def test_parseUrl(self):
"CSSParser.parseUrl()"
if mock:
# parseUrl(self, href, encoding=None, media=None, title=None):
parser = cssutils.CSSParser()
mock("cssutils.util._defaultFetcher",
mock_obj=self._make_fetcher(None, u''))
sheet = parser.parseUrl('http://example.com',
media='tv,print',
title='test')
restore()
#self.assertEqual(sheet, 1)
self.assertEqual(sheet.href, 'http://example.com')
self.assertEqual(sheet.encoding, 'utf-8')
self.assertEqual(sheet.media.mediaText, 'tv, print')
self.assertEqual(sheet.title, 'test')
# URL and content tests
tests = {
# (url, content): isSheet, encoding, cssText
('', None): (False, None, None),
('1', None): (False, None, None),
('mailto:[email protected]', None): (False, None, None),
('http://example.com/x.css', None): (False, None, None),
('http://example.com/x.css', ''): (True, u'utf-8', u''),
# ('http://example.com/x.css', 'a'): (True, u'utf-8', u''),
# ('http://example.com/x.css', 'a {color: red}'): (True, u'utf-8',
# u'a {\n color: red\n }'),
# ('http://example.com/x.css', 'a {color: red}'): (True, u'utf-8',
# u'a {\n color: red\n }'),
# ('http://example.com/x.css', '@charset "ascii";a {color: red}'): (True, u'ascii',
# u'@charset "ascii";\na {\n color: red\n }'),
}
override = 'iso-8859-1'
overrideprefix = u'@charset "iso-8859-1";'
httpencoding = None
for (url, content), (isSheet, expencoding, cssText) in tests.items():
mock("cssutils.util._defaultFetcher",
mock_obj=self._make_fetcher(httpencoding, content))
#parser.setFetcher(self._make_fetcher(httpencoding, content))
sheet1 = parser.parseUrl(url)
sheet2 = parser.parseUrl(url, encoding=override)
restore()
if isSheet:
self.assertEqual(sheet1.encoding, expencoding)
self.assertEqual(sheet1.cssText, cssText)
self.assertEqual(sheet2.encoding, override)
if sheet1.cssText and sheet1.cssText.startswith('@charset'):
self.assertEqual(sheet2.cssText, cssText.replace('ascii', override))
elif sheet1.cssText:
self.assertEqual(sheet2.cssText, overrideprefix + '\n' + cssText)
else:
self.assertEqual(sheet2.cssText, overrideprefix + cssText)
else:
self.assertEqual(sheet1, None)
self.assertEqual(sheet2, None)
self.assertRaises(ValueError, parser.parseUrl, '../not-valid-in-urllib')
self.assertRaises(urllib2.HTTPError, parser.parseUrl, 'http://example.com/not-present.css')
def test_users_from_url(self):
mock('obswatch.http_GET', tracker=self.tt,
returns=StringIO('''<?xml version="1.0" encoding="UTF-8"?>
<project name="superkde" created="2005-01-01T00:00:02+01:00" updated="2007-01-19T10:44:45+01:00">
<title>SuperKDE</title>
<description>SuperKDE is a heavily tuned version of KDE.</description>
<link project="openSUSE:11.2:Update" />
<link project="openSUSE:11.2" />
<person role="maintainer" userid="Geeko"/>
<person role="maintainer" userid="BrownGeeko"/>
<group role="reviewer" groupid="release_team"/>
<build>
<disable />
</build>
<repository name="kde4:factory" rebuild="transitive">
<path project="kde4" repository="factory"/>
<arch>i386</arch>
<arch>x86_64</arch>
</repository>
</project>'''))
mock('obswatch.get_user_email', returns='*****@*****.**')
result = obswatch.get_users_from_url('%ssource/superkde/_meta' %
obswatch.APIURL)
assert_same_trace(self.tt, """Called obswatch.http_GET(
'%ssource/superkde/_meta')""" % obswatch.APIURL)
self.assertEqual(len(result), 2)
self.assertEqual(result['Geeko'], '*****@*****.**')
self.assertEqual(result['BrownGeeko'], '*****@*****.**')
def setUp(self):
self.api = MediaMosaAPI('http://video.example.com')
self.tt = TraceTracker()
mock('self.api.session', tracker=self.tt)
self.response = Mock('requests.Response')
self.response.status_code = 200
self.api.session.get.mock_returns = self.response
def testTripwireTripped(self):
'''Tripwire test, tripped'''
tt = minimock.TraceTracker()
minimock.mock('tripwire.sendEmail', tracker=tt)
datevalue = datetime.date(2011, 8, 16)
dtmock = minimock.Mock('datetime.date')
minimock.mock('datetime.date', mock_obj=dtmock)
dtmock.mock_returns = dtmock
dtmock.today.mock_returns = datevalue
dtmock.today.mock_tracker = tt
#can't just do minimock.mock('datetime.date.today', returns=datevalue, tracker=tt)
#because datetime.date is in an extension (ie, not native python)
#Add another value to make the tripwire trip
self.session.add(model.MeasuredValue(6))
self.session.commit()
tripwire.main()
expected = r'''Called datetime.date.today()
Called tripwire.sendEmail(3.0, datetime.date(2011, 8, 16))'''
self.assertTrue(tt.check(expected), tt.diff(expected))
minimock.restore()
def setUp(self):
self.maxDiff = None
run.Redis = fakeredis.FakeRedis
self.r = fakeredis.FakeStrictRedis()
self.tt = TraceTracker()
self.return_value = ''
mock('run.analyse', tracker=self.tt, returns_func=self.get_return_value)
def setUp(self):
"""
Nadgers haystack SearchView so that:
- we don't need a search backend
- response is a TemplateResponse, not and HttpResponse (so
that in tests we can check context contents)
"""
