class Search:
def __init__(self, space, version, output_format=None, label=None):
LOG.debug('Starting search...')
self.space = space
self.version = version
self.label = label
self.param = Parameters()
self.conveyor = Conveyor()
# identify the workflow type
self.conveyor.setOrigin('sapply')
# load modelID
path = utils.space_path(space, version)
meta = os.path.join(path,'space-meta.pkl')
try:
with open(meta, 'rb') as handle:
modelID = pickle.load(handle)
except:
LOG.critical(f'Unable to load modelID from {meta}. Aborting...')
sys.exit()
self.conveyor.addMeta('modelID', modelID)
LOG.debug (f'Loaded space with modelID: {modelID}')
# assign prediction (search) label
self.conveyor.addVal(label, 'prediction_label', 'prediction label',
'method', 'single',
'Label used to identify the prediction')
success, results = self.param.loadYaml(space, version, isSpace=True)
if not success:
LOG.critical(f'Unable to load space parameters. {results}. Aborting...')
sys.exit()
# 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 != None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format',output_format)
return
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 getVal (self, idict, ikey):
if not ikey in idict:
return None
return idict[ikey]
# def run(self, input_source, runtime_param=None, metric=None, numsel=None, cutoff=None):
def run(self, param_dict):
''' Executes a default predicton workflow '''
metric = None
numsel = None
cutoff = None
# path to endpoint
epd = utils.space_path(self.space, self.version)
if not os.path.isdir(epd):
LOG.error(f'Unable to find space {self.space}')
self.conveyor.setError(f'Unable to find space {self.space}, version {self.version}')
if self.getVal(param_dict,'smarts') is not None:
input_source = param_dict['smarts']
self.param.setVal('input_type', 'smarts')
elif self.getVal(param_dict,'infile') is not None:
input_source = param_dict['infile']
else:
LOG.error(f'Unable to find input_file')
self.conveyor.setError('wrong format in the runtime similarity parameters')
if 'runtime_param' in param_dict:
runtime_param = self.getVal(param_dict, 'runtime_param')
if runtime_param is not None:
LOG.info (f'runtime parameters: {str(runtime_param)}')
try:
with open(runtime_param, 'r') as pfile:
rtparam = yaml.safe_load(pfile)
try:
metric = rtparam['similarity_metric']
numsel = rtparam['similarity_cutoff_num']
cutoff = rtparam['similarity_cutoff_distance']
except:
LOG.error('wrong format in the runtime similarity parameters')
self.conveyor.setError('wrong format in the runtime similarity parameters')
except:
LOG.error('runtime similarity parameter file not found')
self.conveyor.setError('runtime similarity parameter file not found')
else:
try:
metric = param_dict['metric']
numsel = param_dict['numsel']
cutoff = param_dict['cutoff']
except:
LOG.error('wrong format in the runtime similarity parameters')
self.conveyor.setError('wrong format in the runtime similarity parameters')
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]])
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, self.version)
idata_child = importlib.import_module(modpath+".idata_child")
sapply_child = importlib.import_module(modpath+".sapply_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():
# make sure there is X data
if not self.conveyor.isKey('xmatrix'):
if not self.conveyor.isKey ('SMARTS'):
LOG.debug(f'Failed to compute MDs')
self.conveyor.setError(f'Failed to compute MDs')
if not self.conveyor.getError():
# run apply object, in charge of generate a prediction from idata
try:
sapply = sapply_child.SapplyChild(self.param, self.conveyor)
except:
LOG.warning ('Sapply child architecture mismatch, defaulting to Sapply parent')
sapply = Sapply(self.param, self.conveyor)
sapply.run(cutoff, numsel, metric)
LOG.debug(f'sapply child {type(sapply).__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 Predict:
def __init__(self, model, version=0, output_format=None, label=None):
LOG.debug('Starting predict...')
self.model = model
self.version = version
self.param = Parameters()
self.conveyor = Conveyor()
# identify the workflow type
self.conveyor.setOrigin('apply')
# load modelID
success, result = utils.getModelID(model, version, 'model')
if not success:
LOG.critical(f'{result}. Aborting...')
sys.exit()
self.conveyor.addMeta('modelID', result)
LOG.debug (f'Loaded model with modelID: {result}')
# assign prediction label
self.conveyor.addVal(label, 'prediction_label', 'prediction label',
'method', 'single',
'Label used to identify the prediction')
success, results = self.param.loadYaml(model, version)
if not success:
LOG.critical(f'Unable to load model parameters. {results}. Aborting...')
