Merge pull request #1 from sirixdb/master

Merge from upstream

bundles/sirix-core/src/main/java/org/sirix/access/LocalJsonDatabase.java

@@ -23,6 +23,7 @@
 
 import com.google.common.base.MoreObjects;
 import org.sirix.access.json.JsonResourceStore;
+import org.sirix.access.trx.node.AfterCommitState;
 import org.sirix.api.Database;
 import org.sirix.api.ResourceManager;
 import org.sirix.api.json.JsonNodeTrx;
@@ -127,7 +128,7 @@ protected boolean bootstrapResource(ResourceConfiguration resConfig) {
     try (final JsonResourceManager resourceTrxManager = openResourceManager(resConfig.getResource()
                                                                                      .getFileName()
                                                                                      .toString());
-         final JsonNodeTrx wtx = resourceTrxManager.beginNodeTrx()) {
+         final JsonNodeTrx wtx = resourceTrxManager.beginNodeTrx(AfterCommitState.Close)) {
       wtx.commit();
     } catch (final SirixException e) {
       LOGWRAPPER.error(e.getMessage(), e);

bundles/sirix-core/src/main/java/org/sirix/access/ResourceConfiguration.java

@@ -142,7 +142,7 @@ public static int compareStructure(final Path file) {
 
   // FIXED STANDARD FIELDS
   /** Standard storage. */
-  private static final StorageType STORAGE = StorageType.MEMORY_MAPPED;
+  private static final StorageType STORAGE = StorageType.FILE;
 
   /** Standard versioning approach. */
   private static final VersioningType VERSIONING = VersioningType.SLIDING_SNAPSHOT;

bundles/sirix-core/src/main/java/org/sirix/access/trx/node/AbstractResourceManager.java

@@ -129,16 +129,10 @@ public abstract class AbstractResourceManager<R extends NodeReadOnlyTrx & NodeCu
    */
   final User user;
 
-  public enum AfterCommitState {
-    KeepOpen,
-
-    Close
-  }
-
   /**
    * Package private constructor.
    *
-   * @param database      {@link LocalXmlDatabase} for centralized operations on related sessions
+   * @param database      {@link Database} for centralized operations on related sessions
    * @param resourceStore the resource store with which this manager has been created
    * @param resourceConf  {@link DatabaseConfiguration} for general setting about the storage
    * @param bufferManager the cache of in-memory pages shared amongst all resource managers and transactions
@@ -346,44 +340,45 @@ public Path getCommitFile() {
 
   @Override
   public W beginNodeTrx() {
-    return beginNodeTrx(0, TimeUnit.MINUTES, 0, AfterCommitState.KeepOpen);
+    return beginNodeTrx(0, 0, TimeUnit.MILLISECONDS, AfterCommitState.KeepOpen);
   }
 
   @Override
   public W beginNodeTrx(final @Nonnegative int maxNodeCount) {
-    return beginNodeTrx(maxNodeCount, TimeUnit.MINUTES, 0, AfterCommitState.KeepOpen);
+    return beginNodeTrx(maxNodeCount, 0, TimeUnit.MILLISECONDS, AfterCommitState.KeepOpen);
   }
 
   @Override
-  public W beginNodeTrx(final @Nonnull TimeUnit timeUnit, final @Nonnegative int maxTime) {
-    return beginNodeTrx(0, timeUnit, maxTime, AfterCommitState.KeepOpen);
+  public W beginNodeTrx(final @Nonnegative int maxTime, final @Nonnull TimeUnit timeUnit) {
+    return beginNodeTrx(0, maxTime, timeUnit, AfterCommitState.KeepOpen);
   }
 
-  public W beginNodeTrx(final @Nonnegative int maxNodeCount, final @Nonnull TimeUnit timeUnit,
-      final @Nonnegative int maxTime) {
-    return beginNodeTrx(maxNodeCount, timeUnit, maxTime, AfterCommitState.KeepOpen);
+  @Override
+  public W beginNodeTrx(final @Nonnegative int maxNodeCount, final @Nonnegative int maxTime,
+      final @Nonnull TimeUnit timeUnit) {
+    return beginNodeTrx(maxNodeCount, maxTime, timeUnit, AfterCommitState.KeepOpen);
   }
 
   @Override
   public W beginNodeTrx(final @Nonnull AfterCommitState afterCommitState) {
-    return beginNodeTrx(0, TimeUnit.MINUTES, 0, afterCommitState);
+    return beginNodeTrx(0, 0, TimeUnit.MILLISECONDS, afterCommitState);
   }
 
   @Override
   public W beginNodeTrx(final @Nonnegative int maxNodeCount, final @Nonnull AfterCommitState afterCommitState) {
-    return beginNodeTrx(maxNodeCount, TimeUnit.MINUTES, 0);
+    return beginNodeTrx(maxNodeCount, 0, TimeUnit.MILLISECONDS);
   }
 
