def it_shows_error_on_stop_for_slow_start(self):
assert_command(
('pgctl-2015', 'start', 'slow-startup'),
'',
'''\
[pgctl] Starting: slow-startup
[pgctl] Started: slow-startup
''',
0,
)
assert_command(
('pgctl-2015', 'restart', 'slow-startup'),
'''\
==> playground/slow-startup/stdout.log <==
==> playground/slow-startup/stderr.log <==
pgctl-poll-ready: service's ready check succeeded
pgctl-poll-ready: service is stopping -- quitting the poll
''',
S(
self.LOCKERROR.format(service='slow-startup',
time='5',
cmd='sleep 987654')),
1,
)
def it_shows_error_on_stop_for_sweet(self):
assert_command(
('pgctl-2015', 'start', 'sweet'),
'',
'''\
[pgctl] Starting: sweet
[pgctl] Started: sweet
''',
0,
)
assert_command(
('pgctl-2015', 'restart', 'sweet'),
'''\
==> playground/sweet/stdout.log <==
sweet
==> playground/sweet/stderr.log <==
sweet_error
''',
S(
self.LOCKERROR.format(service='sweet',
time='5',
cmd='sleep infinity')),
1,
)
def it_cant_parse_nonsense(self, tmpdir):
conffile = tmpdir.join('my.nonsense')
conffile.write(example1.yaml)
with ShouldRaise(
C.UnrecognizedConfig(
S(r'Unknown config type: .*/my\.nonsense'))):
example1.config.from_file(conffile.strpath)
def test_order_doesnt_matter_ok(self):
capture = LogCapture.make(self)
log.info('Failed to send BAR')
log.info('Sent FOO, length 1234')
log.info('Sent 1 Messages')
capture.check((INFO, S('Sent FOO, length \d+')),
(INFO, 'Failed to send BAR'), (INFO, 'Sent 1 Messages'),
order_matters=False)
def it_displays_correctly_when_the_service_is_up(self, in_example_dir):
check_call(('pgctl-2015', 'start', 'sleep'))
assert_command(
('pgctl-2015', 'status', 'sleep'),
S('sleep: ready \\(pid \\d+\\) \\d+ seconds\\n$'),
'',
0,
)
def it_logs_continuously_when_run_interactively(self, in_example_dir):
check_call(('pgctl', 'start'))
# this pty simulates running in a terminal
read, write = os.openpty()
pty.normalize_newlines(read)
p = Popen(('pgctl', 'log'), stdout=write, stderr=write)
os.close(write)
import fcntl
fl = fcntl.fcntl(read, fcntl.F_GETFL)
fcntl.fcntl(read, fcntl.F_SETFL, fl | os.O_NONBLOCK)
assert p.poll() is None # it's still running
# needs to loop for several seconds because the default event loop
# in tail-f is one second.
# TODO: buf is a list, use wait_for() to append to it
limit = 3.0
wait = .1
buf = b''
while True:
try:
block = os.read(read, 1024)
print('BLOCK:', block)
except OSError as error:
print('ERROR:', error)
if error.errno == 11: # other end didn't write yet
if limit > 0:
import time
time.sleep(wait)
limit -= wait
continue
else:
break
else:
raise
buf += block
from testfixtures import StringComparison as S
buf = norm.pgctl(buf.decode('UTF-8'))
print('NORMED:')
print(buf)
assert buf == S('''(?s)\
==> playground/ohhi/log <==
{TIMESTAMP} [oe].*
==> playground/sweet/log <==
{TIMESTAMP} sweet
{TIMESTAMP} sweet_error
==> playground/ohhi/log <==
.*{TIMESTAMP} .*$''')
assert p.poll() is None # it's still running
p.terminate()
assert p.wait() == -15
def it_explodes_on_ambiguity(self, tmpdir):
conffile = tmpdir.join('example1.ini')
conffile.write(example1.ini)
conffile = tmpdir.join('example1.conf')
conffile.write(example1.ini)
with ShouldRaise(
C.AmbiguousConfig(
S(r'multiple configurations found at .*/example1\.\*'))):
example1.config.from_path_prefix(tmpdir.strpath + '/')
def test_sort(self):
a = S('a')
b = S('b')
c = S('c')
compare(sorted((
'd',
c,
'e',
a,
'a1',
b,
)), [
a,
'a1',
b,
c,
'd',
'e',
])
def it_logs_continuously_when_run_interactively(self, in_example_dir):
check_call(('pgctl-2015', 'start'))
# this pty simulates running in a terminal
read, write = os.openpty()
pty_normalize_newlines(read)
p = Popen(('pgctl-2015', 'log'), stdout=write, stderr=write)
os.close(write)
import fcntl
fl = fcntl.fcntl(read, fcntl.F_GETFL)
fcntl.fcntl(read, fcntl.F_SETFL, fl | os.O_NONBLOCK)
