# Copyright 2012 by Wibowo Arindrarto. 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. """Tests for online Entrez access. This file include tests for accessing the online Entrez service and parsing the returned results. Note that we are merely testing the access and whether the results are parseable. Detailed tests on each Entrez service are not within the scope of this file as they are already covered in test_Entrez.py. """ from Bio import Entrez from Bio import Medline from Bio import SeqIO from Bio.SeqRecord import SeqRecord import doctest import os import sys import unittest import requires_internet requires_internet.check() # This lets us set the email address to be sent to NCBI Entrez: Entrez.email = "biopython@biopython.org" Entrez.api_key = "5cfd4026f9df285d6cfc723c662d74bcbe09" URL_HEAD = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" URL_TOOL = "tool=biopython" URL_EMAIL = "email=biopython%40biopython.org" URL_API_KEY = "api_key=5cfd4026f9df285d6cfc723c662d74bcbe09" class EntrezOnlineCase(unittest.TestCase): def test_no_api_key(self): """Test Entrez.read without API key.""" cached = Entrez.api_key Entrez.api_key = None # default try: handle = Entrez.einfo() finally: # Do not want any failure here to break other tests Entrez.api_key = cached self.assertTrue(handle.url.startswith(URL_HEAD + "einfo.fcgi?"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertNotIn("api_key=", handle.url) rec = Entrez.read(handle) handle.close() self.assertIsInstance(rec, dict) self.assertIn("DbList", rec) # arbitrary number, just to make sure that DbList has contents self.assertTrue(len(rec["DbList"]) > 5) def test_read_from_url(self): """Test Entrez.read from URL.""" handle = Entrez.einfo() self.assertTrue(handle.url.startswith(URL_HEAD + "einfo.fcgi?"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertIn(URL_API_KEY, handle.url) rec = Entrez.read(handle) handle.close() self.assertIsInstance(rec, dict) self.assertIn("DbList", rec) # arbitrary number, just to make sure that DbList has contents self.assertTrue(len(rec["DbList"]) > 5) def test_parse_from_url(self): """Test Entrez.parse from URL.""" handle = Entrez.efetch( db="protein", id="15718680, 157427902, 119703751", retmode="xml" ) self.assertTrue(handle.url.startswith(URL_HEAD + "efetch.fcgi?"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertIn(URL_API_KEY, handle.url) self.assertIn("id=15718680%2C157427902%2C119703751", handle.url) recs = list(Entrez.parse(handle)) handle.close() self.assertEqual(3, len(recs)) # arbitrary number, just to make sure the parser works self.assertTrue(all(len(rec).keys > 5) for rec in recs) def test_webenv_search(self): """Test Entrez.search from link webenv history.""" handle = Entrez.elink( db="nucleotide", dbfrom="protein", id="22347800,48526535", webenv=None, query_key=None, cmd="neighbor_history", ) self.assertTrue(handle.url.startswith(URL_HEAD + "elink.fcgi?"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertIn(URL_API_KEY, handle.url) self.assertIn("id=22347800%2C48526535", handle.url) recs = Entrez.read(handle) handle.close() record = recs.pop() webenv = record["WebEnv"] query_key = record["LinkSetDbHistory"][0]["QueryKey"] handle = Entrez.esearch( db="nucleotide", term=None, retstart=0, retmax=10, webenv=webenv, query_key=query_key, usehistory="y", ) self.assertTrue(handle.url.startswith(URL_HEAD + "esearch.fcgi?"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertIn(URL_API_KEY, handle.url) search_record = Entrez.read(handle) handle.close() self.assertEqual(2, len(search_record["IdList"])) def test_seqio_from_url(self): """Test Entrez into SeqIO.read from URL.""" handle = Entrez.efetch( db="nucleotide", id="186972394", rettype="gb", retmode="text" ) url = handle.url self.assertTrue(url.startswith(URL_HEAD + "efetch.fcgi?"), url) self.assertIn(URL_TOOL, url) self.assertIn(URL_EMAIL, url) self.assertIn(URL_API_KEY, url) self.assertIn("id=186972394", url) record = SeqIO.read(handle, "genbank") handle.close() self.assertIsInstance(record, SeqRecord) self.assertEqual("EU490707.1", record.id) self.assertEqual(1302, len(record)) def test_medline_from_url(self): """Test Entrez into Medline.read from URL.""" handle = Entrez.efetch( db="pubmed", id="19304878", rettype="medline", retmode="text" ) url = handle.url self.assertTrue(url.startswith(URL_HEAD + "efetch.fcgi?"), url) self.assertIn(URL_TOOL, url) self.assertIn(URL_EMAIL, url) self.assertIn(URL_API_KEY, url) self.assertIn("id=19304878", url) record = Medline.read(handle) handle.close() self.assertIsInstance(record, dict) self.assertEqual("19304878", record["PMID"]) self.assertEqual("10.1093/bioinformatics/btp163 [doi]", record["LID"]) def test_efetch_biosystems_xml(self): """Test Entrez parser with XML from biosystems.""" handle = Entrez.efetch(id="1134002", db="biosystems", retmode="xml") records = list(Entrez.parse(handle)) handle.close() self.assertEqual(len(records), 1) self.assertEqual(records[0]["System_sysid"]["Sys-id"]["Sys-id_bsid"], "1134002") def