def __init__(self, configuration, dataStream=None, connect="", exceptions=True):
if isinstance(configuration, config.AugustusConfiguration):
configuration.validate(exception=True)
else:
try:
configuration = xmlbase.loadfile(configuration, config.Config, lineNumbers=True)
except IOError:
configuration = xmlbase.load(configuration, config.Config)
if configuration.exists(config.CustomProcessing):
raise Exception("The Augustus class defines its own <CustomProcessing>; please leave this out of the configuration file.")
self.dataStream = dataStream
if configuration.child(config.DataInput).exists(config.Interactive):
if dataStream is None:
raise Exception("If the configuration has a DataInput <Interactive> block, then a DataStream object must be provided.")
else:
if dataStream is not None:
raise Exception("If the configuration has no DataInput <Interactive> block, then a DataStream object must not be provided.")
persistentStorage = config.PersistentStorage(connect=connect)
persistentStorage.validate()
customProcessing = config.CustomProcessing(persistentStorage)
customProcessing.code = None
customProcessing.callbackClass = self
configuration.children.append(customProcessing)
self.configuration = configuration
self.mainLoop = augustus.engine.mainloop.MainLoop(self.configuration, rethrowExceptions=exceptions, dataStream=self.dataStream)
def post_validate(self):
if "validate" not in self.attrib:
self["validate"] = True
try:
self.data = xmlbase.loadfile(self["fileName"], pmml.X_ODG_PMML, validation=self["validate"])
except XMLValidationError, err:
raise RuntimeError, "PMML file %s failed validation: %s" % (self["fileName"], str(err))
def post_validate(self):
if "validate" not in self.attrib:
self["validate"] = True
try:
self.data = xmlbase.loadfile(self["fileName"], pmml.X_ODG_PMML, validation=self["validate"])
except XMLValidationError, err:
raise RuntimeError("PMML file %s failed validation: %s" % (self["fileName"], str(err)))
def __init__(self,
configuration,
dataStream=None,
connect="",
exceptions=True):
if isinstance(configuration, config.AugustusConfiguration):
configuration.validate(exception=True)
else:
try:
configuration = xmlbase.loadfile(configuration,
config.Config,
lineNumbers=True)
except IOError:
configuration = xmlbase.load(configuration, config.Config)
if configuration.exists(config.CustomProcessing):
raise Exception(
"The Augustus class defines its own <CustomProcessing>; please leave this out of the configuration file."
)
self.dataStream = dataStream
if configuration.child(config.DataInput).exists(config.Interactive):
if dataStream is None:
raise Exception(
"If the configuration has a DataInput <Interactive> block, then a DataStream object must be provided."
)
else:
if dataStream is not None:
raise Exception(
"If the configuration has no DataInput <Interactive> block, then a DataStream object must not be provided."
)
persistentStorage = config.PersistentStorage(connect=connect)
persistentStorage.validate()
customProcessing = config.CustomProcessing(persistentStorage)
customProcessing.code = None
customProcessing.callbackClass = self
configuration.children.append(customProcessing)
self.configuration = configuration
self.mainLoop = augustus.engine.mainloop.MainLoop(
self.configuration,
rethrowExceptions=exceptions,
dataStream=self.dataStream)
def getModel(configOptions):
"""Return a pmmlElement object: the root of the model.
Arguments:
configOptions (XML object, defined in xmlbase):
The XML element <ModelInput>...</ModelInput> which
contains the source location for the PMML model.
"""
#xsd: Assume FromFile/FromFifo, with file name required.
sourceElement = configOptions.child(lambda x: x.tag.startswith("From"))
filename = sourceElement["name"]
if sourceElement.tag.endswith("File"):
selectmode = sourceElement.attrib.get(
"selectmode", "lastAlphabetic")
if filename.startswith("http://") or filename.startswith("https://"):
pass
else:
filelist = glob.glob(filename)
if len(filelist) > 1:
filelist = [
f for f in filelist if _modelExceptionIdentifier not in f]
if len(filelist) == 0 :
raise RuntimeError, "no files matched the given filename/glob: %s" % filename
if selectmode == "mostRecent":
filename = max(filelist, key=lambda x: os.stat(x).st_mtime)
else:
filelist.sort()
filename = filelist[-1]
if _modelExceptionIdentifier in filename:
logging.getLogger().warning("Using a PMML model that was written on exception:File name: %s" % filename)
try:
# TODO: make lineNumbers optional (better diagnostics with them, better performance without them)
model = xmlbase.loadfile(filename, pmml.X_ODG_PMML, lineNumbers=True)
except:
logging.getLogger().error("Error loading PMML model from %s." % filename)
raise
return model, filename
import glob
from augustus.core.xmlbase import loadfile
import augustus.core.pmml41 as pmml
from cassius import *
modelFiles = glob.glob("_out/modelout*.pmml")
modelFiles.sort()
models = []
for modelFile in modelFiles:
model = loadfile(modelFile, pmml.X_ODG_PMML)
models.append(model)
print model.tree()
plots = []
for model in models:
eventNumber = model.descendant(pmml.X_ODG_Eventstamp)["number"]
discretize = model.descendant(pmml.Discretize)
bins = []
for discretizeBin in discretize.matches(pmml.DiscretizeBin):
binName = discretizeBin["binValue"]
leftMargin = discretizeBin.child(pmml.Interval)["leftMargin"]
rightMargin = discretizeBin.child(pmml.Interval)["rightMargin"]
bins.append((binName, leftMargin, rightMargin))
bins.sort(lambda a, b: cmp(a[1], b[1]))
h = HistogramNonUniform([(b[1], b[2]) for b in bins],
fillcolor="yellow",
def __init__(self,
configuration,
model=None,
dataStream=None,
rethrowExceptions=None):
self.model = model
self.dataStream = dataStream
self.rethrowExceptions = rethrowExceptions
self.fileNameOnException = None
# get the configuration, in whatever form you find it
if isinstance(configuration, config.AugustusConfiguration):
pass
elif isinstance(configuration, basestring):
try:
configuration = xmlbase.loadfile(configuration,
config.Config,
lineNumbers=True)
except IOError:
configuration = xmlbase.load(configuration,
config.Config,
lineNumbers=True)
else:
raise ConfigurationError(
"Configuration must be a pre-validated XML object, a fileName, or a literal configuration string."
)
# set up logging
setupLogging(
configuration.matches(
lambda x: isinstance(x, (config.Logging, config.Metadata))))
self.logger = logging.getLogger()
self.metadata = logging.getLogger("metadata")
# begin "initialization" phase
for l in self.logger, self.metadata:
if "initialization" in l.differentLevel:
l.setLevel(l.differentLevel["initialization"])
else:
l.setLevel(l.naturalLevel)
# get the model, in whatever form you find it
self.logger.info("Loading PMML model.")
self.metadata.startTiming("Time to load PMML model")
modelFileName = "(none)"
maturityThreshold = 0
if self.model is None:
modelInput = configuration.child(config.ModelInput, exception=None)
if modelInput is None:
raise ConfigurationError(
"If a model is not provided to MainLoop explicitly, it must be present in the configuration file."
)
fileLocation = modelInput["fileLocation"]
if not fileLocation.startswith(
"http://") and not fileLocation.startswith("https://"):
fileList = glob.glob(fileLocation)
if len(fileList) > 1:
fileList = [
f for f in fileList
if self._modelExceptionIdentifier not in f
]
if len(fileList) == 0:
raise IOError(
"No files matched the ModelInput fileLocation \"%s\"."
