class MedlineTest(TestCase, TestMixin):
def setUp(self):
InitDb(URI, module=dbapi2)
self.sess = Session()
self.klass = Medline
self.entity = namedtuple('Medline', 'pmid status journal pub_date created')
self.defaults = self.entity(1, 'MEDLINE', 'journal', 'published', date.today())
def testCreate(self):
self.assertCreate()
def testEquals(self):
self.assertSame()
self.assertDifference(pmid=2)
self.assertDifference(status='In-Data-Review')
self.assertDifference(journal='other')
self.assertDifference(pub_date='other')
def testBigPmids(self):
big = 987654321098765432 # up to 18 decimals
r = Medline(big, 'MEDLINE', 'journal', 'PubDate', date.today())
self.sess.add(r)
self.sess.commit()
self.assertEqual(big, r.pmid)
self.assertEqual(big, self.sess.query(Medline).first().pmid)
# PMID
def testRequirePmid(self):
self.assertNonNullValue(TypeError, 'pmid')
def testRequirePositivePmid(self):
self.assertPositiveValue(AssertionError, 'pmid')
# STATUS
def testRequireStatus(self):
self.assertNonNullValue(AssertionError, 'status')
def testRequireValidStatus(self):
self.assertBadValue('invalid', AssertionError, 'status')
def testValidStatusNames(self):
d = date.today()
for pmid, status in enumerate(Medline.STATES):
self.sess.add(Medline(pmid + 1, status, 'journal', 'pubdate', d))
self.sess.commit()
self.assertTrue(True)
# JOURNAL
def testRequireJournal(self):
self.assertNonNullValue(AssertionError, 'journal')
def testRequireNonEmptyJournal(self):
self.assertNonEmptyValue(AssertionError, 'journal')
# CREATED
def testRequireCreated(self):
self.assertNonNullValue(AssertionError, 'created')
# COMPLETED
def testRequireCompletedDateOrNone(self):
self.assertBadExtraValue(AssertionError, 'completed', '')
# REVISED
def testRequireRevisedDateOrNone(self):
self.assertBadExtraValue(AssertionError, 'revised', '')
# MODIFIED
def testRequireModifiedDateOrNone(self):
m = Medline(*self.defaults)
m.modified = ''
self.sess.add(m)
self.assertRaises(StatementError, self.sess.commit)
def testAutomaticModified(self):
r = Medline(1, 'MEDLINE', 'journal', 'PubDate', date.today())
self.sess.add(r)
self.sess.commit()
self.assertEqual(date.today(), r.modified)
def testModifiedBefore(self):
today = date.today()
yesterday = today - timedelta(days=1)
m1 = Medline(1, 'MEDLINE', 'Journal 1', 'PubDate', today)
m2 = Medline(2, 'MEDLINE', 'Journal 1', 'PubDate', today)
m1.modified = today
m2.modified = yesterday
self.sess.add(m1)
self.sess.add(m2)
self.sess.commit()
self.assertListEqual([2], list(Medline.modifiedBefore([1, 2], date.today())))
# METHODS
def testToString(self):
d = date.today()
r = Medline(1, 'MEDLINE', 'journal\\.', 'PubDate', d)
line = "1\tMEDLINE\tjournal\\.\tPubDate\t\\N\t\\N\t{}\t\\N\t\\N\t{}\n".format(
d.isoformat(), d.isoformat()
)
self.assertEqual(line, str(r))
def testToRepr(self):
r = Medline(1, 'MEDLINE', 'journal', 'PubDate', date.today())
self.assertEqual("Medline<1>", repr(r))
def testInsert(self):
data = {
Medline.__tablename__: [
dict(pmid=1, status='MEDLINE', journal='Journal', pub_date='PubDate',
created=date.today())
],
Section.__tablename__: [
dict(pmid=1, seq=1, name='Title', content='The title.')
