refactor: simplify ModelAdapter

* Remove the reflection-based machinery around adapter types.
* Adapter builders, store adapters, and model adapters are now only associated
  with each other based on static and runtime types.
* Simplifies writing new adapters.
* Hierarchical syntax for adding adapter builders to the store builder.

9 files changed, 19 insertions, 58 deletions

diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/Reasoning.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/Reasoning.java
deleted file mode 100644
index 3d3df2b2..00000000
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/Reasoning.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.reasoning;
-
-import tools.refinery.store.reasoning.internal.ReasoningBuilderImpl;
-import tools.refinery.store.adapter.ModelAdapterBuilderFactory;
-import tools.refinery.store.model.ModelStoreBuilder;
-import tools.refinery.store.reasoning.representation.PartialRelation;
-
-public final class Reasoning extends ModelAdapterBuilderFactory<ReasoningAdapter,
-                ReasoningStoreAdapter, ReasoningBuilder> {
-        public static final Reasoning ADAPTER = new Reasoning();
-
-        public static final PartialRelation EXISTS = new PartialRelation("exists", 1);
-
-        public static final PartialRelation EQUALS = new PartialRelation("equals", 1);
-
-        private Reasoning() {
-                super(ReasoningAdapter.class, ReasoningStoreAdapter.class, ReasoningBuilder.class);
-        }
-
-        @Override
-        public ReasoningBuilder createBuilder(ModelStoreBuilder storeBuilder) {
-                return new ReasoningBuilderImpl(storeBuilder);
-        }
-}
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java
index 8dedddf7..8f319242 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningAdapter.java
@@ -6,12 +6,15 @@
 package tools.refinery.store.reasoning;
 
 import tools.refinery.store.adapter.ModelAdapter;
+import tools.refinery.store.query.ResultSet;
+import tools.refinery.store.query.dnf.Dnf;
 import tools.refinery.store.reasoning.representation.AnyPartialSymbol;
+import tools.refinery.store.reasoning.representation.PartialRelation;
 import tools.refinery.store.reasoning.representation.PartialSymbol;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.ResultSet;
 
 public interface ReasoningAdapter extends ModelAdapter {
+        PartialRelation EXISTS = new PartialRelation("exists", 1);
+
         @Override
         ReasoningStoreAdapter getStoreAdapter();
 
@@ -23,5 +26,5 @@ public interface ReasoningAdapter extends ModelAdapter {
 
         <A, C> PartialInterpretation<A, C> getPartialInterpretation(PartialSymbol<A, C> partialSymbol);
 
-        ResultSet getLiftedResultSet(Dnf query);
+        ResultSet<Boolean> getLiftedResultSet(Dnf query);
 }
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java
index df7b6e4d..d3a337e8 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/ReasoningBuilder.java
@@ -29,5 +29,5 @@ public interface ReasoningBuilder extends ModelAdapterBuilder {
         Dnf lift(Modality modality, Dnf query);
 
         @Override
-        ReasoningStoreAdapter createStoreAdapter(ModelStore store);
+        ReasoningStoreAdapter build(ModelStore store);
 }
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 96514d36..33b6f3c6 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
@@ -37,7 +37,7 @@ public class ReasoningAdapterImpl implements ReasoningAdapter {
         }
 
         @Override
-        public ResultSet getLiftedResultSet(Dnf query) {
+        public ResultSet<Boolean> getLiftedResultSet(Dnf query) {
                 return null;
         }
 }
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java
index 49f7c7d3..aa71496c 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/internal/ReasoningBuilderImpl.java
@@ -7,16 +7,12 @@ package tools.refinery.store.reasoning.internal;
 
 import tools.refinery.store.adapter.AbstractModelAdapterBuilder;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.model.ModelStoreBuilder;
+import tools.refinery.store.query.dnf.Dnf;
 import tools.refinery.store.reasoning.ReasoningBuilder;
 import tools.refinery.store.reasoning.literal.Modality;
-import tools.refinery.store.query.dnf.Dnf;
-
-public class ReasoningBuilderImpl extends AbstractModelAdapterBuilder implements ReasoningBuilder {
-        public ReasoningBuilderImpl(ModelStoreBuilder storeBuilder) {
-                super(storeBuilder);
-        }
 
+public class ReasoningBuilderImpl extends AbstractModelAdapterBuilder<ReasoningStoreAdapterImpl>
+                implements ReasoningBuilder {
         @Override
         public ReasoningBuilder liftedQuery(Dnf liftedQuery) {
                 return null;
@@ -24,11 +20,12 @@ public class ReasoningBuilderImpl extends AbstractModelAdapterBuilder implements
 
