def __init__(self, argv):
super(TRA_Module, self).__init__(argv)
self.tasks = ["SATISFIES-PATTERN"]
parser = argparse.ArgumentParser()
parser.add_argument("--kappa_url", help="kappa endpoint")
args = parser.parse_args()
if args.kappa_url:
self.kappa_url = args.kappa_url
else:
logger.error("No Kappa URL given.")
sys.exit()
# Generate a basic model as placeholder (for testing)
# model_text = 'MAPK1 binds MAP2K1.'
# pa = PysbAssembler()
# pa.add_statements(trips.process_text(model_text).statements)
# self.model = pa.make_model()
# Send subscribe messages
for task in self.tasks:
msg_txt = "(subscribe :content (request &key :content (%s . *)))" % task
self.send(KQMLPerformative.from_string(msg_txt))
# Instantiate a singleton TRA agent
try:
kappa = kappa_client.KappaRuntime(self.kappa_url)
self.tra = TRA(kappa)
except Exception as e:
logger.error("Could not instantiate TRA with Kappa service.")
self.tra = None
self.ready()
super(TRA_Module, self).start()
def get_content(self):
"""Convert the entry to a message."""
if not self.content:
maxlen = 100000
if len(self.message) <= maxlen:
self.content = KQMLPerformative.from_string(self.message)
else:
raise KQMLException('Message is longer than %d characters'
% maxlen)
return self.content
def __init__(self, argv):
super(MRA_Module, self).__init__(argv)
self.tasks = ["BUILD-MODEL", "EXPAND-MODEL", "MODEL-HAS-MECHANISM"]
self.models = []
for task in self.tasks:
msg_txt = "(subscribe :content (request &key :content (%s . *)))" % task
self.send(KQMLPerformative.from_string(msg_txt))
# Instantiate a singleton MRA agent
self.mra = MRA()
self.ready()
super(MRA_Module, self).start()
def performative(string: str) -> KQMLPerformative:
"""Wrapper for KQMLPerformative.from_string, produces a performative object
from a KQML string
Arguments:
string (str): well formed KQML performative as a string
Returns:
KQMLPerformative
"""
return KQMLPerformative.from_string(string)
def init(self):
'''
Initialize TRIPS module
'''
super(Test_Module, self).init()
# Send subscribe messages
for task, subtasks in self.tasks.iteritems():
for subtask in subtasks:
msg_txt = '(subscribe :content (request &key :content ' +\
'(%s &key :content (%s . *))))' % (task, subtask)
self.send(KQMLPerformative.from_string(msg_txt))
# Send ready message
self.ready()
return None
def __init__(self, argv):
# Call the constructor of TripsModule
super(DTDA_Module, self).__init__(argv)
self.tasks = ['IS-DRUG-TARGET', 'FIND-TARGET-DRUG',
'FIND-DISEASE-TARGETS', 'FIND-TREATMENT']
# Send subscribe messages
for task in self.tasks:
msg_txt =\
'(subscribe :content (request &key :content (%s . *)))' % task
self.send(KQMLPerformative.from_string(msg_txt))
# Instantiate a singleton DTDA agent
self.dtda = DTDA()
# Send ready message
self.ready()
super(DTDA_Module, self).start()
def __init__(self, argv):
super(MEA_Module, self).__init__(argv)
self.tasks = ["SIMULATE-MODEL"]
parser = argparse.ArgumentParser()
parser.add_argument("--kappa_url", help="kappa endpoint")
args = parser.parse_args()
if args.kappa_url:
self.kappa_url = args.kappa_url
# Send subscribe messages
for task in self.tasks:
msg_txt = "(subscribe :content (request &key :content (%s . *)))" % task
self.send(KQMLPerformative.from_string(msg_txt))
# Instantiate a singleton MEA agent
self.mea = MEA()
self.ready()
super(MEA_Module, self).start()
def __init__(self, argv):
# Call the constructor of TripsModule
super(Kappa_Module, self).__init__(argv)
self.tasks = ['KAPPA-VERSION', 'KAPPA-PARSE', 'KAPPA-START',
'KAPPA-STATUS', 'KAPPA-STOP']
parser = argparse.ArgumentParser()
parser.add_argument("--kappa_url", help="kappa endpoint")
args = parser.parse_args()
if args.kappa_url:
self.kappa_url = args.kappa_url
else:
logger.error('No Kappa URL given.')
sys.exit()
# Send subscribe messages
for task in self.tasks:
msg_txt =\
'(subscribe :content (request &key :content (%s . *)))' % task
self.send(KQMLPerformative.from_string(msg_txt))
# Instantiate a kappa runtime
self.kappa = KappaRuntime(self.kappa_url)
# Send ready message
self.ready()
super(Kappa_Module, self).start()
def performative(string: str) -> KQMLPerformative:
return KQMLPerformative.from_string(string)
def get_perf(self, msg_id, msg_txt):
msg_txt = msg_txt.replace('\\n', '\n')
perf = KQMLPerformative.from_string(
'(request :reply-with IO-%d :content %s)' % (msg_id, msg_txt))
return perf