public FileParsingResult ParseFiles(string netPath, string specPath)
{
ParseRuleResponse conditionAndExperiments;
var links = GetConditionAndExperiments(netPath, specPath, out conditionAndExperiments);
var automates =
conditionAndExperiments.Experiments.ToDictionary(s => s.Key,
s => new AutomataFromExperimentCreator().CreateAutomata(s.Value));
var res = new List <GeneNode>();
var availableNodes = new Stack <GeneNode>(automates.Select(a => a.Value).ToList());
var backTrackingNode = AutomataMergeLogic.CreateBackTrackingNodeFromStack(availableNodes, 0);
// find merges
var automataMergeLogic = new AutomataMergeLogic();
automataMergeLogic
.GetFinalMerges(availableNodes, links, res, backTrackingNode);
// handle not merged experiments
availableNodes.Where(d => NotExistInMerges(d, res)).ToList().ForEach(f =>
{
f = automataMergeLogic.ApplyAllPossibleLoops(f, links);
res.Add(f);
});
var merges = res
.Take(100)
.Select(a => a.ToFullViewAutomata(automates))
.ToList();
logger.Info($"Finish merges found {merges.Count} valid merges");
/* var allMerges = new AutomataMergeLogic()
* .GetMerges(automates.Select(a => a.Value).ToList())
* .Take(100)
* .Select(a => a.ToViewAutomata())
* .ToList();
*/
var automatesView = automates
.ToDictionary(a => a.Key, a => a.Value.ToViewAutomata());
var backTrackingAutomata = backTrackingNode?.ToViewAutomata();
logger.Info("BackTracing");
logger.Info(JsonConvert.SerializeObject(backTrackingAutomata, Formatting.Indented));
return(new FileParsingResult()
{
GeneLinks = links,
Conditions = conditionAndExperiments.Conditions,
Experiments = conditionAndExperiments.Experiments,
Automates = automatesView,
Merges = merges,
BackTrackingNode = backTrackingAutomata,
MergeObjects = res
//AllMerges = allMerges
});
}
public void TestMergeWithNullConditionReturnValid()
{
var automata1 = new GeneNode()
{
NodeName = "a1",
CurrentCondition = new Condition()
{
{ "B", true }, { "C", true }
}, // here A is missing
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b1",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
}
}
}
};
var automata2 = new GeneNode()
{
NodeName = "a2",
CurrentCondition = new Condition()
{
{ "A", true }, { "B", true }
}, // Here C is missing
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
}
}
}
};
var mergeLogic = new AutomataMergeLogic();
var res = mergeLogic.GetMerges(automata1, automata2);
Assert.AreEqual(1, res.Count);
Assert.AreEqual(res.First().CurrentCondition["A"], true);
Assert.AreEqual(res.First().CurrentCondition["B"], true);
Assert.AreEqual(res.First().CurrentCondition["C"], true);
}
public void TestMergeWithSameConditionReturnMerged()
{
var automata1 = new GeneNode()
{
NodeName = "a1",
CurrentCondition = new Condition()
{
{ "A", true }, { "B", true }, { "C", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b1",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
}
}
}
};
var automata2 = new GeneNode()
{
NodeName = "a2",
CurrentCondition = new Condition()
{
{ "A", true }, { "B", true }, { "C", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
}
}
}
};
var mergeLogic = new AutomataMergeLogic();
var res = mergeLogic.GetMerges(automata1, automata2);
Assert.AreEqual(1, res.Count);
}
public void TestPrefixLength()
{
var automata1 = new GeneNode()
{
NodeName = "a1",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b1",
CurrentCondition = new Condition()
{
{ "A", true }, { "B", true }, { "C", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "c1"
}
}
}
}
}
}
};
// a2 is prefix, because only b2 will be matched
var automata2 = new GeneNode()
{
NodeName = "a2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", true }, { "C", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "c2"
}
}
}
}
}
}
};
var mergeLogic = new AutomataMergeLogic();
var res = mergeLogic.GetMerges(automata1, automata2);
// length should be 4
// a2 => b2@a1 => b1 => c1
Assert.AreEqual(1, res.Count);
var builder = new StringBuilder();
res.First().AppendPath(builder);
logger.Info(builder.ToString());
Assert.AreEqual(4, res.First().NodeLength);
}
public void TestMergeWhenAutomata2CanBeMergedFromAutomata1Child()
{
var automata1 = new GeneNode()
{
NodeName = "a1",
CurrentCondition = new Condition()
{
{ "A", true }, { "B", true }, { "C", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b1",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "c1"
}
}
}
}
}
}
};
var automata2 = new GeneNode()
{
NodeName = "a2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", false }, { "C", false }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "b2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", true }, { "C", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "c2"
}
}
}
}
}
}
};
var mergeLogic = new AutomataMergeLogic();
var res = mergeLogic.GetMerges(automata1, automata2);
Assert.AreEqual(1, res.Count);
Assert.AreEqual(4, res.First().NodeLength);
}
public void TestToyMultipleLoopTest()
{
var automata1 = new GeneNode()
{
NodeName = "a0",
CurrentCondition = new Condition()
{
{ "A", true }, { "B", true }, { "C", true }, { "S1", false }, { "S2", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "a1",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", true }, { "C", true }, { "S1", false }, { "S2", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "a2",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", true }, { "C", true }, { "S1", false }, { "S2", true }
},
Transitions = new List <GeneTransition>()
{
new GeneTransition()
{
Node = new GeneNode()
{
NodeName = "a3",
CurrentCondition = new Condition()
{
{ "A", false }, { "B", true }, { "C", true }, { "S1", false }, { "S2", true }
},
}
},
}
}
}
}
}
}
}
};
List <GeneLink> booleanNetwok = new List <GeneLink>()
{
new GeneLink()
{
From = "S2", To = "B", IsPositive = true
},
new GeneLink()
{
From = "S1", To = "A", IsPositive = true
},
new GeneLink()
{
From = "S1", To = "S1", IsPositive = true
},
new GeneLink()
{
From = "S2", To = "S2", IsPositive = true
},
};
var mergeLogic = new AutomataMergeLogic();
var res = mergeLogic.ApplyAllPossibleLoops(automata1, booleanNetwok);
Assert.IsNotNull(res);
}
