refactor[ats_PRNVV]: Fix with test database relation integrity health checks

7 files changed, 259 insertions, 50 deletions

diff --git a/plugins/org.eclipse.osee.framework.branch.management/src/org/eclipse/osee/framework/branch/management/internal/OseeBranchService.java b/plugins/org.eclipse.osee.framework.branch.management/src/org/eclipse/osee/framework/branch/management/internal/OseeBranchService.java
index 2381775..36f2eb0 100644
--- a/plugins/org.eclipse.osee.framework.branch.management/src/org/eclipse/osee/framework/branch/management/internal/OseeBranchService.java
+++ b/plugins/org.eclipse.osee.framework.branch.management/src/org/eclipse/osee/framework/branch/management/internal/OseeBranchService.java
@@ -66,7 +66,6 @@ public class OseeBranchService implements IOseeBranchService {
    private final IOseeModelFactoryServiceProvider modelFactory;
 
    public OseeBranchService(IOseeDatabaseServiceProvider oseeDatabaseProvider, IOseeCachingServiceProvider cachingService, IOseeModelFactoryServiceProvider modelFactory) {
-      super();
       this.oseeDatabaseProvider = oseeDatabaseProvider;
       this.cachingService = cachingService;
       this.modelFactory = modelFactory;
diff --git a/plugins/org.eclipse.osee.framework.core.server/src/org/eclipse/osee/framework/core/server/SecureOseeHttpServlet.java b/plugins/org.eclipse.osee.framework.core.server/src/org/eclipse/osee/framework/core/server/SecureOseeHttpServlet.java
index 52e0647..26f5daa 100644
--- a/plugins/org.eclipse.osee.framework.core.server/src/org/eclipse/osee/framework/core/server/SecureOseeHttpServlet.java
+++ b/plugins/org.eclipse.osee.framework.core.server/src/org/eclipse/osee/framework/core/server/SecureOseeHttpServlet.java
@@ -23,7 +23,6 @@ public class SecureOseeHttpServlet extends OseeHttpServlet {
    private final ISessionManager sessionManager;
 
    public SecureOseeHttpServlet(ISessionManager sessionManager) {
-      super();
       this.sessionManager = sessionManager;
    }
 
diff --git a/plugins/org.eclipse.osee.framework.skynet.core/src/org/eclipse/osee/framework/skynet/core/revision/ConflictManagerInternal.java b/plugins/org.eclipse.osee.framework.skynet.core/src/org/eclipse/osee/framework/skynet/core/revision/ConflictManagerInternal.java
index 0253813..5c0e01a 100644
--- a/plugins/org.eclipse.osee.framework.skynet.core/src/org/eclipse/osee/framework/skynet/core/revision/ConflictManagerInternal.java
+++ b/plugins/org.eclipse.osee.framework.skynet.core/src/org/eclipse/osee/framework/skynet/core/revision/ConflictManagerInternal.java
@@ -392,7 +392,7 @@ public class ConflictManagerInternal {
          }
       }
       for (Branch branch : sourceBranches) {
-         if (branch.getParentBranch().equals(commonBranch)) {
+         if (commonBranch.equals(branch.getParentBranch())) {
             sourceTransaction = branch.getBaseTransaction();
             break;
          }
diff --git a/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/cases/ArtifactPasteConfigurationTest.java b/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/cases/ArtifactPasteConfigurationTest.java
index f2ea705..319f739 100644
--- a/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/cases/ArtifactPasteConfigurationTest.java
+++ b/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/cases/ArtifactPasteConfigurationTest.java
@@ -24,27 +24,27 @@ public class ArtifactPasteConfigurationTest {
    @Test
    public void testConstruction() {
       ArtifactPasteConfiguration config = new ArtifactPasteConfiguration();
-      Assert.assertEquals(false, config.isIncludeChildrenOfCopiedElements());
-      Assert.assertEquals(true, config.isKeepRelationOrderSettings());
+      Assert.assertFalse(config.isIncludeChildrenOfCopiedElements());
+      Assert.assertTrue(config.isKeepRelationOrderSettings());
    }
 