import django.template.response
import haystack.views
# SearchView passes a RequestContext to render_to_response,
# but we want to be able to get hold of the request itself
# (to pass on to TemplateResponse).
class RequestContext(django.template.response.RequestContext):
def __init__(self, request):
super(RequestContext, self).__init__(request)
self.request = request
def render_to_response(template, context, context_instance):
return django.template.response.TemplateResponse(
request = context_instance.request,
template = template,
context = context)
self.context_class = RequestContext
minimock.mock("haystack.views.render_to_response", returns_func=render_to_response, tracker=None)
minimock.mock("haystack.views.SearchView.get_results", returns_func=self.get_results, tracker=None)
self.org = OrganizationFactory()
def test_offline(self):
"""Proxy when offline"""
import urllib
minimock.mock('urllib.urlopen', raises=IOError)
get_proxy()
def mock_send_email(request):
"""Mock up smtplib.SMTP and keyring.get_password for send_email."""
import smtplib
import keyring
# capture all calls into mock objects
# (instead of letting output go to stdout)
tracker = minimock.TraceTracker()
# mock up smtplib
minimock.mock('smtplib.SMTP',
returns=minimock.Mock('smtp_connection', tracker=tracker),
tracker=tracker)
# mock up keyring.get_password
minimock.mock('keyring.get_password',
returns='send_email_secret',
tracker=tracker)
def finalizer():
# restore all objects in global module state that minimock replaced
minimock.restore()
request.addfinalizer(finalizer)
return tracker
def setUp(self):
self.api = MediaMosaAPI('http://video.example.com')
self.tt = TraceTracker()
mock('self.api.session', tracker=self.tt)
self.response = Mock('requests.Response')
self.response.status_code = 200
self.api.session.get.mock_returns = self.response
self.item_dict = {u'is_original_file': u'FALSE',
u'is_streamable': u'FALSE', u'is_downloadable': u'FALSE',
u'app_id': u'2', u'transcode_inherits_acl': u'TRUE',
u'tag': '', u'response_metafile_available': u'TRUE',
u'mediafile_id_source': u'u2ilZNiHdl7iNUdexL7BcFMY',
u'asset_id': u'g1QkoSmSeHdWfGkMKlOlldLn',
u'mediafile_id': u'Md2RgaUEVFhfJMeUIbwPOMei',
u'transcode_profile_id': u'17',
u'filename': u'Sintel_Trailer1.1080p.DivX_Plus_HD.mp4',
u'is_protected': u'FALSE', u'ega_stream_url': '',
u'file_extension': u'mp4', 'metadata': {
u'is_inserted_md': u'FALSE', u'fps': u'24', u'bpp': u'0.31',
u'file_duration': u'00:00:52.20', u'colorspace': u'yuv420p',
u'container_type': u'mov;mp4;m4a;3gp;3g2;mj2', u'height': u'478',
u'channels': u'stereo', u'width': u'852', u'sample_rate': u'44100',
u'filesize': u'20543936', u'audio_codec': u'aac',
u'video_codec': u'h264', u'is_hinted': u'TRUE',
u'bitrate': u'3012', u'mime_type': u'video/mp4'},
u'ega_download_url': '', u'ega_play_url': '', u'tool': u'ffmpeg',
u'response_plain_available': u'TRUE', u'owner_id': u'krkeppen',
u'response_object_available': u'TRUE',
u'created': u'2012-07-05 11:38:14',
u'changed': u'2012-07-05 11:38:14', u'uri': '',
u'is_still': u'FALSE', u'command':
u'audiocodec:libfaac;audiobitrate:128000;audiosamplingrate:44100;audiochannels:2;videocodec:libx264;videopreset_quality:slow;videopreset_profile:baseline;2_pass_h264_encoding:2;videobitrate:800000;qmax:17;size:852x480;maintain_aspect_ratio:yes',
u'group_id': ''}
def setUp(self):
from netprintbox.data import OAuthRequestToken
super(DropboxServiceSetupTest, self).setUp()
token = 'oauth_token=token&oauth_token_secret=secret'
token = OAuthRequestToken(key=self.key, token=token)
token.put()
class client(object):
@staticmethod
def account_info():
return {'uid': self.uid,
'email': 'email',
'display_name': 'display_name',
'country': 'JP',
}
class session(object):
@staticmethod
def obtain_access_token(request_token):
pass
class token(object):
key = 'access_key'
secret = 'access_secret'
import dropbox.client
import dropbox.session
mock('dropbox.client.DropboxClient', returns=client)
mock('dropbox.session.DropboxSession', returns=session)
def test_ok(self):
"""OK proxy"""
minimock.mock('flickrapi.FlickrAPI.get_token_part_one')
