distributed reaction system
This commit is contained in:
Artur Meski
305
rs/distributed_reaction_system.py
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305
rs/distributed_reaction_system.py
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#!/usr/bin/env python
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"""
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--- Distributed Reaction Systems Manipulation
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"""
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from sys import exit
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class DistributedReactionSystem(object):
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def __init__(self):
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self.__reactions = []
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self.__background_set = []
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self.__reactions_by_prod = []
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self.__states = []
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self.__transitions = []
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self.__init_state = None
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self.__context_sets_size = None
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@property
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def background_set(self):
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return self.__background_set
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@property
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def set_of_background_ids(self):
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return set(range(len(self.__background_set)))
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@property
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def components_count(self):
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return len(self.__reactions)
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def add_bg_set_entity(self, name):
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if not self.is_in_background_set(name):
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self.__background_set.append(name)
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else:
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print("The entity \"" + str(name) + "\" is already on the list")
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exit(1)
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def add_bg_set_entities(self, names):
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for name in names:
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self.add_bg_set_entity(name)
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def is_in_background_set(self, entity):
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"""Checks if the given name is valid wrt the background set="""
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if entity in self.__background_set:
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return True
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else:
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return False
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def get_entity_id(self, name):
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try:
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return self.__background_set.index(name)
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except ValueError:
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print("Undefined background set entity: " + repr(name))
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exit(1)
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def get_state_ids(self, state):
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ids = []
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for entity in state:
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ids.append(self.get_entity_id(entity))
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return ids
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def get_entity_name(self, entity_id):
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"""Returns the string corresponding to the entity"""
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return self.__background_set[entity_id]
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def ensure_reactions(self, k):
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while len(self.__reactions) <= k:
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self.__reactions.append([])
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def add_reaction(self, k, R, I, P):
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"""Adds a reaction"""
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if R == [] or P == []:
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print("No reactants of products defined")
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raise
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reactants = []
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for entity in R:
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reactants.append(self.get_entity_id(entity))
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inhibitors = []
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for entity in I:
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inhibitors.append(self.get_entity_id(entity))
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products = []
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for entity in P:
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products.append(self.get_entity_id(entity))
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self.ensure_reactions(k)
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self.__reactions[k].append((reactants, inhibitors, products))
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def entities_names_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += entity + ", "
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s = s[:-2]
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return s
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def entities_ids_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += self.get_entity_name(entity) + ", "
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s = s[:-2]
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return s
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def show_reactions(self):
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print("[*] Reactions:")
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for i in range(len(self.__reactions)):
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local_reactions = self.__reactions[i]
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print(" agent = " + str(i))
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for rcts,inhib,prods in local_reactions:
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print("\t - ( R={" + self.entities_ids_set_to_str(rcts) + "}, \tI={" + self.entities_ids_set_to_str(inhib) + "}, \tP={" + self.entities_ids_set_to_str(prods) + "} )")
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def show_background_set(self):
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print("[*] Background set: {" + self.entities_names_set_to_str(self.__background_set) + "}")
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def show(self):
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self.show_background_set()
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self.show_reactions()
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self.show_states()
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self.show_transitions()
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print()
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def reactions_by_product_are_cached(self, component_id):
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if len(self.__reactions_by_prod) > component_id:
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if self.__reactions_by_prod[component_id] != None:
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return True
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return False
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def get_reactions_by_product(self, component_id):
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"""Sorts reactions for the component given by component_id by their products and returns a dictionary of products"""
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if self.reactions_by_product_are_cached(component_id):
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return self.__reactions_by_prod[component_id]
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producible_entities = set()
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for reactants,inhibitors,products in self.__reactions[component_id]:
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producible_entities = producible_entities.union(set(products))
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reactions_by_prod = dict()
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for prod_entity in producible_entities:
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reactions_by_prod[prod_entity] = []
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for reactants,inhibitors,products in self.__reactions[component_id]:
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if prod_entity in products:
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reactions_by_prod[prod_entity].append([reactants,inhibitors])
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# save in cache
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while len(self.__reactions_by_prod) <= component_id: # ensure that the size of cache is right
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self.__reactions_by_prod.append(None)
