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):
'''
Initialize TRIPS module
'''
super(DTDA_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.fromString(msg_txt))
# Instantiate a singleton DTDA agent
self.dtda = DTDA()
# Send ready message
self.ready()
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, **kwargs):
# Instantiate a singleton DTDA agent
self.dtda = DTDA()
super(DTDA_Module, self).__init__(**kwargs)
class DTDA_Module(Bioagent):
"""The DTDA module is a TRIPS module built around the DTDA agent.
Its role is to receive and decode messages and send responses from and
to other agents in the system."""
name = "DTDA"
tasks = [
'IS-DRUG-TARGET', 'FIND-TARGET-DRUG', 'FIND-DISEASE-TARGETS',
'FIND-TREATMENT'
]
def __init__(self, **kwargs):
# Instantiate a singleton DTDA agent
self.dtda = DTDA()
super(DTDA_Module, self).__init__(**kwargs)
def respond_is_drug_target(self, content):
"""Response content to is-drug-target request."""
try:
drug_arg = content.gets('drug')
except:
reply = make_failure('INVALID_DRUG')
try:
drug = self._get_target(drug_arg)
except Exception as e:
reply = make_failure('DRUG_NOT_FOUND')
return reply
drug_name = drug.name
try:
target_arg = content.gets('target')
target = self._get_target(target_arg)
target_name = target.name
except:
reply = make_failure('INVALID_TARGET')
return reply
try:
is_target = self.dtda.is_nominal_drug_target(
drug_name, target_name)
except DrugNotFoundException:
reply = make_failure('DRUG_NOT_FOUND')
return reply
reply = KQMLList('SUCCESS')
reply.set('is-target', 'TRUE' if is_target else 'FALSE')
return reply
def respond_find_target_drug(self, content):
"""Response content to find-target-drug request."""
try:
target_arg = content.gets('target')
target = self._get_target(target_arg)
target_name = target.name
except Exception as e:
reply = make_failure('INVALID_TARGET')
return reply
drug_names, pubchem_ids = self.dtda.find_target_drugs(target_name)
reply = KQMLList('SUCCESS')
drugs = KQMLList()
for dn, pci in zip(drug_names, pubchem_ids):
drug = KQMLList()
drug.set('name', dn.replace(' ', '-'))
if pci:
drug.set('pubchem_id', pci)
drugs.append(drug)
reply.set('drugs', drugs)
return reply
def respond_find_disease_targets(self, content):
"""Response content to find-disease-targets request."""
try:
disease_arg = content.gets('disease')
disease = self.get_disease(disease_arg)
except Exception as e:
logger.error(e)
reply = make_failure('INVALID_DISEASE')
return reply
if disease.disease_type != 'cancer':
reply = make_failure('DISEASE_NOT_FOUND')
return reply
logger.debug('Disease: %s' % disease.name)
try:
mut_protein, mut_percent = \
self.dtda.get_top_mutation(disease.name)
except DiseaseNotFoundException:
reply = make_failure('DISEASE_NOT_FOUND')
return reply
# TODO: get functional effect from actual mutations
# TODO: add list of actual mutations to response
# TODO: get fraction not percentage from DTDA
reply = KQMLList('SUCCESS')
protein = KQMLList()
protein.set('name', mut_protein)
protein.set('hgnc', mut_protein)
reply.set('protein', protein)
reply.set('prevalence', '%.2f' % (mut_percent / 100.0))
reply.set('functional-effect', 'ACTIVE')
return reply
def respond_find_treatment(self, content):
"""Response content to find-treatment request."""
