def setUp(self):
# This test does not start a container so we have to hack creating a FileSystem singleton instance
FileSystem(DotDict())
self.px_ctd = SimpleCtdPublisher()
self.px_ctd.last_time = 0
self.tx_L0 = ctd_L0_all()
self.tx_L0.streams = defaultdict(Mock)
self.tx_L0.conductivity = Mock()
self.tx_L0.temperature = Mock()
self.tx_L0.pressure = Mock()
self.tx_L1_C = CTDL1ConductivityTransform()
self.tx_L1_C.streams = defaultdict(Mock)
self.tx_L1_T = CTDL1TemperatureTransform()
self.tx_L1_T.streams = defaultdict(Mock)
self.tx_L1_P = CTDL1PressureTransform()
self.tx_L1_P.streams = defaultdict(Mock)
self.tx_L2_S = SalinityTransform()
self.tx_L2_S.streams = defaultdict(Mock)
self.tx_L2_D = DensityTransform()
self.tx_L2_D.streams = defaultdict(Mock)
def __init__(self, *args, **kwargs):
BaseContainerAgent.__init__(self, *args, **kwargs)
self._is_started = False
self._capabilities = []
# set container id and cc_agent name (as they are set in base class call)
self.id = get_default_container_id()
self.name = "cc_agent_%s" % self.id
Container.instance = self
from pyon.core import bootstrap
bootstrap.container_instance = self
log.debug("Container (sysname=%s) initializing ..." % bootstrap.get_sys_name())
# DatastoreManager - controls access to Datastores (both mock and couch backed)
self.datastore_manager = DatastoreManager()
self.datastore_manager.start()
self._capabilities.append("DATASTORE_MANAGER")
# Keep track of the overrides from the command-line, so they can trump app/rel file data
self.spawn_args = kwargs
# Instantiate Directory and self-register
# Has the additional side effect of either
# bootstrapping the configuration into the
# directory or read the configuration based
# in the value of the auto_bootstrap setting
self.directory = Directory()
# Create this Container's specific ExchangeManager instance
self.ex_manager = ExchangeManager(self)
# Create this Container's specific ProcManager instance
self.proc_manager = ProcManager(self)
# Create this Container's specific AppManager instance
self.app_manager = AppManager(self)
# File System - Interface to the OS File System, using correct path names and setups
self.file_system = FileSystem(CFG)
# Governance Controller - manages the governance related interceptors
self.governance_controller = GovernanceController(self)
# sFlow manager - controls sFlow stat emission
self.sflow_manager = SFlowManager(self)
# Coordinates the container start
self._status = "INIT"
# protection for when the container itself is used as a Process for clients
self.container = self
log.debug("Container initialized, OK.")
def __init__(self, *args, **kwargs):
BaseContainerAgent.__init__(self, *args, **kwargs)
self._is_started = False
# set id and name (as they are set in base class call)
self.id = string.replace('%s_%d' % (os.uname()[1], os.getpid()), ".",
"_")
self.name = "cc_agent_%s" % self.id
Container.instance = self
# TODO: Bug: Replacing CFG instance not work because references are already public. Update directly
dict_merge(CFG, kwargs, inplace=True)
from pyon.core import bootstrap
bootstrap.container_instance = self
bootstrap.assert_configuration(CFG)
log.debug("Container (sysname=%s) initializing ..." %
bootstrap.get_sys_name())
# Keep track of the overrides from the command-line, so they can trump app/rel file data
self.spawn_args = kwargs
# Load object and service registry etc.
bootstrap_pyon()
# Create this Container's specific ExchangeManager instance
self.ex_manager = ExchangeManager(self)
# Create this Container's specific ProcManager instance
self.proc_manager = ProcManager(self)
# Create this Container's specific AppManager instance
self.app_manager = AppManager(self)
# DatastoreManager - controls access to Datastores (both mock and couch backed)
self.datastore_manager = DatastoreManager()
# File System - Interface to the OS File System, using correct path names and setups
self.file_system = FileSystem(CFG)
# Governance Controller - manages the governance related interceptors
self.governance_controller = GovernanceController(self)
# sFlow manager - controls sFlow stat emission
self.sflow_manager = SFlowManager(self)
# Coordinates the container start
self._is_started = False
self._capabilities = []
self._status = "INIT"
# protection for when the container itself is used as a Process for clients
self.container = self
log.debug("Container initialized, OK.")