sys.exit()
# 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 != None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format',output_format)
if 'ghost' in output_format:
self.param.setVal('output_similar', False)
return
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
endpoint = utils.model_path(self.model, self.version)
# if not os.path.isdir(endpoint):
# self.conveyor.setError(f'Unable to find model {self.model}, version {self.version}')
# #LOG.error(f'Unable to find model {self.model}')
# 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, self.version)
idata_child = importlib.import_module(modpath+".idata_child")
apply_child = importlib.import_module(modpath+".apply_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_apply()
if not success:
self.conveyor.setError(results)
if not self.conveyor.getError():
# make sure there is X data
if not self.conveyor.isKey('xmatrix'):
LOG.debug(f'Failed to compute MDs')
self.conveyor.setError(f'Failed to compute MDs')
# for secret models avoid searching similar compounds
space_pkl = os.path.join(endpoint,'space.pkl')
if not os.path.isfile(space_pkl):
self.param.setVal('output_similar', False)
if not self.conveyor.getError():
if self.param.getVal('output_similar') is True:
from flame.sapply import Sapply
metric = self.param.getVal('similarity_metric')
numsel = self.param.getVal('similarity_cutoff_num')
cutoff = self.param.getVal('similarity_cutoff_distance')
# sapply = Sapply(self.param, self.conveyor)
sapply_child = importlib.import_module(modpath+".sapply_child")
# run apply object, in charge of generate a prediction from idata
try:
sapply = sapply_child.SapplyChild(self.param, self.conveyor)
except:
LOG.warning ('Sapply child architecture mismatch, defaulting to Sapply parent')
sapply = Sapply(self.param, self.conveyor)
sapply.run(cutoff, numsel, metric)
LOG.debug(f'sapply child {type(sapply).__name__} completed `run()`')
if not self.conveyor.getError():
# run apply object, in charge of generate a prediction from idata
try:
apply = apply_child.ApplyChild(self.param, self.conveyor)
except:
LOG.warning ('Apply child architecture mismatch, defaulting to Apply parent')
apply = Apply(self.param, self.conveyor)
apply.run()
LOG.debug(f'apply child {type(apply).__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()
def action_import(model):
'''
Creates a new model tree from a tarbal file with the name "model.tgz"
'''
import re
if not model:
return False, 'Empty model label'
# convert model to endpoint string
base_model = os.path.basename(model)
endpoint = os.path.splitext(base_model)[0]
# find version in case of single version exports
version = None
if re.match("_v[0-9]{6}", endpoint[-8:]):
version = int(endpoint[-6:])
endpoint = endpoint[:-8]
ext = os.path.splitext(base_model)[1]
base_path = utils.model_tree_path(endpoint)
# safety checks
if os.path.isdir(base_path):
return False, f'Endpoint {endpoint} already exists'
if ext != '.tgz':
importfile = os.path.abspath(model + '.tgz')
else:
importfile = model
LOG.info(f'Importing {importfile} ...')
if not os.path.isfile(importfile):
LOG.info(f'Importing package {importfile} not found')
return False, f'Importing package {importfile} not found'
confidential = False
# create directory
try:
os.mkdir(base_path)
except Exception as e:
return False, f'Error creating directory {base_path}: {e}'
# unpack tar.gz. This is done for any kind of export file
with tarfile.open(importfile, 'r:gz') as tar:
tar.extractall(base_path)
# when importing a single version we need to clone the last folder to 'dev'
inner_dirs = os.listdir(base_path)
if not 'dev' in inner_dirs and version is not None:
# assign single version using file name
version_dir = f'ver{version:06d}'
# as a fallback assign the last internal folder
if not os.path.isdir(version_dir):
version_dir = inner_dirs[-1]
version_path = os.path.join(base_path, version_dir)
confidential_model = os.path.join(version_path,
'confidential_model.yaml')
# check if it is a confidential model
if (os.path.isfile(confidential_model)):
confidential = True
flame_source = os.path.dirname(os.path.abspath(__file__))
children_source = os.path.join(flame_source, 'children')
children_names = [
'apply', 'idata', 'odata', 'learn', 'slearn', 'sapply'
]
for cname in children_names:
cpath = os.path.join(children_source, cname + '_child.py')
shutil.copy(cpath, version_path)
LOG.info(f'Adding local children: {cpath} ...')
