improved checks for taints

Author: arcuri82

core/src/main/kotlin/org/evomaster/core/problem/enterprise/EnterpriseIndividual.kt

@@ -180,6 +180,8 @@ abstract class EnterpriseIndividual(
      */
     fun ensureFlattenedStructure() : Boolean{
 
+        Lazy.assert { verifyValidity(); true }
+
         val before = seeAllActions().size
 
         val issues = doFlattenStructure()

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

@@ -154,6 +154,11 @@ class RestIndividual(
                 .sortBy { if ((it as SqlAction).representExistingData) 0 else 1 }
         }
 
+        /*
+            Can't do this, as it can change how the test behave when there are bounded tainted values
+         */
+        //seeAllActions().forEach { it.forceNewTaints() }
+
         /*
             if we move any environment action to the beginning of the individual, it might impact the fitness
          */

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

@@ -103,6 +103,7 @@ class RestIndividualBuilder {
             other.resetLocalIdRecursively()
 
             //avoid possible taint id conflicts
+            base.seeAllActions().forEach { it.forceNewTaints() }
             other.seeAllActions().forEach { it.forceNewTaints() }
 
             val duplicates = base.addInitializingActions(other.seeInitializingActions())
@@ -122,7 +123,7 @@ class RestIndividualBuilder {
             //merge shouldn't lose any actions
             assert(before == (after+duplicates)) { "$after+$duplicates!=$before" }
 
-            base.verifyValidity()
+            base.verifyValidity(true)
 
             return base
         }

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

@@ -180,7 +180,7 @@ abstract class Individual(
      * All invariants should always be satisfied after any modification of the individual.
      * If not, this is a bug.
      */
-    fun verifyValidity(){
+    fun verifyValidity(checkForTaints: Boolean = false){
 
         groupsView()?.verifyGroups()
 
@@ -202,9 +202,18 @@ abstract class Individual(
             throw IllegalStateException("There are invalid local ids:\n" + localIdErrors.joinToString("\n"))
         }
 
-        val taintIdErrors = verifyTaintIds()
-        if(taintIdErrors.isNotEmpty()){
-            throw IllegalStateException("There are invalid taint ids:\n" + taintIdErrors.joinToString("\n"))
+        /*
+            We cannot really verify it all the time.
+            Duplicates might exist due to bounded genes.
+            But flattening (done at minimization, for example) removes the binding, leading
+            this check to fail.
+            further problem, many phases (eg security) are done _after_ minimization...
+         */
+        if(checkForTaints) {
+            val taintIdErrors = verifyTaintIds()
+            if (taintIdErrors.isNotEmpty()) {
+                throw IllegalStateException("There are invalid taint ids:\n" + taintIdErrors.joinToString("\n"))
+            }
         }
     }
 

core/src/main/kotlin/org/evomaster/core/search/service/Sampler.kt

@@ -99,7 +99,7 @@ abstract class Sampler<T> : TrackOperator where T : Individual {
 
         samplePostProcessing(ind)
 
-        org.evomaster.core.Lazy.assert { ind.verifyValidity(); true }
+        org.evomaster.core.Lazy.assert { ind.verifyValidity(true); true }
         return ind
     }
 

core/src/main/kotlin/org/evomaster/core/search/service/mutator/Mutator.kt

@@ -159,7 +159,7 @@ abstract class Mutator<T> : TrackOperator where T : Individual {
                 log.trace("now it is {}th, do addInitializingActions ends", i)
             }
 
-            Lazy.assert{current.individual.verifyValidity(); true}
+            Lazy.assert{current.individual.verifyValidity(true); true}
 
             // skip to mutate the individual if any new harvested external actions are added
             val mutatedInd = if (!anyHarvestedExternalServiceActions)
@@ -171,7 +171,7 @@ abstract class Mutator<T> : TrackOperator where T : Individual {
 
             sampler.applyDerivedParamModifications(mutatedInd)
 
-            Lazy.assert{mutatedInd.verifyValidity(); true}
+            Lazy.assert{mutatedInd.verifyValidity(true); true}
 
             //FIXME: why setOf()??? are we skipping coverage collection here???
             // or always added non-covered from archive? if so, name "targets" is confusing