def predictThread(command, output, temp_dir=''):
print("Thread Start")
success, results = context.predict_cmd(command, output_format=output)
shutil.rmtree(temp_dir)
# print (f"Folder {temp_dir} removed")
print("Thread End")
def put(self, request, modelname, version, format=None):
# get the upladed file with name "file"
try:
file_obj = request.FILES["SDF"]
except MultiValueDictKeyError as e:
return JsonResponse({'error': 'Datatest not provided'},
status=status.HTTP_400_BAD_REQUEST)
# Set the temp filesystem storage
temp_dir = tempfile.mkdtemp(prefix="predict_data_", dir=None)
fs = FileSystemStorage(location=temp_dir)
# save the file to the new filesystem
path = fs.save(file_obj.name, ContentFile(file_obj.read()))
predict_data = os.path.join(temp_dir, path)
arguments = {
'endpoint': modelname,
'version': int(version),
'infile': predict_data
}
try:
success, results = context.predict_cmd(arguments,
output_format='JSON')
except Exception as e:
return Response(str(e), status=status.HTTP_400_BAD_REQUEST)
if success:
return JsonResponse(json.loads(results), status=status.HTTP_200_OK)
else:
return Response(results, status=status.HTTP_404_NOT_FOUND)
def POST(self, ifile, model, version, temp_dir):
ifile = os.path.join(tempfile.gettempdir(),temp_dir,ifile)
# TODO: for now, only working for plain models (no external input sources)
model = {'endpoint' : model,
'version' : numeric_version(version),
'label': 'temp',
'infile' : ifile}
success, results = context.predict_cmd(model, 'JSON')
return results
def main():
LOG.debug('-------------NEW RUN-------------\n')
parser = argparse.ArgumentParser(
description=
'Use Flame to either build a model from or apply a model to the input file.'
)
parser.add_argument('-f', '--infile', help='Input file.', required=False)
parser.add_argument('-e',
'--endpoint',
help='Endpoint model name.',
required=False)
parser.add_argument('-v',
'--version',
help='Endpoint model version.',
required=False)
parser.add_argument('-a',
'--action',
help='Manage action.',
required=False)
parser.add_argument(
'-c',
'--command',
action='store',
choices=['predict', 'build', 'manage', 'config'],
help='Action type: \'predict\' or \'build\' or \'manage\'',
required=True)
# parser.add_argument('-log', '--loglevel',
# help='Logger level of verbosity',)
parser.add_argument('-p',
'--path',
help='Defines de new path for models repository.',
required=False)
args = parser.parse_args()
# init logger Level and set general config
# another way around would be create a handler with the level
# and append it to the global instance of logger
# if args.loglevel:
# numeric_level = getattr(logging, args.loglevel.upper(), None)
# if not isinstance(numeric_level, int):
# raise ValueError('Invalid log level: {}'.format(args.loglevel))
# logging.basicConfig(level=numeric_level)
# make sure flame has been configured before running any command, unless this command if used to
# configure flame
if args.command != 'config':
configuration_warning()
if args.command == 'predict':
if (args.endpoint is None) or (args.infile is None):
print(
'flame predict : endpoint and input file arguments are compulsory'
)
return
version = utils.intver(args.version)
command_predict = {
'endpoint': args.endpoint,
'version': version,
'infile': args.infile
}
LOG.info(f'Starting prediction with model {args.endpoint}'
f' version {version} for file {args.infile}')
success, results = context.predict_cmd(command_predict)
# print('flame predict : ', success, results)
elif args.command == 'build':
if (args.endpoint is None) or (args.infile is None):
print(
'flame build : endpoint and input file arguments are compulsory'
)
return
command_build = {'endpoint': args.endpoint, 'infile': args.infile}
LOG.info(f'Starting building model {args.endpoint}'
f' with file {args.infile}')
success, results = context.build_cmd(command_build)
# print('flame build : ', success, results)
elif args.command == 'manage':
manage_cmd(args)
elif args.command == 'config':
config(args.path)
change_config_status()
def main():
LOG.debug('-------------NEW RUN-------------\n')
parser = argparse.ArgumentParser(
description=
f'Flame version {__version__}. Use Flame to build and manage predictive models or to predict using them.'