try:
disease_arg = content.gets('disease')
disease = self.get_disease(disease_arg)
except Exception as e:
logger.error(e)
reply = make_failure('INVALID_DISEASE')
return reply
if disease.disease_type != 'cancer':
reply = make_failure('DISEASE_NOT_FOUND')
return reply
logger.debug('Disease: %s' % disease.name)
try:
mut_protein, mut_percent = \
self.dtda.get_top_mutation(disease.name)
except DiseaseNotFoundException:
reply = make_failure('DISEASE_NOT_FOUND')
return reply
reply = KQMLList()
# TODO: get functional effect from actual mutations
# TODO: add list of actual mutations to response
# TODO: get fraction not percentage from DTDA
reply1 = KQMLList('SUCCESS')
protein = KQMLList()
protein.set('name', mut_protein)
protein.set('hgnc', mut_protein)
reply1.set('protein', protein)
reply1.set('prevalence', '%.2f' % (mut_percent / 100.0))
reply1.set('functional-effect', 'ACTIVE')
reply.append(reply1)
reply2 = KQMLList('SUCCESS')
drug_names, pubchem_ids = self.dtda.find_target_drugs(mut_protein)
drugs = KQMLList()
for dn, pci in zip(drug_names, pubchem_ids):
drug = KQMLList()
drug.sets('name', dn.replace(' ', '-'))
if pci:
drug.set('pubchem_id', pci)
drugs.append(drug)
reply2.set('drugs', drugs)
reply.append(reply2)
return reply
def _get_target(self, target_str):
tp = TripsProcessor(target_str)
terms = tp.tree.findall('TERM')
term_id = terms[0].attrib['id']
agent = tp._get_agent_by_id(term_id, None)
return agent
def get_disease(self, disease_str):
term = ET.fromstring(disease_str).find('TERM')
disease_type = term.find('type').text
if disease_type.startswith('ONT::'):
disease_type = disease_type[5:].lower()
drum_term = term.find('drum-terms/drum-term')
dbname = drum_term.attrib['name']
dbid = term.attrib['dbid']
dbids = dbid.split('|')
dbid_dict = {k: v for k, v in [d.split(':') for d in dbids]}
disease = Disease(disease_type, dbname, dbid_dict)
return disease
class DTDA_Module(trips_module.TripsModule):
'''
The DTDA module is a TRIPS module built around the DTDA agent.
Its role is to receive and decode messages and send responses from and
to other agents in the system.
'''
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 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
message is then sent back.
'''
content_list = content
task_str = content_list[0].to_string().upper()
if task_str == 'IS-DRUG-TARGET':
reply_content = self.respond_is_drug_target(content_list)
elif task_str == 'FIND-TARGET-DRUG':
reply_content = self.respond_find_target_drug(content_list)
elif task_str == 'FIND-DISEASE-TARGETS':
reply_content = self.respond_find_disease_targets(content_list)
elif task_str == 'FIND-TREATMENT':
reply_content = self.respond_find_treatment(content_list)
if reply_content is None:
self.respond_dont_know(msg,
'(ONT::A X1 :instance-of ONT::DRUG)')
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_dont_know(self, msg, content_string):
resp = '(ONT::TELL :content (ONT::DONT-KNOW :content %s))' %\
content_string
resp_list = KQMLList.from_string(resp)
reply_msg = KQMLPerformative('reply')
reply_msg.set_parameter(':content', resp_list)
self.reply(msg, reply_msg)
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 = target_arg[0].to_string()
reply_content = KQMLList()
try:
is_target = self.dtda.is_nominal_drug_target(drug, target)
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 respond_find_target_drug(self, content_list):
'''
Response content to find-target-drug request
'''
target = content_list.get_keyword_arg(':target')
target_str = target.to_string()[1:-1]
drug_names, chebi_ids = self.dtda.find_target_drugs(target_str)
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 = KQMLList.from_string('(SUCCESS :drugs (' +
drug_list_str + '))')
return reply_content
def respond_find_disease_targets(self, content_list):
'''
Response content to find-disease-targets request
'''
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':
msg_str = '(FAILURE :reason DISEASE_NOT_FOUND)'
reply_content = KQMLList.from_string(msg_str)
return reply_content
logger.debug('Disease: %s' % disease.name)
try:
mut_protein, mut_percent =\
self.dtda.get_top_mutation(disease.name)
except DiseaseNotFoundException:
msg_str = '(FAILURE :reason DISEASE_NOT_FOUND)'
reply_content = KQMLList.from_string(msg_str)
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 =\
KQMLList.from_string(
'(SUCCESS ' +
':protein (:name %s :hgnc %s) ' % (mut_protein, mut_protein) +
':prevalence %.2f ' % (mut_percent/100.0) +
':functional-effect ACTIVE)')
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
@staticmethod
def get_disease(disease_arg):
disease_type = str(disease_arg[0]).lower()
dbname = str(disease_arg.get_keyword_arg(':dbname'))[1:-1]
dbid = str(disease_arg.get_keyword_arg(':dbid'))[1:-1]
dbids = dbid.split('|')
dbid_dict = {k: v for k, v in [d.split(':') for d in dbids]}
disease = Disease(disease_type, dbname, dbid_dict)
return disease
@staticmethod
def get_single_argument(arg):
if arg is None:
return None
arg_str = arg.to_string()
if arg_str[0] == '(' and arg_str[-1] == ')':
arg_str = arg_str[1:-1]
arg_str = arg_str.lower()
return arg_str
class DTDA_Module(trips_module.TripsModule):
'''
The DTDA module is a TRIPS module built around the DTDA agent. Its role is to
receive and decode messages and send responses from and to other agents in
the system.
