proper pages

.github/workflows/server.yml

@@ -43,11 +43,11 @@ jobs:
           distribution: "zulu"
           cache: maven
 
-      - name: Build LazyFS
+      # - name: Build LazyFS
-        run: cd thirdparty/lazyfs/ && ./build.sh
+      #   run: cd thirdparty/lazyfs/ && ./build.sh
 
       - name: Test with Maven
-        run: cd dhfs-parent && mvn -T $(nproc) --batch-mode --update-snapshots package verify
+        run: cd dhfs-parent && mvn -T $(nproc) --batch-mode --update-snapshots javadoc:aggregate
 
       # - name: Build with Maven
       #   run: cd dhfs-parent && mvn --batch-mode --update-snapshots package # -Dquarkus.log.category.\"com.usatiuk.dhfs\".min-level=DEBUG
@@ -57,6 +57,11 @@ jobs:
           name: DHFS Server Package
           path: dhfs-parent/dhfs-fuse/target/quarkus-app
 
+      - uses: actions/upload-artifact@v4
+        with:
+          name: DHFS Javadocs
+          path: dhfs-parent/target/reports/apidocs/
+
       - uses: actions/upload-artifact@v4
         if: ${{ always() }}
         with:
@@ -231,3 +236,37 @@ jobs:
         with:
           name: Run wrapper
           path: ~/run-wrapper.tar.gz
+
+  publish-javadoc:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+
+    needs: [build-webui, build-dhfs]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: DHFS Javadocs
+          path: dhfs-javadocs-downloaded
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload entire repository
+          path: 'dhfs-javadocs-downloaded'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+
+

dhfs-parent/.gitignore

@@ -41,3 +41,5 @@ nb-configuration.xml
 
 # Plugin directory
 /.quarkus/cli/plugins/
+
+.jqwik-database

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/ChunkData.java

@@ -5,6 +5,11 @@ import com.usatiuk.dhfs.remoteobj.JDataRemote;
 import com.usatiuk.dhfs.remoteobj.JDataRemoteDto;
 import com.usatiuk.objects.JObjectKey;
 
+/**
+ * ChunkData is a data structure that represents an immutable binary blob
+ * @param key unique key
+ * @param data binary data
+ */
 public record ChunkData(JObjectKey key, ByteString data) implements JDataRemote, JDataRemoteDto {
     @Override
     public int estimateSize() {

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/ChunkDataProtoSerializer.java

@@ -1,26 +0,0 @@
-package com.usatiuk.dhfsfs.objects;
-
-import com.usatiuk.dhfs.ProtoSerializer;
-import com.usatiuk.dhfs.persistence.ChunkDataP;
-import com.usatiuk.dhfs.persistence.JObjectKeyP;
-import com.usatiuk.objects.JObjectKey;
-import jakarta.inject.Singleton;
-
-@Singleton
-public class ChunkDataProtoSerializer implements ProtoSerializer<ChunkDataP, ChunkData> {
-    @Override
-    public ChunkData deserialize(ChunkDataP message) {
-        return new ChunkData(
-                JObjectKey.of(message.getKey().getName()),
-                message.getData()
-        );
-    }
-
-    @Override
-    public ChunkDataP serialize(ChunkData object) {
-        return ChunkDataP.newBuilder()
-                .setKey(JObjectKeyP.newBuilder().setName(object.key().value()).build())
-                .setData(object.data())
-                .build();
-    }
-}

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/File.java

@@ -9,6 +9,14 @@ import com.usatiuk.objects.JObjectKey;
 import java.util.Collection;
 import java.util.Set;
 
+/**
+ * File is a data structure that represents a file in the file system
+ * @param key unique key
+ * @param mode file mode
+ * @param cTime creation time
+ * @param mTime modification time
+ * @param symlink true if the file is a symlink, false otherwise
+ */
 public record File(JObjectKey key, long mode, long cTime, long mTime,
                    boolean symlink
 ) implements JDataRemote, JMapHolder<JMapLongKey> {

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/FileDto.java

@@ -7,6 +7,11 @@ import org.apache.commons.lang3.tuple.Pair;
 
 import java.util.List;
 
+/**
+ * FileDto is a data transfer object that contains a file and its chunks.
+ * @param file the file
+ * @param chunks the list of chunks, each represented as a pair of a long and a JObjectKey
+ */
 public record FileDto(File file, List<Pair<Long, JObjectKey>> chunks) implements JDataRemoteDto {
     @Override
     public Class<? extends JDataRemote> objClass() {

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/FileDtoMapper.java

@@ -5,6 +5,9 @@ import com.usatiuk.dhfs.syncmap.DtoMapper;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
 
+/**
+ * Maps a {@link File} object to a {@link FileDto} object and vice versa.
+ */
 @ApplicationScoped
 public class FileDtoMapper implements DtoMapper<File, FileDto> {
     @Inject

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/FileHelper.java

@@ -10,11 +10,20 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * Helper class for working with files.
+ */
 @ApplicationScoped
 public class FileHelper {
     @Inject
     JMapHelper jMapHelper;
 
+    /**
+     * Get the chunks of a file.
+     * Transaction is expected to be already started.
+     * @param file the file to get chunks from
+     * @return a list of pairs of chunk offset and chunk key
+     */
     public List<Pair<Long, JObjectKey>> getChunks(File file) {
         ArrayList<Pair<Long, JObjectKey>> chunks = new ArrayList<>();
         try (var it = jMapHelper.getIterator(file)) {
@@ -26,6 +35,13 @@ public class FileHelper {
         return List.copyOf(chunks);
     }
 
+    /**
+     * Replace the chunks of a file.
+     * All previous chunks will be deleted.
+     * Transaction is expected to be already started.
+     * @param file the file to replace chunks in
+     * @param chunks the list of pairs of chunk offset and chunk key
+     */
     public void replaceChunks(File file, List<Pair<Long, JObjectKey>> chunks) {
         jMapHelper.deleteAll(file);
 

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/FileProtoSerializer.java

@@ -1,25 +0,0 @@
-package com.usatiuk.dhfsfs.objects;
-
-import com.usatiuk.dhfs.ProtoSerializer;
-import com.usatiuk.dhfs.persistence.FileDtoP;
-import com.usatiuk.utils.SerializationHelper;
-import jakarta.inject.Singleton;
-
-import java.io.IOException;
-
-@Singleton
-public class FileProtoSerializer implements ProtoSerializer<FileDtoP, FileDto> {
-    @Override
-    public FileDto deserialize(FileDtoP message) {
-        try (var is = message.getSerializedData().newInput()) {
-            return SerializationHelper.deserialize(is);
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        }
-    }
-
-    @Override
-    public FileDtoP serialize(FileDto object) {
-        return FileDtoP.newBuilder().setSerializedData(SerializationHelper.serialize(object)).build();
-    }
-}

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/FileSyncHandler.java

@@ -23,6 +23,9 @@ import javax.annotation.Nullable;
 import java.util.List;
 import java.util.Objects;
 