],
Author.__tablename__: [
dict(pmid=1, pos=1, name='Author')
],
Descriptor.__tablename__: [
dict(pmid=1, num=1, major=True, name='descriptor')
],
Qualifier.__tablename__: [
dict(pmid=1, num=1, sub=1, major=True, name='descriptor')
],
Identifier.__tablename__: [
dict(pmid=1, namespace='ns', value='id')
],
Database.__tablename__: [
dict(pmid=1, name='name', accession='accession')
],
Chemical.__tablename__: [
dict(pmid=1, idx=1, name='name')
],
Keyword.__tablename__: [
dict(pmid=1, owner='NLM', cnt=1, major=True, value='name')
],
}
Medline.insert(data)
for m in self.sess.query(Medline):
self.assertEqual(1, m.pmid)
for t in Medline.CHILDREN:
self.assertEqual(1, list(self.sess.query(t))[0].pmid)
def testInsertMultiple(self):
d = date.today()
data = {Medline.__tablename__: [
dict(pmid=1, status='MEDLINE', journal='Journal 1', pub_date='PubDate', created=d),
dict(pmid=2, status='MEDLINE', journal='Journal 2', pub_date='PubDate', created=d),
dict(pmid=3, status='MEDLINE', journal='Journal 3', pub_date='PubDate', created=d)
]}
Medline.insert(data)
count = 0
for m in self.sess.query(Medline):
if m.pmid not in (1, 2, 3):
self.fail(m)
else:
count += 1
self.assertEqual(3, count)
def addThree(self, d):
self.sess.add(Medline(1, 'MEDLINE', 'Journal 1', 'PubDate', d))
self.sess.add(Medline(2, 'MEDLINE', 'Journal 2', 'PubDate', d))
self.sess.add(Medline(3, 'MEDLINE', 'Journal X', 'PubDate', d))
self.sess.commit()
def testSelect(self):
self.addThree(date.today())
count = 0
for row in Medline.select([1, 2], ['journal']):
self.assertEqual('Journal {}'.format(row['pmid']), row['journal'])
count += 1
self.assertEqual(2, count)
def testSelectAll(self):
d = date.today()
self.addThree(d)
count = 0
for row in Medline.selectAll([1, 2]):
self.assertEqual('Journal {}'.format(row['pmid']), row['journal'])
self.assertEqual(d, row['created'])
self.assertEqual('MEDLINE', row[1])
count += 1
self.assertEqual(2, count)
def testDelete(self):
self.addThree(date.today())
Medline.delete([1, 2])
count = 0
for m in self.sess.query(Medline):
self.assertEqual(3, m.pmid)
count += 1
self.assertEqual(1, count)
def testExisting(self):
self.addThree(date.today())
self.assertListEqual([1, 3], list(Medline.existing([1, 3, 5])))
class CitationTest(TestCase, TestMixin):
def setUp(self):
InitDb(URI, module=dbapi2)
self.sess = Session()
self.klass = Citation
self.entity = namedtuple('Citation',
'pmid status title journal pub_date created')
self.defaults = self.entity(1, 'MEDLINE', 'title', 'journal',
'1990 published', date.today())
def testCreate(self):
self.assertCreate()
def testEquals(self):
self.assertSame()
self.assertDifference(pmid=2)
self.assertDifference(status='In-Data-Review')
self.assertDifference(journal='other')
self.assertDifference(pub_date='1960 other')
def testBigPmids(self):
big = 987654321098765432 # up to 18 decimals
r = DefaultCitation(big)
self.sess.add(r)
self.sess.commit()
self.assertEqual(big, r.pmid)
self.assertEqual(big, self.sess.query(Citation).first().pmid)
# PMID
def testRequirePmid(self):
self.assertNonNullValue(TypeError, 'pmid')
def testRequirePositivePmid(self):
self.assertPositiveValue(AssertionError, 'pmid')
# STATUS
def testRequireStatus(self):
self.assertNonNullValue(AssertionError, 'status')
def testRequireValidStatus(self):
self.assertBadValue('invalid', AssertionError, 'status')
def testValidStatusNames(self):
for pmid, status in enumerate(Citation.STATES):
self.sess.add(DefaultCitation(pmid + 1, status))
self.sess.commit()
self.assertTrue(True)
# JOURNAL
def testRequireJournal(self):
self.assertNonNullValue(AssertionError, 'journal')
def testRequireNonEmptyJournal(self):
self.assertNonEmptyValue(AssertionError, 'journal')
# CREATED
def testRequireCreated(self):
self.assertNonNullValue(AssertionError, 'created')
# COMPLETED
def testRequireCompletedDateOrNone(self):
self.assertBadExtraValue(AssertionError, 'completed', '')
# REVISED
def testRequireRevisedDateOrNone(self):
self.assertBadExtraValue(AssertionError, 'revised', '')
# MODIFIED
def testRequireModifiedDateOrNone(self):
m = Citation(*self.defaults)
m.modified = ''
self.sess.add(m)
self.assertRaises(StatementError, self.sess.commit)
def testAutomaticModified(self):
r = DefaultCitation()
self.sess.add(r)
self.sess.commit()
self.assertEqual(date.today(), r.modified)
def testModifiedBefore(self):
today = date.today()
yesterday = today - timedelta(days=1)
m1 = DefaultCitation()
m2 = DefaultCitation(2)
m1.modified = today
m2.modified = yesterday
self.sess.add(m1)
self.sess.add(m2)
self.sess.commit()
self.assertListEqual([2],
list(Citation.modifiedBefore([1, 2],
date.today())))
# METHODS
def testToString(self):
d = date.today()
r = Citation(1, 'MEDLINE', 'title', 'journal\\.', '1990 PubDate', d)
line = "1\tMEDLINE\t1990\ttitle\tjournal\\\\.\t1990 PubDate\t\\N\t\\N\t{}\t\\N\t\\N\t{}\n".format(
d.isoformat(), d.isoformat())
self.assertEqual(line, str(r))
def testToRepr(self):
r = DefaultCitation(123)
self.assertEqual("Citation<123>", repr(r))
def testInsert(self):
data = {
Citation.__tablename__: [
dict(pmid=1,
status='MEDLINE',
year=1990,
title='Title',
journal='Journal',
pub_date='1990 PubDate',
created=date.today())
],
Abstract.__tablename__: [dict(pmid=1, source='NLM')],
Section.__tablename__: [
dict(pmid=1,
source='NLM',
seq=1,
name='Title',
content='The title.')