'''
def __init__(self, argv):
# Call the constructor of TripsModule
super(DTDA_Module, self).__init__(argv)
self.tasks = {'ONT::PERFORM': ['ONT::IS-DRUG-TARGET',
'ONT::FIND-TARGET-DRUG', 'ONT::FIND-DISEASE-TARGETS',
'ONT::FIND-TREATMENT']}
def init(self):
'''
Initialize TRIPS module
'''
super(DTDA_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.fromString(msg_txt))
# Instantiate a singleton DTDA agent
self.dtda = DTDA()
# Send ready message
self.ready()
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 = cast(KQMLList, content)
task_str = content_list.get(0).toString().upper()
if task_str == 'ONT::PERFORM':
subtask = cast(KQMLList,content_list.getKeywordArg(':content'))
subtask_str = subtask.get(0).toString().upper()
if subtask_str == 'ONT::IS-DRUG-TARGET':
reply_content = self.respond_is_drug_target(content_list)
elif subtask_str == 'ONT::FIND-TARGET-DRUG':
reply_content = self.respond_find_target_drug(content_list)
elif subtask_str == 'ONT::FIND-DISEASE-TARGETS':
reply_content = self.respond_find_disease_targets(content_list)
elif subtask_str == 'ONT::FIND-TREATMENT':
reply_content = self.respond_find_treatment(subtask)
if reply_content is None:
self.respond_dont_know(msg, '(ONT::A X1 :instance-of ONT::DRUG)')
return
else:
self.error_reply(msg, 'unknown request subtask ' + subtask_str)
return
else:
self.error_reply(msg, 'unknown request task ' + task_str)
return
reply_msg = KQMLPerformative('reply')
reply_msg.setParameter(':content', cast(KQMLObject, reply_content))
self.reply(msg, reply_msg)
def respond_dont_know(self, msg, content_string):
resp = '(ONT::TELL :content (ONT::DONT-KNOW :content %s))' % content_string
resp_list = KQMLList.fromString(resp)
reply_msg = KQMLPerformative('reply')
reply_msg.setParameter(':content', cast(KQMLObject, resp_list))
self.reply(msg, reply_msg)
def respond_is_drug_target(self, content_list):
'''
Response content to is-drug-target request
'''
# TODO: get parameters from content
is_target = self.dtda.is_nominal_drug_target('Vemurafenib', 'BRAF')
reply_content = KQMLList()
if is_target:
msg_str = 'TRUE'
else:
msg_str = 'FALSE'
reply_content.add(msg_str)
return reply_content
def respond_find_target_drug(self, content_list):
'''
Response content to find-target-drug request
'''
# TODO: implement
reply_content = KQMLList()
reply_content.add('')
return reply_content
def respond_find_disease_targets(self, content_list):
'''
Response content to find-disease-targets request
'''
# TODO: implement
self.dtda.get_mutation_statistics('pancreatic', 'missense')
reply_content = KQMLList()
reply_content.add('')
return reply_content
def respond_find_treatment(self, content_list):
'''
Response content to find-treatment request
'''
reply_content = KQMLList()
# Parse content
disease_str = content_list.getKeywordArg(':disease')
if disease_str is None:
print 'no disease set'
return None
disease_str = disease_str.toString()
disease_terms = disease_str[1:-1].split(' ')
disease = disease_terms[0]
disease_type = disease_terms[1]
disease_str = disease[3:].lower()
if disease_str not in ['cancer', 'tumor'] and\
disease_str.find('carcinoma') == -1 and\
disease_str.find('cancer') == -1 and\
disease_str.find('melanoma') == -1:
print 'problem with disease name'
return None
if disease_type == '-':
disease_type_filter = disease_str
disease_type_filter = disease_type_filter.replace('cancer', '')
disease_type_filter = disease_type_filter.replace('-', '')
else:
disease_type_filter = disease_type[3:].lower()
print disease_type_filter
# First, look for possible disease targets
mutation_stats = self.dtda.get_mutation_statistics(disease_type_filter, 'missense')
if mutation_stats is None:
print 'no mutation stats'
return None
# Return the top mutation as a possible target
mutations_sorted = sorted(mutation_stats.items(),
key=operator.itemgetter(1), reverse=True)
top_mutation = mutations_sorted[0]
mut_protein = top_mutation[0]
mut_percent = int(top_mutation[1][0]*100.0)
mut_response = KQMLList.fromString('(ONT::TELL :content ' +\
'(ONT::PROPORTION :refset (ONT::CANCER-PATIENT) ' +\
':quan (ONT::PERCENT %d) ' % mut_percent +\
':content (ONT::MUTATION :affected ONT::%s)))' % mut_protein)
# Try to find a drug targeting KRAS
drugs = self.dtda.find_target_drug(mut_protein)
#import ipdb; ipdb.set_trace()
if not drugs:
drug_response = KQMLList.fromString('(ONT::TELL :content (ONT::DONT-KNOW :content (ONT::A X1 :instance-of ONT::DRUG)))')
else:
drugs_str = ', '.join(drugs)
drug_response = KQMLList.fromString('(ONT::TELL :content (%s))' % drugs_str)
reply_content.add(KQMLList(mut_response))
reply_content.add(KQMLList(drug_response))
return reply_content
class DTDA_Module(KQMLModule):
'''
The DTDA module is a TRIPS module built around the DTDA agent.
