7 files changed, 71 insertions, 87 deletions

diff --git a/subprojects/viatra-runtime-rete/build.gradle.kts b/subprojects/viatra-runtime-rete/build.gradle.kts
index 7e795a90..560e8854 100644
--- a/subprojects/viatra-runtime-rete/build.gradle.kts
+++ b/subprojects/viatra-runtime-rete/build.gradle.kts
@@ -6,6 +6,10 @@
 
 plugins {
         id("tools.refinery.gradle.java-library")
+        // Vendor code from Eclipse VIATRA is maintained by the VIATRA project,
+        // so we don't need to keep track of coverage ourselves.
+        // Our own modifications are covered by tests in the `store-query-viatra` subproject.
+        id("tools.refinery.gradle.skip-coverage")
 }
 
 dependencies {
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java
index 38fe7c2f..5f0f1892 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/matcher/RetePatternMatcher.java
@@ -31,10 +31,8 @@ import tools.refinery.viatra.runtime.rete.single.TransformerNode;
 import tools.refinery.viatra.runtime.rete.traceability.RecipeTraceInfo;
 
 import java.util.Collection;
-import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 /**
@@ -78,14 +76,6 @@ public class RetePatternMatcher extends TransformerNode implements IQueryResultP
         return productionNode;
     }
 
-    public Tuple matchOneRandomly(Object[] inputMapping, boolean[] fixed) {
-        List<Tuple> allMatches = matchAll(inputMapping, fixed).collect(Collectors.toList());
-        if (allMatches == null || allMatches.isEmpty())
-            return null;
-        else
-            return allMatches.get((int) (Math.random() * allMatches.size()));
-    }
-
     /**
      * @since 2.0
      */
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java
index b261d19d..bd4d9bf2 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ConnectionFactory.java
@@ -132,17 +132,16 @@ class ConnectionFactory {
      * @return a replacement for the secondary Indexers, if needed
      */
     private Slots avoidActiveNodeConflict(final RecipeTraceInfo primarySlot, final RecipeTraceInfo secondarySlot) {
-        Slots result = new Slots() {
-            {
-                primary = (IterableIndexer) resolveIndexer((ProjectionIndexerRecipe) primarySlot.getRecipe());
-                secondary = resolveIndexer((IndexerRecipe) secondarySlot.getRecipe());
-            }
-        };
-        if (activeNodeConflict(result.primary, result.secondary))
-            if (result.secondary instanceof IterableIndexer)
-                result.secondary = resolveActiveIndexer(secondarySlot);
-            else
-                result.primary = (IterableIndexer) resolveActiveIndexer(primarySlot);
+        Slots result = new Slots();
+        result.primary = (IterableIndexer) resolveIndexer((ProjectionIndexerRecipe) primarySlot.getRecipe());
+        result.secondary = resolveIndexer((IndexerRecipe) secondarySlot.getRecipe());
+        if (activeNodeConflict(result.primary, result.secondary)) {
+                        if (result.secondary instanceof IterableIndexer) {
+                                result.secondary = resolveActiveIndexer(secondarySlot);
+                        } else {
+                                result.primary = (IterableIndexer) resolveActiveIndexer(primarySlot);
+                        }
+                }
         return result;
     }
 
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java
index 64f59ff3..61030ff2 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/Network.java
@@ -3,23 +3,12 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 
 package tools.refinery.viatra.runtime.rete.network;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.concurrent.locks.Lock;
-import java.util.concurrent.locks.ReadWriteLock;
-import java.util.concurrent.locks.ReentrantReadWriteLock;
-
 import tools.refinery.viatra.runtime.matchers.tuple.Tuple;
 import tools.refinery.viatra.runtime.matchers.util.CollectionsFactory;
 import tools.refinery.viatra.runtime.matchers.util.Direction;
@@ -30,9 +19,15 @@ import tools.refinery.viatra.runtime.rete.remote.Address;
 import tools.refinery.viatra.runtime.rete.traceability.RecipeTraceInfo;
 import tools.refinery.viatra.runtime.rete.util.Options;
 