def setUpClass(cls):
# This test does not start a container so we have to hack creating a FileSystem singleton instance
FileSystem(DotDict())
@unittest.skipIf(no_numpy_h5py, 'numpy and/or h5py not imported')
def create_known(dataset_name, rootgrp_name, grp_name):
"""
A known array to compare against during tests
"""
known_array = numpy.random.rand(10, 20)
filename = FileSystem.get_url(FS.TEMP, random_name(), ".hdf5")
# Write an hdf file with known values to compare against
h5pyfile = h5py.File(filename, mode='w', driver='core')
grp = h5pyfile.create_group(rootgrp_name)
subgrp = grp.create_group(grp_name)
dataset = subgrp.create_dataset(dataset_name,
known_array.shape,
known_array.dtype.str,
compression='gzip',
compression_opts=4,
maxshape=(None, None))
dataset.write_direct(known_array)
h5pyfile.close()
# convert the hdf file into a binary string
f = open(filename, mode='rb')
# read the binary string representation of the file
known_hdf_as_string = f.read(
) # this is a known string to compare against during tests
f.close()
# cleaning up
FileSystem.unlink(f.name)
return known_array, known_hdf_as_string
# Use the class method to patch these attributes onto the class.
TestScienceObjectCodec.known_array, TestScienceObjectCodec.known_hdf_as_string = create_known(
TestScienceObjectCodec.dataset_name,
TestScienceObjectCodec.rootgrp_name,
TestScienceObjectCodec.grp_name)
TestScienceObjectCodec.known_hdf_as_sha1 = sha1(
TestScienceObjectCodec.known_hdf_as_string)
def __init__(self, container):
ContainerCapability.__init__(self, container)
self.container.file_system = FileSystem(CFG)
def __init__(self, *args, **kwargs):
BaseContainerAgent.__init__(self, *args, **kwargs)
self._is_started = False
# set container id and cc_agent name (as they are set in base class call)
self.id = get_default_container_id()
self.name = "cc_agent_%s" % self.id
self._capabilities = []
bootstrap.container_instance = self
Container.instance = self
log.debug("Container (sysname=%s) initializing ..." %
bootstrap.get_sys_name())
# Keep track of the overrides from the command-line, so they can trump app/rel file data
self.spawn_args = kwargs
# DatastoreManager - controls access to Datastores (both mock and couch backed)
self.datastore_manager = DatastoreManager()
# TODO: Do not start a capability here. Symmetric start/stop
self.datastore_manager.start()
self._capabilities.append("DATASTORE_MANAGER")
# Instantiate Directory
self.directory = Directory()
# internal router
self.local_router = None
# Create this Container's specific ExchangeManager instance
self.ex_manager = ExchangeManager(self)
# Create this Container's specific ProcManager instance
self.proc_manager = ProcManager(self)
# Create this Container's specific AppManager instance
self.app_manager = AppManager(self)
# File System - Interface to the OS File System, using correct path names and setups
self.file_system = FileSystem(CFG)
# Governance Controller - manages the governance related interceptors
self.governance_controller = GovernanceController(self)
# sFlow manager - controls sFlow stat emission
self.sflow_manager = SFlowManager(self)
# Coordinates the container start
self._status = "INIT"
# protection for when the container itself is used as a Process for clients
self.container = self
# publisher, initialized in start()
self.event_pub = None
# context-local storage
self.context = LocalContextMixin()
log.debug("Container initialized, OK.")
def setUp(self):
import numpy, h5py
FileSystem(DotDict())
#--------------------------------------------------------------------
# Create an hdf file for testing
#--------------------------------------------------------------------
self.salinity = [
0,
] * 3
self.temperature = [
0,
] * 3
self.pressure = [
0,
] * 3
self.salinity[0] = numpy.arange(50)
self.salinity[1] = numpy.arange(50) + 50
self.salinity[2] = numpy.arange(50) + 100
self.temperature[0] = numpy.random.normal(size=50)
self.temperature[1] = numpy.random.normal(size=50)
self.temperature[2] = numpy.random.normal(size=50)
self.pressure[0] = numpy.random.uniform(low=0.0, high=1.0, size=50)
self.pressure[1] = numpy.random.uniform(low=0.0, high=1.0, size=50)
self.pressure[2] = numpy.random.uniform(low=0.0, high=1.0, size=50)
# provide the check_pieces mathod the size of the dataset so that it can do its checking..
self.sl = slice(0, 150)
self.fnames = [
0,
] * 3
for i in range(0, 3):
self.fnames[i] = FileSystem.get_url(FS.TEMP,
'data%d.hdf5' % (i + 1))
for fname, s, t, p in zip(self.fnames, self.salinity, self.temperature,
self.pressure):
file = h5py.File(fname, 'w')
grp1 = file.create_group('fields')
dset1 = grp1.create_dataset("salinity", data=s)
dset2 = grp1.create_dataset("temperature", data=t)
dset3 = grp1.create_dataset("pressure", data=p)
file.close()
# Concatenate the test values for comparison:
self.t_result = numpy.concatenate(
(self.temperature[0], self.temperature[1], self.temperature[2]),
axis=0)
self.s_result = numpy.concatenate(
(self.salinity[0], self.salinity[1], self.salinity[2]), axis=0)
self.p_result = numpy.concatenate(
(self.pressure[0], self.pressure[1], self.pressure[2]), axis=0)