],
Author.__tablename__: [dict(pmid=1, pos=1, name='Author')],
Descriptor.__tablename__:
[dict(pmid=1, num=1, major=True, name='descriptor')],
Qualifier.__tablename__:
[dict(pmid=1, num=1, sub=1, major=True, name='descriptor')],
Identifier.__tablename__:
[dict(pmid=1, namespace='ns', value='id')],
Database.__tablename__:
[dict(pmid=1, name='name', accession='accession')],
Chemical.__tablename__: [dict(pmid=1, idx=1, name='name')],
Keyword.__tablename__:
[dict(pmid=1, owner='NLM', cnt=1, major=True, value='name')],
}
Citation.insert(data)
for m in self.sess.query(Citation):
self.assertEqual(1, m.pmid)
for t in Citation.CHILDREN:
self.assertEqual(1, list(self.sess.query(t))[0].pmid)
def testInsertMultiple(self):
d = date.today()
data = {
Citation.__tablename__: [
dict(pmid=1,
status='MEDLINE',
year=1990,
title='Title 1',
journal='Journal 1',
pub_date='1990 PubDate',
created=d),
dict(pmid=2,
status='MEDLINE',
year=1990,
title='Title 2',
journal='Journal 2',
pub_date='1990 PubDate',
created=d),
dict(pmid=3,
status='MEDLINE',
year=1990,
title='Title 3',
journal='Journal 3',
pub_date='1990 PubDate',
created=d)
]
}
Citation.insert(data)
count = 0
for m in self.sess.query(Citation):
if m.pmid not in (1, 2, 3):
self.fail(m)
else:
count += 1
self.assertEqual(3, count)
def addThree(self, d):
self.sess.add(DefaultCitation(1, journal='Journal 1', created=d))
self.sess.add(DefaultCitation(2, journal='Journal 2', created=d))
self.sess.add(DefaultCitation(3, created=d))
self.sess.commit()
def testSelect(self):
self.addThree(date.today())
count = 0
for row in Citation.select([1, 2], ['journal']):
self.assertEqual('Journal {}'.format(row['pmid']), row['journal'])
count += 1
self.assertEqual(2, count)
def testSelectAll(self):
d = date.today()
self.addThree(d)
count = 0
for row in Citation.selectAll([1, 2]):
self.assertEqual('Journal {}'.format(row['pmid']), row['journal'])
self.assertEqual(d, row['created'])
self.assertEqual('MEDLINE', row[1])
count += 1
self.assertEqual(2, count)
def testDelete(self):
self.addThree(date.today())
Citation.delete([1, 2])
count = 0
for m in self.sess.query(Citation):
self.assertEqual(3, m.pmid)
count += 1
self.assertEqual(1, count)
def testExisting(self):
self.addThree(date.today())
self.assertListEqual([1, 3], list(Citation.existing([1, 3, 5])))
class AuthorTest(TestCase, TestMixin):
def setUp(self):
InitDb(URI, module=dbapi2)
self.sess = Session()
self.M = Medline(1, 'MEDLINE', 'Journal', 'PubDate', date.today())
self.sess.add(self.M)
self.klass = Author
self.entity = namedtuple('Author', 'pmid pos name')
self.defaults = self.entity(1, 1, 'last')
def testCreate(self):
self.assertCreate()
def testEquals(self):
self.assertSame()
self.assertDifference(pos=2)
self.assertDifference(name='other')
# PMID
def testRequirePmid(self):
self.assertNonNullValue(TypeError, 'pmid')
# POS
def testRequirePos(self):
self.assertNonNullValue(TypeError, 'pos')
def testRequirePositivePos(self):
self.assertPositiveValue(AssertionError, 'pos')
# NAME
def testRequireName(self):
self.assertNonNullValue(AssertionError, 'name')
def testRequireNonEmptyName(self):
self.assertNonEmptyValue(AssertionError, 'name')
# INITIALS
def testAssignInitials(self):
self.sess.add(Author(1, 1, 'last', initials='test'))
self.assertEqual('test', self.sess.query(Author).first().initials)
# FORENAME
def testAssignFirstName(self):
self.sess.add(Author(1, 1, 'last', forename='test'))
self.assertEqual('test', self.sess.query(Author).first().forename)
# SUFFIX
def testAssignSuffix(self):
self.sess.add(Author(1, 1, 'last', suffix='test'))
self.assertEqual('test', self.sess.query(Author).first().suffix)
