Sync-base: more javadocs 2

and some more

.github/workflows/server.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          submodules: 'recursive'
+          submodules: "recursive"
 
       - name: Install sudo for ACT
         run: apt-get update && apt-get install -y sudo
@@ -32,7 +32,7 @@ jobs:
 
       - name: User allow other for fuse
         run: echo "user_allow_other" | sudo tee -a /etc/fuse.conf
-      
+
       - name: Dump fuse.conf
         run: cat /etc/fuse.conf
 
@@ -47,7 +47,7 @@ jobs:
         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 package verify 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
@@ -55,7 +55,12 @@ jobs:
       - uses: actions/upload-artifact@v4
         with:
           name: DHFS Server Package
-          path: dhfs-parent/dhfs-app/target/quarkus-app
+          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() }}
@@ -212,7 +217,7 @@ jobs:
         run: mkdir -p run-wrapper-out/dhfs/data && mkdir -p run-wrapper-out/dhfs/fuse && mkdir -p run-wrapper-out/dhfs/app
 
       - name: Copy DHFS
-        run: cp -r ./dhfs-package-downloaded "run-wrapper-out/dhfs/app/DHFS Package"
+        run: cp -r ./dhfs-package-downloaded "run-wrapper-out/dhfs/app/Server"
 
       - name: Copy Webui
         run: cp -r ./webui-dist-downloaded "run-wrapper-out/dhfs/app/Webui"
@@ -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/.run/Main 2.run.xml

@@ -1,17 +1,16 @@
 <component name="ProjectRunConfigurationManager">
-    <configuration default="false" name="Main 2" type="QsApplicationConfigurationType" factoryName="QuarkusApplication">
-        <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsapp.Main"/>
-        <module name="dhfs-app"/>
-        <option name="VM_PARAMETERS"
-                value="-XX:+UnlockDiagnosticVMOptions -XX:+DebugNonSafepoints --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx2G -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/2/fuse -Ddhfs.objects.persistence.files.root=${HOME}/dhfs_test/2/data -Ddhfs.objects.persistence.stuff.root=${HOME}/dhfs_test/2/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=false -Dquarkus.http.port=9020 -Dquarkus.http.ssl-port=9021 -Ddhfs.peerdiscovery.preset-uuid=22000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=11000000-0000-0000-0000-000000000000:127.0.0.1:9010:9011"/>
-        <extension name="coverage">
-            <pattern>
-                <option name="PATTERN" value="com.usatiuk.dhfs.remoteobj.*"/>
-                <option name="ENABLED" value="true"/>
-            </pattern>
-        </extension>
-        <method v="2">
-            <option name="Make" enabled="true"/>
-        </method>
-    </configuration>
+  <configuration default="false" name="Main 2" type="QsApplicationConfigurationType" factoryName="QuarkusApplication">
+    <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsfuse.Main" />
+    <module name="dhfs-fuse" />
+    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseParallelGC -XX:+DebugNonSafepoints --enable-preview --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx512M -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/2/fuse -Ddhfs.objects.persistence.files.root=${HOME}/dhfs_test/2/data -Ddhfs.objects.persistence.stuff.root=${HOME}/dhfs_test/2/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=false -Dquarkus.http.port=9020 -Dquarkus.http.ssl-port=9021 -Ddhfs.peerdiscovery.preset-uuid=22000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=11000000-0000-0000-0000-000000000000:127.0.0.1:9010:9011" />
+    <extension name="coverage">
+      <pattern>
+        <option name="PATTERN" value="com.usatiuk.dhfs.remoteobj.*" />
+        <option name="ENABLED" value="true" />
+      </pattern>
+    </extension>
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
 </component>

dhfs-parent/.run/Main.run.xml

@@ -1,18 +1,16 @@
 <component name="ProjectRunConfigurationManager">
-    <configuration default="false" name="Main" type="QsApplicationConfigurationType" factoryName="QuarkusApplication"
-                   nameIsGenerated="true">
-        <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsapp.Main"/>
-        <module name="dhfs-app"/>
-        <option name="VM_PARAMETERS"
-                value="-XX:+UnlockDiagnosticVMOptions -XX:+UseParallelGC -XX:+DebugNonSafepoints --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx2G -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/1/fuse -Ddhfs.objects.persistence.files.root=${HOME}/dhfs_test/1/data -Ddhfs.objects.persistence.stuff.root=${HOME}/dhfs_test/1/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=true -Dquarkus.http.port=9010 -Dquarkus.http.ssl-port=9011 -Ddhfs.peerdiscovery.preset-uuid=11000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=22000000-0000-0000-0000-000000000000:127.0.0.1:9020:9021 -Dquarkus.http.host=0.0.0.0"/>
-        <extension name="coverage">
-            <pattern>
-                <option name="PATTERN" value="com.usatiuk.dhfs.remoteobj.*"/>
-                <option name="ENABLED" value="true"/>
-            </pattern>
-        </extension>
-        <method v="2">
-            <option name="Make" enabled="true"/>
-        </method>
-    </configuration>
+  <configuration default="false" name="Main" type="QsApplicationConfigurationType" factoryName="QuarkusApplication" nameIsGenerated="true">
+    <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsfuse.Main" />
+    <module name="dhfs-fuse" />
+    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseZGC -XX:+ZGenerational --enable-preview -XX:+DebugNonSafepoints --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx1G -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/1/fuse -Ddhfs.objects.persistence.files.root=${HOME}/dhfs_test/1/data -Ddhfs.objects.persistence.stuff.root=${HOME}/dhfs_test/1/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=true -Dquarkus.http.port=9010 -Dquarkus.http.ssl-port=9011 -Ddhfs.peerdiscovery.preset-uuid=11000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=22000000-0000-0000-0000-000000000000:127.0.0.1:9020:9021 -Dquarkus.http.host=0.0.0.0" />
+    <extension name="coverage">
+      <pattern>
+        <option name="PATTERN" value="com.usatiuk.dhfs.remoteobj.*" />
+        <option name="ENABLED" value="true" />
+      </pattern>
+    </extension>
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
 </component>

dhfs-parent/dhfs-app/.dockerignore

@@ -1,5 +0,0 @@
-*
-!target/*-runner
-!target/*-runner.jar
-!target/lib/*
-!target/quarkus-app/*

dhfs-parent/dhfs-app/.gitignore

@@ -1,43 +0,0 @@
-#Maven
-target/
-pom.xml.tag
-pom.xml.releaseBackup
-pom.xml.versionsBackup
-release.properties
-.flattened-pom.xml
-
-# Eclipse
-.project
-.classpath
-.settings/
-bin/
-
-# IntelliJ
-.idea
-*.ipr
-*.iml
-*.iws
-
-# NetBeans
-nb-configuration.xml
-
-# Visual Studio Code
-.vscode
-.factorypath
-
-# OSX
-.DS_Store
-
-# Vim
-*.swp
-*.swo
-
-# patch
-*.orig
-*.rej
-
-# Local environment
-.env
-
-# Plugin directory
-/.quarkus/cli/plugins/

dhfs-parent/dhfs-app/Dockerfile

@@ -1,2 +0,0 @@
-FROM azul/zulu-openjdk-debian:21-jre-latest
-RUN apt update && apt install -y libfuse2 curl

dhfs-parent/dhfs-app/docker-compose.yml

@@ -1,43 +0,0 @@
-version: "3.2"
-
-services:
-  dhfs1:
-    build: .
-    privileged: true
-    devices:
-      - /dev/fuse
-    volumes:
-      - $HOME/dhfs/dhfs1:/dhfs_root
-      - $HOME/dhfs/dhfs1_f:/dhfs_root/fuse:rshared
-      - ./target/quarkus-app:/app
-    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
-     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0 
-     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005
-     -jar /app/quarkus-run.jar"
-    ports:
-      - 8080:8080
-      - 8081:8443
-      - 5005:5005
-  dhfs2:
-    build: .
-    privileged: true
-    devices:
-      - /dev/fuse
-    volumes:
-      - $HOME/dhfs/dhfs2:/dhfs_root
-      - $HOME/dhfs/dhfs2_f:/dhfs_root/fuse:rshared
-      - ./target/quarkus-app:/app
-    command: "java --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
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
-     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0
-     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5010
-     -jar /app/quarkus-run.jar"
-    ports:
-      - 8090:8080
-      - 8091:8443
-      - 5010:5010

dhfs-parent/dhfs-app/pom.xml

@@ -1,172 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <modelVersion>4.0.0</modelVersion>
-    <groupId>com.usatiuk.dhfs</groupId>
-    <artifactId>dhfs-app</artifactId>
-    <version>1.0-SNAPSHOT</version>
-
-    <parent>
-        <groupId>com.usatiuk.dhfs</groupId>
-        <artifactId>parent</artifactId>
-        <version>1.0-SNAPSHOT</version>
-    </parent>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-params</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.testcontainers</groupId>
-            <artifactId>testcontainers</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.awaitility</groupId>
-            <artifactId>awaitility</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk18on</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcpkix-jdk18on</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-security</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>net.openhft</groupId>
-            <artifactId>zero-allocation-hashing</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-grpc</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-arc</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client-jsonb</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-jsonb</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-scheduler</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-junit5</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-lang3</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.jboss.slf4j</groupId>
-            <artifactId>slf4j-jboss-logmanager</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>commons-codec</groupId>
-            <artifactId>commons-codec</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-collections4</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.pcollections</groupId>
-            <artifactId>pcollections</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-math3</artifactId>
-            <version>3.6.1</version>
-        </dependency>
-        <dependency>
-            <groupId>com.usatiuk.dhfs</groupId>
-            <artifactId>dhfs-fuse</artifactId>
-            <version>1.0-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>com.usatiuk.dhfs</groupId>
-            <artifactId>utils</artifactId>
-            <version>1.0-SNAPSHOT</version>
-        </dependency>
-    </dependencies>
-
-    <build>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <configuration>
-                    <forkCount>1C</forkCount>
-                    <reuseForks>false</reuseForks>
-                    <parallel>classes</parallel>
-                    <systemPropertyVariables>
-                        <junit.jupiter.execution.parallel.enabled>
-                            false
-                        </junit.jupiter.execution.parallel.enabled>
-                    </systemPropertyVariables>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-failsafe-plugin</artifactId>
-                <configuration>
-                    <forkCount>1C</forkCount>
-                    <reuseForks>false</reuseForks>
-                    <parallel>classes</parallel>
-                    <systemPropertyVariables>
-                        <junit.jupiter.execution.parallel.enabled>
-                            false
-                        </junit.jupiter.execution.parallel.enabled>
-                        <junit.platform.output.capture.stdout>true</junit.platform.output.capture.stdout>
-                        <junit.platform.output.capture.stderr>true</junit.platform.output.capture.stderr>
-                    </systemPropertyVariables>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>${quarkus.platform.group-id}</groupId>
-                <artifactId>quarkus-maven-plugin</artifactId>
-                <version>${quarkus.platform.version}</version>
-                <extensions>true</extensions>
-                <executions>
-                    <execution>
-                        <id>quarkus-plugin</id>
-                        <goals>
-                            <goal>build</goal>
-                            <goal>generate-code</goal>
-                            <goal>generate-code-tests</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-        </plugins>
-    </build>
-</project>

dhfs-parent/dhfs-app/src/main/docker/Dockerfile.jvm

@@ -1,97 +0,0 @@
-####
-# This Dockerfile is used in order to build a container that runs the Quarkus application in JVM mode
-#
-# Before building the container image run:
-#
-# ./mvnw package
-#
-# Then, build the image with:
-#
-# docker build -f src/main/docker/Dockerfile.jvm -t quarkus/server-jvm .
-#
-# Then run the container using:
-#
-# docker run -i --rm -p 8080:8080 quarkus/server-jvm
-#
-# If you want to include the debug port into your docker image
-# you will have to expose the debug port (default 5005 being the default) like this :  EXPOSE 8080 5005.
-# Additionally you will have to set -e JAVA_DEBUG=true and -e JAVA_DEBUG_PORT=*:5005
-# when running the container
-#
-# Then run the container using :
-#
-# docker run -i --rm -p 8080:8080 quarkus/server-jvm
-#
-# This image uses the `run-java.sh` script to run the application.
-# This scripts computes the command line to execute your Java application, and
-# includes memory/GC tuning.
-# You can configure the behavior using the following environment properties:
-# - JAVA_OPTS: JVM options passed to the `java` command (example: "-verbose:class")
-# - JAVA_OPTS_APPEND: User specified Java options to be appended to generated options
-#   in JAVA_OPTS (example: "-Dsome.property=foo")
-# - JAVA_MAX_MEM_RATIO: Is used when no `-Xmx` option is given in JAVA_OPTS. This is
-#   used to calculate a default maximal heap memory based on a containers restriction.
-#   If used in a container without any memory constraints for the container then this
-#   option has no effect. If there is a memory constraint then `-Xmx` is set to a ratio
-#   of the container available memory as set here. The default is `50` which means 50%
-#   of the available memory is used as an upper boundary. You can skip this mechanism by
-#   setting this value to `0` in which case no `-Xmx` option is added.
-# - JAVA_INITIAL_MEM_RATIO: Is used when no `-Xms` option is given in JAVA_OPTS. This
-#   is used to calculate a default initial heap memory based on the maximum heap memory.
-#   If used in a container without any memory constraints for the container then this
-#   option has no effect. If there is a memory constraint then `-Xms` is set to a ratio
-#   of the `-Xmx` memory as set here. The default is `25` which means 25% of the `-Xmx`
-#   is used as the initial heap size. You can skip this mechanism by setting this value
-#   to `0` in which case no `-Xms` option is added (example: "25")
-# - JAVA_MAX_INITIAL_MEM: Is used when no `-Xms` option is given in JAVA_OPTS.
-#   This is used to calculate the maximum value of the initial heap memory. If used in
-#   a container without any memory constraints for the container then this option has
-#   no effect. If there is a memory constraint then `-Xms` is limited to the value set
-#   here. The default is 4096MB which means the calculated value of `-Xms` never will
-#   be greater than 4096MB. The value of this variable is expressed in MB (example: "4096")
-# - JAVA_DIAGNOSTICS: Set this to get some diagnostics information to standard output
-#   when things are happening. This option, if set to true, will set
-#  `-XX:+UnlockDiagnosticVMOptions`. Disabled by default (example: "true").
-# - JAVA_DEBUG: If set remote debugging will be switched on. Disabled by default (example:
-#    true").
-# - JAVA_DEBUG_PORT: Port used for remote debugging. Defaults to 5005 (example: "8787").
-# - CONTAINER_CORE_LIMIT: A calculated core limit as described in
-#   https://www.kernel.org/doc/Documentation/scheduler/sched-bwc.txt. (example: "2")
-# - CONTAINER_MAX_MEMORY: Memory limit given to the container (example: "1024").
-# - GC_MIN_HEAP_FREE_RATIO: Minimum percentage of heap free after GC to avoid expansion.
-#   (example: "20")
-# - GC_MAX_HEAP_FREE_RATIO: Maximum percentage of heap free after GC to avoid shrinking.
-#   (example: "40")
-# - GC_TIME_RATIO: Specifies the ratio of the time spent outside the garbage collection.
-#   (example: "4")
-# - GC_ADAPTIVE_SIZE_POLICY_WEIGHT: The weighting given to the current GC time versus
-#   previous GC times. (example: "90")
-# - GC_METASPACE_SIZE: The initial metaspace size. (example: "20")
-# - GC_MAX_METASPACE_SIZE: The maximum metaspace size. (example: "100")
-# - GC_CONTAINER_OPTIONS: Specify Java GC to use. The value of this variable should
-#   contain the necessary JRE command-line options to specify the required GC, which
-#   will override the default of `-XX:+UseParallelGC` (example: -XX:+UseG1GC).
-# - HTTPS_PROXY: The location of the https proxy. (example: "myuser@127.0.0.1:8080")
-# - HTTP_PROXY: The location of the http proxy. (example: "myuser@127.0.0.1:8080")
-# - NO_PROXY: A comma separated lists of hosts, IP addresses or domains that can be
-#   accessed directly. (example: "foo.example.com,bar.example.com")
-#
-###
-FROM registry.access.redhat.com/ubi8/openjdk-21:1.18
-
-ENV LANGUAGE='en_US:en'
-
-
-# We make four distinct layers so if there are application changes the library layers can be re-used
-COPY --chown=185 target/quarkus-app/lib/ /deployments/lib/
-COPY --chown=185 target/quarkus-app/*.jar /deployments/
-COPY --chown=185 target/quarkus-app/app/ /deployments/app/
-COPY --chown=185 target/quarkus-app/quarkus/ /deployments/quarkus/
-
-EXPOSE 8080
-USER 185
-ENV JAVA_OPTS_APPEND="-Dquarkus.http.host=0.0.0.0 -Djava.util.logging.manager=org.jboss.logmanager.LogManager"
-ENV JAVA_APP_JAR="/deployments/quarkus-run.jar"
-
-ENTRYPOINT [ "/opt/jboss/container/java/run/run-java.sh" ]
-

dhfs-parent/dhfs-app/src/main/docker/Dockerfile.legacy-jar

@@ -1,93 +0,0 @@
-####
-# This Dockerfile is used in order to build a container that runs the Quarkus application in JVM mode
-#
-# Before building the container image run:
-#
-# ./mvnw package -Dquarkus.package.jar.type=legacy-jar
-#
-# Then, build the image with:
-#
-# docker build -f src/main/docker/Dockerfile.legacy-jar -t quarkus/server-legacy-jar .
-#
-# Then run the container using:
-#
-# docker run -i --rm -p 8080:8080 quarkus/server-legacy-jar
-#
-# If you want to include the debug port into your docker image
-# you will have to expose the debug port (default 5005 being the default) like this :  EXPOSE 8080 5005.
-# Additionally you will have to set -e JAVA_DEBUG=true and -e JAVA_DEBUG_PORT=*:5005
-# when running the container
-#
-# Then run the container using :
-#
-# docker run -i --rm -p 8080:8080 quarkus/server-legacy-jar
-#
-# This image uses the `run-java.sh` script to run the application.
-# This scripts computes the command line to execute your Java application, and
-# includes memory/GC tuning.
-# You can configure the behavior using the following environment properties:
-# - JAVA_OPTS: JVM options passed to the `java` command (example: "-verbose:class")
-# - JAVA_OPTS_APPEND: User specified Java options to be appended to generated options
-#   in JAVA_OPTS (example: "-Dsome.property=foo")
-# - JAVA_MAX_MEM_RATIO: Is used when no `-Xmx` option is given in JAVA_OPTS. This is
-#   used to calculate a default maximal heap memory based on a containers restriction.
-#   If used in a container without any memory constraints for the container then this
-#   option has no effect. If there is a memory constraint then `-Xmx` is set to a ratio
-#   of the container available memory as set here. The default is `50` which means 50%
-#   of the available memory is used as an upper boundary. You can skip this mechanism by
-#   setting this value to `0` in which case no `-Xmx` option is added.
-# - JAVA_INITIAL_MEM_RATIO: Is used when no `-Xms` option is given in JAVA_OPTS. This
-#   is used to calculate a default initial heap memory based on the maximum heap memory.
-#   If used in a container without any memory constraints for the container then this
-#   option has no effect. If there is a memory constraint then `-Xms` is set to a ratio
-#   of the `-Xmx` memory as set here. The default is `25` which means 25% of the `-Xmx`
-#   is used as the initial heap size. You can skip this mechanism by setting this value
-#   to `0` in which case no `-Xms` option is added (example: "25")
-# - JAVA_MAX_INITIAL_MEM: Is used when no `-Xms` option is given in JAVA_OPTS.
-#   This is used to calculate the maximum value of the initial heap memory. If used in
-#   a container without any memory constraints for the container then this option has
-#   no effect. If there is a memory constraint then `-Xms` is limited to the value set
-#   here. The default is 4096MB which means the calculated value of `-Xms` never will
-#   be greater than 4096MB. The value of this variable is expressed in MB (example: "4096")
-# - JAVA_DIAGNOSTICS: Set this to get some diagnostics information to standard output
-#   when things are happening. This option, if set to true, will set
-#  `-XX:+UnlockDiagnosticVMOptions`. Disabled by default (example: "true").
-# - JAVA_DEBUG: If set remote debugging will be switched on. Disabled by default (example:
-#    true").
-# - JAVA_DEBUG_PORT: Port used for remote debugging. Defaults to 5005 (example: "8787").
-# - CONTAINER_CORE_LIMIT: A calculated core limit as described in
-#   https://www.kernel.org/doc/Documentation/scheduler/sched-bwc.txt. (example: "2")
-# - CONTAINER_MAX_MEMORY: Memory limit given to the container (example: "1024").
-# - GC_MIN_HEAP_FREE_RATIO: Minimum percentage of heap free after GC to avoid expansion.
-#   (example: "20")
-# - GC_MAX_HEAP_FREE_RATIO: Maximum percentage of heap free after GC to avoid shrinking.
-#   (example: "40")
-# - GC_TIME_RATIO: Specifies the ratio of the time spent outside the garbage collection.
-#   (example: "4")
-# - GC_ADAPTIVE_SIZE_POLICY_WEIGHT: The weighting given to the current GC time versus
-#   previous GC times. (example: "90")
-# - GC_METASPACE_SIZE: The initial metaspace size. (example: "20")
-# - GC_MAX_METASPACE_SIZE: The maximum metaspace size. (example: "100")
-# - GC_CONTAINER_OPTIONS: Specify Java GC to use. The value of this variable should
-#   contain the necessary JRE command-line options to specify the required GC, which
-#   will override the default of `-XX:+UseParallelGC` (example: -XX:+UseG1GC).
-# - HTTPS_PROXY: The location of the https proxy. (example: "myuser@127.0.0.1:8080")
-# - HTTP_PROXY: The location of the http proxy. (example: "myuser@127.0.0.1:8080")
-# - NO_PROXY: A comma separated lists of hosts, IP addresses or domains that can be
-#   accessed directly. (example: "foo.example.com,bar.example.com")
-#
-###
-FROM registry.access.redhat.com/ubi8/openjdk-21:1.18
-
-ENV LANGUAGE='en_US:en'
-
-
-COPY target/lib/* /deployments/lib/
-COPY target/*-runner.jar /deployments/quarkus-run.jar
-
-EXPOSE 8080
-USER 185
-ENV JAVA_OPTS_APPEND="-Dquarkus.http.host=0.0.0.0 -Djava.util.logging.manager=org.jboss.logmanager.LogManager"
-ENV JAVA_APP_JAR="/deployments/quarkus-run.jar"
-
-ENTRYPOINT [ "/opt/jboss/container/java/run/run-java.sh" ]

dhfs-parent/dhfs-app/src/main/docker/Dockerfile.native

@@ -1,27 +0,0 @@
-####
-# This Dockerfile is used in order to build a container that runs the Quarkus application in native (no JVM) mode.
-#
-# Before building the container image run:
-#
-# ./mvnw package -Dnative
-#
-# Then, build the image with:
-#
-# docker build -f src/main/docker/Dockerfile.native -t quarkus/server .
-#
-# Then run the container using:
-#
-# docker run -i --rm -p 8080:8080 quarkus/server
-#
-###
-FROM registry.access.redhat.com/ubi8/ubi-minimal:8.9
-WORKDIR /work/
-RUN chown 1001 /work \
-    && chmod "g+rwX" /work \
-    && chown 1001:root /work
-COPY --chown=1001:root target/*-runner /work/application
-
-EXPOSE 8080
-USER 1001
-
-ENTRYPOINT ["./application", "-Dquarkus.http.host=0.0.0.0"]

