Moving on

klab.core.api/src/main/java/org/integratedmodelling/klab/api/data/KnowledgeGraph.java

@@ -66,16 +66,14 @@ interface Operation extends Closeable {
 
         /**
          * Link the two passed assets.
-         * <p>
-         * FIXME remove scope when the other is gone
-         *
+         * <p>*
          * @param source
          * @param destination
          * @param additionalProperties any pair of properties we want overridden. Pass pairs and do it right
          *                             or you'll get an exception.
          */
         void link(RuntimeAsset source, RuntimeAsset destination,
-                  DigitalTwin.Relationship relationship, Scope scope,
+                  DigitalTwin.Relationship relationship,
                   Object... additionalProperties);
 
         //

klab.core.api/src/main/java/org/integratedmodelling/klab/api/services/resolver/ResolutionConstraint.java

@@ -112,7 +112,7 @@ private Type(Class<?> dataClass, boolean incremental) {
      */
     ResolutionConstraint merge(ResolutionConstraint constraint);
 
-    static ResolutionConstraint of(Type type, Object data) {
+    static ResolutionConstraint of(Type type, Object... data) {
         return new ResolutionConstraintImpl(type, data);
     }
 

klab.core.api/src/main/java/org/integratedmodelling/klab/api/services/resolver/objects/ResolutionConstraintImpl.java

@@ -24,7 +24,9 @@ public ResolutionConstraintImpl(Type type, Object... data) {
                 throw new KlabIllegalArgumentException("Cannot create resolution constraint: illegal data " +
                         "content");
             }
-            this.data.add(o);
+            if (o != null) {
+                this.data.add(o);
+            }
         }
     }
 

klab.core.common/src/main/java/org/integratedmodelling/common/data/jackson/JacksonConfiguration.java

@@ -32,6 +32,9 @@
 import org.integratedmodelling.klab.api.lang.kactors.KActorsBehavior;
 import org.integratedmodelling.klab.api.lang.kdl.KdlDataflow;
 import org.integratedmodelling.klab.api.lang.kim.*;
+import org.integratedmodelling.klab.api.provenance.Activity;
+import org.integratedmodelling.klab.api.provenance.Agent;
+import org.integratedmodelling.klab.api.provenance.Provenance;
 import org.integratedmodelling.klab.api.services.resolver.ResolutionConstraint;
 import org.integratedmodelling.klab.api.services.runtime.Actuator;
 import org.integratedmodelling.klab.api.services.runtime.Dataflow;
@@ -252,7 +255,8 @@ public static void configureObjectMapperForKlabTypes(ObjectMapper mapper) {
                                       Currency.class, Message.class, Worldview.class, Workspace.class,
                                       Concept.class, Observable.class, Resource.class, KimOntology.class,
                                       KimNamespace.class, KimObservationStrategyDocument.class,
-                                      KdlDataflow.class, KActorsBehavior.class, KimModel.class,
+                                      KActorsBehavior.class, KimModel.class, Activity.class,
+                                      Agent.class, Provenance.Node.class, Provenance.class,
                                       KimSymbolDefinition.class, Contextualizable.class, Identifier.class,
                                       KimConcept.class, KimObservable.class, Quantity.class,
                                       Model.class, ServiceCall.class, Observation.class,

klab.services.runtime/src/main/java/org/integratedmodelling/klab/services/runtime/RuntimeService.java

@@ -11,6 +11,7 @@
 import org.integratedmodelling.klab.api.data.RuntimeAsset;
 import org.integratedmodelling.klab.api.digitaltwin.DigitalTwin;
 import org.integratedmodelling.klab.api.exceptions.KlabIllegalArgumentException;
+import org.integratedmodelling.klab.api.exceptions.KlabIllegalStateException;
 import org.integratedmodelling.klab.api.exceptions.KlabInternalErrorException;
 import org.integratedmodelling.klab.api.knowledge.observation.Observation;
 import org.integratedmodelling.klab.api.knowledge.observation.impl.ObservationImpl;
@@ -271,20 +272,37 @@ public String registerContext(ContextScope contextScope) {
 
     @Override
     public long submit(Observation observation, ContextScope scope) {
+
+        if (observation.isResolved()) {
+            // TODO there may be a context for this at some point.
+            throw new KlabIllegalStateException("A resolved observation cannot be submitted to the " +
+                    "knowledge graph for now");
+        }
+
         if (scope instanceof ServiceContextScope serviceContextScope) {
             var digitalTwin = getDigitalTwin(scope);
             var parentActivity = getInstantiationActivity(observation, scope);
             var agent = getAgent(scope);
             var instantiation = digitalTwin.knowledgeGraph().operation(agent, parentActivity,
                     Activity.Type.INSTANTIATION, observation);
+
             try (instantiation) {
                 var ret = instantiation.store(observation);
+                if (scope.getContextObservation() != null) {
+                    instantiation.link(scope.getContextObservation(), observation,
+                            DigitalTwin.Relationship.HAS_CHILD);
+                }
+                if (scope.getObserver() != null) {
+                    instantiation.link(observation, scope.getObserver(),
+                            DigitalTwin.Relationship.HAS_OBSERVER);
+                }
                 instantiation.success(scope, observation);
                 return ret;
             } catch (Throwable t) {
                 instantiation.fail(scope, observation);
             }
         }
+
         return Observation.UNASSIGNED_ID;
     }
 
