class Sbuild:
def __init__(self,
space,
param_file=None,
param_string=None,
output_format=None):
LOG.debug('Starting sbuild...')
self.space = space
self.param = Parameters()
self.conveyor = Conveyor()
# identify the workflow type
self.conveyor.setOrigin('slearn')
# generate a unique modelID
self.conveyor.addMeta('modelID', utils.id_generator())
LOG.debug(
f'Generated new space with modelID: {self.conveyor.getMeta("modelID")}'
)
# load parameters
if param_file is not None:
# use the param_file to update existing parameters at the space
# directory and save changes to make them persistent
success, message = self.param.delta(space,
0,
param_file,
iformat='YAML',
isSpace=True)
elif param_string is not None:
success, message = self.param.delta(space,
0,
param_string,
iformat='JSONS',
isSpace=True)
else:
# load parameter file at the space directory
success, message = self.param.loadYaml(space, 0, isSpace=True)
# being unable to load parameters is a critical error
if not success:
LOG.critical(
f'Unable to load space parameters. {message}. Aborting...')
sys.exit(1)
md = self.param.getVal('computeMD_method')
if utils.isFingerprint(md) and len(md) > 1:
LOG.warning(
f'When using fingerprints, only a single type of MD can be used to build spaces. Selecting {md[0]}'
)
self.conveyor.setWarning(
f'When using fingerprints, only a single type of MD can be used to build spaces. Selecting {md[0]}'
)
self.param.setVal('computeMD_method', [md[0]])
# add additional output formats included in the constructor
# this is requiered to add JSON format as output when the object is
# instantiated from a web service call, requiring this output
if output_format is not None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format', output_format)
def set_single_CPU(self) -> None:
''' Forces the use of a single CPU '''
LOG.debug('parameter "numCPUs" forced to be 1')
self.param.setVal('numCPUs', 1)
def run(self, input_source):
''' Executes a default chemical space building workflow '''
# path to endpoint
epd = utils.space_path(self.space, 0)
if not os.path.isdir(epd):
self.conveyor.setError(f'Unable to find space {self.space}')
#LOG.error(f'Unable to find space {self.space}')
# import ichild classes
if not self.conveyor.getError():
# uses the child classes within the 'space' folder,
# to allow customization of the processing applied to each space
modpath = utils.smodule_path(self.space, 0)
idata_child = importlib.import_module(modpath + ".idata_child")
slearn_child = importlib.import_module(modpath + ".slearn_child")
odata_child = importlib.import_module(modpath + ".odata_child")
# run idata object, in charge of generate space data from input
try:
idata = idata_child.IdataChild(self.param, self.conveyor,
input_source)
except:
LOG.warning(
'Idata child architecture mismatch, defaulting to Idata parent'
)
idata = Idata(self.param, self.conveyor, input_source)
idata.run()
LOG.debug(f'idata child {type(idata).__name__} completed `run()`')
if not self.conveyor.getError():
success, results = idata.preprocess_create()
if not success:
self.conveyor.setError(results)
if not self.conveyor.getError():
# check there is a suitable X and Y
if not self.conveyor.isKey('xmatrix'):
self.conveyor.setError(f'Failed to compute MDs')
if not self.conveyor.getError():
# instantiate learn (build a space from idata) and run it
try:
slearn = slearn_child.SlearnChild(self.param, self.conveyor)
except:
LOG.warning(
'Slearn child architecture mismatch, defaulting to Learn parent'
)
slearn = Slearn(self.param, self.conveyor)
slearn.run()
LOG.debug(
f'slearn child {type(slearn).__name__} completed `run()`')
# run odata object, in charge of formatting the prediction results
# note that if any of the above steps failed, an error has been inserted in the
# conveyor and odata will take case of showing an error message
try:
odata = odata_child.OdataChild(self.param, self.conveyor)
except:
LOG.warning(
'Odata child architecture mismatch, defaulting to Odata parent'
)
odata = Odata(self.param, self.conveyor)
return odata.run()
class Build:
def __init__(self,
model,
param_file=None,
param_string=None,
output_format=None):
LOG.debug('Starting build...')
