Merge branch 'master' into phg/enumGene

Author: Pgarrett

README.md

@@ -198,6 +198,8 @@ Examples of Fortune 500 companies using _EvoMaster_ are:
 
 ![](docs/img/video-player-flaticon.png)
 
+* A [45-minute talk given at TestCon'25](https://www.youtube.com/watch?v=uKKRo3LrNiw&list=PLqYhGsQ9iSEoXaRmW9WQjjXJK_1NbLlZ6&index=15) on Fuzz Testing Web APIs gives an overview of what can be expected from this kind of fuzzers.   
+
 * A [short video](https://youtu.be/3mYxjgnhLEo) (5 minutes)
   shows the use of _EvoMaster_ on one of the
   case studies in [EMB](https://github.com/WebFuzzing/EMB).

core/src/main/kotlin/org/evomaster/core/EMConfig.kt

@@ -1162,7 +1162,7 @@ class EMConfig {
 
     enum class Algorithm {
         DEFAULT, SMARTS, MIO, RANDOM, WTS, MOSA, RW,
-        StandardGA, MonotonicGA, SteadyStateGA, BreederGA, CellularGA, OnePlusLambdaLambdaGA, MuLambdaEA, MuPlusLambdaEA // GA variants still work-in-progress.
+        StandardGA, MonotonicGA, SteadyStateGA, BreederGA, CellularGA, OnePlusLambdaLambdaGA, MuLambdaEA, MuPlusLambdaEA, LIPS, CRO // GA variants still work-in-progress.
     }
 
     @Cfg("The algorithm used to generate test cases. The default depends on whether black-box or white-box testing is done.")
@@ -1575,6 +1575,27 @@ class EMConfig {
     @Min(1.0)
     var tournamentSize = 10
 
+    // --- Chemical Reaction Optimization (CRO) parameters ---
+    @Cfg("CRO: Molecular collision rate c_r (probability of binary reactions)")
+    @Probability
+    var croMolecularCollisionRate: Double = 0.2
+
+    @Cfg("CRO: Kinetic energy loss rate k_r (lower bound of retained fraction after on-wall)")
+    @Probability
+    var croKineticEnergyLossRate: Double = 0.2
+
+    @Cfg("CRO: Initial kinetic energy assigned to each molecule")
+    @Min(0.0)
+    var croInitialKineticEnergy: Double = 1000.0
+
+    @Cfg("CRO: Decomposition threshold d_t (min number of collisions before decomposition)")
+    @Min(0.0)
+    var croDecompositionThreshold: Int = 500
+
+    @Cfg("CRO: Synthesis KE threshold s_t (molecule can synthesize if KE ≤ s_t)")
+    @Min(0.0)
+    var croSynthesisThreshold: Double = 10.0
+
     @Cfg("When sampling new test cases to evaluate, probability of using some smart strategy instead of plain random")
     @Probability
     var probOfSmartSampling = 0.95

core/src/main/kotlin/org/evomaster/core/Main.kt

@@ -645,6 +645,8 @@ class Main {
                 EMConfig.Algorithm.StandardGA ->
                     Key.get(object : TypeLiteral<StandardGeneticAlgorithm<GraphQLIndividual>>() {})
 
+                EMConfig.Algorithm.LIPS ->
+                    Key.get(object : TypeLiteral<org.evomaster.core.search.algorithms.LIPSAlgorithm<GraphQLIndividual>>() {})
                 EMConfig.Algorithm.MuPlusLambdaEA ->
                     Key.get(object : TypeLiteral<MuPlusLambdaEvolutionaryAlgorithm<GraphQLIndividual>>() {})
 
@@ -684,6 +686,8 @@ class Main {
 
                 EMConfig.Algorithm.RW ->
                     Key.get(object : TypeLiteral<RandomWalkAlgorithm<RPCIndividual>>() {})
+                EMConfig.Algorithm.LIPS ->
+                    Key.get(object : TypeLiteral<org.evomaster.core.search.algorithms.LIPSAlgorithm<RPCIndividual>>() {})
 
                 EMConfig.Algorithm.MuPlusLambdaEA ->
                     Key.get(object : TypeLiteral<MuPlusLambdaEvolutionaryAlgorithm<RPCIndividual>>() {})
@@ -722,6 +726,8 @@ class Main {
 
                 EMConfig.Algorithm.RW ->
                     Key.get(object : TypeLiteral<RandomWalkAlgorithm<WebIndividual>>() {})
+                EMConfig.Algorithm.LIPS ->
+                    Key.get(object : TypeLiteral<org.evomaster.core.search.algorithms.LIPSAlgorithm<WebIndividual>>() {})
 
                 EMConfig.Algorithm.MuPlusLambdaEA ->
                     Key.get(object : TypeLiteral<MuPlusLambdaEvolutionaryAlgorithm<WebIndividual>>() {})
@@ -769,6 +775,8 @@ class Main {
 
                 EMConfig.Algorithm.RW ->
                     Key.get(object : TypeLiteral<RandomWalkAlgorithm<RestIndividual>>() {})
+                EMConfig.Algorithm.LIPS ->
+                    Key.get(object : TypeLiteral<org.evomaster.core.search.algorithms.LIPSAlgorithm<RestIndividual>>() {})
                 EMConfig.Algorithm.MuPlusLambdaEA ->
                     Key.get(object : TypeLiteral<MuPlusLambdaEvolutionaryAlgorithm<RestIndividual>>() {})
                 EMConfig.Algorithm.MuLambdaEA ->
@@ -783,6 +791,9 @@ class Main {
                 EMConfig.Algorithm.OnePlusLambdaLambdaGA ->
                     Key.get(object : TypeLiteral<OnePlusLambdaLambdaGeneticAlgorithm<RestIndividual>>() {})
 