    @Test
    public void testSetIncludeChildren() {
       ArtifactPasteConfiguration config = new ArtifactPasteConfiguration();
       config.setIncludeChildrenOfCopiedElements(true);
-      Assert.assertEquals(true, config.isIncludeChildrenOfCopiedElements());
+      Assert.assertTrue(config.isIncludeChildrenOfCopiedElements());
 
       config.setIncludeChildrenOfCopiedElements(false);
-      Assert.assertEquals(false, config.isIncludeChildrenOfCopiedElements());
+      Assert.assertFalse(config.isIncludeChildrenOfCopiedElements());
    }
 
    @Test
    public void testSetKeepRelationOrder() {
       ArtifactPasteConfiguration config = new ArtifactPasteConfiguration();
       config.setKeepRelationOrderSettings(true);
-      Assert.assertEquals(true, config.isKeepRelationOrderSettings());
+      Assert.assertTrue(config.isKeepRelationOrderSettings());
 
       config.setKeepRelationOrderSettings(false);
-      Assert.assertEquals(false, config.isKeepRelationOrderSettings());
+      Assert.assertFalse(config.isKeepRelationOrderSettings());
    }
 }
diff --git a/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/dbHealth/RelationIntegrityCheckTest.java b/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/dbHealth/RelationIntegrityCheckTest.java
new file mode 100644
index 0000000..7fb7977
--- a/dev/null
+++ b/plugins/org.eclipse.osee.framework.ui.skynet.test/src/org/eclipse/osee/framework/ui/skynet/test/dbHealth/RelationIntegrityCheckTest.java
@@ -0,0 +1,148 @@
+/*******************************************************************************
+ * Copyright (c) 2011 Boeing.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     Boeing - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.osee.framework.ui.skynet.test.dbHealth;
+
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import junit.framework.Assert;
+import org.eclipse.osee.framework.core.data.SystemUser;
+import org.eclipse.osee.framework.core.data.TokenFactory;
+import org.eclipse.osee.framework.core.enums.CoreArtifactTypes;
+import org.eclipse.osee.framework.core.exception.OseeCoreException;
+import org.eclipse.osee.framework.core.exception.OseeDataStoreException;
+import org.eclipse.osee.framework.core.model.Branch;
+import org.eclipse.osee.framework.database.core.ConnectionHandler;
+import org.eclipse.osee.framework.database.core.IOseeStatement;
+import org.eclipse.osee.framework.jdk.core.type.DoubleKeyHashMap;
+import org.eclipse.osee.framework.jdk.core.util.GUID;
+import org.eclipse.osee.framework.skynet.core.UserManager;
+import org.eclipse.osee.framework.skynet.core.artifact.Artifact;
+import org.eclipse.osee.framework.skynet.core.artifact.ArtifactTypeManager;
+import org.eclipse.osee.framework.skynet.core.artifact.BranchManager;
+import org.eclipse.osee.framework.skynet.core.artifact.search.ArtifactQuery;
+import org.eclipse.osee.framework.skynet.core.conflict.ConflictManagerExternal;
+import org.eclipse.osee.framework.ui.skynet.dbHealth.RelationIntegrityCheck;
+import org.eclipse.osee.framework.ui.skynet.dbHealth.RelationIntegrityCheck.LocalRelationLink;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * {@link RelationIntegrityCheck}
+ * <p>
+ * Tests data integrity case where a new relation is persisted on a deleted artifact. Checks that if the situation
+ * exists, applyFix can resolve the issue.
+ * </p>
+ *
+ * @author Karol M. Wilk
+ */
+public class RelationIntegrityCheckTest {
+
+   private final DoubleKeyHashMap<Integer, Integer, LocalRelationLink> map =
+      new DoubleKeyHashMap<Integer, Integer, LocalRelationLink>();
+   private Branch parentBranch;
+   private Branch workingBranch;
+
+   @Test
+   public void testNewRelationOnDeletedArtifact() throws Exception {
+      runQuery(RelationIntegrityCheck.DELETED_A_ARTIFACTS);
+      runQuery(RelationIntegrityCheck.DELETED_B_ARTIFACTS);
+
+      applyFix();
+
+      Assert.assertTrue(checkIfAllFixed());
+   }
+
+   private boolean checkIfAllFixed() throws OseeCoreException {
+      map.clear();
+      runQuery(RelationIntegrityCheck.DELETED_A_ARTIFACTS);
+      runQuery(RelationIntegrityCheck.DELETED_B_ARTIFACTS);
+      return map.isEmpty();
+   }
+
