def __getEc2PrivateIpv4s(self, additionalVariables):
try:
dir = File(self.__basedir)
dir = dir.getParentFile().getParentFile().getParentFile()
fileReader = FileReader(File(dir, "engine-session.properties"))
props = Properties()
props.load(fileReader)
ec2PrivateIpv4s = props.getProperty("ec2PrivateIpv4s")
if ec2PrivateIpv4s:
ipList = ec2PrivateIpv4s.split()
logger.info("Ec2 Private IPv4s:" + list2str(ipList))
engineInstance = getVariableValue("ENGINE_INSTANCE")
engineInstance = int(engineInstance)
if len(ipList) > engineInstance:
self.__dockerHostIp = ipList[engineInstance]
logger.info("Setting DOCKER_HOST_IP:" +
self.__dockerHostIp)
additionalVariables.add(
RuntimeContextVariable(
"DOCKER_HOST_IP", self.__dockerHostIp,
RuntimeContextVariable.STRING_TYPE,
"Docker Host IP", False,
RuntimeContextVariable.NO_INCREMENT))
else:
self.__dockerHostIp = getVariableValue("LISTEN_ADDRESS")
additionalVariables.add(
RuntimeContextVariable(
"DOCKER_HOST_IP", self.__dockerHostIp,
RuntimeContextVariable.STRING_TYPE,
"Docker Host IP", False,
RuntimeContextVariable.NO_INCREMENT))
except:
type, value, traceback = sys.exc_info()
logger.warning("read engine session properties error:" + ` value `)
def restoreJSystemProperties(self):
if self.userDir is None:
return
orig = File(self.userDir, "jsystem.properties")
back = File(orig.getParentFile(), "jsystem.properties.back")
FileUtils.copyFile(back, orig)
def test_image_example_dir_iteration(self):
f = File(str(inspect.getfile( inspect.currentframe() )))
example_dir = File(File(f.getParentFile().getParentFile().getParentFile(),"character_examples"),"A")
image_example_dir = ImageExampleDir(example_dir.getCanonicalPath())
for label, image in image_example_dir:
if label != "A":
raise "The label of the examples in this dir should be A"
def setUp(self):
if not os.path.exists(self._execution_dir):
os.makedirs(self._execution_dir)
wlst_dir = File(System.getProperty('unit-test-wlst-dir'))
self._oracle_home = wlst_dir.getParentFile().getParentFile(
).getParentFile().getCanonicalPath()
return
def get_example_image(self):
f = File(str(inspect.getfile(inspect.currentframe())))
example_dir = File(
File(f.getParentFile().getParentFile().getParentFile(),
"character_examples"), "A")
image_example_dir = ImageExampleDir(example_dir.getCanonicalPath())
label, image = image_example_dir.__iter__().next()
return image
def save_session(req,remember,session_dir,**kwargs):
session=JsonObject()
id=str(uuid.uuid1())
session.putString("id", id)
for name,value in kwargs.iteritems():
session.putString(name, value)
print("remember = "+remember)
cookie = 'mvcx.sessionID=%s' % id.strip()
if remember=="1":
cookie += ";max-age=864000"
req.response.put_header('set-cookie', cookie)
session_file=File("%s/%s.json" % (session_dir,id))
print("session_path:"+str(session_file.getAbsolutePath()))
session_file.getParentFile().mkdirs()
Files.write(str(session),session_file)
def test_extract_label_examples_tuples_for_library(self):
extractor = SimpleImageFeatureExtractor(nr_of_divisions=7,
size_classification_factor=1.3)
f = File(str(inspect.getfile( inspect.currentframe() )))
library_path = File(f.getParentFile().getParentFile().getParentFile(),
"character_examples").getCanonicalPath()
training_examples = extractor.extract_label_examples_tuples_for_library(library_path)
print("test_extract_label_examples_tuples_for_library")
print(training_examples)
def test_extract_label_examples_tuples_for_library(self):
extractor = SimpleImageFeatureExtractor(nr_of_divisions=7,
size_classification_factor=1.3)
f = File(str(inspect.getfile(inspect.currentframe())))
library_path = File(f.getParentFile().getParentFile().getParentFile(),
"character_examples").getCanonicalPath()