+import java.util.*;
+import java.util.Map.Entry;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReadWriteLock;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
+
 /**
  * @author Gabor Bergmann
- * 
+ *
  */
 public class Network {
     final int threads;
@@ -43,7 +38,7 @@ public class Network {
     private int nextContainer = 0;
 
     // the following fields exist only if threads > 0
-    protected Map<ReteContainer, Long> globalTerminationCriteria = null;
+    protected final Map<ReteContainer, Long> globalTerminationCriteria;
     protected Map<ReteContainer, Long> reportedClocks = null;
     protected Lock updateLock = null; // grab during normal update operations
     protected Lock structuralChangeLock = null; // grab if the network structure
@@ -104,9 +99,10 @@ public class Network {
             structuralChangeLock = rwl.writeLock();
             for (int i = 0; i < threads; ++i)
                 containers.add(new ReteContainer(this, true));
-        } else
-            containers.add(new ReteContainer(this, false));
-
+        } else {
+                        containers.add(new ReteContainer(this, false));
+                        globalTerminationCriteria = null;
+                }
         headContainer = containers.get(0);
     }
 
@@ -138,7 +134,7 @@ public class Network {
 
     /**
      * Internal message delivery method.
-     * 
+     *
      * @pre threads > 0
      */
     private void sendUpdate(Address<? extends Receiver> receiver, Direction direction, Tuple updateElement) {
@@ -151,7 +147,7 @@ public class Network {
 
     /**
      * Internal message delivery method for single-threaded operation
-     * 
+     *
      * @pre threads == 0
      */
     private void sendUpdateSingleThreaded(Address<? extends Receiver> receiver, Direction direction,
@@ -162,7 +158,7 @@ public class Network {
 
     /**
      * Internal message delivery method.
-     * 
+     *
      * @pre threads > 0
      */
     private void sendUpdates(Address<? extends Receiver> receiver, Direction direction,
@@ -180,7 +176,7 @@ public class Network {
      * Sends an update message to the receiver node, indicating a newly found or lost partial matching. The node may
      * reside in any of the containers associated with this network. To be called from a user thread during normal
      * operation, NOT during construction.
-     * 
+     *
      * @since 2.4
      */
     public void sendExternalUpdate(Address<? extends Receiver> receiver, Direction direction, Tuple updateElement) {
@@ -201,10 +197,10 @@ public class Network {
      * Sends an update message to the receiver node, indicating a newly found or lost partial matching. The node may
      * reside in any of the containers associated with this network. To be called from a user thread during
      * construction.
-     * 
+     *
      * @pre: structuralChangeLock MUST be grabbed by the sequence (but not necessarily this thread, as the sequence may
      *       span through network calls, that's why it's not enforced here )
-     * 
+     *
      * @return the value of the target container's clock at the time when the message was accepted into its message
      *         queue
      * @since 2.4
@@ -222,10 +218,10 @@ public class Network {
      * Sends multiple update messages atomically to the receiver node, indicating a newly found or lost partial
      * matching. The node may reside in any of the containers associated with this network. To be called from a user
      * thread during construction.
-     * 
+     *
      * @pre: structuralChangeLock MUST be grabbed by the sequence (but not necessarily this thread, as the sequence may
      *       span through network calls, that's why it's not enforced here )
-     * 
+     *
      * @since 2.4
      */
     public void sendConstructionUpdates(Address<? extends Receiver> receiver, Direction direction,
@@ -241,7 +237,7 @@ public class Network {
     /**
      * Establishes connection between a supplier and a receiver node, regardless which container they are in. Not to be
      * called remotely, because this method enforces the structural lock.
-     * 
+     *
      * @param supplier
      * @param receiver
      * @param synchronise
@@ -262,7 +258,7 @@ public class Network {
     /**
      * Severs connection between a supplier and a receiver node, regardless which container they are in. Not to be
      * called remotely, because this method enforces the structural lock.
-     * 
+     *
      * @param supplier
      * @param receiver
      * @param desynchronise
@@ -282,9 +278,9 @@ public class Network {
 
