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 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 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 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 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())))
def testDoi2Pmid(self):
self.sess.add(Identifier(1, 'doi', 'id'))
self.sess.add(Medline(2, 'MEDLINE', 'Journal', 'PubDate',
date.today()))
self.sess.commit()
self.assertEqual(1, Identifier.doi2pmid('id'))
self.assertEqual(None, Identifier.doi2pmid('other'))
def MedlineCitation(self, element):
options = {}
for name, key in (('DateCompleted', 'completed'),
('DateCreated', 'created'),
('DateRevised', 'revised')):
e = element.find(name)
if e is not None:
options[key] = ParseDate(e)
created = options['created']
del options['created']
status = element.get('Status')
journal = element.find('MedlineJournalInfo').find('MedlineTA').text.strip()
article = element.find('Article')
pub_date = self.parsePubDate(article.find('Journal/JournalIssue/PubDate'))
issue = self.parseIssue(article.find('Journal/JournalIssue'))
pagination = self.parsePagination(article.find('Pagination/MedlinePgn'))
if issue:
options['issue'] = issue
if pagination:
options['pagination'] = pagination
return Medline(self.pmid, status, journal, pub_date, created, **options)
def testPmid2Doi(self):
self.sess.add(Identifier(1, 'doi', 'id'))
self.sess.add(Medline(2, 'MEDLINE', 'Journal', 'PubDate',
date.today()))
self.sess.commit()
self.assertEqual('id', Identifier.pmid2doi(1))
self.assertEqual(None, Identifier.pmid2doi(2))
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)
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 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 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 = Section
self.entity = namedtuple('Section', 'pmid seq name content')
self.defaults = self.entity(1, 1, 'Title', 'The Title')
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 = PublicationType
self.entity = namedtuple('PublicationType', 'pmid value')
self.defaults = self.entity(1, 'type')
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)
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 = Chemical
self.entity = namedtuple('Chemical', 'pmid idx name')
self.defaults = self.entity(1, 1, 'chem')
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 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 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 = Identifier
self.entity = namedtuple('Identifier', 'pmid namespace value')
self.defaults = self.entity(1, 'ns', 'id')
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 = Database
self.entity = namedtuple('Database', 'pmid name accession')
self.defaults = self.entity(1, 'name', 'accession')
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 = Keyword
self.entity = namedtuple('Keyword', 'pmid owner cnt name')
self.defaults = self.entity(1, 'NASA', 1, 'keyword')
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.D = Descriptor(1, 1, 'd_name', True)
self.sess.add(self.D)
self.klass = Qualifier
self.entity = namedtuple('Qualifier', 'pmid num sub name')
self.defaults = self.entity(1, 1, 1, 'name')
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 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 testMapPmids2Dois(self):
self.sess.add(Identifier(1, 'doi', 'id1'))
self.sess.add(Medline(2, 'MEDLINE', 'Journal', 'PubDate',
date.today()))
self.sess.add(Identifier(2, 'doi', 'id2'))
self.sess.commit()
self.assertDictEqual({
1: 'id1',
2: 'id2'
}, Identifier.mapPmids2Dois([1, 2, 3]))
self.assertDictEqual({}, Identifier.mapPmids2Dois([3, 4]))
def testMapDois2Pmids(self):
self.sess.add(Identifier(1, 'doi', 'id1'))
self.sess.add(Medline(2, 'MEDLINE', 'Journal', 'PubDate',
date.today()))
self.sess.add(Identifier(2, 'doi', 'id2'))
self.sess.commit()
self.assertDictEqual({
'id1': 1,
'id2': 2
}, Identifier.mapDois2Pmids(['id1', 'id2', 'id3']))
self.assertDictEqual({}, Identifier.mapDois2Pmids(['id3', 'id4']))
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 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())))
def testToRepr(self):
r = Medline(1, 'MEDLINE', 'journal', 'PubDate', date.today())
self.assertEqual("Medline<1>", repr(r))
def testExisting(self):
self.addThree(date.today())
self.assertListEqual([1, 3], list(Medline.existing([1, 3, 5])))
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 testExisting(self):
self.addThree(date.today())
self.assertListEqual([1, 3], list(Medline.existing([1, 3, 5])))
def testRequireModifiedDateOrNone(self):
m = Medline(*self.defaults)
m.modified = ''
self.sess.add(m)
self.assertRaises(StatementError, self.sess.commit)
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 parse(self, _):
for i in self.instances:
yield i
class TestDump(unittest.TestCase):
def setUp(self):
self.out = {
def testRequireModifiedDateOrNone(self):
m = Medline(*self.defaults)
m.modified = ''
self.sess.add(m)
self.assertRaises(StatementError, self.sess.commit)
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 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()