def testEquals(self):
self.assertSame()
self.assertDifference(num=2)
self.assertDifference(sub=2)
self.assertDifference(name='other')
self.assertNotEqual(Qualifier(1, 1, 1, 'q_name', True),
Qualifier(1, 1, 1, 'q_name', False))
def testSelectAll(self):
self.sess.add(Qualifier(1, 1, 1, 'q1'))
self.sess.add(Qualifier(1, 1, 2, 'q2'))
self.sess.add(Qualifier(1, 1, 3, 'q3'))
self.sess.commit()
for row in Qualifier.selectAll((1, 1)):
if row['sub'] == 1:
self.assertEqual(row['name'], 'q1')
elif row['sub'] == 2:
self.assertFalse(row[Qualifier.major.name])
elif row['sub'] == 3:
self.assertEqual(row['name'], 'q3')
else:
self.fail(str(row))
def testSelect(self):
self.sess.add(Qualifier(1, 1, 1, 'q1'))
self.sess.add(Qualifier(1, 1, 2, 'q2'))
self.sess.add(Qualifier(1, 1, 3, 'q3'))
self.sess.commit()
for row in Qualifier.select((1, 1), ['sub', 'name']):
if row['sub'] == 1:
self.assertEqual(row['name'], 'q1')
elif row[0] == 2:
self.assertEqual(row[1], 'q2')
elif row[0] == 3:
self.assertEqual(row[1], 'q3')
else:
self.fail(str(row))
def testRelations(self):
q = Qualifier(1, 1, 1, 'name')
self.sess.add(q)
self.sess.commit()
self.assertListEqual([q], self.M.qualifiers)
self.assertEqual(self.M, q.citation)
self.assertEqual(self.D, q.descriptor)
def parseQualifier(self, num, sub, element):
return Qualifier(
self.pmid,
num + 1,
sub + 1,
element.text.strip(),
element.get('MajorTopicYN', 'N') == 'Y',
)
def testSelectAll(self):
self.sess.add(Qualifier(1, 1, 1, 'q1'))
self.sess.add(Qualifier(1, 1, 2, 'q2'))
self.sess.add(Qualifier(1, 1, 3, 'q3'))
self.sess.commit()
for row in Qualifier.selectAll((1, 1)):
if row['sub'] == 1:
self.assertEqual(row['name'], 'q1')
elif row['sub'] == 2:
self.assertFalse(row[Qualifier.major.name])
elif row['sub'] == 3:
self.assertEqual(row['name'], 'q3')
else:
self.fail(str(row))
def testSelect(self):
self.sess.add(Qualifier(1, 1, 1, 'q1'))
self.sess.add(Qualifier(1, 1, 2, 'q2'))
self.sess.add(Qualifier(1, 1, 3, 'q3'))
self.sess.commit()
for row in Qualifier.select((1, 1), ['sub', 'name']):
if row['sub'] == 1:
self.assertEqual(row['name'], 'q1')
elif row[0] == 2:
self.assertEqual(row[1], 'q2')
elif row[0] == 3:
self.assertEqual(row[1], 'q3')
else:
self.fail(str(row))
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 testToRepr(self):
self.assertEqual('Qualifier<1:2:3>', repr(Qualifier(1, 2, 3, 'name')))
def testToString(self):
self.assertEqual('1\t1\t1\tT\tmajor\n',
str(Qualifier(1, 1, 1, 'major', True)))
self.assertEqual('1\t1\t1\tF\tminor\n',
str(Qualifier(1, 1, 1, 'minor')))
def testMajorIsBool(self):
self.sess.add(Qualifier(1, 1, 1, 'q_name', None))
self.assertRaises(IntegrityError, self.sess.commit)
def testRequireExistingDescriptor(self):
self.sess.add(Qualifier(1, 2, 1, 'q_name'))
self.assertRaises(IntegrityError, self.sess.commit)
