Fix MID-4407: Closure not recomputed correctly

Add-with-overwrite repo method was (probably for a very long time)
broken with respect for org closure maintenance. Hopefully, other
methods (standard addObject, modifyObject, deleteObject) were not
affected.

infra/prism/src/main/java/com/evolveum/midpoint/prism/PrismContainerValue.java

@@ -1096,7 +1096,7 @@ void diffItems(PrismContainerValue<C> thisValue, PrismContainerValue<C> other,
 		if (thisValue.getItems() !=  null) {
 			for (Item<?,?> thisItem: thisValue.getItems()) {
 				Item otherItem = other.findItem(thisItem.getElementName());
-				if (!isLiteral) {
+				if (!isLiteral) {       // here should be perhaps ignoreMetadata instead
 					ItemDefinition itemDef = thisItem.getDefinition();
 					if (itemDef == null && other.getDefinition() != null) {
 						itemDef = other.getDefinition().findItemDefinition(thisItem.getElementName());
@@ -1118,7 +1118,7 @@ void diffItems(PrismContainerValue<C> thisValue, PrismContainerValue<C> other,
 					// Already processed in previous loop
 					continue;
 				}
-				if (!isLiteral) {
+				if (!isLiteral) {       // here should be perhaps ignoreMetadata instead
 					ItemDefinition itemDef = otherItem.getDefinition();
 					if (itemDef == null && thisValue.getDefinition() != null) {
 						itemDef = thisValue.getDefinition().findItemDefinition(otherItem.getElementName());

infra/prism/src/main/java/com/evolveum/midpoint/prism/delta/ObjectDelta.java

@@ -221,6 +221,7 @@ public void setObjectToAdd(PrismObject<T> objectToAdd) {
         }
     }
 
+    @NotNull
     public Collection<? extends ItemDelta<?,?>> getModifications() {
         return modifications;
     }

repo/repo-sql-impl-test/src/test/java/com/evolveum/midpoint/repo/sql/closure/OrgClosureOverwriteAddTest.java

@@ -0,0 +1,83 @@
+/*
+ * Copyright (c) 2010-2018 Evolveum
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.evolveum.midpoint.repo.sql.closure;
+
+import com.evolveum.midpoint.prism.PrismObject;
+import com.evolveum.midpoint.repo.api.RepoAddOptions;
+import com.evolveum.midpoint.schema.result.OperationResult;
+import com.evolveum.midpoint.util.logging.Trace;
+import com.evolveum.midpoint.util.logging.TraceManager;
+import com.evolveum.midpoint.xml.ns._public.common.common_3.OrgType;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.testng.annotations.Test;
+
+import static org.testng.AssertJUnit.assertFalse;
+
+/**
+ * MID-4407
+ *
+ * @author mederly
+ */
+@ContextConfiguration(locations = {"../../../../../../ctx-test.xml"})
+@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
+public class OrgClosureOverwriteAddTest extends AbstractOrgClosureTest {
+
+	private static final Trace LOGGER = TraceManager.getTrace(OrgClosureOverwriteAddTest.class);
+
+    private static final int[] ORG_CHILDREN_IN_LEVEL  = { 1, 1  };
+    private static final int[] USER_CHILDREN_IN_LEVEL = null;
+    private static final int[] PARENTS_IN_LEVEL       = { 0, 1  };
+
+    private OrgClosureTestConfiguration configuration;
+
+    public OrgClosureOverwriteAddTest() {
+        configuration = new OrgClosureTestConfiguration();
+        configuration.setCheckChildrenSets(true);
+        configuration.setCheckClosureMatrix(true);
+        configuration.setDeletionsToClosureTest(1);
+        configuration.setOrgChildrenInLevel(ORG_CHILDREN_IN_LEVEL);
+        configuration.setUserChildrenInLevel(USER_CHILDREN_IN_LEVEL);
+        configuration.setParentsInLevel(PARENTS_IN_LEVEL);
+    }
+
+    @Test
+    public void test100AddWithOverwrite() throws Exception {
+        OperationResult opResult = new OperationResult("===[ test100AddWithOverwrite ]===");
+
+        _test100LoadOrgStructure();
+        _test150CheckClosure();
+
+        String parentOid = orgsByLevels.get(0).get(0);
+        String childOid = orgsByLevels.get(1).get(0);
+        PrismObject<OrgType> childOrg = repositoryService.getObject(OrgType.class, childOid, null, opResult);
+        childOrg.asObjectable().getParentOrgRef().clear();
+
+        LOGGER.info("+++ adding object with 'overwrite' option +++");
+        repositoryService.addObject(childOrg, RepoAddOptions.createOverwrite(), opResult);
+
+	    orgGraph.removeEdge(childOid, parentOid);
+	    checkOrgGraph();
+        boolean problem = checkClosureMatrix();
+        assertFalse("Closure problem was detected", problem);
+    }
+
+    @Override
+    public OrgClosureTestConfiguration getConfiguration() {
+        return configuration;
+    }
+}

repo/repo-sql-impl-test/testng-integration.xml

@@ -39,6 +39,7 @@
             <class name="com.evolveum.midpoint.repo.sql.ListAccountShadowOwnerTest"/>
             <class name="com.evolveum.midpoint.repo.sql.OrgStructTest"/>
             <class name="com.evolveum.midpoint.repo.sql.closure.OrgClosureCorrectnessTest"/>
+            <class name="com.evolveum.midpoint.repo.sql.closure.OrgClosureOverwriteAddTest"/>
             <class name="com.evolveum.midpoint.repo.sql.SearchTest"/>
             <class name="com.evolveum.midpoint.repo.sql.CleanupTest"/>
             <class name="com.evolveum.midpoint.repo.sql.SearchShadowOwnerTest"/>

repo/repo-sql-impl/src/main/java/com/evolveum/midpoint/repo/sql/helpers/ObjectUpdater.java

@@ -179,7 +179,7 @@ private <T extends ObjectType> String overwriteAddObjectAttempt(PrismObject<T> o
         if (originalOid != null) {
             try {
                 oldObject = objectRetriever.getObjectInternal(session, object.getCompileTimeClass(), originalOid, null, true, result);
-                ObjectDelta<T> delta = object.diff(oldObject);
+                ObjectDelta<T> delta = oldObject.diff(object, false, true);
                 modifications = delta.getModifications();
 
                 LOGGER.trace("overwriteAddObjectAttempt: originalOid={}, modifications={}", originalOid, modifications);