training_examples = extractor.extract_label_examples_tuples_for_library(
library_path)
print("test_extract_label_examples_tuples_for_library")
print(training_examples)
def test_extract_feature_strings_for_dir(self):
extractor = SimpleImageFeatureExtractor(nr_of_divisions=7,
size_classification_factor=1.3)
f = File(str(inspect.getfile(inspect.currentframe())))
example_dir_path = File(
File(f.getParentFile().getParentFile().getParentFile(),
"character_examples"), "A").getCanonicalPath()
training_examples, test_examples = extractor.extract_feature_strings_for_dir(
example_dir_path,
nr_of_training_examples=90,
nr_of_test_examples=10)
if len(training_examples) == 90 and len(test_examples) == 10:
pass
else:
raise "wrong number in retuned list"
print("test_extract_feature_strings_for_dir")
print(training_examples, test_examples)
def test_extract_feature_strings_for_dir(self):
extractor = SimpleImageFeatureExtractor(nr_of_divisions=7,
size_classification_factor=1.3)
f = File(str(inspect.getfile( inspect.currentframe() )))
example_dir_path = File(File(f.getParentFile().getParentFile().getParentFile(),
"character_examples"),
"A").getCanonicalPath()
training_examples,test_examples = extractor.extract_feature_strings_for_dir(
example_dir_path,
nr_of_training_examples=90,
nr_of_test_examples=10)
if len(training_examples)==90 and len(test_examples) == 10:
pass
else:
raise "wrong number in retuned list"
print("test_extract_feature_strings_for_dir")
print(training_examples,test_examples )
def use_jar(fname, root=__file__, isglobal=False):
from org.gvsig.scripting import ScriptingLocator
from java.io import File
import sys
import os
if isinstance(fname, File):
f = fname
fname = f.getPath()
else:
f = File(fname)
if not f.isAbsolute():
rf = File(root)
if rf.isFile():
rf = rf.getParentFile()
f = File(rf, fname)
fname = f.getCanonicalPath()
use_libs(fname, isglobal=isglobal)
def __getEc2PrivateIpv4s(self, additionalVariables):
try:
dir = File(self.__basedir)
dir = dir.getParentFile().getParentFile().getParentFile()
fileReader = FileReader(File(dir, "engine-session.properties" ))
props = Properties()
props.load(fileReader)
ec2PrivateIpv4s = props.getProperty("ec2PrivateIpv4s")
if ec2PrivateIpv4s:
ipList = ec2PrivateIpv4s.split()
logger.info("Ec2 Private IPv4s:" + list2str(ipList))
engineInstance = getVariableValue("ENGINE_INSTANCE")
engineInstance = int(engineInstance)
if len(ipList) > engineInstance:
self.__dockerHostIp = ipList[engineInstance]
logger.info("Setting DOCKER_HOST_IP:" +self.__dockerHostIp)
additionalVariables.add(RuntimeContextVariable("DOCKER_HOST_IP", self.__dockerHostIp, RuntimeContextVariable.STRING_TYPE, "Docker Host IP", False, RuntimeContextVariable.NO_INCREMENT))
else:
self.__dockerHostIp = getVariableValue("LISTEN_ADDRESS")
additionalVariables.add(RuntimeContextVariable("DOCKER_HOST_IP", self.__dockerHostIp , RuntimeContextVariable.STRING_TYPE, "Docker Host IP", False, RuntimeContextVariable.NO_INCREMENT))
except:
type, value, traceback = sys.exc_info()
logger.warning("read engine session properties error:" + `value`)
for maxElecLenIndex in range(0,len(maxElecLens)):
maxElecLen = maxElecLens[maxElecLenIndex]
for sim in simulators:
recompSuffix = "_"+str(maxElecLen)
simRefPrefix = (simAllPrefix+simConfigName+"_").replace(' ', '')
simRef = simRefPrefix+"_"+sim+recompSuffix
simDir = File(projFile.getParentFile(), "/simulations/"+simRef)
timeFile = File(simDir, "time.dat")
if not timeFile.exists():
print "\n------- Error loading data from simulation in directory: %s\n"%simDir.getCanonicalPath()
else:
if verbose: print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
time.sleep(1) # wait a while...
