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# Copyright 2015 by Carlos Pena. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Offline tests for two Entrez features.
(1) the URL construction of NCBI's Entrez services.
(2) setting a custom directory for DTD and XSD downloads.
"""
import unittest
import warnings
from Bio import Entrez
from Bio.Entrez import Parser
# This lets us set the email address to be sent to NCBI Entrez:
Entrez.email = "biopython@biopython.org"
Entrez.api_key = "5cfd4026f9df285d6cfc723c662d74bcbe09"
URL_HEAD = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
URL_TOOL = "tool=biopython"
URL_EMAIL = "email=biopython%40biopython.org"
URL_API_KEY = "api_key=5cfd4026f9df285d6cfc723c662d74bcbe09"
class TestURLConstruction(unittest.TestCase):
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_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)
self.assertIn(URL_API_KEY, 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_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_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_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_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)
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)
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.assertIn("id=15718680%2C157427902%2C119703751", result_url, result_url)
self.assertIn(URL_API_KEY, result_url)
class CustomDirectoryTest(unittest.TestCase):
"""Offline unit test for custom directory feature.
Allow user to specify a custom directory for Entrez DTD/XSD files by setting
Parser.DataHandler.directory.
"""
def test_custom_directory(self):
import tempfile
import os
import shutil
handler = Parser.DataHandler(validate=False, escape=False)
# Create a temporary directory
tmpdir = tempfile.mkdtemp()
# Set the custom directory to the temporary directory.
# This assignment statement will also initialize the local DTD and XSD
# directories.
handler.directory = tmpdir
# Confirm that the two temp directories are named what we want.
self.assertEqual(
handler.local_dtd_dir,
os.path.join(handler.directory, "Bio", "Entrez", "DTDs"),
)
self.assertEqual(
handler.local_xsd_dir,
os.path.join(handler.directory, "Bio", "Entrez", "XSDs"),
)
# And that they were created.
self.assertTrue(os.path.isdir(handler.local_dtd_dir))
self.assertTrue(os.path.isdir(handler.local_xsd_dir))
shutil.rmtree(tmpdir)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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