def article_chunks(self, count, **kwargs):
'''
:param count: chunk size if requested, default is 20
'''
entrez = OpenEmoryEntrezClient()
self.date_opts = self._date_opts(self.min_date, self.max_date, self.auto_date)
qs = entrez.get_emory_articles(**self.date_opts)
return Paginator(qs, count)
def article_chunks(self, count, **kwargs):
'''
:param count: chunk size if requested, default is 20
'''
entrez = OpenEmoryEntrezClient()
self.date_opts = self._date_opts(self.min_date, self.max_date, self.auto_date)
qs = entrez.get_emory_articles(**self.date_opts)
return Paginator(qs, count)
def setUp(self):
self.entrez = OpenEmoryEntrezClient()
class EntrezTest(TestCase):
def setUp(self):
self.entrez = OpenEmoryEntrezClient()
@patch('openemory.harvest.entrez.sleep')
@patch('openemory.harvest.entrez.xmlmap')
def test_get_emory_articles(self, mock_xmlmap, mock_sleep):
'''Verify that test_emory_articles makes an appropriate request to
E-Utils and interprets the result appropriately.'''
# set up mocks
def mock_load(url, xmlclass):
'''mock-like method wrapping load_xmlobject_from_file without
actually making a network query, but still calling the requested
xmlclass constructor.
'''
# figure out what fixture to return
fixture = (mock_load.return_fixtures[mock_load.call_count]
if mock_load.call_count < len(mock_load.return_fixtures)
else mock_load.return_fixtures[-1])
mock_load.call_count += 1
mock_load.urls.append(url)
test_response_path = fixture_path(fixture)
test_response_obj = xmlmap.load_xmlobject_from_file(test_response_path,
xmlclass=xmlclass)
return test_response_obj
mock_load.call_count = 0
mock_load.urls = []
mock_xmlmap.load_xmlobject_from_file = mock_load
# configure the return values
mock_load.return_fixtures = [
'esearch-response-withhist.xml',
'efetch-retrieval-from-hist.xml',
]
# make the call
article_qs = self.entrez.get_emory_articles()
self.assertEqual(mock_xmlmap.load_xmlobject_from_file.call_count, 1)
# check the first query url
self.assertTrue('esearch.fcgi' in mock_load.urls[0])
# these should always be in there per E-Utils policy (see entrez.py)
self.assertTrue('tool=' in mock_load.urls[0])
self.assertTrue('email=' in mock_load.urls[0])
# these are what we're currently querying for. note that these may
# change as our implementation develops. if they do (causing these
# assertions to fail) then we probably need to update our fixture.
self.assertTrue('db=pmc' in mock_load.urls[0])
self.assertTrue('term=emory' in mock_load.urls[0])
self.assertTrue('field=affl' in mock_load.urls[0])
self.assertTrue('usehistory=y' in mock_load.urls[0])
# fetch one
articles = article_qs[:20] # grab a slice to limit the query
articles[0]
self.assertEqual(mock_xmlmap.load_xmlobject_from_file.call_count, 2)
# check that we slept between calls (reqd by eutils policies)
self.assertEqual(mock_sleep.call_count, 1)
sleep_args, sleep_kwargs = mock_sleep.call_args
self.assertTrue(sleep_args[0] >= 0.3)
# check the second query url
self.assertTrue('efetch.fcgi' in mock_load.urls[1])
# always required
self.assertTrue('tool=' in mock_load.urls[1])
self.assertTrue('email=' in mock_load.urls[1])
# what we're currently querying for
self.assertTrue('db=pmc' in mock_load.urls[1])
self.assertTrue('usehistory=y' in mock_load.urls[1])
self.assertTrue('query_key=' in mock_load.urls[1])
self.assertTrue('WebEnv=' in mock_load.urls[1])
self.assertTrue('retmode=xml' in mock_load.urls[1])
self.assertTrue('retstart=0' in mock_load.urls[1])
self.assertTrue('retmax=20' in mock_load.urls[1])
def setUp(self):
self.entrez = OpenEmoryEntrezClient()
class EntrezTest(TestCase):
def setUp(self):
self.entrez = OpenEmoryEntrezClient()
@patch('openemory.harvest.entrez.sleep')
@patch('openemory.harvest.entrez.xmlmap')
def test_get_emory_articles(self, mock_xmlmap, mock_sleep):
'''Verify that test_emory_articles makes an appropriate request to
E-Utils and interprets the result appropriately.'''
# set up mocks
def mock_load(url, xmlclass):
'''mock-like method wrapping load_xmlobject_from_file without
actually making a network query, but still calling the requested
xmlclass constructor.
'''
# figure out what fixture to return
fixture = (mock_load.return_fixtures[mock_load.call_count]
if mock_load.call_count < len(mock_load.return_fixtures)
else mock_load.return_fixtures[-1])
mock_load.call_count += 1
mock_load.urls.append(url)
test_response_path = fixture_path(fixture)
test_response_obj = xmlmap.load_xmlobject_from_file(
test_response_path, xmlclass=xmlclass)
return test_response_obj
mock_load.call_count = 0
mock_load.urls = []
mock_xmlmap.load_xmlobject_from_file = mock_load
# configure the return values
mock_load.return_fixtures = [
'esearch-response-withhist.xml',
'efetch-retrieval-from-hist.xml',
]
# make the call
article_qs = self.entrez.get_emory_articles()
self.assertEqual(mock_xmlmap.load_xmlobject_from_file.call_count, 1)
# check the first query url
self.assertTrue('esearch.fcgi' in mock_load.urls[0])
# these should always be in there per E-Utils policy (see entrez.py)
self.assertTrue('tool=' in mock_load.urls[0])
self.assertTrue('email=' in mock_load.urls[0])
# these are what we're currently querying for. note that these may
# change as our implementation develops. if they do (causing these
# assertions to fail) then we probably need to update our fixture.
self.assertTrue('db=pmc' in mock_load.urls[0])
self.assertTrue('term=emory' in mock_load.urls[0])
self.assertTrue('field=affl' in mock_load.urls[0])
self.assertTrue('usehistory=y' in mock_load.urls[0])
# fetch one
articles = article_qs[:20] # grab a slice to limit the query
articles[0]
self.assertEqual(mock_xmlmap.load_xmlobject_from_file.call_count, 2)
# check that we slept between calls (reqd by eutils policies)
self.assertEqual(mock_sleep.call_count, 1)
sleep_args, sleep_kwargs = mock_sleep.call_args
self.assertTrue(sleep_args[0] >= 0.3)
# check the second query url
self.assertTrue('efetch.fcgi' in mock_load.urls[1])
# always required
self.assertTrue('tool=' in mock_load.urls[1])
self.assertTrue('email=' in mock_load.urls[1])
# what we're currently querying for
self.assertTrue('db=pmc' in mock_load.urls[1])
self.assertTrue('usehistory=y' in mock_load.urls[1])
self.assertTrue('query_key=' in mock_load.urls[1])
self.assertTrue('WebEnv=' in mock_load.urls[1])
self.assertTrue('retmode=xml' in mock_load.urls[1])
self.assertTrue('retstart=0' in mock_load.urls[1])
self.assertTrue('retmax=20' in mock_load.urls[1])