def __init__(self, **kwargs):
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
# Instantiate a singleton MEA agent
self.mea = MEA()
super(MEA_Module, self).__init__(**kwargs)
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):
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()
class MEA_Module(KQMLModule):
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 receive_request(self, msg, content):
"""
If a "request" message is received, decode the task and the content
and call the appropriate function to prepare the response. A reply
"tell" message is then sent back.
"""
content_list = content
task_str = content_list[0].to_string().upper()
if task_str == "SIMULATE-MODEL":
try:
reply_content = self.respond_simulate_model(content_list)
except Exception as e:
self.error_reply(msg, "Error in performing simulation task.")
return
else:
self.error_reply(msg, "Unknown request task " + task_str)
return
reply_msg = KQMLPerformative("reply")
reply_msg.set_parameter(":content", reply_content)
self.reply(msg, reply_msg)
def respond_simulate_model(self, content_list):
"""
Response content to simulate-model request
"""
model_str = content_list.get_keyword_arg(":model")
try:
# model_str = model_str.to_string()
model = self.decode_model(model_str)
except InvalidModelDescriptionError as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason INVALID_MODEL)")
return reply_content
except Exception as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason INVALID_MODEL)")
return reply_content
target_entity = content_list.get_keyword_arg(":target_entity")
if target_entity is not None:
target_entity = target_entity.to_string()[1:-1]
else:
reply_content = KQMLList.from_string("(FAILURE :reason MISSING_PARAMETER)")
return reply_content
target_pattern = content_list.get_keyword_arg(":target_pattern")
if target_pattern is not None:
target_pattern = target_pattern.to_string().lower()
else:
reply_content = KQMLList.from_string("(FAILURE :reason MISSING_PARAMETER)")
return reply_content
condition_entity = content_list.get_keyword_arg(":condition_entity")
if condition_entity is not None:
condition_entity = condition_entity.to_string()[1:-1]
condition_type = content_list.get_keyword_arg(":condition_type")
if condition_type is not None:
condition_type = condition_type.to_string().lower()
self.get_context(model)
if condition_entity is None:
target_match = self.mea.check_pattern(model, target_entity, target_pattern)
else:
target_match = self.mea.compare_conditions(
model, target_entity, target_pattern, condition_entity, condition_type
)
target_match_str = "TRUE" if target_match else "FALSE"
reply_content = KQMLList()
reply_content.add("SUCCESS :content (:target_match %s)" % target_match_str)
return reply_content
@staticmethod
def get_context(model):
# TODO: Here we will have to query the context
# for now it is hard coded
kras = model.monomers["KRAS"]
try:
p = Parameter("kras_act_0", 100)
model.add_component(p)
model.initial(kras(act="active"), p)
except ComponentDuplicateNameError:
model.parameters["kras_act_0"].value = 100
@staticmethod
def decode_model(model_enc_str):
model_str = model_enc_str
model = MEA_Module.model_from_string(model_str)
return model
@staticmethod
def model_from_string(model_kqml_str):
try:
model_str = model_kqml_str.to_string()
model_str = model_str[1:-1]
with open("tmp_model.py", "wt") as fh:
fh.write(model_str)
# TODO: executing the model string is not safe
# we should do this through a safer method
exec model_str
except Exception as e:
raise InvalidModelDescriptionError(e)
logger.debug("\n\n")
logger.debug("------BEGIN received model------")
logger.debug("%s" % model_str)
logger.debug("%s" % model.monomers)
logger.debug("%s" % model.rules)
logger.debug("%s" % model.parameters)
logger.debug("%s" % model.initial_conditions)
logger.debug("%s" % model.observables)
logger.debug("-------END received model------")
logger.debug("\n\n")
return model
from mea import MEA
from mea import LIST
mea = MEA()
lst = LIST()
# returns a encrypted or a decrypted list
enclist = lst.enlist("hello world")
declist = lst.delist("208 202 216 216 222 64 238 222 228 216 200"
) # don't forget to add the space between every ascii
# returns an encrypted or a decrpyted string
encstring = mea.encrypt("hello world")
decstring = mea.decrypt(encstring)
class MEA_Module(trips_module.TripsModule):
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 receive_request(self, msg, content):
'''
If a "request" message is received, decode the task and the content
and call the appropriate function to prepare the response. A reply
"tell" message is then sent back.
