def __init__(self, argv):
super(MRA_Module, self).__init__(argv)
self.tasks = ['BUILD-MODEL', 'EXPAND-MODEL']
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 __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()
class MRA_Module(KQMLModule):
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 receive_tell(self, msg, content):
tell_content = content[0].to_string().upper()
if tell_content == "START-CONVERSATION":
logger.info("MRA resetting")
# self.mra = MRA()
# self.models = []
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.
"""
try:
task_str = content[0].to_string().upper()
except Exception as e:
logger.error("Could not get task string from request.")
logger.error(e)
self.error_reply(msg, "Invalid task")
if task_str == "BUILD-MODEL":
try:
reply_content = self.respond_build_model(content)
except InvalidModelDescriptionError as e:
logger.error("Invalid model description.")
logger.error(e)
fail_msg = "(FAILURE :reason INVALID_DESCRIPTION)"
reply_content = KQMLList.from_string(fail_msg)
elif task_str == "EXPAND-MODEL":
try:
reply_content = self.respond_expand_model(content)
except InvalidModelIdError as e:
logger.error("Invalid model ID.")
logger.error(e)
fail_msg = "(FAILURE :reason INVALID_MODEL_ID)"
reply_content = KQMLList.from_string(fail_msg)
except InvalidModelDescriptionError as e:
logger.error("Invalid model description.")
logger.error(e)
fail_msg = "(FAILURE :reason INVALID_DESCRIPTION)"
reply_content = KQMLList.from_string(fail_msg)
elif task_str == "MODEL-HAS-MECHANISM":
reply_content = self.respond_has_mechanism(content)
else:
self.error_reply(msg, "Unknown task " + task_str)
return
reply_msg = KQMLPerformative("reply")
reply_msg.set_parameter(":content", reply_content)
self.reply(msg, reply_msg)
def respond_build_model(self, content_list):
"""
Response content to build-model request
"""
try:
descr_arg = content_list.get_keyword_arg(":description")
descr = descr_arg[0].to_string()
descr = self.decode_description(descr)
model = self.mra.build_model_from_ekb(descr)
except Exception as e:
raise InvalidModelDescriptionError(e)
if model is None:
raise InvalidModelDescriptionError
self.get_context(model)
self.models.append(model)
model_id = len(self.models)
model_enc = self.encode_model(model)
try:
model_diagram = self.get_model_diagram(model, model_id)
except DiagramGenerationError as e:
logger.error("Could not generate model diagram.")
logger.error(e)
model_diagram = ""
except DiagramConversionError as e:
logger.error("Could not save model diagram.")
logger.error(e)
model_diagram = ""
reply_content = KQMLList.from_string(
'(SUCCESS :model-id %s :model "%s" :diagram "%s")' % (model_id, model_enc, model_diagram)
)
return reply_content
def respond_expand_model(self, content_list):
"""
Response content to expand-model request
"""
try:
descr_arg = content_list.get_keyword_arg(":description")
descr = descr_arg[0].to_string()
descr = self.decode_description(descr)
except Exception as e:
raise InvalidModelDescriptionError(e)
model_id_arg = content_list.get_keyword_arg(":model-id")
if model_id_arg is None:
logger.error("Model ID missing.")
raise InvalidModelIdError
try:
model_id_str = model_id_arg.to_string()
model_id = int(model_id_str)
except Exception as e:
logger.error("Could not get model ID as integer.")
raise InvalidModelIdError(e)
if model_id < 1 or model_id > len(self.models):
logger.error("Model ID does not refer to an existing model.")
raise InvalidModelIdError
try:
model = self.mra.expand_model_from_ekb(descr, model_id)
except Exception as e:
raise InvalidModelDescriptionError
self.get_context(model)
self.models.append(model)
new_model_id = len(self.models)
model_enc = self.encode_model(model)
try:
model_diagram = self.get_model_diagram(model, new_model_id)
except DiagramGenerationError:
model_diagram = ""
except DiagramConversionError:
model_diagram = ""
reply_content = KQMLList.from_string(
'(SUCCESS :model-id %s :model "%s" :diagram "%s")' % (new_model_id, model_enc, model_diagram)
)
return reply_content
def respond_has_mechanism(self, content_list):
"""
Response content to model-has-mechanism request
"""
try:
descr_arg = content_list.get_keyword_arg(":description")
descr = descr_arg[0].to_string()
descr = self.decode_description(descr)
except Exception as e:
raise InvalidModelDescriptionError(e)
model_id_arg = content_list.get_keyword_arg(":model-id")
if model_id_arg is None:
logger.error("Model ID missing.")