minimock.mock('flickrapi.FlickrAPI.get_token_part_two', returns=True)
assert isinstance(get_proxy(), flickrapi.FlickrAPI)
def test_cb(self):
"""Callback from proxy"""
minimock.mock('flickrapi.FlickrAPI.get_token_part_one', returns=('token', 'frob'))
def _bad_api(auth_response):
raise FlickrError('Error: 108: Invalid frob')
minimock.mock('flickrapi.FlickrAPI.get_token_part_two',
returns_func=_bad_api)
self.hit_cb = False
def _cb(proxy, perms, token, frob):
assert perms == 'write'
assert token == 'token'
assert frob == 'frob'
if self.hit_cb:
return True
else:
self.hit_cb = True
assert_raises(FlickrError, get_proxy, wait_callback=_cb)
assert self.hit_cb
def mock_set_password(request):
"""Mock up getpass.getpass and keyring.set_password for set_password."""
import getpass
import keyring
# capture all calls into mock objects
# (instead of letting output go to stdout)
tracker = minimock.TraceTracker()
# mock up getpass.getpass
minimock.mock('getpass.getpass',
returns='set_password_secret',
tracker=tracker)
# mock up keyring.set_password
minimock.mock('keyring.set_password',
tracker=tracker)
def finalizer():
# restore all objects in global module state that minimock replaced
minimock.restore()
request.addfinalizer(finalizer)
return tracker
def test_bad_xml(self):
"""Bad XML from proxy"""
minimock.mock('flickrapi.FlickrAPI.get_token_part_one',
raises=ExpatError)
get_proxy()
def setUp(self):
super(FanInMergeJoinDispatchTest, self).setUp()
setUpByString(self, FAN_IN_MACHINE, machineName='FanInMachine', instanceName='foo')
mock('config.currentConfiguration', returns=self.currentConfig, tracker=None)
for i in range(20):
SimpleModel(key_name='%d' % i).put()
memcache.set('calls', 0)
memcache.set('raise', False)
context = self.factory.createFSMInstance(self.machineConfig.name, instanceName='foo')
context[constants.STEPS_PARAM] = 1
obj = TemporaryStateObject()
obj[constants.TASK_NAME_PARAM] = 'taskName'
obj[constants.RETRY_COUNT_PARAM] = 0
self.context = None
self.obj = None
random.seed(0)
context.dispatch('pseudo-init', obj) # write down a work package
self.index = context[constants.INDEX_PARAM]
self.assertEqual(1, _FantasmFanIn.all().count())
self.assertEqual('foo--InitialState--ok--FanInState--step-2-2957927341',
_FantasmFanIn.all().get().workIndex)
def test_multipleLevelMountPointExtraPathInfo(self):
url = '/other/mount/point/fsm/MyMachine/state1/to/state2'
request = buildRequest(path=url)
from fantasm import config
mock('config.currentConfiguration', returns=MockConfigRootUrl('/other/mount/point/'), tracker=None)
name = getMachineNameFromRequest(request)
self.assertEquals(name, 'MyMachine')
def setUp(self):
super(StartStateMachineTests, self).setUp()
filename = 'test-TaskQueueFSMTests.yaml'
setUpByFilename(self, filename)
self.machineName = getMachineNameByFilename(filename)
self.mockQueue = TaskQueueDouble()
mock(name='Queue.add', returns_func=self.mockQueue.add, tracker=None)
def test_successful_authentication(self):
# setup
mock('self.api._login_challenge', returns='xxx', tracker=self.tt)
mock('self.api._login_response', returns=True, tracker=self.tt)
# test
success = self.api.authenticate(self.username, self.secret)
# validate
self.assertEquals(success, True)
def test_post_put_hook_sends_log_line_to_channel(self):
tracker = minimock.TraceTracker()
minimock.mock('channel.ServerChannels.get_client_ids', returns=['client_id'], tracker=None)
minimock.mock('channel.ServerChannels.send_message', tracker=tracker)
log_line = models.LogLine.create(self.server, LOG_LINE, TIME_ZONE)
minimock.assert_same_trace(
tracker, """Called channel.ServerChannels.send_message({0}, u'chat')""".format(log_line)
)
def setUp(self):
super(ScreenShotBlurredTaskTest, self).setUp()
minimock.mock('image.NdbImage.post_data', returns_func=self.mock_post_data, tracker=None)
self.server = models.Server.create()
self.image_data = None
blob_info = self.create_blob_info(IMAGE_PATH)
self.screenshot = models.ScreenShot.create(self.server.key, None, blob_info=blob_info)
self.assertEqual(1, models.ScreenShot.query().count())
def test_reject(self):
"""Rejected proxy"""
