dump

.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 javadoc:aggregate
+        run: cd dhfs-parent && mvn -T $(nproc) --batch-mode --update-snapshots package verify
 
       # - name: Build with Maven
       #   run: cd dhfs-parent && mvn --batch-mode --update-snapshots package # -Dquarkus.log.category.\"com.usatiuk.dhfs\".min-level=DEBUG
@@ -55,12 +55,7 @@ jobs:
       - uses: actions/upload-artifact@v4
         with:
           name: DHFS Server Package
-          path: dhfs-parent/dhfs-fuse/target/quarkus-app
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: DHFS Javadocs
-          path: dhfs-parent/target/reports/apidocs/
+          path: dhfs-parent/dhfs-app/target/quarkus-app
 
       - uses: actions/upload-artifact@v4
         if: ${{ always() }}
@@ -217,7 +212,7 @@ 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/Server"
+        run: cp -r ./dhfs-package-downloaded "run-wrapper-out/dhfs/app/DHFS Package"
 
       - name: Copy Webui
         run: cp -r ./webui-dist-downloaded "run-wrapper-out/dhfs/app/Webui"
@@ -236,37 +231,3 @@ 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
-
-

README.md

@@ -16,36 +16,7 @@ the DHFS server in the background, and update itself (hopefully!)
 
 ## How to use it?
 
-### General prerequisites
 
-Java should be available as `java` in path, and Java 21+ is required.
-
-FUSE 2 userspace library also should be available:
-
-- On Ubuntu `libfuse2` package can be installed.
-
-- On Windows, [WinFsp](https://winfsp.dev/) should be installed. 
-
-- On macOS, [macFUSE](https://macfuse.github.io/).
-
-In the run-wrapper, 3 scripts are available.
-
-- `run` script starts the filesystem
-- `stop` script stops it
-- `update` script will update the filesystem to the newest available CI build
-
-On Windows, Powershell alternatives should be used. For them to work, it might be required to allow execution of unsigned scripts using `set-executionpolicy remotesigned`.
-
-Additional options for the filesystem can be specified in the `extra-opts` file in the same directory with the run scripts.
-
-One line in the `extra-opts` file corresponds to one option passed to the JVM when starting the filesystem. 
-
-Some extra possible configuration options are:
-
-- `-Ddhfs.fuse.root=` specifies the root where filesystem should be mounted. By default it is the `fuse` path under the `run-wrapper` root. For windows, it should be a disk letter, by default `Z:\`.
-- `-Ddhfs.objects.last-seen.timeout=` specifies the period of time (in seconds) after which unavailable peers will be ignored for gabgage collection and resynchronized after being reconnected. The default is 43200 (30 days), if set to `-1`, this feature is disabled.
-- `-Ddhfs.objects.autosync.download-all=` specifies whether all objects (files and their data) should be downloaded to this peer. `true` or `false`, the default is `false`.
-
-On Windows, the entire space for the filesystem should also be preallocated, the `-Ddhfs.objects.persistence.lmdb.size=` option controls the size (the value is in bytes), on Windows the default is 100GB.
+Unpack the run-wrapper and run the `run` script. The filesystem should be mounted to the `fuse` folder in the run-wrapper root directory.
 
 Then, a web interface will be available at `losthost:8080`, that can be used to connect with other peers.

dhfs-parent/.gitignore

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

dhfs-parent/.run/Main 2.run.xml

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

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

@@ -1,8 +1,8 @@
 <component name="ProjectRunConfigurationManager">
   <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=${HOME}/dhfs_test/1/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=true -Dquarkus.http.port=9010 -Dquarkus.http.ssl-port=9011 -Ddhfs.peerdiscovery.preset-uuid=11000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=22000000-0000-0000-0000-000000000000:127.0.0.1:9020:9021 -Dquarkus.http.host=0.0.0.0" />
+    <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsapp.Main" />
+    <module name="dhfs-app" />
+    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseParallelGC --enable-preview -XX:+DebugNonSafepoints --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx2G -Ddhfs.webui.root=$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.*" />

dhfs-parent/dhfs-app/.dockerignore

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

dhfs-parent/dhfs-app/.gitignore

@@ -0,0 +1,43 @@
+#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

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

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

@@ -0,0 +1,43 @@
+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

@@ -0,0 +1,172 @@
+<?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

@@ -0,0 +1,97 @@
+####
+# 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

@@ -0,0 +1,93 @@
+####
+# 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

@@ -0,0 +1,27 @@
+####
+# 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

@@ -0,0 +1,30 @@
+####
+# 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/java/com/usatiuk/dhfsapp/Main.java

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

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

@@ -0,0 +1,35 @@
+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=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.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=INFO
+quarkus.log.category."com.usatiuk".level=INFO
+quarkus.http.insecure-requests=enabled
+quarkus.http.ssl.client-auth=required

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

@@ -0,0 +1,29 @@
+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

@@ -0,0 +1,44 @@
+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/java/com/usatiuk/dhfsapp/integration/DhfsFuseIT.java

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsfuse.integration;
+package com.usatiuk.dhfsapp.integration;
 
 import com.github.dockerjava.api.model.Device;
 import io.quarkus.logging.Log;
@@ -40,11 +40,11 @@ public class DhfsFuseIT {
         container1 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
         container2 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
 
         Stream.of(container1, container2).parallel().forEach(GenericContainer::start);
 
@@ -55,9 +55,6 @@ public class DhfsFuseIT {
         var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFuseIT.class)).withPrefix("2-" + testInfo.getDisplayName());
         container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
 
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-
         c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
         c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
 
@@ -171,6 +168,35 @@ 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());
@@ -195,28 +221,6 @@ 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-app/src/test/java/com/usatiuk/dhfsapp/integration/DhfsFusex3IT.java