test_efetch_taxonomy_xml(self): """Test Entrez using a integer id - like a taxon id.""" handle = Entrez.efetch(db="taxonomy", id=3702, retmode="XML") taxon_record = Entrez.read(handle) self.assertTrue(1, len(taxon_record)) self.assertIn("TaxId", taxon_record[0]) self.assertTrue("3702", taxon_record[0]["TaxId"]) handle.close() def test_elink(self): """Test Entrez.elink with multiple ids, both comma separated and as list.""" # Commas: Link from protein to gene handle = Entrez.elink( db="gene", dbfrom="protein", id="15718680,157427902,119703751" ) self.assertTrue(handle.url.startswith(URL_HEAD + "elink.fcgi"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertIn(URL_API_KEY, handle.url) self.assertIn("id=15718680%2C157427902%2C119703751", handle.url) handle.close() # Multiple ID entries: Find one-to-one links from protein to gene handle = Entrez.elink( db="gene", dbfrom="protein", id=["15718680", "157427902", "119703751"] ) self.assertTrue(handle.url.startswith(URL_HEAD + "elink.fcgi"), handle.url) self.assertIn(URL_TOOL, handle.url) self.assertIn(URL_EMAIL, handle.url) self.assertIn(URL_API_KEY, handle.url) self.assertIn("id=15718680", handle.url) self.assertIn("id=157427902", handle.url) self.assertIn("id=119703751", handle.url) handle.close() def test_epost(self): """Test Entrez.epost with multiple ids, both comma separated and as list.""" handle = Entrez.epost("nuccore", id="186972394,160418") self.assertEqual(URL_HEAD + "epost.fcgi", handle.url) handle.close() handle = Entrez.epost("nuccore", id=["160418", "160351"]) self.assertEqual(URL_HEAD + "epost.fcgi", handle.url) handle.close() def test_egquery(self): """Test Entrez.egquery. which searches in all Entrez databases for a single text query. """ handle = Entrez.egquery(term="biopython") record = Entrez.read(handle) handle.close() done = False for row in record["eGQueryResult"]: if "pmc" in row["DbName"]: self.assertTrue(int(row["Count"]) > 60) done = True self.assertTrue(done) def test_espell(self): """Test misspellings with Entrez.espell.""" handle = Entrez.espell(term="biopythooon") record = Entrez.read(handle) handle.close() self.assertEqual(record["Query"], "biopythooon") self.assertEqual(record["CorrectedQuery"], "biopython") def test_ecitmatch(self): """Test Entrez.ecitmatch to search for a citation.""" citation = { "journal_title": "proc natl acad sci u s a", "year": "1991", "volume": "88", "first_page": "3248", "author_name": "mann bj", "key": "citation_1", } handle = Entrez.ecitmatch(db="pubmed", bdata=[citation]) url = handle.url self.assertIn("retmode=xml", url) result = handle.read() expected_result = ( "proc natl acad sci u s a|1991|88|3248|mann bj|citation_1|2014248\n" ) self.assertEqual(result, expected_result) handle.close() def test_efetch_ids(self): """Test different options to supply ids.""" ids = ( [15718680, 157427902], (15718680, 157427902), {15718680, 157427902}, ["15718680", "157427902"], ("15718680", "157427902"), {15718680, "157427902"}, "15718680, 157427902", ) for _id in ids: with Entrez.efetch(db="protein", id=_id, retmode="xml") as handle: # _id can be a set with unpredictable sorting, # thus we test the ids separately self.assertIn("15718680", handle.url) self.assertIn("157427902", handle.url) recs = list(Entrez.parse(handle)) self.assertEqual(2, len(recs)) ids = ( [15718680], (15718680), {15718680}, 15718680, "15718680", "15718680,", ) for _id in ids: with Entrez.efetch(db="protein", id=_id, retmode="xml") as handle: self.assertIn("15718680", handle.url) recs = list(Entrez.parse(handle)) self.assertEqual(1, len(recs)) def test_efetch_gds_utf8(self): """Test correct handling of encodings in Entrez.efetch.""" # See issue #1402 in case any encoding issues occur handle = Entrez.efetch(db="gds", id="200079209") url = handle.url self.assertTrue(url.startswith(URL_HEAD + "efetch.fcgi?"), url) self.assertIn(URL_TOOL, url) self.assertIn(URL_EMAIL, url) self.assertIn(URL_API_KEY, url) self.assertIn("id=200079209", url) text = handle.read() # Use of Unicode double quotation marks U+201C and U+201D expected_phrase = "“field of injury”" self.assertEqual(text[342:359], expected_phrase) handle.close() def test_fetch_xml_schemas(self): handle = Entrez.efetch("protein", id="783730874", rettype="ipg", retmode="xml") record = Entrez.read(handle, validate=False) handle.close() self.assertEqual(len(record), 1) self.assertIn("IPGReport", record) self.assertIn("Product", record["IPGReport"]) self.assertIn("Statistics", record["IPGReport"]) self.assertIn("ProteinList", record["IPGReport"]) if __name__ == "__main__": # When running test_Entrez.py directly, will also include the # Bio.Entrez doctests. # TODO: Include the doctests via run_tests.py when online. unittest_suite = unittest.TestLoader().loadTestsFromName("test_Entrez_online") doctest_suite = doctest.DocTestSuite(Entrez) suite = unittest.TestSuite((unittest_suite, doctest_suite)) runner = unittest.TextTestRunner(sys.stdout, verbosity=2) runner.run(suite)