Merge pull request #57 from kris7t/logic-extract

Refactor logic expressions

26 files changed, 35 insertions, 38 deletions

diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java
index 5b86a5e1..a6c58381 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java
@@ -9,7 +9,7 @@ import tools.refinery.store.dse.modification.ModificationAdapter;
 import tools.refinery.store.dse.transition.actions.AbstractActionLiteral;
 import tools.refinery.store.dse.transition.actions.BoundActionLiteral;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java
index 18ad2b9d..e13e9c11 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java
@@ -10,7 +10,7 @@ import tools.refinery.store.dse.modification.ModificationAdapter;
 import tools.refinery.store.dse.transition.actions.AbstractActionLiteral;
 import tools.refinery.store.dse.transition.actions.BoundActionLiteral;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 import tools.refinery.store.tuple.Tuple;
 
 import java.util.List;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java
index 31f50ac7..4de482f0 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.modification.actions;
 
 import tools.refinery.store.dse.modification.DanglingEdges;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 public class ModificationActionLiterals {
         private ModificationActionLiterals() {
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java
index ff45ed3e..14a9c556 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/Rule.java
@@ -9,7 +9,7 @@ import tools.refinery.store.dse.transition.actions.Action;
 import tools.refinery.store.dse.transition.actions.BoundAction;
 import tools.refinery.store.dse.transition.callback.*;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.logic.dnf.RelationalQuery;
 
 public class Rule {
         private final String name;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java
index 865ac369..c2e43e0d 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/RuleBuilder.java
@@ -8,9 +8,9 @@ package tools.refinery.store.dse.transition;
 import tools.refinery.store.dse.transition.actions.Action;
 import tools.refinery.store.dse.transition.actions.ActionLiteral;
 import tools.refinery.store.dse.transition.callback.*;
-import tools.refinery.store.query.dnf.AbstractQueryBuilder;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.term.Variable;
+import tools.refinery.logic.dnf.AbstractQueryBuilder;
+import tools.refinery.logic.dnf.Dnf;
+import tools.refinery.logic.term.Variable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java
index d63ddfdd..0ce0c3a4 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/Action.java
@@ -9,9 +9,9 @@ import org.eclipse.collections.api.factory.primitive.ObjectIntMaps;
 import org.eclipse.collections.api.map.primitive.MutableObjectIntMap;
 import org.jetbrains.annotations.Nullable;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.dnf.RelationalQuery;
+import tools.refinery.logic.dnf.SymbolicParameter;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.*;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java
index a721ef73..86b4e3cd 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiteral.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.actions;
 
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java
index 275e1e25..d06e2479 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/ActionLiterals.java
@@ -5,7 +5,7 @@
  */
 package tools.refinery.store.dse.transition.actions;
 
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 import tools.refinery.store.representation.Symbol;
 
 import java.util.List;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java
index 86288921..6657b157 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/actions/PutActionLiteral.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.actions;
 
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.tuple.Tuple;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java
index 869f1a96..7e1dd5b7 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback1.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.actions.ActionLiteral;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java
index a648fc93..1361482d 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback2.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.actions.ActionLiteral;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java
index a9b1d334..870ba088 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback3.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.actions.ActionLiteral;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java
index aef1351c..46c056ef 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/ActionCallback4.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.actions.ActionLiteral;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 import java.util.List;
 
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java
index bd7bf4f5..603500ae 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback1.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.RuleBuilder;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 @FunctionalInterface
 public interface RuleCallback1 {
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java
index 7b02b68a..88d3e43c 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback2.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.RuleBuilder;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 @FunctionalInterface
 public interface RuleCallback2 {
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java
index 6f112d48..d4d35e19 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback3.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.RuleBuilder;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 @FunctionalInterface
 public interface RuleCallback3 {
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java
index dbcf8567..67690169 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/callback/RuleCallback4.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.dse.transition.callback;
 
 import tools.refinery.store.dse.transition.RuleBuilder;
-import tools.refinery.store.query.term.NodeVariable;
+import tools.refinery.logic.term.NodeVariable;
 