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsfuse.integration;
+package com.usatiuk.dhfsapp.integration;
 
 import com.github.dockerjava.api.model.Device;
 import io.quarkus.logging.Log;
@@ -48,42 +48,39 @@ public class DhfsFusex3IT {
         container1 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
         container2 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
         container3 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+
 
         Stream.of(container1, container2, container3).parallel().forEach(GenericContainer::start);
 
-        waitingConsumer1 = new WaitingConsumer();
-        var loggingConsumer1 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
-                .withPrefix(1 + "-" + testInfo.getDisplayName());
-        container1.followOutput(loggingConsumer1.andThen(waitingConsumer1));
-        waitingConsumer2 = new WaitingConsumer();
-        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
-                .withPrefix(2 + "-" + testInfo.getDisplayName());
-        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
-        waitingConsumer3 = new WaitingConsumer();
-        var loggingConsumer3 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
-                .withPrefix(3 + "-" + testInfo.getDisplayName());
-        container3.followOutput(loggingConsumer3.andThen(waitingConsumer3));
-
-        waitingConsumer3.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-
         c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
         c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
         c3uuid = container3.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
 
-        Log.info(container1.getContainerId() + "=" + c1uuid + " = 1");
-        Log.info(container2.getContainerId() + "=" + c2uuid + " = 2");
-        Log.info(container3.getContainerId() + "=" + c3uuid + " = 3");
+        Log.info(container1.getContainerId() + "=" + c1uuid);
+        Log.info(container2.getContainerId() + "=" + c2uuid);
+        Log.info(container3.getContainerId() + "=" + c3uuid);
+
+        waitingConsumer1 = new WaitingConsumer();
+        var loggingConsumer1 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
+                .withPrefix(c1uuid.substring(0, 4) + "-" + testInfo.getDisplayName());
+        container1.followOutput(loggingConsumer1.andThen(waitingConsumer1));
+        waitingConsumer2 = new WaitingConsumer();
+        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
+                .withPrefix(c2uuid.substring(0, 4) + "-" + testInfo.getDisplayName());
+        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
+        waitingConsumer3 = new WaitingConsumer();
+        var loggingConsumer3 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
+                .withPrefix(c3uuid.substring(0, 4) + "-" + testInfo.getDisplayName());
+        container3.followOutput(loggingConsumer3.andThen(waitingConsumer3));
 
         Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
         Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));

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

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsfuse.integration;
+package com.usatiuk.dhfsapp.integration;
 
 import io.quarkus.logging.Log;
 import org.jetbrains.annotations.NotNull;
@@ -70,7 +70,6 @@ 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",
@@ -79,8 +78,6 @@ 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-app/src/test/java/com/usatiuk/dhfsapp/integration/KillIT.java

@@ -1,7 +1,7 @@
-package com.usatiuk.dhfsfuse.integration;
+package com.usatiuk.dhfsapp.integration;
 
 import com.github.dockerjava.api.model.Device;
-import com.usatiuk.dhfsfuse.TestDataCleaner;
+import com.usatiuk.dhfsapp.TestDataCleaner;
 import io.quarkus.logging.Log;
 import org.junit.jupiter.api.*;
 import org.slf4j.LoggerFactory;
@@ -52,12 +52,12 @@ public class KillIT {
         container1 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network)
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
                 .withFileSystemBind(data1.getAbsolutePath(), "/dhfs_test/data");
         container2 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network)
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
                 .withFileSystemBind(data2.getAbsolutePath(), "/dhfs_test/data");
 
         Stream.of(container1, container2).parallel().forEach(GenericContainer::start);
@@ -69,9 +69,6 @@ public class KillIT {
         var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(KillIT.class)).withPrefix("2-" + testInfo.getDisplayName());
         container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
 
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-
         c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
         c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
 

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

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

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

@@ -1,7 +1,7 @@
-package com.usatiuk.dhfsfuse.integration;
+package com.usatiuk.dhfsapp.integration;
 
 import com.github.dockerjava.api.model.Device;
-import com.usatiuk.dhfsfuse.TestDataCleaner;
+import com.usatiuk.dhfsapp.TestDataCleaner;
 import io.quarkus.logging.Log;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -64,12 +64,12 @@ public class LazyFsIT {
         container1 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network)
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
                 .withFileSystemBind(data1.getAbsolutePath(), "/dhfs_test/data");
         container2 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network)
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
                 .withFileSystemBind(data2.getAbsolutePath(), "/dhfs_test/data");
 
         Stream.of(container1, container2).parallel().forEach(GenericContainer::start);
@@ -81,9 +81,6 @@ public class LazyFsIT {
         var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(LazyFsIT.class)).withPrefix("2-" + testInfo.getDisplayName());
         container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
 
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-
         c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
         c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
 
@@ -157,7 +154,7 @@ public class LazyFsIT {
         Thread.sleep(3000);
         Log.info("Killing");
         lazyFs1.crash();
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container1.getContainerId()).exec();
         container1.stop();
@@ -198,7 +195,7 @@ public class LazyFsIT {
             lazyFs1.crash();
         }
         try {
-            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());
@@ -240,7 +237,7 @@ public class LazyFsIT {
         Thread.sleep(3000);
         Log.info("Killing");
         lazyFs1.crash();
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container1.getContainerId()).exec();
         container1.stop();
@@ -282,7 +279,7 @@ public class LazyFsIT {
             lazyFs1.crash();
         }
         try {
-            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+            waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());
@@ -325,7 +322,7 @@ public class LazyFsIT {
         Log.info("Killing");
         lazyFs2.crash();
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting1");
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container2.getContainerId()).exec();
         container2.stop();
@@ -369,7 +366,7 @@ public class LazyFsIT {
         }
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting2");
         try {
-            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());
@@ -412,7 +409,7 @@ public class LazyFsIT {
         Log.info("Killing");
         lazyFs2.crash();
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting1");
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         var client = DockerClientFactory.instance().client();
         client.killContainerCmd(container2.getContainerId()).exec();
         container2.stop();
@@ -456,7 +453,7 @@ public class LazyFsIT {
         }
         container1.execInContainer("/bin/sh", "-c", "touch /tmp/stopprinting2");
         try {
-            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("org.lmdbjava.LmdbNativeException"), 60, TimeUnit.SECONDS);
+            waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Caused by: org.lmdbjava"), 60, TimeUnit.SECONDS);
         } catch (TimeoutException e) {
             // Sometimes crash doesn't work
             Log.info("Failed to crash: " + testInfo.getDisplayName());

