fix: further Dnf tests and fixes

11 files changed, 56 insertions, 28 deletions

diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
index e841da9e..c0995e53 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
@@ -32,7 +32,9 @@ public interface Constraint {
                 return equals(other);
         }
 
-        String toReferenceString();
+        default String toReferenceString() {
+                return name();
+        }
 
         default CallLiteral call(CallPolarity polarity, List<Variable> arguments) {
                 return new CallLiteral(polarity, this, arguments);
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
index dd45ecd4..b5e7092b 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
@@ -106,7 +106,7 @@ class ClausePostProcessor {
         private Set<NodeVariable> getEquivalentVariables(NodeVariable variable) {
                 var representative = getRepresentative(variable);
                 if (!representative.equals(variable)) {
-                        throw new IllegalStateException("NodeVariable %s already has a representative %s"
+                        throw new AssertionError("NodeVariable %s already has a representative %s"
                                         .formatted(variable, representative));
                 }
                 return equivalencePartition.computeIfAbsent(variable, key -> {
@@ -249,7 +249,7 @@ class ClausePostProcessor {
 
                 private void bindVariable(Variable input) {
                         if (!remainingInputs.remove(input)) {
-                                throw new IllegalStateException("Already processed input %s of literal %s".formatted(input, literal));
+                                throw new AssertionError("Already processed input %s of literal %s".formatted(input, literal));
                         }
                         if (allInputsBound()) {
                                 addToAllInputsBoundQueue();
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
index dcf7611d..8e38ca6b 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
@@ -223,7 +223,8 @@ public final class DnfBuilder {
                         } else if (result instanceof ClausePostProcessor.ConstantResult constantResult) {
                                 switch (constantResult) {
                                 case ALWAYS_TRUE -> {
-                                        return List.of(new DnfClause(Set.of(), List.of()));
+                                        var inputVariables = getInputVariables();
+                                        return List.of(new DnfClause(inputVariables, List.of()));
                                 }
                                 case ALWAYS_FALSE -> {
                                         // Skip this clause because it can never match.
@@ -248,4 +249,14 @@ public final class DnfBuilder {
                 }
                 return Collections.unmodifiableMap(mutableParameterInfoMap);
         }
+
+        private Set<Variable> getInputVariables() {
+                var inputParameters = new LinkedHashSet<Variable>();
+                for (var parameter : parameters) {
+                        if (parameter.getDirection() == ParameterDirection.IN) {
+                                inputParameters.add(parameter.getVariable());
+                        }
+                }
+                return Collections.unmodifiableSet(inputParameters);
+        }
 }
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/exceptions/IncompatibleParameterDirectionException.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/exceptions/IncompatibleParameterDirectionException.java
deleted file mode 100644
index 52da20ae..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/exceptions/IncompatibleParameterDirectionException.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.exceptions;
-
-public class IncompatibleParameterDirectionException extends RuntimeException {
-        public IncompatibleParameterDirectionException(String message) {
-                super(message);
-        }
-
-        public IncompatibleParameterDirectionException(String message, Throwable cause) {
-                super(message, cause);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
index ed7d3401..8ef8e8b4 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
@@ -19,6 +19,8 @@ public abstract class AbstractCallLiteral implements Literal {
         private final Set<Variable> inArguments;
         private final Set<Variable> outArguments;
 
+        // Use exhaustive switch over enums.
+        @SuppressWarnings("squid:S1301")
         protected AbstractCallLiteral(Constraint target, List<Variable> arguments) {
                 int arity = target.arity();
                 if (arguments.size() != arity) {
@@ -59,14 +61,14 @@ public abstract class AbstractCallLiteral implements Literal {
 
         private static void checkInOutUnifiable(Variable argument) {
                 if (!argument.isUnifiable()) {
-                        throw new IllegalArgumentException("Arguments %s cannot appear with both %s and %s direction"
+                        throw new IllegalArgumentException("Argument %s cannot appear with both %s and %s direction"
                                         .formatted(argument, ParameterDirection.IN, ParameterDirection.OUT));
                 }
         }
 
         private static void checkDuplicateOutUnifiable(Variable argument) {
                 if (!argument.isUnifiable()) {
-                        throw new IllegalArgumentException("Arguments %s cannot be bound multiple times".formatted(argument));
+                        throw new IllegalArgumentException("Argument %s cannot be bound multiple times".formatted(argument));
                 }
         }
 
