10 files changed, 340 insertions, 0 deletions

diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/DanglingEdges.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/DanglingEdges.java
new file mode 100644
index 00000000..ac9d125b
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/DanglingEdges.java
@@ -0,0 +1,12 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+
+public enum DanglingEdges {
+        IGNORE,
+        DELETE,
+        FAIL
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationAdapter.java
new file mode 100644
index 00000000..58b60499
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationAdapter.java
@@ -0,0 +1,24 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.dse.modification.internal.ModificationBuilderImpl;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.Tuple1;
+
+public interface ModificationAdapter extends ModelAdapter {
+
+        int getModelSize();
+
+        Tuple1 createObject();
+
+        boolean deleteObject(Tuple tuple, DanglingEdges danglingEdges);
+
+        static ModificationBuilder builder() {
+                return new ModificationBuilderImpl();
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationBuilder.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationBuilder.java
new file mode 100644
index 00000000..48c22bdf
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationBuilder.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+
+import tools.refinery.store.adapter.ModelAdapterBuilder;
+
+public interface ModificationBuilder extends ModelAdapterBuilder {
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationStoreAdapter.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationStoreAdapter.java
new file mode 100644
index 00000000..144c4d05
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/ModificationStoreAdapter.java
@@ -0,0 +1,11 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification;
+
+import tools.refinery.store.adapter.ModelStoreAdapter;
+
+public interface ModificationStoreAdapter extends ModelStoreAdapter {
+}
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
new file mode 100644
index 00000000..5b86a5e1
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/CreateActionLiteral.java
@@ -0,0 +1,43 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.actions;
+
+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 java.util.List;
+
+public class CreateActionLiteral extends AbstractActionLiteral {
+        private final NodeVariable variable;
+
+        public CreateActionLiteral(NodeVariable variable) {
+
+                this.variable = variable;
+        }
+
+        public NodeVariable getVariable() {
+                return variable;
+        }
+
+        @Override
+        public List<NodeVariable> getInputVariables() {
+                return List.of();
+        }
+
+        @Override
+        public List<NodeVariable> getOutputVariables() {
+                return List.of(variable);
+        }
+
+        @Override
+        public BoundActionLiteral bindToModel(Model model) {
+                var adapter = model.getAdapter(ModificationAdapter.class);
+                return ignoredTuple -> adapter.createObject();
+        }
+}
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
new file mode 100644
index 00000000..18ad2b9d
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/DeleteActionLiteral.java
@@ -0,0 +1,51 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.actions;
+
+import tools.refinery.store.dse.modification.DanglingEdges;
+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.store.tuple.Tuple;
+
+import java.util.List;
+
+public class DeleteActionLiteral extends AbstractActionLiteral {
+        private final NodeVariable variable;
+        private final DanglingEdges danglingEdges;
+
+        public DeleteActionLiteral(NodeVariable variable, DanglingEdges danglingEdges) {
+
+                this.variable = variable;
+                this.danglingEdges = danglingEdges;
+        }
+
+        public NodeVariable getVariable() {
+                return variable;
+        }
+
+        public DanglingEdges getDanglingEdges() {
+                return danglingEdges;
+        }
+
+        @Override
+        public List<NodeVariable> getInputVariables() {
+                return List.of(variable);
+        }
+
+        @Override
+        public List<NodeVariable> getOutputVariables() {
+                return List.of();
+        }
+
+        @Override
+        public BoundActionLiteral bindToModel(Model model) {
+                var adapter = model.getAdapter(ModificationAdapter.class);
+                return tuple -> adapter.deleteObject(tuple, danglingEdges) ? Tuple.of() : null;
+        }
+}
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
new file mode 100644
index 00000000..31f50ac7
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/actions/ModificationActionLiterals.java
@@ -0,0 +1,23 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.actions;
+
+import tools.refinery.store.dse.modification.DanglingEdges;
+import tools.refinery.store.query.term.NodeVariable;
+
+public class ModificationActionLiterals {
+        private ModificationActionLiterals() {
+                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
+        }
+
+        public static CreateActionLiteral create(NodeVariable variable) {
+                return new CreateActionLiteral(variable);
+        }
+
+        public static DeleteActionLiteral delete(NodeVariable variable, DanglingEdges danglingEdges) {
+                return new DeleteActionLiteral(variable, danglingEdges);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationAdapterImpl.java
new file mode 100644
index 00000000..4e77c462
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationAdapterImpl.java
@@ -0,0 +1,107 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.internal;
+
+import tools.refinery.store.adapter.ModelStoreAdapter;
+import tools.refinery.store.dse.modification.DanglingEdges;
+import tools.refinery.store.dse.modification.ModificationAdapter;
+import tools.refinery.store.model.Interpretation;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.representation.Symbol;
