def response_error(self, error):
reply_content = KQMLList()
for e in error:
error_msg = '"%s"' %\
str(e).encode('string-escape').replace('"', '\\"')
reply_content.add(error_msg)
return self.format_error(reply_content.to_string())
def response_error(self, error):
reply_content = KQMLList()
for e in error:
error_msg = '"%s"' %\
str(e).encode('string-escape').replace('"', '\\"')
reply_content.add(error_msg)
return self.format_error(reply_content.to_string())
def reply(self,):
reply_msg = KQMLPerformative('reply')
reply_content = KQMLList()
for t in self.tests:
print 'reply {0}'.format(t)
t_content = t.get_content()
if t_content:
reply_content.add(t_content.to_string())
reply_msg.setParameter(':content', reply_content)
return reply_msg
def respond_satisfies_pattern(self, content_list):
"""
Response content to satisfies-pattern request
"""
model_token = content_list.get_keyword_arg(":model")
pattern_lst = content_list.get_keyword_arg(":pattern")
conditions_lst = content_list.get_keyword_arg(":conditions")
try:
model_str = str(model_token)
model = decode_model(model_str)
except Exception as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason INVALID_MODEL)")
return reply_content
try:
pattern = get_temporal_pattern(pattern_lst)
except InvalidTimeUnitError as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason INVALID_TIME_LIMIT)")
return reply_content
except Exception as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason INVALID_PATTERN)")
return reply_content
if conditions_lst is None:
conditions = None
else:
try:
conditions = []
for condition_lst in conditions_lst:
condition = get_molecular_condition(condition_lst)
conditions.append(condition)
except Exception as e:
logger.error(e)
msg_str = "(FAILURE :reason INVALID_CONDITIONS)"
reply_content = KQMLList.from_string(msg_str)
return reply_content
try:
sat_rate, num_sim = self.tra.check_property(model, pattern, conditions)
except SimulatorError as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason KAPPA_FAILURE)")
return reply_content
except Exception as e:
logger.error(e)
reply_content = KQMLList.from_string("(FAILURE :reason INVALID_PATTERN)")
return reply_content
reply_content = KQMLList()
msg_str = "(:satisfies-rate %.1f :num-sim %d)" % (sat_rate, num_sim)
reply_content.add("SUCCESS :content %s" % msg_str)
return reply_content
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
def respond_test(self):
'''
Response content to version message
'''
reply_content = KQMLList()
version_response = KQMLList.from_string( '' +\
'(ONT::TELL :content ' +\
')')
reply_content.add(KQMLList(version_response))
return reply_content
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
def respond_find_treatment(self, content_list):
'''
Response content to find-treatment request
'''
reply_content = KQMLList()
#TODO: eliminate code duplication here
disease_arg = content_list.get_keyword_arg(':disease')
try:
disease = self.get_disease(disease_arg)
except Exception as e:
logger.error(e)
msg_str = '(FAILURE :reason INVALID_DISEASE)'
reply_content = KQMLList.from_string(msg_str)
return reply_content
if disease.disease_type != 'cancer':
reply_content.add('FAILURE :reason DISEASE_NOT_FOUND')
return reply_content
logger.debug('Disease: %s' % disease.name)
try:
mut_protein, mut_percent = \
self.dtda.get_top_mutation(disease.name)
except DiseaseNotFoundException:
reply_content.add('FAILURE :reason DISEASE_NOT_FOUND')
return reply_content
# TODO: get functional effect from actual mutations
# TODO: add list of actual mutations to response
# TODO: get fraction not percentage from DTDA
reply_content.add(KQMLList.from_string(
'(SUCCESS ' +
':protein (:name %s :hgnc %s) ' % (mut_protein, mut_protein) +
':prevalence %.2f ' % (mut_percent/100.0) +
':functional-effect ACTIVE)'))
# Try to find a drug
drug_names, chebi_ids = self.dtda.find_target_drugs(mut_protein)
drug_list_str = ''
for dn, ci in zip(drug_names, chebi_ids):
if ci is None:
drug_list_str += '(:name %s) ' % dn.encode('ascii', 'ignore')
else:
drug_list_str += '(:name %s :chebi_id %s) ' % (dn, ci)
reply_content.add(KQMLList.from_string(
'(SUCCESS :drugs (' + drug_list_str + '))'))
return reply_content
def respond_is_drug_target(self, content_list):
'''
Response content to is-drug-target request
'''
drug_arg = content_list.get_keyword_arg(':drug')
drug = drug_arg[0].to_string()
target_arg = content_list.get_keyword_arg(':target')
target = self._get_target(target_arg)
target_name = target.name
reply_content = KQMLList()
try:
is_target = self.dtda.is_nominal_drug_target(drug, target_name)
except DrugNotFoundException:
reply_content.add('FAILURE :reason DRUG_NOT_FOUND')
return reply_content
status = 'SUCCESS'
if is_target:
is_target_str = 'TRUE'
else:
is_target_str = 'FALSE'
msg_str = '%s :is-target %s' %\