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

@@ -1,4 +1,4 @@
-package com.usatiuk.dhfsfuse.integration;
+package com.usatiuk.dhfsapp.integration;
 
 import com.github.dockerjava.api.model.Device;
 import org.junit.jupiter.api.*;
@@ -38,11 +38,11 @@ public class ResyncIT {
         container1 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
         container2 = new GenericContainer<>(DhfsImage.getInstance())
                 .withPrivilegedMode(true)
                 .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .withNetwork(network);
+                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
 
         Stream.of(container1, container2).parallel().forEach(GenericContainer::start);
 
@@ -52,9 +52,6 @@ public class ResyncIT {
         waitingConsumer2 = new WaitingConsumer();
         var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFuseIT.class)).withPrefix("2-" + testInfo.getDisplayName());
         container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
-
-        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
-        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
     }
 
     @AfterEach

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

@@ -0,0 +1,11 @@
+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

@@ -5,11 +5,6 @@ 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

@@ -0,0 +1,26 @@
+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

@@ -9,15 +9,6 @@ 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   inode modification 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> {
@@ -41,10 +32,6 @@ public record File(JObjectKey key, long mode, long cTime, long mTime,
         return new File(key, mode, cTime, System.currentTimeMillis(), symlink);
     }
 
-    public File withCurrentCTime() {
-        return new File(key, mode, System.currentTimeMillis(), mTime, symlink);
-    }
-
     @Override
     public Collection<JObjectKey> collectRefsTo() {
         return Set.of();

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

@@ -7,11 +7,6 @@ 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

@@ -5,9 +5,6 @@ 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

@@ -10,20 +10,11 @@ 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)) {
@@ -35,13 +26,6 @@ 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

@@ -0,0 +1,25 @@
+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

@@ -8,6 +8,7 @@ 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;
@@ -23,9 +24,6 @@ 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
@@ -44,18 +42,14 @@ public class FileSyncHandler implements ObjSyncHandler<File, FileDto> {
     @Inject
     DhfsFileService fileService;
 
-    private JKleppmannTreeManager.JKleppmannTree getTree() {
+    private JKleppmannTreeManager.JKleppmannTree getTreeW() {
         return jKleppmannTreeManager.getTree(JObjectKey.of("fs")).orElseThrow();
     }
 
-    /**
-     * Resolve conflict between two file versions, update the file in storage and create a conflict file.
-     *
-     * @param from              the peer that sent the update
-     * @param key               the key of the file
-     * @param receivedChangelog the changelog of the received file
-     * @param receivedData      the received file data
-     */
+    private JKleppmannTreeManager.JKleppmannTree getTreeR() {
+        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), LockingStrategy.OPTIMISTIC).orElseThrow();
+    }
+
     private void resolveConflict(PeerId from, JObjectKey key, PMap<PeerId, Long> receivedChangelog,
                                  @Nullable FileDto receivedData) {
         var oursCurMeta = curTx.get(RemoteObjectMeta.class, key).orElse(null);
@@ -137,12 +131,12 @@ public class FileSyncHandler implements ObjSyncHandler<File, FileDto> {
 
             do {
                 try {
-                    getTree().move(parent.getRight(),
+                    getTreeW().move(parent.getRight(),
                             new JKleppmannTreeNodeMetaFile(
                                     parent.getLeft() + ".fconflict." + persistentPeerDataService.getSelfUuid() + "." + otherHostname.toString() + "." + i,
                                     newFile.key()
                             ),
-                            getTree().getNewNodeId()
+                            getTreeW().getNewNodeId()
                     );
                 } catch (AlreadyExistsException aex) {
                     i++;

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

@@ -6,10 +6,6 @@ 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

@@ -6,11 +6,6 @@ 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

@@ -2,803 +2,47 @@ 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.stores.ObjectPersistentStore;
-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;
+import java.util.Optional;
 
-/**
- * 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;
+public interface DhfsFileService {
+    Optional<JObjectKey> open(String name);
 
-    @Inject
-    Transaction curTx;
-    @Inject
-    RemoteTransaction remoteTx;
-    @Inject
-    TransactionManager jObjectTxManager;
-    @Inject
-    JKleppmannTreeManager jKleppmannTreeManager;
-    @Inject
-    JMapHelper jMapHelper;
-    @Inject
-    ObjectPersistentStore objectPersistentStore;
+    Optional<JObjectKey> create(String name, long mode);
 
-    private JKleppmannTreeManager.JKleppmannTree getTree() {
-        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), () -> new JKleppmannTreeNodeMetaDirectory(""));
-    }
+    Pair<String, JObjectKey> inoToParent(JObjectKey ino);
 
-    /**
-     * 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;
-    }
+    void mkdir(String name, long mode);
 
-    void init(@Observes @Priority(500) StartupEvent event) {
-        Log.info("Initializing file service");
-        getTree();
-    }
+    Optional<GetattrRes> getattr(JObjectKey name);
 