raise InvalidModelIdError
try:
model_id_str = model_id_arg.to_string()
model_id = int(model_id_str)
except Exception as e:
logger.error("Could not get model ID as integer.")
raise InvalidModelIdError(e)
if model_id < 1 or model_id > len(self.models):
logger.error("Model ID does not refer to an existing model.")
raise InvalidModelIdError
try:
has_mechanism = self.mra.has_mechanism(descr, model_id)
except Exception as e:
raise InvalidModelDescriptionError
reply_content = KQMLList.from_string("(SUCCESS :model-id %s :has-mechanism %s)" % (model_id, has_mechanism))
return reply_content
@staticmethod
def get_model_diagram(model, model_id=None):
try:
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
fname = "model%d" % ("" if model_id is None else model_id)
diagram_dot = render_reactions.run(model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
raise DiagramGenerationError(e)
try:
with open(fname + ".dot", "wt") as fh:
fh.write(diagram_dot)
subprocess.call(("dot -T png -o %s.png %s.dot" % (fname, fname)).split(" "))
abs_path = os.path.abspath(os.getcwd())
if abs_path[-1] != "/":
abs_path = abs_path + "/"
full_path = abs_path + fname + ".png"
except Exception as e:
raise DiagramConversionError(e)
return full_path
@staticmethod
def get_context(model):
# TODO: Here we will have to query the context
# for now it is not used
pass
@staticmethod
def decode_description(descr):
if descr[0] == '"':
descr = descr[1:]
if descr[-1] == '"':
descr = descr[:-1]
descr = descr.replace('\\"', '"')
return descr
@staticmethod
def encode_model(model):
model_str = pysb.export.export(model, "pysb_flat")
model_str = str(model_str.strip())
model_str = model_str.replace('"', '\\"')
return model_str
urlmap(style, "styles", ())
# Layers, layer styles and data fields:
urlmap(layers, "layers")
urlmap(layer, "layers", ())
urlmap(layerstyles, "layers", (), "styles")
urlmap(layerstyle, "layers", (), "styles", ())
urlmap(layerfields, "layers", (), "fields")
# Layergroups:
urlmap(layergroups, "layergroups")
urlmap(layergroup, "layergroups", ())
# OGC Web Services:
urlmap(OWSGlobalSettings, "services", "(wms|wfs|wcs)", "settings")
urls = tuple(urlmap)
mra = MRA(os.path.join(sys.path[0], "mra.yaml"))
mralogs.setup(mra.config["logging"]["level"], mra.config["logging"]["file"],
mra.config["logging"]["format"])
web.config.debug = mra.config["debug"].get("web_debug", False)
webapp.exceptionManager.raise_all = mra.config["debug"].get("raise_all", False)
HTTPCompatible.return_logs = mra.config["logging"].get("web_logs", False)
for pdir in mra.config["plugins"].get("loadpaths", []):
plugins.load_plugins_dir(pdir)
app = web.application(urls, globals())
if __name__ == "__main__":
app.run()
def __init__(self, **kwargs):
# Instantiate a singleton MRA agent
self.mra = MRA()
super(MRA_Module, self).__init__(**kwargs)
class MRA_Module(Bioagent):
name = "MRA"
tasks = [
'BUILD-MODEL', 'EXPAND-MODEL', 'MODEL-HAS-MECHANISM',
'MODEL-REPLACE-MECHANISM', 'MODEL-REMOVE-MECHANISM', 'MODEL-UNDO',
'MODEL-GET-UPSTREAM'
]
def __init__(self, **kwargs):
# Instantiate a singleton MRA agent
self.mra = MRA()
super(MRA_Module, self).__init__(**kwargs)
def receive_tell(self, msg, content):
tell_content = content.head().upper()
if tell_content == 'START-CONVERSATION':
logger.info('MRA resetting')
def receive_request(self, msg, content):
"""Handle request messages and respond.
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.