(status, is_target_str)
reply_content.add(msg_str)
return reply_content
def render_status(status):
reply_content = KQMLList()
reply_content.add(":status")
if 'plot' in status:
plot_data = status['plot']
plot = KQMLList()
plot.add(':plot')
if 'legend' in plot_data:
legend = KQMLList()
legend.add(':legend')
for label in plot_data['legend']:
legend.add('"' + label + '"')
plot.add(legend)
if 'observables' in plot_data:
observables = KQMLList()
observables.add(':observables')
for o in plot_data['observables']:
observation = KQMLList()
observation.add(':observation')
if 'time' in o:
time = KQMLList()
time.add(':time')
time.add(render_value(o['time']))
observation.add(time)
if 'values' in o:
values = KQMLList()
values.add(':values')
for f in o['values']:
values.add(render_value(f))
observation.add(values)
observables.add(observation)
plot.add(observables)
reply_content.add(plot)
if 'tracked_events' in status:
tracked_events = KQMLList()
tracked_events.add(':tracked_events')
tracked_events.add(render_value(status['tracked_events']))
plot.add(tracked_events)
if 'is_running' in status:
is_running = KQMLList()
is_running.add(':is_running')
is_running.add(render_value(status['is_running']))
plot.add(is_running)
if 'event_percentage' in status:
event_percentage = KQMLList()
event_percentage.add(':event_percentage')
event_percentage.add(render_value(status['event_percentage']))
plot.add(event_percentage)
if 'time_percentage' in status:
time_percentage = KQMLList()
time_percentage.add(':time_percentage')
time_percentage.add(render_value(status['time_percentage']))
plot.add(time_percentage)
if 'time' in status:
time = KQMLList()
time.add(':time')
time.add(render_value(status['time']))
plot.add(time)
if 'event' in status:
event = KQMLList()
event.add(':event')
event.add(render_value(status['event']))
plot.add(event)
# trips is not happy with this not sure why
# if 'log_messages':
# log_messages = KQMLList()
# log_messages.add(':log_messages')
# for message in status['log_messages']:
# log_messages.add("'"+render_value(message)+"'")
# plot.add(log_messages)
return reply_content
def render_status(status):
reply_content = KQMLList()
reply_content.add(":status")
if 'plot' in status:
plot_data = status['plot']
plot = KQMLList()
plot.add(':plot')
if 'legend' in plot_data:
legend = KQMLList()
legend.add(':legend')
for label in plot_data['legend']:
legend.add('"'+label+'"')
plot.add(legend)
if 'observables' in plot_data:
observables = KQMLList()
observables.add(':observables')
for o in plot_data['observables']:
observation = KQMLList()
observation.add(':observation')
if 'time' in o:
time = KQMLList()
time.add(':time')
time.add(render_value(o['time']))
observation.add(time)
if 'values' in o:
values = KQMLList()
values.add(':values')
for f in o['values']:
values.add(render_value(f))
observation.add(values)
observables.add(observation)
plot.add(observables)
reply_content.add(plot)
if 'tracked_events' in status:
tracked_events = KQMLList()
tracked_events.add(':tracked_events')
tracked_events.add(render_value(status['tracked_events']))
plot.add(tracked_events)
if 'is_running' in status:
is_running = KQMLList()
is_running.add(':is_running')
is_running.add(render_value(status['is_running']))
plot.add(is_running)
if 'event_percentage' in status:
event_percentage = KQMLList()
event_percentage.add(':event_percentage')
event_percentage.add(render_value(status['event_percentage']))
plot.add(event_percentage)
if 'time_percentage' in status:
time_percentage = KQMLList()
time_percentage.add(':time_percentage')
time_percentage.add(render_value(status['time_percentage']))
plot.add(time_percentage)
if 'time' in status:
time = KQMLList()
time.add(':time')
time.add(render_value(status['time']))
plot.add(time)
if 'event' in status:
event = KQMLList()
event.add(':event')
event.add(render_value(status['event']))
plot.add(event)
# trips is not happy with this not sure why
# if 'log_messages':
# log_messages = KQMLList()
# log_messages.add(':log_messages')
# for message in status['log_messages']:
# log_messages.add("'"+render_value(message)+"'")
# plot.add(log_messages)
return reply_content
def get_content(self):
reply_content = KQMLList()
if self.get_actual():
actual_string = self.get_actual().to_string()
expected_string = self.get_expected().to_string()
print 'get_content:actual_string {0}'.format(actual_string)
print 'get_content:expected_string {0}'.format(expected_string)
if expected_string in actual_string:
return None
else:
reply_content.add(":request")
reply_content.add(self.get_request())
reply_content.add(":expected")
reply_content.add(self.get_expected())
reply_content.add(":actual")
reply_content.add(self.get_actual())
else:
reply_content.add(":request")
reply_content.add(self.get_request())
reply_content.add(":noresponse")
return reply_content