% fileLocation)
selectmode = modelInput.attrib.get("selectmode",
"lastAlphabetic")
if selectmode == "mostRecent":
fileLocation = max(fileList,
key=lambda x: os.stat(x).st_mtime)
elif selectmode == "lastAlphabetic":
fileList.sort()
fileLocation = fileList[-1]
else:
assert False
if self._modelExceptionIdentifier in fileLocation:
self.logger.warning(
"Using a PMML model that was written on exception (fileName \"%s\")"
% fileLocation)
self.model = xmlbase.loadfile(fileLocation,
pmml.X_ODG_PMML,
lineNumbers=True)
if "maturityThreshold" in modelInput.attrib:
maturityThreshold = modelInput["maturityThreshold"]
elif isinstance(self.model, pmml.PMML):
pass
elif isinstance(self.model, basestring):
try:
self.model, modelFileName = xmlbase.loadfile(
self.model, pmml.X_ODG_PMML, lineNumbers=True), self.model
except IOError:
self.model = xmlbase.load(self.model,
pmml.X_ODG_PMML,
lineNumbers=True)
else:
raise ConfigurationError(
"Model must be a pre-validated XML object, a fileName, or a literal PMML string."
)
self.metadata.stopTiming("Time to load PMML model")
self.metadata.data["PMML model file"] = modelFileName
# globally set random number seeds
if "randomSeed" in configuration.attrib:
augustusRandomSeed = configuration["randomSeed"]
random.seed(augustusRandomSeed)
numpy.random.seed(augustusRandomSeed + 1)
else:
augustusRandomSeed = "unspecified"
# globally set numpy error handling
numpy.seterr(divide="raise",
over="raise",
under="ignore",
invalid="raise")
# update schemes (producerUpdateScheme may be redefined below)
consumerUpdateScheme = self._getUpdateScheme(
configuration.child(config.ConsumerBlending, exception=False))
producerUpdateScheme = self._getUpdateScheme(None)
# set up scoring output
outputConfig = configuration.child(config.Output, exception=False)
if outputConfig is None:
self.outputWriter = None
else:
outputParams = {
"pmmlFileName": modelFileName,
"mode": outputConfig.destination.attrib.get("type",
"XML").lower()
}
if isinstance(outputConfig.destination, config.ToFile):
if outputConfig.destination.attrib.get("overwrite", False):
outputStream = codecs.open(
outputConfig.destination["name"],
"w",
encoding="utf-8")
else:
outputStream = codecs.open(
outputConfig.destination["name"],
"a",
encoding="utf-8")
elif isinstance(outputConfig.destination, config.ToStandardError):
outputStream = sys.stderr
elif isinstance(outputConfig.destination, config.ToStandardOut):
outputStream = sys.stdout
else:
assert False
reportTag = outputConfig.child("ReportTag", exception=False)
if reportTag:
outputParams["reportName"] = reportTag.attrib.get(
"name", "Report")
eventTag = outputConfig.child("EventTag", exception=False)
if eventTag:
outputParams["eventName"] = eventTag.attrib.get(
"name", "Event")
outputParams["pseudoEventName"] = eventTag.attrib.get(
"pseudoName", "pseudoEvent")
self.outputWriter = OutputWriter(outputStream, **outputParams)
# initialize for the case of no output model
engineSettings = {
"maturityThreshold": maturityThreshold,
"augustusRandomSeed": augustusRandomSeed
}
self.modelWriter = None
segmentationScheme = SegmentationScheme(None, self.model)
self.updateFlag = False
self.aggregateUpdateFlag = False
producerAlgorithm = dict(config.producerAlgorithmDefaults)
for pa in producerAlgorithm.values():
validationResult = pa.validate()
assert validationResult is None
# set up output model, if present in the configuration
modelSetup = configuration.child(config.ModelSetup, exception=False)
engineSettings["hasProducer"] = modelSetup is not None
if engineSettings["hasProducer"]:
self.logger.info("Setting up model updating/producing.")
producerBlending = modelSetup.child(config.ProducerBlending,
exception=False)
producerUpdateScheme = self._getUpdateScheme(producerBlending)
if producerBlending is not None and producerBlending.contains(
config.MaturityThreshold):
maturityConfig = producerBlending.child(
config.MaturityThreshold)
engineSettings["maturityThreshold"] = int(
maturityConfig.attrib.get("threshold", 1))
try:
engineSettings["lockingThreshold"] = int(
maturityConfig.attrib["lockingThreshold"])
except KeyError:
engineSettings["lockingThreshold"] = None
engineSettings["lockAllSegments"] = modelSetup.attrib.get(
"mode", None) == "lockExisting"
if engineSettings[
"lockAllSegments"] and segmentationScheme is not None and not segmentationScheme._generic and not segmentationScheme._whiteList:
self.logger.warning(
"The model is locked and no new segments are specified...new model files will be unchanged."
)
self.modelWriter = getModelWriter(modelSetup)
if self.modelWriter is not None:
if self.modelWriter.baseName is None:
self.fileNameOnException = self._modelExceptionIdentifier + ".pmml"
else:
self.fileNameOnException = "".join([
self.modelWriter.baseName,
self._modelExceptionIdentifier, ".pmml"
])
else:
self.logger.warning(
"There is no outputFile attribute in the ModelSetup; no new model file will be created."
)
segmentationScheme = SegmentationScheme(
modelSetup.child(config.SegmentationSchema, exception=False),
self.model)
self.updateFlag = modelSetup.attrib.get("updateEvery",
"event") in ("event",
"both")
self.aggregateUpdateFlag = modelSetup.attrib.get(
"updateEvery", "event") in ("aggregate", "both")
for pa in modelSetup.matches(config.ProducerAlgorithm):
producerAlgorithm[pa["model"]] = pa
if modelSetup.attrib.get("mode", None) == "updateExisting":
for pa in producerAlgorithm.values():
pa.parameters["updateExisting"] = True
if modelSetup.attrib.get("mode", None) == "replaceExisting":
for pa in producerAlgorithm.values():
pa.parameters["updateExisting"] = False
# to score or not to score
eventSettings = configuration.child(config.EventSettings,
exception=False)
if eventSettings is not None:
self.logger.info("Setting up output.")
self.scoreFlag = eventSettings["score"]
self.outputFlag = eventSettings["output"]
else:
self.scoreFlag = False
self.outputFlag = False
aggregationConfig = configuration.child(config.AggregationSettings,
exception=False)
if aggregationConfig is not None:
self.aggregateScoreFlag = aggregationConfig["score"]
self.aggregateOutputFlag = aggregationConfig["output"]
self.aggregationSettings = dict(aggregationConfig.attrib)
else:
self.aggregateScoreFlag = False
self.aggregateOutputFlag = False
self.aggregationSettings = None
self.metadata.data[
"Update model"] = "true" if self.updateFlag or self.aggregateUpdateFlag else "false"
# build a scoring engine once without a dataStream (to evaluate any verification blocks)
self.engine = Engine(self.model, None, producerUpdateScheme,
consumerUpdateScheme, segmentationScheme,
producerAlgorithm, **engineSettings)
self.engine.initialize()
if self.outputWriter is not None: self.outputWriter.open()
# begin "verification" phase
for l in self.logger, self.metadata:
if "verification" in l.differentLevel:
l.eventLogLevel = l.differentLevel["verification"]
l.setLevel(l.differentLevel["verification"])
else:
l.eventLogLevel = l.naturalLevel
l.setLevel(l.naturalLevel)
# evaluate verification blocks
modelVerificationConfig = configuration.child(config.ModelVerification,
exception=False)
if modelVerificationConfig is not None:
verify(modelVerificationConfig, self.engine, self.logger,
self.outputWriter)
# verification can increment aggregate variables, but
# aggregates should all start at zero at the start of real
# processing, whether verification happened or not
self.engine.flushAggregates()
# get the dataStream, in whatever form you find it
self.logger.info("Setting up data input.")
if self.dataStream is None:
configDataInput = configuration.child(config.DataInput,
exception=None)
if configDataInput is None:
raise ConfigurationError(
"If a dataStream is not provided to MainLoop explicitly, it must be present in the configuration file."