+   private void applyFix() throws OseeCoreException {
+      List<Object[]> rowsToDelete = new LinkedList<Object[]>();
+      for (LocalRelationLink relLink : map.allValues()) {
+         rowsToDelete.add(new Object[] {relLink.gammaId, relLink.relTransId, relLink.branchId});
+      }
+
+      if (!rowsToDelete.isEmpty()) {
+         ConnectionHandler.runBatchUpdate(RelationIntegrityCheck.DEL_FROM_TXS_W_SPEC_BRANCH_ID, rowsToDelete);
+      }
+   }
+
+   private void runQuery(String sqlQuery) throws OseeDataStoreException, OseeCoreException {
+      IOseeStatement chStmt = ConnectionHandler.getStatement();
+      try {
+         chStmt.runPreparedQuery(sqlQuery);
+         while (chStmt.next()) {
+            //@formatter:off
+            int gammaId =              chStmt.getInt("gamma_id");
+            int transactionId =        chStmt.getInt("transaction_id");
+            int relationId =           chStmt.getInt("rel_link_id");
+            int branchId =             chStmt.getInt("branch_id");
+            int a_sideArtifactId =     chStmt.getInt("a_art_id");
+            int b_sideArtifactId =     chStmt.getInt("b_art_id");
+            int deletedTransaction =   chStmt.getInt("deleted_tran");
+
+            int commitTransId =        chStmt.getInt("commit_trans_art_id");
+            int modType =              chStmt.getInt("creating_trans_mod_type");
+            //@formatter:on
+
+            if (!map.containsKey(gammaId, transactionId)) {
+               if (commitTransId > 0 && modType == 1) {
+                  map.put(gammaId, transactionId, new LocalRelationLink(relationId, gammaId, transactionId, branchId,
+                     a_sideArtifactId, b_sideArtifactId, deletedTransaction, commitTransId, modType));
+               }
+            }
+         }
+      } finally {
+         chStmt.close();
+      }
+   }
+
+   @Before
+   public void setUp() throws Exception {
+
+      parentBranch = BranchManager.createTopLevelBranch("1");
+
+      Artifact art_A = ArtifactTypeManager.addArtifact(CoreArtifactTypes.Folder, parentBranch, "A");
+      art_A.persist();
+      BranchManager.persist(parentBranch);
+
+      workingBranch =
+         BranchManager.createWorkingBranch(parentBranch, TokenFactory.createBranch(GUID.create(), "2"),
+            UserManager.getUser(SystemUser.OseeSystem));
+
+      art_A.deleteAndPersist();
+
+      Artifact art_A_prime = ArtifactQuery.getArtifactFromTypeAndName(CoreArtifactTypes.Folder, "A", workingBranch);
+      //Sample artifact to create a relation to...
+      Artifact child = ArtifactTypeManager.addArtifact(CoreArtifactTypes.Folder, workingBranch, "Child");
+
+      //cause a change on the branch
+      art_A_prime.persist();
+
+      //create a new relation on A' to child
+      art_A_prime.addChild(child);
+      art_A_prime.persist();
+
+      //commit branch 2 into 1
+      ConflictManagerExternal conflictManager = new ConflictManagerExternal(parentBranch, workingBranch);
+      BranchManager.commitBranch(null, conflictManager, false, true);
+   }
+
+   @After
+   public void tearDown() throws Exception {
+      BranchManager.purgeBranch(Arrays.asList(workingBranch, parentBranch));
+   }
+}
diff --git a/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/blam/operation/DatabaseHealth.java b/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/blam/operation/DatabaseHealth.java
index f9ba776..2ba4e434 100644
--- a/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/blam/operation/DatabaseHealth.java
+++ b/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/blam/operation/DatabaseHealth.java
@@ -77,24 +77,24 @@ public class DatabaseHealth extends AbstractBlam {
       builder.append("<XWidget xwidgetType=\"XLabel\" displayName=\" \"/>");
       builder.append("<XWidget xwidgetType=\"XLabel\" displayName=\"Select Verification Operations to Run:\"/>");
       for (DatabaseHealthOperation healthOp : DatabaseHealthOpsExtensionManager.getVerifyOperations()) {
-         builder.append(getOperationsCheckBoxes(healthOp, false));
+         builder.append(getOperationsCheckBoxes(healthOp.getVerifyTaskName(), healthOp.getCheckDescription()));
       }
 