dhfs-parent/dhfs-app/src/main/docker/Dockerfile.native-micro

@@ -1,30 +0,0 @@
-####
-# This Dockerfile is used in order to build a container that runs the Quarkus application in native (no JVM) mode.
-# It uses a micro base image, tuned for Quarkus native executables.
-# It reduces the size of the resulting container image.
-# Check https://quarkus.io/guides/quarkus-runtime-base-image for further information about this image.
-#
-# Before building the container image run:
-#
-# ./mvnw package -Dnative
-#
-# Then, build the image with:
-#
-# docker build -f src/main/docker/Dockerfile.native-micro -t quarkus/server .
-#
-# Then run the container using:
-#
-# docker run -i --rm -p 8080:8080 quarkus/server
-#
-###
-FROM quay.io/quarkus/quarkus-micro-image:2.0
-WORKDIR /work/
-RUN chown 1001 /work \
-    && chmod "g+rwX" /work \
-    && chown 1001:root /work
-COPY --chown=1001:root target/*-runner /work/application
-
-EXPOSE 8080
-USER 1001
-
-ENTRYPOINT ["./application", "-Dquarkus.http.host=0.0.0.0"]

dhfs-parent/dhfs-app/src/main/resources/application.properties

@@ -1,34 +0,0 @@
-quarkus.grpc.server.use-separate-server=false
-dhfs.objects.peerdiscovery.port=42069
-dhfs.objects.peerdiscovery.interval=4s
-dhfs.objects.peerdiscovery.broadcast=true
-dhfs.objects.sync.timeout=30
-dhfs.objects.sync.ping.timeout=5
-dhfs.objects.invalidation.threads=16
-dhfs.objects.invalidation.delay=1000
-dhfs.objects.reconnect_interval=5s
-dhfs.objects.write_log=false
-dhfs.objects.periodic-push-op-interval=5m
-dhfs.fuse.root=${HOME}/dhfs_default/fuse
-dhfs.objects.persistence.stuff.root=${HOME}/dhfs_default/data/stuff
-dhfs.fuse.debug=false
-dhfs.fuse.enabled=true
-dhfs.files.allow_recursive_delete=false
-dhfs.files.target_chunk_size=2097152
-dhfs.files.target_chunk_alignment=19
-dhfs.objects.deletion.delay=1000
-dhfs.objects.deletion.can-delete-retry-delay=10000
-dhfs.objects.ref_verification=true
-dhfs.files.use_hash_for_chunks=false
-dhfs.objects.autosync.threads=16
-dhfs.objects.autosync.download-all=false
-dhfs.objects.move-processor.threads=16
-dhfs.objects.ref-processor.threads=16
-dhfs.objects.opsender.batch-size=100
-dhfs.objects.lock_timeout_secs=2
-dhfs.local-discovery=true
-dhfs.peerdiscovery.timeout=10000
-quarkus.log.category."com.usatiuk".min-level=TRACE
-quarkus.log.category."com.usatiuk".level=TRACE
-quarkus.http.insecure-requests=enabled
-quarkus.http.ssl.client-auth=required

dhfs-parent/dhfs-app/src/test/java/com/usatiuk/dhfsapp/TempDataProfile.java

@@ -1,29 +0,0 @@
-package com.usatiuk.dhfsapp;
-
-import io.quarkus.test.junit.QuarkusTestProfile;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.HashMap;
-import java.util.Map;
-
-abstract public class TempDataProfile implements QuarkusTestProfile {
-    protected void getConfigOverrides(Map<String, String> toPut) {
-    }
-
-    @Override
-    final public Map<String, String> getConfigOverrides() {
-        Path tempDirWithPrefix;
-        try {
-            tempDirWithPrefix = Files.createTempDirectory("dhfs-test");
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        }
-        var ret = new HashMap<String, String>();
-        ret.put("dhfs.objects.persistence.files.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
-        ret.put("dhfs.fuse.root", tempDirWithPrefix.resolve("dhfs_fuse_root_test").toString());
-        getConfigOverrides(ret);
-        return ret;
-    }
-}

dhfs-parent/dhfs-app/src/test/java/com/usatiuk/dhfsapp/TestDataCleaner.java

@@ -1,44 +0,0 @@
-package com.usatiuk.dhfsapp;
-
-import io.quarkus.logging.Log;
-import io.quarkus.runtime.ShutdownEvent;
-import io.quarkus.runtime.StartupEvent;
-import jakarta.annotation.Priority;
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.enterprise.event.Observes;
-import org.eclipse.microprofile.config.inject.ConfigProperty;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.Objects;
-
-@ApplicationScoped
-public class TestDataCleaner {
-    @ConfigProperty(name = "dhfs.objects.persistence.files.root")
-    String tempDirectory;
-
-    public static void purgeDirectory(File dir) {
-        try {
-            for (File file : Objects.requireNonNull(dir.listFiles())) {
-                if (file.isDirectory())
-                    purgeDirectory(file);
-                file.delete();
-            }
-        } catch (Exception e) {
-            Log.error("Couldn't purge directory " + dir, e);
-        }
-    }
-
-    void init(@Observes @Priority(1) StartupEvent event) throws IOException {
-        try {
-            purgeDirectory(Path.of(tempDirectory).toFile());
-        } catch (Exception ignored) {
-            Log.warn("Couldn't cleanup test data on init");
-        }
-    }
-
-    void shutdown(@Observes @Priority(1000000000) ShutdownEvent event) throws IOException {
-        purgeDirectory(Path.of(tempDirectory).toFile());
-    }
-}

dhfs-parent/dhfs-app/src/test/resources/application.properties

@@ -1,11 +0,0 @@
-dhfs.objects.persistence.files.root=${HOME}/dhfs_data/dhfs_root_test
-dhfs.objects.root=${HOME}/dhfs_data/dhfs_root_d_test
-dhfs.fuse.root=${HOME}/dhfs_data/dhfs_fuse_root_test
-dhfs.objects.ref_verification=true
-dhfs.objects.deletion.delay=0
-quarkus.log.category."com.usatiuk.dhfs".level=TRACE
-quarkus.log.category."com.usatiuk.dhfs".min-level=TRACE
-quarkus.http.test-port=0
-quarkus.http.test-ssl-port=0
-dhfs.local-discovery=false
-dhfs.objects.persistence.snapshot-extra-checks=true

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

@@ -8,7 +8,6 @@ import com.usatiuk.dhfs.remoteobj.*;
 import com.usatiuk.dhfsfs.service.DhfsFileService;
 import com.usatiuk.kleppmanntree.AlreadyExistsException;
 import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.transaction.LockingStrategy;
 import com.usatiuk.objects.transaction.Transaction;
 import io.grpc.Status;
 import io.grpc.StatusRuntimeException;
@@ -24,6 +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
@@ -42,14 +44,18 @@ public class FileSyncHandler implements ObjSyncHandler<File, FileDto> {
     @Inject
     DhfsFileService fileService;
 
-    private JKleppmannTreeManager.JKleppmannTree getTreeW() {
+    private JKleppmannTreeManager.JKleppmannTree getTree() {
         return jKleppmannTreeManager.getTree(JObjectKey.of("fs")).orElseThrow();
     }
 
-    private JKleppmannTreeManager.JKleppmannTree getTreeR() {
-        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), LockingStrategy.OPTIMISTIC).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);
@@ -131,12 +137,12 @@ public class FileSyncHandler implements ObjSyncHandler<File, FileDto> {
 
             do {
                 try {
-                    getTreeW().move(parent.getRight(),
+                    getTree().move(parent.getRight(),
                             new JKleppmannTreeNodeMetaFile(
                                     parent.getLeft() + ".fconflict." + persistentPeerDataService.getSelfUuid() + "." + otherHostname.toString() + "." + i,
                                     newFile.key()
                             ),
-                            getTreeW().getNewNodeId()
+                            getTree().getNewNodeId()
                     );
                 } catch (AlreadyExistsException aex) {
                     i++;

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

@@ -2,47 +2,783 @@ package com.usatiuk.dhfsfs.service;
 
 import com.google.protobuf.ByteString;
 import com.google.protobuf.UnsafeByteOperations;
+import com.usatiuk.dhfs.jkleppmanntree.JKleppmannTreeManager;
+import com.usatiuk.dhfs.jkleppmanntree.structs.JKleppmannTreeNode;
+import com.usatiuk.dhfs.jkleppmanntree.structs.JKleppmannTreeNodeHolder;
+import com.usatiuk.dhfs.jkleppmanntree.structs.JKleppmannTreeNodeMeta;
+import com.usatiuk.dhfs.jmap.JMapEntry;
+import com.usatiuk.dhfs.jmap.JMapHelper;
+import com.usatiuk.dhfs.jmap.JMapLongKey;
+import com.usatiuk.dhfs.remoteobj.JDataRemote;
+import com.usatiuk.dhfs.remoteobj.RemoteObjectMeta;
+import com.usatiuk.dhfs.remoteobj.RemoteTransaction;
+import com.usatiuk.dhfsfs.objects.ChunkData;
+import com.usatiuk.dhfsfs.objects.File;
+import com.usatiuk.dhfsfs.objects.JKleppmannTreeNodeMetaDirectory;
+import com.usatiuk.dhfsfs.objects.JKleppmannTreeNodeMetaFile;
+import com.usatiuk.objects.JData;
 import com.usatiuk.objects.JObjectKey;
+import com.usatiuk.objects.iterators.IteratorStart;
+import com.usatiuk.objects.transaction.Transaction;
+import com.usatiuk.objects.transaction.TransactionManager;
+import com.usatiuk.utils.StatusRuntimeExceptionNoStacktrace;
+import io.grpc.Status;
+import io.grpc.StatusRuntimeException;
+import io.quarkus.logging.Log;
+import io.quarkus.runtime.StartupEvent;
+import jakarta.annotation.Priority;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.enterprise.event.Observes;
+import jakarta.inject.Inject;
 import org.apache.commons.lang3.tuple.Pair;
+import org.eclipse.microprofile.config.inject.ConfigProperty;
 
-import java.util.Optional;
+import java.nio.ByteBuffer;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
+import java.util.*;
+import java.util.stream.StreamSupport;
 
-public interface DhfsFileService {
-    Optional<JObjectKey> open(String name);
+/**
+ * Actual filesystem implementation.
+ */
+@ApplicationScoped
+public class DhfsFileService {
+    @ConfigProperty(name = "dhfs.files.target_chunk_alignment")
+    int targetChunkAlignment;
+    @ConfigProperty(name = "dhfs.files.target_chunk_size")
+    int targetChunkSize;
+    @ConfigProperty(name = "dhfs.files.max_chunk_size", defaultValue = "524288")
+    int maxChunkSize;
+    @ConfigProperty(name = "dhfs.files.use_hash_for_chunks")
+    boolean useHashForChunks;
+    @ConfigProperty(name = "dhfs.files.allow_recursive_delete")
+    boolean allowRecursiveDelete;
+    @ConfigProperty(name = "dhfs.objects.ref_verification")
+    boolean refVerification;
+    @ConfigProperty(name = "dhfs.objects.write_log")
+    boolean writeLogging;
 
-    Optional<JObjectKey> create(String name, long mode);
+    @Inject
+    Transaction curTx;
+    @Inject
+    RemoteTransaction remoteTx;
+    @Inject
+    TransactionManager jObjectTxManager;
+    @Inject
+    JKleppmannTreeManager jKleppmannTreeManager;
+    @Inject
+    JMapHelper jMapHelper;
 
-    Pair<String, JObjectKey> inoToParent(JObjectKey ino);
-
-    void mkdir(String name, long mode);
-
-    Optional<GetattrRes> getattr(JObjectKey name);
-
-    Boolean chmod(JObjectKey name, long mode);
-
-    void unlink(String name);
-
-    Boolean rename(String from, String to);
-
-    Boolean setTimes(JObjectKey fileUuid, long atimeMs, long mtimeMs);
-
-    Iterable<String> readDir(String name);
-
-    long size(JObjectKey fileUuid);
-
-    ByteString read(JObjectKey fileUuid, long offset, int length);
-
-    Long write(JObjectKey fileUuid, long offset, ByteString data);
-
-    default Long write(JObjectKey fileUuid, long offset, byte[] data) {
-        return write(fileUuid, offset, UnsafeByteOperations.unsafeWrap(data));
+    private JKleppmannTreeManager.JKleppmannTree getTree() {
+        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), () -> new JKleppmannTreeNodeMetaDirectory(""));
     }
 
-    Boolean truncate(JObjectKey fileUuid, long length);
+    /**
+     * 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);
+        return newChunk;
+    }
 
-    String readlink(JObjectKey uuid);
+    void init(@Observes @Priority(500) StartupEvent event) {
+        Log.info("Initializing file service");
+        getTree();
+    }
 
-    ByteString readlinkBS(JObjectKey uuid);
+    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;
+    }
 
-    JObjectKey symlink(String oldpath, String newpath);
+    private Optional<JKleppmannTreeNode> getDirEntryOpt(String name) {
+        var res = getTree().traverse(StreamSupport.stream(Path.of(name).spliterator(), false).map(p -> p.toString()).toList());
+        if (res == null) return Optional.empty();
+        var ret = curTx.get(JKleppmannTreeNodeHolder.class, res).map(JKleppmannTreeNodeHolder::node);
+        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);
+            if (ref == null) return Optional.empty();
+            GetattrRes ret;
+            if (ref instanceof RemoteObjectMeta r) {
+                var remote = remoteTx.getData(JDataRemote.class, uuid).orElse(null);
+                if (remote instanceof File f) {
+                    ret = new GetattrRes(f.mTime(), f.cTime(), f.mode(), f.symlink() ? GetattrType.SYMLINK : GetattrType.FILE);
+                } else {
+                    throw new StatusRuntimeException(Status.DATA_LOSS.withDescription("FsNode is not an FsNode: " + ref.key()));
+                }
+            } else if (ref instanceof JKleppmannTreeNodeHolder) {
+                ret = new GetattrRes(100, 100, 0700, GetattrType.DIRECTORY);
+            } else {
+                throw new StatusRuntimeException(Status.DATA_LOSS.withDescription("FsNode is not an FsNode: " + ref.key()));
+            }
+            return Optional.of(ret);
+        });
+    }
+
+    /**
+     * 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 = getDirEntry(name);
+                return switch (ret.meta()) {
+                    case JKleppmannTreeNodeMetaFile f -> Optional.of(f.fileIno());
+                    case JKleppmannTreeNodeMetaDirectory f -> Optional.of(ret.key());
+                    default -> Optional.empty();
+                };
+            } catch (StatusRuntimeException e) {
+                if (e.getStatus().getCode() == Status.Code.NOT_FOUND) {
+                    return Optional.empty();
+                }
+                throw e;
+            }
+        });
+    }
+
+    private void ensureDir(JKleppmannTreeNode entry) {
+        if (!(entry.meta() instanceof JKleppmannTreeNodeMetaDirectory))
+            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 = getDirEntry(path.getParent().toString());
+
+            ensureDir(parent);
+
+            String fname = path.getFileName().toString();
+
+            var fuuid = UUID.randomUUID();
+            Log.debug("Creating file " + fuuid);
+            File f = new File(JObjectKey.of(fuuid.toString()), mode, System.currentTimeMillis(), System.currentTimeMillis(), false);
+            remoteTx.putData(f);
+
+            try {
+                getTree().move(parent.key(), new JKleppmannTreeNodeMetaFile(fname, f.key()), getTree().getNewNodeId());
+            } catch (Exception e) {
+//                fobj.getMeta().removeRef(newNodeId);
+                throw e;
+            }
+            return Optional.of(f.key());
+        });
+    }
+
+    /**
+     * 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);
+                return false;
+            });
+        });
+    }
+
+    /**
+     * 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 = 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);
+            if (node == null)
+                throw new StatusRuntimeException(Status.NOT_FOUND.withDescription("File not found when trying to unlink: " + name));
+            if (node.meta() instanceof JKleppmannTreeNodeMetaDirectory f) {
+                if (!allowRecursiveDelete && !node.children().isEmpty())
+                    throw new DirectoryNotEmptyException();
+            }
+            getTree().trash(node.meta(), node.key());
+        });
+    }
+
+    /**
+     * 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 = getDirEntry(from);
+            JKleppmannTreeNodeMeta meta = node.meta();
+
+            var toPath = Path.of(to);
+            var toDentry = getDirEntry(toPath.getParent().toString());
+            ensureDir(toDentry);
+
+            getTree().move(toDentry.key(), meta.withName(toPath.getFileName().toString()), node.key());
+            return true;
+        });
+    }
+
+    /**
+     * 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));
+
+            if (dent instanceof JKleppmannTreeNodeHolder) {
+                return true;
+            } else if (dent instanceof RemoteObjectMeta) {
+                var remote = remoteTx.getData(JDataRemote.class, uuid).orElse(null);
+                if (remote instanceof File f) {
+                    remoteTx.putData(f.withMode(mode).withCurrentMTime());
+                    return true;
+                } else {
+                    throw new IllegalArgumentException(uuid + " is not a file");
+                }
+            } else {
+                throw new IllegalArgumentException(uuid + " is not a file");
+            }
+        });
+    }
+
+    /**
+     * 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 = getDirEntry(name);
+
+            if (!(found.meta() instanceof JKleppmannTreeNodeMetaDirectory md))
+                throw new StatusRuntimeException(Status.INVALID_ARGUMENT);
+
+            return found.children().keySet();
+        });
+    }
+
+    /**
+     * 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)
+                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Length should be more than zero: " + length));
+            if (offset < 0)
+                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Offset should be more than zero: " + offset));
+
+            var file = remoteTx.getData(File.class, fileUuid).orElse(null);
+            if (file == null) {
+                Log.error("File not found when trying to read: " + fileUuid);
+                throw new StatusRuntimeException(Status.NOT_FOUND.withDescription("File not found when trying to read: " + fileUuid));
+            }
+
+            try (var it = jMapHelper.getIterator(file, IteratorStart.LE, JMapLongKey.of(offset))) {
+                if (!it.hasNext())
+                    return ByteString.empty();
+
+//                if (it.peekNextKey().key() != offset) {
+//                    Log.warnv("Read over the end of file: {0} {1} {2}, next chunk: {3}", fileUuid, offset, length, it.peekNextKey());
+//                    return Optional.of(ByteString.empty());
+//                }
+                long curPos = offset;
+                ByteString buf = ByteString.empty();
+
+                var chunk = it.next();
+
+                while (curPos < offset + length) {
+                    var chunkPos = chunk.getKey().key();
+
+                    long offInChunk = curPos - chunkPos;
+
+                    long toReadInChunk = (offset + length) - curPos;
+
+                    var chunkBytes = readChunk(chunk.getValue().ref());
+
+                    long readableLen = chunkBytes.size() - offInChunk;
+
+                    var toReadReally = Math.min(readableLen, toReadInChunk);
+
+                    if (toReadReally < 0) break;
+
+                    buf = buf.concat(chunkBytes.substring((int) offInChunk, (int) (offInChunk + toReadReally)));
+
+                    curPos += toReadReally;
+
+                    if (readableLen > toReadInChunk)
+                        break;
+
+                    if (!it.hasNext()) break;
+
+                    chunk = it.next();
+                }
+
+                return buf;
+            } catch (Exception e) {
+                Log.error("Error reading file: " + fileUuid, e);
+                throw new StatusRuntimeException(Status.INTERNAL.withDescription("Error reading file: " + fileUuid));
+            }
+        });
+    }
+
+    /**
+     * 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);
+
+        if (chunkRead == null) {
+            Log.error("Chunk requested not found: " + uuid);
+            throw new StatusRuntimeException(Status.NOT_FOUND);
+        }
+
+        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();
+    }
+
+    private long alignDown(long num, long n) {
+        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)
+                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Offset should be more than zero: " + offset));
+
+            var file = remoteTx.getData(File.class, fileUuid).orElse(null);
+            if (file == null) {
+                throw new StatusRuntimeException(Status.NOT_FOUND.withDescription("File not found when trying to write: " + fileUuid));
+            }
+
+            Map<Long, JObjectKey> removedChunks = new HashMap<>();
+
+            long realOffset = targetChunkAlignment >= 0 ? alignDown(offset, targetChunkAlignment) : offset;
+            long writeEnd = offset + data.size();
+            long start = realOffset;
+            long existingEnd = 0;
+            ByteString pendingPrefix = ByteString.empty();
+            ByteString pendingSuffix = ByteString.empty();
+
+            try (var it = jMapHelper.getIterator(file, IteratorStart.LE, JMapLongKey.of(realOffset))) {
+                while (it.hasNext()) {
+                    var curEntry = it.next();
+                    long curChunkStart = curEntry.getKey().key();
+                    var curChunkId = curEntry.getValue().ref();
+                    long curChunkEnd = it.hasNext() ? it.peekNextKey().key() : curChunkStart + getChunkSize(curChunkId);
+                    existingEnd = curChunkEnd;
+                    if (curChunkEnd <= realOffset) break;
+
+                    removedChunks.put(curEntry.getKey().key(), curChunkId);
+
+                    if (curChunkStart < offset) {
+                        if (curChunkStart < start)
+                            start = curChunkStart;
+
+                        var readChunk = readChunk(curChunkId);
+                        pendingPrefix = pendingPrefix.concat(readChunk.substring(0, Math.min(readChunk.size(), (int) (offset - curChunkStart))));
+                    }
+
+                    if (curChunkEnd > writeEnd) {
+                        var readChunk = readChunk(curChunkId);
+                        pendingSuffix = pendingSuffix.concat(readChunk.substring((int) (writeEnd - curChunkStart), readChunk.size()));
+                    }
+
+                    if (curChunkEnd >= writeEnd) break;
+                }
+            }
+
+
+            Map<Long, JObjectKey> newChunks = new HashMap<>();
+
+            if (existingEnd < offset) {
+                if (!pendingPrefix.isEmpty()) {
+                    int diff = Math.toIntExact(offset - existingEnd);
+                    pendingPrefix = pendingPrefix.concat(UnsafeByteOperations.unsafeWrap(ByteBuffer.allocateDirect(diff)));
+                } else {
+                    fillZeros(existingEnd, offset, newChunks);
+                    start = offset;
+                }
+            }
+
+            ByteString pendingWrites = pendingPrefix.concat(data).concat(pendingSuffix);
+
+            int combinedSize = pendingWrites.size();
+
+            {
+                int cur = 0;
+                while (cur < combinedSize) {
+                    int end;
+
+                    if (combinedSize - cur < maxChunkSize)
+                        end = combinedSize;
+                    else if (targetChunkAlignment < 0)
+                        end = combinedSize;
+                    else
+                        end = Math.min(cur + targetChunkSize, combinedSize);
+
+                    var thisChunk = pendingWrites.substring(cur, end);
+
+                    ChunkData newChunkData = createChunk(thisChunk);
+                    newChunks.put(start, newChunkData.key());
+
+                    start += thisChunk.size();
+                    cur = end;
+                }
+            }
+
+            for (var e : removedChunks.entrySet()) {
+//                Log.tracev("Removing chunk {0}-{1}", e.getKey(), e.getValue());
+                jMapHelper.delete(file, JMapLongKey.of(e.getKey()));
+            }
+
+            for (var e : newChunks.entrySet()) {
+//                Log.tracev("Adding chunk {0}-{1}", e.getKey(), e.getValue());
+                jMapHelper.put(file, JMapLongKey.of(e.getKey()), e.getValue());
+            }
+
+            remoteTx.putData(file.withCurrentMTime());
+
+            return (long) data.size();
+        });
+    }
+
+    /**
+     * 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)
+                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Length should be more than zero: " + length));
+
+            var file = remoteTx.getData(File.class, fileUuid).orElse(null);
+            if (file == null) {
+                Log.error("File not found when trying to write: " + fileUuid);
+                return false;
+            }
+
+            if (length == 0) {
+                jMapHelper.deleteAll(file);
+                remoteTx.putData(file);
+                return true;
+            }
+
+            var curSize = size(fileUuid);
+            if (curSize == length) return true;
+
+            NavigableMap<Long, JObjectKey> removedChunks = new TreeMap<>();
+            NavigableMap<Long, JObjectKey> newChunks = new TreeMap<>();
+
+            if (curSize < length) {
+                fillZeros(curSize, length, newChunks);
+            } else {
+//                Pair<JMapLongKey, JMapEntry<JMapLongKey>> first;
+                Pair<JMapLongKey, JMapEntry<JMapLongKey>> last;
+                try (var it = jMapHelper.getIterator(file, IteratorStart.LT, JMapLongKey.of(length))) {
+                    last = it.hasNext() ? it.next() : null;
+                    while (it.hasNext()) {
+                        var next = it.next();
+                        removedChunks.put(next.getKey().key(), next.getValue().ref());
+                    }
+                }
+                removedChunks.put(last.getKey().key(), last.getValue().ref());
+//
+//                NavigableMap<Long, JObjectKey> removedChunks = new TreeMap<>();
+//
+//                long start = 0;
+//
+//                try (var it = jMapHelper.getIterator(file, IteratorStart.LE, JMapLongKey.of(offset))) {
+//                    first = it.hasNext() ? it.next() : null;
+//                    boolean empty = last == null;
+//                    if (first != null && getChunkSize(first.getValue().ref()) + first.getKey().key() <= offset) {
+//                        first = null;
+//                        last = null;
+//                        start = offset;
+//                    } else if (!empty) {
+//                        assert first != null;
+//                        removedChunks.put(first.getKey().key(), first.getValue().ref());
+//                        while (it.hasNext() && it.peekNextKey() != last.getKey()) {
+//                            var next = it.next();
+//                            removedChunks.put(next.getKey().key(), next.getValue().ref());
+//                        }
+//                        removedChunks.put(last.getKey().key(), last.getValue().ref());
+//                    }
+//                }
+//
+//                var tail = chunksAll.lowerEntry(length);
+//                var afterTail = chunksAll.tailMap(tail.getKey(), false);
+//
+//                removedChunks.put(tail.getKey(), tail.getValue());
+//                removedChunks.putAll(afterTail);
+
+                var tailBytes = readChunk(last.getValue().ref());
+                var newChunk = tailBytes.substring(0, (int) (length - last.getKey().key()));
+
+                ChunkData newChunkData = createChunk(newChunk);
+                newChunks.put(last.getKey().key(), newChunkData.key());
+            }
+
+//            file = file.withChunks(file.chunks().minusAll(removedChunks.keySet()).plusAll(newChunks)).withMTime(System.currentTimeMillis());
+
+            for (var e : removedChunks.entrySet()) {
+//                Log.tracev("Removing chunk {0}-{1}", e.getKey(), e.getValue());
+                jMapHelper.delete(file, JMapLongKey.of(e.getKey()));
+            }
+
+            for (var e : newChunks.entrySet()) {
+//                Log.tracev("Adding chunk {0}-{1}", e.getKey(), e.getValue());
+                jMapHelper.put(file, JMapLongKey.of(e.getKey()), e.getValue());
+            }
+
+            remoteTx.putData(file.withCurrentMTime());
+            return true;
+        });
+    }
+
+    /**
+     * 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);
+
+        long start = fillStart;
+
+        // Hack
+        HashMap<Long, ChunkData> zeroCache = new HashMap<>();
+
+        {
+            long cur = 0;
+            while (cur < combinedSize) {
+                long end;
+
+                if (targetChunkSize <= 0)
+                    end = combinedSize;
+                else {
+                    if ((combinedSize - cur) > (targetChunkSize * 1.5)) {
+                        end = cur + targetChunkSize;
+                    } else {
+                        end = combinedSize;
+                    }
+                }
+
+                if (!zeroCache.containsKey(end - cur))
+                    zeroCache.put(end - cur, createChunk(UnsafeByteOperations.unsafeWrap(ByteBuffer.allocateDirect(Math.toIntExact(end - cur)))));
+
+                ChunkData newChunkData = zeroCache.get(end - cur);
+                newChunks.put(start, newChunkData.key());
+
+                start += newChunkData.data().size();
+                cur = end;
+            }
+        }
+    }
+
+    /**
+     * 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)));
+            return read(uuid, 0, Math.toIntExact(size(uuid)));
+        });
+    }
+
+    /**
+     * 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 = getDirEntry(path.getParent().toString());
+
+            ensureDir(parent);
+
+            String fname = path.getFileName().toString();
+
+            var fuuid = UUID.randomUUID();
+            Log.debug("Creating file " + fuuid);
+
+            ChunkData newChunkData = createChunk(UnsafeByteOperations.unsafeWrap(oldpath.getBytes(StandardCharsets.UTF_8)));
+            File f = new File(JObjectKey.of(fuuid.toString()), 0, System.currentTimeMillis(), System.currentTimeMillis(), true);
+            jMapHelper.put(f, JMapLongKey.of(0), newChunkData.key());
+
+            remoteTx.putData(f);
+            getTree().move(parent.key(), new JKleppmannTreeNodeMetaFile(fname, f.key()), getTree().getNewNodeId());
+            return f.key();
+        });
+    }
+
+    /**
+     * 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));
+
+            // FIXME:
+            if (dent instanceof JKleppmannTreeNodeHolder) {
+                return true;
+            } else if (dent instanceof RemoteObjectMeta) {
+                var remote = remoteTx.getData(JDataRemote.class, fileUuid).orElse(null);
+                if (remote instanceof File f) {
+                    remoteTx.putData(f.withCTime(atimeMs).withMTime(mtimeMs));
+                    return true;
+                } else {
+                    throw new IllegalArgumentException(fileUuid + " is not a file");
+                }
+            } else {
+                throw new IllegalArgumentException(fileUuid + " is not a file");
+            }
+        });
+    }
+
+    /**
+     * 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;
+            var file = remoteTx.getData(File.class, fileUuid)
+                    .orElseThrow(() -> new StatusRuntimeException(Status.NOT_FOUND));
+
+            Pair<JMapLongKey, JMapEntry<JMapLongKey>> last;
+            try (var it = jMapHelper.getIterator(file, IteratorStart.LT, JMapLongKey.max())) {
+                last = it.hasNext() ? it.next() : null;
+            }
+
+            if (last != null) {
+                realSize = last.getKey().key() + getChunkSize(last.getValue().ref());
+            }
+
+            return realSize;
+        });
+    }
+
+    /**
+     * 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/DhfsFileServiceImpl.java