minimock.mock('flickrapi.FlickrAPI.get_token_part_one')
minimock.mock('flickrapi.FlickrAPI.get_token_part_two',
raises=FlickrError)
get_proxy()
def test_finalStateDispatchWithEventEmitsNoEventAsTask(self):
mockQueue = TaskQueueDouble()
mock(name='Queue.add', returns_func=mockQueue.add, tracker=None)
self.context.currentState = self.stateNormal
self.context.dispatch('next-event', {})
self.assertEquals(len(mockQueue.tasks), 0)
def test_maxDoublingsAddedToQueuedTask(self):
def execute(context, obj):
return 'ok5'
mock(name='CountExecuteCalls.execute', returns_func=execute, tracker=None)
self.context.dispatch(self.initEvent, TemporaryStateObject())
self.assertEquals(len(self.mockQueue.tasks), 1)
task = self.mockQueue.tasks[0][0]
self.assertEquals(task.retry_options.max_doublings, 5)
def test(self):
gv = tap.ext.GoogleVisualization(username="******", password="******", key="dummy")
assert isinstance(gv, tap.ext.GoogleVisualization)
assert list(gv.query("select *")) == [{u'A': u'Japan', u'Population Density': 339.0}]
mock("atom.service.AtomService.request", returns=ErrorResponse())
assert list(gv.query("select *")) == []
self.expected_logs = [('ERROR', 'gae/tap/ext.py', 'query', "[{u'reason': u'invalid_query', u'detailed_message': u'Query parse error: Encountered...', u'message': u'Invalid query'}]")]
def setUp(self):
super(FanInTxnException, self).setUp()
setUpByString(self, FAN_IN_MACHINE, machineName='FanInMachine')
mock('config.currentConfiguration', returns=self.currentConfig, tracker=None)
for i in range(20):
SimpleModel(key_name='%d' % i).put()
memcache.set('calls', 0)
memcache.set('raise', True)
def test_get_fail(self):
"""Fail shorthash retrieval"""
self.make_mock_photo('123')
minimock.mock('urllib2.urlopen', raises=IOError)
self.index.refresh()
def test_get_fail_bad(self):
"""Failed shorthash retrieval passes fatal exceptions"""
self.make_mock_photo('123')
minimock.mock('urllib2.urlopen', raises=SystemError)
self.index.refresh()
def setUp(self):
super(BaseTest, self).setUp()
setUpByString(self, FAN_IN_MACHINE, machineName=self.MACHINE_NAME)
mock('config.currentConfiguration', returns=self.currentConfig, tracker=None)
mock('FSMFanInCleanupHandler.post', returns=None, tracker=None)
for i in range(10):
ContinuationFanInModel(value=i).put()
self.context['event'] = self.EVENT
def testLights(self):
minimock.mock("executor.dim.set_dim_level", returns=None)
for i in ['12', '50']:
self.assertEqual("Lights turned %s" % str(i), executor.lights(i))
for i in ['lala', '234$', '12 12', '-12', '0', '50.5', 'off']:
self.assertEqual("Lights turned 0", executor.lights(i))
for i in ['100', '34674', '1111111111', 'on']:
self.assertEqual("Lights turned 100", executor.lights(i))
def stub(name, **kw): kw['tracker'] = minimock.Printer(open(os.devnull, "w")) stack = inspect.stack() globals_ = stack[1][0].f_globals locals_ = stack[1][0].f_locals kw['nsdicts'] = (locals_, globals_, __builtin__.__dict__) minimock.mock(name, **kw)
def setUp(self):
""" Set up test fixtures """
self.mock_outfile = StringIO()
self.app_class_name = self.application_class.__name__
self.mock_app = Mock("test_app", outfile=self.mock_outfile)
self.mock_app_class = Mock(self.app_class_name,
outfile=self.mock_outfile)
self.mock_app_class.mock_returns = self.mock_app
mock(self.app_class_name,
mock_obj=self.mock_app_class,
nsdicts=[self.program_module.__dict__])
super(Test_ProgramMain, self).setUp()
def _check_make_server(self, backend):
mocked_backend = minimock.Mock('Backend', returns='backend_impl', tracker=self.tt)
minimock.mock('chaussette.server.get', returns=mocked_backend, tracker=self.tt)
server = chaussette.server.make_server('app', 'host', 'port', backend)
minimock.assert_same_trace(self.tt, '\n'.join([
"Called chaussette.server.get('%s')" % backend,
"Called Backend(",
" ('host', 'port'),",
" 'app',",
" address_family=2,",
" backlog=2048,",
"socket_type=1)"
]))
self.assertEqual(server, 'backend_impl')
def setUp(self):
super(FanInQueueDispatchTest, self).setUp()
setUpByString(self,
FAN_IN_MACHINE,
machineName='FanInMachine',
instanceName='foo')