       builder.append("<XWidget xwidgetType=\"XLabel\" displayName=\" \"/>");
       builder.append("<XWidget xwidgetType=\"XLabel\" displayName=\"Select Clean Up Operations to Run:\"/>");
       for (DatabaseHealthOperation fixOp : DatabaseHealthOpsExtensionManager.getFixOperations()) {
-         builder.append(getOperationsCheckBoxes(fixOp, true));
+         builder.append(getOperationsCheckBoxes(fixOp.getFixTaskName(), fixOp.getFixDescription()));
       }
 
       builder.append("</xWidgets>");
       return builder.toString();
    }
 
-   private String getOperationsCheckBoxes(DatabaseHealthOperation fixOp, boolean fix) {
+   private String getOperationsCheckBoxes(String taskName, String description) {
       StringBuilder builder = new StringBuilder();
       builder.append("<XWidget xwidgetType=\"XCheckBox\" displayName=\"");
-      builder.append(fix ? fixOp.getFixTaskName() : fixOp.getVerifyTaskName());
-      String toolTip = AXml.textToXml((fix ? fixOp.getFixDescription() : fixOp.getCheckDescription()));
+      builder.append(taskName);
+      String toolTip = AXml.textToXml(description);
       builder.append("\" labelAfter=\"true\" horizontalLabel=\"true\"  toolTip=\"" + toolTip + "\"/>");
       return builder.toString();
    }
diff --git a/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/dbHealth/RelationIntegrityCheck.java b/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/dbHealth/RelationIntegrityCheck.java
index 1c178b1..8a50c9f 100644
--- a/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/dbHealth/RelationIntegrityCheck.java
+++ b/plugins/org.eclipse.osee.framework.ui.skynet/src/org/eclipse/osee/framework/ui/skynet/dbHealth/RelationIntegrityCheck.java
@@ -26,20 +26,16 @@ import org.eclipse.osee.framework.ui.skynet.results.XResultData;
 import org.eclipse.osee.framework.ui.skynet.results.html.XResultPage.Manipulations;
 
 /**
+ * {@link RelationIntegrityCheckTest }
+ *
  * @author Theron Virgin
  */
 public class RelationIntegrityCheck extends DatabaseHealthOperation {
-   private static class LocalRelationLink {
-      public int relLinkId;
-      public int gammaId;
-      public int relTransId;
-      public int branchId;
-      public int aArtId;
-      public int bArtId;
-      public int transIdForArtifactDeletion;
-
-      public LocalRelationLink(int relLinkId, int gammaId, int transactionId, int branchId, int aArtId, int bArtId, int transIdForArtifactDeletion) {
-         super();
+   public static class LocalRelationLink {
+      public int relLinkId, gammaId, relTransId, branchId, aArtId, bArtId, transIdForArtifactDeletion, commitTrans,
+         modType;
+
+      public LocalRelationLink(int relLinkId, int gammaId, int transactionId, int branchId, int aArtId, int bArtId, int transIdForArtifactDeletion, int commitTrans, int modType) {
          this.aArtId = aArtId;
          this.bArtId = bArtId;
          this.branchId = branchId;
@@ -47,26 +43,63 @@ public class RelationIntegrityCheck extends DatabaseHealthOperation {
          this.relLinkId = relLinkId;
          this.relTransId = transactionId;
          this.transIdForArtifactDeletion = transIdForArtifactDeletion;
+         this.commitTrans = commitTrans;
+         this.modType = modType;
       }
-   }
 
