def test_identify_library_by_url(self):
assert_raises_regexp(
Exception,
"Could not locate library with URL http://bar/. Available URLs: http://foo/",
self.script.set_secret,
self._db, "http://bar/", "vendorid", "libraryname", "secret", None
)
def test_attempt_renew_with_local_loan_and_no_available_copies(self):
"""We have a local loan and a remote loan but the patron tried to
borrow again -- probably to renew their loan.
"""
# Local loan.
loan, ignore = self.pool.loan_to(self.patron)
# Remote loan.
self.circulation.add_remote_loan(
self.identifier.type, self.identifier.identifier, self.YESTERDAY,
self.IN_TWO_WEEKS
)
# NoAvailableCopies can happen if there are already people
# waiting in line for the book. This case gives a more
# specific error message.
#
# Contrast with the way NoAvailableCopies is handled in
# test_loan_becomes_hold_if_no_available_copies.
self.remote.queue_checkout(NoAvailableCopies())
assert_raises_regexp(
CannotRenew,
"You cannot renew a loan if other patrons have the work on hold.",
self.borrow
)
def test_lane_loading(self):
# The default setup loads lane IDs properly.
gate = COPPAGate(self._default_library, self.integration)
eq_(self.lane1.id, gate.yes_lane_id)
eq_(self.lane2.id, gate.no_lane_id)
# If a lane isn't associated with the right library, the
# COPPAGate is misconfigured and cannot be instantiated.
library = self._library()
self.lane1.library = library
self._db.commit()
assert_raises_regexp(
CannotLoadConfiguration,
"Lane .* is for the wrong library",
COPPAGate,
self._default_library, self.integration
)
self.lane1.library_id = self._default_library.id
# If the lane ID doesn't correspond to a real lane, the
# COPPAGate cannot be instantiated.
ConfigurationSetting.for_library_and_externalintegration(
self._db, COPPAGate.REQUIREMENT_MET_LANE, self._default_library,
self.integration
).value = -100
assert_raises_regexp(
CannotLoadConfiguration, "No lane with ID: -100",
COPPAGate, self._default_library, self.integration
)
def error_is_raised_if_init_value_is_missing():
User = dodge.data_class("User", ["username", "password"])
assert_raises_regexp(
TypeError, "^Missing argument: 'password'$",
lambda: User("bob")
)
def test_get_plot_point_colors_invalid_input(self):
# column provided without df
with npt.assert_raises(ValueError):
self.min_ord_results._get_plot_point_colors(None, 'numeric',
['B', 'C'], 'jet')
# df provided without column
with npt.assert_raises(ValueError):
self.min_ord_results._get_plot_point_colors(self.df, None,
['B', 'C'], 'jet')
# column not in df
with assert_raises_regexp(ValueError, 'missingcol'):
self.min_ord_results._get_plot_point_colors(self.df, 'missingcol',
['B', 'C'], 'jet')
# id not in df
with assert_raises_regexp(ValueError, 'numeric'):
self.min_ord_results._get_plot_point_colors(
self.df, 'numeric', ['B', 'C', 'missingid', 'A'], 'jet')
# missing data in df
with assert_raises_regexp(ValueError, 'nancolumn'):
self.min_ord_results._get_plot_point_colors(self.df, 'nancolumn',
['B', 'C', 'A'], 'jet')
def test_simple(self):
p = SimpleAuthenticationProvider
integration = self._external_integration(self._str)
assert_raises_regexp(
CannotLoadConfiguration,
"Test identifier and password not set.",
p, self._default_library, integration
)
integration.setting(p.TEST_IDENTIFIER).value = "barcode"
integration.setting(p.TEST_PASSWORD).value = "pass"
provider = p(self._default_library, integration)
eq_(None, provider.remote_authenticate("user", "wrongpass"))
eq_(None, provider.remote_authenticate("user", None))
eq_(None, provider.remote_authenticate(None, "pass"))
user = provider.remote_authenticate("barcode", "pass")
assert isinstance(user, PatronData)
eq_("barcode", user.authorization_identifier)
eq_("barcode_id", user.permanent_id)
eq_("barcode_username", user.username)
# User can also authenticate by their 'username'
user2 = provider.remote_authenticate("barcode_username", "pass")
eq_("barcode", user2.authorization_identifier)
def test_untied_biases():
x = tensor.tensor4('x')
num_channels = 4
num_filters = 3
batch_size = 5
filter_size = (3, 3)
conv = Convolutional(filter_size, num_filters, num_channels,
weights_init=Constant(1.), biases_init=Constant(2.),
image_size=(28, 30), tied_biases=False)
conv.initialize()
y = conv.apply(x)
func = function([x], y)
# Untied biases provide a bias for every individual output
assert_allclose(conv.b.eval().shape, (3, 26, 28))
# Untied biases require images of a specific size
x_val_1 = numpy.ones((batch_size, num_channels, 28, 30),
dtype=theano.config.floatX)
assert_allclose(func(x_val_1),
numpy.prod(filter_size) * num_channels *
numpy.ones((batch_size, num_filters, 26, 28)) + 2)
x_val_2 = numpy.ones((batch_size, num_channels, 23, 19),
dtype=theano.config.floatX)
def wrongsize():
func(x_val_2)
assert_raises_regexp(AssertionError, 'AbstractConv shape mismatch',
wrongsize)
def test_tutorial_create_hands_on_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.create_hands_on_tutorial`."""