# open confidential_model.yaml
with open(confidential_model, 'r') as fc:
cmodel = yaml.safe_load(fc)
# create model-results.pkl
model_building_info = [('nobj', '', cmodel['nobj'])]
model_building_info += [('nvarx', '', cmodel['nvarx'])]
model_building_info += [('model', '', cmodel['model'])]
model_type_info = [('quantitative', '', cmodel['quantitative'])]
model_type_info += [('conformal', '', cmodel['conformal'])]
model_type_info += [('conformal_confidence', '',
cmodel['conformal_confidence'])]
model_type_info += [('ensemble', '', False)]
model_type_info += [('ensemble_names', '', [])]
model_type_info += [('ensemble_versions', '', [])]
model_type_info += [('confidential', '', True)]
model_type_info += [('secret', '', True)]
if cmodel['quantitative']:
model_validation_info = [('R2', '', cmodel['R2'])]
model_validation_info += [('Q2', '', cmodel['Q2'])]
model_validation_info += [('SDEC', '', cmodel['SDEC'])]
model_validation_info += [('SDEP', '', cmodel['SDEP'])]
model_validation_info += [('scoringP', '', cmodel['scoringP'])]
model_validation_info += [('scoringR', '', cmodel['scoringR'])]
else:
model_validation_info = [('MCC_f', '', cmodel['MCC_f'])]
model_validation_info += [('MCC', '', cmodel['MCC'])]
model_validation_info += [('Sensitivity_f', '',
cmodel['Sensitivity_f'])]
model_validation_info += [('Sensitivity', '',
cmodel['Sensitivity'])]
model_validation_info += [('Specificity_f', '',
cmodel['Specificity_f'])]
model_validation_info += [('Specificity', '',
cmodel['Specificity'])]
model_validation_info += [('FP_f', '', cmodel['FP_f'])]
model_validation_info += [('FP', '', cmodel['FP'])]
model_validation_info += [('FN_f', '', cmodel['FN_f'])]
model_validation_info += [('FN', '', cmodel['FN'])]
model_validation_info += [('TP_f', '', cmodel['TP_f'])]
model_validation_info += [('TP', '', cmodel['TP'])]
model_validation_info += [('TN_f', '', cmodel['TN_f'])]
model_validation_info += [('TN', '', cmodel['TN'])]
conveyor = Conveyor()
conveyor.addMeta('modelID', cmodel['modelID'])
conveyor.addMeta('endpoint', endpoint)
conveyor.addMeta('version', version)
conveyor.addMeta('quantitative', True)
conveyor.addMeta('secret', True)
conveyor.addVal(model_building_info, 'model_build_info',
'model building information', 'method', 'single',
'Information about the model building')
conveyor.addVal(model_validation_info, 'model_valid_info',
'model validation information', 'method', 'single',
'Information about the model validation')
conveyor.addVal(model_type_info, 'model_type_info',
'model type information', 'method', 'single',
'Information about the model type')
results_file_name = os.path.join(version_path, 'model-results.pkl')
with open(results_file_name, 'wb') as handle:
conveyor.save(handle)
meta_file_name = os.path.join(version_path, 'model-meta.pkl')
with open(meta_file_name, 'wb') as handle:
pickle.dump(cmodel['modelID'], handle)
pickle.dump(None, handle)
pickle.dump(None, handle)
pickle.dump(model_building_info, handle)
pickle.dump(model_validation_info, handle)
pickle.dump(model_type_info, handle)
# clone the version in dev
shutil.copytree(version_path, os.path.join(base_path, 'dev'))
LOG.info(f'Cloning version {version} to version 0 ...')
if confidential:
LOG.info(
f'Import of CONFIDENTIAL model {model} version {version} was successfull'
)
return True, 'OK'
# get libraries
message = f'Endpoint {endpoint} imported OK'
for x in os.listdir(base_path):
model_path = os.path.join(base_path, x)
model_pkl = os.path.join(model_path, 'estimator.pkl')
dict_estimator = {}
if os.path.isfile(model_pkl):
with open(model_pkl, "rb") as input_file:
try:
dict_estimator = pickle.load(input_file)
except Exception as e:
return False, f'Incompatible libraries found!. Import aborted with message "{str(e)}"'
# check if the libraries used to build this model are similar to current libraries
if 'libraries' in dict_estimator:
# print (dict_estimator['libraries'])
success, results = utils.compatible_modules(
dict_estimator['libraries'])
if not success:
message = f"WARNING: Incompatible libraries detected, {results}. Use at your own risk"
return False, message
LOG.info(
'Libraries used to generate the imported model are compatible with local libraries'
)
LOG.info(message)
return True, message
class Predict:
def __init__(self, model, version=0, output_format=None, label=None):
LOG.debug('Starting predict...')