+/**
+ * Handles synchronization of file objects.
+ */
 @ApplicationScoped
 public class FileSyncHandler implements ObjSyncHandler<File, FileDto> {
     @Inject
@@ -45,6 +48,14 @@ public class FileSyncHandler implements ObjSyncHandler<File, FileDto> {
         return jKleppmannTreeManager.getTree(JObjectKey.of("fs")).orElseThrow();
     }
 
+    /**
+     * Resolve conflict between two file versions, update the file in storage and create a conflict file.
+     *
+     * @param from              the peer that sent the update
+     * @param key               the key of the file
+     * @param receivedChangelog the changelog of the received file
+     * @param receivedData      the received file data
+     */
     private void resolveConflict(PeerId from, JObjectKey key, PMap<PeerId, Long> receivedChangelog,
                                  @Nullable FileDto receivedData) {
         var oursCurMeta = curTx.get(RemoteObjectMeta.class, key).orElse(null);

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/JKleppmannTreeNodeMetaDirectory.java

@@ -6,6 +6,10 @@ import com.usatiuk.objects.JObjectKey;
 import java.util.Collection;
 import java.util.List;
 
+/**
+ * JKleppmannTreeNodeMetaDirectory is a record that represents a directory in the JKleppmann tree.
+ * @param name the name of the directory
+ */
 public record JKleppmannTreeNodeMetaDirectory(String name) implements JKleppmannTreeNodeMeta {
     public JKleppmannTreeNodeMeta withName(String name) {
         return new JKleppmannTreeNodeMetaDirectory(name);

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/JKleppmannTreeNodeMetaFile.java

@@ -6,6 +6,11 @@ import com.usatiuk.objects.JObjectKey;
 import java.util.Collection;
 import java.util.List;
 
+/**
+ * JKleppmannTreeNodeMetaFile is a record that represents a file in the JKleppmann tree.
+ * @param name the name of the file
+ * @param fileIno a reference to the `File` object
+ */
 public record JKleppmannTreeNodeMetaFile(String name, JObjectKey fileIno) implements JKleppmannTreeNodeMeta {
     @Override
     public JKleppmannTreeNodeMeta withName(String name) {

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/service/DhfsFileService.java

@@ -39,6 +39,9 @@ import java.nio.file.Path;
 import java.util.*;
 import java.util.stream.StreamSupport;
 
+/**
+ * Actual filesystem implementation.
+ */
 @ApplicationScoped
 public class DhfsFileService {
     @ConfigProperty(name = "dhfs.files.target_chunk_alignment")
@@ -71,6 +74,12 @@ public class DhfsFileService {
         return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), () -> new JKleppmannTreeNodeMetaDirectory(""));
     }
 
+    /**
+     * Create a new chunk with the given data and a new unique ID.
+     *
+     * @param bytes the data to store in the chunk
+     * @return the created chunk
+     */
     private ChunkData createChunk(ByteString bytes) {
         var newChunk = new ChunkData(JObjectKey.of(UUID.randomUUID().toString()), bytes);
         remoteTx.putDataNew(newChunk);
@@ -82,14 +91,7 @@ public class DhfsFileService {
         getTree();
     }
 
-    private JKleppmannTreeNode getDirEntryW(String name) {
+    private JKleppmannTreeNode getDirEntry(String name) {
-        var res = getTree().traverse(StreamSupport.stream(Path.of(name).spliterator(), false).map(p -> p.toString()).toList());
-        if (res == null) throw new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND);
-        var ret = curTx.get(JKleppmannTreeNodeHolder.class, res).map(JKleppmannTreeNodeHolder::node).orElseThrow(() -> new StatusRuntimeException(Status.NOT_FOUND.withDescription("Tree node exists but not found as jObject: " + name)));
-        return ret;
-    }
-
-    private JKleppmannTreeNode getDirEntryR(String name) {
         var res = getTree().traverse(StreamSupport.stream(Path.of(name).spliterator(), false).map(p -> p.toString()).toList());
         if (res == null) throw new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND);
         var ret = curTx.get(JKleppmannTreeNodeHolder.class, res).map(JKleppmannTreeNodeHolder::node).orElseThrow(() -> new StatusRuntimeException(Status.NOT_FOUND.withDescription("Tree node exists but not found as jObject: " + name)));
@@ -103,6 +105,11 @@ public class DhfsFileService {
         return ret;
     }
 
+    /**
+     * Get the attributes of a file or directory.
+     * @param uuid the UUID of the file or directory
+     * @return the attributes of the file or directory
+     */
     public Optional<GetattrRes> getattr(JObjectKey uuid) {
         return jObjectTxManager.executeTx(() -> {
             var ref = curTx.get(JData.class, uuid).orElse(null);
@@ -124,10 +131,15 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Try to resolve a path to a file or directory.
+     * @param name the path to resolve
+     * @return the key of the file or directory, or an empty optional if it does not exist
+     */
     public Optional<JObjectKey> open(String name) {
         return jObjectTxManager.executeTx(() -> {
             try {
-                var ret = getDirEntryR(name);
+                var ret = getDirEntry(name);
                 return switch (ret.meta()) {
                     case JKleppmannTreeNodeMetaFile f -> Optional.of(f.fileIno());
                     case JKleppmannTreeNodeMetaDirectory f -> Optional.of(ret.key());
@@ -147,10 +159,16 @@ public class DhfsFileService {
             throw new StatusRuntimeExceptionNoStacktrace(Status.INVALID_ARGUMENT.withDescription("Not a directory: " + entry.key()));
     }
 
+    /**
+     * Create a new file with the given name and mode.
+     * @param name the name of the file
+     * @param mode the mode of the file
+     * @return the key of the created file
+     */
     public Optional<JObjectKey> create(String name, long mode) {
         return jObjectTxManager.executeTx(() -> {
             Path path = Path.of(name);
-            var parent = getDirEntryW(path.getParent().toString());
+            var parent = getDirEntry(path.getParent().toString());
 
             ensureDir(parent);
 
@@ -171,9 +189,14 @@ public class DhfsFileService {
         });
     }
 
-    //FIXME: Slow..
+    /**
+     * Get the parent directory of a file or directory.
+     * @param ino the key of the file or directory
+     * @return the parent directory
+     */
     public Pair<String, JObjectKey> inoToParent(JObjectKey ino) {
         return jObjectTxManager.executeTx(() -> {
+            // FIXME: Slow
             return getTree().findParent(w -> {
                 if (w.meta() instanceof JKleppmannTreeNodeMetaFile f)
                     return f.fileIno().equals(ino);
@@ -182,20 +205,31 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Create a new directory with the given name and mode.
+     * @param name the name of the directory
+     * @param mode the mode of the directory
+     */
     public void mkdir(String name, long mode) {
         jObjectTxManager.executeTx(() -> {
             Path path = Path.of(name);
-            var parent = getDirEntryW(path.getParent().toString());
+            var parent = getDirEntry(path.getParent().toString());
             ensureDir(parent);
 
             String dname = path.getFileName().toString();
 
             Log.debug("Creating directory " + name);
 
+            // TODO: No modes for directories yet
             getTree().move(parent.key(), new JKleppmannTreeNodeMetaDirectory(dname), getTree().getNewNodeId());
         });
     }
 