tuto = Tutorial(
training=training,
topic=topic)
os.makedirs(tuto.wf_dir)
# with init_wf_id and no Galaxy URL
tuto.init_wf_id = 'ID'
tuto.training.galaxy_url = None
exp_exception = "No Galaxy URL given"
with assert_raises_regexp(Exception, exp_exception):
tuto.create_hands_on_tutorial(CTX)
# with init_wf_id and no Galaxy API key
tuto.init_wf_id = 'ID'
tuto.training.galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
tuto.training.galaxy_api_key = None
exp_exception = "No API key to access the given Galaxy instance"
with assert_raises_regexp(Exception, exp_exception):
tuto.create_hands_on_tutorial(CTX)
# with init_wf_id
assert is_galaxy_engine(**KWDS)
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
tuto.init_wf_id = config.workflow_id(WF_FP)
tuto.training.galaxy_api_key = config.user_api_key
tuto.create_hands_on_tutorial(CTX)
assert os.path.exists(tuto.tuto_fp)
os.remove(tuto.tuto_fp)
# with init_wf_fp
tuto.init_wf_id = None
tuto.init_wf_fp = WF_FP
tuto.create_hands_on_tutorial(CTX)
assert os.path.exists(tuto.tuto_fp)
shutil.rmtree("topics")
def test_worked_hours_custom_end_time(self):
day_1 = day.Day("2014-09-01")
nt.assert_raises_regexp(
errors.ChronoError,
"Custom end times can only be tried on days in progress.",
day_1.worked_hours,
end_time=datetime.datetime(2014, 9, 1, hour=17))
day_1.report_start_time("8:00")
nt.assert_equal(
day_1.worked_hours(
end_time=datetime.datetime(2014, 9, 1, hour=16, minute=30)),
datetime.timedelta(hours=8, minutes=30))
day_1.report_lunch_duration("0:30")
nt.assert_equal(
day_1.worked_hours(
end_time=datetime.datetime(2014, 9, 1, hour=16, minute=30)),
datetime.timedelta(hours=8))
day_1.report_deviation("0:45")
nt.assert_equal(
day_1.worked_hours(
end_time=datetime.datetime(2014, 9, 1, hour=16, minute=30)),
datetime.timedelta(hours=7, minutes=15))
day_1.report_end_time("17:00")
nt.assert_raises_regexp(
errors.ChronoError,
"Custom end times can only be tried on days in progress.",
day_1.worked_hours,
end_time=datetime.datetime(2014, 9, 1, hour=16, minute=30))
def test_by_name_and_protocol(self):
name = "A name"
protocol = ExternalIntegration.OVERDRIVE
key = (name, protocol)
# Cache is empty.
eq_(HasFullTableCache.RESET, Collection._cache)
collection1, is_new = Collection.by_name_and_protocol(
self._db, name, ExternalIntegration.OVERDRIVE
)
eq_(True, is_new)
# Cache was populated and then reset because we created a new
# Collection.
eq_(HasFullTableCache.RESET, Collection._cache)
collection2, is_new = Collection.by_name_and_protocol(
self._db, name, ExternalIntegration.OVERDRIVE
)
eq_(collection1, collection2)
eq_(False, is_new)
# This time the cache was not reset after being populated.
eq_(collection1, Collection._cache[key])
# You'll get an exception if you look up an existing name
# but the protocol doesn't match.
assert_raises_regexp(
ValueError,
'Collection "A name" does not use protocol "Bibliotheca".',
Collection.by_name_and_protocol,
self._db, name, ExternalIntegration.BIBLIOTHECA
)
def test_add_flow_with_only_source(self):
"""Test plugin deny add flow with only source."""
data = {
"kind": "Access Control List",
"rules": [{
"action": "permit",
"description": "Restrict environment",
"icmp-options": {
"icmp-code": "0",
"icmp-type": "8"
},
"id": "82325",
"owner": "networkapi",
"protocol": "icmp",
"source": "0.0.0.0/0"
}]
}
rule = dumps(data['rules'][0], sort_keys=True)
assert_raises_regexp(
ValueError,
"Error building ACL Json. Malformed input data: \n%s" %
rule,
self.odl.add_flow,
data
)
def test_bad_connection_remote_pin_test(self):
api = self.mock_api(bad_connection=True)
assert_raises_regexp(
RemoteInitiatedServerError,
"Could not connect!",
api.remote_pin_test, "key", "pin"
)
def test_broken_service_remote_pin_test(self):
api = self.mock_api(failure_status_code=502)
assert_raises_regexp(
RemoteInitiatedServerError,
"Got unexpected response code 502. Content: Error 502",
api.remote_pin_test, "key", "pin"
)
def test_protocol_enforcement(self):
"""A CollectionMonitor can require that it be instantiated
with a Collection that implements a certain protocol.
"""
class NoProtocolMonitor(CollectionMonitor):
SERVICE_NAME = "Test Monitor 1"
PROTOCOL = None
class OverdriveMonitor(CollectionMonitor):
SERVICE_NAME = "Test Monitor 2"
PROTOCOL = ExternalIntegration.OVERDRIVE
# Two collections.
c1 = self._collection(protocol=ExternalIntegration.OVERDRIVE)
c2 = self._collection(protocol=ExternalIntegration.BIBLIOTHECA)
# The NoProtocolMonitor can be instantiated with either one,
# or with no Collection at all.
NoProtocolMonitor(self._db, c1)
NoProtocolMonitor(self._db, c2)
NoProtocolMonitor(self._db, None)