)
if configDataInput.contains(config.FromFile):
self.dataStream = DataStreamer(
configDataInput.child(config.FromFile),
self.engine.pmmlModel)
elif configDataInput.contains(config.FromStandardIn):
self.dataStream = DataStreamer(
configDataInput.child(config.FromStandardIn),
self.engine.pmmlModel)
elif configDataInput.contains(config.FromHTTP):
self.dataStream = AugustusHTTPDataStream(
configDataInput.child(config.FromHTTP))
if self.outputWriter is None:
self.dataStream.respond = False
if self.dataStream.respond:
self.dataStream.setupOutput(self.outputWriter)
else:
assert False
# begin "eventLoop" phase
for l in self.logger, self.metadata:
if "eventloop" in l.differentLevel:
l.eventLogLevel = l.differentLevel["eventloop"]
l.setLevel(l.differentLevel["eventloop"])
else:
l.eventLogLevel = l.naturalLevel
l.setLevel(l.naturalLevel)
# possibly set up custom processing
self.customProcessing = configuration.child(config.CustomProcessing,
exception=False)
if self.customProcessing is not None:
constants = self.engine.pmmlModel.child(pmml.Extension,
exception=False)
if constants is None:
constants = NameSpaceReadOnly()
else:
constants = constants.child(
pmml.X_ODG_CustomProcessingConstants, exception=False)
if constants is None:
constants = NameSpaceReadOnly()
else:
constants = constants.nameSpace
atoms = {
"INVALID": INVALID,
"MISSING": MISSING,
"IMMATURE": IMMATURE,
"MATURE": MATURE,
"LOCKED": LOCKED,
"UNINITIALIZED": UNINITIALIZED
}
for thing in pmml.OutputField.__dict__.values(
) + pmml.X_ODG_OutputField.__dict__.values():
if isinstance(thing, Atom):
atoms[repr(thing)] = thing
self.customProcessing.initialize(
self.model, self.engine.pmmlModel, constants,
[s.userFriendly
for s in self.engine.segmentRecords], atoms, self.logger,
self.metadata, consumerUpdateScheme, producerUpdateScheme)
self.engine.customProcessing = self.customProcessing
self.engine.reinitialize()
else:
# only turn off circular garbage collection if there is no CustomProcessing or AugustusInterface
gc.disable()
def post_validate(self):
self.config = xmlbase.loadfile(self["fileName"], augustus.applications.scoresAwk.root, lineNumbers=True)
def post_validate(self):
self.config = xmlbase.loadfile(self["fileName"], augustus.core.config.Config, lineNumbers=True)
def post_validate(self):
self.data = xmlbase.loadfile(self["fileName"],
pmml.X_ODG_PMML,
validation=False)
def post_validate(self):
self.config = xmlbase.loadfile(self["fileName"], augustus.applications.scoresAwk.root, lineNumbers=True)
def main(config_file=None, rethrowExceptions=False):
"""From the configuration, set up the Augustus engine.
Set up segments, PMML tree, I/O, and logging for the
ProducerConsumer. Identify what task is to be done:
Producing, Consuming, or Automatic Incremental Model
updates (AIM). Identify the model type and start that
model, passing the segments, PMML tree, and I/O information.
Arguments:
config_file (string):
Path to the configuration file.
"""
# Get the configuration settings (as an XML instance)
if isinstance(config_file, config.AugustusConfiguration):
configRoot = config_file
else:
configRoot = xmlbase.loadfile(config_file,
config.Config,
lineNumbers=True)
setupLogging(
configRoot.matches(lambda x: x.tag in ("Logging", "Metadata")))
logger = logging.getLogger()
metadata = logging.getLogger('metadata')
logger.info("Loading PMML model.")
child = configRoot.child(config.ModelInput, exception=False)
metadata.startTiming("Time to load PMML model")
pmmlModel, pmmlFileName = getModel(child)
metadata.stopTiming("Time to load PMML model")
metadata.data["PMML model file"] = pmmlFileName
logger.info("Setting up data input.")
child = configRoot.child(config.DataInput, exception=False)
dataStreamer = getDataStreamer(child)
child = configRoot.child(config.ConsumerBlending, exception=False)
consumerUpdateScheme = getUpdateScheme(child)
child = configRoot.child(config.ModelSetup, exception=False)
# Default Model setup parameters
modelWriter = getModelWriter(None)
engineSettings = dict(maturityThreshold=0)
producerParameters = {}
filenameOnException = None
producerUpdateScheme = getUpdateScheme(None)
segmentationScheme = SegmentationScheme(None, pmmlModel)
aggregateUpdateFlag = updateFlag = False
# Model setup
if child:
logger.info("Setting up model updating/producing.")
modelWriter = getModelWriter(child)
segmentationScheme = SegmentationScheme(
child.child(config.SegmentationSchema, exception=False), pmmlModel)
if modelWriter is not None:
engineSettings['lockAllSegments'] = child.attrib.get(
"mode", None) == "lockExisting"
producerParameters['resume'] = child.attrib.get(
"mode", None) == "updateExisting"
updateFlag = child.attrib.get("updateEvery",
"event") in ("event", "both")
aggregateUpdateFlag = child.attrib.get("updateEvery",
"event") in ("aggregate",
"both")
filenameOnException = "".join(
[modelWriter.baseName, _modelExceptionIdentifier, ".pmml"])
child = child.child(config.ProducerBlending, exception=False)
producerUpdateScheme = getUpdateScheme(child)
if child and child.exists(config.MaturityThreshold):
maturityConfig = child.child(config.MaturityThreshold)
engineSettings['maturityThreshold'] = int(
maturityConfig.attrib.get("threshold", 1))
engineSettings['lockingThreshold'] = \
None if "lockingThreshold" not in \
maturityConfig.attrib \
else int(maturityConfig["lockingThreshold"])
if engineSettings[
'lockAllSegments'] and not segmentationScheme._generic and not segmentationScheme.whiteList:
logger.warning(
"The model is locked and no new segments are specified...new model files will be unchanged."
)
else:
logger.warning(
"There is no outputFile attribute in the ModelSetup; no new model file will be created."
)
# Set up output
child = configRoot.child(config.Output, exception=False)
outputWriter = getOutputWriter(child, pmmlFileName)
child = configRoot.child(config.EventSettings, exception=False)
if child is not None:
logger.info("Setting up output.")
# not in a dictionary to reduce the number of lookups while looping
scoreFlag = child.attrib['score']
outputFlag = child.attrib['output']
else:
scoreFlag = outputFlag = False
child = configRoot.child(config.AggregationSettings, exception=False)
if child is not None:
aggregateScoreFlag = child.attrib['score']
aggregateOutputFlag = child.attrib['output']
aggregationSettings = child.attrib
else:
aggregationSettings = None
metadata.data[
'Update model'] = "true" if updateFlag or aggregateUpdateFlag else "false"
# build engine once without a data stream
engine = Engine(pmmlModel, None, producerUpdateScheme,
consumerUpdateScheme, segmentationScheme, **engineSettings)
engine.initialize(producerParameters=producerParameters)
if outputWriter: outputWriter.open()
# score fake data from <ModelVerifications>
modelVerificationConfig = configRoot.child(config.ModelVerification,
exception=False)
if modelVerificationConfig is not None:
augustus.engine.verification.verify(modelVerificationConfig, engine,
logger, outputWriter)
# start of real data
logger.info("Setting up Augustus's main engine.")
engine.resetDataStream(dataStreamer)
dataStreamer.start_streaming()
metadata.data['Events'] = 0
logger.info("Calculating.")