@@ -326,8 +344,7 @@ public Future<Observation> resolve(long id, ContextScope scope) {
                 This will commit or rollback at close()
                  */
                 var resolution = digitalTwin.knowledgeGraph().operation(digitalTwin.knowledgeGraph().klab()
-                        , parentActivity,
-                        Activity.Type.RESOLUTION);
+                        , parentActivity, Activity.Type.RESOLUTION);
 
                 try (resolution) {
                     result = observation;
@@ -363,13 +380,12 @@ this will commit all resources at close()
                      */
                     var contextualization =
                             digitalTwin.knowledgeGraph().operation(digitalTwin.knowledgeGraph().klab(),
-                                    resolutionActivity,
-                            Activity.Type.CONTEXTUALIZATION);
+                                    resolutionActivity, Activity.Type.CONTEXTUALIZATION);
 
                     try (contextualization) {
                         // TODO contextualization gets its own activities to use in operations
                         //  (dependent on resolution) linked to actuators by runDataflow
-                        result = runDataflow(dataflow, scope);
+                        result = runDataflow(dataflow, scope, contextualization);
                         ret.complete(result);
                         contextualization.success(scope, dataflow, result);
                     } catch (Throwable t) {
@@ -388,13 +404,12 @@ this will commit all resources at close()
 
     @Override
     public Observation runDataflow(Dataflow<Observation> dataflow, ContextScope contextScope) {
-        var activity = new ActivityImpl();
-        // TODO fill in the activity for an external dataflow run
-        return runDataflow(dataflow, contextScope, activity);
+        // TODO fill in the operation representing an external dataflow run
+        return runDataflow(dataflow, contextScope, null);
     }
 
     public Observation runDataflow(Dataflow<Observation> dataflow, ContextScope contextScope,
-                                   Activity activity) {
+                                   KnowledgeGraph.Operation contextualization) {
 
         var digitalTwin = getDigitalTwin(contextScope);
 

klab.services.runtime/src/main/java/org/integratedmodelling/klab/services/runtime/neo4j/AbstractKnowledgeGraph.java

@@ -46,11 +46,12 @@ public RuntimeAsset load(Long key) throws Exception {
      */
     public class OperationImpl implements Operation {
 
-        ActivityImpl activity;
-        AgentImpl agent;
-        Transaction transaction;
-        Scope.Status outcome;
-        Throwable exception;
+        private ActivityImpl activity;
+        private AgentImpl agent;
+        // FIXME ACH no this must be in the Neo4j implementation
+        private Transaction transaction;
+        private Scope.Status outcome;
+        private Throwable exception;
 
         /**
          * What should be passed: an agent that will own the activity; the current context scope for graph
@@ -71,7 +72,7 @@ public OperationImpl(Object... arguments) {
 
             // select arguments and put them where they belong
 
-            // validate arguments and complain loudly if anything is missing
+            // validate arguments and complain loudly if anything is missing. Must have agent and activity
 
             // create and commit the activity record as a node, possibly linked to a parent
             // activity.
@@ -81,41 +82,55 @@ public OperationImpl(Object... arguments) {
 
         @Override
         public Agent getAgent() {
-            return null;
+            return this.agent;
         }
 
         @Override
         public Activity getActivity() {
-            return null;
+            return this.activity;
         }
 
         @Override
         public long store(RuntimeAsset asset, Object... additionalProperties) {
-            return 0;
+            // FIXME NO use transactional version!
+            return AbstractKnowledgeGraph.this.store(asset, scope, additionalProperties);
         }
 
         @Override
         public void link(RuntimeAsset source, RuntimeAsset destination,
-                         DigitalTwin.Relationship relationship, Scope scope, Object... additionalProperties) {
-
+                         DigitalTwin.Relationship relationship, Object... additionalProperties) {
+            // FIXME NO use transactional version!
+            AbstractKnowledgeGraph.this.link(source, destination, relationship, scope,
+                    additionalProperties);
         }
 
         @Override
         public Operation success(ContextScope scope, Object... assets) {
-            // commit
-            return null;
+            this.outcome = Scope.Status.FINISHED;
+            // updates as needed (activity end, observation resolved if type == resolution, context timestamp
+            return this;
         }
 
         @Override
         public Operation fail(ContextScope scope, Object... assets) {
-            // rollback
+            // rollback; update activity end and context timestamp only, if we have an error or throwable
+            // update activity
+            this.outcome = Scope.Status.ABORTED;
             return null;
         }
 
         @Override
         public void close() throws IOException {
             // TODO commit or rollback based on status after success() or fail(). If none has been
             // called, status is null and this is an internal error, logged with the activity
+            if (outcome == null) {
+                // Log an internal failure (no success or failure, should not happen)
+                transaction.rollback();
+            } else if (outcome == Scope.Status.FINISHED) {
+                transaction.commit();
+            } else if (outcome == Scope.Status.ABORTED) {
+                transaction.rollback();
+            }
         }
     }