@@ -1,667 +0,0 @@
-package com.usatiuk.dhfsfs.service;
-
-import com.google.protobuf.ByteString;
-import com.google.protobuf.UnsafeByteOperations;
-import com.usatiuk.dhfs.jkleppmanntree.JKleppmannTreeManager;
-import com.usatiuk.dhfs.jkleppmanntree.structs.JKleppmannTreeNode;
-import com.usatiuk.dhfs.jkleppmanntree.structs.JKleppmannTreeNodeHolder;
-import com.usatiuk.dhfs.jkleppmanntree.structs.JKleppmannTreeNodeMeta;
-import com.usatiuk.dhfs.jmap.JMapEntry;
-import com.usatiuk.dhfs.jmap.JMapHelper;
-import com.usatiuk.dhfs.jmap.JMapLongKey;
-import com.usatiuk.dhfs.remoteobj.JDataRemote;
-import com.usatiuk.dhfs.remoteobj.RemoteObjectMeta;
-import com.usatiuk.dhfs.remoteobj.RemoteTransaction;
-import com.usatiuk.dhfsfs.objects.ChunkData;
-import com.usatiuk.dhfsfs.objects.File;
-import com.usatiuk.dhfsfs.objects.JKleppmannTreeNodeMetaDirectory;
-import com.usatiuk.dhfsfs.objects.JKleppmannTreeNodeMetaFile;
-import com.usatiuk.objects.JData;
-import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.iterators.IteratorStart;
-import com.usatiuk.objects.transaction.LockingStrategy;
-import com.usatiuk.objects.transaction.Transaction;
-import com.usatiuk.objects.transaction.TransactionManager;
-import com.usatiuk.utils.StatusRuntimeExceptionNoStacktrace;
-import io.grpc.Status;
-import io.grpc.StatusRuntimeException;
-import io.quarkus.logging.Log;
-import io.quarkus.runtime.StartupEvent;
-import jakarta.annotation.Priority;
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.enterprise.event.Observes;
-import jakarta.inject.Inject;
-import org.apache.commons.lang3.tuple.Pair;
-import org.eclipse.microprofile.config.inject.ConfigProperty;
-
-import java.nio.ByteBuffer;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Path;
-import java.util.*;
-import java.util.stream.StreamSupport;
-
-@ApplicationScoped
-public class DhfsFileServiceImpl implements DhfsFileService {
-    @Inject
-    Transaction curTx;
-    @Inject
-    RemoteTransaction remoteTx;
-    @Inject
-    TransactionManager jObjectTxManager;
-
-    @ConfigProperty(name = "dhfs.files.target_chunk_alignment")
-    int targetChunkAlignment;
-
-    @ConfigProperty(name = "dhfs.files.target_chunk_size")
-    int targetChunkSize;
-
-    @ConfigProperty(name = "dhfs.files.use_hash_for_chunks")
-    boolean useHashForChunks;
-
-    @ConfigProperty(name = "dhfs.files.allow_recursive_delete")
-    boolean allowRecursiveDelete;
-
-    @ConfigProperty(name = "dhfs.objects.ref_verification")
-    boolean refVerification;
-
-    @ConfigProperty(name = "dhfs.objects.write_log")
-    boolean writeLogging;
-
-    @Inject
-    JKleppmannTreeManager jKleppmannTreeManager;
-
-    @Inject
-    JMapHelper jMapHelper;
-
-    private JKleppmannTreeManager.JKleppmannTree getTreeW() {
-        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), () -> new JKleppmannTreeNodeMetaDirectory(""));
-    }
-
-    private JKleppmannTreeManager.JKleppmannTree getTreeR() {
-        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), LockingStrategy.OPTIMISTIC, () -> new JKleppmannTreeNodeMetaDirectory(""));
-    }
-
-    private ChunkData createChunk(ByteString bytes) {
-        var newChunk = new ChunkData(JObjectKey.of(UUID.randomUUID().toString()), bytes);
-        remoteTx.putData(newChunk);
-        return newChunk;
-    }
-
-    void init(@Observes @Priority(500) StartupEvent event) {
-        Log.info("Initializing file service");
-        getTreeW();
-    }
-
-    private JKleppmannTreeNode getDirEntryW(String name) {
-        var res = getTreeW().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 = getTreeR().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 Optional<JKleppmannTreeNode> getDirEntryOpt(String name) {
-        var res = getTreeW().traverse(StreamSupport.stream(Path.of(name).spliterator(), false).map(p -> p.toString()).toList());
-        if (res == null) return Optional.empty();
-        var ret = curTx.get(JKleppmannTreeNodeHolder.class, res).map(JKleppmannTreeNodeHolder::node);
-        return ret;
-    }
-
-    @Override
-    public Optional<GetattrRes> getattr(JObjectKey uuid) {
-        return jObjectTxManager.executeTx(() -> {
-            var ref = curTx.get(JData.class, uuid).orElse(null);
-            if (ref == null) return Optional.empty();
-            GetattrRes ret;
-            if (ref instanceof RemoteObjectMeta r) {
-                var remote = remoteTx.getData(JDataRemote.class, uuid).orElse(null);
-                if (remote instanceof File f) {
-                    ret = new GetattrRes(f.mTime(), f.cTime(), f.mode(), f.symlink() ? GetattrType.SYMLINK : GetattrType.FILE);
-                } else {
-                    throw new StatusRuntimeException(Status.DATA_LOSS.withDescription("FsNode is not an FsNode: " + ref.key()));
-                }
-            } else if (ref instanceof JKleppmannTreeNodeHolder) {
-                ret = new GetattrRes(100, 100, 0700, GetattrType.DIRECTORY);
-            } else {
-                throw new StatusRuntimeException(Status.DATA_LOSS.withDescription("FsNode is not an FsNode: " + ref.key()));
-            }
-            return Optional.of(ret);
-        });
-    }
-
-    @Override
-    public Optional<JObjectKey> open(String name) {
-        return jObjectTxManager.executeTx(() -> {
-            try {
-                var ret = getDirEntryR(name);
-                return switch (ret.meta()) {
-                    case JKleppmannTreeNodeMetaFile f -> Optional.of(f.fileIno());
-                    case JKleppmannTreeNodeMetaDirectory f -> Optional.of(ret.key());
-                    default -> Optional.empty();
-                };
-            } catch (StatusRuntimeException e) {
-                if (e.getStatus().getCode() == Status.Code.NOT_FOUND) {
-                    return Optional.empty();
-                }
-                throw e;
-            }
-        });
-    }
-
-    private void ensureDir(JKleppmannTreeNode entry) {
-        if (!(entry.meta() instanceof JKleppmannTreeNodeMetaDirectory))
-            throw new StatusRuntimeExceptionNoStacktrace(Status.INVALID_ARGUMENT.withDescription("Not a directory: " + entry.key()));
-    }
-
-    @Override
-    public Optional<JObjectKey> create(String name, long mode) {
-        return jObjectTxManager.executeTx(() -> {
-            Path path = Path.of(name);
-            var parent = getDirEntryW(path.getParent().toString());
-
-            ensureDir(parent);
-
-            String fname = path.getFileName().toString();
-
-            var fuuid = UUID.randomUUID();
-            Log.debug("Creating file " + fuuid);
-            File f = new File(JObjectKey.of(fuuid.toString()), mode, System.currentTimeMillis(), System.currentTimeMillis(), false);
-            remoteTx.putData(f);
-
-            try {
-                getTreeW().move(parent.key(), new JKleppmannTreeNodeMetaFile(fname, f.key()), getTreeW().getNewNodeId());
-            } catch (Exception e) {
-//                fobj.getMeta().removeRef(newNodeId);
-                throw e;
-            }
-            return Optional.of(f.key());
-        });
-    }
-
-    //FIXME: Slow..
-    @Override
-    public Pair<String, JObjectKey> inoToParent(JObjectKey ino) {
-        return jObjectTxManager.executeTx(() -> {
-            return getTreeW().findParent(w -> {
-                if (w.meta() instanceof JKleppmannTreeNodeMetaFile f)
-                    return f.fileIno().equals(ino);
-                return false;
-            });
-        });
-    }
-
-    @Override
-    public void mkdir(String name, long mode) {
-        jObjectTxManager.executeTx(() -> {
-            Path path = Path.of(name);
-            var parent = getDirEntryW(path.getParent().toString());
-            ensureDir(parent);
-
-            String dname = path.getFileName().toString();
-
-            Log.debug("Creating directory " + name);
-
-            getTreeW().move(parent.key(), new JKleppmannTreeNodeMetaDirectory(dname), getTreeW().getNewNodeId());
-        });
-    }
-
-    @Override
-    public void unlink(String name) {
-        jObjectTxManager.executeTx(() -> {
-            var node = getDirEntryOpt(name).orElse(null);
-            if (node.meta() instanceof JKleppmannTreeNodeMetaDirectory f) {
-                if (!allowRecursiveDelete && !node.children().isEmpty())
-                    throw new DirectoryNotEmptyException();
-            }
-            getTreeW().trash(node.meta(), node.key());
-        });
-    }
-
-    @Override
-    public Boolean rename(String from, String to) {
-        return jObjectTxManager.executeTx(() -> {
-            var node = getDirEntryW(from);
-            JKleppmannTreeNodeMeta meta = node.meta();
-
-            var toPath = Path.of(to);
-            var toDentry = getDirEntryW(toPath.getParent().toString());
-            ensureDir(toDentry);
-
-            getTreeW().move(toDentry.key(), meta.withName(toPath.getFileName().toString()), node.key());
-            return true;
-        });
-    }
-
-    @Override
-    public Boolean chmod(JObjectKey uuid, long mode) {
-        return jObjectTxManager.executeTx(() -> {
-            var dent = curTx.get(JData.class, uuid).orElseThrow(() -> new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND));
-
-            if (dent instanceof JKleppmannTreeNodeHolder) {
-                return true;
-            } else if (dent instanceof RemoteObjectMeta) {
-                var remote = remoteTx.getData(JDataRemote.class, uuid).orElse(null);
-                if (remote instanceof File f) {
-                    remoteTx.putData(f.withMode(mode).withCurrentMTime());
-                    return true;
-                } else {
-                    throw new IllegalArgumentException(uuid + " is not a file");
-                }
-            } else {
-                throw new IllegalArgumentException(uuid + " is not a file");
-            }
-        });
-    }
-
-    @Override
-    public Iterable<String> readDir(String name) {
-        return jObjectTxManager.executeTx(() -> {
-            var found = getDirEntryW(name);
-
-            if (!(found.meta() instanceof JKleppmannTreeNodeMetaDirectory md))
-                throw new StatusRuntimeException(Status.INVALID_ARGUMENT);
-
-            return found.children().keySet();
-        });
-    }
-
-    @Override
-    public ByteString read(JObjectKey fileUuid, long offset, int length) {
-        return jObjectTxManager.executeTx(() -> {
-            if (length < 0)
-                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Length should be more than zero: " + length));
-            if (offset < 0)
-                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Offset should be more than zero: " + offset));
-
-            var file = remoteTx.getData(File.class, fileUuid).orElse(null);
-            if (file == null) {
-                Log.error("File not found when trying to read: " + fileUuid);
-                throw new StatusRuntimeException(Status.NOT_FOUND.withDescription("File not found when trying to read: " + fileUuid));
-            }
-
-            try (var it = jMapHelper.getIterator(file, IteratorStart.LE, JMapLongKey.of(offset))) {
-                if (!it.hasNext())
-                    return ByteString.empty();
-
-//                if (it.peekNextKey().key() != offset) {
-//                    Log.warnv("Read over the end of file: {0} {1} {2}, next chunk: {3}", fileUuid, offset, length, it.peekNextKey());
-//                    return Optional.of(ByteString.empty());
-//                }
-                long curPos = offset;
-                ByteString buf = ByteString.empty();
-
-                var chunk = it.next();
-
-                while (curPos < offset + length) {
-                    var chunkPos = chunk.getKey().key();
-
-                    long offInChunk = curPos - chunkPos;
-
-                    long toReadInChunk = (offset + length) - curPos;
-
-                    var chunkBytes = readChunk(chunk.getValue().ref());
-
-                    long readableLen = chunkBytes.size() - offInChunk;
-
-                    var toReadReally = Math.min(readableLen, toReadInChunk);
-
-                    if (toReadReally < 0) break;
-
-                    buf = buf.concat(chunkBytes.substring((int) offInChunk, (int) (offInChunk + toReadReally)));
-
-                    curPos += toReadReally;
-
-                    if (readableLen > toReadInChunk)
-                        break;
-
-                    if (!it.hasNext()) break;
-
-                    chunk = it.next();
-                }
-
-                return buf;
-            } catch (Exception e) {
-                Log.error("Error reading file: " + fileUuid, e);
-                throw new StatusRuntimeException(Status.INTERNAL.withDescription("Error reading file: " + fileUuid));
-            }
-        });
-    }
-
-    private ByteString readChunk(JObjectKey uuid) {
-        var chunkRead = remoteTx.getData(ChunkData.class, uuid).orElse(null);
-
-        if (chunkRead == null) {
-            Log.error("Chunk requested not found: " + uuid);
-            throw new StatusRuntimeException(Status.NOT_FOUND);
-        }
-
-        return chunkRead.data();
-    }
-
-    private int getChunkSize(JObjectKey uuid) {
-        return readChunk(uuid).size();
-    }
-
-    private long alignDown(long num, long n) {
-        return num & -(1L << n);
-    }
-
-    @Override
-    public Long write(JObjectKey fileUuid, long offset, ByteString data) {
-        return jObjectTxManager.executeTx(() -> {
-            if (offset < 0)
-                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Offset should be more than zero: " + offset));
-
-            var file = remoteTx.getData(File.class, fileUuid, LockingStrategy.WRITE).orElse(null);
-            if (file == null) {
-                Log.error("File not found when trying to write: " + fileUuid);
-                return -1L;
-            }
-
-            if (writeLogging) {
-                Log.info("Writing to file: " + file.key() + " size=" + size(fileUuid) + " "
-                        + offset + " " + data.size());
-            }
-
-            NavigableMap<Long, JObjectKey> removedChunks = new TreeMap<>();
-
-            long realOffset = targetChunkAlignment >= 0 ? alignDown(offset, targetChunkAlignment) : offset;
-            long writeEnd = offset + data.size();
-            long start = realOffset;
-            long existingEnd = 0;
-            ByteString pendingPrefix = ByteString.empty();
-            ByteString pendingSuffix = ByteString.empty();
-
-            try (var it = jMapHelper.getIterator(file, IteratorStart.LE, JMapLongKey.of(realOffset))) {
-                while (it.hasNext()) {
-                    var curEntry = it.next();
-                    long curChunkStart = curEntry.getKey().key();
-                    var curChunkId = curEntry.getValue().ref();
-                    long curChunkEnd = it.hasNext() ? it.peekNextKey().key() : curChunkStart + getChunkSize(curChunkId);
-                    existingEnd = curChunkEnd;
-                    if (curChunkEnd <= realOffset) break;
-
-                    removedChunks.put(curEntry.getKey().key(), curChunkId);
-
-                    if (curChunkStart < offset) {
-                        if (curChunkStart < start)
-                            start = curChunkStart;
-
-                        var readChunk = readChunk(curChunkId);
-                        pendingPrefix = pendingPrefix.concat(readChunk.substring(0, Math.min(readChunk.size(), (int) (offset - curChunkStart))));
-                    }
-
-                    if (curChunkEnd > writeEnd) {
-                        var readChunk = readChunk(curChunkId);
-                        pendingSuffix = pendingSuffix.concat(readChunk.substring((int) (writeEnd - curChunkStart), readChunk.size()));
-                    }
-
-                    if (curChunkEnd >= writeEnd) break;
-                }
-            }
-
-
-            NavigableMap<Long, JObjectKey> newChunks = new TreeMap<>();
-
-            if (existingEnd < offset) {
-                if (!pendingPrefix.isEmpty()) {
-                    int diff = Math.toIntExact(offset - existingEnd);
-                    pendingPrefix = pendingPrefix.concat(UnsafeByteOperations.unsafeWrap(ByteBuffer.allocateDirect(diff)));
-                } else {
-                    fillZeros(existingEnd, offset, newChunks);
-                    start = offset;
-                }
-            }
-
-            ByteString pendingWrites = pendingPrefix.concat(data).concat(pendingSuffix);
-
-            int combinedSize = pendingWrites.size();
-
-            {
-                int targetChunkSize = 1 << targetChunkAlignment;
-                int cur = 0;
-                while (cur < combinedSize) {
-                    int end;
-
-                    if (targetChunkAlignment < 0)
-                        end = combinedSize;
-                    else
-                        end = Math.min(cur + targetChunkSize, combinedSize);
-
-                    var thisChunk = pendingWrites.substring(cur, end);
-
-                    ChunkData newChunkData = createChunk(thisChunk);
-                    newChunks.put(start, newChunkData.key());
-
-                    start += thisChunk.size();
-                    cur = end;
-                }
-            }
-
-            for (var e : removedChunks.entrySet()) {
-//                Log.tracev("Removing chunk {0}-{1}", e.getKey(), e.getValue());
-                jMapHelper.delete(file, JMapLongKey.of(e.getKey()));
-            }
-
-            for (var e : newChunks.entrySet()) {
-//                Log.tracev("Adding chunk {0}-{1}", e.getKey(), e.getValue());
-                jMapHelper.put(file, JMapLongKey.of(e.getKey()), e.getValue());
-            }
-
-            remoteTx.putData(file.withCurrentMTime());
-
-            return (long) data.size();
-        });
-    }
-
-    @Override
-    public Boolean truncate(JObjectKey fileUuid, long length) {
-        return jObjectTxManager.executeTx(() -> {
-            if (length < 0)
-                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Length should be more than zero: " + length));
-
-            var file = remoteTx.getData(File.class, fileUuid).orElse(null);
-            if (file == null) {
-                Log.error("File not found when trying to write: " + fileUuid);
-                return false;
-            }
-
-            if (length == 0) {
-                jMapHelper.deleteAll(file);
-                remoteTx.putData(file);
-                return true;
-            }
-
-            var curSize = size(fileUuid);
-            if (curSize == length) return true;
-
-            NavigableMap<Long, JObjectKey> removedChunks = new TreeMap<>();
-            NavigableMap<Long, JObjectKey> newChunks = new TreeMap<>();
-
-            if (curSize < length) {
-                fillZeros(curSize, length, newChunks);
-            } else {
-//                Pair<JMapLongKey, JMapEntry<JMapLongKey>> first;
-                Pair<JMapLongKey, JMapEntry<JMapLongKey>> last;
-                try (var it = jMapHelper.getIterator(file, IteratorStart.LT, JMapLongKey.of(length))) {
-                    last = it.hasNext() ? it.next() : null;
-                    while (it.hasNext()) {
-                        var next = it.next();
-                        removedChunks.put(next.getKey().key(), next.getValue().ref());
-                    }
-                }
-                removedChunks.put(last.getKey().key(), last.getValue().ref());
-//
-//                NavigableMap<Long, JObjectKey> removedChunks = new TreeMap<>();
-//
-//                long start = 0;
-//
-//                try (var it = jMapHelper.getIterator(file, IteratorStart.LE, JMapLongKey.of(offset))) {
-//                    first = it.hasNext() ? it.next() : null;
-//                    boolean empty = last == null;
-//                    if (first != null && getChunkSize(first.getValue().ref()) + first.getKey().key() <= offset) {
-//                        first = null;
-//                        last = null;
-//                        start = offset;
-//                    } else if (!empty) {
-//                        assert first != null;
-//                        removedChunks.put(first.getKey().key(), first.getValue().ref());
-//                        while (it.hasNext() && it.peekNextKey() != last.getKey()) {
-//                            var next = it.next();
-//                            removedChunks.put(next.getKey().key(), next.getValue().ref());
-//                        }
-//                        removedChunks.put(last.getKey().key(), last.getValue().ref());
-//                    }
-//                }
-//
-//                var tail = chunksAll.lowerEntry(length);
-//                var afterTail = chunksAll.tailMap(tail.getKey(), false);
-//
-//                removedChunks.put(tail.getKey(), tail.getValue());
-//                removedChunks.putAll(afterTail);
-
-                var tailBytes = readChunk(last.getValue().ref());
-                var newChunk = tailBytes.substring(0, (int) (length - last.getKey().key()));
-
-                ChunkData newChunkData = createChunk(newChunk);
-                newChunks.put(last.getKey().key(), newChunkData.key());
-            }
-
-//            file = file.withChunks(file.chunks().minusAll(removedChunks.keySet()).plusAll(newChunks)).withMTime(System.currentTimeMillis());
-
-            for (var e : removedChunks.entrySet()) {
-//                Log.tracev("Removing chunk {0}-{1}", e.getKey(), e.getValue());
-                jMapHelper.delete(file, JMapLongKey.of(e.getKey()));
-            }
-
-            for (var e : newChunks.entrySet()) {
-//                Log.tracev("Adding chunk {0}-{1}", e.getKey(), e.getValue());
-                jMapHelper.put(file, JMapLongKey.of(e.getKey()), e.getValue());
-            }
-
-            remoteTx.putData(file.withCurrentMTime());
-            return true;
-        });
-    }
-
-    private void fillZeros(long fillStart, long length, NavigableMap<Long, JObjectKey> newChunks) {
-        long combinedSize = (length - fillStart);
-
-        long start = fillStart;
-
-        // Hack
-        HashMap<Long, ChunkData> zeroCache = new HashMap<>();
-
-        {
-            long cur = 0;
-            while (cur < combinedSize) {
-                long end;
-
-                if (targetChunkSize <= 0)
-                    end = combinedSize;
-                else {
-                    if ((combinedSize - cur) > (targetChunkSize * 1.5)) {
-                        end = cur + targetChunkSize;
-                    } else {
-                        end = combinedSize;
-                    }
-                }
-
-                if (!zeroCache.containsKey(end - cur))
-                    zeroCache.put(end - cur, createChunk(UnsafeByteOperations.unsafeWrap(ByteBuffer.allocateDirect(Math.toIntExact(end - cur)))));
-
-                ChunkData newChunkData = zeroCache.get(end - cur);
-                newChunks.put(start, newChunkData.key());
-
-                start += newChunkData.data().size();
-                cur = end;
-            }
-        }
-    }
-
-    @Override
-    public String readlink(JObjectKey uuid) {
-        return jObjectTxManager.executeTx(() -> {
-            return readlinkBS(uuid).toStringUtf8();
-        });
-    }
-
-    @Override
-    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)));
-            return read(uuid, 0, Math.toIntExact(size(uuid)));
-        });
-    }
-
-    @Override
-    public JObjectKey symlink(String oldpath, String newpath) {
-        return jObjectTxManager.executeTx(() -> {
-            Path path = Path.of(newpath);
-            var parent = getDirEntryW(path.getParent().toString());
-
-            ensureDir(parent);
-
-            String fname = path.getFileName().toString();
-
-            var fuuid = UUID.randomUUID();
-            Log.debug("Creating file " + fuuid);
-
-            ChunkData newChunkData = createChunk(UnsafeByteOperations.unsafeWrap(oldpath.getBytes(StandardCharsets.UTF_8)));
-            File f = new File(JObjectKey.of(fuuid.toString()), 0, System.currentTimeMillis(), System.currentTimeMillis(), true);
-            jMapHelper.put(f, JMapLongKey.of(0), newChunkData.key());
-
-            remoteTx.putData(f);
-            getTreeW().move(parent.key(), new JKleppmannTreeNodeMetaFile(fname, f.key()), getTreeW().getNewNodeId());
-            return f.key();
-        });
-    }
-
-    @Override
-    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));
-
-            // FIXME:
-            if (dent instanceof JKleppmannTreeNodeHolder) {
-                return true;
-            } else if (dent instanceof RemoteObjectMeta) {
-                var remote = remoteTx.getData(JDataRemote.class, fileUuid).orElse(null);
-                if (remote instanceof File f) {
-                    remoteTx.putData(f.withCTime(atimeMs).withMTime(mtimeMs));
-                    return true;
-                } else {
-                    throw new IllegalArgumentException(fileUuid + " is not a file");
-                }
-            } else {
-                throw new IllegalArgumentException(fileUuid + " is not a file");
-            }
-        });
-    }
-
-    @Override
-    public long size(JObjectKey fileUuid) {
-        return jObjectTxManager.executeTx(() -> {
-            long realSize = 0;
-            var file = remoteTx.getData(File.class, fileUuid)
-                    .orElseThrow(() -> new StatusRuntimeException(Status.NOT_FOUND));
-
-            Pair<JMapLongKey, JMapEntry<JMapLongKey>> last;
-            try (var it = jMapHelper.getIterator(file, IteratorStart.LT, JMapLongKey.max())) {
-                last = it.hasNext() ? it.next() : null;
-            }
-
-            if (last != null) {
-                realSize = last.getKey().key() + getChunkSize(last.getValue().ref());
-            }
-
-            return realSize;
-        });
-    }
-}