+import tools.refinery.store.tuple.Tuple;
+import tools.refinery.store.tuple.Tuple1;
+
+import java.util.HashSet;
+
+public class ModificationAdapterImpl implements ModificationAdapter {
+        static final Symbol<Integer> NEXT_ID = Symbol.of("NEXT_ID", 0, Integer.class, 0);
+
+        final ModelStoreAdapter storeAdapter;
+        final Model model;
+        Interpretation<Integer> nodeCountInterpretation;
+
+        ModificationAdapterImpl(ModelStoreAdapter storeAdapter, Model model) {
+                this.storeAdapter = storeAdapter;
+                this.model = model;
+                this.nodeCountInterpretation = model.getInterpretation(NEXT_ID);
+        }
+
+        @Override
+        public Model getModel() {
+                return model;
+        }
+
+        @Override
+        public ModelStoreAdapter getStoreAdapter() {
+                return storeAdapter;
+        }
+
+        @Override
+        public int getModelSize() {
+                return nodeCountInterpretation.get(Tuple.of());
+        }
+
+        @Override
+        public Tuple1 createObject() {
+                var newNodeId = getModelSize();
+                nodeCountInterpretation.put(Tuple.of(), newNodeId + 1);
+                return Tuple.of(newNodeId);
+        }
+
+        @Override
+        public boolean deleteObject(Tuple tuple, DanglingEdges danglingEdges) {
+                if (tuple.getSize() != 1) {
+                        throw new IllegalArgumentException("Tuple size must be 1");
+                }
+                int objectId = tuple.get(0);
+                if (danglingEdges == DanglingEdges.DELETE) {
+                        deleteDanglingEdges(objectId);
+                } else if (danglingEdges == DanglingEdges.FAIL && hasDanglingEdges(objectId)) {
+                        return false;
+
+                }
+                int modelSize = getModelSize();
+                if (objectId == modelSize - 1) {
+                        nodeCountInterpretation.put(Tuple.of(), modelSize - 1);
+                }
+                return true;
+        }
+
+        private void deleteDanglingEdges(int objectId) {
+                for (var symbol : model.getStore().getSymbols()) {
+                        deleteDanglingEdges(objectId, (Symbol<?>) symbol);
+                }
+        }
+
+        private <T> void deleteDanglingEdges(int objectId, Symbol<T> symbol) {
+                var interpretation = model.getInterpretation(symbol);
+                var toDelete = new HashSet<Tuple>();
+                int arity = symbol.arity();
+                for (int i = 0; i < arity; i++) {
+                        var cursor = interpretation.getAdjacent(i, objectId);
+                        while (cursor.move()) {
+                                toDelete.add(cursor.getKey());
+                        }
+                }
+                var defaultValue = symbol.defaultValue();
+                for (var tuple : toDelete) {
+                        interpretation.put(tuple, defaultValue);
+                }
+        }
+
+        private boolean hasDanglingEdges(int objectId) {
+                for (var symbol : model.getStore().getSymbols()) {
+                        var interpretation = model.getInterpretation(symbol);
+                        int arity = symbol.arity();
+                        for (int i = 0; i < arity; i++) {
+                                if (interpretation.getAdjacentSize(i, objectId) > 0) {
+                                        return true;
+                                }
+                        }
+                }
+                return false;
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationBuilderImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationBuilderImpl.java
new file mode 100644
index 00000000..c4d38d22
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationBuilderImpl.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.internal;
+
+import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
+import tools.refinery.store.dse.modification.ModificationBuilder;
+import tools.refinery.store.dse.modification.ModificationStoreAdapter;
+import tools.refinery.store.model.ModelStore;
+import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.statecoding.StateCoderBuilder;
+
+public class ModificationBuilderImpl extends AbstractModelAdapterBuilder<ModificationStoreAdapter> implements ModificationBuilder {
+
+        @Override
+        protected void doConfigure(ModelStoreBuilder storeBuilder) {
+                storeBuilder.symbols(ModificationAdapterImpl.NEXT_ID);
+                storeBuilder.tryGetAdapter(StateCoderBuilder.class).ifPresent(
+                                coderBuilder -> coderBuilder.exclude(ModificationAdapterImpl.NEXT_ID));
+                super.doConfigure(storeBuilder);
+        }
+
+        @Override
+        protected ModificationStoreAdapter doBuild(ModelStore store) {
+                return new ModificationStoreAdapterImpl(store);
+        }
+}
diff --git a/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationStoreAdapterImpl.java b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationStoreAdapterImpl.java
new file mode 100644
index 00000000..62e4227b
--- /dev/null
+++ b/subprojects/store-dse/src/main/java/tools/refinery/store/dse/modification/internal/ModificationStoreAdapterImpl.java
@@ -0,0 +1,29 @@
+/*
+ * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.store.dse.modification.internal;
+
+import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.dse.modification.ModificationStoreAdapter;
+import tools.refinery.store.model.Model;
+import tools.refinery.store.model.ModelStore;
+
+public class ModificationStoreAdapterImpl implements ModificationStoreAdapter {
+        ModelStore store;
+
+        ModificationStoreAdapterImpl(ModelStore store) {
+                this.store = store;
+        }
+
+        @Override
+        public ModelStore getStore() {
+                return store;
+        }
+
+        @Override
+        public ModelAdapter createModelAdapter(Model model) {
+                return new ModificationAdapterImpl(this, model);
+        }
+}