+                EMConfig.Algorithm.CRO ->
+                    Key.get(object : TypeLiteral<CroAlgorithm<RestIndividual>>() {})
+
                 else -> throw IllegalStateException("Unrecognized algorithm ${config.algorithm}")
             }
         }

core/src/main/kotlin/org/evomaster/core/problem/externalservice/httpws/service/HarvestActualHttpWsResponseHandler.kt

@@ -532,10 +532,11 @@ class HarvestActualHttpWsResponseHandler {
         try {
             val template = getACopyOfItsActualResponseIfExist(geneToMutate, probability)?.responseBody ?: return false
 
-            val v = ParamUtil.getValueGene(geneToMutate)
-            val t = ParamUtil.getValueGene(template)
+            val v = geneToMutate.getLeafGene()
+            val t = template.getLeafGene()
             if (v::class.java == t::class.java) {
                 v.copyValueFrom(t)
+                v.forceNewTaints()
                 return true
             } else if (v is StringGene) {
                 // add template as part of specialization

core/src/main/kotlin/org/evomaster/core/problem/rest/data/RestCallAction.kt

@@ -191,7 +191,9 @@ class RestCallAction(
                     For example, they could be a ChoiceGene when dealing with "examples" or Regex when having patterns
                     only defined on some endpoints
                  */
-                parameters[i].primaryGene().copyValueFrom(k.primaryGene())
+                val g = parameters[i].primaryGene()
+                g.copyValueFrom(k.primaryGene())
+                g.forceNewTaints()
             }
         }
     }

core/src/main/kotlin/org/evomaster/core/problem/rest/service/RestIndividualBuilder.kt

@@ -102,6 +102,9 @@ class RestIndividualBuilder {
                 .forEach { it.revertToWeakReference() }
             other.resetLocalIdRecursively()
 
+            //avoid possible taint id conflicts
+            other.seeAllActions().forEach { it.forceNewTaints() }
+
             val duplicates = base.addInitializingActions(other.seeInitializingActions())
 
             other.getFlattenMainEnterpriseActionGroup()!!.forEach { group ->

core/src/main/kotlin/org/evomaster/core/problem/util/BindingBuilder.kt

@@ -109,14 +109,14 @@ object BindingBuilder {
     }
 
     private fun bindValues(p: Pair<Gene,Gene>, doBuildBindingGene: Boolean){
-        val ok = p.first.setFromDifferentGene(p.second)
+        val ok = p.first.copyValueFrom(p.second)
         if (ok && doBuildBindingGene){
             p.first.addBindingGene(p.second)
             p.second.addBindingGene(p.first)
         }
 
-        val first = ParamUtil.getValueGene(p.first)
-        val second = ParamUtil.getValueGene(p.second)
+        val first = p.first.getLeafGene()
+        val second = p.second.getLeafGene()
         if(ok && !doBuildBindingGene && first is StringGene && TaintInputName.isTaintInput(first.value)){
             //do not use same tainted value in non-bound genes
             if(second is StringGene){

core/src/main/kotlin/org/evomaster/core/problem/util/ParamUtil.kt

@@ -16,7 +16,6 @@ import org.evomaster.core.search.gene.numeric.LongGene
 import org.evomaster.core.search.gene.wrapper.CustomMutationRateGene
 import org.evomaster.core.search.gene.wrapper.OptionalGene
 import org.evomaster.core.search.gene.string.StringGene
-import org.evomaster.core.search.gene.utils.GeneUtils
 
 /**
  * this class used to handle binding values among params
@@ -100,7 +99,7 @@ class ParamUtil {
          */
         fun compareGenesWithValue(geneA: Gene, geneB: Gene): Boolean {
             val geneAWithGeneBType = geneB.copy()
-            geneAWithGeneBType.setFromDifferentGene(geneA)
+            geneAWithGeneBType.copyValueFrom(geneA)
             return when (geneB) {
                 is StringGene -> geneB.value == (geneAWithGeneBType as StringGene).value
                 is IntegerGene -> geneB.value == (geneAWithGeneBType as IntegerGene).value
@@ -275,7 +274,7 @@ class ParamUtil {
 
         fun generateParamId(list: Array<String>): String = list.joinToString(separator)
 
-        @Deprecated(message = "Rather use GeneUtils.getWrappedValueGene(gene)",
+        @Deprecated(message = "Rather use getLeafGene()",
             replaceWith = ReplaceWith("GeneUtils.getWrappedValueGene(gene)"))
         fun getValueGene(gene: Gene): Gene {
            return gene.getLeafGene()!!

core/src/main/kotlin/org/evomaster/core/search/Individual.kt

@@ -527,7 +527,7 @@ abstract class Individual(
                       y !=x && !y.hasAnyBindingRelationship(x)
                }
            }){
-               errors.add("Taint id ${d.key} has duplicate genes that are not related}")
+               errors.add("Taint id ${d.key} has duplicate genes that are not related")
            }
         }
         return errors

core/src/main/kotlin/org/evomaster/core/search/action/Action.kt

@@ -79,11 +79,7 @@ abstract class Action(children: List<StructuralElement>) : ActionComponent(
 
     fun forceNewTaints(){
         seeTopGenes().forEach { g ->
-            g.flatView().forEach { r ->
-                if(r is TaintableGene && !r.isDependentTaint()){
-                    r.forceNewTaintId()
-                }
-            }
+            g.forceNewTaints()
         }
     }