self.model = model
self.param = Parameters()
self.conveyor = Conveyor()
# load parameters
if param_file is not None:
# use the param_file to update existing parameters at the model
# directory and save changes to make them persistent
success, message = self.param.delta(model,
0,
param_file,
iformat='YAML')
elif param_string is not None:
success, message = self.param.delta(model,
0,
param_string,
iformat='JSONS')
else:
# load parameter file at the model directory
success, message = self.param.loadYaml(model, 0)
# being unable to load parameters is a critical error
if not success:
LOG.critical(
f'Unable to load model parameters. "{message}" Aborting...')
sys.exit(1)
# add additional output formats included in the constructor
# this is requiered to add JSON format as output when the object is
# instantiated from a web service call, requiring this output
if output_format is not None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format', output_format)
def get_ensemble(self):
''' Returns a Boolean indicating if the model uses external input
sources and a list with these sources '''
return self.param.getEnsemble()
def set_single_CPU(self) -> None:
''' Forces the use of a single CPU '''
LOG.debug('parameter "numCPUs" forced to be 1')
self.param.setVal('numCPUs', 1)
def run(self, input_source):
''' Executes a default predicton workflow '''
# path to endpoint
epd = utils.model_path(self.model, 0)
if not os.path.isdir(epd):
self.conveyor.setError(f'Unable to find model {self.model}')
#LOG.error(f'Unable to find model {self.model}')
# import ichild classes
if not self.conveyor.getError():
# uses the child classes within the 'model' folder,
# to allow customization of the processing applied to each model
modpath = utils.module_path(self.model, 0)
idata_child = importlib.import_module(modpath + ".idata_child")
learn_child = importlib.import_module(modpath + ".learn_child")
odata_child = importlib.import_module(modpath + ".odata_child")
# run idata object, in charge of generate model data from input
try:
idata = idata_child.IdataChild(self.param, self.conveyor,
input_source)
except:
LOG.warning(
'Idata child architecture mismatch, defaulting to Idata parent'
)
idata = Idata(self.param, self.conveyor, input_source)
idata.run()
LOG.debug(f'idata child {type(idata).__name__} completed `run()`')
if not self.conveyor.getError():
# check there is a suitable X and Y
if not self.conveyor.isKey('xmatrix'):
self.conveyor.setError(f'Failed to compute MDs')
if not self.conveyor.isKey('ymatrix'):
self.conveyor.setError(
f'No activity data (Y) found in training series')
if not self.conveyor.getError():
# instantiate learn (build a model from idata) and run it
learn = learn_child.LearnChild(self.param, self.conveyor)
learn.run()
try:
learn = learn_child.LearnChild(self.param, self.conveyor)
except:
LOG.warning(
'Learn child architecture mismatch, defaulting to Learn parent'
)
learn = Learn(self.param, self.conveyor)
LOG.debug(f'learn child {type(learn).__name__} completed `run()`')
# run odata object, in charge of formatting the prediction results
# note that if any of the above steps failed, an error has been inserted in the
# conveyor and odata will take case of showing an error message
try:
odata = odata_child.OdataChild(self.param, self.conveyor)
except:
LOG.warning(
'Odata child architecture mismatch, defaulting to Odata parent'
)
odata = Odata(self.param, self.conveyor)
return odata.run()
class Build:
def __init__(self, model, param_file=None, param_string=None, output_format=None):
LOG.debug('Starting build...')
self.model = model
self.param = Parameters()
self.conveyor = Conveyor()
# identify the workflow type
self.conveyor.setOrigin('learn')
# generate a unique modelID
self.conveyor.addMeta('modelID',utils.id_generator())
LOG.debug(f'Generated new model with modelID: {self.conveyor.getMeta("modelID")}')
# load parameters
if param_file is not None:
# use the param_file to update existing parameters at the model
# directory and save changes to make them persistent
success, message = self.param.delta(model, 0, param_file, iformat='YAML')
elif param_string is not None:
success, message = self.param.delta(model, 0, param_string, iformat='JSONS')
else:
# load parameter file at the model directory
success, message = self.param.loadYaml(model, 0)
# being unable to load parameters is a critical error
if not success:
LOG.critical(f'Unable to load model parameters. {message}. Aborting...')