-    private JKleppmannTreeNode getDirEntry(String name) {
-        var res = getTree().traverse(StreamSupport.stream(Path.of(name).spliterator(), false).map(p -> p.toString()).toList());
-        if (res == null) throw new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND);
-        var ret = curTx.get(JKleppmannTreeNodeHolder.class, res).map(JKleppmannTreeNodeHolder::node).orElseThrow(() -> new StatusRuntimeException(Status.NOT_FOUND.withDescription("Tree node exists but not found as jObject: " + name)));
-        return ret;
-    }
+    Boolean chmod(JObjectKey name, long mode);
 
-    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;
-    }
+    void unlink(String name);
 
-    /**
-     * 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);
-        });
-    }
+    Boolean rename(String from, String to);
 
-    /**
-     * 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;
-            }
-        });
-    }
+    Boolean setTimes(JObjectKey fileUuid, long atimeMs, long mtimeMs);
 
-    private void ensureDir(JKleppmannTreeNode entry) {
-        if (!(entry.meta() instanceof JKleppmannTreeNodeMetaDirectory))
-            throw new StatusRuntimeExceptionNoStacktrace(Status.INVALID_ARGUMENT.withDescription("Not a directory: " + entry.key()));
-    }
+    Iterable<String> readDir(String name);
 
-    /**
-     * 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());
+    long size(JObjectKey fileUuid);
 
-            ensureDir(parent);
+    ByteString read(JObjectKey fileUuid, long offset, int length);
 
-            String fname = path.getFileName().toString();
+    Long write(JObjectKey fileUuid, long offset, ByteString data);
 
-            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).withCurrentCTime());
-                    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 mtimeMs  the modification time in milliseconds
-     * @return true if the times were set successfully, false otherwise
-     */
-    public Boolean setTimes(JObjectKey fileUuid, 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(System.currentTimeMillis()).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) {
+    default Long write(JObjectKey fileUuid, long offset, byte[] data) {
         return write(fileUuid, offset, UnsafeByteOperations.unsafeWrap(data));
     }
 
-    /**
-     * Get the free space on the filesystem.
-     *
-     * @return the free space in bytes
-     */
-    public long getFreeSpace() {
-        return objectPersistentStore.getFreeSpace();
-    }
+    Boolean truncate(JObjectKey fileUuid, long length);
 
-    /**
-     * Get the total space on the filesystem.
-     *
-     * @return the total space in bytes
-     */
-    public long getTotalSpace() {
-        return objectPersistentStore.getTotalSpace();
-    }
+    String readlink(JObjectKey uuid);
+
+    ByteString readlinkBS(JObjectKey uuid);
+
+    JObjectKey symlink(String oldpath, String newpath);
 }

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

@@ -0,0 +1,665 @@
+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.max_chunk_size")
+    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;
+
+    @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.putDataNew(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) {
+                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();
+        });
+    }
+
+    @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, 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;
+            }
+        }
+    }
+
+    @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

@@ -1,10 +1,5 @@
 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

@@ -1,11 +1,4 @@
 package com.usatiuk.dhfsfs.service;
 
-/**
- * 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) {
+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());
     }
 
-    public void purgeDirectory(File dir) {
+    void purgeDirectory(File dir) {
         for (File file : Objects.requireNonNull(dir.listFiles())) {
             if (file.isDirectory())
                 purgeDirectory(file);

dhfs-parent/dhfs-fuse/pom.xml

@@ -139,13 +139,16 @@
                 <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
+                            true
                         </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

@@ -1,7 +1,6 @@
 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;
@@ -20,17 +19,16 @@ 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.*;
+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 java.nio.ByteBuffer;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Optional;
@@ -39,9 +37,6 @@ 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;
@@ -54,15 +49,11 @@ public class DhfsFuse extends FuseStubFS {
     boolean enabled;
     @ConfigProperty(name = "dhfs.fuse.debug")
     Boolean debug;
+    @ConfigProperty(name = "dhfs.files.target_chunk_size")
+    int targetChunkSize;
     @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();
@@ -73,15 +64,8 @@ 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) {
-        if (handle == 0)
-            throw new IllegalStateException("Handle is 0");
+        assert handle != 0;
         return _openHandles.get(handle);
     }
 
@@ -112,6 +96,7 @@ public class DhfsFuse extends FuseStubFS {
                 opts.add("-o");
                 opts.add("iosize=" + iosize);
             } else if (SystemUtils.IS_OS_LINUX) {
+                // FIXME: There's something else missing: the writes still seem to be 32k max
 //            opts.add("-o");
 //            opts.add("large_read");
                 opts.add("-o");
@@ -143,12 +128,13 @@ public class DhfsFuse extends FuseStubFS {
         try {
             stbuf.f_frsize.set(blksize);
             stbuf.f_bsize.set(blksize);
-            stbuf.f_blocks.set(fileService.getTotalSpace() / blksize); // total data blocks in file system
-            stbuf.f_bfree.set(fileService.getFreeSpace() / blksize);  // free blocks in fs
-            stbuf.f_bavail.set(fileService.getFreeSpace() / blksize); // avail blocks in fs
-            stbuf.f_files.set(1000); // TODO: Calculate real file counts?
-            stbuf.f_ffree.set(Integer.MAX_VALUE - 1000);
-            stbuf.f_favail.set(Integer.MAX_VALUE - 1000);
+            // FIXME:
+            stbuf.f_blocks.set(1024 * 1024 * 1024 / blksize); // total data blocks in file system
+            stbuf.f_bfree.set(1024 * 1024 * 1024 / blksize);  // free blocks in fs
+            stbuf.f_bavail.set(1024 * 1024 * 1024 / blksize); // avail blocks in fs
+            stbuf.f_files.set(1000); //FIXME:
+            stbuf.f_ffree.set(Integer.MAX_VALUE - 2000); //FIXME:
+            stbuf.f_favail.set(Integer.MAX_VALUE - 2000); //FIXME:
             stbuf.f_namemax.set(2048);
             return super.statfs(path, stbuf);
         } catch (Throwable e) {
@@ -184,13 +170,13 @@ public class DhfsFuse extends FuseStubFS {
                 }
             }
 