# METHODS
def testFullNameDefault(self):
a = Author(1, 1, 'last', initials='init', forename='first', suffix='suffix')
self.assertEqual('first last suffix', a.fullName())
def testFullNameNoFirst(self):
a = Author(1, 1, 'last', initials='init', forename='', suffix='suffix')
self.assertEqual('init last suffix', a.fullName())
def testFullNameNoFirstOrInitials(self):
a = Author(1, 1, 'last', initials='', forename='', suffix='suffix')
self.assertEqual('last suffix', a.fullName())
def testFullNameNoSuffix(self):
a = Author(1, 1, 'last', initials='init', forename='first', suffix='')
self.assertEqual('first last', a.fullName())
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 testShortNameNoFirstOrInitials(self):
a = Author(1, 1, 'last', initials='', forename='', suffix='suffix')
self.assertEqual('last', a.shortName())
def testToString(self):
self.assertEqual('1\t1\tlast\t\\N\tfirst\t\n',
str(Author(1, 1, 'last', forename='first', suffix='')))
def testToRepr(self):
self.assertEqual('Author<1:1>', repr(Author(1, 1, 'name')))
def testMedlineRelations(self):
a = Author(1, 1, 'last')
self.sess.add(a)
self.sess.commit()
self.assertListEqual([a], self.M.authors)
self.assertEqual(self.M, a.medline)
class AuthorTest(TestCase, TestMixin):
def setUp(self):
InitDb(URI, module=dbapi2)
self.sess = Session()
self.M = DefaultCitation()
self.sess.add(self.M)
self.klass = Author
self.entity = namedtuple('Author', 'pmid pos name')
self.defaults = self.entity(1, 1, 'last')
def testCreate(self):
self.assertCreate()
def testEquals(self):
self.assertSame()
self.assertDifference(pos=2)
self.assertDifference(name='other')
# PMID
def testRequirePmid(self):
self.assertNonNullValue(TypeError, 'pmid')
# POS
def testRequirePos(self):
self.assertNonNullValue(TypeError, 'pos')
def testRequirePositivePos(self):
self.assertPositiveValue(AssertionError, 'pos')
# NAME
def testRequireName(self):
self.assertNonNullValue(AssertionError, 'name')
def testRequireNonEmptyName(self):
self.assertNonEmptyValue(AssertionError, 'name')
# INITIALS
def testAssignInitials(self):
self.sess.add(Author(1, 1, 'last', initials='test'))
self.assertEqual('test', self.sess.query(Author).first().initials)
# FORENAME
def testAssignFirstName(self):
self.sess.add(Author(1, 1, 'last', forename='test'))
self.assertEqual('test', self.sess.query(Author).first().forename)
# SUFFIX
def testAssignSuffix(self):
self.sess.add(Author(1, 1, 'last', suffix='test'))
self.assertEqual('test', self.sess.query(Author).first().suffix)
# METHODS
def testFullNameDefault(self):
a = Author(1,
1,
'last',
initials='init',
forename='first',
suffix='suffix')
self.assertEqual('first last suffix', a.fullName())
def testFullNameNoFirst(self):
a = Author(1, 1, 'last', initials='init', forename='', suffix='suffix')
self.assertEqual('init last suffix', a.fullName())
def testFullNameNoFirstOrInitials(self):
a = Author(1, 1, 'last', initials='', forename='', suffix='suffix')
self.assertEqual('last suffix', a.fullName())
def testFullNameNoSuffix(self):
a = Author(1, 1, 'last', initials='init', forename='first', suffix='')
self.assertEqual('first last', a.fullName())
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 testShortNameNoFirstOrInitials(self):
a = Author(1, 1, 'last', initials='', forename='', suffix='suffix')
self.assertEqual('last', a.shortName())
def testToString(self):
self.assertEqual(
'1\t1\tlast\t\\N\tfirst\t\n',
str(Author(1, 1, 'last', forename='first', suffix='')))
def testToRepr(self):
self.assertEqual('Author<1:1>', repr(Author(1, 1, 'name')))
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)