assert p.poll() is None # it's still running
# needs to loop for at least two seconds because the default event loop
# in tail-f is one second.
retries = 20
buf = ''
while True:
try:
block = os.read(read, 1024)
print('BLOCK:', block)
except OSError as error:
print('ERROR:', error)
if error.errno == 11: # other end didn't write yet
if retries > 0:
retries -= 1
import time
time.sleep(.1)
continue
else:
break
else:
raise
buf += block
assert buf == S('''(?s)\
==> playground/ohhi/stdout\\.log <==
o.*
==> playground/ohhi/stderr\\.log <==
e.*
==> playground/sweet/stdout\\.log <==
sweet
==> playground/sweet/stderr\\.log <==
sweet_error
.*$''')
assert p.poll() is None # it's still running
p.terminate()
assert p.wait() == -15
def it_displays_the_status_of_all_services(self, in_example_dir):
"""Expect all services to provide status when no service is specified"""
check_call(('pgctl-2015', 'start', 'tail'))
assert_command(
('pgctl-2015', 'status'),
S('''\
sleep: down
tail: ready \\(pid \\d+\\) \\d+ seconds
$'''),
'',
0,
)
def it_displays_the_status_of_multiple_services(self, in_example_dir):
"""Expect multiple services with status and PID"""
check_call(('pgctl-2015', 'start', 'sleep'))
assert_command(
('pgctl-2015', 'status', 'sleep', 'tail'),
S('''\
sleep: ready \\(pid \\d+\\) \\d+ seconds
tail: down
$'''),
'',
0,
)
def test_warning_no_csq_for_variants(self):
logging.disable(logging.NOTSET)
with LogCapture() as l:
temp_path = tempfile.TemporaryDirectory()
os.symlink(os.path.join(self.test_data_dir, 'input.no_csq.vcf'), os.path.join(temp_path.name, 'input.vcf'))
command = [
os.path.join(temp_path.name, 'input.vcf'),
os.path.join(self.test_data_dir, 'genes.fpkm_tracking'),
'cufflinks',
'gene',
]
vcf_expression_annotator.main(command)
temp_path.cleanup()
l.check_present(('root', 'WARNING', S("Variant is missing VEP annotation. INFO column doesn't contain CSQ field for variant")))
def test_class(self):
class SomethingElse:
pass
if PY2:
text = ("<class mortar_rdb.tests.test_controlled_schema."
"SomethingElse at [0-9a-zA-Z]+>")
else:
text = ("<class 'mortar_rdb.tests.test_controlled_schema."
"TestSource.test_class.<locals>.SomethingElse'>")
with ShouldRaise(
TypeError(
S(text + " must be a "
"Table object or a declaratively mapped model class."))):
s = Source(SomethingElse)
def it_fails_by_default(self):
check_call(('pgctl-2015', 'start'))
assert_svstat('playground/sweet', state='up')
assert_command(
('pgctl-2015', 'stop'),
'''\
==> playground/sweet/stdout.log <==
sweet
==> playground/sweet/stderr.log <==
sweet_error
''',
S(
self.LOCKERROR.format(service='sweet',
time='1\\.5',
cmd='sleep 2\\.25')),
1,
)
def test_order_doesnt_matter_extra_in_expected(self):
capture = LogCapture.make(self)
log.info('Failed to send BAR')
log.info('Sent FOO, length 1234')
with ShouldAssert("entries not as expected:\n"
"\n"
"expected and found:\n"
"[(<LogLevel=info>, 'Failed to send BAR'),\n"
" (<LogLevel=info>, <S:Sent FOO, length 1234>)]\n"
"\n"
"expected but not found:\n"
"[(<LogLevel=info>, 'Sent 1 Messages')]\n"
"\n"
"other entries:\n"
"[]"):
capture.check((INFO, S('Sent FOO, length 1234')),
(INFO, 'Failed to send BAR'),
(INFO, 'Sent 1 Messages'),
order_matters=False)
def test_order_doesnt_matter_failure(self):
capture = LogCapture.make(self)
log.info('Failed to send BAR')
log.info('Sent FOO, length 1234')
log.info('Sent 1 Messages')
with ShouldAssert(
"entries not as expected:\n"
"\n"
"expected and found:\n"
"[(<LogLevel=info>, 'Failed to send BAR'), (<LogLevel=info>, 'Sent 1 Messages')]\n"
"\n"
"expected but not found:\n"
"[(<LogLevel=info>, <S:Sent FOO, length abc>)]\n"
"\n"
"other entries:\n"
"[(<LogLevel=info>, {}'Sent FOO, length 1234')]".format(
'' if PY3 else 'u')):
capture.check((INFO, S('Sent FOO, length abc')),
(INFO, 'Failed to send BAR'),
(INFO, 'Sent 1 Messages'),
order_matters=False)
def test_cmp_no(self):
self.failUnless(cmp(S('on \d+'), 'on xx'))
def test_cmp_yes(self):
self.failIf(cmp(S('on \d+'), 'on 4040'))
def test_flags_names(self):
compare(S(".*BaR", dotall=True, ignorecase=True), actual="foo\nbar")
def test_str(self):
compare('<S:on \\d+>', str(S('on \d+')))
def test_repr(self):
compare('<S:on \\d+>', repr(S('on \d+')))
def test_not_string(self):
self.failIf(40220 == S('on \d+'))
def test_comp_in_sequence(self):
self.failUnless((1, 2, 'on 40220') == (1, 2, S('on \d+')))
def test_not_equal_no(self):
self.failUnless('on xxx' != S('on \d+'))
def test_not_equal_yes(self):
self.failIf('on 40220' != S('on \d+'))
def test_equal_yes(self):
self.failUnless('on 40220' == S('on \d+'))
def test_flags_parameter(self):
compare(S(".*bar", flags=re.DOTALL), actual="foo\nbar")
def test_equal_no(self):
self.failIf('on xxx' == S('on \d+'))
def test_flags_argument(self):
compare(S(".*bar", re.DOTALL), actual="foo\nbar")
