author provided')
if not 'title' in metadata or not metadata['title']:
raise ValueError('No title')
# the upstream function ensures that there is a non-empty title
if not 'DOI' in metadata or not metadata['DOI']:
raise ValueError("No DOI, skipping")
doi = to_doi(metadata['DOI'])
pubdate = get_publication_date(metadata)
if pubdate is None:
raise ValueError('No pubdate')
title = metadata['title']
# CrossRef metadata stores titles in lists
if type(title) == list:
title = title[0]
subtitle = metadata.get('subtitle')
if subtitle:
if type(subtitle) == list:
subtitle = subtitle[0]
title += ': '+subtitle
authors = map(name_lookup_cache.lookup, map(convert_to_name_pair, metadata['author']))
authors = filter(lambda x: x != None, authors)
if (not allow_unknown_authors and all(not elem.is_known for elem in authors)) or authors == []:
raise ValueError('No known author')
def get_affiliation(author_elem):
# First, look for an ORCID id
orcid = validate_orcid(author_elem.get('ORCID'))
if orcid:
return orcid
# Otherwise return the plain affiliation, if any
for dct in author_elem.get('affiliation', []):
if 'name' in dct:
return dct['name']
affiliations = map(get_affiliation, metadata['author'])
if extra_affiliations and len(affiliations) == len(extra_affiliations):
for i in range(len(affiliations)):
if affiliation_is_greater(extra_affiliations[i],affiliations[i]):
affiliations[i] = extra_affiliations[i]
paper = BarePaper.create(title, authors, pubdate,
'VISIBLE', affiliations)
result = create_publication(paper, metadata)
if result is None: # Creating the publication failed!
paper.update_visibility()
# Make sure the paper only appears if it is still associated
# with another source.
# TODO add unit test for this
else:
paper = result[0]
return paper
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