try:
simData = SimulationData(simDir)
simData.initialise()
times = simData.getAllTimes()
def __getHistoryFile(self):
f = File(System.getProperty("user.home"), ".fascinator/blog/history.txt")
if not f.exists():
f.getParentFile().mkdirs()
return f
def get_example_image(self):
f = File(str(inspect.getfile( inspect.currentframe() )))
example_dir = File(File(f.getParentFile().getParentFile().getParentFile(),"character_examples"),"A")
image_example_dir = ImageExampleDir(example_dir.getCanonicalPath())
label, image = image_example_dir.__iter__().next()
return image
def SingleCellNML2generator(projString=" ",ConfigDict={},ElecLenList=[],somaNseg=None,savingDir=None,shell=None):
projFile=File(os.getcwd(),projString)
pm=ProjectManager()
for config in ConfigDict.keys():
project=pm.loadProject(projFile)
nmlfm = NeuroMLFileManager(project)
compSummary={}
compSummary[config]={}
if " " in config:
configPath=config.replace(" ","_")
else:
configPath=config
if savingDir !=None:
full_path_to_config=r'../%s/%s'%(savingDir,configPath)
else:
full_path_to_config=r'../%s'%(configPath)
for maxElecLen in ElecLenList:
compSummary[config][str(maxElecLen)]={}
cell=project.cellManager.getCell(ConfigDict[config])
if maxElecLen > 0:
info = CellTopologyHelper.recompartmentaliseCell(cell, maxElecLen, project)
print "Recompartmentalising cell %s"%ConfigDict[config]
if somaNseg != None:
cell.getSegmentWithId(0).getSection().setNumberInternalDivisions(somaNseg)
if savingDir !=None:
cellpath = r'../%s/%s/%s_%f'%(savingDir,configPath,configPath,maxElecLen)
else:
cellpath = r'../%s/%s_%f'%(configPath,configPath,maxElecLen)
else:
if savingDir !=None:
cellpath = r'../%s/%s/%s_default'%(savingDir,configPath,configPath)
else:
cellpath = r'../%s/%s_default'%(configPath,configPath)
summary=str(cell.getMorphSummary())
summary_string=summary.split("_")
for feature in summary_string:
feature_split=feature.split(":")
compSummary[config][str(maxElecLen)][feature_split[0]]=feature_split[1]
# the format of summary : Segs:122_Secs:61_IntDivs:1458
print("Will be printing a cell morphology summary")
print compSummary[config][str(maxElecLen)]
######### it turns out that this does not save recompartmentalized cells - all saved cells have identical spatial discretization;
##### generateNeuroML2 receives the parent projFile but not the loaded project which is modified by the CellTopologyHelper.recompartmentaliseCell()
##################### neuroConstruct block #############################################################################
neuroConstructSeed=1234
verbose=True
pm.doGenerate(config, neuroConstructSeed)
while pm.isGenerating():
if verbose:
print("Waiting for the project to be generated with Simulation Configuration: "+config)
time.sleep(5)
simConfig = project.simConfigInfo.getSimConfig(config)
seed=1234
genDir = File(projFile.getParentFile(), "generatedNeuroML2")
nmlfm.generateNeuroMLFiles(simConfig,
NeuroMLConstants.NeuroMLVersion.getLatestVersion(),
LemsConstants.LemsOption.LEMS_WITHOUT_EXECUTE_MODEL,
OriginalCompartmentalisation(),
seed,
False,
True,
genDir,
"GENESIS Physiological Units",
False)
########################################################################################################################
if not os.path.exists(cellpath):
print("Creating a new directory %s"%cellpath)
os.makedirs(cellpath)
else:
print("A directory %s already exists"%cellpath)
src_files = os.listdir("../../neuroConstruct/generatedNeuroML2/")
for file_name in src_files:
full_file_name = os.path.join("../../neuroConstruct/generatedNeuroML2/", file_name)
if (os.path.isfile(full_file_name)):
print("Moving generated NeuroML2 to files to %s"%cellpath)
shutil.copy(full_file_name, cellpath)
with open(os.path.join(full_path_to_config,"compSummary.json"),'w') as fout:
json.dump(compSummary, fout)
if shell ==None:
extension='sh'
else:
extension=shell
os.chdir("../../neuroConstruct/pythonScripts")
subprocess.call("%s/nC.%s -python ../../neuroConstruct/pythonScripts/RegenerateNml2.py -f"%(os.environ["NC_HOME"],extension),shell=True)
os.chdir("../../NeuroML2/pythonScripts")
totNumSpikes = -1
for maxElecLenIndex in range(0, len(maxElecLens)):
maxElecLen = maxElecLens[maxElecLenIndex]
for sim in simulators:
recompSuffix = "_" + str(maxElecLen)
simRefPrefix = (simAllPrefix + simConfigName + "_").replace(
' ', '')
simRef = simRefPrefix + "_" + sim + recompSuffix
simDir = File(projFile.getParentFile(), "/simulations/" + simRef)
timeFile = File(simDir, "time.dat")
if not timeFile.exists():
print "\n------- Error loading data from simulation in directory: %s\n" % simDir.getCanonicalPath(
)
else:
if verbose:
print "--- Reloading data from simulation in directory: %s" % simDir.getCanonicalPath(
)
time.sleep(1) # wait a while...
try:
simData = SimulationData(simDir)
simData.initialise()
times = simData.getAllTimes()
def backupJSystemProperties(self):
self.userDir = self.jsystem.getUserDir()
orig = File(self.userDir, "jsystem.properties")
back = File(orig.getParentFile(), "jsystem.properties.back")
FileUtils.copyFile(orig, back)
def SingleCellNML2generator(projString=" ",
ConfigDict={},
ElecLenList=[],
somaNseg=None,
savingDir=None):
projFile = File(os.getcwd(), projString)
pm = ProjectManager()
compSummary = {}
for config in ConfigDict.keys():
project = pm.loadProject(projFile)
nmlfm = NeuroMLFileManager(project)
compSummary[config] = {}
if " " in config:
configPath = config.replace(" ", "_")
else:
configPath = config
for maxElecLen in ElecLenList:
compSummary[config][str(maxElecLen)] = {}
cell = project.cellManager.getCell(ConfigDict[config])
if maxElecLen > 0:
info = CellTopologyHelper.recompartmentaliseCell(
cell, maxElecLen, project)
print "Recompartmentalising cell %s" % ConfigDict[config]
if somaNseg != None:
cell.getSegmentWithId(
0).getSection().setNumberInternalDivisions(somaNseg)
if savingDir != None:
cellpath = r'../../NeuroML2/%s/%s/%s_%f' % (
savingDir, configPath, configPath, maxElecLen)
else:
cellpath = r'../../NeuroML2/%s/%s_%f' % (
configPath, configPath, maxElecLen)
else:
if savingDir != None:
cellpath = r'../../NeuroML2/%s/%s/%s_default' % (
savingDir, configPath, configPath)
else:
cellpath = r'../../NeuroML2/%s/%s_default' % (configPath,
configPath)
summary = str(cell.getMorphSummary())
summary_string = summary.split("_")
for feature in summary_string:
feature_split = feature.split(":")
compSummary[config][str(maxElecLen)][
feature_split[0]] = feature_split[1]
# the format of summary : Segs:122_Secs:61_IntDivs:1458
print("Will be printing a cell morphology summary")
print compSummary[config][str(maxElecLen)]
######### it turns out that this does not save recompartmentalized cells - all saved cells have identical spatial discretization;
##### generateNeuroML2 receives the parent projFile but not the loaded project which is modified by the CellTopologyHelper.recompartmentaliseCell()
##################### neuroConstruct block #############################################################################
neuroConstructSeed = 1234
verbose = True
pm.doGenerate(config, neuroConstructSeed)
while pm.isGenerating():
if verbose:
print(
"Waiting for the project to be generated with Simulation Configuration: "
+ config)
time.sleep(5)
simConfig = project.simConfigInfo.getSimConfig(config)
seed = 1234
genDir = File(projFile.getParentFile(), "generatedNeuroML2")
nmlfm.generateNeuroMLFiles(
simConfig, NeuroMLConstants.NeuroMLVersion.getLatestVersion(),
LemsConstants.LemsOption.LEMS_WITHOUT_EXECUTE_MODEL,