   @Override
-  public W beginNodeTrx(final @Nonnull TimeUnit timeUnit, final @Nonnegative int maxTime,
+  public W beginNodeTrx(final @Nonnegative int maxTime, final @Nonnull TimeUnit timeUnit,
       final @Nonnull AfterCommitState afterCommitState) {
-    return beginNodeTrx(0, timeUnit, maxTime, afterCommitState);
+    return beginNodeTrx(0, maxTime, timeUnit, afterCommitState);
   }
 
   @SuppressWarnings("unchecked")
   @Override
-  public synchronized W beginNodeTrx(final @Nonnegative int maxNodeCount, final @Nonnull TimeUnit timeUnit,
-      final @Nonnegative int maxTime, final @Nonnull AfterCommitState afterCommitState) {
+  public synchronized W beginNodeTrx(final @Nonnegative int maxNodeCount, final @Nonnegative int maxTime,
+      final @Nonnull TimeUnit timeUnit, final @Nonnull AfterCommitState afterCommitState) {
     // Checks.
     assertAccess(lastCommittedUberPage.get().getRevision());
     if (maxNodeCount < 0 || maxTime < 0) {

bundles/sirix-core/src/main/java/org/sirix/access/trx/node/AfterCommitState.java

@@ -0,0 +1,7 @@
+package org.sirix.access.trx.node;
+
+public enum AfterCommitState {
+    KeepOpen,
+
+    Close
+}

bundles/sirix-core/src/main/java/org/sirix/access/trx/node/json/JsonNodeTrxImpl.java

@@ -30,7 +30,7 @@
 import org.brackit.xquery.atomic.QNm;
 import org.sirix.access.ResourceConfiguration;
 import org.sirix.access.User;
-import org.sirix.access.trx.node.AbstractResourceManager;
+import org.sirix.access.trx.node.AfterCommitState;
 import org.sirix.access.trx.node.CommitCredentials;
 import org.sirix.access.trx.node.HashType;
 import org.sirix.access.trx.node.InternalResourceManager;
@@ -128,7 +128,7 @@ final class JsonNodeTrxImpl extends AbstractForwardingJsonNodeReadOnlyTrx implem
   /**
    * After commit state: keep open or close.
    */
-  private final AbstractResourceManager.AfterCommitState afterCommitState;
+  private final AfterCommitState afterCommitState;
 
   /**
    * Hashes nodes.
@@ -232,7 +232,7 @@ final class JsonNodeTrxImpl extends AbstractForwardingJsonNodeReadOnlyTrx implem
 
   private final boolean isAutoCommitting;
 
-  private State state;
+  private volatile State state;
 
   private enum State {
     Running,
@@ -262,7 +262,7 @@ private enum State {
       final InternalJsonNodeReadOnlyTrx nodeReadTrx, final PathSummaryWriter<JsonNodeReadOnlyTrx> pathSummaryWriter,
       final @Nonnegative int maxNodeCount, final TimeUnit timeUnit, final @Nonnegative int maxTime,
       final @Nonnull JsonNodeHashing nodeHashing, final JsonNodeFactory nodeFactory,
-      final @Nonnull AbstractResourceManager.AfterCommitState afterCommitState) {
+      final @Nonnull AfterCommitState afterCommitState) {
     // Do not accept negative values.
     Preconditions.checkArgument(maxNodeCount >= 0 && maxTime >= 0,
                                 "Negative arguments for maxNodeCount and maxTime are not accepted.");
@@ -348,32 +348,46 @@ private void unLockIfNecessary() {
 
   @Override
   public JsonNodeTrx insertSubtreeAsFirstChild(final JsonReader reader) {
-    return insertSubtree(reader, InsertPosition.AS_FIRST_CHILD, true);
+    return insertSubtree(reader, InsertPosition.AS_FIRST_CHILD, Commit.Implicit, CheckParentNode.Yes);
   }
 
   @Override
-  public JsonNodeTrx insertSubtreeAsFirstChild(final JsonReader reader, boolean doImplicitCommit) {
-    return insertSubtree(reader, InsertPosition.AS_FIRST_CHILD, doImplicitCommit);
+  public JsonNodeTrx insertSubtreeAsFirstChild(final JsonReader reader, Commit commit) {
+    return insertSubtree(reader, InsertPosition.AS_FIRST_CHILD, commit, CheckParentNode.Yes);
+  }
+
+  @Override
+  public JsonNodeTrx insertSubtreeAsFirstChild(final JsonReader reader, Commit commit,
+      CheckParentNode checkParentNode) {
+    return insertSubtree(reader, InsertPosition.AS_FIRST_CHILD, commit, checkParentNode);
   }
 