+      @Override
+      public String toString() {
+         //System.out.println("gamma_id \t transaction_id \t rel_link_id \t branch_d \t a_art_id \t b_art_id \t deleted_tran \t commit trans \t commit trans mod type");
+         return String.format("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s", gammaId, relTransId, relLinkId, branchId, aArtId,
+            bArtId, transIdForArtifactDeletion, commitTrans, modType);
+      }
+   }
+   //@formatter:off
+   private static final String DELETED_ARTIFACTS_QUERY =
+      " SELECT    " +
+      "     tx1.gamma_id, " +
+      "     tx1.transaction_id, " +
+      "     tx1.branch_id, " +
+      "     rel1.rel_link_id, " +
+      "     rel1.a_art_id, " +
+      "     rel1.b_art_id, " +
+      "     tx2.transaction_id AS deleted_tran, " +
+      "     txd.commit_art_id AS commit_trans_art_id, " +
+      "     tx1.mod_type AS creating_trans_mod_type " +
+      " FROM " +
+      "     osee_txs tx1, " +
+      "     osee_txs tx2, " +
+      "     osee_relation_link rel1, " +
+      "     osee_artifact av1, " +
+      "     osee_tx_details txd " +
+      " WHERE " +
+      "     tx1.branch_id = tx2.branch_id AND " +
+      "     tx1.tx_current = " + TxChange.CURRENT.getValue() + " AND " +
+      "     tx2.tx_current = " + TxChange.DELETED.getValue() + " AND " +
+      "     tx1.gamma_id = rel1.gamma_id AND " +
+      "     tx2.gamma_id = av1.gamma_id AND " +
+      "     av1.art_id = rel1.%s AND " +
+      "     tx1.transaction_id = txd.transaction_id ";
+    //@formatter:on
+
+   // relations that reference deleted artifacts on side A
+   public static final String DELETED_A_ARTIFACTS = String.format(DELETED_ARTIFACTS_QUERY, "a_art_id");
+   public static final String DELETED_B_ARTIFACTS = String.format(DELETED_ARTIFACTS_QUERY, "b_art_id");
+
+   public static final String DELETE_FROM_TXS = "DELETE FROM osee_txs where gamma_id = ? AND transaction_id = ?";
+
+   public static final String DEL_FROM_TXS_W_SPEC_BRANCH_ID =
+      "DELETE FROM osee_txs where gamma_id = ? AND transaction_id = ? AND branch_id = ?";
+
+   // relations that no artifact (on side A of relation) references
    private static final String NO_ADDRESSING_ARTIFACTS_A =
       "SELECT tx1.gamma_id, tx1.transaction_id, rel1.rel_link_id, tx1.branch_id, rel1.a_art_id, rel1.b_art_id, 0 AS deleted_tran FROM osee_txs tx1, osee_relation_link rel1 WHERE tx1.gamma_id = rel1.gamma_id AND NOT EXISTS (SELECT 'x' FROM osee_txs tx2, osee_artifact av1 WHERE tx1.branch_id = tx2.branch_id AND tx2.gamma_id = av1.gamma_id AND av1.art_id = rel1.a_art_id)";
-
+   // relations that no artifact (on side B of relation) references
    private static final String NO_ADDRESSING_ARTIFACTS_B =
       "SELECT tx1.gamma_id, tx1.transaction_id, rel1.rel_link_id, tx1.branch_id, rel1.a_art_id, rel1.b_art_id, 0 AS deleted_tran FROM osee_txs tx1, osee_relation_link rel1 WHERE tx1.gamma_id = rel1.gamma_id AND NOT EXISTS (SELECT 'x' FROM osee_txs tx2, osee_artifact av1 WHERE tx1.branch_id = tx2.branch_id AND tx2.gamma_id = av1.gamma_id AND av1.art_id = rel1.b_art_id)";
 