# The OverdriveMonitor can only be instantiated with the first one.
OverdriveMonitor(self._db, c1)
assert_raises_regexp(
ValueError,
"Collection protocol \(Bibliotheca\) does not match Monitor protocol \(Overdrive\)",
OverdriveMonitor, self._db, c2
)
assert_raises(
CollectionMissing,
OverdriveMonitor, self._db, None
)
def test_internal_server_error(self):
data = self.sample_data("invalid_error_code.xml")
parser = HoldReleaseResponseParser()
assert_raises_regexp(
RemoteInitiatedServerError, "Invalid response code from Axis 360: abcd",
parser.process_all, data
)
def test_missing_error_code(self):
data = self.sample_data("missing_error_code.xml")
parser = HoldReleaseResponseParser()
assert_raises_regexp(
RemoteInitiatedServerError, "No status code!",
parser.process_all, data
)
def test_for_collection(self):
# This collection has no mirror_integration, so
# there is no MirrorUploader for it.
collection = self._collection()
eq_(None, MirrorUploader.for_collection(collection))
# We can tell the method that we're okay with a sitewide
# integration instead of an integration specifically for this
# collection.
sitewide_integration = self._integration
uploader = MirrorUploader.for_collection(collection, use_sitewide=True)
assert isinstance(uploader, MirrorUploader)
# This collection has a properly configured mirror_integration,
# so it can have an MirrorUploader.
collection.mirror_integration = self._integration
uploader = MirrorUploader.for_collection(collection)
assert isinstance(uploader, MirrorUploader)
# This collection has a mirror_integration but it has the
# wrong goal, so attempting to make an MirrorUploader for it
# raises an exception.
collection.mirror_integration.goal = ExternalIntegration.LICENSE_GOAL
assert_raises_regexp(
CannotLoadConfiguration,
"from an integration with goal=licenses",
MirrorUploader.for_collection, collection
)
def test_internal_server_error(self):
data = self.sample_data("internal_server_error.xml")
parser = HoldReleaseResponseParser()
assert_raises_regexp(
RemoteInitiatedServerError, "Internal Server Error",
parser.process_all, data
)
def test_empty_token(self):
# Test the behavior when a credential is empty.
# First, create a token with an empty credential.
data_source = DataSource.lookup(self._db, DataSource.ADOBE)
token, is_new = Credential.persistent_token_create(
self._db, data_source, "i am empty", None
)
token.credential = None
# If allow_empty_token is true, the token is returned as-is
# and the refresher method is not called.
def refresher(self):
raise Exception("Refresher method was called")
args = self._db, data_source, token.type, None, refresher,
again_token = Credential.lookup(
*args, allow_persistent_token=True, allow_empty_token=True
)
eq_(again_token, token)
# If allow_empty_token is False, the refresher method is
# created.
assert_raises_regexp(
Exception, "Refresher method was called",
Credential.lookup, *args,
allow_persistent_token=True, allow_empty_token=False
)
def test_add_flow_without_icmp_code_and_icmp_type(self):
"""Test plugin deny add flow without icmp-code and icmp-type."""
data = {
"kind": "Access Control List",
"rules": [{
"id": 1,
"protocol": "icmp",
"source": "10.0.0.1/32",
"destination": "10.0.0.2/32",
"icmp-options": {
}
}]
}
rule = dumps(data['rules'][0], sort_keys=True)
assert_raises_regexp(
ValueError,
"Error building ACL Json. Malformed input data: \n"
"Missing icmp-code or icmp-type icmp options:\n%s" %
rule,
self.odl.add_flow,
data
)
def test_calling_atom_raises_exception():
"""A function call to a non-function should result in an error."""
with assert_raises_regexp(LispError, "not a function"):
evaluate(parse("(#t 'foo 'bar)"), Environment())
with assert_raises_regexp(LispError, "not a function"):
evaluate(parse("(42)"), Environment())
def test_add_flow_without_source_and_destination(self):
"""Test plugin deny add flow without source and destination."""
data = {
"kind": "default#acl",
"rules": [{
"action": "permit",
"description": "generic",
"icmp-options": {
"icmp-code": "0",
"icmp-type": "8"
},
"id": "82325",
"owner": "networkapi",
"protocol": "icmp"
}]
}
rule = dumps(data['rules'][0], sort_keys=True)
assert_raises_regexp(
ValueError,
"Error building ACL Json. Malformed input data: \n%s" %
rule,
self.odl.add_flow,
data
)
def error_is_raised_if_too_many_positional_arguments_are_passed_to_init():
User = dodge.data_class("User", ["username", "password"])
assert_raises_regexp(
TypeError, r"takes 2 positional arguments but 3 were given",
lambda: User("bob", "password1", "salty")
)
def test_create_external_integration(self):
# A newly created Collection has no associated ExternalIntegration.
collection, ignore = get_one_or_create(
self._db, Collection, name=self._str
)
eq_(None, collection.external_integration_id)
assert_raises_regexp(
ValueError,
"No known external integration for collection",
getattr, collection, 'external_integration'
)
# We can create one with create_external_integration().
overdrive = ExternalIntegration.OVERDRIVE
integration = collection.create_external_integration(protocol=overdrive)
eq_(integration.id, collection.external_integration_id)
eq_(overdrive, integration.protocol)
# If we call create_external_integration() again we get the same
# ExternalIntegration as before.
integration2 = collection.create_external_integration(protocol=overdrive)
eq_(integration, integration2)