 @FunctionalInterface
 public interface RuleCallback4 {
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java
index 0ad2b7a4..2a02ff14 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/AndCriterion.java
@@ -5,9 +5,9 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
+import tools.refinery.logic.literal.Reduction;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.literal.Reduction;
 
 import java.util.ArrayList;
 import java.util.Collection;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java
index 5746cc7e..1f2defab 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CompositeCriterion.java
@@ -5,11 +5,11 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
-import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.query.literal.Reduction;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.LinkedHashSet;
+import java.util.List;
 
 public abstract sealed class CompositeCriterion implements Criterion permits AndCriterion, OrCriterion {
         private final List<Criterion> criteria;
@@ -32,9 +32,6 @@ public abstract sealed class CompositeCriterion implements Criterion permits And
         }
 
         @Override
-        public abstract Reduction getReduction(ModelStore store);
-
-        @Override
         public void configure(ModelStoreBuilder storeBuilder) {
                 for (var criterion : criteria) {
                         criterion.configure(storeBuilder);
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java
index fbd05ded..f9fe1459 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/CountObjective.java
@@ -5,14 +5,14 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
+import tools.refinery.logic.dnf.RelationalQuery;
+import tools.refinery.logic.literal.Reduction;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
 import tools.refinery.store.query.ModelQueryAdapter;
 import tools.refinery.store.query.ModelQueryBuilder;
 import tools.refinery.store.query.ModelQueryStoreAdapter;
-import tools.refinery.store.query.dnf.RelationalQuery;
-import tools.refinery.store.query.literal.Reduction;
 
 public class CountObjective implements Objective {
         private final RelationalQuery query;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java
index 0e4ec5c9..7d4c97ad 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criteria.java
@@ -5,7 +5,7 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
-import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.logic.dnf.AnyQuery;
 
 import java.util.Collection;
 import java.util.List;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java
index c827f20e..da6b2102 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Criterion.java
@@ -5,10 +5,10 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
+import tools.refinery.logic.literal.Reduction;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.query.literal.Reduction;
 
 public interface Criterion {
         default void configure(ModelStoreBuilder storeBuilder) {
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java
index e552d14c..d2364c6a 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/Objectives.java
@@ -5,8 +5,8 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
-import tools.refinery.store.query.dnf.FunctionalQuery;
-import tools.refinery.store.query.dnf.RelationalQuery;
+import tools.refinery.logic.dnf.FunctionalQuery;
+import tools.refinery.logic.dnf.RelationalQuery;
 
 import java.util.Collection;
 import java.util.List;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java
index 7a8d7778..4f7fcb26 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/OrCriterion.java
@@ -5,9 +5,9 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
+import tools.refinery.logic.literal.Reduction;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.literal.Reduction;
 
 import java.util.ArrayList;
 import java.util.Collection;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java
index e15e4e41..82dd8712 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryCriterion.java
@@ -5,14 +5,14 @@
  */
 package tools.refinery.store.dse.transition.objectives;
 
+import tools.refinery.logic.dnf.AnyQuery;
+import tools.refinery.logic.literal.Reduction;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStore;
 import tools.refinery.store.model.ModelStoreBuilder;
 import tools.refinery.store.query.ModelQueryAdapter;
 import tools.refinery.store.query.ModelQueryBuilder;
 import tools.refinery.store.query.ModelQueryStoreAdapter;
-import tools.refinery.store.query.dnf.AnyQuery;
-import tools.refinery.store.query.literal.Reduction;
 
 public class QueryCriterion implements Criterion {
         protected final boolean satisfiedIfHasMatch;
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java
index 5a7ba8f4..1fa6327e 100644
--- a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/transition/objectives/QueryObjective.java
@@ -9,7 +9,7 @@ import tools.refinery.store.model.Model;
 import tools.refinery.store.model.ModelStoreBuilder;
 import tools.refinery.store.query.ModelQueryAdapter;
 import tools.refinery.store.query.ModelQueryBuilder;
-import tools.refinery.store.query.dnf.FunctionalQuery;
+import tools.refinery.logic.dnf.FunctionalQuery;
 
 public class QueryObjective implements Objective {
         protected final FunctionalQuery<? extends Number> objectiveFunction;