def autocomplete_documentation(self):
"""
Auto complete fields in model documentation
"""
#ID, Model identifier.
self.fields['ID']['value'] = utils.getModelID(self.model, self.version,
'model')[1]
#Version
self.fields['Version']['value'] = str(self.version)
#Date, Date of model development and Date of QMRF.
today = date.today().strftime("%B %d, %Y")
self.fields['Date']['value'] = today
self.fields['Date_of_QMRF']['value'] = today
#format, Format used(SDF,TSV)
if self.parameters.getVal('input_type') == 'data':
self.fields['Data_info']['value']['format']['value'] = 'TSV'
else:
self.fields['Data_info']['value']['format']['value'] = 'SDF'
#Algorithm, type: QSAR.
self.fields['Algorithm']['value']['type']['value'] = 'QSAR'
#Model, Main modelling program, version, description and license.
software = "Flame, 1.0rc3"
fieldsapplysoftware = ['model', 'descriptors', 'applicability_domain']
for field in fieldsapplysoftware:
if field == 'applicability_domain':
if self.parameters.getVal('conformal'):
self.fields['Software']['value'][field]['value'] = software
else:
self.fields['Software']['value'][field]['value'] = software
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 build_cmd(arguments, output_format=None):
'''
Instantiates a Build object to build a model using the given
input file and model.
This method must be self-contained and suitable for being called in
cascade, by models which use the output of other models as input
'''
from flame.build import Build
# safety check if model exists
endpoint_dir = utils.model_path(arguments['endpoint'], 0)
if not os.path.isdir(endpoint_dir):
return False, 'Endpoint name not found in model repository.'
# remove pre-existing results file
results_file = os.path.join(endpoint_dir, 'model-results.pkl')
if os.path.isfile(results_file):
os.remove(results_file)
meta_file = os.path.join(endpoint_dir, 'model-meta.pkl')
if os.path.isfile(meta_file):
os.remove(meta_file)
# input file provided in the command
ifile = arguments['infile']
if ifile is not None and not os.path.isfile (ifile):
return False, f'Wrong training series file {ifile}'
# lfile is the "training_series" copied internally to the endpoint folder
endpoint_path = utils.model_path(arguments['endpoint'], 0)
lfile = os.path.join(endpoint_path, 'training_series')
if 'param_file' in arguments:
build = Build(arguments['endpoint'], param_file=arguments['param_file'], output_format=output_format)
elif 'param_string' in arguments:
build = Build(arguments['endpoint'], param_string=arguments['param_string'], output_format=output_format)
else:
build = Build(arguments['endpoint'], output_format=output_format)
if utils.isSingleThread():
build.set_single_CPU()
ensemble = build.get_ensemble()
# ensemble[0] Boolean with True for ensemble models and False otherwyse
# ensemble[1] List of ensemble model model_names
# ensemble[2] List of ensemble model versions
if ensemble[0]:
emodels = ensemble[1]
evers = ensemble[2]
if ifile is None:
if not os.path.isfile (lfile):
return False, 'no training series detected'
else:
try:
safe_copy(ifile, lfile)
# shutil.copy(ifile, lfile)
except:
return False, 'Unable to copy input file to model directory'
success, model_res = get_ensemble_input(build, emodels, evers, lfile)
if not success:
return False, model_res
for i in range(len (emodels)):
success, iID = utils.getModelID(emodels[i], evers[i], 'model')
if success:
build.extend_modelID(iID)
LOG.debug(f'New modelID is: {build.conveyor.getMeta("modelID")}')
# now run the model using the data from the external sources
success, results = build.run(model_res)
else:
# when a new training series is provided in the command line
# try to copy it to the model directory
if ifile is not None:
# in case of incremental training, add the input file at the end of existing file
if arguments['incremental']:
if arguments['incremental'] and os.path.isfile(lfile):
LOG.info(f'Merging file {ifile} with existing training series')
new_training = os.path.join(endpoint_path, 'temp_training')
with open(new_training, 'w') as outfile:
# handling the extra newline of SDFiles is problematic. We are delaying the
# output of the newline by striping newlines and adding an universal newline
# at the next line for the first block
first = True
with codecs.open(lfile, 'r', encoding='utf-8', errors='ignore') as infile:
for line in infile:
if first:
outfile.write(f'{line.rstrip()}')
first = False
else:
outfile.write(f'\n{line.rstrip()}')
# for the second block we add the preceding newline in all lines
with codecs.open(ifile, 'r', encoding='utf-8', errors='ignore') as infile:
for line in infile:
outfile.write(f'\n{line.rstrip()}')
shutil.move(new_training, lfile)
else:
try:
safe_copy (ifile, lfile)
# shutil.copy(ifile, lfile)
except:
return False, 'Unable to copy input file to model directory'
# check that the local copy of the input file exists
if not os.path.isfile(lfile):
return False, 'No training series found'
# run the model with the input file
success, results = build.run(lfile)
return success, results
def predict_cmd(arguments, output_format=None):
'''
Instantiates a Predict object to run a prediction using the given input
file and model.
This method must be self-contained and suitable for being called in
cascade, by models which use the output of other models as input.
'''
from flame.predict import Predict
# safety check if model exists
endpoint_dir = utils.model_path(arguments['endpoint'], 0)
if not os.path.isdir(endpoint_dir):
return False, 'Endpoint name not found in model repository.'
# ** DEPRECATE **
# this is a back-compatibility trick for older versions of APIs
# not supporting the label argument
if 'label' not in arguments:
arguments['label'] = 'temp'
if 'output_format' in arguments:
output_format = arguments['output_format']
predict = Predict(arguments['endpoint'], version=arguments['version'], output_format=output_format, label=arguments['label'])
if utils.isSingleThread():
predict.set_single_CPU()
ensemble = predict.get_ensemble()
# ensemble[0] Boolean with True for ensemble models and False otherwyse
# ensemble[1] List of ensemble model model_names
# ensemble[2] List of ensemble model versions
if ensemble[0]:
if arguments['infile'] is None:
return False, 'ensemble models require allways an input file'
emodels = ensemble[1]
evers = ensemble[2]
success, model_res = get_ensemble_input(predict, emodels, evers, arguments['infile'])
if not success:
predict.conveyor.setError (model_res)
LOG.error (model_res)
# return False, model_res # TO-DO, comment this line and run prediction to allow odata to generate error info
# check the presence of changes in the inner models
modelID = predict.conveyor.getMeta('modelID')
for i in range(len (emodels)):
success, iID = utils.getModelID(emodels[i], evers[i], 'model')
if success:
if iID not in modelID:
predict.conveyor.setWarning (f'Inner model {emodels[i]}.{evers[i]} has been updated. Rebuilding of ensemble model is recommended')
LOG.warning (f'Inner model {emodels[i]}.{evers[i]} has been updated. Rebuilding of ensemble model is recommended')
# now run the model using the data from the external sources
success, results = predict.run(model_res)
else:
# run the model with the input file
success, results = predict.run(arguments['infile'])
LOG.info('Prediction completed...')
return success, results