-   private static final String DELETED_A_ARTIFACTS =
-      "SELECT tx1.gamma_id, tx1.transaction_id, rel1.rel_link_id, tx1.branch_id, rel1.a_art_id, rel1.b_art_id, tx2.transaction_id AS deleted_tran FROM osee_txs tx1, osee_txs tx2, osee_relation_link rel1, osee_artifact av1 WHERE tx1.gamma_id = rel1.gamma_id AND tx1.tx_current = 1 AND tx1.branch_id = tx2.branch_id AND tx2.gamma_id = av1.gamma_id AND tx2.tx_current = 2 AND av1.art_id = rel1.a_art_id";
-
-   private static final String DELETED_B_ARTIFACTS =
-      "SELECT tx1.gamma_id, tx1.transaction_id, rel1.rel_link_id, tx1.branch_id, rel1.a_art_id, rel1.b_art_id, tx2.transaction_id AS deleted_tran FROM osee_txs tx1, osee_txs tx2, osee_relation_link rel1, osee_artifact av1 WHERE tx1.gamma_id = rel1.gamma_id AND tx1.tx_current = 1 AND tx1.branch_id = tx2.branch_id AND tx2.gamma_id = av1.gamma_id AND tx2.tx_current = 2 AND av1.art_id = rel1.b_art_id";
-
-   private static final String DELETE_FROM_TXS = "DELETE FROM osee_txs where gamma_id = ? AND transaction_id = ?";
-
    private static final String UPDATE_TXS_PREVIOUS =
       "UPDATE osee_txs SET tx_current = 0 WHERE gamma_id = ? AND transaction_id = ?";
-
    private static final String UPDATE_TXS_CURRENT =
       "UPDATE osee_txs SET tx_current = " + TxChange.ARTIFACT_DELETED.getValue() + ", mod_type = " + ModificationType.ARTIFACT_DELETED.getValue() + " WHERE gamma_id = ? AND transaction_id = ?";
 
@@ -162,7 +195,7 @@ public class RelationIntegrityCheck extends DatabaseHealthOperation {
          rowsToDelete.add(new Object[] {relLink.gammaId, relLink.relTransId});
       }
 
-      monitor.subTask("Deleting Relation Addressing with non existent Artifacts");
+      monitor.subTask("Deleting Relation Addressing with " + TxChange.DELETED + " Artifact");
       if (rowsToDelete.size() != 0) {
          ConnectionHandler.runBatchUpdate(DELETE_FROM_TXS, rowsToDelete);
       }
@@ -172,15 +205,31 @@ public class RelationIntegrityCheck extends DatabaseHealthOperation {
    }
 
    private void fix() throws OseeCoreException {
+
+      //fix for NO_ADDRESSING_ARTIFACTS_A or NO_ADDRESSING_ARTIFACTS_B
       deleteInvalidRelationAddressing();
 
       List<Object[]> insertArtifactDeleted = new LinkedList<Object[]>();
       List<Object[]> updatePreviousAddressing = new LinkedList<Object[]>();
       List<Object[]> updateCurrentAddressing = new LinkedList<Object[]>();
-      List<LocalRelationLink> pathologicalCases = new ArrayList<LocalRelationLink>();
+      List<LocalRelationLink> unExpectedCases = new ArrayList<LocalRelationLink>();
+      List<Object[]> commitOfNewRelationOnDeletedArtifactCases = new ArrayList<Object[]>();
+
       for (LocalRelationLink relLink : updateMap.allValues()) {
          if (relLink.relTransId > relLink.transIdForArtifactDeletion) {
-            pathologicalCases.add(relLink);
+
+            if (relLink.commitTrans > 0 && relLink.modType == 1) {
+               commitOfNewRelationOnDeletedArtifactCases.add(new Object[] {
+                  relLink.gammaId,
+                  relLink.relTransId,
+                  relLink.branchId}); //typically during a merge of a branch
+               //displayUnexpectedRelLinks(unExpectedCases);
+            } else {
+               //NO POST PROCESSING HERE, subset of relLink(s) that are not understood to be classified.
+               //At minimum they should be displayed.
+               unExpectedCases.add(relLink);
+            }
+
          } else if (relLink.relTransId == relLink.transIdForArtifactDeletion) {
             updateCurrentAddressing.add(new Object[] {relLink.gammaId, relLink.relTransId});
          } else {
@@ -192,22 +241,29 @@ public class RelationIntegrityCheck extends DatabaseHealthOperation {
          }
       }
 