Its role is to receive and decode messages and send responses from and
to other agents in the system.
'''
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 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
message is then sent back.
'''
content_list = content
task_str = content_list[0].to_string().upper()
if task_str == 'IS-DRUG-TARGET':
reply_content = self.respond_is_drug_target(content_list)
elif task_str == 'FIND-TARGET-DRUG':
reply_content = self.respond_find_target_drug(content_list)
elif task_str == 'FIND-DISEASE-TARGETS':
reply_content = self.respond_find_disease_targets(content_list)
elif task_str == 'FIND-TREATMENT':
reply_content = self.respond_find_treatment(content_list)
if reply_content is None:
self.respond_dont_know(msg,
'(ONT::A X1 :instance-of ONT::DRUG)')
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_dont_know(self, msg, content_string):
resp = '(ONT::TELL :content (ONT::DONT-KNOW :content %s))' %\
content_string
resp_list = KQMLList.from_string(resp)
reply_msg = KQMLPerformative('reply')
reply_msg.set_parameter(':content', resp_list)
self.reply(msg, reply_msg)
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 respond_find_target_drug(self, content_list):
'''
Response content to find-target-drug request
'''
target_arg = content_list.get_keyword_arg(':target')
target = self._get_target(target_arg)
target_name = target.name
drug_names, chebi_ids = self.dtda.find_target_drugs(target_name)
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 = KQMLList.from_string(
'(SUCCESS :drugs (' + drug_list_str + '))')
return reply_content
def respond_find_disease_targets(self, content_list):
'''
Response content to find-disease-targets request
'''
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':
msg_str = '(FAILURE :reason DISEASE_NOT_FOUND)'
reply_content = KQMLList.from_string(msg_str)
return reply_content
logger.debug('Disease: %s' % disease.name)
try:
mut_protein, mut_percent =\
self.dtda.get_top_mutation(disease.name)
except DiseaseNotFoundException:
msg_str = '(FAILURE :reason DISEASE_NOT_FOUND)'
reply_content = KQMLList.from_string(msg_str)
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 =\
KQMLList.from_string(
'(SUCCESS ' +
':protein (:name %s :hgnc %s) ' % (mut_protein, mut_protein) +
':prevalence %.2f ' % (mut_percent/100.0) +
':functional-effect ACTIVE)')
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 _get_target(self, target_arg):
target_str = str(target_arg)
target_str = self.decode_description('<ekb>' + target_str + '</ekb>')
tp = TripsProcessor(target_str)
terms = tp.tree.findall('TERM')
term_id = terms[0].attrib['id']
agent = tp._get_agent_by_id(term_id, None)
return agent
def get_disease(self, disease_arg):
disease_str = str(disease_arg)
disease_str = self.decode_description(disease_str)
term = ET.fromstring(disease_str)
disease_type = term.find('type').text
if disease_type.startswith('ONT::'):
disease_type = disease_type[5:].lower()
drum_term = term.find('drum-terms/drum-term')
dbname = drum_term.attrib['name']
dbid = term.attrib['dbid']
dbids = dbid.split('|')
dbid_dict = {k: v for k, v in [d.split(':') for d in dbids]}
disease = Disease(disease_type, dbname, dbid_dict)
return disease
@staticmethod
def get_single_argument(arg):
if arg is None:
return None
arg_str = arg.to_string()
if arg_str[0] == '(' and arg_str[-1] == ')':
arg_str = arg_str[1:-1]
arg_str = arg_str.lower()
return arg_str
@staticmethod
def decode_description(descr):
if descr[0] == '"':
descr = descr[1:]
if descr[-1] == '"':
descr = descr[:-1]
descr = descr.replace('\\"', '"')
return descr