@@ -87,12 +89,17 @@ public abstract class AbstractCallLiteral implements Literal {
 
         @Override
         public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return getArgumentsOfDirection(ParameterDirection.IN);
+                var inputVariables = new LinkedHashSet<>(getArgumentsOfDirection(ParameterDirection.OUT));
+                inputVariables.retainAll(positiveVariablesInClause);
+                inputVariables.addAll(getArgumentsOfDirection(ParameterDirection.IN));
+                return Collections.unmodifiableSet(inputVariables);
         }
 
         @Override
         public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
+                var privateVariables = new LinkedHashSet<>(getArgumentsOfDirection(ParameterDirection.OUT));
+                privateVariables.removeAll(positiveVariablesInClause);
+                return Collections.unmodifiableSet(privateVariables);
         }
 
         @Override
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
index b2fec430..3a5eb5c7 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
@@ -61,6 +61,14 @@ public class AggregationLiteral<R, T> extends AbstractCallLiteral {
         }
 
         @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                if (positiveVariablesInClause.contains(inputVariable)) {
+                        throw new IllegalArgumentException("Aggregation variable %s must not be bound".formatted(inputVariable));
+                }
+                return super.getInputVariables(positiveVariablesInClause);
+        }
+
+        @Override
         public Literal reduce() {
                 var reduction = getTarget().getReduction();
                 return switch (reduction) {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
index 27d8ad60..29772aee 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
@@ -49,6 +49,22 @@ public final class CallLiteral extends AbstractCallLiteral implements CanNegate<
         }
 
         @Override
+        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
+                if (polarity.isPositive()) {
+                        return getArgumentsOfDirection(ParameterDirection.IN);
+                }
+                return super.getInputVariables(positiveVariablesInClause);
+        }
+
+        @Override
+        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
+                if (polarity.isPositive()) {
+                        return Set.of();
+                }
+                return super.getPrivateVariables(positiveVariablesInClause);
+        }
+
+        @Override
         public Literal reduce() {
                 var reduction = getTarget().getReduction();
                 var negatedReduction = polarity.isPositive() ? reduction : reduction.negate();
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
index 0fe297ab..e5a0cdf1 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
@@ -9,7 +9,7 @@ import java.util.Objects;
 import java.util.Optional;
 
 public class Parameter {
-        public static final Parameter NODE_IN_OUT = new Parameter(null, ParameterDirection.OUT);
+        public static final Parameter NODE_OUT = new Parameter(null, ParameterDirection.OUT);
 
         private final Class<?> dataType;
         private final ParameterDirection direction;
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
index c6f3dd43..c1f9d688 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
@@ -105,7 +105,7 @@ public abstract class AbstractFunctionView<T> extends SymbolView<T> {
 
         private static List<Parameter> createParameters(int symbolArity, Parameter outParameter) {
                 var parameters = new Parameter[symbolArity + 1];
-                Arrays.fill(parameters, Parameter.NODE_IN_OUT);
+                Arrays.fill(parameters, Parameter.NODE_OUT);
                 parameters[symbolArity] = outParameter;
                 return List.of(parameters);
         }
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
index e9785c67..fcf11506 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
@@ -11,7 +11,7 @@ import tools.refinery.store.tuple.Tuple1;
 
 public final class NodeFunctionView extends AbstractFunctionView<Tuple1> {
         public NodeFunctionView(Symbol<Tuple1> symbol, String name) {
-                super(symbol, name, Parameter.NODE_IN_OUT);
+                super(symbol, name, Parameter.NODE_OUT);
         }
 
         public NodeFunctionView(Symbol<Tuple1> symbol) {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
index 7e5b7788..6bc5a708 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
@@ -76,7 +76,7 @@ public abstract class TuplePreservingView<T> extends SymbolView<T> {
 
         private static List<Parameter> createParameters(int arity) {
                 var parameters = new Parameter[arity];
-                Arrays.fill(parameters, Parameter.NODE_IN_OUT);
+                Arrays.fill(parameters, Parameter.NODE_OUT);
                 return List.of(parameters);
         }
 }