   @Override
   public JsonNodeTrx insertSubtreeAsRightSibling(final JsonReader reader) {
-    return insertSubtree(reader, InsertPosition.AS_RIGHT_SIBLING, true);
+    return insertSubtree(reader, InsertPosition.AS_RIGHT_SIBLING, Commit.Implicit, CheckParentNode.Yes);
+  }
+
+  @Override
+  public JsonNodeTrx insertSubtreeAsRightSibling(final JsonReader reader, Commit commit) {
+    return insertSubtree(reader, InsertPosition.AS_RIGHT_SIBLING, commit, CheckParentNode.Yes);
   }
 
   @Override
-  public JsonNodeTrx insertSubtreeAsRightSibling(final JsonReader reader, boolean doImplicitCommit) {
-    return insertSubtree(reader, InsertPosition.AS_RIGHT_SIBLING, false);
+  public JsonNodeTrx insertSubtreeAsRightSibling(final JsonReader reader, Commit commit,
+      CheckParentNode checkParentNode) {
+    return insertSubtree(reader, InsertPosition.AS_RIGHT_SIBLING, commit, checkParentNode);
   }
 
-  private JsonNodeTrx insertSubtree(final JsonReader reader, final InsertPosition insertionPosition,
-      boolean doImplicitCommit) {
+  private JsonNodeTrx insertSubtree(final JsonReader reader, final InsertPosition insertionPosition, Commit commit,
+      CheckParentNode checkParentNode) {
     nodeReadOnlyTrx.assertNotClosed();
-    checkState();
     checkNotNull(reader);
     assert insertionPosition != null;
 
+    acquireLockIfNecessary();
+
     try {
+      checkState();
       final var peekedJsonToken = reader.peek();
 
       if (peekedJsonToken != JsonToken.BEGIN_OBJECT && peekedJsonToken != JsonToken.BEGIN_ARRAY)
@@ -403,9 +417,11 @@ private JsonNodeTrx insertSubtree(final JsonReader reader, final InsertPosition
           }
         }
         case AS_RIGHT_SIBLING -> {
-          final NodeKind parentKind = getParentKind();
-          if (parentKind != NodeKind.ARRAY) {
-            throw new IllegalStateException("Current parent node must be an array node.");
+          if (checkParentNode == CheckParentNode.Yes) {
+            final NodeKind parentKind = getParentKind();
+            if (parentKind != NodeKind.ARRAY) {
+              throw new IllegalStateException("Current parent node must be an array node.");
+            }
           }
         }
         default -> throw new UnsupportedOperationException();
@@ -448,11 +464,13 @@ private JsonNodeTrx insertSubtree(final JsonReader reader, final InsertPosition
 
       nodeHashing.setBulkInsert(false);
 
-      if (doImplicitCommit) {
+      if (commit == Commit.Implicit) {
         commit();
       }
     } catch (final IOException e) {
       throw new UncheckedIOException(e);
+    } finally {
+      unLockIfNecessary();
     }
     return this;
   }
@@ -515,8 +533,10 @@ public JsonNodeTrx insertObjectAsRightSibling() {
     try {
       checkAccessAndCommit();
 
-      if (getParentKind() != NodeKind.ARRAY) {
-        throw new SirixUsageException("Insert is not allowed if parent node is not an array node!");
+      if (!nodeHashing.isBulkInsert()) {
+        if (getParentKind() != NodeKind.ARRAY) {
+          throw new SirixUsageException("Insert is not allowed if parent node is not an array node!");
+        }
       }
 
       final StructNode currentNode = nodeReadOnlyTrx.getStructuralNode();
@@ -846,7 +866,7 @@ private long getPathNodeKey(StructNode structNode) {
   private void adaptNodesAndHashesForInsertAsFirstChild(final ImmutableJsonNode node) {
     // Adapt local nodes and hashes.
     nodeReadOnlyTrx.setCurrentNode(node);
-    adaptForInsert((StructNode) node, InsertPos.ASFIRSTCHILD);
+    adaptForInsert((StructNode) node);
     nodeReadOnlyTrx.setCurrentNode(node);
     nodeHashing.adaptHashesWithAdd();
   }
@@ -956,14 +976,15 @@ public JsonNodeTrx insertBooleanValueAsRightSibling(boolean value) {
   }
 
   private void checkPrecondition() {
-    if (getParentKind() != NodeKind.ARRAY)
+    if (!nodeHashing.isBulkInsert() && getParentKind() != NodeKind.ARRAY) {
       throw new SirixUsageException("Insert is not allowed if parent node is not an array node!");
+    }
   }
 
   private void insertAsRightSibling(final ImmutableJsonNode node) {
     // Adapt local nodes and hashes.
     nodeReadOnlyTrx.setCurrentNode(node);
-    adaptForInsert((StructNode) node, InsertPos.ASRIGHTSIBLING);
+    adaptForInsert((StructNode) node);
     nodeReadOnlyTrx.setCurrentNode(node);
     nodeHashing.adaptHashesWithAdd();
 