+    /**
+     * Unlink a file or directory.
+     * @param name the name of the file or directory
+     * @throws DirectoryNotEmptyException if the directory is not empty and recursive delete is not allowed
+     */
     public void unlink(String name) {
         jObjectTxManager.executeTx(() -> {
             var node = getDirEntryOpt(name).orElse(null);
@@ -209,13 +243,19 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Rename a file or directory.
+     * @param from the old name
+     * @param to the new name
+     * @return true if the rename was successful, false otherwise
+     */
     public Boolean rename(String from, String to) {
         return jObjectTxManager.executeTx(() -> {
-            var node = getDirEntryW(from);
+            var node = getDirEntry(from);
             JKleppmannTreeNodeMeta meta = node.meta();
 
             var toPath = Path.of(to);
-            var toDentry = getDirEntryW(toPath.getParent().toString());
+            var toDentry = getDirEntry(toPath.getParent().toString());
             ensureDir(toDentry);
 
             getTree().move(toDentry.key(), meta.withName(toPath.getFileName().toString()), node.key());
@@ -223,6 +263,12 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Change the mode of a file or directory.
+     * @param uuid the ID of the file or directory
+     * @param mode the new mode
+     * @return true if the mode was changed successfully, false otherwise
+     */
     public Boolean chmod(JObjectKey uuid, long mode) {
         return jObjectTxManager.executeTx(() -> {
             var dent = curTx.get(JData.class, uuid).orElseThrow(() -> new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND));
@@ -243,9 +289,14 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Read the contents of a directory.
+     * @param name the path of the directory
+     * @return an iterable of the names of the files in the directory
+     */
     public Iterable<String> readDir(String name) {
         return jObjectTxManager.executeTx(() -> {
-            var found = getDirEntryW(name);
+            var found = getDirEntry(name);
 
             if (!(found.meta() instanceof JKleppmannTreeNodeMetaDirectory md))
                 throw new StatusRuntimeException(Status.INVALID_ARGUMENT);
@@ -254,6 +305,13 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Read the contents of a file.
+     * @param fileUuid the ID of the file
+     * @param offset the offset to start reading from
+     * @param length the number of bytes to read
+     * @return the contents of the file as a ByteString
+     */
     public ByteString read(JObjectKey fileUuid, long offset, int length) {
         return jObjectTxManager.executeTx(() -> {
             if (length < 0)
@@ -315,6 +373,11 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Get the size of a file.
+     * @param uuid the ID of the file
+     * @return the size of the file
+     */
     private ByteString readChunk(JObjectKey uuid) {
         var chunkRead = remoteTx.getData(ChunkData.class, uuid).orElse(null);
 
@@ -326,6 +389,11 @@ public class DhfsFileService {
         return chunkRead.data();
     }
 
+    /**
+     * Get the size of a chunk.
+     * @param uuid the ID of the chunk
+     * @return the size of the chunk
+     */
     private int getChunkSize(JObjectKey uuid) {
         return readChunk(uuid).size();
     }
@@ -334,6 +402,13 @@ public class DhfsFileService {
         return num & -(1L << n);
     }
 
+    /**
+     * Write data to a file.
+     * @param fileUuid the ID of the file
+     * @param offset the offset to write to
+     * @param data the data to write
+     * @return the number of bytes written
+     */
     public Long write(JObjectKey fileUuid, long offset, ByteString data) {
         return jObjectTxManager.executeTx(() -> {
             if (offset < 0)
@@ -436,6 +511,12 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Truncate a file to the given length.
+     * @param fileUuid the ID of the file
+     * @param length the new length of the file
+     * @return true if the truncate was successful, false otherwise
+     */
     public Boolean truncate(JObjectKey fileUuid, long length) {
         return jObjectTxManager.executeTx(() -> {
             if (length < 0)
@@ -525,6 +606,12 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Fill the given range with zeroes.
+     * @param fillStart the start of the range
+     * @param length the end of the range
+     * @param newChunks the map to store the new chunks in
+     */
     private void fillZeros(long fillStart, long length, Map<Long, JObjectKey> newChunks) {
         long combinedSize = (length - fillStart);
 
@@ -560,12 +647,22 @@ public class DhfsFileService {
         }
     }
 
+    /**
+     * Read the contents of a symlink.
+     * @param uuid the ID of the symlink
+     * @return the contents of the symlink as a string
+     */
     public String readlink(JObjectKey uuid) {
         return jObjectTxManager.executeTx(() -> {
             return readlinkBS(uuid).toStringUtf8();
         });
     }
 
+    /**
+     * Read the contents of a symlink as a ByteString.
+     * @param uuid the ID of the symlink
+     * @return the contents of the symlink as a ByteString
+     */
     public ByteString readlinkBS(JObjectKey uuid) {
         return jObjectTxManager.executeTx(() -> {
             var fileOpt = remoteTx.getData(File.class, uuid).orElseThrow(() -> new StatusRuntimeException(Status.NOT_FOUND.withDescription("File not found when trying to readlink: " + uuid)));
@@ -573,10 +670,16 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Create a symlink.
+     * @param oldpath the target of the symlink
+     * @param newpath the path of the symlink
+     * @return the key of the created symlink
+     */
     public JObjectKey symlink(String oldpath, String newpath) {
         return jObjectTxManager.executeTx(() -> {
             Path path = Path.of(newpath);
-            var parent = getDirEntryW(path.getParent().toString());
+            var parent = getDirEntry(path.getParent().toString());
 
             ensureDir(parent);
 
@@ -595,6 +698,13 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Set the access and modification times of a file.
+     * @param fileUuid the ID of the file
+     * @param atimeMs the access time in milliseconds
+     * @param mtimeMs the modification time in milliseconds
+     * @return true if the times were set successfully, false otherwise
+     */
     public Boolean setTimes(JObjectKey fileUuid, long atimeMs, long mtimeMs) {
         return jObjectTxManager.executeTx(() -> {
             var dent = curTx.get(JData.class, fileUuid).orElseThrow(() -> new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND));
@@ -616,6 +726,11 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Get the size of a file.
+     * @param fileUuid the ID of the file
+     * @return the size of the file
+     */
     public long size(JObjectKey fileUuid) {
         return jObjectTxManager.executeTx(() -> {
             long realSize = 0;
@@ -635,6 +750,13 @@ public class DhfsFileService {
         });
     }
 
+    /**
+     * Write data to a file.
+     * @param fileUuid the ID of the file
+     * @param offset the offset to write to
+     * @param data the data to write
+     * @return the number of bytes written
+     */
     public Long write(JObjectKey fileUuid, long offset, byte[] data) {
         return write(fileUuid, offset, UnsafeByteOperations.unsafeWrap(data));
     }

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/service/DirectoryNotEmptyException.java

@@ -1,5 +1,10 @@
 package com.usatiuk.dhfsfs.service;
 
+/**
+ * DirectoryNotEmptyException is thrown when a directory is not empty.
+ * This exception is used to indicate that a directory cannot be deleted
+ * because it contains files or subdirectories.
+ */
 public class DirectoryNotEmptyException extends RuntimeException {
     @Override
     public synchronized Throwable fillInStackTrace() {

dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/service/GetattrRes.java

@@ -1,4 +1,11 @@
 package com.usatiuk.dhfsfs.service;
 
