[1411] Add standard libraries migration participants

CHANGELOG.adoc

@@ -24,6 +24,7 @@
 
 - https://github.com/eclipse-syson/syson/issues/893[#893] [explorer] Fix _Expand All_ tool in SysON _Explorer_ view
 - https://github.com/eclipse-syson/syson/issues/1398[#1398] [explorer] Fix an issue where a d'n'd of an `Element` in a diagram exposed the `Element` twice in the `ViewUsage` associated to the diagram.
+- https://github.com/eclipse-syson/syson/issues/1411[#1411] [syson] Fix an issue where model and diagrams referencing standard libraries elements might not correctly loaded.
 
 === Improvements
 

backend/application/syson-application-configuration/src/main/java/org/eclipse/syson/application/migration/StandardLibrariesElementsDiagramMigrationParticipant.java

@@ -0,0 +1,78 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Obeo.
+ * This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v2.0
+ * which accompanies this distribution, and is available at
+ * https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *     Obeo - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.syson.application.migration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.databind.node.TextNode;
+
+import java.util.Objects;
+
+import org.eclipse.sirius.components.collaborative.representations.migration.IRepresentationMigrationParticipant;
+import org.eclipse.sirius.components.core.api.IEditingContext;
+import org.eclipse.sirius.components.core.api.IObjectSearchService;
+import org.eclipse.syson.sysml.Element;
+import org.eclipse.syson.sysml.util.ElementUtil;
+import org.springframework.stereotype.Service;
+
+/**
+ * Diagram migration participant used to migrate SysON diagrams with diagram elements having "targetObjectId" pointing
+ * to standard libraries Elements previous to 2025.8.0.
+ *
+ * Let's say we have a Start node pointing to the Actions::Action::start Element from the standard library. This node
+ * had for "targetObjectId" the "id" of the object instead of its "elementId". But the "id" property changes each time
+ * the standard libraries are updated. So the "targetObjectId" reference was pointing to nothing after the update. With
+ * this migration participant, the "targetObjectId" now all point to the "elementId" property which is stable
+ * before/after standard libraries updates.
+ *
+ * This migration participant has been added at the same time than the update of SysONIdentityService which allows to
+ * get the "elementId" instead of the "id" when it is a library Element.
+ *
+ * @author arichard
+ */
+@Service
+public class StandardLibrariesElementsDiagramMigrationParticipant implements IRepresentationMigrationParticipant {
+
+    private static final String PARTICIPANT_VERSION = "2025.8.0-202506301700";
+
+    private final IObjectSearchService objectSearchService;
+
+    public StandardLibrariesElementsDiagramMigrationParticipant(IObjectSearchService objectSearchService) {
+        this.objectSearchService = Objects.requireNonNull(objectSearchService);
+    }
+
+    @Override
+    public String getVersion() {
+        return PARTICIPANT_VERSION;
+    }
+
+    @Override
+    public String getKind() {
+        return "siriusComponents://representation?type=Diagram";
+    }
+
+    @Override
+    public void replaceJsonNode(IEditingContext editingContext, ObjectNode root, String currentAttribute, JsonNode currentValue) {
+        if (currentAttribute.equals("targetObjectId") && currentValue instanceof TextNode textNode) {
+            var optElement = this.objectSearchService.getObject(editingContext, textNode.asText())
+                    .filter(Element.class::isInstance)
+                    .map(Element.class::cast);
+            if (optElement.isPresent()) {
+                var element = optElement.get();
+                if (ElementUtil.isStandardLibraryResource(element.eResource())) {
+                    root.put("targetObjectId", element.getElementId());
+                }
+            }
+        }
+    }
+}

backend/application/syson-application-configuration/src/main/java/org/eclipse/syson/application/migration/StandardLibrariesElementsReferencesMigrationParticipant.java