# If we try to initialize an ExternalIntegration with a different
# protocol, we get an error.
assert_raises_regexp(
ValueError,
"Located ExternalIntegration, but its protocol \(Overdrive\) does not match desired protocol \(blah\).",
collection.create_external_integration,
protocol="blah"
)
def test_for_foreign_id_rejects_invalid_identifiers(self):
assert_raises_regexp(
ValueError,
'"foo/bar" is not a valid Bibliotheca ID.',
Identifier.for_foreign_id,
self._db, Identifier.BIBLIOTHECA_ID, "foo/bar"
)
def test_verb_alias_config_initialization():
cwd = os.getcwd()
test_folder = os.path.join(cwd, 'test')
# Test target directory does not exist failure
with assert_raises_regexp(RuntimeError, "Cannot initialize verb aliases because catkin configuration path"):
config.initialize_verb_aliases(test_folder)
# Test normal case
os.makedirs(test_folder)
config.initialize_verb_aliases(test_folder)
assert os.path.isdir(test_folder)
assert os.path.isdir(os.path.join(test_folder, 'verb_aliases'))
defaults_path = os.path.join(test_folder, 'verb_aliases', '00-default-aliases.yaml')
assert os.path.isfile(defaults_path)
# Assert a second invocation is fine
config.initialize_verb_aliases(test_folder)
# Check that replacement of defaults works
with open(defaults_path, 'w') as f:
f.write("This should be overwritten (simulation of update needed)")
with redirected_stdio() as (out, err):
config.initialize_verb_aliases(test_folder)
assert "Warning, builtin verb aliases at" in out.getvalue(), out.getvalue()
shutil.rmtree(test_folder)
# Check failure from verb aliases folder existing as a file
os.makedirs(test_folder)
with open(os.path.join(test_folder, 'verb_aliases'), 'w') as f:
f.write("this will cause a RuntimeError")
with assert_raises_regexp(RuntimeError, "The catkin verb aliases config directory"):
config.initialize_verb_aliases(test_folder)
shutil.rmtree(test_folder)
def test_misconfigured_authentication_mode(self):
assert_raises_regexp(
CannotLoadConfiguration,
"Unrecognized Millenium Patron API authentication mode: nosuchauthmode.",
self.mock_api,
auth_mode = 'nosuchauthmode'
)
def test_convolutional_sequence_with_no_input_size():
# suppose x is outputted by some RNN
x = tensor.tensor4('x')
filter_size = (1, 1)
num_filters = 2
num_channels = 1
pooling_size = (1, 1)
conv = Convolutional(filter_size, num_filters, tied_biases=False,
weights_init=Constant(1.), biases_init=Constant(1.))
act = Rectifier()
pool = MaxPooling(pooling_size)
bad_seq = ConvolutionalSequence([conv, act, pool], num_channels,
tied_biases=False)
assert_raises_regexp(ValueError, 'Cannot infer bias size \S+',
bad_seq.initialize)
seq = ConvolutionalSequence([conv, act, pool], num_channels,
tied_biases=True)
try:
seq.initialize()
out = seq.apply(x)
except TypeError:
assert False, "This should have succeeded"
assert out.ndim == 4
def test_define_with_wrong_number_of_arguments():
"""Defines should have exactly two arguments, or raise an error"""
with assert_raises_regexp(LispError, "Wrong number of arguments"):
evaluate(parse("(define x)"), Environment())
with assert_raises_regexp(LispError, "Wrong number of arguments"):
evaluate(parse("(define x 1 2)"), Environment())
def test_invalid_generalization(self):
my_point = Point(1, 3)
assert_raises_regexp(
RecordInstanceError,
"^Record type Point is not a subtype of Point3D$",
Point3D.init_from_specialization,
my_point,
)
def test_circulationdata_may_require_collection(self):
"""Depending on the information provided in a CirculationData
object, it might or might not be possible to call apply()
without providing a Collection.
"""
identifier = IdentifierData(Identifier.OVERDRIVE_ID, "1")
format = FormatData(Representation.EPUB_MEDIA_TYPE,
DeliveryMechanism.NO_DRM,
rights_uri=RightsStatus.IN_COPYRIGHT)
circdata = CirculationData(DataSource.OVERDRIVE,
primary_identifier=identifier,
formats=[format])
circdata.apply(self._db, collection=None)
# apply() has created a LicensePoolDeliveryMechanism for this
# title, even though there are no LicensePools for it.
identifier_obj, ignore = identifier.load(self._db)
eq_([], identifier_obj.licensed_through)
[lpdm] = identifier_obj.delivery_mechanisms
eq_(DataSource.OVERDRIVE, lpdm.data_source.name)
eq_(RightsStatus.IN_COPYRIGHT, lpdm.rights_status.uri)
mechanism = lpdm.delivery_mechanism
eq_(Representation.EPUB_MEDIA_TYPE, mechanism.content_type)
eq_(DeliveryMechanism.NO_DRM, mechanism.drm_scheme)