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-fs/src/test/java/com/usatiuk/dhfsfs/TestDataCleaner.java

@@ -30,7 +30,7 @@ public class TestDataCleaner {
         purgeDirectory(Path.of(tempDirectory).toFile());
     }
 
-    void purgeDirectory(File dir) {
+    public void purgeDirectory(File dir) {
         for (File file : Objects.requireNonNull(dir.listFiles())) {
             if (file.isDirectory())
                 purgeDirectory(file);

dhfs-parent/dhfs-fuse/pom.xml

@@ -139,16 +139,13 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
                 <configuration>
+                    <forkCount>1C</forkCount>
+                    <reuseForks>false</reuseForks>
+                    <parallel>classes</parallel>
                     <systemPropertyVariables>
                         <junit.jupiter.execution.parallel.enabled>
-                            true
+                            false
                         </junit.jupiter.execution.parallel.enabled>
-                        <junit.jupiter.execution.parallel.mode.default>
-                            concurrent
-                        </junit.jupiter.execution.parallel.mode.default>
-                        <junit.jupiter.execution.parallel.config.dynamic.factor>
-                            0.5
-                        </junit.jupiter.execution.parallel.config.dynamic.factor>
                         <junit.platform.output.capture.stdout>true</junit.platform.output.capture.stdout>
                         <junit.platform.output.capture.stderr>true</junit.platform.output.capture.stderr>
                     </systemPropertyVariables>

dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/DhfsFuse.java

@@ -1,12 +1,15 @@
 package com.usatiuk.dhfsfuse;
 
 import com.google.protobuf.UnsafeByteOperations;
+import com.kenai.jffi.MemoryIO;
 import com.sun.security.auth.module.UnixSystem;
 import com.usatiuk.dhfsfs.service.DhfsFileService;
 import com.usatiuk.dhfsfs.service.DirectoryNotEmptyException;
 import com.usatiuk.dhfsfs.service.GetattrRes;
 import com.usatiuk.kleppmanntree.AlreadyExistsException;
 import com.usatiuk.objects.JObjectKey;
+import com.usatiuk.utils.UninitializedByteBuffer;
+import com.usatiuk.utils.UnsafeAccessor;
 import io.grpc.Status;
 import io.grpc.StatusRuntimeException;
 import io.quarkus.logging.Log;
@@ -17,15 +20,15 @@ import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.enterprise.event.Observes;
 import jakarta.inject.Inject;
 import jnr.ffi.Pointer;
+import jnr.ffi.Runtime;
+import jnr.ffi.Struct;
+import jnr.ffi.types.off_t;
 import org.apache.commons.lang3.SystemUtils;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
 import ru.serce.jnrfuse.ErrorCodes;
 import ru.serce.jnrfuse.FuseFillDir;
 import ru.serce.jnrfuse.FuseStubFS;
-import ru.serce.jnrfuse.struct.FileStat;
-import ru.serce.jnrfuse.struct.FuseFileInfo;
-import ru.serce.jnrfuse.struct.Statvfs;
-import ru.serce.jnrfuse.struct.Timespec;
+import ru.serce.jnrfuse.struct.*;
 
 import java.nio.ByteBuffer;
 import java.nio.file.Paths;
@@ -36,6 +39,9 @@ import java.util.concurrent.atomic.AtomicLong;
 
 import static jnr.posix.FileStat.*;
 
+/**
+ * FUSE file system implementation.
+ */
 @ApplicationScoped
 public class DhfsFuse extends FuseStubFS {
     private static final int blksize = 1048576;
@@ -51,10 +57,13 @@ public class DhfsFuse extends FuseStubFS {
     @ConfigProperty(name = "dhfs.files.target_chunk_size")
     int targetChunkSize;
     @Inject
-    JnrPtrByteOutputAccessors jnrPtrByteOutputAccessors;
-    @Inject
     DhfsFileService fileService;
 
+    /**
+     * Allocate a handle for the given key.
+     * @param key the key to allocate a handle for
+     * @return the allocated handle, not 0
+     */
     private long allocateHandle(JObjectKey key) {
         while (true) {
             var newFh = _fh.getAndIncrement();
@@ -65,8 +74,14 @@ public class DhfsFuse extends FuseStubFS {
         }
     }
 
+    /**
+     * Get the key from the handle.
+     * @param handle the handle to get the key from
+     * @return the key, or null if not found
+     */
     private JObjectKey getFromHandle(long handle) {
-        assert handle != 0;
+        if(handle == 0)
+            throw new IllegalStateException("Handle is 0");
         return _openHandles.get(handle);
     }
 
@@ -231,7 +246,7 @@ public class DhfsFuse extends FuseStubFS {
             var fileKey = getFromHandle(fi.fh.get());
             var read = fileService.read(fileKey, offset, (int) size);
             if (read.isEmpty()) return 0;
-            UnsafeByteOperations.unsafeWriteTo(read, new JnrPtrByteOutput(jnrPtrByteOutputAccessors, buf, size));
+            UnsafeByteOperations.unsafeWriteTo(read, new JnrPtrByteOutput(buf, size));
             return read.size();
         } catch (Throwable e) {
             Log.error("When reading " + path, e);
@@ -241,24 +256,22 @@ public class DhfsFuse extends FuseStubFS {
 
     @Override
     public int write(String path, Pointer buf, long size, long offset, FuseFileInfo fi) {
+        var buffer = UninitializedByteBuffer.allocate((int) size);
+        UnsafeAccessor.UNSAFE.copyMemory(
+                buf.address(),
+                UnsafeAccessor.NIO.getBufferAddress(buffer),
+                size
+        );
+        return write(path, buffer, offset, fi);
+    }
+
+    public int write(String path, ByteBuffer buffer, long offset, FuseFileInfo fi) {
         if (offset < 0) return -ErrorCodes.EINVAL();
         try {
             var fileKey = getFromHandle(fi.fh.get());
-            var buffer = ByteBuffer.allocateDirect((int) size);
-
-            if (buffer.isDirect()) {
-                jnrPtrByteOutputAccessors.getUnsafe().copyMemory(
-                        buf.address(),
-                        jnrPtrByteOutputAccessors.getNioAccess().getBufferAddress(buffer),
-                        size
-                );
-            } else {
-                buf.get(0, buffer.array(), 0, (int) size);
-            }
-
             var written = fileService.write(fileKey, offset, UnsafeByteOperations.unsafeWrap(buffer));
             return written.intValue();
-        } catch (Throwable e) {
+        } catch (Exception e) {
             Log.error("When writing " + path, e);
             return -ErrorCodes.EIO();
         }
@@ -394,7 +407,7 @@ public class DhfsFuse extends FuseStubFS {
             var file = fileOpt.get();
             var read = fileService.readlinkBS(fileOpt.get());
             if (read.isEmpty()) return 0;
-            UnsafeByteOperations.unsafeWriteTo(read, new JnrPtrByteOutput(jnrPtrByteOutputAccessors, buf, size));
+            UnsafeByteOperations.unsafeWriteTo(read, new JnrPtrByteOutput(buf, size));
             buf.putByte(Math.min(size - 1, read.size()), (byte) 0);
             return 0;
         } catch (Throwable e) {
@@ -426,4 +439,29 @@ public class DhfsFuse extends FuseStubFS {
             return -ErrorCodes.EIO();
         }
     }
+
+    @Override
+    public int write_buf(String path, FuseBufvec buf, @off_t long off, FuseFileInfo fi) {
+        int size = (int) libFuse.fuse_buf_size(buf);
+        FuseBufvec tmpVec = new FuseBufvec(Runtime.getSystemRuntime());
+        long tmpVecAddr = MemoryIO.getInstance().allocateMemory(Struct.size(tmpVec), false);
+        try {
+            tmpVec.useMemory(Pointer.wrap(Runtime.getSystemRuntime(), tmpVecAddr));
+            FuseBufvec.init(tmpVec, size);
+            var bb = UninitializedByteBuffer.allocate(size);
+            var mem = UninitializedByteBuffer.getAddress(bb);
+            tmpVec.buf.mem.set(mem);
+            tmpVec.buf.size.set(size);
+            int res = (int) libFuse.fuse_buf_copy(tmpVec, buf, 0);
+            if (res != size) {
+                Log.errorv("fuse_buf_copy failed: {0} != {1}", res, size);
+                return -ErrorCodes.ENOMEM();
+            }
+            return write(path, bb, off, fi);
+        } finally {
+            if (tmpVecAddr != 0) {
+                MemoryIO.getInstance().freeMemory(tmpVecAddr);
+            }
+        }
+    }
 }

dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/JnrPtrByteOutput.java

@@ -1,22 +1,24 @@
 package com.usatiuk.dhfsfuse;
 
 import com.google.protobuf.ByteOutput;
+import com.usatiuk.utils.UnsafeAccessor;
 import jnr.ffi.Pointer;
 
 import java.nio.ByteBuffer;
 import java.nio.MappedByteBuffer;
 
+/**
+ * JnrPtrByteOutput is a ByteOutput implementation that writes to a `jnr.ffi.Pointer`.
+ */
 public class JnrPtrByteOutput extends ByteOutput {
     private final Pointer _backing;
     private final long _size;
-    private final JnrPtrByteOutputAccessors _accessors;
     private long _pos;
 
-    public JnrPtrByteOutput(JnrPtrByteOutputAccessors accessors, Pointer backing, long size) {
+    public JnrPtrByteOutput(Pointer backing, long size) {
         _backing = backing;
         _size = size;
         _pos = 0;
-        _accessors = accessors;
     }
 
     @Override
@@ -47,9 +49,9 @@ public class JnrPtrByteOutput extends ByteOutput {
             if (value instanceof MappedByteBuffer mb) {
                 mb.load();
             }
-            long addr = _accessors.getNioAccess().getBufferAddress(value) + value.position();
+            long addr = UnsafeAccessor.NIO.getBufferAddress(value) + value.position();
             var out = _backing.address() + _pos;
-            _accessors.getUnsafe().copyMemory(addr, out, rem);
+            UnsafeAccessor.UNSAFE.copyMemory(addr, out, rem);
         } else {
             _backing.put(_pos, value.array(), value.arrayOffset() + value.position(), rem);
         }

dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/JnrPtrByteOutputAccessors.java

@@ -1,29 +0,0 @@
-package com.usatiuk.dhfsfuse;
-
-import jakarta.inject.Singleton;
-import jdk.internal.access.JavaNioAccess;
-import jdk.internal.access.SharedSecrets;
-import sun.misc.Unsafe;
-
-import java.lang.reflect.Field;
-
-@Singleton
-class JnrPtrByteOutputAccessors {
-    JavaNioAccess _nioAccess;
-    Unsafe _unsafe;
-
-    JnrPtrByteOutputAccessors() throws NoSuchFieldException, IllegalAccessException {
-        _nioAccess = SharedSecrets.getJavaNioAccess();
-        Field f = Unsafe.class.getDeclaredField("theUnsafe");
-        f.setAccessible(true);
-        _unsafe = (Unsafe) f.get(null);
-    }
-
-    public JavaNioAccess getNioAccess() {
-        return _nioAccess;
-    }
-
-    public Unsafe getUnsafe() {
-        return _unsafe;
-    }
-}

dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/Main.java

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsapp;
+package com.usatiuk.dhfsfuse;
 
 import io.quarkus.runtime.Quarkus;
 import io.quarkus.runtime.QuarkusApplication;

dhfs-parent/dhfs-fuse/src/main/resources/application.properties

@@ -14,8 +14,9 @@ dhfs.objects.persistence.stuff.root=${HOME}/dhfs_default/data/stuff
 dhfs.fuse.debug=false
 dhfs.fuse.enabled=true
 dhfs.files.allow_recursive_delete=false
-dhfs.files.target_chunk_size=2097152
-dhfs.files.target_chunk_alignment=19
+dhfs.files.target_chunk_size=524288
+dhfs.files.max_chunk_size=524288
+dhfs.files.target_chunk_alignment=17
 dhfs.objects.deletion.delay=1000
 dhfs.objects.deletion.can-delete-retry-delay=10000
 dhfs.objects.ref_verification=true

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

@@ -30,7 +30,7 @@ public class TestDataCleaner {
         purgeDirectory(Path.of(tempDirectory).toFile());
     }
 
-    void purgeDirectory(File dir) {
+    public static void purgeDirectory(File dir) {
         for (File file : Objects.requireNonNull(dir.listFiles())) {
             if (file.isDirectory())
                 purgeDirectory(file);

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

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import com.github.dockerjava.api.model.Device;
 import io.quarkus.logging.Log;
@@ -168,35 +168,6 @@ public class DhfsFuseIT {
                 "rewritten\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));
     }
 
-    // TODO: How this fits with the tree?
-    @Test
-    @Disabled
-    void deleteDelayedTest() throws IOException, InterruptedException, TimeoutException {
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo tesempty > /dhfs_test/fuse/testf1").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> "tesempty\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));
-        await().atMost(45, TimeUnit.SECONDS).until(() -> "tesempty\n".equals(container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));
-
-        var client = DockerClientFactory.instance().client();
-        client.pauseContainerCmd(container2.getContainerId()).exec();
-
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS);
-
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "rm /dhfs_test/fuse/testf1").getExitCode());
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Delaying deletion check"), 60, TimeUnit.SECONDS, 1);
-
-        client.unpauseContainerCmd(container2.getContainerId()).exec();
-
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS);
-
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "ls /dhfs_test/fuse").getExitCode());
-
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Deleting from persistent"), 60, TimeUnit.SECONDS, 1);
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Deleting from persistent"), 60, TimeUnit.SECONDS, 3);
-
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 1 == container2.execInContainer("/bin/sh", "-c", "test -f /dhfs_test/fuse/testf1").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 1 == container1.execInContainer("/bin/sh", "-c", "test -f /dhfs_test/fuse/testf1").getExitCode());
-    }
-
     @Test
     void deleteTest() throws IOException, InterruptedException, TimeoutException {
         await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo tesempty > /dhfs_test/fuse/testf1").getExitCode());
@@ -221,6 +192,28 @@ public class DhfsFuseIT {
                 1 == container1.execInContainer("/bin/sh", "-c", "test -f /dhfs_test/fuse/testf1").getExitCode());
     }
 
+    @Test
+    void deleteTestKickedOut() throws IOException, InterruptedException, TimeoutException {
+        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo tesempty > /dhfs_test/fuse/testf1").getExitCode());
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                "tesempty\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                "tesempty\n".equals(container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));
+
+        container2.stop();
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("kicked"), 60, TimeUnit.SECONDS, 1);
+
+        Log.info("Deleting");
+        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "rm /dhfs_test/fuse/testf1").getExitCode());
+        Log.info("Deleted");
+
+        // FIXME?
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Deleting from persistent"), 60, TimeUnit.SECONDS, 3);
+
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                1 == container1.execInContainer("/bin/sh", "-c", "test -f /dhfs_test/fuse/testf1").getExitCode());
+    }
+
     @Test
     void moveFileTest() throws IOException, InterruptedException, TimeoutException {
         Log.info("Creating");

dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsFusex3IT.java

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import com.github.dockerjava.api.model.Device;
 import io.quarkus.logging.Log;