mock('config.currentConfiguration',
returns=self.currentConfig,
tracker=None)
for i in range(20):
SimpleModel(key_name='%d' % i).put()
FanInAction.CALLS = 0
self.context = None
self.obj = None
def test_initialDispatchEmitsEventAsTask(self):
mockQueue = TaskQueueDouble()
mock(name='Queue.add', returns_func=mockQueue.add, tracker=None)
event = self.context.initialize()
self.assertEquals(len(mockQueue.tasks), 1)
self.context.dispatch(event, {})
self.assertEquals(len(mockQueue.tasks), 2)
(task, transactional) = mockQueue.tasks[1]
# state-initial is the state we're transitioning FROM
self.assertTaskUrlHasStateAndEvent(task, 'state-initial', 'next-event')
def setUp(self):
super(TaskQueueFSMRetryTests, self).setUp()
filename = 'test-TaskQueueFSMRetryTests.yaml'
machineName = getMachineNameByFilename(filename)
self.factory = getFSMFactoryByFilename(filename)
self.context = self.factory.createFSMInstance(machineName)
self.mockQueue = TaskQueueDouble()
mock(name='Queue.add', returns_func=self.mockQueue.add, tracker=None)
self.loggingDouble = getLoggingDouble()
# drive the machine to ready
self.initEvent = self.context.initialize()
self.mockQueue.purge() # clear the initialization task
def setUp(self):
super(SpawnTests, self).setUp()
filename = 'test-TaskQueueFSMTests.yaml'
setUpByFilename(self, filename)
self.machineName = getMachineNameByFilename(filename)
self.mockQueue = TaskQueueDouble()
mock(name='Queue.add', returns_func=self.mockQueue.add, tracker=None)
# dispatch initial event to get context in correct state
self.taskName = 'foo'
self.obj = {TASK_NAME_PARAM: self.taskName}
self.context.dispatch(FSM.PSEUDO_INIT, self.obj)
# but now flush the task queue to remove the event that we just dispatched;
# we're only interested in testing spawn tasks
self.mockQueue.purge()
def test_pksi_dh(self):
with umock.patch.object(active_site_finder.common.ActiveSiteAnalysis, "scaffold_matches") as mocked_match:
mocked_match.return_value = True
for values in ["GGP", "HPP", "HGG", "NNN", "HGP"]:
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment(values, {5: values[0], 39: values[1], 44: values[2]})])
pairings = analysis.asp_pksi_dh(self.record)
assert pairings == [(values, "catalytic triad H,G,P found: %s" % (values == "HGP"))]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment("incon", {})])
pairings = analysis.asp_pksi_dh(self.record)
assert pairings == [("incon", "catalytic triad H,G,P inconclusive")]
def test_kr_stereo(self):
for char in string.ascii_uppercase:
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment("match", {102: char})])
pairings = analysis.pksi_kr_stereo(self.record)
if char == "D":
assert pairings == [(
"match",
"KR domain putatively catalyzing D-configuration product formation"
)]
else:
assert pairings == [(
"match",
"KR domain putatively catalyzing L-configuration product formation"
)]
def test_taskQueueOnQueueSpecifiedAtTransitionLevel(self):
mockQueue = TaskQueueDouble()
mock(name='Queue.__init__',
returns_func=mockQueue.__init__,
tracker=None)
mock(name='Queue.add', returns_func=mockQueue.add, tracker=None)
self.transNormalToFinal.queueName = 'fantasm-queue' # should be this one (dest state)
self.transInitialToNormal.queueName = 'barfoo'
self.context.queueName = 'foobar'
self.context.currentState = self.stateInitial
self.context.dispatch('next-event', {})
self.assertEquals(mockQueue.name, 'fantasm-queue')
def test_get_git_vesion(self):
"Test utils.get_git_version()"
mock('utils.execute', tracker=self.tt, returns=('deadbeef', '', 0))
expected_trace = r""" Called utils.execute(['git', 'rev-parse', '--short', 'HEAD'])
Called utils.execute(['git', 'rev-parse', '--short', 'HEAD'])"""
ret = utils.get_git_version()
self.assertEqual(ret, 'deadbeef')
mock('utils.execute', tracker=self.tt, raises=OSError)
ret = utils.get_git_version()
self.assertEqual(ret, '')
assert_same_trace(self.tt, expected_trace)
def test_KS_N(self):
mock("subprocessing.run_hmmpfam2",
returns=parse_hmmpfam_results("KS_N.output"))
results = analysis.asp_ks(self.record)
expected = {
"PKS_KS0":
'found active site cysteine: False, scaffold matched GSSS: True',