-public record GetattrRes(long mtime, long ctime, long mode, GetattrType type) {
+/**
+ * GetattrRes is a record that represents the result of a getattr operation.
+ * @param mtime File modification time
+ * @param ctime File creation time
+ * @param mode File mode
+ * @param type File type
+ */
+ public record GetattrRes(long mtime, long ctime, long mode, GetattrType type) {
 }

dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/LazyFsIT.java

@@ -154,7 +154,7 @@ public class LazyFsIT {
         Thread.sleep(3000);
         Log.info("Killing");
         lazyFs1.crash();
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container1.getContainerId()).exec();
         container1.stop();
@@ -195,7 +195,7 @@ public class LazyFsIT {
             lazyFs1.crash();
         }
         try {
-            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());
@@ -237,7 +237,7 @@ public class LazyFsIT {
         Thread.sleep(3000);
         Log.info("Killing");
         lazyFs1.crash();
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container1.getContainerId()).exec();
         container1.stop();
@@ -279,7 +279,7 @@ public class LazyFsIT {
             lazyFs1.crash();
         }
         try {
-            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());
@@ -322,7 +322,7 @@ public class LazyFsIT {
         Log.info("Killing");
         lazyFs2.crash();
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting1");
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container2.getContainerId()).exec();
         container2.stop();
@@ -366,7 +366,7 @@ public class LazyFsIT {
         }
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting2");
         try {
-            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());
@@ -409,7 +409,7 @@ public class LazyFsIT {
         Log.info("Killing");
         lazyFs2.crash();
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting1");
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container2.getContainerId()).exec();
         container2.stop();
@@ -453,7 +453,7 @@ public class LazyFsIT {
         }
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting2");
         try {
-            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
+            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());

dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/AtomicClock.java

@@ -1,32 +0,0 @@
-package com.usatiuk.kleppmanntree;
-
-import java.io.Serializable;
-
-public class AtomicClock implements Clock<Long>, Serializable {
-    private long _max = 0;
-
-    public AtomicClock(long counter) {
-        _max = counter;
-    }
-
-    @Override
-    public Long getTimestamp() {
-        return ++_max;
-    }
-
-    public void setTimestamp(Long timestamp) {
-        _max = timestamp;
-    }
-
-    @Override
-    public Long peekTimestamp() {
-        return _max;
-    }
-
-    @Override
-    public Long updateTimestamp(Long receivedTimestamp) {
-        var old = _max;
-        _max = Math.max(_max, receivedTimestamp) + 1;
-        return old;
-    }
-}

dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/CloseableKvIterator.java

@@ -1,11 +1,10 @@
 package com.usatiuk.objects.iterators;
 
-import com.usatiuk.utils.AutoCloseableNoThrow;
 import org.apache.commons.lang3.tuple.Pair;
 
 import java.util.Iterator;
 
-public interface CloseableKvIterator<K extends Comparable<? super K>, V> extends Iterator<Pair<K, V>>, AutoCloseableNoThrow {
+public interface CloseableKvIterator<K extends Comparable<? super K>, V> extends Iterator<Pair<K, V>>, AutoCloseable {
     K peekNextKey();
 
     void skip();
@@ -21,4 +20,7 @@ public interface CloseableKvIterator<K extends Comparable<? super K>, V> extends
     default CloseableKvIterator<K, V> reversed() {
         return new ReversedKvIterator<K, V>(this);
     }
+
+    @Override
+    void close();
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/snapshot/Snapshot.java

@@ -3,19 +3,20 @@ package com.usatiuk.objects.snapshot;
 import com.usatiuk.objects.iterators.CloseableKvIterator;
 import com.usatiuk.objects.iterators.IteratorStart;
 import com.usatiuk.objects.iterators.MaybeTombstone;
-import com.usatiuk.objects.iterators.Tombstone;
-import com.usatiuk.utils.AutoCloseableNoThrow;
 
 import javax.annotation.Nonnull;
 import java.util.List;
 import java.util.Optional;
-import java.util.stream.Stream;
 
-public interface Snapshot<K extends Comparable<K>, V> extends AutoCloseableNoThrow {
+public interface Snapshot<K extends Comparable<K>, V> extends AutoCloseable {
     List<CloseableKvIterator<K, MaybeTombstone<V>>> getIterator(IteratorStart start, K key);
 
     @Nonnull
     Optional<V> readObject(K name);
 
     long id();
+
+    @Override
+    void close();
+
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/CachingObjectPersistentStore.java

@@ -31,7 +31,6 @@ public class CachingObjectPersistentStore {
     SerializingObjectPersistentStore delegate;
     @ConfigProperty(name = "dhfs.objects.lru.print-stats")
     boolean printStats;
-    private ExecutorService _commitExecutor;
     private ExecutorService _statusExecutor;
     private AtomicLong _cached = new AtomicLong();
     private AtomicLong _cacheTries = new AtomicLong();
@@ -47,7 +46,6 @@ public class CachingObjectPersistentStore {
             _cache.set(_cache.get().withVersion(s.id()));
         }
 
-        _commitExecutor = Executors.newSingleThreadExecutor();
         if (printStats) {
             _statusExecutor = Executors.newSingleThreadExecutor();
             _statusExecutor.submit(() -> {
@@ -68,7 +66,6 @@ public class CachingObjectPersistentStore {
         Log.tracev("Committing: {0} writes, {1} deletes", objs.written().size(), objs.deleted().size());
 
         var cache = _cache.get();
-        var commitFuture = _commitExecutor.submit(() -> delegate.prepareTx(objs, txId).run());
         for (var write : objs.written()) {
             cache = cache.withPut(write.getLeft(), Optional.of(write.getRight()));
         }
@@ -76,11 +73,7 @@ public class CachingObjectPersistentStore {
             cache = cache.withPut(del, Optional.empty());
         }
         cache = cache.withVersion(txId);
-        try {
+        delegate.commitTx(objs, txId);
-            commitFuture.get();
-        } catch (Exception e) {
-            throw new RuntimeException(e);
-        }
         _cache.set(cache);
 
         Log.tracev("Committed: {0} writes, {1} deletes", objs.written().size(), objs.deleted().size());

dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/LmdbObjectPersistentStore.java

@@ -145,10 +145,9 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
     }
 
     @Override
-    public Runnable prepareTx(TxManifestRaw names, long txId) {
+    public void commitTx(TxManifestRaw names, long txId) {
         verifyReady();
-        var txn = _env.txnWrite();
+        try (var txn = _env.txnWrite()) {
-        try {
             for (var written : names.written()) {
                 var putBb = _db.reserve(txn, written.getKey().toByteBuffer(), written.getValue().size());
                 written.getValue().copyTo(putBb);
@@ -163,17 +162,8 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
             bbData.putLong(txId);
             bbData.flip();
             _db.put(txn, DB_VER_OBJ_NAME.asReadOnlyBuffer(), bbData);
-        } catch (Throwable t) {
+            txn.commit();
-            txn.close();
-            throw t;
         }
-        return () -> {
-            try {
-                txn.commit();
-            } finally {
-                txn.close();
-            }
-        };
     }
 