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

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import io.quarkus.logging.Log;
 import org.jetbrains.annotations.NotNull;
@@ -70,6 +70,7 @@ public class DhfsImage implements Future<String> {
                                         "--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",
                                         "-Ddhfs.objects.peerdiscovery.interval=1s",
                                         "-Ddhfs.objects.invalidation.delay=100",
                                         "-Ddhfs.objects.deletion.delay=0",
@@ -78,6 +79,8 @@ public class DhfsImage implements Future<String> {
                                         "-Ddhfs.objects.sync.timeout=30",
                                         "-Ddhfs.objects.sync.ping.timeout=5",
                                         "-Ddhfs.objects.reconnect_interval=1s",
+                                        "-Ddhfs.objects.last-seen.timeout=30",
+                                        "-Ddhfs.objects.last-seen.update=10",
                                         "-Ddhfs.sync.cert-check=false",
                                         "-Dquarkus.log.category.\"com.usatiuk\".level=TRACE",
                                         "-Dquarkus.log.category.\"com.usatiuk.dhfs\".level=TRACE",

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

@@ -1,7 +1,7 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import com.github.dockerjava.api.model.Device;
-import com.usatiuk.dhfsapp.TestDataCleaner;
+import com.usatiuk.dhfsfuse.TestDataCleaner;
 import io.quarkus.logging.Log;
 import org.junit.jupiter.api.*;
 import org.slf4j.LoggerFactory;

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

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import io.quarkus.logging.Log;
 

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

@@ -1,7 +1,7 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import com.github.dockerjava.api.model.Device;
-import com.usatiuk.dhfsapp.TestDataCleaner;
+import com.usatiuk.dhfsfuse.TestDataCleaner;
 import io.quarkus.logging.Log;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -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/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/ResyncIT.java

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsapp.integration;
+package com.usatiuk.dhfsfuse.integration;
 
 import com.github.dockerjava.api.model.Device;
 import org.junit.jupiter.api.*;

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

@@ -1,5 +1,8 @@
 package com.usatiuk.kleppmanntree;
 
+/**
+ * Exception thrown when an attempt is made to create a new tree node as a child with a name that already exists.
+ */
 public class AlreadyExistsException extends RuntimeException {
     public AlreadyExistsException(String message) {
         super(message);

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/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/Clock.java

@@ -1,9 +1,26 @@
 package com.usatiuk.kleppmanntree;
 
+/**
+ * Clock interface
+ */
 public interface Clock<TimestampT extends Comparable<TimestampT>> {
+    /**
+     * Increment and get the current timestamp.
+     * @return the incremented timestamp
+     */
     TimestampT getTimestamp();
 
+    /**
+     * Get the current timestamp without incrementing it.
+     * @return the current timestamp
+     */
     TimestampT peekTimestamp();
 
+    /**
+     * Update the timestamp with an externally received timestamp.
+     * Will set the currently stored timestamp to <code>max(receivedTimestamp, currentTimestamp) + 1</code>
+     * @param receivedTimestamp the received timestamp
+     * @return the previous timestamp
+     */
     TimestampT updateTimestamp(TimestampT receivedTimestamp);
 }

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

@@ -3,6 +3,13 @@ package com.usatiuk.kleppmanntree;
 import java.io.Serializable;
 import java.util.Comparator;
 
+/**
+ * CombinedTimestamp is a record that represents a timestamp and a node ID, ordered first by timestamp and then by node ID.
+ * @param timestamp the timestamp
+ * @param nodeId the node ID. If null, then only the timestamp is used for ordering.
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the node ID
+ */
 public record CombinedTimestamp<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>>
         (TimestampT timestamp,
          PeerIdT nodeId) implements Comparable<CombinedTimestamp<TimestampT, PeerIdT>>, Serializable {

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

@@ -8,6 +8,14 @@ import java.util.function.Function;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+/**
+ * An implementation of a tree as described in <a href="https://martin.kleppmann.com/papers/move-op.pdf">A highly-available move operation for replicated trees</a>
+ *
+ * @param <TimestampT> Type of the timestamp
+ * @param <PeerIdT>    Type of the peer ID
+ * @param <MetaT>      Type of the node metadata
+ * @param <NodeIdT>    Type of the node ID
+ */
 public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT> {
     private static final Logger LOGGER = Logger.getLogger(KleppmannTree.class.getName());
 
@@ -16,6 +24,14 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
     private final Clock<TimestampT> _clock;
     private final OpRecorder<TimestampT, PeerIdT, MetaT, NodeIdT> _opRecorder;
 
+    /**
+     * Constructor with all the dependencies
+     *
+     * @param storage    Storage interface
+     * @param peers      Peer interface
+     * @param clock      Clock interface
+     * @param opRecorder Operation recorder interface
+     */
     public KleppmannTree(StorageInterface<TimestampT, PeerIdT, MetaT, NodeIdT> storage,
                          PeerInterface<PeerIdT> peers,
                          Clock<TimestampT> clock,
@@ -26,6 +42,13 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         _opRecorder = opRecorder;
     }
 
+    /**
+     * Traverse the tree from the given node ID using the given list of names
+     *
+     * @param fromId The starting node ID
+     * @param names  The list of names to traverse
+     * @return The resulting node ID or null if not found
+     */
     private NodeIdT traverseImpl(NodeIdT fromId, List<String> names) {
         if (names.isEmpty()) return fromId;
 
@@ -39,14 +62,21 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         return traverseImpl(childId, names.subList(1, names.size()));
     }
 
-    public NodeIdT traverse(NodeIdT fromId, List<String> names) {
-        return traverseImpl(fromId, names.subList(1, names.size()));
-    }
-
+    /**
+     * Traverse the tree from its root node using the given list of names
+     *
+     * @param names The list of names to traverse
+     * @return The resulting node ID or null if not found
+     */
     public NodeIdT traverse(List<String> names) {
         return traverseImpl(_storage.getRootId(), names);
     }
 
+    /**
+     * Undo the effect of a log effect
+     *
+     * @param effect The log effect to undo
+     */
     private void undoEffect(LogEffect<TimestampT, PeerIdT, MetaT, NodeIdT> effect) {
         if (effect.oldInfo() != null) {
             var node = _storage.getById(effect.childId());
@@ -89,6 +119,11 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         }
     }
 
+    /**
+     * Undo the effects of a log record
+     *
+     * @param op The log record to undo
+     */
     private void undoOp(LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> op) {
         LOGGER.finer(() -> "Will undo op: " + op);
         if (op.effects() != null)
@@ -96,16 +131,32 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
                 undoEffect(e);
     }
 
+    /**
+     * Redo the operation in a log record
+     *
+     * @param entry The log record to redo
+     */
     private void redoOp(Map.Entry<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> entry) {
         var newEffects = doOp(entry.getValue().op(), false);
         _storage.getLog().replace(entry.getKey(), newEffects);
     }
 
+    /**
+     * Perform the operation and put it in the log
+     *
+     * @param op                   The operation to perform
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
     private void doAndPut(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
         var res = doOp(op, failCreatingIfExists);
         _storage.getLog().put(res.op().timestamp(), res);
     }
 
+    /**
+     * Try to trim the log to the causality threshold
+     */
     private void tryTrimLog() {
         var log = _storage.getLog();
         var timeLog = _storage.getPeerTimestampLog();
@@ -161,22 +212,52 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         }
     }
 
+    /**
+     * Move a node to a new parent with new metadata
+     *
+     * @param newParent The new parent node ID
+     * @param newMeta   The new metadata
+     * @param child     The child node ID
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
     public <LocalMetaT extends MetaT> void move(NodeIdT newParent, LocalMetaT newMeta, NodeIdT child) {
         move(newParent, newMeta, child, true);
     }
 
+    /**
+     * Move a node to a new parent with new metadata
+     *
+     * @param newParent            The new parent node ID
+     * @param newMeta              The new metadata
+     * @param child                The child node ID
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
     public void move(NodeIdT newParent, MetaT newMeta, NodeIdT child, boolean failCreatingIfExists) {
         var createdMove = createMove(newParent, newMeta, child);
         applyOp(_peers.getSelfId(), createdMove, failCreatingIfExists);
         _opRecorder.recordOp(createdMove);
     }
 
+    /**
+     * Apply an external operation from a remote peer
+     *
+     * @param from The peer ID
+     * @param op   The operation to apply
+     */
     public void applyExternalOp(PeerIdT from, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op) {
         _clock.updateTimestamp(op.timestamp().timestamp());
         applyOp(from, op, false);
     }
 
-    // Returns true if the timestamp is newer than what's seen, false otherwise
+    /**
+     * Update the causality threshold timestamp for a peer
+     *
+     * @param from         The peer ID
+     * @param newTimestamp The timestamp received from it
+     * @return True if the timestamp was updated, false otherwise
+     */
     private boolean updateTimestampImpl(PeerIdT from, TimestampT newTimestamp) {
         TimestampT oldRef = _storage.getPeerTimestampLog().getForPeer(from);
         if (oldRef != null && oldRef.compareTo(newTimestamp) >= 0) { // FIXME?
@@ -187,6 +268,12 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         return true;
     }
 
+    /**
+     * Update the causality threshold timestamp for a peer
+     *
+     * @param from      The peer ID
+     * @param timestamp The timestamp received from it
+     */
     public void updateExternalTimestamp(PeerIdT from, TimestampT timestamp) {
         var gotExt = _storage.getPeerTimestampLog().getForPeer(from);
         var gotSelf = _storage.getPeerTimestampLog().getForPeer(_peers.getSelfId());
@@ -197,6 +284,15 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         tryTrimLog();
     }
 
+    /**
+     * Apply an operation from a peer
+     *
+     * @param from                 The peer ID
+     * @param op                   The operation to apply
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
     private void applyOp(PeerIdT from, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
         if (!updateTimestampImpl(op.timestamp().nodeId(), op.timestamp().timestamp())) return;
 
@@ -229,14 +325,36 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         }
     }
 
+    /**
+     * Get a new timestamp, incrementing the one in storage
+     *
+     * @return A new timestamp
+     */
     private CombinedTimestamp<TimestampT, PeerIdT> getTimestamp() {
         return new CombinedTimestamp<>(_clock.getTimestamp(), _peers.getSelfId());
     }
 
+    /**
+     * Create a new move operation
+     *
+     * @param newParent The new parent node ID
+     * @param newMeta   The new metadata
+     * @param node      The child node ID
+     * @return A new move operation
+     */
     private <LocalMetaT extends MetaT> OpMove<TimestampT, PeerIdT, LocalMetaT, NodeIdT> createMove(NodeIdT newParent, LocalMetaT newMeta, NodeIdT node) {
         return new OpMove<>(getTimestamp(), newParent, newMeta, node);
     }
 
+    /**
+     * Perform the operation and return the log record
+     *
+     * @param op                   The operation to perform
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @return The log record
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
     private LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> doOp(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
         LOGGER.finer(() -> "Doing op: " + op);
         LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> computed;
@@ -253,10 +371,24 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         return computed;
     }
 
+    /**
+     * Get a new node from storage
+     *
+     * @param key    The node ID
+     * @param parent The parent node ID
+     * @param meta   The metadata
+     * @return A new tree node
+     */
     private TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> getNewNode(NodeIdT key, NodeIdT parent, MetaT meta) {
         return _storage.createNewNode(key, parent, meta);
     }
 
+    /**
+     * Apply the effects of a log record
+     *
+     * @param sourceOp The source operation
+     * @param effects  The list of log effects
+     */
     private void applyEffects(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> sourceOp, List<LogEffect<TimestampT, PeerIdT, MetaT, NodeIdT>> effects) {
         for (var effect : effects) {
             LOGGER.finer(() -> "Applying effect: " + effect + " from op " + sourceOp);
@@ -297,6 +429,15 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         }
     }
 
+    /**
+     * Compute the effects of a move operation
+     *
+     * @param op                   The operation to process
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @return The log record with the computed effects
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
     private LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> computeEffects(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
         var node = _storage.getById(op.childId());
 
@@ -380,6 +521,13 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         ));
     }
 
+    /**
+     * Check if a node is an ancestor of another node
+     *
+     * @param child  The child node ID
+     * @param parent The parent node ID
+     * @return True if the child is an ancestor of the parent, false otherwise
+     */
     private boolean isAncestor(NodeIdT child, NodeIdT parent) {
         var node = _storage.getById(parent);
         NodeIdT curParent;
@@ -390,6 +538,11 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         return false;
     }
 
+    /**
+     * Walk the tree and apply the given consumer to each node
+     *
+     * @param consumer The consumer to apply to each node
+     */
     public void walkTree(Consumer<TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT>> consumer) {
         ArrayDeque<NodeIdT> queue = new ArrayDeque<>();
         queue.push(_storage.getRootId());
@@ -403,6 +556,12 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         }
     }
 
+    /**
+     * Find the parent of a node that matches the given predicate
+     *
+     * @param kidPredicate The predicate to match the child node
+     * @return A pair containing the name of the child and the ID of the parent, or null if not found
+     */
     public Pair<String, NodeIdT> findParent(Function<TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT>, Boolean> kidPredicate) {
         ArrayDeque<NodeIdT> queue = new ArrayDeque<>();
         queue.push(_storage.getRootId());
@@ -423,6 +582,13 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         return null;
     }
 
+    /**
+     * Record the bootstrap operations for a given peer
+     * Will visit all nodes of the tree and add their effective operations to both the queue to be sent to the peer,
+     * and to the global operation log.
+     *
+     * @param host The peer ID
+     */
     public void recordBoostrapFor(PeerIdT host) {
         TreeMap<CombinedTimestamp<TimestampT, PeerIdT>, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT>> result = new TreeMap<>();
 

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

@@ -2,6 +2,18 @@ package com.usatiuk.kleppmanntree;
 
 import java.io.Serializable;
 
+/**
+ * LogEffect is a record that represents the effect of a log entry on a tree node.
+ * @param oldInfo the old information about the node, before it was moved. Null if the node did not exist before
+ * @param effectiveOp the operation that had caused this effect to be applied
+ * @param newParentId the ID of the new parent node
+ * @param newMeta the new metadata of the node
+ * @param childId the ID of the child node
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public record LogEffect<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>(
         LogEffectOld<TimestampT, PeerIdT, MetaT, NodeIdT> oldInfo,
         OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> effectiveOp,

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

@@ -2,6 +2,16 @@ package com.usatiuk.kleppmanntree;
 
 import java.io.Serializable;
 
+/**
+ * Represents the old information about a node before it was moved.
+ * @param oldEffectiveMove the old effective move that had caused this effect to be applied
+ * @param oldParent the ID of the old parent node
+ * @param oldMeta the old metadata of the node
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public record LogEffectOld<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>
         (OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> oldEffectiveMove,
          NodeIdT oldParent,

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

@@ -4,29 +4,82 @@ import org.apache.commons.lang3.tuple.Pair;
 
 import java.util.List;
 
+/**
+ * LogInterface is an interface that allows accessing the log of operations
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public interface LogInterface<
         TimestampT extends Comparable<TimestampT>,
         PeerIdT extends Comparable<PeerIdT>,
         MetaT extends NodeMeta,
         NodeIdT> {
+    /**
+     * Peek the oldest log entry.
+     * @return the oldest log entry
+     */
     Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> peekOldest();
 
+    /**
+     * Take the oldest log entry.
+     * @return the oldest log entry
+     */
     Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> takeOldest();
 
+    /**
+     * Peek the newest log entry.
+     * @return the newest log entry
+     */
     Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> peekNewest();
 
+    /**
+     * Return all log entries that are newer than the given timestamp.
+     * @param since the timestamp to compare with
+     * @param inclusive if true, include the log entry with the given timestamp
+     * @return a list of log entries that are newer than the given timestamp
+     */
     List<Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>>>
     newestSlice(CombinedTimestamp<TimestampT, PeerIdT> since, boolean inclusive);
 
+    /**
+     * Return all the log entries
+     * @return a list of all log entries
+     */
     List<Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>>> getAll();
 
+    /**
+     * Checks if the log is empty.
+     * @return true if the log is empty, false otherwise
+     */
     boolean isEmpty();
 
+    /**
+     * Checks if the log contains the given timestamp.
+     * @param timestamp the timestamp to check
+     * @return true if the log contains the given timestamp, false otherwise
+     */
     boolean containsKey(CombinedTimestamp<TimestampT, PeerIdT> timestamp);
 
+    /**
+     * Get the size of the log.
+     * @return the size of the log (number of entries)
+     */
     long size();
 
+    /**
+     * Add a log entry to the log.
+     * @param timestamp the timestamp of the log entry
+     * @param record the log entry
+     * @throws IllegalStateException if the log entry already exists
+     */
     void put(CombinedTimestamp<TimestampT, PeerIdT> timestamp, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> record);
 
+    /**
+     * Replace a log entry in the log.
+     * @param timestamp the timestamp of the log entry
+     * @param record the log entry
+     */
     void replace(CombinedTimestamp<TimestampT, PeerIdT> timestamp, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> record);
 }

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

@@ -3,6 +3,15 @@ package com.usatiuk.kleppmanntree;
 import java.io.Serializable;
 import java.util.List;
 
+/**
+ * Represents a log record in the Kleppmann tree.
+ * @param op the operation that is stored in this log record
+ * @param effects the effects of the operation (resulting moves)
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public record LogRecord<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>
         (OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op,
          List<LogEffect<TimestampT, PeerIdT, MetaT, NodeIdT>> effects) implements Serializable {

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

@@ -2,8 +2,24 @@ package com.usatiuk.kleppmanntree;
 
 import java.io.Serializable;
 
+/**
+ * Represents metadata associated with a node in the Kleppmann tree.
+ * This interface is used to define the metadata that can be associated with nodes in the tree.
+ * Implementations of this interface should provide a name for the node and a method to create a copy of it with a new name.
+ */
 public interface NodeMeta extends Serializable {
+    /**
+     * Returns the name of the node.
+     *
+     * @return the name of the node
+     */
     String name();
 
+    /**
+     * Creates a copy of the metadata with a new name.
+     *
+     * @param name the new name for the metadata
+     * @return a new instance of NodeMeta with the specified name
+     */
     NodeMeta withName(String name);
 }

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

@@ -2,9 +2,27 @@ package com.usatiuk.kleppmanntree;
 
 import java.io.Serializable;
 
+/**
+ * Operation that moves a child node to a new parent node.
+ *
+ * @param timestamp    the timestamp of the operation
+ * @param newParentId  the ID of the new parent node
+ * @param newMeta      the new metadata of the node, can be null
+ * @param childId      the ID of the child node (the node that is being moved)
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT>    the type of the peer ID
+ * @param <MetaT>      the type of the node metadata
+ * @param <NodeIdT>    the type of the node ID
+ */
 public record OpMove<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>
         (CombinedTimestamp<TimestampT, PeerIdT> timestamp, NodeIdT newParentId, MetaT newMeta,
          NodeIdT childId) implements Serializable {
+    /**
+     * Returns the new name of the node: name extracted from the new metadata if available,
+     * otherwise the child ID converted to string.
+     *
+     * @return the new name of the node
+     */
     public String newName() {
         if (newMeta != null)
             return newMeta.name();

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

@@ -1,7 +1,26 @@
 package com.usatiuk.kleppmanntree;
 
+/**
+ * Interface to provide recording operations to be sent to peers asynchronously.
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public interface OpRecorder<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT> {
+    /**
+     * Records an operation to be sent to peers asynchronously.
+     * The operation will be sent to all known peers in the system.
+     *
+     * @param op the operation to be recorded
+     */
     void recordOp(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op);
 
+    /**
+     * Records an operation to be sent to a specific peer asynchronously.
+     *
+     * @param peer the ID of the peer to send the operation to
+     * @param op   the operation to be recorded
+     */
     void recordOpForPeer(PeerIdT peer, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op);
 }

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

@@ -2,8 +2,22 @@ package com.usatiuk.kleppmanntree;
 
 import java.util.Collection;
 
+/**
+ * Interface providing access to a list of known peers.
+ * @param <PeerIdT> the type of the peer ID
+ */
 public interface PeerInterface<PeerIdT extends Comparable<PeerIdT>> {
+    /**
+     * Returns the ID of the current peer.
+     *
+     * @return the ID of the current peer
+     */
     PeerIdT getSelfId();
 
+    /**
+     * Returns a collection of all known peers.
+     *
+     * @return a collection of all known peers
+     */
     Collection<PeerIdT> getAllPeers();
 }

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

@@ -1,11 +1,26 @@
 package com.usatiuk.kleppmanntree;
 
+/**
+ * Interface providing a map of newest received timestamps for each peer. (causality thresholds)
+ * If a peer has some timestamp recorded in this map,
+ * it means that all messages coming from this peer will have a newer timestamp.
+ * @param <TimestampT>
+ * @param <PeerIdT>
+ */
 public interface PeerTimestampLogInterface<
         TimestampT extends Comparable<TimestampT>,
         PeerIdT extends Comparable<PeerIdT>> {
 
+    /**
+     * Get the timestamp for a specific peer.
+     * @param peerId the ID of the peer
+     * @return the timestamp for the peer
+     */
     TimestampT getForPeer(PeerIdT peerId);
 
+    /**
+     * Get the timestamp for the current peer.
+     */
     void putForPeer(PeerIdT peerId, TimestampT timestamp);
 
 }

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

@@ -1,28 +1,89 @@
 package com.usatiuk.kleppmanntree;
 
+/**
+ * Storage interface for the Kleppmann tree.
+ *
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT>    the type of the peer ID
+ * @param <MetaT>      the type of the node metadata
+ * @param <NodeIdT>    the type of the node ID
+ */
 public interface StorageInterface<
         TimestampT extends Comparable<TimestampT>,
         PeerIdT extends Comparable<PeerIdT>,
         MetaT extends NodeMeta,
         NodeIdT> {
+    /**
+     * Get the root node ID.
+     *
+     * @return the root node IDx
+     */
     NodeIdT getRootId();
 
+    /**
+     * Get the trash node ID.
+     *
+     * @return the trash node ID
+     */
     NodeIdT getTrashId();
 
+    /**
+     * Get the lost and found node ID.
+     *
+     * @return the lost and found node ID
+     */
     NodeIdT getLostFoundId();
 
+    /**
+     * Get the new node ID.
+     *
+     * @return the new node ID
+     */
     NodeIdT getNewNodeId();
 
+    /**
+     * Get the node by its ID.
+     *
+     * @param id the ID of the node
+     * @return the node with the specified ID, or null if not found
+     */
     TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> getById(NodeIdT id);
 
-    // Creates a node, returned wrapper is RW-locked
+    /**
+     * Create a new node with the specified key, parent, and metadata.
+     *
+     * @param key    the ID of the new node
+     * @param parent the ID of the parent node
+     * @param meta   the metadata of the new node
+     * @return the new node
+     */
     TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> createNewNode(NodeIdT key, NodeIdT parent, MetaT meta);
 
+    /**
+     * Put a node into the storage.
+     *
+     * @param node the node to put into the storage
+     */
     void putNode(TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> node);
 