"PKS_KS1":
'found active site cysteine: False, scaffold matched GSSS: False',
"PKS_KS2":
'found active site cysteine: False, scaffold matched GSSS: False',
"PKS_KS3":
'found active site cysteine: False, scaffold matched GSSS: False'
}
assert {dom.domain_id: message for dom, message in results} == expected
def test_AT(self):
mock("subprocessing.run_hmmpfam2",
returns=parse_hmmpfam_results("AT.output"))
results = analysis.asp_at(self.record)
expected = {
"PKS_AT0":
"found active site serine: True, scaffold matched GHGE: False",
"PKS_AT1":
"found active site serine: False, scaffold matched GHGE: True",
"PKS_AT2":
"found active site serine: False, scaffold matched GHGE: True",
"PKS_AT3":
"found active site serine: False, scaffold matched GHGE: False"
}
assert {dom.domain_id: message for dom, message in results} == expected
def test_p450(self):
with umock.patch.object(active_site_finder.common.ActiveSiteAnalysis, "scaffold_matches") as mocked_match:
mocked_match.return_value = True
for char in string.ascii_uppercase:
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment(char, {407: char})])
pairings = analysis.asp_p450_oxy(self.record)
assert pairings == [(char, "active site cysteine present: %s" % (char == "C"))]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment("incon", {})])
pairings = analysis.asp_p450_oxy(self.record)
assert pairings == [("incon", "active site cysteine inconclusive")]
def setUp(self):
super(SendLogLineTest, self).setUp()
self.server = models.Server.create()
models.User.create_user('1234', email='*****@*****.**')
self.user = models.User.lookup(email='*****@*****.**')
self.interesting_log_line = models.LogLine.create(
self.server, self.INTERESTING_LOG_LINE, 'US/Central')
self.uninteresting_log_line = models.LogLine.create(
self.server, self.UNINTERESTING_LOG_LINE, 'US/Central')
self.tracker = minimock.TraceTracker()
minimock.mock('channel.ServerChannels.get_client_ids',
returns=['client_id'],
tracker=None)
minimock.mock('channel.ServerChannels.send_message',
tracker=self.tracker)
def setUp(self):
self.user = UserFactory()
self.decision = DecisionFactory()
# Ensure value of "now" always increases by amount sufficient
# to show up as a change, even if db resolution for datetime
# is one second.
def now_iter(start):
t = start
while True:
t += datetime.timedelta(hours=1)
yield t
minimock.mock("timezone.now",
returns_iter=now_iter(timezone.now()),
tracker=None)
def test_generate_namespace(self):
"test generate_namespace() method"
mydb = db.aSDB(self.options)
mock('BioSeqDatabase.DBServer.new_database',
tracker=self.trace_tracker,
returns=["mock result"])
expected = """Called BioSeqDatabase.DBServer.new_database(
db_name='test',
description='test namespace for nosetests')
"""
mydb.generate_namespace(self.options.BioSQLnamespace,
'test namespace for nosetests')
assert_same_trace(self.trace_tracker, expected)
def setUp(self):
self.domains = [
'Condensation', 'AMP-binding', 'PP-binding', 'Condensation',
'A-OX', 'PP-binding', 'PKS_AT', 'hyb_KS', 'PP-binding', 'PF00561',
'Peptidase_S9', 'LANC_like', 'Pkinase', 'p450', 'Abi', 'DUF4135',
'Condensation', 'AMP-binding', 'PP-binding', 'Condensation',
'AMP-binding', 'PP-binding', 'PF07366', 'adh_short',
'adh_short_C2', 'p450', 'PF12697', 'PP-binding', 'PKS_AT',
'mod_KS', 'hyb_KS', 'adh_short', 'PP-binding', 'PKS_AT', 'mod_KS',
'adh_short', 'PP-binding', 'PKS_AT', 'mod_KS', 'adh_short',
'NAD_binding_4', 'Condensation', 'PP-binding'
]
mock("lanthi.run_rodeo", returns=20)
self.cds = DummyCDS(38, 48)
# an all_orf detected gene at 7922405:7922549 in CP013129.1, with a C appended
self.cds.translation = "VCGPRDHGRQRTSAPHAFHSDSMDRAASRPVEYGDYSGSPLSQGLGGC"
def test_encode_failed_returncode_1(self):
"""encode test with failed"""
mock('encoder.subprocess.Popen', returns=Mock(
'proc',
communicate=Mock(
'proc.communicate',
returns=(b'', b'')),
returncode=1))
dummy_src_file = 'aaa.m2ts'
args = (dummy_src_file, 'bbb.mp4')
kwargs = {'reso': '1280x720', 'vb_mbps': 2, 'ab_kbps': 256, 'is_deint': False}
self.assertRaises(ConvertError, encoder.encode, *args, **kwargs)
