feat: generator facade timeout and non-existent objects

Quality of life improvements for the semantics and generator facade APIs.

3 files changed, 23 insertions, 4 deletions

diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java
index 386ae1d8..b83d162e 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningAdapterImpl.java
@@ -204,6 +204,8 @@ class ReasoningAdapterImpl implements ReasoningAdapter {
                 if (nodeToDelete == currentModelSize - 1) {
                         nodeCountInterpretation.put(Tuple.of(), nodeToDelete);
                 }
+                // We mustn't reuse the ID of {@code nodeToDelete} in any circumstance, because clients may depend on stable
+                // node IDs for nodes in the initial partial model.
                 return true;
         }
 
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/CleanupPropagator.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/CleanupPropagator.java
index f14b4783..6feccae3 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/CleanupPropagator.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/CleanupPropagator.java
@@ -11,6 +11,7 @@ import tools.refinery.logic.term.uppercardinality.UpperCardinalities;
 import tools.refinery.logic.term.uppercardinality.UpperCardinality;
 import tools.refinery.logic.term.uppercardinality.UpperCardinalityTerms;
 import tools.refinery.store.dse.propagation.BoundPropagator;
+import tools.refinery.store.dse.propagation.PropagationRejectedResult;
 import tools.refinery.store.dse.propagation.PropagationResult;
 import tools.refinery.store.dse.propagation.Propagator;
 import tools.refinery.store.model.Model;
@@ -48,7 +49,7 @@ public class CleanupPropagator implements Propagator {
                 return new BoundCleanupPropagator(model);
         }
 
-        private static class BoundCleanupPropagator implements BoundPropagator {
+        private class BoundCleanupPropagator implements BoundPropagator {
                 private final Model model;
                 private final ModelQueryAdapter queryEngine;
                 private final ResultSet<Boolean> resultSet;
@@ -70,7 +71,11 @@ public class CleanupPropagator implements Propagator {
                         var cursor = resultSet.getAll();
                         while (cursor.move()) {
                                 propagated = true;
-                                reasoningAdapter.cleanup(cursor.getKey().get(0));
+                                var nodeToDelete = cursor.getKey().get(0);
+                                if (!reasoningAdapter.cleanup(nodeToDelete)) {
+                                        return new PropagationRejectedResult(CleanupPropagator.this,
+                            "Failed to remove node: " + nodeToDelete, true);
+                                }
                         }
                         return propagated ? PropagationResult.PROPAGATED : PropagationResult.UNCHANGED;
                 }
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectTranslator.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectTranslator.java
index 05d96689..7b3be76d 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectTranslator.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectTranslator.java
@@ -41,6 +41,16 @@ public class MultiObjectTranslator implements ModelStoreConfiguration {
         public static final PartialFunction<CardinalityInterval, Integer> COUNT_SYMBOL = new PartialFunction<>("COUNT", 1,
                         CardinalityDomain.INSTANCE);
 
+        private final boolean keepNonExistingObjects;
+
+        public MultiObjectTranslator(boolean keepNonExistingObjects) {
+                this.keepNonExistingObjects = keepNonExistingObjects;
+        }
+
+        public MultiObjectTranslator() {
+                this(true);
+        }
+
         @Override
         public void apply(ModelStoreBuilder storeBuilder) {
                 storeBuilder.symbol(COUNT_STORAGE);
@@ -90,7 +100,9 @@ public class MultiObjectTranslator implements ModelStoreConfiguration {
                 reasoningBuilder.initializer(new MultiObjectInitializer(COUNT_STORAGE));
                 reasoningBuilder.storageRefiner(COUNT_STORAGE, MultiObjectStorageRefiner::new);
 
-                storeBuilder.tryGetAdapter(PropagationBuilder.class)
-                                .ifPresent(propagationBuilder -> propagationBuilder.propagator(new CleanupPropagator()));
+                if (!keepNonExistingObjects) {
+                        storeBuilder.tryGetAdapter(PropagationBuilder.class)
+                                        .ifPresent(propagationBuilder -> propagationBuilder.propagator(new CleanupPropagator()));
+                }
         }
 }