         @Override
         public Dnf lift(Modality modality, Dnf query) {
+                checkNotConfigured();
                 return null;
         }
 
         @Override
-        public ReasoningStoreAdapterImpl createStoreAdapter(ModelStore store) {
+        public ReasoningStoreAdapterImpl doBuild(ModelStore store) {
                 return null;
         }
 }
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java
index 157f06e8..594005f1 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/lifting/DnfLifter.java
@@ -14,7 +14,7 @@ import tools.refinery.store.query.literal.CallPolarity;
 import tools.refinery.store.query.literal.Literal;
 import tools.refinery.store.query.term.DataVariable;
 import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.reasoning.Reasoning;
+import tools.refinery.store.reasoning.ReasoningAdapter;
 import tools.refinery.store.reasoning.literal.ModalConstraint;
 import tools.refinery.store.reasoning.literal.Modality;
 import tools.refinery.store.reasoning.literal.PartialLiterals;
@@ -74,8 +74,8 @@ public class DnfLifter {
                 }
                 for (var quantifiedVariable : quantifiedVariables) {
                         // Quantify over data variables that are not already quantified with the expected modality.
-                        liftedLiterals.add(new CallLiteral(CallPolarity.POSITIVE, new ModalConstraint(modality, Reasoning.EXISTS),
-                                        List.of(quantifiedVariable)));
+                        liftedLiterals.add(new CallLiteral(CallPolarity.POSITIVE,
+                                        new ModalConstraint(modality, ReasoningAdapter.EXISTS), List.of(quantifiedVariable)));
                 }
                 builder.clause(liftedLiterals);
                 return changed || !quantifiedVariables.isEmpty();
@@ -87,7 +87,7 @@ public class DnfLifter {
                                 callLiteral.getPolarity() == CallPolarity.POSITIVE &&
                                 callLiteral.getTarget() instanceof ModalConstraint modalConstraint &&
                                 modalConstraint.modality() == modality &&
-                                modalConstraint.constraint().equals(Reasoning.EXISTS)) {
+                                modalConstraint.constraint().equals(ReasoningAdapter.EXISTS)) {
                         return callLiteral.getArguments().get(0);
                 }
                 return null;
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/rule/RelationRefinementAction.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/rule/RelationRefinementAction.java
index e4c702ea..0beee248 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/rule/RelationRefinementAction.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/rule/RelationRefinementAction.java
@@ -5,7 +5,7 @@
  */
 package tools.refinery.store.reasoning.rule;
 
-import tools.refinery.store.reasoning.Reasoning;
+import tools.refinery.store.reasoning.ReasoningAdapter;
 import tools.refinery.store.reasoning.representation.PartialRelation;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.query.term.Variable;
@@ -28,7 +28,7 @@ public record RelationRefinementAction(PartialRelation target, List<Variable> ar
 
         @Override
         public RuleActionExecutor createExecutor(int[] argumentIndices, Model model) {
-                var targetInterpretation = model.getAdapter(Reasoning.ADAPTER).getPartialInterpretation(target);
+                var targetInterpretation = model.getAdapter(ReasoningAdapter.class).getPartialInterpretation(target);
                 return activationTuple -> {
                         int arity = argumentIndices.length;
                         var arguments = new int[arity];
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java
index 7f01122b..6e44a7d7 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/TranslationUnit.java
@@ -6,7 +6,6 @@
 package tools.refinery.store.reasoning.translator;
 
 import tools.refinery.store.model.Model;
-import tools.refinery.store.model.ModelStoreBuilder;
 import tools.refinery.store.reasoning.ReasoningBuilder;
 
 import java.util.Collection;
@@ -23,10 +22,6 @@ public abstract class TranslationUnit {
                 configureReasoningBuilder();
         }
 
-        protected ModelStoreBuilder getModelStoreBuilder() {
-                return reasoningBuilder.getStoreBuilder();
-        }
-
         protected void configureReasoningBuilder() {
                 // Nothing to configure by default.
         }
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java
index d41e11c6..405e58ac 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/base/BaseDecisionTranslationUnit.java
@@ -37,11 +37,6 @@ public class BaseDecisionTranslationUnit extends TranslationUnit {
         }
 
         @Override
-        protected void configureReasoningBuilder() {
-                getModelStoreBuilder().symbol(symbol);
-        }
-
-        @Override
         public Collection<TranslatedRelation> getTranslatedRelations() {
                 return List.of(new TranslatedBaseDecision(getReasoningBuilder(), partialRelation, symbol));
         }