'''
content_list = content
task_str = content_list[0].to_string().upper()
if task_str == 'SIMULATE-MODEL':
try:
reply_content = self.respond_simulate_model(content_list)
except Exception as e:
self.error_reply(msg, 'Error in performing simulation task.')
return
else:
self.error_reply(msg, 'Unknown request task ' + task_str)
return
reply_msg = KQMLPerformative('reply')
reply_msg.set_parameter(':content', reply_content)
self.reply(msg, reply_msg)
def respond_simulate_model(self, content_list):
'''
Response content to simulate-model request
'''
model_str = content_list.get_keyword_arg(':model')
try:
#model_str = model_str.to_string()
model = self.decode_model(model_str)
except InvalidModelDescriptionError as e:
logger.error(e)
reply_content =\
KQMLList.from_string('(FAILURE :reason INVALID_MODEL)')
return reply_content
except Exception as e:
logger.error(e)
reply_content =\
KQMLList.from_string('(FAILURE :reason INVALID_MODEL)')
return reply_content
target_entity = content_list.get_keyword_arg(':target_entity')
if target_entity is not None:
target_entity = target_entity.to_string()[1:-1]
else:
reply_content =\
KQMLList.from_string('(FAILURE :reason MISSING_PARAMETER)')
return reply_content
target_pattern = content_list.get_keyword_arg(':target_pattern')
if target_pattern is not None:
target_pattern = target_pattern.to_string().lower()
else:
reply_content =\
KQMLList.from_string('(FAILURE :reason MISSING_PARAMETER)')
return reply_content
condition_entity = content_list.get_keyword_arg(':condition_entity')
if condition_entity is not None:
condition_entity = condition_entity.to_string()[1:-1]
condition_type = content_list.get_keyword_arg(':condition_type')
if condition_type is not None:
condition_type = condition_type.to_string().lower()
self.get_context(model)
if condition_entity is None:
target_match = self.mea.check_pattern(model, target_entity,
target_pattern)
else:
target_match = self.mea.compare_conditions(model, target_entity,
target_pattern,
condition_entity,
condition_type)
target_match_str = 'TRUE' if target_match else 'FALSE'
reply_content = KQMLList()
reply_content.add('SUCCESS :content (:target_match %s)' %
target_match_str)
return reply_content
@staticmethod
def get_context(model):
# TODO: Here we will have to query the context
# for now it is hard coded
kras = model.monomers['KRAS']
try:
p = Parameter('kras_act_0', 100)
model.add_component(p)
model.initial(kras(act='active'), p)
except ComponentDuplicateNameError:
model.parameters['kras_act_0'].value = 100
@staticmethod
def decode_model(model_enc_str):
model_str = model_enc_str
model = MEA_Module.model_from_string(model_str)
return model
@staticmethod
def model_from_string(model_kqml_str):
try:
model_str = model_kqml_str.to_string()
model_str = model_str[1:-1]
with open('tmp_model.py', 'wt') as fh:
fh.write(model_str)
# TODO: executing the model string is not safe
# we should do this through a safer method
exec model_str
except Exception as e:
raise InvalidModelDescriptionError(e)
logger.debug('\n\n')
logger.debug('------BEGIN received model------')
logger.debug('%s' % model_str)
logger.debug('%s' % model.monomers)
logger.debug('%s' % model.rules)
logger.debug('%s' % model.parameters)
logger.debug('%s' % model.initial_conditions)
logger.debug('%s' % model.observables)
logger.debug('-------END received model------')
logger.debug('\n\n')
return model
class MEA_Module(Bioagent):
name = 'MEA'
tasks = ['SIMULATE-MODEL']
def __init__(self, **kwargs):
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
