class TestPubmedFetcher(unittest.TestCase):
def setUp(self):
self.fetch = PubMedFetcher()
def tearDown(self):
pass
def test_pmids_for_query(self):
params = {'journal': 'PLoS One',
'year': 2013,
'author': 'McMurry AJ'}
pmids = self.fetch.pmids_for_query(**params)
assert len(pmids) == 1
assert pmids[0] == '23533569'
# this pubmed ID was deleted
params = {'TA': 'Journal of Neural Transmission',
'pdat': 2014,
'vol': 121,
'aulast': 'Freitag'
}
pmids = self.fetch.pmids_for_query(**params)
assert len(pmids) == 0
def test_medical_genetics_query(self):
# we presume that the results for a fixed year prior to this one will not change.
results = self.fetch.pmids_for_medical_genetics_query('Brugada Syndrome', 'diagnosis', debug=True, year=2013)
assert '24775617' in results
def test_clinical_query(self):
# we presume that the results for a fixed year prior to this one will not change.
results = self.fetch.pmids_for_clinical_query('Global developmental delay', 'etiology', 'narrow', debug=True, year=2013)
assert results[0] == '24257216'
assert results[1] == '24123848'
assert results[2] == '24089199'
def test_specified_return_slice(self):
pmids = self.fetch.pmids_for_query(since='2015/3/1', retmax=1000)
assert len(pmids) == 1000
pmids = self.fetch.pmids_for_query(since='2015/3/1', retstart=200, retmax=500)
assert len(pmids) == 500
def test_pmc_only(self):
params = {'mesh': 'breast neoplasm'}
stuff = self.fetch.pmids_for_query(since='2015/1/1', until='2015/3/1', pmc_only=True, **params)
print(stuff)
def test_ncbi_book_id_to_pubmed(self):
for eg in NCBI_BOOKS:
result = self.fetch.pmids_for_query(eg['book_id'])
if len(result) > 0:
assert result[0] == eg['pmid']
else:
assert eg['pmid'] is None
print(eg, result)
from __future__ import absolute_import, print_function, unicode_literals
from metapub import PubMedFetcher
fetch = PubMedFetcher()
term = 'Global developmental delay'
print('%s: etiology broad' % term)
results = fetch.pmids_for_clinical_query(term,
'etiology',
debug=True,
year=2013)
print('First three results:')
print(results[:3])
print('')
print('%s: etiology narrow' % term)
results = fetch.pmids_for_clinical_query(term,
'etiology',
'narrow',
debug=True,
year=2013)
print('First three results:')
print(results[:3])
print('')
print('tyrosine kinase inhibitor: diagnosis')
results = fetch.pmids_for_clinical_query('tyrosine kinase inhibitor',