+      runInsert(commitOfNewRelationOnDeletedArtifactCases, DEL_FROM_TXS_W_SPEC_BRANCH_ID,
+         "Deleting TXs with relation links made with deleted artifacts.");
       runInsert(insertArtifactDeleted, INSERT_TXS, "Inserting Addressing for Deleted Artifacts");
       runInsert(updatePreviousAddressing, UPDATE_TXS_PREVIOUS, "Updating Addressing for Deleted Artifacts");
       runInsert(updateCurrentAddressing, UPDATE_TXS_CURRENT, "Updating Addressing for Deleted Artifacts");
       updateMap = null;
    }
 
+   @SuppressWarnings("unused")
+   private void displayUnexpectedRelLinks(LocalRelationLink relationLink) {
+      System.out.println("gam_id \t transaction_id \t rel_link_id \t branch_d \t a_art_id \t b_art_id \t deleted_tran \t commit trans \t commit trans mod type");
+      System.out.println(relationLink.toString());
+   }
+
    private void runInsert(List<Object[]> insertParameters, String sql, String taskName) throws OseeCoreException {
       monitor.subTask(taskName);
       if (insertParameters.size() != 0) {
          ConnectionHandler.runBatchUpdate(sql, insertParameters);
       }
       monitor.worked(calculateWork(0.10));
-
    }
 
-   private void endReport() throws OseeCoreException {
+   private void endReport() {
       sbFull.append(AHTML.endMultiColumnTable());
       XResultData rd = new XResultData();
       rd.addRaw(sbFull.toString());
@@ -244,14 +300,22 @@ public class RelationIntegrityCheck extends DatabaseHealthOperation {
       try {
          chStmt.runPreparedQuery(sql);
          while (chStmt.next()) {
-            if (!map.containsKey(chStmt.getInt("gamma_id"), chStmt.getInt("transaction_id")) && (forDelete || !deleteMap.containsKey(
-               chStmt.getInt("gamma_id"), chStmt.getInt("transaction_id")))) {
-               map.put(
-                  chStmt.getInt("gamma_id"),
-                  chStmt.getInt("transaction_id"),
-                  new LocalRelationLink(chStmt.getInt("rel_link_id"), chStmt.getInt("gamma_id"),
-                     chStmt.getInt("transaction_id"), chStmt.getInt("branch_id"), chStmt.getInt("a_art_id"),
-                     chStmt.getInt("b_art_id"), chStmt.getInt("deleted_tran")));
+            //@formatter:off
+            int version =              chStmt.getInt("gamma_id");
+            int transactionId =        chStmt.getInt("transaction_id");
+            int relationId =           chStmt.getInt("rel_link_id");
+            int branchId =             chStmt.getInt("branch_id");
+            int a_sideArtifactId =     chStmt.getInt("a_art_id");
+            int b_sideArtifactId =     chStmt.getInt("b_art_id");
+            int deletedTransaction =   chStmt.getInt("deleted_tran");
+
+            int commitTransId =        chStmt.getInt("commit_trans_art_id");
+            int modType =              chStmt.getInt("creating_trans_mod_type");
+            //@formatter:on
+
+            if (!map.containsKey(version, transactionId) && (forDelete || !deleteMap.containsKey(version, transactionId))) {
+               map.put(version, transactionId, new LocalRelationLink(relationId, version, transactionId, branchId,
+                  a_sideArtifactId, b_sideArtifactId, deletedTransaction, commitTransId, modType));
             } else {
                System.out.print("");
             }
@@ -272,5 +336,4 @@ public class RelationIntegrityCheck extends DatabaseHealthOperation {
    public String getFixDescription() {
       return "Enter Fix Description Here";
    }
-
 }