     @Override
@@ -188,12 +178,6 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
         return _root.toFile().getFreeSpace();
     }
 
-    @Override
-    public long getUsableSpace() {
-        verifyReady();
-        return _root.toFile().getUsableSpace();
-    }
-
     private class LmdbKvIterator extends ReversibleKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>> {
         private static final Cleaner CLEANER = Cleaner.create();
         private final Txn<ByteBuffer> _txn; // Managed by the snapshot

dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/MemoryObjectPersistentStore.java

@@ -53,19 +53,18 @@ public class MemoryObjectPersistentStore implements ObjectPersistentStore {
         }
     }
 
-    public Runnable prepareTx(TxManifestRaw names, long txId) {
+    @Override
-        return () -> {
+    public void commitTx(TxManifestRaw names, long txId) {
-            synchronized (this) {
+        synchronized (this) {
-                for (var written : names.written()) {
+            for (var written : names.written()) {
-                    _objects = _objects.plus(written.getKey(), written.getValue());
+                _objects = _objects.plus(written.getKey(), written.getValue());
-                }
-                for (JObjectKey key : names.deleted()) {
-                    _objects = _objects.minus(key);
-                }
-                assert txId > _lastCommitId;
-                _lastCommitId = txId;
             }
-        };
+            for (JObjectKey key : names.deleted()) {
+                _objects = _objects.minus(key);
+            }
+            assert txId > _lastCommitId;
+            _lastCommitId = txId;
+        }
     }
 
     @Override
@@ -77,9 +76,4 @@ public class MemoryObjectPersistentStore implements ObjectPersistentStore {
     public long getFreeSpace() {
         return 0;
     }
-
-    @Override
-    public long getUsableSpace() {
-        return 0;
-    }
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/ObjectPersistentStore.java

@@ -13,11 +13,9 @@ import java.util.Optional;
 public interface ObjectPersistentStore {
     Snapshot<JObjectKey, ByteBuffer> getSnapshot();
 
-    Runnable prepareTx(TxManifestRaw names, long txId);
+    void commitTx(TxManifestRaw names, long txId);
 
     long getTotalSpace();
 
     long getFreeSpace();
-
-    long getUsableSpace();
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/SerializingObjectPersistentStore.java

@@ -62,7 +62,7 @@ public class SerializingObjectPersistentStore {
                 , objs.deleted());
     }
 
-    Runnable prepareTx(TxManifestObj<? extends JDataVersionedWrapper> objects, long txId) {
+    void commitTx(TxManifestObj<? extends JDataVersionedWrapper> objects, long txId) {
-        return delegateStore.prepareTx(prepareManifest(objects), txId);
+        delegateStore.commitTx(prepareManifest(objects), txId);
     }
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/WritebackObjectPersistentStore.java

@@ -188,7 +188,7 @@ public class WritebackObjectPersistentStore {
         Log.info("Writeback thread exiting");
     }
 
-    public long commitBundle(Collection<TxRecord.TxObjectRecord<?>> writes) {
+    private long commitBundle(Collection<TxRecord.TxObjectRecord<?>> writes) {
         verifyReady();
         _pendingBundleLock.lock();
         try {

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionFactory.java

@@ -1,5 +0,0 @@
-package com.usatiuk.objects.transaction;
-
-public interface TransactionFactory {
-    TransactionPrivate createTransaction();
-}