+            // FIXME: Race?
             stat.st_ctim.tv_sec.set(found.get().ctime() / 1000);
             stat.st_ctim.tv_nsec.set((found.get().ctime() % 1000) * 1000);
             stat.st_mtim.tv_sec.set(found.get().mtime() / 1000);
             stat.st_mtim.tv_nsec.set((found.get().mtime() % 1000) * 1000);
-            var atime = Math.max(found.get().ctime(), found.get().mtime());
-            stat.st_atim.tv_sec.set(atime / 1000);
-            stat.st_atim.tv_nsec.set((atime % 1000) * 1000000L);
+            stat.st_atim.tv_sec.set(found.get().mtime() / 1000);
+            stat.st_atim.tv_nsec.set((found.get().mtime() % 1000) * 1000);
             stat.st_blksize.set(blksize);
         } catch (Throwable e) {
             Log.error("When getattr " + path, e);
@@ -206,7 +192,8 @@ public class DhfsFuse extends FuseStubFS {
             if (fileOpt.isEmpty()) return -ErrorCodes.ENOENT();
             var file = fileOpt.get();
             var res = fileService.setTimes(file,
-                    timespec[1].tv_sec.get() * 1000L + timespec[1].tv_nsec.longValue() / 1000000L);
+                    timespec[0].tv_sec.get() * 1000,
+                    timespec[1].tv_sec.get() * 1000);
             if (!res) return -ErrorCodes.EINVAL();
             else return 0;
         } catch (Throwable e) {
@@ -253,19 +240,17 @@ 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 = UninitializedByteBuffer.allocate((int) size);
+
+            UnsafeAccessor.get().getUnsafe().copyMemory(
+                    buf.address(),
+                    UnsafeAccessor.get().getNioAccess().getBufferAddress(buffer),
+                    size
+            );
+
             var written = fileService.write(fileKey, offset, UnsafeByteOperations.unsafeWrap(buffer));
             return written.intValue();
         } catch (Exception e) {
@@ -436,29 +421,4 @@ 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

@@ -7,9 +7,6 @@ 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;
@@ -49,9 +46,9 @@ public class JnrPtrByteOutput extends ByteOutput {
             if (value instanceof MappedByteBuffer mb) {
                 mb.load();
             }
-            long addr = UnsafeAccessor.NIO.getBufferAddress(value) + value.position();
+            long addr = UnsafeAccessor.get().getNioAccess().getBufferAddress(value) + value.position();
             var out = _backing.address() + _pos;
-            UnsafeAccessor.UNSAFE.copyMemory(addr, out, rem);
+            UnsafeAccessor.get().getUnsafe().copyMemory(addr, out, rem);
         } else {
             _backing.put(_pos, value.array(), value.arrayOffset() + value.position(), rem);
         }

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

@@ -14,9 +14,8 @@ 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=524288
-dhfs.files.max_chunk_size=524288
-dhfs.files.target_chunk_alignment=17
+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-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/TestDataCleaner.java

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

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

@@ -1,8 +1,5 @@
 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

@@ -0,0 +1,32 @@
+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

@@ -1,26 +1,9 @@
 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

@@ -3,13 +3,6 @@ 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

@@ -8,14 +8,6 @@ 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());
 
@@ -24,14 +16,6 @@ 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,
@@ -42,13 +26,6 @@ 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;
 
@@ -62,21 +39,14 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
         return traverseImpl(childId, 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(NodeIdT fromId, List<String> names) {
+        return traverseImpl(fromId, names.subList(1, names.size()));
+    }
+
     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());
@@ -119,11 +89,6 @@ 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)
@@ -131,32 +96,16 @@ 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();
@@ -212,52 +161,22 @@ 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);
     }
 
-    /**
-     * 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
-     */
+    // Returns true if the timestamp is newer than what's seen, false otherwise
     private boolean updateTimestampImpl(PeerIdT from, TimestampT newTimestamp) {
         TimestampT oldRef = _storage.getPeerTimestampLog().getForPeer(from);
         if (oldRef != null && oldRef.compareTo(newTimestamp) >= 0) { // FIXME?
@@ -268,12 +187,6 @@ 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());
@@ -284,15 +197,6 @@ 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;
 
@@ -325,36 +229,14 @@ 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;
@@ -371,24 +253,10 @@ 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);
@@ -429,15 +297,6 @@ 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());
 
@@ -521,13 +380,6 @@ 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;
@@ -538,11 +390,6 @@ 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());
@@ -556,12 +403,6 @@ 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());
@@ -582,13 +423,6 @@ 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

@@ -2,18 +2,6 @@ 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

@@ -2,16 +2,6 @@ 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

@@ -4,82 +4,29 @@ 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

@@ -3,15 +3,6 @@ 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

@@ -2,24 +2,8 @@ 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

@@ -2,27 +2,9 @@ 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

@@ -1,26 +1,7 @@
 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

@@ -2,22 +2,8 @@ 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

@@ -1,26 +1,11 @@
 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

@@ -1,89 +1,28 @@
 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);
 
-    /**
-     * 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
-     */
+    // Creates a node, returned wrapper is RW-locked
     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

@@ -5,92 +5,29 @@ 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

@@ -18,6 +18,11 @@
     </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

@@ -2,20 +2,9 @@ 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

@@ -2,34 +2,15 @@ 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

@@ -4,9 +4,6 @@ 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

@@ -2,35 +2,18 @@ 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

@@ -7,21 +7,11 @@ 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());
@@ -29,13 +19,6 @@ 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

