af26ca543b
- Attempt at implementing an example for DRS - Complete reactions set - New automaton - Formula - Fixed automaton scaling - Proc index in the formula - Benchmark generators - Scripts to reproduce experiments for reaction mining
291 lines
8.1 KiB
Python
Executable File
291 lines
8.1 KiB
Python
Executable File
#!/usr/bin/env python3
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import sys
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import itertools
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class SingleReaction:
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def __init__(self, reactants=None, inhibitors=None, products=None):
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self.reactants = set(reactants) if reactants is not None else set()
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self.inhibitors = set(inhibitors) if inhibitors is not None else set()
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self.products = set(products) if products is not None else set()
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def get_reactants(self):
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return "{" + ", ".join(self.reactants) + "}"
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def get_inhibitors(self):
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return "{" + ", ".join(self.inhibitors) + "}"
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def get_products(self):
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return "{" + ", ".join(self.products) + "}"
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def __str__(self):
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return (
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"{"
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+ f"{self.get_reactants()}, {self.get_inhibitors()} -> {self.get_products()}"
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+ "};"
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)
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class Reactions:
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def __init__(self):
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self.reactions = []
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def add(self, reaction):
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self.reactions.append(reaction)
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def __str__(self):
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ret = ""
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for r in self.reactions:
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ret += f"{r}\n"
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return ret
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class Transition:
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def __init__(self, src, dst, guard, context):
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self.src = src
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self.dst = dst
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self.guard = guard
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self.context = context
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def get_context_str(self):
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r = []
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for proc, entities in self.context:
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ent_str = ",".join(entities)
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r.append(f"{proc}={{{ent_str}}}")
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r = " ".join(r)
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return "{ " + r + " }"
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def __str__(self):
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if self.guard:
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return f"{self.get_context_str()}: {self.src} -> {self.dst} : {self.guard};"
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else:
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return f"{self.get_context_str()}: {self.src} -> {self.dst};"
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class Automaton:
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def __init__(self):
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self.transitions = []
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self.states = []
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self.init_state = None
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def add_transition(self, transition):
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self.transitions.append(transition)
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def add_state(self, state):
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if state not in self.states:
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self.states.append(state)
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def set_init_state(self, state):
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assert state in self.states, f"{state} not in states"
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self.init_state = state
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def __str__(self):
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r = "context-automaton {\n"
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r += "\tstates { " + ", ".join(self.states) + " };\n"
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r += f"\tinit-state {{ {self.init_state} }};\n"
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r += "\ttransitions {\n"
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for tr in self.transitions:
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r += "\t\t" + str(tr) + "\n"
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r += "\t};\n"
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r += "};\n"
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return r
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class DRSGenerator:
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def __init__(self, x, y, z, aut):
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assert y >= z
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assert x >= 2 and y >= 2 and z >= 2
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self.x = x
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self.y = y
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self.z = z
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self.aut_id = aut
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self.n = self.y
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self.reactions = {}
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self.automaton = Automaton()
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self.generate()
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def generate_agent_zero(self):
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rcts = Reactions()
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for i in range(1, self.y + 1):
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rcts.add(SingleReaction(["RTK"], ["h"], [f"RTK{i}"]))
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for j in range(1, self.x + 1):
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rcts.add(SingleReaction([f"EN:{j}_{i}"], ["h"], [f"ENi:{self.x}_{i}"]))
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return rcts
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def generate_reactions_for_component(self, i):
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self.reactions.setdefault(i, Reactions())
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rcts = self.reactions[i]
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rcts.add(SingleReaction(["GF"], ["h"], ["GF"]))
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rcts.add(SingleReaction(["GF"], ["h", f"RTK{i}"], ["RTK"]))
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rcts.add(SingleReaction(["RTK"], [f"ENi:1_{i}"], [f"EN:1_{i}"]))
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for j in range(1, self.x):
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rcts.add(
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SingleReaction([f"EN:{j}_{i}"], [f"ENi:{j+1}_{i}"], [f"EN:{j+1}_{i}"])
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)
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indices = list(range(1, self.y + 1))
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for comb in itertools.combinations(indices, self.z):
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reactants = []
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for i in comb:
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reactants.append(f"EN:{self.x}_{i}")
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rcts.add(SingleReaction(reactants, ["h"], ["TF"]))
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def generate(self):
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print(f"# Generated for: x = {self.x}, y = {self.y}, z = {self.z}")
