def test_guess_db(capsys, hf):
test_in_args = deepcopy(in_args)
test_in_args.guess_database = True
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, Db.DbBuddy(), skip_exit=True)
out, err = capsys.readouterr()
assert 'Nothing to return' in out
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, Db.DbBuddy(",".join(ACCNS) + ",Casp9"), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "4b3edb0272b02d8e18ce591304fdea1d"
def test_error(monkeypatch, capsys):
monkeypatch.setattr(Db, "LiveShell", mock_systemexit)
test_in_args = deepcopy(in_args)
test_in_args.live_shell = True
assert Db.command_line_ui(test_in_args, Db.DbBuddy(), skip_exit=True) is None
monkeypatch.setattr(Db, "LiveShell", mock_fileexistserror)
monkeypatch.setattr(br.TempFile, "save", lambda *_: True)
monkeypatch.setattr(br, "send_traceback", lambda *_: True)
capsys.readouterr()
assert Db.command_line_ui(test_in_args, Db.DbBuddy(), skip_exit=True) is None
out, err = capsys.readouterr()
assert "can be loaded by launching DatabaseBuddy and using the 'load' command." in err
def test_exit(monkeypatch, capsys):
class MockExitUsage(object):
@staticmethod
def increment(*args):
print(args)
return True
@staticmethod
def save():
return True
monkeypatch.setattr(br, "Usage", MockExitUsage)
monkeypatch.setattr(Db, "LiveShell", lambda *_: True)
test_in_args = deepcopy(in_args)
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, Db.DbBuddy())
out, err = capsys.readouterr()
assert "('DatabaseBuddy', '%s', 'LiveShell', 0)" % Db.VERSION.short() in out
def test_retrieve_sequences(monkeypatch, capsys, sb_resources, hf):
# Don't actually run anything, retrieve_summary() is tested elsewhere
monkeypatch.setattr(Db, "retrieve_summary", lambda *_: True)
monkeypatch.setattr(Db, "retrieve_sequences", lambda *_: True)
test_in_args = deepcopy(in_args)
test_in_args.retrieve_sequences = True
dbbuddy = Db.DbBuddy()
dbbuddy.failures = OrderedDict([("Foo", ValueError("Blahh")), ("Bar", AttributeError("Blahh"))])
dbbuddy.records = sb_resources.get_one("f d").records
for rec in dbbuddy.records:
rec.id = re.sub("α", "", rec.id)
rec.description = re.sub("α", "", rec.description)
dbbuddy.records = OrderedDict([(rec.id, rec) for rec in dbbuddy.records])
for accn, rec in dbbuddy.records.items():
rec.size = len(rec)
rec.record = rec
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, dbbuddy)
out, err = capsys.readouterr()
assert dbbuddy.out_format == "fasta"
assert hf.string2hash(out) == "5438dd48c22fd7b6cf2d3da637d333b6"
assert err == """\
# ###################### Failures ###################### #
Foo
Blahh
Bar
Blahh
# ############################################## #
"""
monkeypatch.setattr(br, "ask", lambda _, **kwargs: False)
for accn, rec in dbbuddy.records.items():
rec.size *= 100
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, dbbuddy)
out, err = capsys.readouterr()
assert out == '\x1b[91mAborted...\n\n\x1b[m\x1b[40m'
def test_retrieve_accessions(monkeypatch):
# Don't actually run anything, retrieve_summary() is tested elsewhere
monkeypatch.setattr(Db, "retrieve_summary", lambda *_: True)
test_in_args = deepcopy(in_args)
test_in_args.retrieve_accessions = True
dbbuddy = Db.DbBuddy()
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, dbbuddy)
assert dbbuddy.out_format == "ids"
test_in_args.out_format = "genbank"
dbbuddy = Db.DbBuddy(_out_format="genbank")
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, dbbuddy)
assert dbbuddy.out_format == "ids"
for out_format in ["ids", "accessions", "full-summary", "summary"]:
test_in_args.out_format = out_format
dbbuddy = Db.DbBuddy(_out_format=out_format)
with pytest.raises(SystemExit):
Db.command_line_ui(test_in_args, dbbuddy)
assert dbbuddy.out_format == out_format