"""
ret = None
try:
ret = super(MRA_Module, self).receive_request(msg, content)
except InvalidModelDescriptionError as e:
logger.error('Invalid model description.')
logger.error(e)
reply_content = self.make_failure('INVALID_DESCRIPTION')
except InvalidModelIdError as e:
logger.error('Invalid model ID.')
logger.error(e)
reply_content = self.make_failure('INVALID_MODEL_ID')
except Exception as e:
logger.error(e)
reply_content = self.make_failure('INTERNAL_FAILURE')
if ret is None:
ret = self.reply_with_content(msg, reply_content)
return ret
def respond_build_model(self, content):
"""Return response content to build-model request."""
descr = content.gets('description')
descr_format = content.gets('format')
no_display = content.get('no-display')
try:
if not descr_format or descr_format == 'ekb':
res = self.mra.build_model_from_ekb(descr)
elif descr_format == 'indra_json':
res = self.mra.build_model_from_json(descr)
else:
err_msg = 'Invalid description format: %s' % descr_format
raise InvalidModelDescriptionError(err_msg)
except Exception as e:
raise InvalidModelDescriptionError(e)
model_id = res.get('model_id')
if model_id is None:
raise InvalidModelDescriptionError()
# Start a SUCCESS message
msg = KQMLPerformative('SUCCESS')
# Add the model id
msg.set('model-id', str(model_id))
# Add the INDRA model json
model = res.get('model')
model_msg = encode_indra_stmts(model)
msg.sets('model', model_msg)
# Add the diagrams
diagrams = res.get('diagrams')
if not no_display:
if diagrams:
rxn_diagram = diagrams.get('reactionnetwork')
if rxn_diagram:
msg.sets('diagram', rxn_diagram)
if not self.testing:
self.send_display_model(model_msg, diagrams)
ambiguities = res.get('ambiguities')
if ambiguities:
ambiguities_msg = get_ambiguities_msg(ambiguities)
msg.set('ambiguities', ambiguities_msg)
return msg
def respond_expand_model(self, content):
"""Return response content to expand-model request."""
descr = content.gets('description')
model_id = self._get_model_id(content)
descr_format = content.gets('format')
no_display = content.get('no-display')
try:
if not descr_format or descr_format == 'ekb':
res = self.mra.expand_model_from_ekb(descr, model_id)
elif descr_format == 'indra_json':
res = self.mra.expand_model_from_json(descr, model_id)
else:
err_msg = 'Invalid description format: %s' % descr_format
raise InvalidModelDescriptionError(err_msg)
except Exception as e:
raise InvalidModelDescriptionError(e)
new_model_id = res.get('model_id')
if new_model_id is None:
raise InvalidModelDescriptionError()
# Start a SUCCESS message
msg = KQMLPerformative('SUCCESS')
# Add the model id
msg.set('model-id', str(new_model_id))
# Add the INDRA model json
model = res.get('model')
model_msg = encode_indra_stmts(model)
msg.sets('model', model_msg)
# Add the INDRA model new json
model_new = res.get('model_new')
if model_new:
model_new_msg = encode_indra_stmts(model_new)
msg.sets('model-new', model_new_msg)
# Add the diagram
if not no_display:
diagrams = res.get('diagrams')
if diagrams:
rxn_diagram = diagrams.get('reactionnetwork')
if rxn_diagram:
msg.sets('diagram', rxn_diagram)
if not self.testing:
self.send_display_model(model_msg, diagrams)
ambiguities = res.get('ambiguities')
if ambiguities:
ambiguities_msg = get_ambiguities_msg(ambiguities)
msg.set('ambiguities', ambiguities_msg)
return msg
def respond_model_undo(self, content):
"""Return response content to model-undo request."""
res = self.mra.model_undo()
no_display = content.get('no-display')
new_model_id = res.get('model_id')
# Start a SUCCESS message
msg = KQMLPerformative('SUCCESS')
# Add the model id
msg.set('model-id', str(new_model_id))
# Add the INDRA model json
model = res.get('model')
model_msg = encode_indra_stmts(model)
msg.sets('model', model_msg)
# Add the diagram
diagrams = res.get('diagrams')
if not no_display:
if diagrams:
rxn_diagram = diagrams.get('reactionnetwork')
if rxn_diagram:
msg.sets('diagram', rxn_diagram)
if not self.testing:
self.send_display_model(model_msg, diagrams)
return msg
def respond_has_mechanism(self, content):
"""Return response content to model-has-mechanism request."""