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self.__reactions_by_prod[component_id] = reactions_by_prod
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return reactions_by_prod
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@property
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def states(self):
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return self.__states
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@property
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def transitions(self):
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return self.__transitions
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def add_state(self, name):
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if name not in self.__states:
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self.__states.append(name)
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else:
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print("\'%s\' already added. skipping..." % (name,))
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def add_init_state(self, name):
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self.add_state(name)
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self.__init_state = self.__states.index(name)
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def get_init_state_name(self):
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if self.__init_state == None:
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return None
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return self.__states[self.__init_state]
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def is_state(self, name):
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if name in self.__states:
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return True
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else:
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return False
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def get_state_id(self, name):
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try:
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return self.__states.index(name)
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except ValueError:
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print("Undefined context automaton state: " + repr(name))
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exit(1)
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def get_init_state_id(self):
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return self.__init_state
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def print_states(self):
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for state in self.__states:
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print(state)
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def is_valid_context_sets(self, context_sets):
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for c in context_sets:
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if not self.is_valid_context(c):
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return False
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return True
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def is_valid_context(self, context):
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if set(context).issubset(self.__background_set):
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return True
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else:
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return False
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def add_transition(self, src, label, dst):
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recipients = label[0]
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context_sets = label[1]
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if not type(context_sets) is list:
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print("Context sets must be of type list")
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exit(1)
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for s in context_sets:
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if not type(s) is set and not type(s) is list:
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print("Each context set must be of type set or list")
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exit(1)
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if self.__context_sets_size == None:
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self.__context_sets_size = len(context_sets)
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else:
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if len(context_sets) != self.__context_sets_size:
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print("Inconsistent size of the context sets: " + str(len(context_sets)) + " != " + str(self.__context_sets_size))
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exit(1)
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if not self.is_valid_context_sets(context_sets):
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raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
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if not self.is_state(src):
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raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
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if not self.is_state(dst):
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raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
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new_context_sets = []
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for c in context_sets:
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new_c_set = set()
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for e in set(c):
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new_c_set.add(self.get_entity_id(e))
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new_context_sets.append(new_c_set)
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recipients = set(recipients)
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self.__transitions.append((self.get_state_id(src),(recipients,new_context_sets),self.get_state_id(dst)))
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def context2str(self, context_sets):
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"""Converts the set of entities ids into the string with their names"""
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s = "["
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for ctx in context_sets:
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if len(ctx) == 0:
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s += " 0"
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else:
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s += " {"
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for c in ctx:
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s += " " + self.get_entity_name(c)
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s += " }"
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s += " ]"
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return s
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def show_transitions(self):
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print("[*] Context automaton transitions:")
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for transition in self.__transitions:
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str_transition = str(transition[0]) + " --( "
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str_transition += str(list(transition[1][0])) + "<=" + self.context2str(transition[1][1])
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str_transition += " )--> " + str(transition[2])
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print("\t- " + str_transition)
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def show_states(self):
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init_state_name = self.get_init_state_name()
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print("[*] Context automaton states:")
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for state in self.__states:
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print("\t- " + state, end="")
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if state == init_state_name:
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print(" [init]")
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else:
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print()
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def sanity_check(self):
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"""Performs a sanity check of the defined distributed reaction system"""
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print("[i] Performing sanity check of the DRS")
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if self.__reactions == []:
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print("No reactions defined")
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exit(1)
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if self.__background_set == []:
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print("Empty background set")
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exit(1)
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if self.__init_state == None:
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print("Initial state not specified")
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exit(1)
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if self.__context_sets_size != len(self.__reactions):
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print("Inconsistent sizes of the context sets with respect to the number of components/agents/processes: " + str(self.__context_sets_size) + " != " + str(len(self.__reactions)))
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exit(1)
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