metadata.startTiming("Run time")
try:
while True:
try:
score = engine.event(score=scoreFlag, update=updateFlag)
metadata.data['Events'] += 1
if outputWriter and outputFlag:
try:
outputWriter.write(score)
except IOError:
## FIXME: this exception should be raised to the top level; I do not
## undersand why it is handled here, nor why a 'good' model is written...--tanya
if modelWriter:
modelWriter.write(pmmlModel)
break
if modelWriter:
modelWriter.serialize(pmmlModel, metadata.data['Events'])
if aggregationSettings:
if engine.checkPseudoeventReadiness(aggregationSettings):
score = engine.pseudoevent(score=aggregateScoreFlag,
update=aggregateUpdateFlag)
if outputWriter and outputOnAggregate:
outputWriter.write(score)
except StopIteration:
if modelWriter:
if modelWriter.serialization:
modelWriter.serialize(pmmlModel,
metadata.data['Events'])
else:
modelWriter.write(pmmlModel)
break
if aggregationSettings is not None and aggregationSettings['atEnd']:
score = engine.pseudoevent(score=aggregateScoreFlag,
update=aggregateUpdateFlag)
if outputWriter and aggregateOutputFlag:
outputWriter.write(score)
except (Exception, KeyboardInterrupt), err:
if rethrowExceptions: raise
logger.error("Shutting down on exception...")
excinfo = sys.exc_info()
logger.error("...%s" % excinfo[0])
logger.error("...%s" % excinfo[1])
logger.error("...%s" % traceback.format_exc())
if filenameOnException:
logger.error("Writing last model in location %s" %
filenameOnException)
pmmlModel.write(filenameOnException)
sys.exit(
"Shutting down on exception; for more information check the logfile (if logging is enabled)...\n%s"
% traceback.format_exc())
for line in input_file:
number_of_rows += 1
if number_of_rows <= 3:
print "\t", line.strip()
print "\t", line
checkForQuit()
print "To load an XML file using Augustus' xmlbase library, first include the library"
print "from augustus.core import xmlbase # type this at the top of a script"
print "\nthen load the file:"
print """
filename = "../results/example_scores.xml"
root_element = xmlbase.loadfile(filename)
"""
checkForQuit()
root_element = xmlbase.loadfile(filename)
print "To access a tag of an xml element, use 'element.tag' for example,"
print "if we type:"
print ">>> root_element.tag"
checkForQuit()
print "we get:"
print root_element.tag
checkForQuit()
print "The element's attributes are stored as a Python dictionary."
print "The dictionary is named 'attrib', so for example,"
print ">>> root_element.attrib"
checkForQuit()
print "gets:"
def post_validate(self):
self.data = xmlbase.loadfile(self["fileName"], pmml.X_ODG_PMML, validation=False)
def __init__(self, configuration, model=None, dataStream=None, rethrowExceptions=None):
self.model = model
self.dataStream = dataStream
self.rethrowExceptions = rethrowExceptions
self.fileNameOnException = None
# get the configuration, in whatever form you find it
if isinstance(configuration, config.AugustusConfiguration):
pass
elif isinstance(configuration, basestring):
try:
configuration = xmlbase.loadfile(configuration, config.Config, lineNumbers=True)
except IOError:
configuration = xmlbase.load(configuration, config.Config, lineNumbers=True)
else:
raise ConfigurationError("Configuration must be a pre-validated XML object, a fileName, or a literal configuration string.")
# set up logging
setupLogging(configuration.matches(lambda x: isinstance(x, (config.Logging, config.Metadata))))
self.logger = logging.getLogger()
self.metadata = logging.getLogger("metadata")
# begin "initialization" phase
for l in self.logger, self.metadata:
if "initialization" in l.differentLevel:
l.setLevel(l.differentLevel["initialization"])
else:
l.setLevel(l.naturalLevel)
# get the model, in whatever form you find it
self.logger.info("Loading PMML model.")
self.metadata.startTiming("Time to load PMML model")
modelFileName = "(none)"
maturityThreshold = 0
if self.model is None:
modelInput = configuration.child(config.ModelInput, exception=None)
if modelInput is None:
raise ConfigurationError("If a model is not provided to MainLoop explicitly, it must be present in the configuration file.")
fileLocation = modelInput["fileLocation"]
if not fileLocation.startswith("http://") and not fileLocation.startswith("https://"):
fileList = glob.glob(fileLocation)
if len(fileList) > 1:
fileList = [f for f in fileList if self._modelExceptionIdentifier not in f]
if len(fileList) == 0:
raise IOError("No files matched the ModelInput fileLocation \"%s\"." % fileLocation)
selectmode = modelInput.attrib.get("selectmode", "lastAlphabetic")
if selectmode == "mostRecent":
fileLocation = max(fileList, key=lambda x: os.stat(x).st_mtime)
elif selectmode == "lastAlphabetic":
fileList.sort()
fileLocation = fileList[-1]
else:
assert False
if self._modelExceptionIdentifier in fileLocation:
self.logger.warning("Using a PMML model that was written on exception (fileName \"%s\")" % fileLocation)
self.model = xmlbase.loadfile(fileLocation, pmml.X_ODG_PMML, lineNumbers=True)
if "maturityThreshold" in modelInput.attrib: maturityThreshold = modelInput["maturityThreshold"]
elif isinstance(self.model, pmml.PMML):
pass
elif isinstance(self.model, basestring):
try:
self.model, modelFileName = xmlbase.loadfile(self.model, pmml.X_ODG_PMML, lineNumbers=True), self.model
except IOError:
self.model = xmlbase.load(self.model, pmml.X_ODG_PMML, lineNumbers=True)
else:
raise ConfigurationError("Model must be a pre-validated XML object, a fileName, or a literal PMML string.")
self.metadata.stopTiming("Time to load PMML model")
self.metadata.data["PMML model file"] = modelFileName
# globally set random number seeds
if "randomSeed" in configuration.attrib:
augustusRandomSeed = configuration["randomSeed"]
random.seed(augustusRandomSeed)
numpy.random.seed(augustusRandomSeed + 1)
else:
augustusRandomSeed = "unspecified"
# globally set numpy error handling
numpy.seterr(divide="raise", over="raise", under="ignore", invalid="raise")
# update schemes (producerUpdateScheme may be redefined below)
consumerUpdateScheme = self._getUpdateScheme(configuration.child(config.ConsumerBlending, exception=False))
producerUpdateScheme = self._getUpdateScheme(None)
# set up scoring output
outputConfig = configuration.child(config.Output, exception=False)
if outputConfig is None:
self.outputWriter = None
else:
outputParams = {"pmmlFileName": modelFileName, "mode": outputConfig.destination.attrib.get("type", "XML").lower()}
if isinstance(outputConfig.destination, config.ToFile):
if outputConfig.destination.attrib.get("overwrite", False):
outputStream = codecs.open(outputConfig.destination["name"], "w", encoding="utf-8")
else:
outputStream = codecs.open(outputConfig.destination["name"], "a", encoding="utf-8")
elif isinstance(outputConfig.destination, config.ToStandardError):
outputStream = sys.stderr
elif isinstance(outputConfig.destination, config.ToStandardOut):
outputStream = sys.stdout
else:
assert False
reportTag = outputConfig.child("ReportTag", exception=False)
if reportTag:
outputParams["reportName"] = reportTag.attrib.get("name", "Report")
eventTag = outputConfig.child("EventTag", exception=False)
if eventTag:
outputParams["eventName"] = eventTag.attrib.get("name", "Event")
outputParams["pseudoEventName"] = eventTag.attrib.get("pseudoName", "pseudoEvent")
self.outputWriter = OutputWriter(outputStream, **outputParams)
# initialize for the case of no output model
engineSettings = {"maturityThreshold": maturityThreshold, "augustusRandomSeed": augustusRandomSeed}
self.modelWriter = None
segmentationScheme = SegmentationScheme(None, self.model)
self.updateFlag = False
self.aggregateUpdateFlag = False
producerAlgorithm = dict(config.producerAlgorithmDefaults)
for pa in producerAlgorithm.values():
validationResult = pa.validate()
assert validationResult is None
# set up output model, if present in the configuration
modelSetup = configuration.child(config.ModelSetup, exception=False)
engineSettings["hasProducer"] = modelSetup is not None
if engineSettings["hasProducer"]:
self.logger.info("Setting up model updating/producing.")