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionFactoryImpl.java

@@ -1,262 +0,0 @@
-package com.usatiuk.objects.transaction;
-
-import com.usatiuk.objects.JData;
-import com.usatiuk.objects.JDataVersionedWrapper;
-import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.iterators.*;
-import com.usatiuk.objects.snapshot.Snapshot;
-import com.usatiuk.objects.stores.WritebackObjectPersistentStore;
-import com.usatiuk.utils.ListUtils;
-import io.quarkus.logging.Log;
-import jakarta.inject.Inject;
-import jakarta.inject.Singleton;
-import org.apache.commons.lang3.tuple.Pair;
-import org.eclipse.microprofile.config.inject.ConfigProperty;
-
-import java.util.*;
-
-@Singleton
-public class TransactionFactoryImpl implements TransactionFactory {
-    @Inject
-    WritebackObjectPersistentStore writebackObjectPersistentStore;
-
-    @Override
-    public TransactionPrivate createTransaction() {
-        return new TransactionImpl();
-    }
-
-    private interface ReadTrackingInternalCrap {
-        boolean fromSource();
-
-        JData obj();
-    }
-
-    // FIXME:
-    private record ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped) implements ReadTrackingInternalCrap {
-        @Override
-        public boolean fromSource() {
-            return true;
-        }
-
-        @Override
-        public JData obj() {
-            return wrapped.data();
-        }
-    }
-
-    private record ReadTrackingInternalCrapTx(JData obj) implements ReadTrackingInternalCrap {
-        @Override
-        public boolean fromSource() {
-            return false;
-        }
-    }
-
-    private class TransactionImpl implements TransactionPrivate {
-        private final Map<JObjectKey, Optional<JDataVersionedWrapper>> _readSet = new HashMap<>();
-        private final NavigableMap<JObjectKey, TxRecord.TxObjectRecord<?>> _writes = new TreeMap<>();
-        private final List<Runnable> _onCommit = new LinkedList<>();
-        private final List<Runnable> _onFlush = new LinkedList<>();
-        private final HashSet<JObjectKey> _knownNew = new HashSet<>();
-        private final Snapshot<JObjectKey, JDataVersionedWrapper> _snapshot;
-        private boolean _closed = false;
-
-        private boolean _writeTrack = false;
-        private Map<JObjectKey, TxRecord.TxObjectRecord<?>> _newWrites = new HashMap<>();
-
-        private TransactionImpl() {
-            _snapshot = writebackObjectPersistentStore.getSnapshot();
-        }
-
-        @Override
-        public void onCommit(Runnable runnable) {
-            _onCommit.add(runnable);
-        }
-
-        @Override
-        public void onFlush(Runnable runnable) {
-            _onFlush.add(runnable);
-        }
-
-        @Override
-        public Collection<Runnable> getOnCommit() {
-            return Collections.unmodifiableCollection(_onCommit);
-        }
-
-        @Override
-        public Snapshot<JObjectKey, JDataVersionedWrapper> snapshot() {
-            return _snapshot;
-        }
-
-        @Override
-        public Collection<Runnable> getOnFlush() {
-            return Collections.unmodifiableCollection(_onFlush);
-        }
-
-        @Override
-        public <T extends JData> Optional<T> getFromSource(Class<T> type, JObjectKey key) {
-            if (_knownNew.contains(key)) {
-                return Optional.empty();
-            }
-
-            return _readSet.computeIfAbsent(key, _snapshot::readObject)
-                    .map(JDataVersionedWrapper::data)
-                    .map(type::cast);
-        }
-
-        @Override
-        public <T extends JData> Optional<T> get(Class<T> type, JObjectKey key) {
-            return switch (_writes.get(key)) {
-                case TxRecord.TxObjectRecordWrite<?> write -> Optional.of(type.cast(write.data()));
-                case TxRecord.TxObjectRecordDeleted deleted -> Optional.empty();
-                case null -> getFromSource(type, key);
-            };
-        }
-
-        @Override
-        public void delete(JObjectKey key) {
-            var record = new TxRecord.TxObjectRecordDeleted(key);
-            if (_writes.put(key, record) instanceof TxRecord.TxObjectRecordDeleted) {
-                return;
-            }
-            if (_writeTrack)
-                _newWrites.put(key, record);
-        }
-
-        @Override
-        public CloseableKvIterator<JObjectKey, JData> getIterator(IteratorStart start, JObjectKey key) {
-            Log.tracev("Getting tx iterator with start={0}, key={1}", start, key);
-            return new ReadTrackingIterator(new TombstoneSkippingIterator<JObjectKey, ReadTrackingInternalCrap>(start, key,
-                    ListUtils.prependAndMap(
-                            new MappingKvIterator<>(new NavigableMapKvIterator<>(_writes, start, key),
-                                    t -> switch (t) {
-                                        case TxRecord.TxObjectRecordWrite<?> write ->
-                                                new DataWrapper<ReadTrackingInternalCrap>(new ReadTrackingInternalCrapTx(write.data()));
-                                        case TxRecord.TxObjectRecordDeleted deleted ->
-                                                new TombstoneImpl<ReadTrackingInternalCrap>();
-                                        case null, default -> null;
-                                    }),
-                            _snapshot.getIterator(start, key),
-                            itin -> new MappingKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>, MaybeTombstone<ReadTrackingInternalCrap>>(itin,
-                                    d -> switch (d) {
-                                        case Data<JDataVersionedWrapper> w ->
-                                                new DataWrapper<>(new ReadTrackingInternalCrapSource(w.value()));
-                                        case Tombstone<JDataVersionedWrapper> t -> new TombstoneImpl<>();
-                                        case null, default -> null;
-                                    }))));
-        }
-
-        @Override
-        public void put(JData obj) {
-            var key = obj.key();
-            var read = _readSet.get(key);
-            if (read != null && (read.map(JDataVersionedWrapper::data).orElse(null) == obj)) {
-                return;
-            }
-
-            var record = new TxRecord.TxObjectRecordWrite<>(obj);
-            _writes.put(key, record);
-            if (_writeTrack)
-                _newWrites.put(key, record);
-        }
-
-        @Override
-        public void putNew(JData obj) {
-            var key = obj.key();
-            _knownNew.add(key);
-
-            var record = new TxRecord.TxObjectRecordWrite<>(obj);
-            _writes.put(key, record);
-            if (_writeTrack)
-                _newWrites.put(key, record);
-        }
-
-        @Override
-        public Collection<TxRecord.TxObjectRecord<?>> drainNewWrites() {
-            if (!_writeTrack) {
-                _writeTrack = true;
-                return Collections.unmodifiableCollection(_writes.values());
-            }
-            var ret = _newWrites;
-            _newWrites = new HashMap<>();
-            return ret.values();
-        }
-
-        @Override
-        public Map<JObjectKey, Optional<JDataVersionedWrapper>> reads() {
-            return _readSet;
-        }
-
-        @Override
-        public Set<JObjectKey> knownNew() {
-            return _knownNew;
-        }
-
-        @Override
-        public void close() {
-            if (_closed) return;
-            _closed = true;
-            _snapshot.close();
-        }
-
-        private class ReadTrackingIterator implements CloseableKvIterator<JObjectKey, JData> {
-            private final CloseableKvIterator<JObjectKey, ReadTrackingInternalCrap> _backing;
-
-            public ReadTrackingIterator(CloseableKvIterator<JObjectKey, ReadTrackingInternalCrap> backing) {
-                _backing = backing;
-            }
-
-            @Override
-            public JObjectKey peekNextKey() {
-                return _backing.peekNextKey();
-            }
-
-            @Override
-            public void skip() {
-                _backing.skip();
-            }
-
-            @Override
-            public JObjectKey peekPrevKey() {
-                return _backing.peekPrevKey();
-            }
-
-            @Override
-            public Pair<JObjectKey, JData> prev() {
-                var got = _backing.prev();
-                if (got.getValue() instanceof ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped)) {
-                    _readSet.putIfAbsent(got.getKey(), Optional.of(wrapped));
-                }
-                return Pair.of(got.getKey(), got.getValue().obj());
-            }
-
-            @Override
-            public boolean hasPrev() {
-                return _backing.hasPrev();
-            }
-
-            @Override
-            public void skipPrev() {
-                _backing.skipPrev();
-            }
-
-            @Override
-            public void close() {
-                _backing.close();
-            }
-
-            @Override
-            public boolean hasNext() {
-                return _backing.hasNext();
-            }
-
-            @Override
-            public Pair<JObjectKey, JData> next() {
-                var got = _backing.next();
-                if (got.getValue() instanceof ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped)) {
-                    _readSet.putIfAbsent(got.getKey(), Optional.of(wrapped));
-                }
-                return Pair.of(got.getKey(), got.getValue().obj());
-            }
-        }
-    }
-}

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionHandlePrivate.java

@@ -1,7 +0,0 @@
-package com.usatiuk.objects.transaction;
-
-import java.util.Collection;
-
-public interface TransactionHandlePrivate extends TransactionHandle {
-    Collection<Runnable> getOnFlush();
-}