# Instantiate a singleton MEA agent
self.mea = MEA()
super(MEA_Module, self).__init__(**kwargs)
def respond_simulate_model(self, content_list):
'''
Response content to simulate-model request
'''
model_str = content_list.get_keyword_arg(':model')
try:
#model_str = model_str.to_string()
model = self.decode_model(model_str)
except InvalidModelDescriptionError as e:
logger.error(e)
reply_content =\
KQMLList.from_string('(FAILURE :reason INVALID_MODEL)')
return reply_content
except Exception as e:
logger.error(e)
reply_content =\
KQMLList.from_string('(FAILURE :reason INVALID_MODEL)')
return reply_content
target_entity = content_list.get_keyword_arg(':target_entity')
if target_entity is not None:
target_entity = target_entity.to_string()[1:-1]
else:
reply_content =\
KQMLList.from_string('(FAILURE :reason MISSING_PARAMETER)')
return reply_content
target_pattern = content_list.get_keyword_arg(':target_pattern')
if target_pattern is not None:
target_pattern = target_pattern.to_string().lower()
else:
reply_content =\
KQMLList.from_string('(FAILURE :reason MISSING_PARAMETER)')
return reply_content
condition_entity = content_list.get_keyword_arg(':condition_entity')
if condition_entity is not None:
condition_entity = condition_entity.to_string()[1:-1]
condition_type = content_list.get_keyword_arg(':condition_type')
if condition_type is not None:
condition_type = condition_type.to_string().lower()
self.get_context(model)
if condition_entity is None:
target_match = self.mea.check_pattern(model, target_entity,
target_pattern)
else:
target_match = self.mea.compare_conditions(model, target_entity,
target_pattern,
condition_entity,
condition_type)
target_match_str = 'TRUE' if target_match else 'FALSE'
reply_content = KQMLList()
reply_content.add('SUCCESS :content (:target_match %s)' %
target_match_str)
return reply_content
@staticmethod
def get_context(model):
# TODO: Here we will have to query the context
# for now it is hard coded
kras = model.monomers['KRAS']
try:
p = Parameter('kras_act_0', 100)
model.add_component(p)
model.initial(kras(act='active'), p)
except ComponentDuplicateNameError:
model.parameters['kras_act_0'].value = 100
@staticmethod
def decode_model(model_enc_str):
model_str = model_enc_str
model = MEA_Module.model_from_string(model_str)
return model
@staticmethod
def model_from_string(model_kqml_str):
try:
model_str = model_kqml_str.to_string()
model_str = model_str[1:-1]
with open('tmp_model.py', 'wt') as fh:
fh.write(model_str)
# TODO: executing the model string is not safe
# we should do this through a safer method
exec model_str
except Exception as e:
raise InvalidModelDescriptionError(e)
logger.debug('\n\n')
logger.debug('------BEGIN received model------')
logger.debug('%s' % model_str)
logger.debug('%s' % model.monomers)
logger.debug('%s' % model.rules)
logger.debug('%s' % model.parameters)
logger.debug('%s' % model.initial_conditions)
logger.debug('%s' % model.observables)
logger.debug('-------END received model------')
logger.debug('\n\n')
return model
# -*- coding: utf-8 -*-
from __future__ import (print_function, division, absolute_import,
unicode_literals)
import matplotlib.pyplot as plt
from mea import MEA
def draw_raster(mea):
""" Draw a raster plot from MEA data """
fig = plt.figure()
for i in range(60):
plt.eventplot(mea[i], lineoffsets=i+0.5, colors=[(0, 0, 0)])
plt.xlim(0, mea.dur)
plt.ylim(0, 60)
return fig
if __name__ == '__main__':
mea = MEA()
mea.dur = 20
mea[0] = range(3, 19, 3)
mea[15] = range(1, 12)
mea[30] = range(2, 18, 2)
fig = draw_raster(mea)
plt.show()