+    /**
+     * Remove a node from the storage.
+     *
+     * @param id the ID of the node to remove
+     */
     void removeNode(NodeIdT id);
 
+    /**
+     * Get the log interface.
+     *
+     * @return the log interface
+     */
     LogInterface<TimestampT, PeerIdT, MetaT, NodeIdT> getLog();
 
+    /**
+     * Get the peer timestamp log interface.
+     *
+     * @return the peer timestamp log interface
+     */
     PeerTimestampLogInterface<TimestampT, PeerIdT> getPeerTimestampLog();
 }

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

@@ -5,29 +5,92 @@ import org.pcollections.PMap;
 
 import java.io.Serializable;
 
+/**
+ * Represents a node in the Kleppmann tree.
+ *
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT>    the type of the peer ID
+ * @param <MetaT>      the type of the node metadata
+ * @param <NodeIdT>    the type of the node ID
+ */
 public interface TreeNode<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT> extends Serializable {
+    /**
+     * Get the ID of the node.
+     *
+     * @return the ID of the node
+     */
     NodeIdT key();
 
+    /**
+     * Get the ID of the parent node.
+     *
+     * @return the ID of the parent node
+     */
     NodeIdT parent();
 
+    /**
+     * Get the last effective operation that moved this node.
+     *
+     * @return the last effective operation
+     */
     OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> lastEffectiveOp();
 
+    /**
+     * Get the metadata stored in this node.
+     *
+     * @return the metadata of the node
+     */
     @Nullable
     MetaT meta();
 
+    /**
+     * Get the name of the node.
+     * If the node has metadata, the name is extracted from it, otherwise the key is converted to string.
+     *
+     * @return the name of the node
+     */
     default String name() {
         var meta = meta();
         if (meta != null) return meta.name();
         return key().toString();
     }
 
+    /**
+     * Get the children of this node.
+     *
+     * @return a map of child IDs to their respective nodes
+     */
     PMap<String, NodeIdT> children();
 
+    /**
+     * Make a copy of this node with a new parent.
+     *
+     * @param parent the ID of the new parent node
+     * @return a new TreeNode instance with the updated parent
+     */
     TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withParent(NodeIdT parent);
 
+    /**
+     * Make a copy of this node with a new last effective operation.
+     *
+     * @param lastEffectiveOp the new last effective operation
+     * @return a new TreeNode instance with the updated last effective operation
+     */
     TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withLastEffectiveOp(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> lastEffectiveOp);
 
+    /**
+     * Make a copy of this node with new metadata.
+     *
+     * @param meta the new metadata
+     * @return a new TreeNode instance with the updated metadata
+     */
     TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withMeta(MetaT meta);
 
+    /**
+     * Make a copy of this node with new children.
+     *
+     * @param children the new children
+     * @return a new TreeNode instance with the updated children
+     */
     TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withChildren(PMap<String, NodeIdT> children);
 }

dhfs-parent/objects/pom.xml

@@ -18,11 +18,6 @@
     </properties>
 
     <dependencies>
-        <dependency>
-            <groupId>org.apache.fury</groupId>
-            <artifactId>fury-core</artifactId>
-            <version>0.10.1</version>
-        </dependency>
         <dependency>
             <groupId>net.jqwik</groupId>
             <artifactId>jqwik</artifactId>

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JData.java

@@ -2,9 +2,20 @@ package com.usatiuk.objects;
 
 import java.io.Serializable;
 
+/**
+ * JData is a marker interface for all objects that can be stored in the object store.
+ */
 public interface JData extends Serializable {
+    /**
+     * Returns the key of the object.
+     * @return the key of the object
+     */
     JObjectKey key();
 
+    /**
+     * Returns the estimated size of the object in bytes.
+     * @return the estimated size of the object in bytes
+     */
     default int estimateSize() {
         return 100;
     }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapper.java

@@ -2,15 +2,34 @@ package com.usatiuk.objects;
 
 import com.usatiuk.objects.iterators.Data;
 
+/**
+ * JDataVersionedWrapper is a wrapper for JData that contains its version number
+ * (the id of the transaction that had changed it last)
+ */
 public sealed interface JDataVersionedWrapper extends Data<JDataVersionedWrapper> permits JDataVersionedWrapperLazy, JDataVersionedWrapperImpl {
     @Override
     default JDataVersionedWrapper value() {
         return this;
     }
 
+    /**
+     * Returns the wrapped object.
+     *
+     * @return the wrapped object
+     */
     JData data();
 
+    /**
+     * Returns the version number of the object.
+     *
+     * @return the version number of the object
+     */
     long version();
 
+    /**
+     * Returns the estimated size of the object in bytes.
+     *
+     * @return the estimated size of the object in bytes
+     */
     int estimateSize();
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperImpl.java

@@ -4,6 +4,9 @@ import jakarta.annotation.Nonnull;
 
 import java.io.Serializable;
 
+/**
+ * Simple wrapper for an already-existing JData object with a version.
+ */
 public record JDataVersionedWrapperImpl(@Nonnull JData data,
                                         long version) implements Serializable, JDataVersionedWrapper {
     @Override

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperLazy.java

@@ -2,18 +2,35 @@ package com.usatiuk.objects;
 
 import java.util.function.Supplier;
 
+/**
+ * Lazy JDataVersionedWrapper implementation.
+ * The object is deserialized only when data() is called for the first time.
+ * Also allows to set a callback to be called when the data is loaded (e.g. to cache it).
+ */
 public final class JDataVersionedWrapperLazy implements JDataVersionedWrapper {
     private final long _version;
     private final int _estimatedSize;
     private JData _data;
     private Supplier<JData> _producer;
 
+    /**
+     * Creates a new JDataVersionedWrapperLazy object.
+     *
+     * @param version       the version number of the object
+     * @param estimatedSize the estimated size of the object in bytes
+     * @param producer      a supplier that produces the wrapped object
+     */
     public JDataVersionedWrapperLazy(long version, int estimatedSize, Supplier<JData> producer) {
         _version = version;
         _estimatedSize = estimatedSize;
         _producer = producer;
     }
 
+    /**
+     * Set a callback to be called when the data is loaded.
+     *
+     * @param cacheCallback the callback to be called
+     */
     public void setCacheCallback(Runnable cacheCallback) {
         if (_data != null) {
             throw new IllegalStateException("Cache callback can be set only before data is loaded");

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperSerializer.java

@@ -7,11 +7,21 @@ import jakarta.inject.Singleton;
 
 import java.nio.ByteBuffer;
 
+/**
+ * Serializer for JDataVersionedWrapper objects.
+ * The objects are stored in a simple format: first is 8-byte long, then the serialized object.
+ */
 @Singleton
 public class JDataVersionedWrapperSerializer {
     @Inject
     ObjectSerializer<JData> dataSerializer;
 
+    /**
+     * Serializes a JDataVersionedWrapper object to a ByteString.
+     *
+     * @param obj the object to serialize
+     * @return the serialized object as a ByteString
+     */
     public ByteString serialize(JDataVersionedWrapper obj) {
         ByteBuffer buffer = ByteBuffer.allocate(Long.BYTES);
         buffer.putLong(obj.version());
@@ -19,6 +29,13 @@ public class JDataVersionedWrapperSerializer {
         return ByteString.copyFrom(buffer).concat(dataSerializer.serialize(obj.data()));
     }
 
+    /**
+     * Deserializes a JDataVersionedWrapper object from a ByteBuffer.
+     * Returns a lazy wrapper (JDataVersionedWrapperLazy).
+     *
+     * @param data the ByteBuffer containing the serialized object
+     * @return the deserialized object
+     */
     public JDataVersionedWrapper deserialize(ByteBuffer data) {
         var version = data.getLong();
         return new JDataVersionedWrapperLazy(version, data.remaining(),

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKey.java

@@ -5,30 +5,68 @@ import java.nio.ByteBuffer;
 import java.nio.charset.StandardCharsets;
 import java.util.UUID;
 
+/**
+ * JObjectKey is an interface for object keys to be used in the object store.
+ */
 public sealed interface JObjectKey extends Serializable, Comparable<JObjectKey> permits JObjectKeyImpl, JObjectKeyMax, JObjectKeyMin {
     JObjectKeyMin MIN = new JObjectKeyMin();
     JObjectKeyMax MAX = new JObjectKeyMax();
 
+    /**
+     * Creates a new JObjectKey from a string value.
+     *
+     * @param value the string value of the key
+     * @return a new JObjectKey
+     */
     static JObjectKey of(String value) {
         return new JObjectKeyImpl(value);
     }
 
+    /**
+     * Creates a new JObjectKey with a random UUID.
+     *
+     * @return a new JObjectKey with a random UUID
+     */
     static JObjectKey random() {
         return new JObjectKeyImpl(UUID.randomUUID().toString());
     }
 
+    /**
+     * Returns a JObjectKey that compares less than all other keys.
+     * Calling value on this key will result in an exception.
+     *
+     * @return a JObjectKey that compares less than all other keys
+     */
     static JObjectKey first() {
         return MIN;
     }
 
+    /**
+     * Returns a JObjectKey that compares greater than all other keys.
+     * Calling value on this key will result in an exception.
+     *
+     * @return a JObjectKey that compares greater than all other keys
+     */
     static JObjectKey last() {
         return MAX;
     }
 
+    /**
+     * Creates a new JObjectKey from a byte array.
+     *
+     * @param bytes the byte array representing the key
+     * @return a new JObjectKey
+     */
     static JObjectKey fromBytes(byte[] bytes) {
         return new JObjectKeyImpl(new String(bytes, StandardCharsets.ISO_8859_1));
     }
 
+    /**
+     * Creates a new JObjectKey from a ByteBuffer.
+     *
+     * @param buff the ByteBuffer representing the key
+     * @return a new JObjectKey
+     */
     static JObjectKey fromByteBuffer(ByteBuffer buff) {
         byte[] bytes = new byte[buff.remaining()];
         buff.get(bytes);
@@ -41,7 +79,17 @@ public sealed interface JObjectKey extends Serializable, Comparable<JObjectKey>
     @Override
     String toString();
 
+    /**
+     * Returns the byte buffer representation of the key.
+     *
+     * @return the byte buffer representation of the key
+     */
     ByteBuffer toByteBuffer();
 
+    /**
+     * Returns the string value of the key.
+     *
+     * @return the string value of the key
+     */
     String value();
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyImpl.java

@@ -1,10 +1,15 @@
 package com.usatiuk.objects;
 
+import com.usatiuk.utils.UninitializedByteBuffer;
+
 import java.io.Serial;
 import java.nio.ByteBuffer;
 import java.nio.charset.StandardCharsets;
 import java.util.Objects;
 
+/**
+ * A "real" implementation of JObjectKey, containing an underlying string, and a cached lazily created byte buffer.
+ */
 public final class JObjectKeyImpl implements JObjectKey {
     @Serial
     private static final long serialVersionUID = 0L;
@@ -46,7 +51,7 @@ public final class JObjectKeyImpl implements JObjectKey {
         synchronized (this) {
             if (_bb != null) return _bb;
             var bytes = value.getBytes(StandardCharsets.ISO_8859_1);
-            var directBb = ByteBuffer.allocateDirect(bytes.length);
+            var directBb = UninitializedByteBuffer.allocate(bytes.length);
             directBb.put(bytes);
             directBb.flip();
             _bb = directBb;
@@ -69,7 +74,7 @@ public final class JObjectKeyImpl implements JObjectKey {
 
     @Override
     public int hashCode() {
-        return Objects.hash(value);
+        return value.hashCode();
     }
 
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyMax.java

@@ -2,6 +2,9 @@ package com.usatiuk.objects;
 
 import java.nio.ByteBuffer;
 
+/**
+ * JObjectKey implementation that compares greater than all other keys.
+ */
 public record JObjectKeyMax() implements JObjectKey {
     @Override
     public int compareTo(JObjectKey o) {

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyMin.java

@@ -2,6 +2,9 @@ package com.usatiuk.objects;
 
 import java.nio.ByteBuffer;
 
+/**
+ * JObjectKey implementation that compares less than all other keys.
+ */
 public record JObjectKeyMin() implements JObjectKey {
     @Override
     public int compareTo(JObjectKey o) {

dhfs-parent/objects/src/main/java/com/usatiuk/objects/JavaDataSerializer.java

@@ -3,30 +3,29 @@ package com.usatiuk.objects;
 
 import com.google.protobuf.ByteString;
 import com.google.protobuf.UnsafeByteOperations;
+import com.usatiuk.utils.SerializationHelper;
 import io.quarkus.arc.DefaultBean;
 import jakarta.enterprise.context.ApplicationScoped;
-import org.apache.fury.Fury;
-import org.apache.fury.ThreadSafeFury;
-import org.apache.fury.config.Language;
 
+import java.io.IOException;
 import java.nio.ByteBuffer;
 
+/**
+ * Simple Java object serializer.
+ */
 @ApplicationScoped
 @DefaultBean
 public class JavaDataSerializer implements ObjectSerializer<JData> {
-    private static final ThreadSafeFury fury = Fury.builder().withLanguage(Language.JAVA)
-            // Allow to deserialize objects unknown types,
-            // more flexible but less secure.
-            .requireClassRegistration(false)
-            .buildThreadSafeFury();
-
     @Override
     public ByteString serialize(JData obj) {
-        return UnsafeByteOperations.unsafeWrap(fury.serialize(obj));
+        return SerializationHelper.serialize(obj);
     }
 
-    @Override
     public JData deserialize(ByteBuffer data) {
-        return (JData) fury.deserialize(data);
+        try (var is = UnsafeByteOperations.unsafeWrap(data).newInput()) {
+            return SerializationHelper.deserialize(is);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
     }
 }

dhfs-parent/objects/src/main/java/com/usatiuk/objects/ObjectSerializer.java

@@ -4,8 +4,25 @@ import com.google.protobuf.ByteString;
 
 import java.nio.ByteBuffer;
 
+/**
+ * Interface for serializing and deserializing objects.
+ *
+ * @param <T> the type of object to serialize/deserialize
+ */
 public interface ObjectSerializer<T> {
+    /**
+     * Serialize an object to a ByteString.
+     *
+     * @param obj the object to serialize
+     * @return the serialized object as a ByteString
+     */
     ByteString serialize(T obj);
 
+    /**
+     * Deserialize an object from a ByteBuffer.
+     *
+     * @param data the ByteBuffer containing the serialized object
+     * @return the deserialized object
+     */
     T deserialize(ByteBuffer data);
 }

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

@@ -1,24 +1,70 @@
 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 {
+
+/**
+ * An iterator over key-value pairs that can be closed and supports peek and skip operations, in both directions.
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
+public interface CloseableKvIterator<K extends Comparable<? super K>, V> extends Iterator<Pair<K, V>>, AutoCloseable {
+    /**
+     * Returns the upcoming key in the forward direction without advancing the iterator.
+     *
+     * @return the current key
+     * @throws IllegalStateException if there is no next element
+     */
     K peekNextKey();
 
+    /**
+     * Skips the next element in the forward direction.
+     *
+     * @throws IllegalStateException if there is no next element
+     */
     void skip();
 
+    /**
+     * Checks if there is a next element in the forward direction.
+     *
+     * @return true if there is a next element, false otherwise
+     * @throws IllegalStateException if there is no next element
+     */
     K peekPrevKey();
 
+    /**
+     * Returns the key-value pair in the reverse direction, and advances the iterator.
+     *
+     * @return the previous key-value pair
+     * @throws IllegalStateException if there is no previous element
+     */
     Pair<K, V> prev();
 
+    /**
+     * Checks if there is a previous element in the reverse direction.
+     *
+     * @return true if there is a previous element, false otherwise
+     */
     boolean hasPrev();
 
+    /**
+     * Skips the previous element in the reverse direction.
+     *
+     * @throws IllegalStateException if there is no previous element
+     */
     void skipPrev();
 
+    /**
+     * Returns a reversed iterator that iterates in the reverse direction.
+     *
+     * @return a new CloseableKvIterator that iterates in the reverse direction
+     */
     default CloseableKvIterator<K, V> reversed() {
         return new ReversedKvIterator<K, V>(this);
     }
+
+    @Override
+    void close();
 }

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

@@ -1,5 +1,13 @@
 package com.usatiuk.objects.iterators;
 
+/**
+ * Interface indicating that data is present.
+ * @param <V> the type of the value
+ */
 public interface Data<V> extends MaybeTombstone<V> {
+    /**
+     * Get the value.
+     * @return the value
+     */
     V value();
 }

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

@@ -1,4 +1,9 @@
 package com.usatiuk.objects.iterators;
 
+/**
+ * Simple implementation of the Data interface.
+ * @param value the value
+ * @param <V> the type of the value
+ */
 public record DataWrapper<V>(V value) implements Data<V> {
 }

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

@@ -1,6 +0,0 @@
-package com.usatiuk.objects.iterators;
-
-@FunctionalInterface
-public interface IterProdFn<K extends Comparable<K>, V> {
-    CloseableKvIterator<K, V> get(IteratorStart start, K key);
-}

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

@@ -1,5 +1,8 @@
 package com.usatiuk.objects.iterators;
 
+/**
+ * Allows to specify initial positioning of the iterator relative to the requested key.
+ */
 public enum IteratorStart {
     LT,
     LE,

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

@@ -5,11 +5,25 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.util.NoSuchElementException;
 import java.util.function.Function;
 
+/**
+ * A key-value iterator that filters keys based on a predicate.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class KeyPredicateKvIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
     private final CloseableKvIterator<K, V> _backing;
     private final Function<K, Boolean> _filter;
     private K _next;
 
+    /**
+     * Constructs a KeyPredicateKvIterator with the specified backing iterator, start position, and filter.
+     *
+     * @param backing  the backing iterator
+     * @param start    the starting position relative to the startKey
+     * @param startKey the starting key
+     * @param filter   the filter function to apply to keys. Only keys for which this function returns true will be included in the iteration.
+     */
     public KeyPredicateKvIterator(CloseableKvIterator<K, V> backing, IteratorStart start, K startKey, Function<K, Boolean> filter) {
         _goingForward = true;
         _backing = backing;

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

@@ -4,10 +4,23 @@ import org.apache.commons.lang3.tuple.Pair;
 
 import java.util.function.Function;
 
+/**
+ * A mapping key-value iterator that transforms the values of a backing iterator using a specified function.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values in the backing iterator
+ * @param <V_T> the type of the transformed values
+ */
 public class MappingKvIterator<K extends Comparable<K>, V, V_T> implements CloseableKvIterator<K, V_T> {
     private final CloseableKvIterator<K, V> _backing;
     private final Function<V, V_T> _transformer;
 
+    /**
+     * Constructs a MappingKvIterator with the specified backing iterator and transformer function.
+     *
+     * @param backing     the backing iterator
+     * @param transformer the function to transform values
+     */
     public MappingKvIterator(CloseableKvIterator<K, V> backing, Function<V, V_T> transformer) {
         _backing = backing;
         _transformer = transformer;

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

@@ -1,4 +1,8 @@
 package com.usatiuk.objects.iterators;
 
+/**
+ * Optional-like interface, can either be {@link Data} or {@link Tombstone}.
+ * @param <T> the type of the value
+ */
 public interface MaybeTombstone<T> {
 }

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

@@ -9,19 +9,32 @@ import java.util.NavigableMap;
 import java.util.NoSuchElementException;
 import java.util.TreeMap;
 
+/**
+ * A merging key-value iterator that combines multiple iterators into a single iterator.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class MergingKvIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
     private final NavigableMap<K, IteratorEntry<K, V>> _sortedIterators = new TreeMap<>();
-    private final String _name;
     private final List<IteratorEntry<K, V>> _iterators;
-    public MergingKvIterator(String name, IteratorStart startType, K startKey, List<IterProdFn<K, V>> iterators) {
-        _goingForward = true;
-        _name = name;
 
-        // Why streams are so slow?
+    /**
+     * Constructs a MergingKvIterator with the specified start type, start key, and list of iterators.
+     * The iterators have priority based on their order in the list: if two iterators have the same key,
+     * the one that is in the beginning of the list will be used.
+     *
+     * @param startType the starting position relative to the startKey
+     * @param startKey  the starting key
+     * @param iterators the list of iterators to merge
+     */
+    public MergingKvIterator(IteratorStart startType, K startKey, List<CloseableKvIterator<K, V>> iterators) {
+        _goingForward = true;
+
         {
             IteratorEntry<K, V>[] iteratorEntries = new IteratorEntry[iterators.size()];
             for (int i = 0; i < iterators.size(); i++) {
-                iteratorEntries[i] = new IteratorEntry<>(i, iterators.get(i).get(startType, startKey));
+                iteratorEntries[i] = new IteratorEntry<>(i, iterators.get(i));
             }
             _iterators = List.of(iteratorEntries);
         }
@@ -90,9 +103,18 @@ public class MergingKvIterator<K extends Comparable<K>, V> extends ReversibleKvI
 //        }
     }
 
+    /**
+     * Constructs a MergingKvIterator with the specified start type, start key, and array of iterators.
+     * The iterators have priority based on their order in the array: if two iterators have the same key,
+     * the one that is in the beginning of the array will be used.
+     *
+     * @param startType the starting position relative to the startKey
+     * @param startKey  the starting key
+     * @param iterators the array of iterators to merge
+     */
     @SafeVarargs
-    public MergingKvIterator(String name, IteratorStart startType, K startKey, IterProdFn<K, V>... iterators) {
-        this(name, startType, startKey, List.of(iterators));
+    public MergingKvIterator(IteratorStart startType, K startKey, CloseableKvIterator<K, V>... iterators) {
+        this(startType, startKey, List.of(iterators));
     }
 
     private void advanceIterator(IteratorEntry<K, V> iteratorEntry) {
@@ -151,7 +173,6 @@ public class MergingKvIterator<K extends Comparable<K>, V> extends ReversibleKvI
                 || (!_goingForward && peekImpl().compareTo(cur.getKey()) >= 0))) {
             skipImpl();
         }
-        Log.tracev("{0} Reversed to {1}", _name, _sortedIterators);
     }
 
     @Override
@@ -199,28 +220,14 @@ public class MergingKvIterator<K extends Comparable<K>, V> extends ReversibleKvI
     @Override
     public String toString() {
         return "MergingKvIterator{" +
-                "_name='" + _name + '\'' +
                 ", _sortedIterators=" + _sortedIterators.keySet() +
                 ", _iterators=" + _iterators +
                 '}';
     }
 
-    private interface FirstMatchState<K extends Comparable<K>, V> {
-    }
-
     private record IteratorEntry<K extends Comparable<K>, V>(int priority, CloseableKvIterator<K, V> iterator) {
         public IteratorEntry<K, V> reversed() {
             return new IteratorEntry<>(priority, iterator.reversed());
         }
     }
-
-    private record FirstMatchNone<K extends Comparable<K>, V>() implements FirstMatchState<K, V> {
-    }
-
-    private record FirstMatchFound<K extends Comparable<K>, V>(
-            CloseableKvIterator<K, V> iterator) implements FirstMatchState<K, V> {
-    }
-
-    private record FirstMatchConsumed<K extends Comparable<K>, V>() implements FirstMatchState<K, V> {
-    }
 }

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

@@ -4,11 +4,25 @@ import org.apache.commons.lang3.tuple.Pair;
 
 import java.util.*;
 