producerBlending = modelSetup.child(config.ProducerBlending, exception=False)
producerUpdateScheme = self._getUpdateScheme(producerBlending)
if producerBlending is not None and producerBlending.contains(config.MaturityThreshold):
maturityConfig = producerBlending.child(config.MaturityThreshold)
engineSettings["maturityThreshold"] = int(maturityConfig.attrib.get("threshold", 1))
try:
engineSettings["lockingThreshold"] = int(maturityConfig.attrib["lockingThreshold"])
except KeyError:
engineSettings["lockingThreshold"] = None
engineSettings["lockAllSegments"] = modelSetup.attrib.get("mode", None) == "lockExisting"
if engineSettings["lockAllSegments"] and segmentationScheme is not None and not segmentationScheme._generic and not segmentationScheme._whiteList:
self.logger.warning("The model is locked and no new segments are specified...new model files will be unchanged.")
self.modelWriter = getModelWriter(modelSetup)
if self.modelWriter is not None:
if self.modelWriter.baseName is None:
self.fileNameOnException = self._modelExceptionIdentifier + ".pmml"
else:
self.fileNameOnException = "".join([self.modelWriter.baseName, self._modelExceptionIdentifier, ".pmml"])
else:
self.logger.warning("There is no outputFile attribute in the ModelSetup; no new model file will be created.")
segmentationScheme = SegmentationScheme(modelSetup.child(config.SegmentationSchema, exception=False), self.model)
self.updateFlag = modelSetup.attrib.get("updateEvery", "event") in ("event", "both")
self.aggregateUpdateFlag = modelSetup.attrib.get("updateEvery", "event") in ("aggregate", "both")
for pa in modelSetup.matches(config.ProducerAlgorithm):
producerAlgorithm[pa["model"]] = pa
if modelSetup.attrib.get("mode", None) == "updateExisting":
for pa in producerAlgorithm.values():
pa.parameters["updateExisting"] = True
if modelSetup.attrib.get("mode", None) == "replaceExisting":
for pa in producerAlgorithm.values():
pa.parameters["updateExisting"] = False
# to score or not to score
eventSettings = configuration.child(config.EventSettings, exception=False)
if eventSettings is not None:
self.logger.info("Setting up output.")
self.scoreFlag = eventSettings["score"]
self.outputFlag = eventSettings["output"]
else:
self.scoreFlag = False
self.outputFlag = False
aggregationConfig = configuration.child(config.AggregationSettings, exception=False)
if aggregationConfig is not None:
self.aggregateScoreFlag = aggregationConfig["score"]
self.aggregateOutputFlag = aggregationConfig["output"]
self.aggregationSettings = dict(aggregationConfig.attrib)
else:
self.aggregateScoreFlag = False
self.aggregateOutputFlag = False
self.aggregationSettings = None
self.metadata.data["Update model"] = "true" if self.updateFlag or self.aggregateUpdateFlag else "false"
# build a scoring engine once without a dataStream (to evaluate any verification blocks)
self.engine = Engine(self.model, None, producerUpdateScheme, consumerUpdateScheme, segmentationScheme, producerAlgorithm, **engineSettings)
self.engine.initialize()
if self.outputWriter is not None: self.outputWriter.open()
# begin "verification" phase
for l in self.logger, self.metadata:
if "verification" in l.differentLevel:
l.eventLogLevel = l.differentLevel["verification"]
l.setLevel(l.differentLevel["verification"])
else:
l.eventLogLevel = l.naturalLevel
l.setLevel(l.naturalLevel)
# evaluate verification blocks
modelVerificationConfig = configuration.child(config.ModelVerification, exception=False)
if modelVerificationConfig is not None:
verify(modelVerificationConfig, self.engine, self.logger, self.outputWriter)
# verification can increment aggregate variables, but
# aggregates should all start at zero at the start of real
# processing, whether verification happened or not
self.engine.flushAggregates()
# get the dataStream, in whatever form you find it
self.logger.info("Setting up data input.")
if self.dataStream is None:
configDataInput = configuration.child(config.DataInput, exception=None)
if configDataInput is None:
raise ConfigurationError("If a dataStream is not provided to MainLoop explicitly, it must be present in the configuration file.")
if configDataInput.contains(config.FromFile):
self.dataStream = DataStreamer(configDataInput.child(config.FromFile), self.engine.pmmlModel)
elif configDataInput.contains(config.FromStandardIn):
self.dataStream = DataStreamer(configDataInput.child(config.FromStandardIn), self.engine.pmmlModel)
elif configDataInput.contains(config.FromHTTP):
self.dataStream = AugustusHTTPDataStream(configDataInput.child(config.FromHTTP))
if self.outputWriter is None:
self.dataStream.respond = False
if self.dataStream.respond:
self.dataStream.setupOutput(self.outputWriter)
else:
assert False
# begin "eventLoop" phase
for l in self.logger, self.metadata:
if "eventloop" in l.differentLevel:
l.eventLogLevel = l.differentLevel["eventloop"]
l.setLevel(l.differentLevel["eventloop"])
else:
l.eventLogLevel = l.naturalLevel
l.setLevel(l.naturalLevel)
# possibly set up custom processing
self.customProcessing = configuration.child(config.CustomProcessing, exception=False)
if self.customProcessing is not None:
constants = self.engine.pmmlModel.child(pmml.Extension, exception=False)
if constants is None:
constants = NameSpaceReadOnly()
else:
constants = constants.child(pmml.X_ODG_CustomProcessingConstants, exception=False)
if constants is None:
constants = NameSpaceReadOnly()
else:
constants = constants.nameSpace
atoms = {"INVALID": INVALID, "MISSING": MISSING, "IMMATURE": IMMATURE, "MATURE": MATURE, "LOCKED": LOCKED, "UNINITIALIZED": UNINITIALIZED}
for thing in pmml.OutputField.__dict__.values() + pmml.X_ODG_OutputField.__dict__.values():
if isinstance(thing, Atom):
atoms[repr(thing)] = thing
self.customProcessing.initialize(self.model, self.engine.pmmlModel, constants, [s.userFriendly for s in self.engine.segmentRecords], atoms, self.logger, self.metadata, consumerUpdateScheme, producerUpdateScheme)
self.engine.customProcessing = self.customProcessing
self.engine.reinitialize()
else:
# only turn off circular garbage collection if there is no CustomProcessing or AugustusInterface
gc.disable()
def main(config_file=None, rethrowExceptions=False):
"""From the configuration, set up the Augustus engine.
Set up segments, PMML tree, I/O, and logging for the
ProducerConsumer. Identify what task is to be done:
Producing, Consuming, or Automatic Incremental Model
updates (AIM). Identify the model type and start that
model, passing the segments, PMML tree, and I/O information.
Arguments:
config_file (string):
Path to the configuration file.