@@ -1642,12 +1663,10 @@ private void checkAccessAndCommit() {
    * Adapting everything for insert operations.
    *
    * @param structNode pointer of the new node to be inserted
-   * @param insertPos  determines the position where to insert
    * @throws SirixIOException if anything weird happens
    */
-  private void adaptForInsert(final StructNode structNode, final InsertPos insertPos) {
+  private void adaptForInsert(final StructNode structNode) {
     assert structNode != null;
-    assert insertPos != null;
 
     final StructNode parent =
         (StructNode) pageWriteTrx.prepareEntryForModification(structNode.getParentKey(), PageKind.RECORDPAGE, -1);
@@ -1831,11 +1850,12 @@ public CommitCredentials getCommitCredentials() {
   @Override
   public JsonNodeTrx commit(final String commitMessage) {
     nodeReadOnlyTrx.assertNotClosed();
-    state = State.Committing;
 
     // Optionally lock while commiting and assigning new instances.
     acquireLockIfNecessary();
     try {
+      state = State.Committing;
+
       // Execute pre-commit hooks.
       for (final PreCommitHook hook : preCommitHooks) {
         hook.preCommit(this);
@@ -1854,7 +1874,7 @@ public JsonNodeTrx commit(final String commitMessage) {
       }
 
       // Reinstantiate everything.
-      if (afterCommitState == AbstractResourceManager.AfterCommitState.KeepOpen) {
+      if (afterCommitState == AfterCommitState.KeepOpen) {
         reInstantiate(getId(), getRevisionNumber());
         state = State.Running;
       } else {

bundles/sirix-core/src/main/java/org/sirix/access/trx/node/json/JsonResourceManagerImpl.java

@@ -26,8 +26,8 @@
 import org.sirix.access.User;
 import org.sirix.access.json.JsonResourceStore;
 import org.sirix.access.trx.node.AbstractResourceManager;
+import org.sirix.access.trx.node.AfterCommitState;
 import org.sirix.access.trx.node.InternalResourceManager;
-import org.sirix.access.trx.node.xml.XmlIndexController;
 import org.sirix.api.Database;
 import org.sirix.api.PageReadOnlyTrx;
 import org.sirix.api.PageTrx;

bundles/sirix-core/src/main/java/org/sirix/access/trx/node/xml/XmlNodeTrxImpl.java

@@ -26,7 +26,7 @@
 import com.google.common.base.Preconditions;
 import org.brackit.xquery.atomic.QNm;
 import org.sirix.access.User;
-import org.sirix.access.trx.node.AbstractResourceManager;
+import org.sirix.access.trx.node.AfterCommitState;
 import org.sirix.access.trx.node.CommitCredentials;
 import org.sirix.access.trx.node.HashType;
 import org.sirix.access.trx.node.InternalResourceManager;
@@ -114,7 +114,7 @@ final class XmlNodeTrxImpl extends AbstractForwardingXmlNodeReadOnlyTrx implemen
    */
   private final XmlDeweyIDManager deweyIDManager;
 
-  private final AbstractResourceManager.AfterCommitState afterCommitState;
+  private final AfterCommitState afterCommitState;
 
   /**
    * Modification counter.
@@ -220,7 +220,7 @@ final class XmlNodeTrxImpl extends AbstractForwardingXmlNodeReadOnlyTrx implemen
       final InternalXmlNodeReadOnlyTrx nodeReadOnlyTrx, final PathSummaryWriter<XmlNodeReadOnlyTrx> pathSummaryWriter,
       final @Nonnegative int maxNodeCount, final TimeUnit timeUnit, final @Nonnegative int maxTime,
       final @Nonnull XmlNodeHashing nodeHashing, final XmlNodeFactory nodeFactory,
-      final AbstractResourceManager.AfterCommitState afterCommitState) {
+      final @Nonnull AfterCommitState afterCommitState) {
     // Do not accept negative values.
     Preconditions.checkArgument(maxNodeCount >= 0 && maxTime >= 0,
                                 "Negative arguments for maxNodeCount and maxTime are not accepted.");

bundles/sirix-core/src/main/java/org/sirix/access/trx/node/xml/XmlResourceManagerImpl.java

@@ -25,6 +25,7 @@
 import org.sirix.access.ResourceConfiguration;
 import org.sirix.access.User;
 import org.sirix.access.trx.node.AbstractResourceManager;
+import org.sirix.access.trx.node.AfterCommitState;
 import org.sirix.access.trx.node.InternalResourceManager;
 import org.sirix.access.xml.XmlResourceStore;
 import org.sirix.api.Database;