+/**
+ * A key-value iterator for a {@link NavigableMap}.
+ * It allows iterating over the keys and values in a sorted order.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class NavigableMapKvIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
     private final NavigableMap<K, V> _map;
     private Iterator<Map.Entry<K, V>> _iterator;
     private Map.Entry<K, V> _next;
 
+    /**
+     * Constructs a NavigableMapKvIterator with the specified map, start type, and start key.
+     *
+     * @param map   the map to iterate over
+     * @param start the starting position relative to the startKey
+     * @param key   the starting key
+     */
     public NavigableMapKvIterator(NavigableMap<K, ? extends V> map, IteratorStart start, K key) {
         _map = (NavigableMap<K, V>) map;
         SortedMap<K, V> _view;

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

@@ -2,9 +2,19 @@ package com.usatiuk.objects.iterators;
 
 import org.apache.commons.lang3.tuple.Pair;
 
+/**
+ * A wrapper for a key-value iterator that iterates in reverse order.
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class ReversedKvIterator<K extends Comparable<? super K>, V> implements CloseableKvIterator<K, V> {
     private final CloseableKvIterator<K, V> _backing;
 
+    /**
+     * Constructs a ReversedKvIterator with the specified backing iterator.
+     *
+     * @param backing the backing iterator
+     */
     public ReversedKvIterator(CloseableKvIterator<K, V> backing) {
         _backing = backing;
     }

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

@@ -2,9 +2,21 @@ package com.usatiuk.objects.iterators;
 
 import org.apache.commons.lang3.tuple.Pair;
 
+/**
+ * Base class for a reversible key-value iterator.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public abstract class ReversibleKvIterator<K extends Comparable<K>, V> implements CloseableKvIterator<K, V> {
+    /**
+     * The current direction of the iterator.
+     */
     protected boolean _goingForward;
 
+    /**
+     * Reverses the current direction of the iterator.
+     */
     protected abstract void reverse();
 
     private void ensureForward() {
@@ -19,12 +31,33 @@ public abstract class ReversibleKvIterator<K extends Comparable<K>, V> implement
         }
     }
 
+    /**
+     * Fills the next element in the iterator, depending on the current direction.
+     *
+     * @throws IllegalStateException if there is no next element
+     */
     abstract protected K peekImpl();
 
+    /**
+     * Skips the next element in the iterator, depending on the current direction.
+     *
+     * @throws IllegalStateException if there is no next element
+     */
     abstract protected void skipImpl();
 
+    /**
+     * Checks if there is a next element in the iterator, depending on the current direction.
+     *
+     * @return true if there is a next element, false otherwise
+     */
     abstract protected boolean hasImpl();
 
+    /**
+     * Returns the next element in the iterator, depending on the current direction.
+     *
+     * @return the next element
+     * @throws IllegalStateException if there is no next element
+     */
     abstract protected Pair<K, V> nextImpl();
 
     @Override

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

@@ -1,4 +1,8 @@
 package com.usatiuk.objects.iterators;
 
+/**
+ * Indicates that the value is a tombstone.
+ * @param <V> the type of the value
+ */
 public interface Tombstone<V> extends MaybeTombstone<V> {
 }

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

@@ -1,4 +1,8 @@
 package com.usatiuk.objects.iterators;
 
+/**
+ * Simple implementation of the Tombstone interface.
+ * @param <V> the type of the value
+ */
 public record TombstoneImpl<V>() implements Tombstone<V> {
 }

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

@@ -1,22 +0,0 @@
-package com.usatiuk.objects.iterators;
-
-import java.util.List;
-
-public abstract class TombstoneMergingKvIterator {
-    public static <K extends Comparable<K>, V> CloseableKvIterator<K, V> of(String name, IteratorStart startType, K startKey, List<IterProdFn<K, MaybeTombstone<V>>> iterators) {
-        return new PredicateKvIterator<K, MaybeTombstone<V>, V>(
-                new MergingKvIterator<K, MaybeTombstone<V>>(name + "-merging", startType, startKey, iterators),
-                startType, startKey,
-                pair -> {
-//                    Log.tracev("{0} - Processing pair {1}", name, pair);
-                    if (pair instanceof Tombstone<V>) {
-                        return null;
-                    }
-                    return ((Data<V>) pair).value();
-                });
-    }
-
-    public static <K extends Comparable<K>, V> CloseableKvIterator<K, V> of(String name, IteratorStart startType, K startKey, IterProdFn<K, MaybeTombstone<V>>... iterators) {
-        return of(name, startType, startKey, List.of(iterators));
-    }
-}

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

@@ -2,26 +2,40 @@ package com.usatiuk.objects.iterators;
 
 import org.apache.commons.lang3.tuple.Pair;
 
+import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.function.Function;
 
-public class PredicateKvIterator<K extends Comparable<K>, V, V_T> extends ReversibleKvIterator<K, V_T> {
-    private final CloseableKvIterator<K, V> _backing;
-    private final Function<V, V_T> _transformer;
-    private Pair<K, V_T> _next = null;
+/**
+ * A key-value iterator that skips tombstones.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
+public class TombstoneSkippingIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
+    private final MergingKvIterator<K, MaybeTombstone<V>> _backing;
+    private Pair<K, V> _next = null;
     private boolean _checkedNext = false;
 
-    public PredicateKvIterator(CloseableKvIterator<K, V> backing, IteratorStart start, K startKey, Function<V, V_T> transformer) {
+    /**
+     * Constructs a TombstoneSkippingIterator with the specified start position, start key, and list of iterators.
+     * Like {@link MappingKvIterator}, iterators have a priority depending on their order in the list.
+     *
+     * @param start     the starting position relative to the startKey
+     * @param startKey  the starting key
+     * @param iterators the list of iterators to merge
+     */
+    public TombstoneSkippingIterator(IteratorStart start, K startKey, List<CloseableKvIterator<K, MaybeTombstone<V>>> iterators) {
         _goingForward = true;
-        _backing = backing;
-        _transformer = transformer;
+        _backing = new MergingKvIterator<>(start, startKey, iterators);
 
         if (start == IteratorStart.GE || start == IteratorStart.GT)
             return;
 
-        fillNext();
-
         boolean shouldGoBack = false;
+        if (canHaveNext())
+            tryFillNext();
+
         if (start == IteratorStart.LE) {
             if (_next == null || _next.getKey().compareTo(startKey) > 0) {
                 shouldGoBack = true;
@@ -38,34 +52,27 @@ public class PredicateKvIterator<K extends Comparable<K>, V, V_T> extends Revers
             _backing.skipPrev();
             fillNext();
             _goingForward = true;
-            _backing.skip();
+            if (_next != null)
+                _backing.skip();
             fillNext();
         }
+    }
 
+    private boolean canHaveNext() {
+        return (_goingForward ? _backing.hasNext() : _backing.hasPrev());
+    }
 
-//        switch (start) {
-//            case LT -> {
-////                assert _next == null || _next.getKey().compareTo(startKey) < 0;
-//            }
-//            case LE -> {
-////                assert _next == null || _next.getKey().compareTo(startKey) <= 0;
-//            }
-//            case GT -> {
-//                assert _next == null || _next.getKey().compareTo(startKey) > 0;
-//            }
-//            case GE -> {
-//                assert _next == null || _next.getKey().compareTo(startKey) >= 0;
-//            }
-//        }
+    private boolean tryFillNext() {
+        var next = _goingForward ? _backing.next() : _backing.prev();
+        if (next.getValue() instanceof Tombstone<?>)
+            return false;
+        _next = Pair.of(next.getKey(), ((Data<V>) next.getValue()).value());
+        return true;
     }
 
     private void fillNext() {
-        while ((_goingForward ? _backing.hasNext() : _backing.hasPrev()) && _next == null) {
-            var next = _goingForward ? _backing.next() : _backing.prev();
-            var transformed = _transformer.apply(next.getValue());
-            if (transformed == null)
-                continue;
-            _next = Pair.of(next.getKey(), transformed);
+        while (_next == null && canHaveNext()) {
+            tryFillNext();
         }
         _checkedNext = true;
     }
@@ -80,9 +87,6 @@ public class PredicateKvIterator<K extends Comparable<K>, V, V_T> extends Revers
         else if (!_goingForward && !wasAtEnd)
             _backing.skipPrev();
 
-//        if (!wasAtEnd)
-//            Log.tracev("Skipped in reverse: {0}", _next);
-
         _next = null;
         _checkedNext = false;
     }
@@ -117,7 +121,7 @@ public class PredicateKvIterator<K extends Comparable<K>, V, V_T> extends Revers
     }
 
     @Override
-    protected Pair<K, V_T> nextImpl() {
+    protected Pair<K, V> nextImpl() {
         if (!_checkedNext)
             fillNext();
 
@@ -137,7 +141,6 @@ public class PredicateKvIterator<K extends Comparable<K>, V, V_T> extends Revers
     @Override
     public String toString() {
         return "PredicateKvIterator{" +
-                "_backing=" + _backing +
                 ", _next=" + _next +
                 '}';
     }

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

@@ -2,16 +2,45 @@ package com.usatiuk.objects.snapshot;
 
 import com.usatiuk.objects.iterators.CloseableKvIterator;
 import com.usatiuk.objects.iterators.IteratorStart;
-import com.usatiuk.utils.AutoCloseableNoThrow;
+import com.usatiuk.objects.iterators.MaybeTombstone;
 
 import javax.annotation.Nonnull;
+import java.util.List;
 import java.util.Optional;
 
-public interface Snapshot<K extends Comparable<K>, V> extends AutoCloseableNoThrow {
-    CloseableKvIterator<K, V> getIterator(IteratorStart start, K key);
+/**
+ * Interface for a snapshot of a database.
+ * Represents a point-in-time view of a storage, with a unique ID.
+ *
+ * @param <K> the type of the key
+ * @param <V> the type of the value
+ */
+public interface Snapshot<K extends Comparable<K>, V> extends AutoCloseable {
+    /**
+     * Get a list of iterators representing the snapshot.
+     * The iterators have priority: the first one in the list is the highest.
+     * The data type of the iterator is a tombstone: a tombstone represents a deleted value that does not exist anymore.
+     * The list of iterators is intended to be consumed by {@link com.usatiuk.objects.iterators.TombstoneSkippingIterator}
+     *
+     * @return a list of iterators
+     */
+    List<CloseableKvIterator<K, MaybeTombstone<V>>> getIterator(IteratorStart start, K key);
 
+    /**
+     * Read an object from the snapshot.
+     * @param name the name of the object
+     * @return an optional containing the object if it exists, or an empty optional if it does not
+     */
     @Nonnull
     Optional<V> readObject(K name);
 
+    /**
+     * Get the ID of the snapshot.
+     * @return the ID of the snapshot
+     */
     long id();
+
+    @Override
+    void close();
+
 }

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

@@ -5,6 +5,7 @@ import com.usatiuk.objects.JDataVersionedWrapperLazy;
 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 io.quarkus.runtime.StartupEvent;
 import jakarta.annotation.Priority;
@@ -16,12 +17,18 @@ import org.eclipse.microprofile.config.inject.ConfigProperty;
 import org.pcollections.TreePMap;
 
 import javax.annotation.Nonnull;
+import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReference;
 
+/**
+ * CachingObjectPersistentStore is a caching layer for the SerializingObjectPersistentStore
+ * It stores the already deserialized objects in memory.
+ * Not (yet) thread safe for writes.
+ */
 @ApplicationScoped
 public class CachingObjectPersistentStore {
     private final AtomicReference<Cache> _cache;
@@ -29,10 +36,10 @@ 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();
+
     public CachingObjectPersistentStore(@ConfigProperty(name = "dhfs.objects.lru.limit") int sizeLimit) {
         _cache = new AtomicReference<>(
                 new Cache(TreePMap.empty(), 0, -1, sizeLimit)
@@ -44,7 +51,6 @@ public class CachingObjectPersistentStore {
             _cache.set(_cache.get().withVersion(s.id()));
         }
 
-        _commitExecutor = Executors.newSingleThreadExecutor();
         if (printStats) {
             _statusExecutor = Executors.newSingleThreadExecutor();
             _statusExecutor.submit(() -> {
@@ -61,11 +67,16 @@ public class CachingObjectPersistentStore {
         }
     }
 
+    /**
+     * Commit the transaction to the underlying store and update the cache.
+     * Once this function returns, the transaction is committed and the cache is updated.
+     * @param objs the transaction manifest object
+     * @param txId the transaction ID
+     */
     public void commitTx(TxManifestObj<? extends JDataVersionedWrapper> objs, long txId) {
         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()));
         }
@@ -73,16 +84,18 @@ public class CachingObjectPersistentStore {
             cache = cache.withPut(del, Optional.empty());
         }
         cache = cache.withVersion(txId);
-        try {
-            commitFuture.get();
-        } catch (Exception e) {
-            throw new RuntimeException(e);
-        }
+        delegate.commitTx(objs, txId);
         _cache.set(cache);
 
         Log.tracev("Committed: {0} writes, {1} deletes", objs.written().size(), objs.deleted().size());
     }
 
+    /**
+     * Get a snapshot of underlying store and the cache.
+     * Objects are read from the cache if possible, if not, they are read from the underlying store,
+     * then possibly lazily cached when their data is accessed.
+     * @return a snapshot of the cached store
+     */
     public Snapshot<JObjectKey, JDataVersionedWrapper> getSnapshot() {
         while (true) {
             var cache = _cache.get();
@@ -150,10 +163,12 @@ public class CachingObjectPersistentStore {
                     }
 
                     @Override
-                    public CloseableKvIterator<JObjectKey, JDataVersionedWrapper> getIterator(IteratorStart start, JObjectKey key) {
-                        return TombstoneMergingKvIterator.<JObjectKey, JDataVersionedWrapper>of("cache", start, key,
-                                (mS, mK) -> new NavigableMapKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>(_curCache.map(), mS, mK),
-                                (mS, mK) -> new CachingKvIterator(_backing.getIterator(start, key)));
+                    public List<CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>> getIterator(IteratorStart start, JObjectKey key) {
+                        return ListUtils.prependAndMap(
+                                new NavigableMapKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>(_curCache.map(), start, key),
+                                _backing.getIterator(start, key),
+                                i -> new CachingKvIterator((CloseableKvIterator<JObjectKey, JDataVersionedWrapper>) (CloseableKvIterator<JObjectKey, ?>) i)
+                        );
                     }
 
                     @Nonnull

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

@@ -3,10 +3,7 @@ package com.usatiuk.objects.stores;
 import com.usatiuk.objects.JObjectKey;
 import com.usatiuk.objects.JObjectKeyMax;
 import com.usatiuk.objects.JObjectKeyMin;
-import com.usatiuk.objects.iterators.CloseableKvIterator;
-import com.usatiuk.objects.iterators.IteratorStart;
-import com.usatiuk.objects.iterators.KeyPredicateKvIterator;
-import com.usatiuk.objects.iterators.ReversibleKvIterator;
+import com.usatiuk.objects.iterators.*;
 import com.usatiuk.objects.snapshot.Snapshot;
 import io.quarkus.arc.properties.IfBuildProperty;
 import io.quarkus.logging.Log;
@@ -26,16 +23,22 @@ import java.lang.ref.Cleaner;
 import java.nio.ByteBuffer;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
+import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.Optional;
 
 import static org.lmdbjava.DbiFlags.MDB_CREATE;
 import static org.lmdbjava.Env.create;
 
+/**
+ * Persistent object storage using LMDB
+ */
 @ApplicationScoped
 @IfBuildProperty(name = "dhfs.objects.persistence", stringValue = "lmdb")
 public class LmdbObjectPersistentStore implements ObjectPersistentStore {
     private static final String DB_NAME = "objects";
+
+    // LMDB object name for the transaction id
     private static final String DB_VER_OBJ_NAME_STR = "__DB_VER_OBJ";
     private static final ByteBuffer DB_VER_OBJ_NAME;
 
@@ -101,6 +104,12 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
         if (!_ready) throw new IllegalStateException("Wrong service order!");
     }
 
+    /**
+     * Get a snapshot of the database.
+     * Note that the ByteBuffers are invalid after the snapshot is closed.
+     *
+     * @return a snapshot of the database
+     */
     @Override
     public Snapshot<JObjectKey, ByteBuffer> getSnapshot() {
         var txn = _env.txnRead();
@@ -112,9 +121,9 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
                 private boolean _closed = false;
 
                 @Override
-                public CloseableKvIterator<JObjectKey, ByteBuffer> getIterator(IteratorStart start, JObjectKey key) {
+                public List<CloseableKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>>> getIterator(IteratorStart start, JObjectKey key) {
                     assert !_closed;
-                    return new KeyPredicateKvIterator<>(new LmdbKvIterator(_txn, start, key), start, key, (k) -> !k.value().equals(DB_VER_OBJ_NAME_STR));
+                    return List.of(new KeyPredicateKvIterator<>(new LmdbKvIterator(_txn, start, key), start, key, (k) -> !k.value().equals(DB_VER_OBJ_NAME_STR)));
                 }
 
                 @Nonnull
@@ -146,10 +155,9 @@ 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 {
+        try (var txn = _env.txnWrite()) {
             for (var written : names.written()) {
                 var putBb = _db.reserve(txn, written.getKey().toByteBuffer(), written.getValue().size());
                 written.getValue().copyTo(putBb);
@@ -164,17 +172,8 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
             bbData.putLong(txId);
             bbData.flip();
             _db.put(txn, DB_VER_OBJ_NAME.asReadOnlyBuffer(), bbData);
-        } catch (Throwable t) {
-            txn.close();
-            throw t;
+            txn.commit();
         }
-        return () -> {
-            try {
-                txn.commit();
-            } finally {
-                txn.close();
-            }
-        };
     }
 
     @Override
@@ -189,13 +188,7 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
         return _root.toFile().getFreeSpace();
     }
 
-    @Override
-    public long getUsableSpace() {
-        verifyReady();
-        return _root.toFile().getUsableSpace();
-    }
-
-    private class LmdbKvIterator extends ReversibleKvIterator<JObjectKey, ByteBuffer> {
+    private class LmdbKvIterator extends ReversibleKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>> {
         private static final Cleaner CLEANER = Cleaner.create();
         private final Txn<ByteBuffer> _txn; // Managed by the snapshot
         private final Cursor<ByteBuffer> _cursor;
@@ -350,13 +343,13 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
         }
 
         @Override
-        protected Pair<JObjectKey, ByteBuffer> nextImpl() {
+        protected Pair<JObjectKey, MaybeTombstone<ByteBuffer>> nextImpl() {
             if (!_hasNext) {
                 throw new NoSuchElementException("No more elements");
             }
             // TODO: Right now with java serialization it doesn't matter, it's all copied to arrays anyway
             var val = _cursor.val();
-            var ret = Pair.of(JObjectKey.fromByteBuffer(_cursor.key()), val.asReadOnlyBuffer());
+            Pair<JObjectKey, MaybeTombstone<ByteBuffer>> ret = Pair.of(JObjectKey.fromByteBuffer(_cursor.key()), new DataWrapper<>(val.asReadOnlyBuffer()));
             if (_goingForward)
                 _hasNext = _cursor.next();
             else

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

@@ -2,10 +2,7 @@ package com.usatiuk.objects.stores;
 
 import com.google.protobuf.ByteString;
 import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.iterators.CloseableKvIterator;
-import com.usatiuk.objects.iterators.IteratorStart;
-import com.usatiuk.objects.iterators.MappingKvIterator;
-import com.usatiuk.objects.iterators.NavigableMapKvIterator;
+import com.usatiuk.objects.iterators.*;
 import com.usatiuk.objects.snapshot.Snapshot;
 import io.quarkus.arc.properties.IfBuildProperty;
 import jakarta.enterprise.context.ApplicationScoped;
@@ -13,9 +10,15 @@ import org.pcollections.TreePMap;
 
 import javax.annotation.Nonnull;
 import java.nio.ByteBuffer;
+import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
+import java.util.stream.Stream;
 
+/**
+ * In-memory implementation of the ObjectPersistentStore interface.
+ * For testing purposes.
+ */
 @ApplicationScoped
 @IfBuildProperty(name = "dhfs.objects.persistence", stringValue = "memory")
 public class MemoryObjectPersistentStore implements ObjectPersistentStore {
@@ -31,8 +34,8 @@ public class MemoryObjectPersistentStore implements ObjectPersistentStore {
                 private final long _lastCommitId = MemoryObjectPersistentStore.this._lastCommitId;
 
                 @Override
-                public CloseableKvIterator<JObjectKey, ByteBuffer> getIterator(IteratorStart start, JObjectKey key) {
-                    return new MappingKvIterator<>(new NavigableMapKvIterator<>(_objects, start, key), ByteString::asReadOnlyByteBuffer);
+                public List<CloseableKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>>> getIterator(IteratorStart start, JObjectKey key) {
+                    return List.of(new MappingKvIterator<>(new NavigableMapKvIterator<>(_objects, start, key), s -> new DataWrapper<>(s.asReadOnlyByteBuffer())));
                 }
 
                 @Nonnull
@@ -54,19 +57,18 @@ public class MemoryObjectPersistentStore implements ObjectPersistentStore {
         }
     }
 
-    public Runnable prepareTx(TxManifestRaw names, long txId) {
-        return () -> {
-            synchronized (this) {
-                for (var written : names.written()) {
-                    _objects = _objects.plus(written.getKey(), written.getValue());
-                }
-                for (JObjectKey key : names.deleted()) {
-                    _objects = _objects.minus(key);
-                }
-                assert txId > _lastCommitId;
-                _lastCommitId = txId;
+    @Override
+    public void commitTx(TxManifestRaw names, long txId) {
+        synchronized (this) {
+            for (var written : names.written()) {
+                _objects = _objects.plus(written.getKey(), written.getValue());
             }
-        };
+            for (JObjectKey key : names.deleted()) {
+                _objects = _objects.minus(key);
+            }
+            assert txId > _lastCommitId;
+            _lastCommitId = txId;
+        }
     }
 
     @Override
@@ -78,9 +80,4 @@ 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

@@ -8,16 +8,33 @@ import javax.annotation.Nonnull;
 import java.nio.ByteBuffer;
 import java.util.Optional;
 
-// Persistent storage of objects
-// All changes are written as sequential transactions
+/**
+ * Interface for a persistent store of objects.
+ * Does not have to be thread-safe! (yet), it is expected that all commits are done by the same thread.
+ */
 public interface ObjectPersistentStore {
+    /**
+     * Get a snapshot of the persistent store.
+     * @return a snapshot of the persistent store
+     */
     Snapshot<JObjectKey, ByteBuffer> getSnapshot();
 
-    Runnable prepareTx(TxManifestRaw names, long txId);
+    /**
+     * Commit a transaction to the persistent store.
+     * @param names the transaction manifest
+     * @param txId the transaction ID
+     */
+    void commitTx(TxManifestRaw names, long txId);
 
+    /**
+     * Get the size of the persistent store.
+     * @return the size of the persistent store
+     */
     long getTotalSpace();
 
+    /**
+     * Get the free space of the persistent store.
+     * @return the free space of the persistent store
+     */
     long getFreeSpace();
-
-    long getUsableSpace();
 }

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

@@ -1,22 +1,26 @@
 package com.usatiuk.objects.stores;
 