OriginalCompartmentalisation(), seed, False, True, genDir,
"GENESIS Physiological Units", False)
########################################################################################################################
if not os.path.exists(cellpath):
print("Creating a new directory %s" % cellpath)
os.makedirs(cellpath)
else:
print("A directory %s already exists" % cellpath)
src_files = os.listdir("../generatedNeuroML2/")
for file_name in src_files:
full_file_name = os.path.join("../generatedNeuroML2/",
file_name)
if (os.path.isfile(full_file_name)):
print("Moving generated NeuroML2 to files to %s" %
cellpath)
shutil.copy(full_file_name, cellpath)
#with open("compSummary.json",'w') as fout:
#json.dump(compSummary, fout)
subprocess.call(["~/neuroConstruct/nC.sh -python RegenerateNml2.py -f"],
shell=True)
#subprocess.call(["cp compSummary.json ~/Thalamocortical/NeuroML2/"],shell=True)
quit()
def _update_server(self, name, dictionary, config_location):
_method_name = '_update_server'
# these imports are local, since they are only present in JRF environments.
# this method is only called after that check has been made.
from oracle.core.ojdl.weblogic.ODLConfiguration import CONFIG_DIR
from oracle.core.ojdl.weblogic.ODLConfiguration import CONFIG_FILE
from oracle.core.ojdl.logging.config import LoggingConfigurationDocument
config_dir = File(self.model_context.get_domain_home(), CONFIG_DIR)
server_dir = File(config_dir, name)
config_file = File(server_dir, CONFIG_FILE)
log_template_dir = config_dir.getParentFile()
try:
if config_file.exists():
source_file = config_file
FileUtils.validateWritableFile(config_file.getPath())
else:
# for dynamic servers, the logging config does not exist until the server is started.
# read the from template file, verify that the server directory is present and writable.
source_file = File(log_template_dir, LOGGING_TEMPLATE_FILE)
FileUtils.validateExistingFile(source_file)
if not server_dir.exists() and not server_dir.mkdirs():
ex = exception_helper.create_deploy_exception(
'WLSDPLY-19710', server_dir)
self.logger.throwing(ex,
class_name=self.__class_name,
method_name=_method_name)
raise ex
FileUtils.validateWritableDirectory(server_dir.getPath())
document = LoggingConfigurationDocument(
FileInputStream(source_file))
# configure AddJvmNumber
add_jvm_number = dictionary_utils.get_element(
dictionary, _ADD_JVM_NUMBER)
if add_jvm_number is not None:
document.setAddJvmNumber(
alias_utils.convert_boolean(add_jvm_number))
# configure HandlerDefaults
handler_defaults = dictionary_utils.get_dictionary_element(
dictionary, _HANDLER_DEFAULTS)
if handler_defaults is not None:
for key in handler_defaults:
value = handler_defaults[key]
document.setHandlerDefault(key, _get_property_text(value))
# configure Handlers
# do these before loggers, in case new handlers are assigned to loggers
existing_handler_names = document.getHandlerNames()
handlers = dictionary_utils.get_dictionary_element(
dictionary, _HANDLER)
if handlers is not None:
for handler_name in handlers:
handler = handlers[handler_name]
self._configure_handler(handler_name, handler, document,
existing_handler_names,
config_location)
# configure Loggers
existing_logger_names = document.getLoggerNames()
loggers = dictionary_utils.get_dictionary_element(
dictionary, _LOGGER)
if loggers is not None:
for logger_name in loggers:
logger = loggers[logger_name]
self._configure_logger(logger_name, logger, document,
existing_logger_names,
config_location)
document.writeDocument(FileOutputStream(config_file))
except (ParserConfigurationException, SAXException, IOException,
IllegalArgumentException), ex:
self.logger.severe('WLSDPLY-19707',
name,
ex.getLocalizedMessage(),
class_name=self.__class_name,
method_name=_method_name)