# But if we put some information in the CirculationData
# that can only be stored in a LicensePool, there's trouble.
circdata.licenses_owned = 0
assert_raises_regexp(
ValueError,
'Cannot store circulation information because no Collection was provided.',
circdata.apply,
self._db,
collection=None)
def test_report_lunch(self):
day_1 = day.Day("2014-09-01")
nt.assert_equal(day_1.lunch_duration, None)
nt.assert_raises_regexp(
errors.ReportError,
"^Date 2014-09-01 must have a start time before a lunch duration "
"can be reported.",
day_1.report_lunch_duration,
"1:00")
day_1.report_start_time("8:00")
day_1.report_lunch_duration("1:00")
nt.assert_equal(day_1.lunch_duration, datetime.timedelta(hours=1))
day_2 = day.Day("2014-09-02")
day_2.report_start_time("8:10")
day_2.report_lunch_duration("0:45")
nt.assert_equal(day_2.lunch_duration, datetime.timedelta(minutes=45))
nt.assert_raises_regexp(
errors.ReportError,
"^Date 2014-09-01 allready has a lunch duration.",
day_1.report_lunch_duration,
"1:00")
def test_config_initialization(patched_func):
cwd = os.getcwd()
test_folder = os.path.join(cwd, 'test')
# Test normal case
config.initialize_config(test_folder)
assert os.path.isdir(test_folder)
assert not os.path.exists(os.path.join(test_folder, 'verb_aliases'))
# Assert a second invocation is fine
config.initialize_config(test_folder)
shutil.rmtree(test_folder)
# Test failure with file for target config path
with open(test_folder, 'w') as f:
f.write('this will cause a RuntimeError')
with assert_raises_regexp(RuntimeError, "The catkin config directory"):
config.initialize_config(test_folder)
def no_call_pure_virtual_method(mthd, *args, **kwargs):
"""
Catches a RuntimeError raised by attempting to call a bound method
with an interface implementation. Used to test that a pybind11
trampoline pattern applied to an interface class behaves correctly
Will raise exception if not virtual method
:param: mthd: The method to be called
:param: *args: Args forwarded to method call
:param: **kwargs: Kwargs forwarded to method call
:return:
"""
with nt.assert_raises_regexp(
RuntimeError, "Tried to call pure virtual function",
):
mthd(*args, **kwargs)
def test_simple(self):
p = SimpleAuthenticationProvider
integration = self._external_integration(self._str)
assert_raises_regexp(CannotLoadConfiguration,
"Test identifier and password not set.", p,
self._default_library, integration)
integration.setting(p.TEST_IDENTIFIER).value = "barcode"
integration.setting(p.TEST_PASSWORD).value = "pass"
provider = p(self._default_library, integration)
eq_(None, provider.remote_authenticate("user", "wrongpass"))
eq_(None, provider.remote_authenticate("user", None))
eq_(None, provider.remote_authenticate(None, "pass"))
user = provider.remote_authenticate("barcode", "pass")
assert isinstance(user, PatronData)
eq_("barcode", user.authorization_identifier)
eq_("barcode_id", user.permanent_id)
eq_("barcode_username", user.username)
# User can also authenticate by their 'username'
user2 = provider.remote_authenticate("barcode_username", "pass")
eq_("barcode", user2.authorization_identifier)
def test_check_axis_angle():
"""Test input validation for axis-angle representation."""
a_list = [1, 0, 0, 0]
a = check_axis_angle(a_list)
assert_array_almost_equal(a_list, a)
assert_equal(type(a), np.ndarray)
assert_equal(a.dtype, np.float)
random_state = np.random.RandomState(0)
a = np.empty(4)
a[:3] = random_vector(random_state, 3)
a[3] = random_state.randn() * 4.0 * np.pi
a2 = check_axis_angle(a)
assert_axis_angle_equal(a, a2)
assert_almost_equal(np.linalg.norm(a2[:3]), 1.0)
assert_greater(a2[3], 0)
assert_greater(np.pi, a2[3])
assert_raises_regexp(ValueError,
"Expected axis and angle in array with shape",
check_axis_angle, np.zeros(3))
assert_raises_regexp(ValueError,
"Expected axis and angle in array with shape",
check_axis_angle, np.zeros((3, 3)))
def test_request_failure(self):
"""Verify that certain unexpected HTTP results are turned into
IntegrationExceptions.
"""
self.api.api_key = "some key"
def result_403(*args, **kwargs):
return 403, None, None
self.api.do_get = result_403
assert_raises_regexp(IntegrationException, "API authentication failed",
self.api.request, "some path")
def result_500(*args, **kwargs):
return 500, {}, "bad value"
self.api.do_get = result_500
try:
self.api.request("some path")
raise Exception("Expected an IntegrationException!")
except IntegrationException, e:
eq_("Unknown API error (status 500)", e.message)
assert e.debug_message.startswith("Response from")
assert e.debug_message.endswith("was: 'bad value'")
def test_verify_status_code(self):
success = dict(Status=dict(Code=0000))
failure = dict(Status=dict(Code=1000, Message="A message"))
missing = dict()
m = JSONResponseParser.verify_status_code
# If the document's Status object indicates success, nothing
# happens.
m(success)
# If it indicates failure, an appropriate exception is raised.
assert_raises_regexp(
PatronAuthorizationFailedException, "A message",
m, failure
)
# If the Status object is missing, a more generic exception is
# raised.
assert_raises_regexp(
RemoteInitiatedServerError,
"Required key Status not present in Axis 360 fulfillment document",
m, missing
)
def test_read_conv_pp():
my_dir = os.path.join(os.path.expanduser("~"), "reegis_opsd_test")
os.makedirs(my_dir, exist_ok=True)
cfg.tmp_set("paths_pattern", "opsd", my_dir)
cfg.tmp_set("paths", "powerplants", my_dir)
with assert_raises_regexp(ValueError, "Category 'conv' is not valid."):
opsd.load_original_opsd_file("conv", True)
df = opsd.load_original_opsd_file("conventional", True)
for f in [
"conventional_readme.md",
"conventional_datapackage.json",
"conventional_power_plants_DE.csv",
]:
ok_(os.path.isfile(os.path.join(my_dir, f)))
rmtree(my_dir)
eq_(int(df["capacity_net_bnetza"].sum()), 118684)
def test_tutorial_init_from_existing_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.init_from_existing_tutorial`."""