@@ -0,0 +1,74 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Obeo.
+ * This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v2.0
+ * which accompanies this distribution, and is available at
+ * https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *     Obeo - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.syson.application.migration;
+
+import org.eclipse.emf.common.util.URI;
+import org.eclipse.emf.ecore.EObject;
+import org.eclipse.emf.ecore.EReference;
+import org.eclipse.emf.ecore.resource.ResourceSet;
+import org.eclipse.sirius.components.emf.migration.api.IMigrationParticipant;
+import org.eclipse.sirius.emfjson.resource.JsonResource;
+import org.eclipse.syson.sysml.Element;
+import org.eclipse.syson.sysml.util.ElementUtil;
+import org.springframework.stereotype.Service;
+
+/**
+ * Diagram migration participant used to migrate SysON diagrams with diagram elements having "targetObjectId" pointing
+ * to standard libraries Elements previous to 2025.8.0.
+ *
+ * Let's say we have a FeatureTyping pointing to the SclaraValues::String Element from the standard library. This
+ * element had for "targetObjectId" the "id" of the object instead of its "elementId". But the "id" property changes
+ * each time the standard libraries are updated. So the "targetObjectId" reference was pointing to nothing after the
+ * update. With this migration participant, the "targetObjectId" now all point to the "elementId" property which is
+ * stable before/after standard libraries updates.
+ *
+ * This migration participant has been added at the same time than the update of SysONIdentityService which allows to
+ * get the "elementId" instead of the "id" when it is a library Element.
+ *
+ * @author arichard
+ */
+@Service
+public class StandardLibrariesElementsReferencesMigrationParticipant implements IMigrationParticipant {
+
+    private static final String PARTICIPANT_VERSION = "2025.8.0-202506301600";
+
+    @Override
+    public String getVersion() {
+        return PARTICIPANT_VERSION;
+    }
+
+    @Override
+    public String getEObjectUri(JsonResource resource, EObject eObject, EReference eReference, String uri) {
+        if (!eReference.isContainment() && (uri.contains(ElementUtil.SYSML_LIBRARY_SCHEME) || uri.contains(ElementUtil.KERML_LIBRARY_SCHEME))) {
+            ResourceSet resourceSet = resource.getResourceSet();
+            String uriWithoutPrefixedType = uri;
+            if (uri.startsWith("sysml:")) {
+                if (uri.contains(ElementUtil.SYSML_LIBRARY_SCHEME)) {
+                    int indexOf = uri.indexOf(ElementUtil.SYSML_LIBRARY_SCHEME);
+                    uriWithoutPrefixedType = uri.substring(indexOf);
+                } else if (uri.contains(ElementUtil.KERML_LIBRARY_SCHEME)) {
+                    int indexOf = uri.indexOf(ElementUtil.KERML_LIBRARY_SCHEME);
+                    uriWithoutPrefixedType = uri.substring(indexOf);
+                }
+            }
+            URI uriAsURI = URI.createURI(uriWithoutPrefixedType);
+            EObject referencedEObject = resourceSet.getEObject(uriAsURI, false);
+            if (referencedEObject instanceof Element element) {
+                int uriFragmentIndex = uri.indexOf('#');
+                var prefix = uri.substring(0, uriFragmentIndex + 1);
+                return prefix + element.getElementId();
+            }
+        }
+        return uri;
+    }
+}

backend/application/syson-application-configuration/src/main/java/org/eclipse/syson/application/services/SysONIdentityService.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2024 Obeo.
+ * Copyright (c) 2024, 2025 Obeo.
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v2.0
  * which accompanies this distribution, and is available at
@@ -17,6 +17,7 @@
 import org.eclipse.sirius.components.core.api.IDefaultIdentityService;
 import org.eclipse.sirius.components.core.api.IIdentityServiceDelegate;
 import org.eclipse.sirius.components.emf.services.IDAdapter;
+import org.eclipse.syson.sysml.Element;
 import org.eclipse.syson.sysml.Relationship;
 import org.eclipse.syson.sysml.util.ElementUtil;
 import org.springframework.stereotype.Service;
@@ -39,12 +40,17 @@ public SysONIdentityService(IDefaultIdentityService defaultIdentityService) {
 
     @Override
     public boolean canHandle(Object object) {
-        return object instanceof Relationship;
+        return object instanceof Element;
     }
 
     @Override
     public String getId(Object object) {
-        var id = this.defaultIdentityService.getId(object);
+        String id = null;
+        if (object instanceof Element element && ElementUtil.isFromStandardLibrary(element)) {
+            id = element.getElementId();
+        } else {
+            id = this.defaultIdentityService.getId(object);
+        }
         if (id == null && object instanceof Relationship relationship && relationship.isIsImplied()) {
             var idAdapter = new IDAdapter(ElementUtil.generateUUID(relationship));
             relationship.eAdapters().add(idAdapter);

backend/application/syson-application/src/test/java/org/eclipse/syson/application/controllers/diagrams/general/view/GVAnnotatingElementTests.java

