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"""Testing code for the EUtils interface for retrieving from Entrez.
"""
import requires_internet
import os
import sys
import unittest
import StringIO
from Bio import EUtils
from Bio.EUtils import HistoryClient
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [HistoryClientTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class HistoryClientTest(unittest.TestCase):
"""Tests for the EUtils HistoryClient interface.
"""
def setUp(self):
self.client = HistoryClient.HistoryClient()
def tearDown(self):
pass
def t_simple_search(self):
"""Simple text search from PubMed.
"""
search = self.client.search("narrow sheath")
assert len(search) > 0
def t_retrieve_search(self):
"""Search and retrieval of PubMed records.
"""
num_to_fetch = 3
search = self.client.search("opuntia ficus indica")
results = search[:num_to_fetch].efetch(retmode = "text",
rettype = "docsum").read()
num_records = 0
for line in results.split("\n"):
if line.find("PMID:") == 0:
num_records += 1
assert num_records == num_to_fetch, results
def t_retrieve_many(self):
"""Retrieving more than 500 sequences from nucleotide database.
"""
search = self.client.search("Arabidopsis", db = "nucleotide",
daterange = EUtils.DateRange("1995/01/01", "1995/04/15",
"mdat"))
results = search.efetch(retmode = "text", rettype = "seqid").read()
num_records = 0
for line in results.split("\n"):
if line.find("::= gi ") > 0:
num_records += 1
assert num_records > 500, num_records
def t_retrieve_by_accession(self):
"""Retrieve a single nucleotide record by accession.
"""
search = self.client.search("AA759046", db="nucleotide")
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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