)
parser.add_argument('-f', '--infile', help='Input file.', required=False)
parser.add_argument('-e',
'--endpoint',
help='Endpoint model name.',
required=False)
parser.add_argument('-s',
'--space',
help='Chemical space name.',
required=False)
parser.add_argument('-v',
'--version',
help='Endpoint model version.',
required=False)
parser.add_argument('-a',
'--action',
help='Manage action.',
required=False)
parser.add_argument('-p',
'--parameters',
help='File with parameters for the current action.',
required=False)
parser.add_argument(
'-c',
'--command',
action='store',
choices=['predict', 'search', 'build', 'sbuild', 'manage', 'config'],
help=
'Action type: \'predict\' or \'search\' or \'build\' \'sbuild\' or \'manage\' or \'config\'',
required=True)
# parser.add_argument('-log', '--loglevel',
# help='Logger level of verbosity',)
parser.add_argument(
'-d',
'--directory',
help=
'Defines the root directory for the models and spaces repositories.',
required=False)
parser.add_argument('-t',
'--documentation_file',
help='File with manually filled documentation fields.',
required=False)
parser.add_argument(
'-l',
'--label',
help='Label for facilitating the identification of the prediction.',
required=False)
parser.add_argument(
'-inc',
'--incremental',
help=
'The input file must be added to the existing training series. Only for "build" command.',
action='store_true',
required=False)
parser.add_argument('--smarts',
help='SMARTS string used as input for similarity',
required=False)
args = parser.parse_args()
# init logger Level and set general config
# another way around would be create a handler with the level
# and append it to the global instance of logger
# if args.loglevel:
# numeric_level = getattr(logging, args.loglevel.upper(), None)
# if not isinstance(numeric_level, int):
# raise ValueError('Invalid log level: {}'.format(args.loglevel))
# logging.basicConfig(level=numeric_level)
if args.infile is not None:
if not os.path.isfile(args.infile):
LOG.error(f'Input file {args.infile} not found')
return
# make sure flame has been configured before running any command, unless this command if used to
# configure flame
if args.command != 'config':
utils.config_test()
if args.command == 'predict':
if (args.endpoint is None) or (args.infile is None):
LOG.error(
'flame predict : endpoint and input file arguments are compulsory'
)
return
version = utils.intver(args.version)
if args.label is None:
label = 'temp'
else:
label = args.label
command_predict = {
'endpoint': args.endpoint,
'version': version,
'label': label,
'infile': args.infile
}
LOG.info(
f'Starting prediction with model {args.endpoint}'
f' version {version} for file {args.infile}, labelled as {label}')
success, results = context.predict_cmd(command_predict)
if not success:
LOG.error(results)
elif args.command == 'search':
if (args.space is None) or (args.infile is None
and args.smarts is None):
LOG.error(
'flame search : space and input file arguments are compulsory')
return
version = utils.intver(args.version)
if args.label is None:
label = 'temp'
else:
label = args.label
command_search = {
'space': args.space,
'version': version,
'infile': args.infile,
'smarts': args.smarts,
'runtime_param': args.parameters,
'label': label
}
LOG.info(
f'Starting search on space {args.space}'
f' version {version} for file {args.infile}, labelled as {label}')
success, results = context.search_cmd(command_search)
if not success:
LOG.error(results)
elif args.command == 'build':
if (args.endpoint is None):
LOG.error('flame build : endpoint argument is compulsory')
return
command_build = {
'endpoint': args.endpoint,
'infile': args.infile,
'param_file': args.parameters,
'incremental': args.incremental
}
LOG.info(f'Starting building model {args.endpoint}'
f' with file {args.infile} and parameters {args.parameters}')
success, results = context.build_cmd(command_build)
if not success:
LOG.error(results)
elif args.command == 'sbuild':
if (args.space is None):
LOG.error('flame sbuild : space argument is compulsory')
return
command_build = {
'space': args.space,
'infile': args.infile,
'param_file': args.parameters
}
LOG.info(f'Starting building model {args.space}'
f' with file {args.infile} and parameters {args.parameters}')
success, results = context.sbuild_cmd(command_build)
if not success:
LOG.error(results)
elif args.command == 'manage':
success, results = context.manage_cmd(args)
if not success:
LOG.error(results)
elif args.command == 'config':
success, results = config.configure(args.directory,
(args.action == 'silent'))
if not success:
LOG.error(f'{results}, configuration unchanged')