"""
# Get the configuration settings (as an XML instance)
if isinstance(config_file, config.AugustusConfiguration):
configRoot = config_file
else:
configRoot = xmlbase.loadfile(config_file, config.Config, lineNumbers=True)
setupLogging(configRoot.matches(lambda x: x.tag in ("Logging", "Metadata")))
logger = logging.getLogger()
metadata = logging.getLogger('metadata')
logger.info("Loading PMML model.")
child = configRoot.child(config.ModelInput, exception=False)
metadata.startTiming("Time to load PMML model")
pmmlModel, pmmlFileName = getModel(child)
metadata.stopTiming("Time to load PMML model")
metadata.data["PMML model file"] = pmmlFileName
logger.info("Setting up data input.")
child = configRoot.child(config.DataInput, exception=False)
dataStreamer = getDataStreamer(child)
child = configRoot.child(config.ConsumerBlending, exception=False)
consumerUpdateScheme = getUpdateScheme(child)
child = configRoot.child(config.ModelSetup, exception=False)
# Default Model setup parameters
modelWriter = getModelWriter(None)
engineSettings = dict(maturityThreshold=0)
producerParameters = {}
filenameOnException = None
producerUpdateScheme = getUpdateScheme(None)
segmentationScheme = SegmentationScheme(None, pmmlModel)
aggregateUpdateFlag = updateFlag = False
# Model setup
if child:
logger.info("Setting up model updating/producing.")
modelWriter = getModelWriter(child)
segmentationScheme = SegmentationScheme(child.child(config.SegmentationSchema, exception=False), pmmlModel)
if modelWriter is not None:
engineSettings['lockAllSegments'] = child.attrib.get("mode", None) == "lockExisting"
producerParameters['resume'] = child.attrib.get("mode", None) == "updateExisting"
updateFlag = child.attrib.get("updateEvery", "event") in ("event", "both")
aggregateUpdateFlag = child.attrib.get("updateEvery", "event") in ("aggregate", "both")
filenameOnException = "".join([modelWriter.baseName, _modelExceptionIdentifier, ".pmml"])
child = child.child(config.ProducerBlending, exception=False)
producerUpdateScheme = getUpdateScheme(child)
if child and child.exists(config.MaturityThreshold):
maturityConfig = child.child(config.MaturityThreshold)
engineSettings['maturityThreshold'] = int(maturityConfig.attrib.get("threshold", 1))
engineSettings['lockingThreshold'] = \
None if "lockingThreshold" not in \
maturityConfig.attrib \
else int(maturityConfig["lockingThreshold"])
if engineSettings['lockAllSegments'] and not segmentationScheme._generic and not segmentationScheme.whiteList:
logger.warning("The model is locked and no new segments are specified...new model files will be unchanged.")
else:
logger.warning("There is no outputFile attribute in the ModelSetup; no new model file will be created.")
# Set up output
child = configRoot.child(config.Output, exception=False)
outputWriter = getOutputWriter(child, pmmlFileName)
child = configRoot.child(config.EventSettings, exception=False)
if child is not None:
logger.info("Setting up output.")
# not in a dictionary to reduce the number of lookups while looping
scoreFlag = child.attrib['score']
outputFlag = child.attrib['output']
else:
scoreFlag = outputFlag = False
child = configRoot.child(config.AggregationSettings, exception=False)
if child is not None:
aggregateScoreFlag = child.attrib['score']
aggregateOutputFlag = child.attrib['output']
aggregationSettings = child.attrib
else:
aggregationSettings = None
metadata.data['Update model'] = "true" if updateFlag or aggregateUpdateFlag else "false"
# build engine once without a data stream
engine = Engine(pmmlModel, None, producerUpdateScheme, consumerUpdateScheme, segmentationScheme, **engineSettings)
engine.initialize(producerParameters=producerParameters)
if outputWriter: outputWriter.open()
# score fake data from <ModelVerifications>
modelVerificationConfig = configRoot.child(config.ModelVerification, exception=False)
if modelVerificationConfig is not None:
augustus.engine.verification.verify(modelVerificationConfig, engine, logger, outputWriter)
# start of real data
logger.info("Setting up Augustus's main engine.")
engine.resetDataStream(dataStreamer)
dataStreamer.start_streaming()
metadata.data['Events'] = 0
logger.info("Calculating.")
metadata.startTiming("Run time")
try:
while True:
try:
score = engine.event(score=scoreFlag, update=updateFlag)
metadata.data['Events'] += 1
if outputWriter and outputFlag:
try:
outputWriter.write(score)
except IOError:
## FIXME: this exception should be raised to the top level; I do not
## undersand why it is handled here, nor why a 'good' model is written...--tanya
if modelWriter:
modelWriter.write(pmmlModel)
break
if modelWriter:
modelWriter.serialize(pmmlModel, metadata.data['Events'])
if aggregationSettings:
if engine.checkPseudoeventReadiness(aggregationSettings):
score = engine.pseudoevent(score=aggregateScoreFlag, update=aggregateUpdateFlag)
if outputWriter and outputOnAggregate:
outputWriter.write(score)
except StopIteration:
if modelWriter:
if modelWriter.serialization:
modelWriter.serialize(pmmlModel, metadata.data['Events'])
else:
modelWriter.write(pmmlModel)
break
if aggregationSettings is not None and aggregationSettings['atEnd']:
score = engine.pseudoevent(score=aggregateScoreFlag, update=aggregateUpdateFlag)
if outputWriter and aggregateOutputFlag:
outputWriter.write(score)
except (Exception, KeyboardInterrupt), err:
if rethrowExceptions: raise
logger.error("Shutting down on exception...")
excinfo = sys.exc_info()
logger.error("...%s" % excinfo[0])
logger.error("...%s" % excinfo[1])
logger.error("...%s" % traceback.format_exc())
if filenameOnException:
logger.error("Writing last model in location %s" % filenameOnException)
pmmlModel.write(filenameOnException)
sys.exit("Shutting down on exception; for more information check the logfile (if logging is enabled)...\n%s" % traceback.format_exc())
def post_validate(self):
self.config = xmlbase.loadfile(self["fileName"], augustus.core.config.Config, lineNumbers=True)
for line in input_file:
number_of_rows += 1
if number_of_rows <= 3:
print "\t", line.strip()
print "\t", line
checkForQuit()
print "To load an XML file using Augustus' xmlbase library, first include the library"
print "from augustus.core import xmlbase # type this at the top of a script"
print "\nthen load the file:"
print """
filename = "../results/example_scores.xml"
root_element = xmlbase.loadfile(filename)
"""
checkForQuit()
root_element = xmlbase.loadfile(filename)
print "To access a tag of an xml element, use 'element.tag' for example,"
print "if we type:"
print ">>> root_element.tag"
checkForQuit()
print "we get:"
print root_element.tag
checkForQuit()
print "The element's attributes are stored as a Python dictionary."
print "The dictionary is named 'attrib', so for example,"
print ">>> root_element.attrib"
checkForQuit()
print "gets:"
print root_element.attrib
def __init__(self, config_file=None, rethrowExceptions=False, dataStream=None):
# Get the configuration settings (as an XML instance)
if isinstance(config_file, config.AugustusConfiguration):
configRoot = config_file
else:
configRoot = xmlbase.loadfile(config_file, config.Config, lineNumbers=True)
if "randomSeed" in configRoot.attrib:
augustusRandomSeed = configRoot.attrib["randomSeed"]
random.seed(augustusRandomSeed)
numpy.random.seed(augustusRandomSeed + 1)
else:
augustusRandomSeed = "unspecified"
setupLogging(configRoot.matches(lambda x: x.tag in ("Logging", "Metadata")))
logger = logging.getLogger()
metadata = logging.getLogger("metadata")
for l in logger, metadata:
if "initialization" in l.differentLevel:
l.setLevel(l.differentLevel["initialization"])
else:
l.setLevel(l.naturalLevel)
logger.info("Loading PMML model.")
modelInput = configRoot.child(config.ModelInput, exception=False)
metadata.startTiming("Time to load PMML model")
pmmlModel, pmmlFileName = getModel(modelInput)
metadata.stopTiming("Time to load PMML model")
metadata.data["PMML model file"] = pmmlFileName
logger.info("Setting up data input.")