     /**
      * Containers use this method to report whenever they run out of messages in their queue.
-     * 
+     *
      * To be called from the thread of the reporting container.
-     * 
+     *
      * @pre threads > 0.
      * @param reportingContainer
      *            the container reporting the emptiness of its message queue.
@@ -328,7 +324,7 @@ public class Network {
     /**
      * Waits until all rete update operations are settled in all containers. Returns immediately, if no updates are
      * pending.
-     * 
+     *
      * To be called from any user thread.
      */
     public void waitForReteTermination() {
@@ -338,7 +334,7 @@ public class Network {
                     try {
                         globalTerminationCriteria.wait();
                     } catch (InterruptedException e) {
-
+                                                Thread.currentThread().interrupt();
                     }
                 }
             }
@@ -350,10 +346,10 @@ public class Network {
      * Waits to execute action until all rete update operations are settled in all containers. Runs action and returns
      * immediately, if no updates are pending. The given action is guaranteed to be run when the terminated state still
      * persists.
-     * 
+     *
      * @param action
      *            the action to be run when reaching the steady-state.
-     * 
+     *
      *            To be called from any user thread.
      */
     public void waitForReteTermination(Runnable action) {
@@ -363,7 +359,7 @@ public class Network {
                     try {
                         globalTerminationCriteria.wait();
                     } catch (InterruptedException e) {
-
+                                                Thread.currentThread().interrupt();
                     }
                 }
                 action.run();
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java
index 79e0526d..d058417f 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/ReteContainer.java
@@ -514,6 +514,7 @@ public final class ReteContainer {
                             try {
                                 externalMessageLock.wait();
                             } catch (InterruptedException e) {
+                                                                Thread.currentThread().interrupt();
                                 if (killed)
                                     return;
                             }
@@ -565,7 +566,9 @@ public final class ReteContainer {
                                         + group.getRepresentative() + " has already been processed!");
                     }
 
-                    group.deliverMessages();
+                                        if (group != null) {
+                                                group.deliverMessages();
+                                        }
 
                     lastGroup = group;
                 }
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java
index d244e644..9c2fbb9a 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/network/communication/CommunicationTracker.java
@@ -8,33 +8,15 @@
  *******************************************************************************/
 package tools.refinery.viatra.runtime.rete.network.communication;
 
