fixed wrong handling of bindings in copy

Author: arcuri82

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

@@ -115,8 +115,8 @@ object BindingBuilder {
             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/search/gene/Gene.kt

@@ -911,19 +911,22 @@ abstract class Gene(
      * sync [bindingGenes] based on [this]
      */
     fun syncBindingGenesBasedOnThis(all: MutableSet<Gene> = mutableSetOf()) {
-        if (bindingGenes.isEmpty()) return
+        if (bindingGenes.isEmpty()){
+            return
+        }
         all.add(this)
         bindingGenes.filterNot { all.contains(it) }.forEach { b ->
             all.add(b)
-            if (!b.copyValueFrom(this))
-                LoggingUtil.uniqueWarn(
-                    log,
-                    "fail to bind the gene (${b.name} with the type ${b::class.java.simpleName}) based on this gene (${this.name} with ${this::class.java.simpleName})"
-                )
+            if (!b.copyValueFrom(this)) {
+                LoggingUtil.uniqueWarn(log, "fail to bind the gene (${b.name} with the type ${b::class.java.simpleName})" +
+                            " based on this gene (${this.name} with ${this::class.java.simpleName})")
+            }
             b.syncBindingGenesBasedOnThis(all)
         }
 
-        children.filterNot { all.contains(it) }.forEach { it.syncBindingGenesBasedOnThis(all) }
+        children.filterNot { all.contains(it) }.forEach {
+            it.syncBindingGenesBasedOnThis(all)
+        }
     }
 
     /**

core/src/main/kotlin/org/evomaster/core/search/gene/string/StringGene.kt

@@ -985,6 +985,10 @@ class StringGene(
 
     override fun unsafeCopyValueFrom(other: Gene): Boolean {
 
+        /*
+            TODO aren't we ignoring here if this gene is using a specialization?
+         */
+
         //TODO should this be handled with phenotype or wrapper? need to double-check
         if(other is ChoiceGene<*>){
             val x = other.activeGene()
@@ -1029,19 +1033,20 @@ class StringGene(
             }
         }
 
-        if(other is StringGene) {
-            this.selectedSpecialization = other.selectedSpecialization
-
-            this.specializations.clear()
-            this.specializations.addAll(other.specializations)
-
-            killAllChildren()
-            addChildren(other.specializationGenes.map { it.copy() })
-
-            this.tainted = other.tainted
-            this.bindingIds.clear()
-            this.bindingIds.addAll(other.bindingIds)
-        }
+        //TODO would need updating...
+//        if(other is StringGene) {
+//            this.selectedSpecialization = other.selectedSpecialization
+//
+//            this.specializations.clear()
+//            this.specializations.addAll(other.specializations)
+//
+//            killAllChildren()
+//            addChildren(other.specializationGenes.map { it.copy() })
+//
+//            this.tainted = other.tainted
+//            this.bindingIds.clear()
+//            this.bindingIds.addAll(other.bindingIds)
+//        }
 
         return true
     }