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print("options { use-context-automaton; make-progressive; };")
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print("reactions {")
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for i in range(1, self.y + 1):
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self.generate_reactions_for_component(i)
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rcts_0 = self.generate_agent_zero()
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print("proc0 {")
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print(rcts_0)
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print("};")
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for proc, reactions in self.reactions.items():
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print(f"proc{proc} {{")
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print(reactions)
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print("};")
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print("};")
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if self.aut_id == "a":
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self.generate_automaton_4(self.n)
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elif self.aut_id == "b":
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self.generate_automaton_5(self.n)
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else:
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raise RuntimeError(f"Unknown automaton identifier: {self.aut_id}")
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self.generate_formula()
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def generate_automaton_4(self, n):
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aut = self.automaton
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aut.add_state("qI")
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aut.add_state("qS")
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for i in range(1, n + 1):
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aut.add_state(f"q{i}A")
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aut.add_state(f"q{i}B")
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aut.add_state(f"q{i}C")
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aut.add_state(f"q{i}D")
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aut.set_init_state("qI")
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aut.add_transition(
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Transition("qI", "qS", "", [(f"proc{i}", ["GF"]) for i in range(0, n + 1)])
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)
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for i in range(1, n + 1):
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aut.add_transition(Transition("qS", f"q{i}A", "", [(f"proc{i}", [])]))
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aut.add_transition(
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Transition(
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f"q{i}A", f"q{i}B", "", [(f"proc{v}", []) for v in range(0, n + 1)]
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)
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)
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aut.add_transition(Transition(f"q{i}B", f"q{i}C", "", [(f"proc{i}", [])]))
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aut.add_transition(
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Transition(
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f"q{i}C", f"q{i}D", "", [(f"proc{v}", []) for v in range(0, n + 1)]
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)
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)
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for i in range(1, n + 1):
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for j in range(1, n + 1):
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if i == j:
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continue
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aut.add_transition(
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Transition(f"q{i}B", f"q{j}A", "", [(f"proc{j}", [])])
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)
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aut.add_transition(
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Transition(f"q{i}D", f"q{j}A", "", [(f"proc{j}", [])])
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)
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print(aut)
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def generate_automaton_5(self, n):
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aut = self.automaton
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for i in range(0, (4 * n + 1)):
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aut.add_state(f"q{i}")
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aut.set_init_state("q0")
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aut.add_transition(
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Transition("q0", "q1", "", [(f"proc{i}", ["GF"]) for i in range(0, n + 1)])
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)
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for i in range(0, n): # 0, ..., n-1
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aut.add_transition(
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Transition(f"q{4*i+1}", f"q{4*i+2}", "", [(f"proc{i+1}", [])])
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)
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aut.add_transition(
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Transition(
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f"q{4*i+2}",
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f"q{4*i+3}",
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"",
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[(f"proc{v}", []) for v in range(0, n + 1)],
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)
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)
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aut.add_transition(
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Transition(f"q{4*i+3}", f"q{4*i+4}", "", [(f"proc{i+1}", [])])
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)
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for i in range(0, n - 1): # 0, ..., n-2
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aut.add_transition(
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Transition(
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f"q{4*i+4}",
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f"q{4*i+5}",
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"",
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[(f"proc{v}", []) for v in range(0, n + 1)],
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)
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)
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aut.add_transition(
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Transition(f"q{4*n}", "q1", "", [(f"proc{i}", []) for i in range(0, n + 1)])
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)
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print(aut)
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def generate_formula(self):
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disjunction = " OR ".join([f"proc{i}.TF" for i in range(1, self.y + 1)])
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conjunction = " AND ".join([f"~proc{i}.TF" for i in range(1, self.y + 1)])
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r = (
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"rsctlk-property { f0 : AG( K[proc0]( "
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+ disjunction
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+ " ) OR K[proc0]( "
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+ conjunction
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+ " ) ) };"
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)
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print(r)
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def main():
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if len(sys.argv) < 1 + 4:
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print(f"Usage: {sys.argv[0]} <x> <y> <z> <Aut>")
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print("\twhere x,y,z >= 2 and y >= z")
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print("\tAut: a, b")
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sys.exit(1)
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g = DRSGenerator(
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x=int(sys.argv[1]),
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y=int(sys.argv[2]),
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z=int(sys.argv[3]),
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aut=sys.argv[4],
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)
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if __name__ == "__main__":
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main()
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