@@ -5,68 +5,30 @@ 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);
@@ -79,17 +41,7 @@ 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

@@ -7,9 +7,6 @@ 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;

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

@@ -2,9 +2,6 @@ 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

@@ -2,9 +2,6 @@ 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

@@ -3,29 +3,30 @@ 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 SerializationHelper.serialize(obj);
+        return UnsafeByteOperations.unsafeWrap(fury.serialize(obj));
     }
 
+    @Override
     public JData deserialize(ByteBuffer data) {
-        try (var is = UnsafeByteOperations.unsafeWrap(data).newInput()) {
-            return SerializationHelper.deserialize(is);
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        }
+        return (JData) fury.deserialize(data);
     }
 }

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

@@ -4,25 +4,8 @@ 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

@@ -1,70 +1,24 @@
 package com.usatiuk.objects.iterators;
 
+import com.usatiuk.utils.AutoCloseableNoThrow;
 import org.apache.commons.lang3.tuple.Pair;
 
 import java.util.Iterator;
 
-
-/**
- * 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
-     */
+public interface CloseableKvIterator<K extends Comparable<? super K>, V> extends Iterator<Pair<K, V>>, AutoCloseableNoThrow {
     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

@@ -1,13 +1,5 @@
 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

@@ -1,9 +1,4 @@
 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

@@ -0,0 +1,6 @@
+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/IterProdFn2.java

@@ -0,0 +1,8 @@
+package com.usatiuk.objects.iterators;
+
+import java.util.stream.Stream;
+
+@FunctionalInterface
+public interface IterProdFn2<K extends Comparable<K>, V> {
+    Stream<CloseableKvIterator<K, MaybeTombstone<V>>> get(IteratorStart start, K key);
+}

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

@@ -1,8 +1,5 @@
 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

@@ -5,25 +5,11 @@ 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

@@ -4,23 +4,10 @@ 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

@@ -1,8 +1,4 @@
 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

@@ -9,32 +9,98 @@ 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;
 
-    /**
-     * 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) {
+    public MergingKvIterator(String name, IteratorStart startType, K startKey, List<IterProdFn<K, V>> iterators) {
         _goingForward = true;
+        _name = name;
 
+        // Why streams are so slow?
         {
             IteratorEntry<K, V>[] iteratorEntries = new IteratorEntry[iterators.size()];
             for (int i = 0; i < iterators.size(); i++) {
-                iteratorEntries[i] = new IteratorEntry<>(i, iterators.get(i));
+                iteratorEntries[i] = new IteratorEntry<>(i, iterators.get(i).get(startType, startKey));
+            }
+            _iterators = List.of(iteratorEntries);
+        }
+
+        if (startType == IteratorStart.LT || startType == IteratorStart.LE) {
+            // Starting at a greatest key less than/less or equal than:
+            // We have a bunch of iterators that have given us theirs "greatest LT/LE key"
+            // now we need to pick the greatest of those to start with
+            // But if some of them don't have a lesser key, we need to pick the smallest of those
+
+            K greatestLess = null;
+            K smallestMore = null;
+
+            for (var ite : _iterators) {
+                var it = ite.iterator();
+                if (it.hasNext()) {
+                    var peeked = it.peekNextKey();
+                    if (startType == IteratorStart.LE ? peeked.compareTo(startKey) <= 0 : peeked.compareTo(startKey) < 0) {
+                        if (greatestLess == null || peeked.compareTo(greatestLess) > 0) {
+                            greatestLess = peeked;
+                        }
+                    } else {
+                        if (smallestMore == null || peeked.compareTo(smallestMore) < 0) {
+                            smallestMore = peeked;
+                        }
+                    }
+                }
+            }
+
+            K initialMaxValue;
+            if (greatestLess != null)
+                initialMaxValue = greatestLess;
+            else
+                initialMaxValue = smallestMore;
+
+            if (initialMaxValue == null) {
+                // Empty iterators
+            }
+
+            for (var ite : _iterators) {
+                var iterator = ite.iterator();
+                while (iterator.hasNext() && iterator.peekNextKey().compareTo(initialMaxValue) < 0) {
+                    iterator.skip();
+                }
+            }
+        }
+
+        for (IteratorEntry<K, V> iterator : _iterators) {
+            advanceIterator(iterator);
+        }
+
+//        Log.tracev("{0} Initialized: {1}", _name, _sortedIterators);
+//        switch (startType) {
+////            case LT -> {
+////                assert _sortedIterators.isEmpty() || _sortedIterators.firstKey().compareTo(initialStartKey) < 0;
+////            }
+////            case LE -> {
+////                assert _sortedIterators.isEmpty() || _sortedIterators.firstKey().compareTo(initialStartKey) <= 0;
+////            }
+//            case GT -> {
+//                assert _sortedIterators.isEmpty() || _sortedIterators.firstKey().compareTo(startKey) > 0;
+//            }
+//            case GE -> {
+//                assert _sortedIterators.isEmpty() || _sortedIterators.firstKey().compareTo(startKey) >= 0;
+//            }
+//        }
+    }
+
+    public MergingKvIterator(String name, IteratorStart startType, K startKey, IterProdFn2<K, V> iteratorsProd) {
+        _goingForward = true;
+        _name = name;
+
+        // Why streams are so slow?
+        {
+            var iterators = iteratorsProd.get(startType, startKey).toList();
+            IteratorEntry<K, V>[] iteratorEntries = new IteratorEntry[iterators.size()];
+            for (int i = 0; i < iterators.size(); i++) {
+                iteratorEntries[i] = new IteratorEntry<>(i, (CloseableKvIterator<K, V>) iterators.get(i));
             }
             _iterators = List.of(iteratorEntries);
         }
@@ -103,18 +169,9 @@ 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(IteratorStart startType, K startKey, CloseableKvIterator<K, V>... iterators) {
-        this(startType, startKey, List.of(iterators));
+    public MergingKvIterator(String name, IteratorStart startType, K startKey, IterProdFn<K, V>... iterators) {
+        this(name, startType, startKey, List.of(iterators));
     }
 
     private void advanceIterator(IteratorEntry<K, V> iteratorEntry) {
@@ -173,6 +230,7 @@ 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
@@ -220,14 +278,28 @@ 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