child = configRoot.child(config.DataInput, exception=False)
if dataStream is None:
fromHTTP = child.child(config.FromHTTP, exception=False)
if fromHTTP is None:
dataStreamer = getDataStreamer(child)
else:
dataStreamer = AugustusHTTPDataStream(fromHTTP)
else:
dataStreamer = dataStream
child = configRoot.child(config.ConsumerBlending, exception=False)
consumerUpdateScheme = getUpdateScheme(child)
child = configRoot.child(config.ModelSetup, exception=False)
# Default Model setup parameters
modelWriter = getModelWriter(None)
engineSettings = {"maturityThreshold": modelInput.attrib.get("maturityThreshold", 0),
"augustusRandomSeed": augustusRandomSeed,
"hasProducer": True,
}
filenameOnException = None
producerUpdateScheme = getUpdateScheme(None)
segmentationScheme = SegmentationScheme(None, pmmlModel)
aggregateUpdateFlag = updateFlag = False
producerAlgorithm = config.producerAlgorithmDefaults
for pa in producerAlgorithm.values():
if pa.validate() is not None:
raise Exception, "Programmer error in producerAlgorithmDefaults"
if child is not None:
for pa in child.matches(config.ProducerAlgorithm):
producerAlgorithm[pa.attrib["model"]] = pa
# Model setup
if child:
logger.info("Setting up model updating/producing.")
modelWriter = getModelWriter(child)
segmentationScheme = SegmentationScheme(child.child(config.SegmentationSchema, exception=False), pmmlModel)
if modelWriter is not None:
engineSettings["lockAllSegments"] = child.attrib.get("mode", None) == "lockExisting"
if child.attrib.get("mode", None) == "updateExisting":
for pa in producerAlgorithm.values():
pa.parameters["updateExisting"] = True
if child.attrib.get("mode", None) == "replaceExisting":
for pa in producerAlgorithm.values():
pa.parameters["updateExisting"] = False
updateFlag = child.attrib.get("updateEvery", "event") in ("event", "both")
aggregateUpdateFlag = child.attrib.get("updateEvery", "event") in ("aggregate", "both")
filenameOnException = "".join([modelWriter.baseName, _modelExceptionIdentifier, ".pmml"])
child = child.child(config.ProducerBlending, exception=False)
producerUpdateScheme = getUpdateScheme(child)
if child and child.exists(config.MaturityThreshold):
maturityConfig = child.child(config.MaturityThreshold)
engineSettings["maturityThreshold"] = int(maturityConfig.attrib.get("threshold", 1))
engineSettings["lockingThreshold"] = \
None if "lockingThreshold" not in \
maturityConfig.attrib \
else int(maturityConfig["lockingThreshold"])
if engineSettings["lockAllSegments"] and segmentationScheme is not None and not segmentationScheme._generic and not segmentationScheme._whiteList:
logger.warning("The model is locked and no new segments are specified...new model files will be unchanged.")
else:
logger.warning("There is no outputFile attribute in the ModelSetup; no new model file will be created.")
else:
engineSettings["hasProducer"] = False
# Set up output
child = configRoot.child(config.Output, exception=False)
outputWriter = getOutputWriter(child, pmmlFileName)
child = configRoot.child(config.EventSettings, exception=False)
if child is not None:
logger.info("Setting up output.")
# not in a dictionary to reduce the number of lookups while looping
scoreFlag = child.attrib["score"]
outputFlag = child.attrib["output"]
else:
scoreFlag = outputFlag = False
child = configRoot.child(config.AggregationSettings, exception=False)
if child is not None:
aggregateScoreFlag = child.attrib["score"]
aggregateOutputFlag = child.attrib["output"]
aggregationSettings = child.attrib
else:
aggregateScoreFlag = False
aggregateOutputFlag = False
aggregationSettings = None
metadata.data["Update model"] = "true" if updateFlag or aggregateUpdateFlag else "false"
# build engine once without a data stream
engine = Engine(pmmlModel, None, producerUpdateScheme, consumerUpdateScheme, segmentationScheme, producerAlgorithm, **engineSettings)
engine.initialize()
if outputWriter: outputWriter.open()
for l in logger, metadata:
if "verification" in l.differentLevel:
l.eventLogLevel = l.differentLevel["verification"]
l.setLevel(l.differentLevel["verification"])
else:
l.eventLogLevel = l.naturalLevel
l.setLevel(l.naturalLevel)
# score fake data from <ModelVerifications>
modelVerificationConfig = configRoot.child(config.ModelVerification, exception=False)
if modelVerificationConfig is not None:
augustus.engine.verification.verify(modelVerificationConfig, engine, logger, outputWriter)
# verification can increment aggregate variables, but
# aggregates should all start at zero at the start of real
# processing, whether verification happened or not
engine.flushAggregates()
if isinstance(dataStreamer, AugustusHTTPDataStream):
if outputWriter is None:
dataStreamer.respond = False
if dataStreamer.respond:
dataStreamer.setupOutput(outputWriter)
for l in logger, metadata:
if "eventloop" in l.differentLevel:
l.eventLogLevel = l.differentLevel["eventloop"]
l.setLevel(l.differentLevel["eventloop"])
else:
l.eventLogLevel = l.naturalLevel
l.setLevel(l.naturalLevel)
# possibly set up custom processing
customProcessing = configRoot.child(config.CustomProcessing, exception=False)
if customProcessing is not None:
constants = engine.pmmlModel.child(pmml.Extension, exception=False)
if constants is None:
constants = NameSpaceReadOnly()
else:
constants = constants.child(pmml.X_ODG_CustomProcessingConstants, exception=False)
if constants is None:
constants = NameSpaceReadOnly()
else:
constants = constants.nameSpace
atoms = {"INVALID": INVALID, "MISSING": MISSING, "IMMATURE": IMMATURE, "MATURE": MATURE, "LOCKED": LOCKED, "UNINITIALIZED": UNINITIALIZED}
for thing in pmml.OutputField.__dict__.values() + pmml.X_ODG_OutputField.__dict__.values():
if isinstance(thing, Atom):
atoms[repr(thing)] = thing
customProcessing.initialize(pmmlModel, engine.pmmlModel, constants, [s.userFriendly for s in engine.segmentRecords], atoms, logger, metadata, consumerUpdateScheme, producerUpdateScheme)
engine.customProcessing = customProcessing
engine.reinitialize()
else:
# only shut off circular garbage collection if there is no CustomProcessing or AugustusInterface
gc.disable()
self.dataStreamer = dataStreamer
self.logger = logger
self.engine = engine
self.metadata = metadata
self.aggregationSettings = aggregationSettings
self.rethrowExceptions = rethrowExceptions
self.scoreFlag = scoreFlag
self.updateFlag = updateFlag
self.outputWriter = outputWriter
self.outputFlag = outputFlag
self.modelWriter = modelWriter
self.filenameOnException = filenameOnException
self.pmmlModel = pmmlModel
self.aggregateScoreFlag = aggregateScoreFlag
self.aggregateUpdateFlag = aggregateUpdateFlag
self.aggregateOutputFlag = aggregateOutputFlag
self.customProcessing = customProcessing
def pmmlDiff(name1,
name2,
validate=False,
numSigfigs=6,
header=False,
extensions=False):
if validate:
file1 = loadfile(name1, pmml.X_ODG_PMML, lineNumbers=True)
file2 = loadfile(name2, pmml.X_ODG_PMML, lineNumbers=True)
else:
file1 = loadfile(name1, lineNumbers=True)
file2 = loadfile(name2, lineNumbers=True)
if not header:
index = file1.index(lambda x: x.tag == "Header")