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionImpl.java

@@ -0,0 +1,240 @@
+package com.usatiuk.objects.transaction;
+
+import com.usatiuk.objects.JData;
+import com.usatiuk.objects.JDataVersionedWrapper;
+import com.usatiuk.objects.JObjectKey;
+import com.usatiuk.objects.iterators.*;
+import com.usatiuk.objects.snapshot.Snapshot;
+import com.usatiuk.utils.ListUtils;
+import io.quarkus.logging.Log;
+import org.apache.commons.lang3.tuple.Pair;
+
+import java.util.*;
+
+class TransactionImpl implements Transaction, AutoCloseable {
+    private final Map<JObjectKey, Optional<JDataVersionedWrapper>> _readSet = new HashMap<>();
+    private final NavigableMap<JObjectKey, TxRecord.TxObjectRecord<?>> _writes = new TreeMap<>();
+    private final List<Runnable> _onCommit = new LinkedList<>();
+    private final List<Runnable> _onFlush = new LinkedList<>();
+    private final HashSet<JObjectKey> _knownNew = new HashSet<>();
+    private final Snapshot<JObjectKey, JDataVersionedWrapper> _snapshot;
+    private boolean _closed = false;
+
+    private boolean _writeTrack = false;
+    private Map<JObjectKey, TxRecord.TxObjectRecord<?>> _newWrites = new HashMap<>();
+
+    private interface ReadTrackingInternalCrap {
+        boolean fromSource();
+
+        JData obj();
+    }
+
+    // FIXME:
+    private record ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped) implements ReadTrackingInternalCrap {
+        @Override
+        public boolean fromSource() {
+            return true;
+        }
+
+        @Override
+        public JData obj() {
+            return wrapped.data();
+        }
+    }
+
+    private record ReadTrackingInternalCrapTx(JData obj) implements ReadTrackingInternalCrap {
+        @Override
+        public boolean fromSource() {
+            return false;
+        }
+    }
+
+    TransactionImpl(Snapshot<JObjectKey, JDataVersionedWrapper> snapshot) {
+        _snapshot = snapshot;
+    }
+
+    @Override
+    public void onCommit(Runnable runnable) {
+        _onCommit.add(runnable);
+    }
+
+    @Override
+    public void onFlush(Runnable runnable) {
+        _onFlush.add(runnable);
+    }
+
+    Collection<Runnable> getOnCommit() {
+        return Collections.unmodifiableCollection(_onCommit);
+    }
+
+    Snapshot<JObjectKey, JDataVersionedWrapper> snapshot() {
+        return _snapshot;
+    }
+
+    Collection<Runnable> getOnFlush() {
+        return Collections.unmodifiableCollection(_onFlush);
+    }
+
+    <T extends JData> Optional<T> getFromSource(Class<T> type, JObjectKey key) {
+        if (_knownNew.contains(key)) {
+            return Optional.empty();
+        }
+
+        return _readSet.computeIfAbsent(key, _snapshot::readObject)
+                .map(JDataVersionedWrapper::data)
+                .map(type::cast);
+    }
+
+    @Override
+    public <T extends JData> Optional<T> get(Class<T> type, JObjectKey key) {
+        return switch (_writes.get(key)) {
+            case TxRecord.TxObjectRecordWrite<?> write -> Optional.of(type.cast(write.data()));
+            case TxRecord.TxObjectRecordDeleted deleted -> Optional.empty();
+            case null -> getFromSource(type, key);
+        };
+    }
+
+    @Override
+    public void delete(JObjectKey key) {
+        var record = new TxRecord.TxObjectRecordDeleted(key);
+        if (_writes.put(key, record) instanceof TxRecord.TxObjectRecordDeleted) {
+            return;
+        }
+        if (_writeTrack)
+            _newWrites.put(key, record);
+    }
+
+    @Override
+    public CloseableKvIterator<JObjectKey, JData> getIterator(IteratorStart start, JObjectKey key) {
+        Log.tracev("Getting tx iterator with start={0}, key={1}", start, key);
+        return new ReadTrackingIterator(new TombstoneSkippingIterator<JObjectKey, ReadTrackingInternalCrap>(start, key,
+                ListUtils.prependAndMap(
+                        new MappingKvIterator<>(new NavigableMapKvIterator<>(_writes, start, key),
+                                t -> switch (t) {
+                                    case TxRecord.TxObjectRecordWrite<?> write ->
+                                            new DataWrapper<ReadTrackingInternalCrap>(new ReadTrackingInternalCrapTx(write.data()));
+                                    case TxRecord.TxObjectRecordDeleted deleted ->
+                                            new TombstoneImpl<ReadTrackingInternalCrap>();
+                                    case null, default -> null;
+                                }),
+                        _snapshot.getIterator(start, key),
+                        itin -> new MappingKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>, MaybeTombstone<ReadTrackingInternalCrap>>(itin,
+                                d -> switch (d) {
+                                    case Data<JDataVersionedWrapper> w ->
+                                            new DataWrapper<>(new ReadTrackingInternalCrapSource(w.value()));
+                                    case Tombstone<JDataVersionedWrapper> t -> new TombstoneImpl<>();
+                                    case null, default -> null;
+                                }))));
+    }
+
+    @Override
+    public void put(JData obj) {
+        var key = obj.key();
+        var read = _readSet.get(key);
+        if (read != null && (read.map(JDataVersionedWrapper::data).orElse(null) == obj)) {
+            return;
+        }
+
+        var record = new TxRecord.TxObjectRecordWrite<>(obj);
+        _writes.put(key, record);
+        if (_writeTrack)
+            _newWrites.put(key, record);
+    }
+
+    @Override
+    public void putNew(JData obj) {
+        var key = obj.key();
+        _knownNew.add(key);
+
+        var record = new TxRecord.TxObjectRecordWrite<>(obj);
+        _writes.put(key, record);
+        if (_writeTrack)
+            _newWrites.put(key, record);
+    }
+
+    Collection<TxRecord.TxObjectRecord<?>> drainNewWrites() {
+        if (!_writeTrack) {
+            _writeTrack = true;
+            return Collections.unmodifiableCollection(_writes.values());
+        }
+        var ret = _newWrites;
+        _newWrites = new HashMap<>();
+        return ret.values();
+    }
+
+    Map<JObjectKey, Optional<JDataVersionedWrapper>> reads() {
+        return _readSet;
+    }
+
+    Set<JObjectKey> knownNew() {
+        return _knownNew;
+    }
+
+    @Override
+    public void close() {
+        if (_closed) return;
+        _closed = true;
+        _snapshot.close();
+    }
+
+    private class ReadTrackingIterator implements CloseableKvIterator<JObjectKey, JData> {
+        private final CloseableKvIterator<JObjectKey, ReadTrackingInternalCrap> _backing;
+
+        public ReadTrackingIterator(CloseableKvIterator<JObjectKey, ReadTrackingInternalCrap> backing) {
+            _backing = backing;
+        }
+
+        @Override
+        public JObjectKey peekNextKey() {
+            return _backing.peekNextKey();
+        }
+
+        @Override
+        public void skip() {
+            _backing.skip();
+        }
+
+        @Override
+        public JObjectKey peekPrevKey() {
+            return _backing.peekPrevKey();
+        }
+
+        @Override
+        public Pair<JObjectKey, JData> prev() {
+            var got = _backing.prev();
+            if (got.getValue() instanceof ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped)) {
+                _readSet.putIfAbsent(got.getKey(), Optional.of(wrapped));
+            }
+            return Pair.of(got.getKey(), got.getValue().obj());
+        }
+
+        @Override
+        public boolean hasPrev() {
+            return _backing.hasPrev();
+        }
+
+        @Override
+        public void skipPrev() {
+            _backing.skipPrev();
+        }
+
+        @Override
+        public void close() {
+            _backing.close();
+        }
+
+        @Override
+        public boolean hasNext() {
+            return _backing.hasNext();
+        }
+
+        @Override
+        public Pair<JObjectKey, JData> next() {
+            var got = _backing.next();
+            if (got.getValue() instanceof ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped)) {
+                _readSet.putIfAbsent(got.getKey(), Optional.of(wrapped));
+            }
+            return Pair.of(got.getKey(), got.getValue().obj());
+        }
+    }
+}

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionManager.java

@@ -1,6 +1,5 @@
 package com.usatiuk.objects.transaction;
 
-import com.usatiuk.utils.VoidFn;
 import io.quarkus.logging.Log;
 
 import java.util.function.Supplier;
@@ -41,9 +40,9 @@ public interface TransactionManager {
         }
     }
 
-    default TransactionHandle runTries(VoidFn fn, int tries, boolean nest) {
+    default TransactionHandle runTries(Runnable fn, int tries, boolean nest) {
         if (!nest && current() != null) {
-            fn.apply();
+            fn.run();
             return new TransactionHandle() {
                 @Override
                 public void onFlush(Runnable runnable) {
@@ -56,7 +55,7 @@ public interface TransactionManager {
             begin();
             boolean commit = false;
             try {
-                fn.apply();
+                fn.run();
                 commit = true;
                 var ret = commit();
                 return ret;
@@ -80,11 +79,11 @@ public interface TransactionManager {
         return runTries(supplier, tries, false);
     }
 
