def test_email_warning(self):
"""Test issuing warning when user does not specify email address."""
Entrez.email = None
with warnings.catch_warnings(record=True) as w:
Entrez._construct_params(params=None)
self.assertEqual(len(w), 1)
def test_email_warning(self):
"""Test issuing warning when user does not specify email address."""
Entrez.email = None
with warnings.catch_warnings(record=True) as w:
Entrez._construct_params(params=None)
self.assertEqual(len(w), 1)
def test_construct_cgi_epost2(self):
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'
variables = {'db': 'nuccore', 'id': ["160418", "160351"]}
post = True
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertEqual(URL_HEAD + "epost.fcgi", result_url)
def test_construct_cgi_epost2(self):
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi'
variables = {'db': 'nuccore', 'id': ["160418", "160351"]}
post = True
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertEqual(URL_HEAD + "epost.fcgi", result_url)
def test_construct_cgi_epost1(self):
cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi"
variables = {"db": "nuccore", "id": "186972394,160418"}
post = True
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertEqual(URL_HEAD + "epost.fcgi", result_url)
def test_construct_cgi_einfo(self):
"""Test constructed url for request to Entrez."""
cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"
params = Entrez._construct_params(params=None)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=False, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "einfo.fcgi?"), result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
def test_construct_cgi_einfo(self):
"""Test constructed url for request to Entrez."""
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi'
params = Entrez._construct_params(params=None)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=False, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "einfo.fcgi?"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
def test_construct_cgi_elink1(self):
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
variables = {'cmd': 'neighbor_history', 'db': 'nucleotide',
'dbfrom': 'protein', 'id': '22347800,48526535',
'query_key': None, 'webenv': None}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi?"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertIn("id=22347800%2C48526535", result_url)
def test_construct_cgi_ecitmatch(self):
citation = {
"journal_title": "proc natl acad sci u s a",
"year": "1991", "volume": "88", "first_page": "3248",
"author_name": "mann bj", "key": "citation_1"
}
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi'
variables = Entrez._update_ecitmatch_variables({'db': 'pubmed',
'bdata': [citation]})
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=True, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertIn("retmode=xml", result_url)
def test_construct_cgi_efetch(self):
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
variables = {'db': 'protein', 'id': '15718680,157427902,119703751',
'retmode': 'xml'}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "efetch.fcgi?"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertTrue("id=15718680%2C157427902%2C119703751" in result_url,
result_url)
def test_construct_cgi_elink2(self):
"""Commas: Link from protein to gene."""
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
variables = {'db': 'gene', 'dbfrom': 'protein',
'id': '15718680,157427902,119703751'}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertTrue("id=15718680%2C157427902%2C119703751" in result_url,
result_url)
def test_construct_cgi_elink1(self):
cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
variables = {"cmd": "neighbor_history", "db": "nucleotide",
"dbfrom": "protein", "id": "22347800,48526535",
"query_key": None, "webenv": None}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi?"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertIn("id=22347800%2C48526535", result_url)
self.assertIn(URL_API_KEY, result_url)
def test_construct_cgi_efetch(self):
cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
variables = {"db": "protein", "id": "15718680,157427902,119703751",
"retmode": "xml"}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "efetch.fcgi?"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertTrue("id=15718680%2C157427902%2C119703751" in result_url,
result_url)
self.assertIn(URL_API_KEY, result_url)
def test_construct_cgi_elink3(self):
"""Multiple ID entries: Find one-to-one links from protein to gene."""
cgi = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi'
variables = {'db': 'gene', 'dbfrom': 'protein',
'id': ["15718680", "157427902", "119703751"]}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertIn("id=15718680", result_url)
self.assertIn("id=157427902", result_url)
self.assertIn("id=119703751", result_url)
def test_construct_cgi_elink2(self):
"""Commas: Link from protein to gene."""
cgi = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
variables = {"db": "gene", "dbfrom": "protein",
"id": "15718680,157427902,119703751"}
post = False
params = Entrez._construct_params(variables)
options = Entrez._encode_options(ecitmatch=False, params=params)
result_url = Entrez._construct_cgi(cgi, post=post, options=options)
self.assertTrue(result_url.startswith(URL_HEAD + "elink.fcgi"),
result_url)
self.assertIn(URL_TOOL, result_url)
self.assertIn(URL_EMAIL, result_url)
self.assertIn("id=15718680%2C157427902%2C119703751", result_url,
result_url)
self.assertIn(URL_API_KEY, result_url)