self.assertTrue(os.path.isfile(os.path.splitext(dummy_src_file)[0] + '.log'))
os.remove(os.path.splitext(dummy_src_file)[0] + '.log')
def test_run_hmmsearch(self):
"Test utils.run_hmmsearch()"
mock('Bio.SearchIO.parse', tracker=self.tt, returns=['mock result'])
mock('utils.execute', tracker=self.tt, returns=('output', 'error', 0))
expected = r""" Called utils.execute(
['hmmsearch', '--cpu', '2', '-o', '/dev/null', '--domtblout', 'result.domtab', 'fake.hmm', '-'],
input='>testinput\nMADEUP')
Called Bio.SearchIO.parse(
'result.domtab', 'hmmsearch3-domtab')"""
hits = utils.run_hmmsearch('fake.hmm', ">testinput\nMADEUP")
self.assertEqual(len(hits), 1)
hit = hits.pop()
self.assertEqual('mock result', hit)
assert_same_trace(self.tt, expected)
def test_DatastoreFSMContinuationFanInTests_write_lock_error(self):
obj = TemporaryStateObject()
obj[TASK_NAME_PARAM] = 'taskName'
event = self.context.initialize() # queues the first task
self.assertEqual('pseudo-init', self.context.currentState.name)
event = self.context.dispatch(event, obj)
self.assertEqual('state-initial', self.context.currentState.name)
mock('memcache.incr', returns=1, tracker=None)
# the .dispatch() takes the machine into "state-continuation" and the queueDispatch() looks
# ahead to determine that _queueDispatchFanIn() is required, which raises the expected error
# due to lock acquisition problems
self.assertRaises(FanInWriteLockFailureRuntimeError,
self.context.dispatch, event, obj)
def setUp(self):
"set up database test framework and test for db connection"
self.options = Namespace()
self.options.BioSQLconfig = Namespace()
self.options.BioSQLconfig.dbdriver = 'psycopg2'
self.options.BioSQLconfig.dbuser = '******'
self.options.BioSQLconfig.dbpass = '******'
self.options.BioSQLconfig.dbhost = 'localhost'
self.options.BioSQLconfig.dbport = '5432'
self.options.BioSQLconfig.dbdb = 'antiSMASHnosetest'
self.options.BioSQLnamespace = 'test'
self.trace_tracker = TraceTracker()
# test correct method call for db.asDB)()
mock('BioSeqDatabase.open_database',
tracker=self.trace_tracker,
returns=['mock result'])
expected = """Called BioSeqDatabase.open_database(
db='antiSMASHnosetest',
driver='psycopg2',
host='localhost',
passwd='biosql',
port='5432',
user='******')
"""
mydb = db.aSDB(self.options)
assert_same_trace(self.trace_tracker, expected)
# restore mocked objects that other tests can run with the original code
restore()
self.trace_tracker = TraceTracker()
#test initializing database object db.__init__"
try:
mydb = db.aSDB(self.options)
except Exception:
self.skipTest(
'database connection could not be established, skipping tests')
self.assertIsInstance(mydb, db.aSDB)
self.mydb = mydb
def test__init(self):
"Test active_site_finder.__init__ method"
self.tt = TraceTracker()
class dummyET:
def __init__(self):
pass
def getroot(self):
return dummyET()
def findall(self, a):
return "ET-Subtree"
mock('ET.parse', returns=dummyET(), tracker=self.tt)
#mock('ET.getroot', returns="XMLTree", tracker=self.tt)
#mock('ET.findall', returns="XMLSubtree", tracker=self.tt)
mock(
'antismash.generic_modules.active_site_finder.active_site_finder.check_prereqs',
returns=[],
tracker=self.tt)
expected = """ Called ET.parse(
'.../antismash/generic_modules/active_site_finder/config/SignatureResources.xml')"""
ASF = antismash.generic_modules.active_site_finder.active_site_finder(
self.seq_record, self.options)
assert_same_trace(self.tt, expected)
# restore mocked objects that other tests can run with the original code
restore()
self.tt = TraceTracker()
# now acutally generate ASF object
myASF = antismash.generic_modules.active_site_finder.active_site_finder(
self.seq_record, self.options)
assert_is_instance(
myASF,
antismash.generic_modules.active_site_finder.active_site_finder)
self.my_ASF = myASF
def test__run_external_tool(self):
"Test active_site_finder._run_external_tool method"
self.tt = TraceTracker()
SeqFeatureList = utils.get_all_features_of_type_with_query(
self.seq_record, "PFAM_domain", "domain", "p450")
self.assertEqual(6, len(SeqFeatureList))
mock(
