# 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)