tuto = Tutorial(training=training, topic=topic)
# non existing tutorial
exp_exception = "The tutorial existing_tutorial does not exists. It should be created"
with assert_raises_regexp(Exception, exp_exception):
tuto.init_from_existing_tutorial('existing_tutorial')
# existing tutorial
create_existing_tutorial('existing_tutorial', tuto_fp, tuto.topic)
tuto.init_from_existing_tutorial('existing_tutorial')
assert tuto.title == 'A tutorial to test'
assert "A learning objective" in tuto.objectives
assert tuto.time_estimation == "1H"
assert 'the_best_contributor' in tuto.contributors
assert '# First section' in tuto.body
shutil.rmtree("topics")
def _test_invalid_property_value(
self,
property_,
property_value,
exc_message_template,
):
saved_contacts = make_contacts(1)
connection = \
self._make_connection_for_contacts(saved_contacts, property_)
contact_with_invalid_property_value = \
make_contact(1, {property_.name: property_value})
exc_message = exc_message_template.format(repr(property_value))
with assert_raises_regexp(HubspotPropertyValueError, exc_message):
with connection:
save_contacts([contact_with_invalid_property_value], connection)
def test_offsettransformer__too_many_input_flows():
"""Too many Input Flows defined."""
with tools.assert_raises_regexp(
ValueError, 'OffsetTransformer` must not have more than 1'):
bgas = solph.Bus(label='GasBus')
bcoal = solph.Bus(label='CoalBus')
solph.components.OffsetTransformer(
label='ostf_2_in',
inputs={
bgas: solph.Flow(
nominal_value=60, min=0.5, max=1.0,
nonconvex=solph.NonConvex()),
bcoal: solph.Flow(
nominal_value=30, min=0.3, max=1.0,
nonconvex=solph.NonConvex())
},
coefficients=(20, 0.5))
def test_offsettransformer_too_many_output_flows():
"""Too many Output Flows defined."""
with tools.assert_raises_regexp(
ValueError, 'OffsetTransformer` must not have more than 1'):
bm1 = solph.Bus(label='my_offset_Bus1')
bm2 = solph.Bus(label='my_offset_Bus2')
solph.components.OffsetTransformer(
label='ostf_2_out',
inputs={
bm1: solph.Flow(
nominal_value=60, min=0.5, max=1.0,
nonconvex=solph.NonConvex())
},
outputs={bm1: solph.Flow(),
bm2: solph.Flow()},
coefficients=(20, 0.5))
def test_annuity_exceptions():
"""Test out-of-bounds-error of the annuity tool."""
msg = "Input arguments for 'annuity' out of bounds!"
assert_raises_regexp(ValueError, msg, economics.annuity, 1000, 10, 2)
assert_raises_regexp(ValueError, msg, economics.annuity, 1000, 0.5, 1)
assert_raises_regexp(ValueError,
msg,
economics.annuity,
1000,
10,
0.1,
u=0.3)
assert_raises_regexp(ValueError,
msg,
economics.annuity,
1000,
10,
0.1,
cost_decrease=-1)
def checkPlotfToFileBadArgs(basenames, specs):
# Enable the persistent_inference_trace in order to trigger the
# inference prelude entry skipping hack in error annotation
ripl = get_ripl(persistent_inference_trace=True)
ripl.assume('x', '(normal 0 1)')
infer = """
(let ((d (empty)))
(do (repeat 10
(do (mh default one 10)
(bind (collect x) (curry into d))))
(plotf_to_file (quote {0}) (quote {1}) d)))"""
infer = infer.format(basenames, specs)
with assert_raises_regexp(
VentureException,
'evaluation: The number of specs must match the number of filenames.'
) as cm:
ripl.infer(infer)
assert "stack_trace" in cm.exception.data # I.e., error annotation succeeded.
def test_infeasible_model():
with tools.assert_raises_regexp(ValueError, ''):
with warnings.catch_warnings(record=True) as w:
es = solph.EnergySystem(timeindex=[1])
bel = solph.Bus(label='bus')
es.add(bel)
es.add(
solph.Sink(inputs={
bel:
solph.Flow(nominal_value=5, actual_value=[1], fixed=True)
}))
es.add(
solph.Source(outputs={
bel: solph.Flow(nominal_value=4, variable_costs=5)
}))
m = solph.models.Model(es, timeincrement=1)
m.solve(solver='cbc')
assert "Optimization ended with status" in str(w[0].message)
outputlib.processing.meta_results(m)
def test_BloscpackHeader_accessor_exceptions():
if sys.version_info[0:2] < (2, 7):
raise SkipTest
bloscpack_header = BloscpackHeader()
nt.assert_raises_regexp(KeyError, 'foo not in BloscpackHeader',
bloscpack_header.__getitem__, 'foo')
nt.assert_raises_regexp(KeyError, 'foo not in BloscpackHeader',
bloscpack_header.__setitem__, 'foo', 'bar')
nt.assert_raises_regexp(
NotImplementedError,
'BloscpackHeader does not support __delitem__ or derivatives',
bloscpack_header.__delitem__,
'foo',
)
def test_transform_not_added():
"""Test request for transforms that have not been added."""
