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 testMapPmids2Dois(self):
self.sess.add(Identifier(1, 'doi', 'id1'))
self.sess.add(DefaultCitation(2))
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 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 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 testMapDois2Pmids(self):
self.sess.add(Identifier(1, 'doi', 'id1'))
self.sess.add(DefaultCitation(2))
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 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 testMapPmids2Dois(self):
self.sess.add(Identifier(1, 'doi', 'id1'))
self.sess.add(DefaultCitation(2))
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(DefaultCitation(2))
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 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 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 ArticleId(self, element):
instance = None
ns = element.get('IdType').strip().lower()
text = element.text.strip()
if ns in self.namespaces:
if re.match('\d[\d\.]+/.+', element.text.strip()) and \
'doi' not in self.namespaces:
self.namespaces.add('doi')
instance = Identifier(self.pmid, 'doi', text)
else:
logger.info('skipping duplicate %s identifier "%s"', ns, text)
else:
self.namespaces.add(ns)
instance = Identifier(self.pmid, ns, text)
return instance
def OtherID(self, element):
if element.get('Source', None) == 'NLM':
text = element.text.strip()
if text.startswith('PMC'):
if 'pmc' not in self.namespaces:
self.namespaces.add('pmc')
return Identifier(self.pmid, 'pmc', text.split(' ', 1)[0])
def testPmid2Doi(self):
self.sess.add(Identifier(1, 'doi', 'id'))
self.sess.add(DefaultCitation(2))
self.sess.commit()
self.assertEqual('id', Identifier.pmid2doi(1))
self.assertEqual(None, Identifier.pmid2doi(2))
def ELocationID(self, element):
ns = element.get('EIdType').strip().lower()
if ns not in self.namespaces:
self.namespaces.add(ns)
return Identifier(self.pmid, ns, element.text.strip())
def testDoi2Pmid(self):
self.sess.add(Identifier(1, 'doi', 'id'))
self.sess.add(DefaultCitation(2))
self.sess.commit()
self.assertEqual(1, Identifier.doi2pmid('id'))
self.assertEqual(None, Identifier.doi2pmid('other'))
def testPmid2Doi(self):
self.sess.add(Identifier(1, 'doi', 'id'))
self.sess.add(DefaultCitation(2))
self.sess.commit()
self.assertEqual('id', Identifier.pmid2doi(1))
self.assertEqual(None, Identifier.pmid2doi(2))
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 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'))
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 parse(self, _):
for i in self.instances:
def testToString(self):
self.assertEqual('1\tns\tid\n', str(Identifier(1, 'ns', 'id')))
def testToRepr(self):
self.assertEqual('Identifier<1:ns>', repr(Identifier(1, 'ns', 'id')))
def testDoi2Pmid(self):
self.sess.add(Identifier(1, 'doi', 'id'))
self.sess.add(DefaultCitation(2))
self.sess.commit()
self.assertEqual(1, Identifier.doi2pmid('id'))
self.assertEqual(None, Identifier.doi2pmid('other'))
def testRelations(self):
i = Identifier(1, 'ns', 'id')
self.sess.add(i)
self.sess.commit()
self.assertEqual({'ns': i}, self.M.identifiers)
self.assertEqual(self.M, i.citation)