def test_config_values(monkeypatch):
fake_config = br.TempFile()
fake_config.write(
"[DEFAULT]\nuser_hash = ABCDEFG\ndiagnostics = True\nemail = [email protected]"
"\nshortcuts = /usr/local/sb,/usr/local/alb")
fake_config.close()
config_path = fake_config.path
monkeypatch.setattr(br, "resource_filename", lambda *_: config_path)
options = br.config_values()
assert options["user_hash"] == "ABCDEFG"
assert options["diagnostics"]
assert options["email"] == "*****@*****.**"
assert options["shortcuts"] == ['/usr/local/sb', '/usr/local/alb']
def mock_keyerror(*args, **kwargs):
raise KeyError(args, kwargs)
monkeypatch.setattr(ConfigParser, "getboolean", mock_keyerror)
monkeypatch.setattr(ConfigParser, "get", mock_keyerror)
options = br.config_values()
assert options["user_hash"] == "hashless"
assert not options["diagnostics"]
assert options["email"] == "*****@*****.**"
def mock_distributionerror(*args, **kwargs):
raise DistributionNotFound(args, kwargs)
monkeypatch.setattr(br, "resource_filename", mock_distributionerror)
options = br.config_values()
assert not options["data_dir"]
def uninstall():
if br.ask("Are you sure you want to completely remove BuddySuite from your system y/[n]? ", default="no"):
# Need to run os.path.split() twice to get to the actual install dir
install_dir, toss = os.path.split(buddysuite.__file__)
install_dir, toss = os.path.split(install_dir)
# Delete all custom shortcuts
config = br.config_values()
for shortcut in config["shortcuts"]:
try:
os.remove(shortcut)
except FileNotFoundError:
pass
# Delete all gateway programs
for buddy in ['seqbuddy', 'alignbuddy', 'phylobuddy', 'databasebuddy', 'buddysuite']:
try:
os.remove(shutil.which(buddy))
except FileNotFoundError:
pass
# Delete the main site-packages module
try:
shutil.rmtree(install_dir)
except FileNotFoundError:
pass
return
def test_ncbiclient_init():
dbbuddy = Db.DbBuddy(", ".join(ACCNS[:3]))
client = Db.NCBIClient(dbbuddy)
assert client.Entrez.email == br.config_values()['email']
assert client.Entrez.tool == "buddysuite"
assert hash(dbbuddy) == hash(client.dbbuddy)
assert type(client.http_errors_file) == br.TempFile
assert type(client.results_file) == br.TempFile
assert client.max_url == 1000
assert client.max_attempts == 5