-import com.google.protobuf.ByteString;
 import com.usatiuk.objects.JDataVersionedWrapper;
 import com.usatiuk.objects.JDataVersionedWrapperSerializer;
 import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.ObjectSerializer;
-import com.usatiuk.objects.iterators.CloseableKvIterator;
-import com.usatiuk.objects.iterators.IteratorStart;
-import com.usatiuk.objects.iterators.MappingKvIterator;
+import com.usatiuk.objects.iterators.*;
 import com.usatiuk.objects.snapshot.Snapshot;
+import com.usatiuk.utils.ListUtils;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
 import org.apache.commons.lang3.tuple.Pair;
 
 import javax.annotation.Nonnull;
 import java.nio.ByteBuffer;
+import java.util.List;
 import java.util.Optional;
+import java.util.stream.Stream;
 
+/**
+ * Serializing wrapper for the ObjectPersistentStore.
+ * It serializes the objects before storing them in the persistent store.
+ * It deserializes the objects after reading them from the persistent store.
+ */
 @ApplicationScoped
 public class SerializingObjectPersistentStore {
     @Inject
@@ -25,13 +29,22 @@ public class SerializingObjectPersistentStore {
     @Inject
     ObjectPersistentStore delegateStore;
 
+    /**
+     * Get a snapshot of the persistent store, with deserialized objects.
+     *
+     * The objects are deserialized lazily, only when their data is accessed.
+     *
+     * @return a snapshot of the persistent store
+     */
     public Snapshot<JObjectKey, JDataVersionedWrapper> getSnapshot() {
         return new Snapshot<JObjectKey, JDataVersionedWrapper>() {
             private final Snapshot<JObjectKey, ByteBuffer> _backing = delegateStore.getSnapshot();
 
             @Override
-            public CloseableKvIterator<JObjectKey, JDataVersionedWrapper> getIterator(IteratorStart start, JObjectKey key) {
-                return new MappingKvIterator<>(_backing.getIterator(start, key), d -> serializer.deserialize(d));
+            public List<CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>> getIterator(IteratorStart start, JObjectKey key) {
+                return ListUtils.map(_backing.getIterator(start, key),
+                        i -> new MappingKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>, MaybeTombstone<JDataVersionedWrapper>>(i,
+                                d -> serializer.deserialize(((DataWrapper<ByteBuffer>) d).value())));
             }
 
             @Nonnull
@@ -53,6 +66,12 @@ public class SerializingObjectPersistentStore {
 
     }
 
+
+    /**
+     * Serialize the objects, in parallel
+     * @param objs the objects to serialize
+     * @return the serialized objects
+     */
     private TxManifestRaw prepareManifest(TxManifestObj<? extends JDataVersionedWrapper> objs) {
         return new TxManifestRaw(
                 objs.written().parallelStream()
@@ -61,7 +80,12 @@ public class SerializingObjectPersistentStore {
                 , objs.deleted());
     }
 
-    Runnable prepareTx(TxManifestObj<? extends JDataVersionedWrapper> objects, long txId) {
-        return delegateStore.prepareTx(prepareManifest(objects), txId);
+    /**
+     * Commit a transaction to the persistent store.
+     * @param objects the transaction manifest
+     * @param txId the transaction ID
+     */
+    void commitTx(TxManifestObj<? extends JDataVersionedWrapper> objects, long txId) {
+        delegateStore.commitTx(prepareManifest(objects), txId);
     }
 }

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

@@ -6,7 +6,6 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.io.Serializable;
 import java.util.Collection;
 
-// FIXME: Serializable
 public record TxManifestObj<T>(Collection<Pair<JObjectKey, T>> written,
                                Collection<JObjectKey> deleted) implements Serializable {
 }

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

@@ -7,7 +7,6 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.io.Serializable;
 import java.util.Collection;
 
-// FIXME: Serializable
 public record TxManifestRaw(Collection<Pair<JObjectKey, ByteString>> written,
                             Collection<JObjectKey> deleted) implements Serializable {
 }

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

@@ -3,10 +3,13 @@ package com.usatiuk.objects.stores;
 import com.usatiuk.objects.JDataVersionedWrapper;
 import com.usatiuk.objects.JDataVersionedWrapperImpl;
 import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.iterators.*;
+import com.usatiuk.objects.iterators.CloseableKvIterator;
+import com.usatiuk.objects.iterators.IteratorStart;
+import com.usatiuk.objects.iterators.MaybeTombstone;
+import com.usatiuk.objects.iterators.NavigableMapKvIterator;
 import com.usatiuk.objects.snapshot.Snapshot;
-import com.usatiuk.objects.transaction.TxCommitException;
 import com.usatiuk.objects.transaction.TxRecord;
+import com.usatiuk.utils.ListUtils;
 import io.quarkus.logging.Log;
 import io.quarkus.runtime.ShutdownEvent;
 import io.quarkus.runtime.StartupEvent;
@@ -26,24 +29,42 @@ import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReference;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.function.Consumer;
 
+/**
+ * Asynchronous write cache of objects.
+ * Objects are put into a write queue by commitTx, and written to the storage by a separate thread.
+ */
 @ApplicationScoped
 public class WritebackObjectPersistentStore {
-    private final LinkedList<TxBundle> _pendingBundles = new LinkedList<>();
-    private final LinkedHashMap<Long, TxBundle> _notFlushedBundles = new LinkedHashMap<>();
-    private final AtomicReference<PendingWriteData> _pendingWrites = new AtomicReference<>(null);
-    private final Object _flushWaitSynchronizer = new Object();
-    private final AtomicLong _lastWrittenId = new AtomicLong(-1);
-    private final AtomicLong _lastCommittedId = new AtomicLong();
-    private final AtomicLong _waitedTotal = new AtomicLong(0);
     @Inject
     CachingObjectPersistentStore cachedStore;
+    @Inject
+    ExecutorService _callbackExecutor;
+
     @ConfigProperty(name = "dhfs.objects.writeback.limit")
-    long sizeLimit;
-    private long currentSize = 0;
+    int sizeLimit;
+
+    private TxBundle _pendingBundle = null;
+    private int _curSize = 0;
+
+    private final AtomicReference<PendingWriteData> _pendingWrites = new AtomicReference<>(null);
+
+    private final ReentrantLock _pendingBundleLock = new ReentrantLock();
+
+    private final Condition _newBundleCondition = _pendingBundleLock.newCondition();
+    private final Condition _flushCondition = _pendingBundleLock.newCondition();
+
+    private final AtomicLong _lastFlushedId = new AtomicLong(-1);
+    private final AtomicLong _lastCommittedId = new AtomicLong(-1);
+
+    private final AtomicLong _waitedTotal = new AtomicLong(0);
+
     private ExecutorService _writebackExecutor;
     private ExecutorService _statusExecutor;
+
     private volatile boolean _ready = false;
 
     void init(@Observes @Priority(120) StartupEvent event) {
@@ -61,8 +82,8 @@ public class WritebackObjectPersistentStore {
             try {
                 while (true) {
                     Thread.sleep(1000);
-                    if (currentSize > 0)
-                        Log.info("Tx commit status: size=" + currentSize / 1024 / 1024 + "MB");
+                    if (_curSize > 0)
+                        Log.info("Tx commit status: size=" + _curSize / 1024 / 1024 + "MB");
                 }
             } catch (InterruptedException ignored) {
             }
@@ -72,7 +93,7 @@ public class WritebackObjectPersistentStore {
             lastTxId = s.id();
         }
         _lastCommittedId.set(lastTxId);
-        _lastWrittenId.set(lastTxId);
+        _lastFlushedId.set(lastTxId);
         _pendingWrites.set(new PendingWriteData(TreePMap.empty(), lastTxId, lastTxId));
         _ready = true;
     }
@@ -80,11 +101,14 @@ public class WritebackObjectPersistentStore {
     void shutdown(@Observes @Priority(890) ShutdownEvent event) throws InterruptedException {
         Log.info("Waiting for all transactions to drain");
 
-        synchronized (_flushWaitSynchronizer) {
-            _ready = false;
-            while (currentSize > 0) {
-                _flushWaitSynchronizer.wait();
+        _ready = false;
+        _pendingBundleLock.lock();
+        try {
+            while (_curSize > 0) {
+                _flushCondition.await();
             }
+        } finally {
+            _pendingBundleLock.unlock();
         }
 
         _writebackExecutor.shutdownNow();
@@ -98,21 +122,19 @@ public class WritebackObjectPersistentStore {
     private void writeback() {
         while (!Thread.interrupted()) {
             try {
-                TxBundle bundle = new TxBundle(0);
-                synchronized (_pendingBundles) {
-                    while (_pendingBundles.isEmpty() || !_pendingBundles.peek()._ready)
-                        _pendingBundles.wait();
+                TxBundle bundle;
+                _pendingBundleLock.lock();
+                try {
+                    while (_pendingBundle == null)
+                        _newBundleCondition.await();
+                    bundle = _pendingBundle;
+                    _pendingBundle = null;
 
-                    long diff = 0;
-                    while (!_pendingBundles.isEmpty() && _pendingBundles.peek()._ready) {
-                        var toCompress = _pendingBundles.poll();
-                        diff -= toCompress.size();
-                        bundle.compress(toCompress);
-                    }
-                    diff += bundle.size();
-                    synchronized (_flushWaitSynchronizer) {
-                        currentSize += diff;
-                    }
+                    _curSize -= bundle.size();
+                    assert _curSize == 0;
+                    _flushCondition.signal();
+                } finally {
+                    _pendingBundleLock.unlock();
                 }
 
                 var toWrite = new ArrayList<Pair<JObjectKey, JDataVersionedWrapper>>();
@@ -132,15 +154,12 @@ public class WritebackObjectPersistentStore {
                     }
                 }
 
-                cachedStore.commitTx(
-                        new TxManifestObj<>(
-                                Collections.unmodifiableList(toWrite),
-                                Collections.unmodifiableList(toDelete)
-                        ), bundle.id());
+                cachedStore.commitTx(new TxManifestObj<>(toWrite, toDelete), bundle.id());
 
                 Log.tracev("Bundle {0} committed", bundle.id());
 
-                while (true) {
+                _pendingBundleLock.lock();
+                try {
                     var curPw = _pendingWrites.get();
                     var curPwMap = curPw.pendingWrites();
                     for (var e : bundle._entries.values()) {
@@ -153,25 +172,16 @@ public class WritebackObjectPersistentStore {
                             bundle.id(),
                             curPw.lastCommittedId()
                     );
-                    if (_pendingWrites.compareAndSet(curPw, newCurPw))
-                        break;
+                    _pendingWrites.compareAndSet(curPw, newCurPw);
+                } finally {
+                    _pendingBundleLock.unlock();
                 }
 
-                List<List<Runnable>> callbacks = new ArrayList<>();
-                synchronized (_notFlushedBundles) {
-                    _lastWrittenId.set(bundle.id());
-                    while (!_notFlushedBundles.isEmpty() && _notFlushedBundles.firstEntry().getKey() <= bundle.id()) {
-                        callbacks.add(_notFlushedBundles.pollFirstEntry().getValue().setCommitted());
-                    }
-                }
-                callbacks.forEach(l -> l.forEach(Runnable::run));
-
-                synchronized (_flushWaitSynchronizer) {
-                    currentSize -= bundle.size();
-                    // FIXME:
-                    if (currentSize <= sizeLimit || !_ready)
-                        _flushWaitSynchronizer.notifyAll();
-                }
+                _lastFlushedId.set(bundle.id());
+                var callbacks = bundle.callbacks();
+                _callbackExecutor.submit(() -> {
+                    callbacks.forEach(Runnable::run);
+                });
             } catch (InterruptedException ignored) {
             } catch (Exception e) {
                 Log.error("Uncaught exception in writeback", e);
@@ -182,134 +192,126 @@ public class WritebackObjectPersistentStore {
         Log.info("Writeback thread exiting");
     }
 
-    public long commitBundle(Collection<TxRecord.TxObjectRecord<?>> writes) {
+    private long commitBundle(Collection<TxRecord.TxObjectRecord<?>> writes) {
         verifyReady();
-        boolean wait = false;
-        while (true) {
-            if (wait) {
-                synchronized (_flushWaitSynchronizer) {
-                    long started = System.currentTimeMillis();
-                    while (currentSize > sizeLimit) {
-                        try {
-                            _flushWaitSynchronizer.wait();
-                        } catch (InterruptedException e) {
-                            throw new RuntimeException(e);
-                        }
-                    }
-                    long waited = System.currentTimeMillis() - started;
-                    _waitedTotal.addAndGet(waited);
-                    if (Log.isTraceEnabled())
-                        Log.tracev("Thread {0} waited for tx bundle for {1} ms", Thread.currentThread().getName(), waited);
-                    wait = false;
-                }
+        _pendingBundleLock.lock();
+        try {
+            boolean shouldWake = false;
+            if (_curSize > sizeLimit) {
+                shouldWake = true;
+                long started = System.currentTimeMillis();
+                while (_curSize > sizeLimit)
+                    _flushCondition.await();
+                long waited = System.currentTimeMillis() - started;
+                _waitedTotal.addAndGet(waited);
+                if (Log.isTraceEnabled())
+                    Log.tracev("Thread {0} waited for tx bundle for {1} ms", Thread.currentThread().getName(), waited);
             }
 
-            synchronized (_pendingBundles) {
-                synchronized (_flushWaitSynchronizer) {
-                    if (currentSize > sizeLimit) {
-                        if (!_pendingBundles.isEmpty() && _pendingBundles.peek()._ready) {
-                            var target = _pendingBundles.poll();
+            var oursId = _lastCommittedId.incrementAndGet();
 
-                            long diff = -target.size();
-                            while (!_pendingBundles.isEmpty() && _pendingBundles.peek()._ready) {
-                                var toCompress = _pendingBundles.poll();
-                                diff -= toCompress.size();
-                                target.compress(toCompress);
-                            }
-                            diff += target.size();
-                            currentSize += diff;
-                            _pendingBundles.addFirst(target);
-                        }
+            var curBundle = _pendingBundle;
+            int oldSize = 0;
+            if (curBundle != null) {
+                oldSize = curBundle.size();
+                curBundle.setId(oursId);
+            } else {
+                curBundle = new TxBundle(oursId);
+            }
+
+            var curPw = _pendingWrites.get();
+            var curPwMap = curPw.pendingWrites();
+
+            for (var action : writes) {
+                var key = action.key();
+                switch (action) {
+                    case TxRecord.TxObjectRecordWrite<?> write -> {
+//                            Log.tracev("Flushing object {0}", write.key());
+                        var wrapper = new JDataVersionedWrapperImpl(write.data(), oursId);
+                        curPwMap = curPwMap.plus(key, new PendingWrite(wrapper, oursId));
+                        curBundle.commit(wrapper);
                     }
-
-                    if (currentSize > sizeLimit) {
-                        wait = true;
-                        continue;
+                    case TxRecord.TxObjectRecordDeleted deleted -> {
+//                            Log.tracev("Deleting object {0}", deleted.key());
+                        curPwMap = curPwMap.plus(key, new PendingDelete(key, oursId));
+                        curBundle.delete(key);
                     }
                 }
-
-                TxBundle bundle;
-                synchronized (_notFlushedBundles) {
-                    bundle = new TxBundle(_lastCommittedId.incrementAndGet());
-                    _pendingBundles.addLast(bundle);
-                    _notFlushedBundles.put(bundle.id(), bundle);
-                }
-
-                for (var action : writes) {
-                    switch (action) {
-                        case TxRecord.TxObjectRecordWrite<?> write -> {
-                            Log.tracev("Flushing object {0}", write.key());
-                            bundle.commit(new JDataVersionedWrapperImpl(write.data(), bundle.id()));
-                        }
-                        case TxRecord.TxObjectRecordDeleted deleted -> {
-                            Log.tracev("Deleting object {0}", deleted.key());
-                            bundle.delete(deleted.key());
-                        }
-                        default -> {
-                            throw new TxCommitException("Unexpected value: " + action.key());
-                        }
-                    }
-                }
-
-                while (true) {
-                    var curPw = _pendingWrites.get();
-                    var curPwMap = curPw.pendingWrites();
-                    for (var e : ((TxBundle) bundle)._entries.values()) {
-                        switch (e) {
-                            case TxBundle.CommittedEntry c -> {
-                                curPwMap = curPwMap.plus(c.key(), new PendingWrite(c.data, bundle.id()));
-                            }
-                            case TxBundle.DeletedEntry d -> {
-                                curPwMap = curPwMap.plus(d.key(), new PendingDelete(d.key, bundle.id()));
-                            }
-                            default -> throw new IllegalStateException("Unexpected value: " + e);
-                        }
-                    }
-                    // Now, make the changes visible to new iterators
-                    var newCurPw = new PendingWriteData(
-                            curPwMap,
-                            curPw.lastFlushedId(),
-                            bundle.id()
-                    );
-
-                    if (!_pendingWrites.compareAndSet(curPw, newCurPw))
-                        continue;
-
-                    ((TxBundle) bundle).setReady();
-                    if (_pendingBundles.peek() == bundle)
-                        _pendingBundles.notify();
-                    synchronized (_flushWaitSynchronizer) {
-                        currentSize += ((TxBundle) bundle).size();
-                    }
-
-                    return bundle.id();
-                }
             }
+            // Now, make the changes visible to new iterators
+            var newCurPw = new PendingWriteData(
+                    curPwMap,
+                    curPw.lastFlushedId(),
+                    oursId
+            );
+
+            _pendingWrites.compareAndSet(curPw, newCurPw);
+
+            _pendingBundle = curBundle;
+            _newBundleCondition.signalAll();
+
+            _curSize += (curBundle.size() - oldSize);
+
+            if (shouldWake && _curSize < sizeLimit) {
+                _flushCondition.signal();
+            }
+
+            return oursId;
+        } catch (InterruptedException e) {
+            throw new RuntimeException(e);
+        } finally {
+            _pendingBundleLock.unlock();
         }
     }
 
-    public void asyncFence(long bundleId, Runnable fn) {
+    /**
+     * Run a given callback after the transaction with id txId is committed.
+     * If the transaction is already committed, the callback is run immediately.
+     *
+     * @param txId transaction id to wait for
+     * @param fn   callback to run
+     */
+    public void asyncFence(long txId, Runnable fn) {
         verifyReady();
-        if (bundleId < 0) throw new IllegalArgumentException("txId should be >0!");
-        if (_lastWrittenId.get() >= bundleId) {
+        if (txId < 0) throw new IllegalArgumentException("txId should be >0!");
+        if (_lastFlushedId.get() >= txId) {
             fn.run();
             return;
         }
-        synchronized (_notFlushedBundles) {
-            if (_lastWrittenId.get() >= bundleId) {
+        _pendingBundleLock.lock();
+        try {
+            if (_lastFlushedId.get() >= txId) {
                 fn.run();
                 return;
             }
-            _notFlushedBundles.get(bundleId).addCallback(fn);
+            var pendingBundle = _pendingBundle;
+            if (pendingBundle == null) {
+                fn.run();
+                return;
+            }
+            pendingBundle.addCallback(fn);
+        } finally {
+            _pendingBundleLock.unlock();
         }
     }
 
+    /**
+     * Commit a transaction to the persistent store.
+     *
+     * @param writes the transaction manifest
+     * @return a function that allows to add a callback to be run after the transaction is committed
+     */
     public Consumer<Runnable> commitTx(Collection<TxRecord.TxObjectRecord<?>> writes) {
         long bundleId = commitBundle(writes);
 
         return r -> asyncFence(bundleId, r);
     }
 
+    /**
+     * Get a snapshot of the persistent store, including the pending writes.
+     *
+     * @return a snapshot of the store
+     */
     public Snapshot<JObjectKey, JDataVersionedWrapper> getSnapshot() {
         Snapshot<JObjectKey, JDataVersionedWrapper> cache = null;
         PendingWriteData pw = null;
@@ -341,10 +343,8 @@ public class WritebackObjectPersistentStore {
                 private final long txId = finalPw.lastCommittedId();
 
                 @Override
-                public CloseableKvIterator<JObjectKey, JDataVersionedWrapper> getIterator(IteratorStart start, JObjectKey key) {
-                    return TombstoneMergingKvIterator.<JObjectKey, JDataVersionedWrapper>of("writeback-ps", start, key,
-                            (tS, tK) -> new NavigableMapKvIterator<>(_pendingWrites, tS, tK),
-                            (tS, tK) -> (CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>) (CloseableKvIterator<JObjectKey, ?>) _cache.getIterator(tS, tK));
+                public List<CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>> getIterator(IteratorStart start, JObjectKey key) {
+                    return ListUtils.prepend(new NavigableMapKvIterator<>(_pendingWrites, start, key), _cache.getIterator(start, key));
                 }
 
                 @Nonnull
@@ -381,46 +381,40 @@ public class WritebackObjectPersistentStore {
         }
     }
 
-    public interface VerboseReadResult {
-    }
-
     private record PendingWriteData(TreePMap<JObjectKey, PendingWriteEntry> pendingWrites,
                                     long lastFlushedId,
                                     long lastCommittedId) {
     }
 
     private static class TxBundle {
-        private final LinkedHashMap<JObjectKey, BundleEntry> _entries = new LinkedHashMap<>();
+        private final HashMap<JObjectKey, BundleEntry> _entries = new HashMap<>();
         private final ArrayList<Runnable> _callbacks = new ArrayList<>();
+        private int _size = 0;
         private long _txId;
-        private volatile boolean _ready = false;
-        private long _size = 0;
-        private boolean _wasCommitted = false;
+
+        ArrayList<Runnable> callbacks() {
+            return _callbacks;
+        }
 
         private TxBundle(long txId) {
             _txId = txId;
         }
 
-        public long id() {
-            return _txId;
+        public void setId(long id) {
+            _txId = id;
         }
 
-        public void setReady() {
-            _ready = true;
+        public long id() {
+            return _txId;
+
         }
 
         public void addCallback(Runnable callback) {
-            synchronized (_callbacks) {
-                if (_wasCommitted) throw new IllegalStateException();
-                _callbacks.add(callback);
-            }
+            _callbacks.add(callback);
         }
 
-        public List<Runnable> setCommitted() {
-            synchronized (_callbacks) {
-                _wasCommitted = true;
-                return Collections.unmodifiableList(_callbacks);
-            }
+        public int size() {
+            return _size;
         }
 
         private void putEntry(BundleEntry entry) {
@@ -439,28 +433,7 @@ public class WritebackObjectPersistentStore {
             putEntry(new DeletedEntry(obj));
         }
 
-        public long size() {
-            return _size;
-        }
-
-        public void compress(TxBundle other) {
-            if (_txId >= other._txId)
-                throw new IllegalArgumentException("Compressing an older bundle into newer");
-
-            _txId = other._txId;
-
-            for (var entry : other._entries.values()) {
-                putEntry(entry);
-            }
-
-            synchronized (_callbacks) {
-                assert !_wasCommitted;
-                assert !other._wasCommitted;
-                _callbacks.addAll(other._callbacks);
-            }
-        }
-
-        private interface BundleEntry {
+        private sealed interface BundleEntry permits CommittedEntry, DeletedEntry {
             JObjectKey key();
 
             int size();
@@ -478,10 +451,4 @@ public class WritebackObjectPersistentStore {
             }
         }
     }
-
-    public record VerboseReadResultPersisted(Optional<JDataVersionedWrapper> data) implements VerboseReadResult {
-    }
-
-    public record VerboseReadResultPending(PendingWriteEntry pending) implements VerboseReadResult {
-    }
 }