@@ -4,25 +4,11 @@ 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/PredicateKvIterator.java

@@ -2,40 +2,26 @@ 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;
 
-/**
- * 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;
+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;
     private boolean _checkedNext = false;
 
-    /**
-     * 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) {
+    public PredicateKvIterator(CloseableKvIterator<K, V> backing, IteratorStart start, K startKey, Function<V, V_T> transformer) {
         _goingForward = true;
-        _backing = new MergingKvIterator<>(start, startKey, iterators);
+        _backing = backing;
+        _transformer = transformer;
 
         if (start == IteratorStart.GE || start == IteratorStart.GT)
             return;
 
-        boolean shouldGoBack = false;
-        if (canHaveNext())
-            tryFillNext();
+        fillNext();
 
+        boolean shouldGoBack = false;
         if (start == IteratorStart.LE) {
             if (_next == null || _next.getKey().compareTo(startKey) > 0) {
                 shouldGoBack = true;
@@ -52,27 +38,34 @@ public class TombstoneSkippingIterator<K extends Comparable<K>, V> extends Rever
             _backing.skipPrev();
             fillNext();
             _goingForward = true;
-            if (_next != null)
-                _backing.skip();
+            _backing.skip();
             fillNext();
         }
-    }
 
-    private boolean canHaveNext() {
-        return (_goingForward ? _backing.hasNext() : _backing.hasPrev());
-    }
 
-    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;
+//        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 void fillNext() {
-        while (_next == null && canHaveNext()) {
-            tryFillNext();
+        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);
         }
         _checkedNext = true;
     }
@@ -87,6 +80,9 @@ public class TombstoneSkippingIterator<K extends Comparable<K>, V> extends Rever
         else if (!_goingForward && !wasAtEnd)
             _backing.skipPrev();
 
+//        if (!wasAtEnd)
+//            Log.tracev("Skipped in reverse: {0}", _next);
+
         _next = null;
         _checkedNext = false;
     }
@@ -121,7 +117,7 @@ public class TombstoneSkippingIterator<K extends Comparable<K>, V> extends Rever
     }
 
     @Override
-    protected Pair<K, V> nextImpl() {
+    protected Pair<K, V_T> nextImpl() {
         if (!_checkedNext)
             fillNext();
 
@@ -141,6 +137,7 @@ public class TombstoneSkippingIterator<K extends Comparable<K>, V> extends Rever
     @Override
     public String toString() {
         return "PredicateKvIterator{" +
+                "_backing=" + _backing +
                 ", _next=" + _next +
                 '}';
     }

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

@@ -2,19 +2,9 @@ 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

@@ -2,21 +2,9 @@ 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() {
@@ -31,33 +19,12 @@ 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

@@ -1,8 +1,4 @@
 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

@@ -1,8 +1,4 @@
 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

@@ -0,0 +1,36 @@
+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));
+    }
+
+    public static <K extends Comparable<K>, V> CloseableKvIterator<K, V> of(String name, IteratorStart startType, K startKey, IterProdFn2<K, V> itProd) {
+        return new PredicateKvIterator<K, MaybeTombstone<V>, V>(
+                new MergingKvIterator<K, MaybeTombstone<V>>(name + "-merging", startType, startKey, (IterProdFn2<K, MaybeTombstone<V>>) itProd),
+                startType, startKey,
+                pair -> {
+//                    Log.tracev("{0} - Processing pair {1}", name, pair);
+                    if (pair instanceof Tombstone<V>) {
+                        return null;
+                    }
+                    return ((Data<V>) pair).value();
+                });
+    }
+
+}

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

@@ -3,44 +3,18 @@ package com.usatiuk.objects.snapshot;
 import com.usatiuk.objects.iterators.CloseableKvIterator;
 import com.usatiuk.objects.iterators.IteratorStart;
 import com.usatiuk.objects.iterators.MaybeTombstone;
+import com.usatiuk.objects.iterators.Tombstone;
+import com.usatiuk.utils.AutoCloseableNoThrow;
 
 import javax.annotation.Nonnull;
-import java.util.List;
 import java.util.Optional;
+import java.util.stream.Stream;
 
-/**
- * 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);
+public interface Snapshot<K extends Comparable<K>, V> extends AutoCloseableNoThrow {
+    Stream<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

@@ -5,7 +5,6 @@ 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;
@@ -17,18 +16,13 @@ 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;
+import java.util.stream.Stream;
 
-/**
- * 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;
@@ -36,6 +30,7 @@ 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();
@@ -51,6 +46,7 @@ public class CachingObjectPersistentStore {
             _cache.set(_cache.get().withVersion(s.id()));
         }
 
+        _commitExecutor = Executors.newSingleThreadExecutor();
         if (printStats) {
             _statusExecutor = Executors.newSingleThreadExecutor();
             _statusExecutor.submit(() -> {
@@ -67,16 +63,11 @@ 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()));
         }
@@ -84,18 +75,16 @@ public class CachingObjectPersistentStore {
             cache = cache.withPut(del, Optional.empty());
         }
         cache = cache.withVersion(txId);
-        delegate.commitTx(objs, txId);
+        try {
+            commitFuture.get();
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
         _cache.set(cache);
 