sys.exit(1)
# add additional output formats included in the constructor
# this is requiered to add JSON format as output when the object is
# instantiated from a web service call, requiring this output
if output_format is not None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format',output_format)
if self.param.getVal('confidential'):
self.confidentialAuditParam()
def confidentialAuditParam (self):
import yaml
original_method = self.param.getVal('model')
if self.param.getVal ('quantitative'):
if original_method != 'PLSR':
self.param.setVal('model', 'PLSR')
LOG.info (f'CONFIDENTIALITY AUDIT: the model was set to PLSR, '
f'the original method {original_method} was not suitable to build confidential models')
else:
if original_method != 'PLSDA':
self.param.setVal('model', 'PLSDA')
LOG.info (f'CONFIDENTIALITY AUDIT: the model was set to PLSDA, '
f'the original method {original_method} was not suitable to build confidential models')
# TODO: conformal support
if self.param.getVal('conformal'):
self.param.setVal('conformal', False)
LOG.info ('CONFIDENTIALITY AUDIT: conformal was set to False. '
'Conformal models are not supported for now in confidential models')
parameters_file_path = utils.model_path(self.model, 0)
parameters_file_name = os.path.join (parameters_file_path,
'parameters.yaml')
with open(parameters_file_name, 'w') as pfile:
yaml.dump (self.param.p, pfile)
def get_ensemble(self):
''' Returns a Boolean indicating if the model uses external input
sources and a list with these sources '''
return self.param.getEnsemble()
def extend_modelID (self, ensembleID):
modelID = self.conveyor.getMeta('modelID')
modelID = f'{modelID}-{ensembleID}'
self.conveyor.addMeta('modelID', modelID)
LOG.debug (f'modelID re-defined as {self.conveyor.getVal("modelID")}')
def set_single_CPU(self) -> None:
''' Forces the use of a single CPU '''
LOG.debug('parameter "numCPUs" forced to be 1')
self.param.setVal('numCPUs',1)
def run(self, input_source):
''' Executes a default predicton workflow '''
# path to endpoint
epd = utils.model_path(self.model, 0)
# if not os.path.isdir(epd):
# self.conveyor.setError(f'Unable to find model {self.model}')
# #LOG.error(f'Unable to find model {self.model}')
# import ichild classes
# if not self.conveyor.getError():
# uses the child classes within the 'model' folder,
# to allow customization of the processing applied to each model
modpath = utils.module_path(self.model, 0)
idata_child = importlib.import_module(modpath+".idata_child")
learn_child = importlib.import_module(modpath+".learn_child")
odata_child = importlib.import_module(modpath+".odata_child")
# run idata object, in charge of generate model data from input
try:
idata = idata_child.IdataChild(self.param, self.conveyor, input_source)
except:
LOG.warning ('Idata child architecture mismatch, defaulting to Idata parent')
idata = Idata(self.param, self.conveyor, input_source)
idata.run()
LOG.debug(f'idata child {type(idata).__name__} completed `run()`')
if not self.conveyor.getError():
success, results = idata.preprocess_create()
if not success:
self.conveyor.setError(results)
if not self.conveyor.getError():
# check there is a suitable X and Y
if not self.conveyor.isKey ('xmatrix'):
self.conveyor.setError(f'Failed to compute MDs')
if not self.conveyor.isKey ('ymatrix'):
self.conveyor.setError(f'No activity data (Y) found in training series')
# run optional chemical space building for supporting "closest" training series object
# if self.param.getVal('buildSimilarity'):
if self.param.getVal('output_similar') is True:
from flame.slearn import Slearn
slearn_child = importlib.import_module(modpath+".slearn_child")
if not self.conveyor.getError():
# instantiate learn (build a space from idata) and run it
try:
slearn = slearn_child.SlearnChild(self.param, self.conveyor)
except:
LOG.warning ('Slearn child architecture mismatch, defaulting to Learn parent')
slearn = Slearn(self.param, self.conveyor)
slearn.run()
LOG.debug(f'slearn child {type(slearn).__name__} completed `run()`')
if not self.conveyor.getError():
# instantiate learn (build a model from idata) and run it
try:
learn = learn_child.LearnChild(self.param, self.conveyor)
except:
LOG.warning ('Learn child architecture mismatch, defaulting to Learn parent')
learn = Learn(self.param, self.conveyor)
learn.run()
LOG.debug(f'learn child {type(learn).__name__} completed `run()`')
# run odata object, in charge of formatting the prediction results
# note that if any of the above steps failed, an error has been inserted in the
# conveyor and odata will take case of showing an error message
try:
odata = odata_child.OdataChild(self.param, self.conveyor)
except:
LOG.warning ('Odata child architecture mismatch, defaulting to Odata parent')
odata = Odata(self.param, self.conveyor)
return odata.run()