ekb = content.gets('description')
model_id = self._get_model_id(content)
try:
res = self.mra.has_mechanism(ekb, model_id)
except Exception as e:
raise InvalidModelDescriptionError(e)
# Start a SUCCESS message
msg = KQMLPerformative('SUCCESS')
# Add the model id
msg.set('model-id', str(model_id))
# Add TRUE or FALSE for has-mechanism
has_mechanism_msg = 'TRUE' if res['has_mechanism'] else 'FALSE'
msg.set('has-mechanism', has_mechanism_msg)
query = res.get('query')
if query:
query_msg = encode_indra_stmts([query])
msg.sets('query', query_msg)
return msg
def respond_remove_mechanism(self, content):
"""Return response content to model-remove-mechanism request."""
ekb = content.gets('description')
model_id = self._get_model_id(content)
no_display = content.get('no-display')
try:
res = self.mra.remove_mechanism(ekb, model_id)
except Exception as e:
raise InvalidModelDescriptionError(e)
model_id = res.get('model_id')
if model_id is None:
raise InvalidModelDescriptionError('Could not find model id.')
# Start a SUCCESS message
msg = KQMLPerformative('SUCCESS')
# Add the model id
msg.set('model-id', str(model_id))
# Add the INDRA model json
model = res.get('model')
model_msg = encode_indra_stmts(model)
msg.sets('model', model_msg)
# Add the removed statements
removed = res.get('removed')
if removed:
removed_msg = encode_indra_stmts(removed)
msg.sets('removed', removed_msg)
# Add the diagram
diagrams = res.get('diagrams')
if not no_display:
if diagrams:
rxn_diagram = diagrams.get('reactionnetwork')
if rxn_diagram:
msg.sets('diagram', rxn_diagram)
if not self.testing:
self.send_display_model(model_msg, rxn_diagram)
return msg
def respond_model_get_upstream(self, content):
"""Return response content to model-upstream request."""
target_arg = content.gets('target')
target = get_target(target_arg)
try:
model_id = self._get_model_id(content)
except Exception as e:
model_id = 1
upstream = self.mra.get_upstream(target, model_id)
terms = []
names = []
for agent in upstream:
term = ekb_from_agent(agent)
if term is not None:
names.append(KQMLString(agent.name))
terms.append(KQMLString(term))
reply = KQMLList('SUCCESS')
reply.set('upstream', KQMLList(terms))
reply.set('upstream-names', KQMLList(names))
return reply
def send_display_model(self, model, diagrams):
msg = KQMLPerformative('tell')
content = KQMLList('display-model')
content.set('type', 'indra')
content.sets('model', model)
msg.set('content', content)
self.send(msg)
for diagram_type, path in diagrams.items():
if not path:
continue
msg = KQMLPerformative('tell')
content = KQMLList('display-image')
content.set('type', diagram_type)
content.sets('path', path)
msg.set('content', content)
self.send(msg)
def _get_model_id(self, content):
model_id_arg = content.get('model-id')
if model_id_arg is None:
logger.error('Model ID missing.')
raise InvalidModelIdError
try:
model_id_str = model_id_arg.to_string()
model_id = int(model_id_str)
except Exception as e:
logger.error('Could not get model ID as integer.')
raise InvalidModelIdError(e)
if not self.mra.has_id(model_id):
logger.error('Model ID does not refer to an existing model.')
raise InvalidModelIdError
return model_id
class MRA_Module(trips_module.TripsModule):
def __init__(self, argv):
super(MRA_Module, self).__init__(argv)
self.tasks = ['BUILD-MODEL', 'EXPAND-MODEL']
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 receive_tell(self, msg, content):
tell_content = content[0].to_string().upper()
if tell_content == 'START-CONVERSATION':
logger.info('MRA resetting')
#self.mra = MRA()
#self.models = []
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.