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.PriorityQueue;
-import java.util.Queue;
-import java.util.Set;
-
-import tools.refinery.viatra.runtime.rete.itc.alg.incscc.IncSCCAlg;
-import tools.refinery.viatra.runtime.rete.itc.alg.misc.topsort.TopologicalSorting;
-import tools.refinery.viatra.runtime.rete.itc.graphimpl.Graph;
 import tools.refinery.viatra.runtime.matchers.tuple.TupleMask;
 import tools.refinery.viatra.runtime.rete.aggregation.IAggregatorNode;
 import tools.refinery.viatra.runtime.rete.boundary.ExternalInputEnumeratorNode;
 import tools.refinery.viatra.runtime.rete.eval.RelationEvaluatorNode;
-import tools.refinery.viatra.runtime.rete.index.DualInputNode;
-import tools.refinery.viatra.runtime.rete.index.ExistenceNode;
-import tools.refinery.viatra.runtime.rete.index.Indexer;
-import tools.refinery.viatra.runtime.rete.index.IndexerListener;
-import tools.refinery.viatra.runtime.rete.index.IterableIndexer;
-import tools.refinery.viatra.runtime.rete.index.SpecializedProjectionIndexer;
-import tools.refinery.viatra.runtime.rete.network.IGroupable;
-import tools.refinery.viatra.runtime.rete.network.NetworkStructureChangeSensitiveNode;
-import tools.refinery.viatra.runtime.rete.network.Node;
-import tools.refinery.viatra.runtime.rete.network.ProductionNode;
-import tools.refinery.viatra.runtime.rete.network.Receiver;
-import tools.refinery.viatra.runtime.rete.network.ReteContainer;
+import tools.refinery.viatra.runtime.rete.index.*;
+import tools.refinery.viatra.runtime.rete.itc.alg.incscc.IncSCCAlg;
+import tools.refinery.viatra.runtime.rete.itc.alg.misc.topsort.TopologicalSorting;
+import tools.refinery.viatra.runtime.rete.itc.graphimpl.Graph;
+import tools.refinery.viatra.runtime.rete.network.*;
 import tools.refinery.viatra.runtime.rete.network.communication.timely.TimelyIndexerListenerProxy;
 import tools.refinery.viatra.runtime.rete.network.communication.timely.TimelyMailboxProxy;
 import tools.refinery.viatra.runtime.rete.network.mailbox.FallThroughCapableMailbox;
@@ -43,6 +25,8 @@ import tools.refinery.viatra.runtime.rete.network.mailbox.timeless.BehaviorChang
 import tools.refinery.viatra.runtime.rete.single.TransitiveClosureNode;
 import tools.refinery.viatra.runtime.rete.single.TrimmerNode;
 
+import java.util.*;
+
 /**
  * An instance of this class is associated with every {@link ReteContainer}. The tracker serves two purposes: <br>
  * (1) It allows RETE nodes to register their communication dependencies on-the-fly. These dependencies can be
@@ -263,7 +247,10 @@ public abstract class CommunicationTracker {
 
     public CommunicationGroup getAndRemoveFirstGroup() {
         final CommunicationGroup group = groupQueue.poll();
-        group.isEnqueued = false;
+                if (group == null) {
+                        throw new IllegalStateException("Group queue must not be empty");
+                }
+                group.isEnqueued = false;
         return group;
     }
 
diff --git a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java
index 8b147cf6..6d0d813a 100644
--- a/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java
+++ b/subprojects/viatra-runtime-rete/src/main/java/tools/refinery/viatra/runtime/rete/util/OrderingCompareAgent.java
@@ -3,7 +3,7 @@
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v. 2.0 which is available at
  * http://www.eclipse.org/legal/epl-v20.html.
- * 
+ *
  * SPDX-License-Identifier: EPL-2.0
  *******************************************************************************/
 
@@ -13,9 +13,9 @@ import java.util.Comparator;
 
 /**
  * Comparing agent for an ordering. Terminology: the "preferred" item will register as LESS.
- * 
+ *
  * @author Gabor Bergmann
- * 
+ *
  */
 public abstract class OrderingCompareAgent<T> {
     protected T a;
@@ -25,7 +25,7 @@ public abstract class OrderingCompareAgent<T> {
      * @param a
      * @param b
      */
-    public OrderingCompareAgent(T a, T b) {
+    protected OrderingCompareAgent(T a, T b) {
         super();
         this.a = a;
         this.b = b;
@@ -77,16 +77,21 @@ public abstract class OrderingCompareAgent<T> {
     protected static <U> int preferLess(Comparable<U> c1, U c2) {
         return c1.compareTo(c2);
     }
-    
+
     protected static <U> int preferLess(U c1, U c2, Comparator<U> comp) {
         return comp.compare(c1, c2);
     }
 
     protected static <U> int preferMore(Comparable<U> c1, U c2) {
-        return -c1.compareTo(c2);
+        return reverse(c1.compareTo(c2));
     }
+
     protected static <U> int preferMore(U c1, U c2, Comparator<U> comp) {
-        return -comp.compare(c1, c2);
+        return reverse(comp.compare(c1, c2));
     }
 
+        private static int reverse(int value) {
+                return Integer.compare(0, value);
+        }
+
 }