random_state = np.random.RandomState(0)
A2B = random_transform(random_state)
C2D = random_transform(random_state)
tm = TransformManager()
tm.add_transform("A", "B", A2B)
tm.add_transform("C", "D", C2D)
assert_raises_regexp(KeyError, "Unknown frame", tm.get_transform, "A", "G")
assert_raises_regexp(KeyError, "Unknown frame", tm.get_transform, "G", "D")
assert_raises_regexp(KeyError, "Cannot compute path", tm.get_transform,
"A", "D")
def test_fill_data_library():
"""Test :func:`planemo.training.fill_data_library`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.kwds['hands_on'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_wo_zenodo_fp,
train.topic)
# no Zenodo link
train.kwds['zenodo_link'] = None
exp_exception = "A Zenodo link should be provided either in the metadata file or as argument of the command"
with assert_raises_regexp(Exception, exp_exception):
train.fill_data_library(CTX)
# with a given Zenodo link and no Zenodo in metadata
train.kwds['zenodo_link'] = zenodo_link
train.fill_data_library(CTX)
with open(train.tuto.data_lib_fp, 'r') as fh:
assert 'DOI: 10.5281/zenodo.1321885' in fh.read()
with open(train.tuto.tuto_fp, 'r') as fh:
assert 'zenodo_link: %s' % zenodo_link in fh.read()
# with a given Zenodo link and Zenodo in metadata
new_z_link = 'https://zenodo.org/record/1324204'
train.kwds['zenodo_link'] = new_z_link
train.tuto = None
train.fill_data_library(CTX)
with open(train.tuto.data_lib_fp, 'r') as fh:
assert 'DOI: 10.5281/zenodo.1324204' in fh.read()
with open(train.tuto.tuto_fp, 'r') as fh:
assert 'zenodo_link: %s' % new_z_link in fh.read()
# with no given Zenodo link
train.kwds['zenodo_link'] = None
train.fill_data_library(CTX)
with open(train.tuto.data_lib_fp, 'r') as fh:
assert 'DOI: 10.5281/zenodo.1324204' in fh.read()
with open(train.tuto.tuto_fp, 'r') as fh:
assert 'zenodo_link: %s' % new_z_link in fh.read()
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_generate_tuto_from_wf():
"""Test :func:`planemo.training.generate_tuto_from_wf`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
# no workflow
train.kwds['workflow'] = None
exp_exception = "A path to a local workflow or the id of a workflow on a running Galaxy instance should be provided"
with assert_raises_regexp(Exception, exp_exception):
train.generate_tuto_from_wf(CTX)
# with workflow
train.kwds['workflow'] = WF_FP
train.generate_tuto_from_wf(CTX)
assert '**FastQC** {% icon tool %} with the following parameters:' in open(train.tuto.tuto_fp, 'r').read()
assert os.path.exists(train.tuto.wf_fp)
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_report_start_time(self):
day_1 = day.Day("2014-09-01")
nt.assert_equal(day_1.start_time, None)
day_1.report_start_time("8:00")
nt.assert_equal(day_1.start_time,
datetime.datetime(year=2014, month=9, day=1, hour=8))
day_2 = day.Day("2014-09-02")
day_2.report_start_time("8:30")
nt.assert_equal(
day_2.start_time,
datetime.datetime(year=2014, month=9, day=2, hour=8, minute=30))
nt.assert_raises_regexp(
errors.ReportError,
"^Date 2014-09-01 allready has a start time.",
day_1.report_start_time,
"8.00")
day_3 = day.Day("2014-09-03")
nt.assert_raises_regexp(
errors.BadTimeError,
"^Bad start time: \"8\".",
day_3.report_start_time,
"8")
nt.assert_raises_regexp(
errors.BadTimeError,
"^Bad start time: \"8.30\".",
day_3.report_start_time,
"8.30")
nt.assert_raises_regexp(
errors.BadTimeError,
"^Bad start time: \"8:10:14\".",
day_3.report_start_time,
"8:10:14")
def test_training_check_topic_init_tuto():
"""Test :func:`planemo.training.Training.check_topic_init_tuto`."""
train = Training(KWDS)
# no topic
exp_exception = "The topic my_new_topic does not exists. It should be created"
with assert_raises_regexp(Exception, exp_exception):
train.check_topic_init_tuto()
# add topic
train.kwds['tutorial_name'] = None
train.kwds['slides'] = None
train.kwds['workflow'] = None
train.kwds['workflow_id'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
train.check_topic_init_tuto()
assert train.tuto.name == train.kwds['tutorial_name']
assert train.tuto.datatype_fp
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_bad_data_type():
"""
Notify if column data type is wrong
"""
patient = get_patient()
bad_column_mapping = {
'column': 'data_proxima_consulta',
'data_type': 'omrs_datetime',
'commcare_data_type': 'cc_date',
'property': 'data_proxima_consulta'
}
with get_importer(bad_column_mapping) as importer:
with assert_raises_regexp(
ConfigurationError,
'Errors importing from <OpenmrsImporter None admin@http://www.example.com/openmrs>:\n'
'Unable to deserialize value 1551564000000 '
'in column "data_proxima_consulta" '
'for case property "data_proxima_consulta". '
'OpenMRS data type is given as "omrs_datetime". '
'CommCare data type is given as "cc_date": '
"argument of type 'int' is not iterable"):
get_case_properties(patient, importer)
def test_mutability(self):
""" test immutability """
source = """
np.arange(20)
"""
source = dedent(source)
code = ast.parse(source)
new_num = ast.Num(n=3)
expr1 = Expression(code.body[0])
with nt.assert_raises_regexp(Exception, "This expression is not mutable"):
expr1.replace(new_num, expr1.code.body, 'args', 0)
expr2 = expr1.copy(mutable=True)
old_key = expr2.key
expr2.replace(new_num, expr2.code.body, 'args', 0)
nt.assert_not_equal(expr2.key, old_key)
# expr2 was changed
nt.assert_false(ast_equal(expr1.code, expr2.code))
nt.assert_equal(expr2.get_source(), 'np.arange(3)')
def test_bad_date(self):
nt.assert_raises_regexp(errors.BadDateError,
"^Bad date string: \"\"$",
day.Day,
"")
nt.assert_raises_regexp(errors.BadDateError,
"^Bad date string: \"25-09-2014\"$",
day.Day,
"25-09-2014")
nt.assert_raises_regexp(TypeError,
"^Given date must be a string.$",
day.Day,
datetime.date(2014, 9, 25))
nt.assert_raises(errors.BadDateError, day.Day, "20140925")
def test_batch_concatenate_quaternions_mismatch():
Q1 = np.zeros((1, 2, 4))
Q2 = np.zeros((1, 2, 3, 4))
assert_raises_regexp(
ValueError, "Number of dimensions must be the same.",
pbr.batch_concatenate_quaternions, Q1, Q2)
Q1 = np.zeros((1, 2, 4, 4))
Q2 = np.zeros((1, 2, 3, 4))
assert_raises_regexp(
ValueError, "Size of dimension 3 does not match",
pbr.batch_concatenate_quaternions, Q1, Q2)
Q1 = np.zeros((1, 2, 3, 3))
Q2 = np.zeros((1, 2, 3, 4))
assert_raises_regexp(
ValueError, "Last dimension of first argument does not match.",
pbr.batch_concatenate_quaternions, Q1, Q2)
Q1 = np.zeros((1, 2, 3, 4))
Q2 = np.zeros((1, 2, 3, 3))
assert_raises_regexp(
ValueError, "Last dimension of second argument does not match.",
pbr.batch_concatenate_quaternions, Q1, Q2)
def test_trailblaze_setters(self):
"""Test that the special setters and the global parameter function shortcut are working properly."""