self.model = model
self.version = version
self.param = Parameters()
self.conveyor = Conveyor()
self.conveyor.addVal(label, 'prediction_label', 'prediction label',
'method', 'single',
'Label used to identify the prediction')
if not self.param.loadYaml(model, version):
LOG.critical('Unable to load model parameters. Aborting...')
sys.exit()
# 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 != None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format', output_format)
return
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
# path to endpoint
endpoint = utils.model_path(self.model, self.version)
if not os.path.isdir(endpoint):
self.conveyor.setError(
f'Unable to find model {self.model}, version {self.version}')
#LOG.error(f'Unable to find model {self.model}')
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, self.version)
idata_child = importlib.import_module(modpath + ".idata_child")
apply_child = importlib.import_module(modpath + ".apply_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():
# make sure there is X data
if not self.conveyor.isKey('xmatrix'):
LOG.debug(f'Failed to compute MDs')
self.conveyor.setError(f'Failed to compute MDs')
if not self.conveyor.getError():
# run apply object, in charge of generate a prediction from idata
try:
apply = apply_child.ApplyChild(self.param, self.conveyor)
except:
LOG.warning(
'Apply child architecture mismatch, defaulting to Apply parent'
)
apply = Apply(self.param, self.conveyor)
apply.run()
LOG.debug(f'apply child {type(apply).__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 Search:
def __init__(self, space, version, output_format=None, label=None):
LOG.debug('Starting predict...')
self.space = space
self.version = version
self.label = label
self.param = Parameters()
self.conveyor = Conveyor()
self.conveyor.addVal(label, 'prediction_label', 'prediction label',
'method', 'single',
'Label used to identify the prediction')
if not self.param.loadYaml(space, version, isSpace=True):
LOG.critical('Unable to load space parameters. Aborting...')
sys.exit()
# 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 != None:
if output_format not in self.param.getVal('output_format'):
self.param.appVal('output_format', output_format)
return
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, runtime_param=None, metric=None, numsel=None, cutoff=None):
def run(self, param_dict):
''' Executes a default predicton workflow '''
print('*********', param_dict)
metric = None
numsel = None
cutoff = None
# path to endpoint
epd = utils.space_path(self.space, self.version)
if not os.path.isdir(epd):
self.conveyor.setError(
f'Unable to find space {self.space}, version {self.version}')
#LOG.error(f'Unable to find space {self.space}')
if 'infile' in param_dict:
input_source = param_dict['infile']
else:
LOG.error(f'Unable to find input_file')
self.conveyor.setError(
'wrong format in the runtime similarity parameters')
if 'runtime_param' in param_dict:
runtime_param = param_dict['runtime_param']
if runtime_param is not None:
print(runtime_param)
try:
with open(runtime_param, 'r') as pfile:
rtparam = yaml.safe_load(pfile)
try:
metric = rtparam['similarity_metric']
numsel = rtparam['similarity_cutoff_num']
cutoff = rtparam['similarity_cutoff_distance']
except:
LOG.error(
'wrong format in the runtime similarity parameters'
)
self.conveyor.setError(
'wrong format in the runtime similarity parameters'
)
except:
LOG.error('runtime similarity parameter file not found')
self.conveyor.setError(
'runtime similarity parameter file not found')
else:
try:
metric = param_dict['metric']
numsel = param_dict['numsel']
cutoff = param_dict['cutoff']
except:
LOG.error('wrong format in the runtime similarity parameters')
self.conveyor.setError(
'wrong format in the runtime similarity parameters')
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, self.version)
idata_child = importlib.import_module(modpath + ".idata_child")
sapply_child = importlib.import_module(modpath + ".sapply_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():
# make sure there is X data
if not self.conveyor.isKey('xmatrix'):
LOG.debug(f'Failed to compute MDs')
self.conveyor.setError(f'Failed to compute MDs')
if not self.conveyor.getError():
# run apply object, in charge of generate a prediction from idata
try:
sapply = sapply_child.SapplyChild(self.param, self.conveyor)
except:
LOG.warning(
'Sapply child architecture mismatch, defaulting to Sapply parent'
)
sapply = Sapply(self.param, self.conveyor)
sapply.run(cutoff, numsel, metric)
LOG.debug(
f'sapply child {type(sapply).__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,
self.label)
except:
LOG.warning(
'Odata child architecture mismatch, defaulting to Odata parent'
)
odata = Odata(self.param, self.conveyor, self.label)
return odata.run()