-    default TransactionHandle runTries(VoidFn fn, int tries) {
+    default TransactionHandle runTries(Runnable fn, int tries) {
         return runTries(fn, tries, false);
     }
 
-    default TransactionHandle run(VoidFn fn, boolean nest) {
+    default TransactionHandle run(Runnable fn, boolean nest) {
         return runTries(fn, 10, nest);
     }
 
@@ -92,7 +91,7 @@ public interface TransactionManager {
         return runTries(supplier, 10, nest);
     }
 
-    default TransactionHandle run(VoidFn fn) {
+    default TransactionHandle run(Runnable fn) {
         return run(fn, false);
     }
 
@@ -100,7 +99,7 @@ public interface TransactionManager {
         return run(supplier, false);
     }
 
-    default void executeTx(VoidFn fn) {
+    default void executeTx(Runnable fn) {
         run(fn, false);
     }
 

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionManagerImpl.java

@@ -11,14 +11,14 @@ import java.util.Stack;
 
 @Singleton
 public class TransactionManagerImpl implements TransactionManager {
-    private static final ThreadLocal<Stack<TransactionPrivate>> _currentTransaction = ThreadLocal.withInitial(Stack::new);
+    private static final ThreadLocal<Stack<TransactionImpl>> _currentTransaction = ThreadLocal.withInitial(Stack::new);
     @Inject
-    JObjectManager jObjectManager;
+    TransactionService transactionService;
 
     @Override
     public void begin() {
         Log.trace("Starting transaction");
-        var tx = jObjectManager.createTransaction();
+        var tx = transactionService.createTransaction();
         _currentTransaction.get().push(tx);
     }
 
@@ -34,7 +34,7 @@ public class TransactionManagerImpl implements TransactionManager {
 
         Pair<Collection<Runnable>, TransactionHandle> ret;
         try {
-            ret = jObjectManager.commit(peeked);
+            ret = transactionService.commit(peeked);
         } catch (Throwable e) {
             Log.trace("Transaction commit failed", e);
             throw e;
@@ -64,7 +64,7 @@ public class TransactionManagerImpl implements TransactionManager {
         var peeked = stack.peek();
 
         try {
-            jObjectManager.rollback(peeked);
+            transactionService.rollback(peeked);
         } catch (Throwable e) {
             Log.error("Transaction rollback failed", e);
             throw e;

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionPrivate.java

@@ -1,27 +0,0 @@
-package com.usatiuk.objects.transaction;
-
-import com.usatiuk.objects.JData;
-import com.usatiuk.objects.JDataVersionedWrapper;
-import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.snapshot.Snapshot;
-import com.usatiuk.utils.AutoCloseableNoThrow;
-
-import java.util.Collection;
-import java.util.Map;
-import java.util.Optional;
-import java.util.Set;
-
-// The transaction interface actually used by user code to retrieve objects
-public interface TransactionPrivate extends Transaction, TransactionHandlePrivate, AutoCloseableNoThrow {
-    Collection<TxRecord.TxObjectRecord<?>> drainNewWrites();
-
-    Map<JObjectKey, Optional<JDataVersionedWrapper>> reads();
-
-    Set<JObjectKey> knownNew();
-
-    <T extends JData> Optional<T> getFromSource(Class<T> type, JObjectKey key);
-
-    Collection<Runnable> getOnCommit();
-
-    Snapshot<JObjectKey, JDataVersionedWrapper> snapshot();
-}

dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionService.java

@@ -22,12 +22,10 @@ import java.util.function.Consumer;
 import java.util.function.Function;
 
 @ApplicationScoped
-public class JObjectManager {
+public class TransactionService {
     private static final List<PreCommitTxHook> _preCommitTxHooks;
     @Inject
     WritebackObjectPersistentStore writebackObjectPersistentStore;
-    @Inject
-    TransactionFactory transactionFactory;
 
     private boolean _ready = false;
     private final DataLocker _objLocker = new DataLocker();
@@ -36,7 +34,7 @@ public class JObjectManager {
         _preCommitTxHooks = List.copyOf(CDI.current().select(PreCommitTxHook.class).stream().sorted(Comparator.comparingInt(PreCommitTxHook::getPriority)).toList());
     }
 
-    JObjectManager(Instance<PreCommitTxHook> preCommitTxHooks) {
+    TransactionService(Instance<PreCommitTxHook> preCommitTxHooks) {
         Log.debugv("Pre-commit hooks: {0}", String.join("->", _preCommitTxHooks.stream().map(Objects::toString).toList()));
     }
 
@@ -48,14 +46,14 @@ public class JObjectManager {
         _ready = true;
     }
 
-    public TransactionPrivate createTransaction() {
+    public TransactionImpl createTransaction() {
         verifyReady();
-        var tx = transactionFactory.createTransaction();
+        var tx = new TransactionImpl(writebackObjectPersistentStore.getSnapshot());
         Log.tracev("Created transaction with snapshotId={0}", tx.snapshot().id());
         return tx;
     }
 
-    public Pair<Collection<Runnable>, TransactionHandle> commit(TransactionPrivate tx) {
+    public Pair<Collection<Runnable>, TransactionHandle> commit(TransactionImpl tx) {
         verifyReady();
         var writes = new HashMap<JObjectKey, TxRecord.TxObjectRecord<?>>();
         Snapshot<JObjectKey, JDataVersionedWrapper> commitSnapshot = null;
@@ -259,7 +257,7 @@ public class JObjectManager {
         }
     }
 
-    public void rollback(TransactionPrivate tx) {
+    public void rollback(TransactionImpl tx) {
         verifyReady();
         tx.close();
     }

dhfs-parent/pom.xml

@@ -22,7 +22,6 @@
     <properties>
         <compiler-plugin.version>3.12.1</compiler-plugin.version>
         <!--FIXME-->
-        <maven.compiler.release></maven.compiler.release>
         <maven.compiler.source>21</maven.compiler.source>
         <maven.compiler.target>21</maven.compiler.target>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -87,6 +86,19 @@
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>3.11.2</version>
+                <configuration>
+                    <additionalOptions>
+                        --add-exports java.base/sun.nio.ch=ALL-UNNAMED
+                        --add-exports java.base/jdk.internal.access=ALL-UNNAMED
+                        --add-opens=java.base/java.nio=ALL-UNNAMED
+                        --enable-preview
+                    </additionalOptions>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>${quarkus.platform.group-id}</groupId>
                 <artifactId>quarkus-maven-plugin</artifactId>

dhfs-parent/utils/src/main/java/com/usatiuk/utils/VoidFn.java

@@ -1,7 +0,0 @@
-package com.usatiuk.utils;
-
-@FunctionalInterface
-public interface VoidFn {
-    void apply();
-}
-

dhfs-parent/utils/src/main/java/com/usatiuk/utils/VoidFnThrows.java

@@ -1,7 +0,0 @@
-package com.usatiuk.utils;
-
-@FunctionalInterface
-public interface VoidFnThrows {
-    void apply() throws Throwable;
-}
-