# Create a harmonic oscillator system to test.
compound_state, sampler_state = self.get_harmonic_oscillator()
mcmc_move = self.get_langevin_dynamics_move()
# Assign to the parameter a function and run the
# trailblaze algorithm over the function variable.
global_parameter_functions = {self.PAR_NAME_X0: 'lambda**2'}
function_variables = ['lambda']
# Make sure it's not possible to have a parameter defined as a function and as a parameter state as well.
err_msg = f"Cannot specify {self.PAR_NAME_X0} in 'state_parameters' and 'global_parameter_functions'"
with assert_raises_regexp(ValueError, err_msg):
run_thermodynamic_trailblazing(
compound_state,
sampler_state,
mcmc_move,
state_parameters=[(self.PAR_NAME_X0, [0.0, 1.0])],
global_parameter_functions=global_parameter_functions,
function_variables=function_variables,
)
# Trailblaze returns the protocol for the actual parameters, not for the function variables.
protocol = run_thermodynamic_trailblazing(
compound_state,
sampler_state,
mcmc_move,
state_parameters=[('lambda', [0.0, 1.0])],
global_parameter_functions=global_parameter_functions,
function_variables=function_variables,
)
assert list(protocol.keys()) == [self.PAR_NAME_X0]
parameter_protocol = protocol[self.PAR_NAME_X0]
assert parameter_protocol[0] == 0
assert parameter_protocol[-1] == 1
def test_credential_refresh_failure(self):
"""Verify that a useful error message results when the Odilo bearer
token cannot be refreshed, since this is the most likely point
of failure on a new setup.
"""
self.api.access_token_response = MockRequestsResponse(
200, {"Content-Type": "text/html"},
"Hi, this is the website, not the API."
)
credential = self.api.credential_object(lambda x: x)
assert_raises_regexp(
BadResponseException,
"Bad response from .*: .* may not be the right base URL. Response document was: 'Hi, this is the website, not the API.'",
self.api.refresh_creds,
credential
)
# Also test a 400 response code.
self.api.access_token_response = MockRequestsResponse(
400, {"Content-Type": "application/json"},
json.dumps(dict(errors=[dict(description="Oops")]))
)
assert_raises_regexp(
BadResponseException, "Bad response from .*: Oops",
self.api.refresh_creds,
credential
)
# If there's a 400 response but no error information,
# the generic error message is used.
self.api.access_token_response = MockRequestsResponse(
400, {"Content-Type": "application/json"},
json.dumps(dict())
)
assert_raises_regexp(
BadResponseException, "Bad response from .*: .* may not be the right base URL.",
self.api.refresh_creds,
credential
)
def test_get_oob(self):
f2fs = F2FHomography(5), F2FHomography(HomographyD.random(), 5, 10)
exp_err_msg = "Tried to perform get\\(\\) out of bounds"
for f2f in f2fs:
with nt.assert_raises_regexp(IndexError, exp_err_msg):
f2f.get(3, 0)
with nt.assert_raises_regexp(IndexError, exp_err_msg):
f2f.get(-4, 0)
with nt.assert_raises_regexp(IndexError, exp_err_msg):
f2f.get(0, 3)
with nt.assert_raises_regexp(IndexError, exp_err_msg):
f2f.get(0, -4)
with nt.assert_raises_regexp(IndexError, exp_err_msg):
f2f.get(5, 5)
with nt.assert_raises_regexp(IndexError, exp_err_msg):
f2f.get(-6, -6)
def test_bad_end_time(self):
day_1 = day.Day("2014-09-01")
day_1.report_start_time("8:00")
day_1.report_lunch_duration("1:00")
nt.assert_raises_regexp(
TypeError,
"^Given end time must be a string.",
day_1.report_end_time,
datetime.time(hour=17))
nt.assert_raises_regexp(
errors.BadTimeError,
"^Bad end time: \"24:00\"$",
day_1.report_end_time,
"24:00")
nt.assert_raises_regexp(
errors.BadTimeError,
"^Bad end time: \"17:00:00\"$",
day_1.report_end_time,
"17:00:00")
