def testShortNameDefault(self):
a = Author(1,
1,
'last',
initials='init',
forename='first',
suffix='suffix')
self.assertEqual('init last', a.shortName())
def testShortNameNoInitials(self):
a = Author(1,
1,
'last',
initials='',
forename='first second',
suffix='suffix')
self.assertEqual('fs last', a.shortName())
def parseAuthor(self, pos, element):
name, forename, initials, suffix = self.parseAuthorElements(element.getchildren())
if initials == forename and initials is not None:
# prune the repetition of initials in the forename
forename = None
if name is not None:
return Author(self.pmid, pos + 1, name, initials, forename, suffix)
else:
logger.warning('empty or missing Author/LastName or CollectiveName in %i',
self.pmid)
return None
def testShortNameNoFirstOrInitials(self):
a = Author(1, 1, 'last', initials='', forename='', suffix='suffix')
self.assertEqual('last', a.shortName())
def testShortNameDefault(self):
a = Author(1, 1, 'last', initials='init', forename='first', suffix='suffix')
self.assertEqual('init last', a.shortName())
def testFullNameNoSuffix(self):
a = Author(1, 1, 'last', initials='init', forename='first', suffix='')
self.assertEqual('first last', a.fullName())
def testFullNameNoFirst(self):
a = Author(1, 1, 'last', initials='init', forename='', suffix='suffix')
self.assertEqual('init last suffix', a.fullName())
from collections import defaultdict
from datetime import date
from io import StringIO
from tempfile import TemporaryFile
from medic.orm import Medline, Section, Author, Descriptor, Qualifier, Database, Identifier, \
Chemical, Keyword, PublicationType
from medic.crud import _dump
DATA = [
Section(1, 1, 'Title', 'The Title'),
Section(1, 2, 'Abstract', 'The Abstract'),
Descriptor(1, 1, 'd_name', True),
Descriptor(1, 2, 'd_name'),
Qualifier(1, 1, 1, 'q_name', True),
Author(1, 1, 'first'),
Author(1, 2, 'last'),
Identifier(1, 'ns', 'id'),
Database(1, 'name', 'accession'),
PublicationType(1, 'some'),
PublicationType(1, 'another'),
Chemical(1, 1, 'name', 'uid'),
Keyword(1, 'NOTNLM', 1, 'name', True),
Medline(1, 'MEDLINE', 'journal', 'pub_date', date.today()),
]
class ParserMock:
def __init__(self, instances):
self.instances = instances
def testRelations(self):
a = Author(1, 1, 'last')
self.sess.add(a)
self.sess.commit()
self.assertListEqual([a], self.M.authors)
self.assertEqual(self.M, a.citation)
def testToRepr(self):
self.assertEqual('Author<1:1>', repr(Author(1, 1, 'name')))
def testToString(self):
self.assertEqual(
'1\t1\tlast\t\\N\tfirst\t\n',
str(Author(1, 1, 'last', forename='first', suffix='')))
def testFullNameNoSuffix(self):
a = Author(1, 1, 'last', initials='init', forename='first', suffix='')
self.assertEqual('first last', a.fullName())
def testFullNameNoFirstOrInitials(self):
a = Author(1, 1, 'last', initials='', forename='', suffix='suffix')
self.assertEqual('last suffix', a.fullName())
def testAssignSuffix(self):
self.sess.add(Author(1, 1, 'last', suffix='test'))
self.assertEqual('test', self.sess.query(Author).first().suffix)
def testAssignFirstName(self):
self.sess.add(Author(1, 1, 'last', forename='test'))
self.assertEqual('test', self.sess.query(Author).first().forename)
def testAssignInitials(self):
self.sess.add(Author(1, 1, 'last', initials='test'))
self.assertEqual('test', self.sess.query(Author).first().initials)