'''
try:
task_str = content[0].to_string().upper()
except Exception as e:
logger.error('Could not get task string from request.')
logger.error(e)
self.error_reply(msg, 'Invalid task')
if task_str == 'BUILD-MODEL':
try:
reply_content = self.respond_build_model(content)
except InvalidModelDescriptionError as e:
logger.error('Invalid model description.')
logger.error(e)
fail_msg = '(FAILURE :reason INVALID_DESCRIPTION)'
reply_content = KQMLList.from_string(fail_msg)
elif task_str == 'EXPAND-MODEL':
try:
reply_content = self.respond_expand_model(content)
except InvalidModelIdError as e:
logger.error('Invalid model ID.')
logger.error(e)
fail_msg = '(FAILURE :reason INVALID_MODEL_ID)'
reply_content = KQMLList.from_string(fail_msg)
except InvalidModelDescriptionError as e:
logger.error('Invalid model description.')
logger.error(e)
fail_msg = '(FAILURE :reason INVALID_DESCRIPTION)'
reply_content = KQMLList.from_string(fail_msg)
else:
self.error_reply(msg, 'Unknown task ' + task_str)
return
reply_msg = KQMLPerformative('reply')
reply_msg.set_parameter(':content', reply_content)
self.reply(msg, reply_msg)
def respond_build_model(self, content_list):
'''
Response content to build-model request
'''
try:
descr_arg = content_list.get_keyword_arg(':description')
descr = descr_arg[0].to_string()
descr = self.decode_description(descr)
model = self.mra.build_model_from_ekb(descr)
except Exception as e:
raise InvalidModelDescriptionError(e)
if model is None:
raise InvalidModelDescriptionError
self.get_context(model)
self.models.append(model)
model_id = len(self.models)
model_enc = self.encode_model(model)
try:
model_diagram = self.get_model_diagram(model, model_id)
except DiagramGenerationError as e:
logger.error('Could not generate model diagram.')
logger.error(e)
model_diagram = ''
except DiagramConversionError as e:
logger.error('Could not save model diagram.')
logger.error(e)
model_diagram = ''
reply_content =\
KQMLList.from_string(
'(SUCCESS :model-id %s :model "%s" :diagram "%s")' %\
(model_id, model_enc, model_diagram))
return reply_content
def respond_expand_model(self, content_list):
'''
Response content to expand-model request
'''
try:
descr_arg = content_list.get_keyword_arg(':description')
descr = descr_arg[0].to_string()
descr = self.decode_description(descr)
except Exception as e:
raise InvalidModelDescriptionError(e)
model_id_arg = content_list.get_keyword_arg(':model-id')
if model_id_arg is None:
logger.error('Model ID missing.')
raise InvalidModelIdError
try:
model_id_str = model_id_arg.to_string()
model_id = int(model_id_str)
except Exception as e:
logger.error('Could not get model ID as integer.')
raise InvalidModelIdError(e)
if model_id < 1 or model_id > len(self.models):
logger.error('Model ID does not refer to an existing model.')
raise InvalidModelIdError
try:
model = self.mra.expand_model_from_ekb(descr, model_id)
except Exception as e:
raise InvalidModelDescriptionError
self.get_context(model)
self.models.append(model)
new_model_id = len(self.models)
model_enc = self.encode_model(model)
try:
model_diagram = self.get_model_diagram(model, new_model_id)
except DiagramGenerationError:
model_diagram = ''
except DiagramConversionError:
model_diagram = ''
reply_content =\
KQMLList.from_string(
'(SUCCESS :model-id %s :model "%s" :diagram "%s")' %\
(new_model_id, model_enc, model_diagram))
return reply_content
@staticmethod
def get_model_diagram(model, model_id=None):
try:
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
fname = 'model%d' % ('' if model_id is None else model_id)
diagram_dot = render_reactions.run(model)
#TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
raise DiagramGenerationError(e)
try:
with open(fname + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(
('dot -T png -o %s.png %s.dot' % (fname, fname)).split(' '))
abs_path = os.path.abspath(os.getcwd())
if abs_path[-1] != '/':
abs_path = abs_path + '/'
full_path = abs_path + fname + '.png'
except Exception as e:
raise DiagramConversionError(e)
return full_path
@staticmethod
def get_context(model):
# TODO: Here we will have to query the context
# for now it is not used
pass
@staticmethod
def decode_description(descr):
if descr[0] == '"':
descr = descr[1:]
if descr[-1] == '"':
descr = descr[:-1]
descr = descr.replace('\\"', '"')
return descr
@staticmethod
def encode_model(model):
model_str = pysb.export.export(model, 'pysb_flat')
model_str = str(model_str.strip())
model_str = model_str.replace('"', '\\"')
return model_str