del file1[index]
index = file2.index(lambda x: x.tag == "Header")
del file2[index]
if extensions:
index1 = [i for i, x in file1.walk()]
index1.insert(0, None)
index2 = [i for i, x in file2.walk()]
index2.insert(0, None)
else:
index1 = [
i for i, x in file1.walk(lambda x: isinstance(x, pmml.Extension))
]
index1.insert(0, None)
index2 = [
i for i, x in file2.walk(lambda x: isinstance(x, pmml.Extension))
]
index2.insert(0, None)
if len(index1) < len(index2):
index1 += [BROKEN] * (len(index2) - len(index1))
if len(index2) < len(index1):
index2 += [BROKEN] * (len(index1) - len(index2))
# show problems in the order that they appear in the files
for i, (i1, i2) in enumerate(zip(index1, index2)):
if i1 is None:
elem1 = file1
elif i1 is BROKEN:
elem1 = BROKEN
else:
elem1 = file1[i1]
if i2 is None:
elem2 = file2
elif i2 is BROKEN:
elem2 = BROKEN
else:
elem2 = file2[i2]
# if we have a structure problem
if i1 != i2:
return "Different structure:%s" % _comparitor(
name1, elem1, name2, elem2)
else:
if elem1.tag != elem2.tag:
return "Different tag: \"%s\" vs. \"%s\"%s" % (
elem1.tag, elem2.tag,
_comparitor(name1, elem1, name2, elem2))
if set(elem1.attrib.keys()) != set(elem2.attrib.keys()):
return "Different attributes: %s vs. %s%s" % (
sorted(elem1.attrib.keys()), sorted(elem2.attrib.keys()),
_comparitor(name1, elem1, name2, elem2))
for k in sorted(elem1.attrib.keys()):
value1 = elem1.attrib[k]
value2 = elem2.attrib[k]
if isinstance(value1, float) and isinstance(value2, float):
value1 = sigfigs(value1, numSigfigs)
value2 = sigfigs(value2, numSigfigs)
if value1 != value2:
return "Different attribute value for \"%s\": %s %s vs. %s %s%s" % (
k, value1, str(type(elem1.attrib[k])), value2,
str(type(elem2.attrib[k])),
_comparitor(name1, elem1, name2, elem2))
v1 = getattr(elem1, "value", NOTFOUND)
v2 = getattr(elem2, "value", NOTFOUND)
if v1 is not NOTFOUND or v2 is not NOTFOUND:
value1, value2 = v1, v2
if isinstance(value1, (tuple, list)) and isinstance(
value2, (tuple, list)) and len(value1) == len(value2):
out1, out2 = [], []
for val1, val2 in zip(value1, value2):
if isinstance(val1, float) and isinstance(val2, float):
val1 = sigfigs(val1, numSigfigs)
val2 = sigfigs(val2, numSigfigs)
out1.append(val1)
out2.append(val2)
value1, value2 = out1, out2
elif isinstance(v1, float) and isinstance(v2, float):
value1 = sigfigs(v1, numSigfigs)
value2 = sigfigs(v2, numSigfigs)
if value1 != value2:
return "Different value for \"%s\": %s %s vs. %s %s%s" % (
k, value1, str(type(value1)), value2, str(
type(v2)), _comparitor(name1, elem1, name2, elem2))
# if both elements are leaves
if len(elem1.matches()) == 0 and len(elem2.matches()) == 0:
content1 = elem1.content()
content2 = elem2.content()
if content1 != content2:
return "Different content: \"%s\" vs. \"%s\"%s" % (
content1, content2,
_comparitor(name1, elem1, name2, elem2))
return None
def pmmlDiff(name1, name2, validate=False, numSigfigs=6, header=False, extensions=False):
if validate:
file1 = loadfile(name1, pmml.X_ODG_PMML, lineNumbers=True)
file2 = loadfile(name2, pmml.X_ODG_PMML, lineNumbers=True)
else:
file1 = loadfile(name1, lineNumbers=True)
file2 = loadfile(name2, lineNumbers=True)
if not header:
index = file1.index(lambda x: x.tag=="Header", exception=False)
if index is not None:
del file1[index]
index = file2.index(lambda x: x.tag=="Header", exception=False)
if index is not None:
del file2[index]
if not extensions:
while True:
index = file1.index(lambda x: x.tag == "Extension", maxdepth=None, exception=False)
if index is None:
break
else:
del file1[index]
while True:
index = file2.index(lambda x: x.tag == "Extension", maxdepth=None, exception=False)
if index is None:
break
else:
del file2[index]
index1 = [i for i, x in file1.walk()]; index1.insert(0, None)
index2 = [i for i, x in file2.walk()]; index2.insert(0, None)
if len(index1) < len(index2):
index1 += [BROKEN] * (len(index2) - len(index1))
if len(index2) < len(index1):
index2 += [BROKEN] * (len(index1) - len(index2))
# show problems in the order that they appear in the files
for i, (i1, i2) in enumerate(zip(index1, index2)):
if i1 is None:
elem1 = file1
elif i1 is BROKEN:
elem1 = BROKEN
else:
elem1 = file1[i1]
if i2 is None:
elem2 = file2
elif i2 is BROKEN:
elem2 = BROKEN
else:
elem2 = file2[i2]
# if we have a structure problem
if i1 != i2:
return "Different structure:%s" % _comparitor(name1, elem1, name2, elem2)
else:
if elem1.tag != elem2.tag:
return "Different tag: \"%s\" vs. \"%s\"%s" % (elem1.tag, elem2.tag, _comparitor(name1, elem1, name2, elem2))
if set(elem1.attrib.keys()) != set(elem2.attrib.keys()):
return "Different attributes: %s vs. %s%s" % (sorted(elem1.attrib.keys()), sorted(elem2.attrib.keys()), _comparitor(name1, elem1, name2, elem2))
for k in sorted(elem1.attrib.keys()):
value1 = elem1.attrib[k]
value2 = elem2.attrib[k]
if isinstance(value1, float) and isinstance(value2, float):
value1 = sigfigs(value1, numSigfigs)
value2 = sigfigs(value2, numSigfigs)
if value1 != value2:
return "Different attribute value for \"%s\": %s %s vs. %s %s%s" % (k, value1, str(type(elem1.attrib[k])), value2, str(type(elem2.attrib[k])), _comparitor(name1, elem1, name2, elem2))
v1 = getattr(elem1, "value", NOTFOUND)
v2 = getattr(elem2, "value", NOTFOUND)
if v1 is not NOTFOUND or v2 is not NOTFOUND:
value1, value2 = v1, v2
if isinstance(value1, (tuple, list)) and isinstance(value2, (tuple, list)) and len(value1) == len(value2):
out1, out2 = [], []
for val1, val2 in zip(value1, value2):
if isinstance(val1, float) and isinstance(val2, float):
val1 = sigfigs(val1, numSigfigs)
val2 = sigfigs(val2, numSigfigs)
out1.append(val1)
out2.append(val2)
value1, value2 = out1, out2
elif isinstance(v1, float) and isinstance(v2, float):
value1 = sigfigs(v1, numSigfigs)
value2 = sigfigs(v2, numSigfigs)
if value1 != value2:
return "Different value for \"%s\": %s %s vs. %s %s%s" % (k, value1, str(type(value1)), value2, str(type(v2)), _comparitor(name1, elem1, name2, elem2))
# if both elements are leaves
if len(elem1.matches()) == 0 and len(elem2.matches()) == 0:
content1 = elem1.content()
content2 = elem2.content()
if content1 != content2:
return "Different content: \"%s\" vs. \"%s\"%s" % (content1, content2, _comparitor(name1, elem1, name2, elem2))
return None
import glob
from augustus.core.xmlbase import loadfile
import augustus.core.pmml41 as pmml
from cassius import *
modelFiles = glob.glob("_out/modelout*.pmml")
modelFiles.sort()
models = []
for modelFile in modelFiles:
model = loadfile(modelFile, pmml.X_ODG_PMML)
models.append(model)
print model.tree()
plots = []
for model in models:
eventNumber = model.descendant(pmml.X_ODG_Eventstamp)["number"]
discretize = model.descendant(pmml.Discretize)
bins = []
for discretizeBin in discretize.matches(pmml.DiscretizeBin):
binName = discretizeBin["binValue"]
leftMargin = discretizeBin.child(pmml.Interval)["leftMargin"]
rightMargin = discretizeBin.child(pmml.Interval)["rightMargin"]
bins.append((binName, leftMargin, rightMargin))
bins.sort(lambda a, b: cmp(a[1], b[1]))
h = HistogramNonUniform(
[(b[1], b[2]) for b in bins],