@@ -159,9 +159,10 @@ public void tearDown() {
         }
     }
 
-    @DisplayName("Given a Part Definition, when using the 'New TextualRepresentation' tool, then a new node should be created with an edge connecting it to the PartDefinition")
+    @DisplayName("GIVEN a Part Definition, WHEN using the 'New TextualRepresentation' tool, THEN a new node should be created with an edge connecting it to the PartDefinition")
     @Test
-    @Sql(scripts = { GeneralViewWithTopNodesTestProjectData.SCRIPT_PATH }, executionPhase = Sql.ExecutionPhase.BEFORE_TEST_METHOD)
+    @Sql(scripts = { GeneralViewWithTopNodesTestProjectData.SCRIPT_PATH }, executionPhase = Sql.ExecutionPhase.BEFORE_TEST_METHOD,
+            config = @SqlConfig(transactionMode = SqlConfig.TransactionMode.ISOLATED))
     @Sql(scripts = { "/scripts/cleanup.sql" }, executionPhase = Sql.ExecutionPhase.AFTER_TEST_METHOD, config = @SqlConfig(transactionMode = SqlConfig.TransactionMode.ISOLATED))
     public void createTextualRepresentation() {
         String parentLabel = "part";
@@ -196,9 +197,10 @@ public void createTextualRepresentation() {
         this.semanticCheckerService.checkEditingContext(semanticChecker, this.verifier);
     }
 
-    @DisplayName("Given a TextualRepresentation, when using the 'Direct Edit' tool, then the body of the textual representation should be updated")
+    @DisplayName("GIVEN a TextualRepresentation, WHEN using the 'Direct Edit' tool, THEN the body of the textual representation should be updated")
     @Test
-    @Sql(scripts = { GeneralViewWithTopNodesTestProjectData.SCRIPT_PATH }, executionPhase = Sql.ExecutionPhase.BEFORE_TEST_METHOD)
+    @Sql(scripts = { GeneralViewWithTopNodesTestProjectData.SCRIPT_PATH }, executionPhase = Sql.ExecutionPhase.BEFORE_TEST_METHOD,
+            config = @SqlConfig(transactionMode = SqlConfig.TransactionMode.ISOLATED))
     @Sql(scripts = { "/scripts/cleanup.sql" }, executionPhase = Sql.ExecutionPhase.AFTER_TEST_METHOD, config = @SqlConfig(transactionMode = SqlConfig.TransactionMode.ISOLATED))
     public void directEditTextualRepresentation() {
         this.directEditInitialLabelTester.checkDirectEditInitialLabelOnNode(this.verifier, this.diagram, GeneralViewWithTopNodesTestProjectData.GraphicalIds.PART_DEFINITION_TEXTUAL_REP_ID,

backend/application/syson-application/src/test/java/org/eclipse/syson/application/controllers/diagrams/general/view/GVBorderNodePortCreationTests.java

@@ -114,8 +114,9 @@ public void tearDown() {
         }
     }
 
-    @DisplayName("Given a SysML Project, when New Port tool is requested on a PartUsage, then a new PortUsage border node is created")
-    @Sql(scripts = { GeneralViewWithTopNodesTestProjectData.SCRIPT_PATH }, executionPhase = Sql.ExecutionPhase.BEFORE_TEST_METHOD)
+    @DisplayName("GIVEN a SysML Project, WHEN New Port tool is requested on a PartUsage, THEN a new PortUsage border node is created")
+    @Sql(scripts = { GeneralViewWithTopNodesTestProjectData.SCRIPT_PATH }, executionPhase = Sql.ExecutionPhase.BEFORE_TEST_METHOD,
+            config = @SqlConfig(transactionMode = SqlConfig.TransactionMode.ISOLATED))
     @Sql(scripts = { "/scripts/cleanup.sql" }, executionPhase = Sql.ExecutionPhase.AFTER_TEST_METHOD, config = @SqlConfig(transactionMode = SqlConfig.TransactionMode.ISOLATED))
     @Test
     public void testApplyTool() {

backend/application/syson-application/src/test/java/org/eclipse/syson/application/data/GeneralViewActionTransitionUsagesProjectData.java

@@ -63,8 +63,8 @@ public static final class SemanticIds {
 
         public static final String STOA4_ID = "2889857b-02e6-4f55-9ef3-1d2bfe404098";
 
-        public static final String START_ACTION_USAGE_ID = "03262155-734a-473f-9535-262925cd5b8b";
+        public static final String START_ACTION_USAGE_ID = "9a0d2905-0f9c-5bb4-af74-9780d6db1817";
 
-        public static final String DONE_ACTION_USAGE_ID = "6f9d8315-c293-4910-9688-668196eb8ec5";
+        public static final String DONE_ACTION_USAGE_ID = "0cdc3cd3-b06c-5c32-beda-0cf4ba164a64";
     }
 }