'antismash.generic_modules.active_site_finder.active_site_finder._execute_tool',
returns=["external program call successful"],
tracker=self.tt)
result = self.my_ASF._run_external_tool(self.ETObj.find('./analysis'),
SeqFeatureList)
expected = ["external program call successful"]
self.assertListEqual(result, expected)
def test_run_hmmpfam2(self):
"Test utils.run_hmmpfam2()"
mock('Bio.SearchIO.parse', tracker=self.tt, returns=['mock result'])
mock('utils.execute', tracker=self.tt, returns=('output', 'error', 0))
expected = r""" Called utils.execute(
['hmmpfam2', '--cpu', '2', 'fake.hmm', '-'],
input='>testinput\nMADEUP')
Called Bio.SearchIO.parse(
<cStringIO.StringI object at ...>,
'hmmer2-text')"""
hits = utils.run_hmmpfam2('fake.hmm', ">testinput\nMADEUP")
self.assertEqual(len(hits), 1)
hit = hits.pop()
self.assertEqual('mock result', hit)
assert_same_trace(self.tt, expected)
def test_alignment_generation(self):
pregenerated = list(
SearchIO.parse(
open(path.get_full_path(__file__, 'data', 'KS_N.output')),
"hmmer2-text"))
mock("subprocessing.run_hmmpfam2", returns=pregenerated)
domains = self.generate_domains()
analysis = ActiveSiteAnalysis("PKS_KS", domains, "PKSI-KS_N.hmm2",
[176, 186, 187, 188],
['G', 'S', 'S', 'S'])
assert {"PKS_KS"} == {
domain.domain
for domain in analysis.domains_of_interest
}
alignments = analysis.get_alignments()
assert len(alignments) == 4
assert [align.domain for align in alignments[:4]] == domains[:4]
def test_er_stereo(self):
with umock.patch.object(active_site_finder.common.ActiveSiteAnalysis, "scaffold_matches") as mocked_match:
mocked_match.return_value = True
for char in string.ascii_uppercase:
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment(char, {39: char})])
pairings = analysis.pksi_er_stereo(self.record)
if char == "Y":
assert pairings == [(char, "ER domain putatively catalyzing 2S-configuration product formation")]
else:
assert pairings == [(char, "ER domain putatively catalyzing 2R-configuration product formation")]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment("incon", {})])
pairings = analysis.pksi_er_stereo(self.record)
assert pairings == [("incon", "ER configuration inconclusive")]
def test_acquireReadLock_one_wait_iter(self):
lock = ReadWriteLock('foo', self.context)
index = lock.currentIndex()
self.assertEqual(None, memcache.get(lock.lockKey(index)))
lock.acquireWriteLock(index)
self.assertEqual('65537', memcache.get(lock.lockKey(index)))
def sleepAndRelease(seconds): # pylint: disable-msg=W0613
lock.releaseWriteLock(index)
mock('time.sleep', returns_func=sleepAndRelease, tracker=None)
lock.acquireReadLock(index)
self.assertEqual('32768', memcache.get(lock.lockKey(index)))
self.assertEqual(
["Tried to acquire read lock 'foo-lock-3626764237' 1 times..."],
self.loggingDouble.messages['debug'])
self.assertEqual([
"Gave up waiting for all fan-in work items with read lock 'foo-lock-3626764237'."
], self.loggingDouble.messages['critical'])
def setup(self):
raimei.vim = None
mock("raimei.vim")
raimei.vim.current = Mock(
"current",
window=Mock(
"window",
cursor=Mock("cursor"),
),
range=Mock(
"range",
start=Mock("start"),
end=Mock("end"),
),
)
utils.vim = None
mock("utils.vim")
_eval_func = lambda var: self.eval_var[var]
utils.vim.eval = Mock("eval", returns_func=_eval_func)
def setUp(self):
super(UsernameClaimTest, self).setUp()
self.params = {'username': '******', 'password': '******'}
self.response_data = Object()
self.response_data.content = json.dumps({
"accessToken": "random access token",
"clientToken": "mc-coal",
"availableProfiles": [
{
"id": "profile identifier",
"name": "steve",
}
],
"selectedProfile": {
"id": "profile identifier",
"name": "steve",
}
})
minimock.mock('urlfetch.fetch', returns=self.response_data, tracker=None)
def test_get_fail_intermittent(self):
"""Fail shorthash retrieval twice"""
shs = map(self.make_mock_photo, map(str, range(10)))
fails = []
old_open = urllib2.urlopen
def _(request):
fails.append(True)
if len(fails) < 3:
raise IOError()
else:
return old_open(request)
minimock.mock('urllib2.urlopen', returns_func=_)
assert set(self.index.refresh()) == set(shs)