         Log.tracev("Committed: {0} writes, {1} deletes", objs.written().size(), objs.deleted().size());
     }
 
-    /**
-     * 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();
@@ -163,11 +152,10 @@ public class CachingObjectPersistentStore {
                     }
 
                     @Override
-                    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)
+                    public Stream<CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>> getIterator(IteratorStart start, JObjectKey key) {
+                        return Stream.concat(
+                                Stream.of(new NavigableMapKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>(_curCache.map(), start, key)),
+                                _backing.getIterator(start, key).map(i -> new CachingKvIterator((CloseableKvIterator<JObjectKey, JDataVersionedWrapper>) (CloseableKvIterator<JObjectKey, ?>) i))
                         );
                     }
 

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

@@ -23,22 +23,17 @@ 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 java.util.stream.Stream;
 
 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;
 
@@ -67,15 +62,12 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
             Log.info("Initializing with root " + _root);
             _root.toFile().mkdirs();
         }
-        Log.info("Opening LMDB with root " + _root);
         _env = create()
                 .setMapSize(lmdbSize)
                 .setMaxDbs(1)
                 .open(_root.toFile(), EnvFlags.MDB_NOTLS);
         _db = _env.openDbi(DB_NAME, MDB_CREATE);
 
-        Log.info("Opened LMDB with root " + _root);
-
         try (Txn<ByteBuffer> txn = _env.txnWrite()) {
             var read = readTxId(txn);
             if (read.isPresent()) {
@@ -90,7 +82,6 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
         }
 
         _ready = true;
-        Log.info("LMDB storage ready");
     }
 
     private Optional<Long> readTxId(Txn<ByteBuffer> txn) {
@@ -99,9 +90,6 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
     }
 
     void shutdown(@Observes @Priority(900) ShutdownEvent event) throws IOException {
-        if (!_ready) {
-            return;
-        }
         _ready = false;
         _db.close();
         _env.close();
@@ -111,15 +99,8 @@ 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() {
-        verifyReady();
         var txn = _env.txnRead();
         try {
             long commitId = readTxId(txn).orElseThrow();
@@ -129,9 +110,9 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
                 private boolean _closed = false;
 
                 @Override
-                public List<CloseableKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>>> getIterator(IteratorStart start, JObjectKey key) {
+                public Stream<CloseableKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>>> getIterator(IteratorStart start, JObjectKey key) {
                     assert !_closed;
-                    return List.of(new KeyPredicateKvIterator<>(new LmdbKvIterator(_txn, start, key), start, key, (k) -> !k.value().equals(DB_VER_OBJ_NAME_STR)));
+                    return Stream.of(new KeyPredicateKvIterator<>(new LmdbKvIterator(_txn, start, key), start, key, (k) -> !k.value().equals(DB_VER_OBJ_NAME_STR)));
                 }
 
                 @Nonnull
@@ -163,9 +144,10 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
     }
 
     @Override
-    public void commitTx(TxManifestRaw names, long txId) {
+    public Runnable prepareTx(TxManifestRaw names, long txId) {
         verifyReady();
-        try (var txn = _env.txnWrite()) {
+        var txn = _env.txnWrite();
+        try {
             for (var written : names.written()) {
                 var putBb = _db.reserve(txn, written.getKey().toByteBuffer(), written.getValue().size());
                 written.getValue().copyTo(putBb);
@@ -180,8 +162,17 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
             bbData.putLong(txId);
             bbData.flip();
             _db.put(txn, DB_VER_OBJ_NAME.asReadOnlyBuffer(), bbData);
-            txn.commit();
+        } catch (Throwable t) {
+            txn.close();
+            throw t;
         }
+        return () -> {
+            try {
+                txn.commit();
+            } finally {
+                txn.close();
+            }
+        };
     }
 
     @Override
@@ -196,6 +187,12 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
         return _root.toFile().getFreeSpace();
     }
 
+    @Override
+    public long getUsableSpace() {
+        verifyReady();
+        return _root.toFile().getUsableSpace();
+    }
+
     private class LmdbKvIterator extends ReversibleKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>> {
         private static final Cleaner CLEANER = Cleaner.create();
         private final Txn<ByteBuffer> _txn; // Managed by the snapshot

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

@@ -10,15 +10,10 @@ 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 {
@@ -34,8 +29,8 @@ public class MemoryObjectPersistentStore implements ObjectPersistentStore {
                 private final long _lastCommitId = MemoryObjectPersistentStore.this._lastCommitId;
 
                 @Override
-                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())));
+                public Stream<CloseableKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>>> getIterator(IteratorStart start, JObjectKey key) {
+                    return Stream.of(new MappingKvIterator<>(new NavigableMapKvIterator<>(_objects, start, key), s -> new DataWrapper<>(s.asReadOnlyByteBuffer())));
                 }
 
                 @Nonnull
@@ -57,18 +52,19 @@ public class MemoryObjectPersistentStore implements ObjectPersistentStore {
         }
     }
 
-    @Override
-    public void commitTx(TxManifestRaw names, long txId) {
-        synchronized (this) {
-            for (var written : names.written()) {
-                _objects = _objects.plus(written.getKey(), written.getValue());
+    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;
             }
-            for (JObjectKey key : names.deleted()) {
-                _objects = _objects.minus(key);
-            }
-            assert txId > _lastCommitId;
-            _lastCommitId = txId;
-        }
+        };
     }
 
     @Override
@@ -80,4 +76,9 @@ 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

@@ -8,33 +8,16 @@ import javax.annotation.Nonnull;
 import java.nio.ByteBuffer;
 import java.util.Optional;
 
-/**
- * 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.
- */
+// Persistent storage of objects
+// All changes are written as sequential transactions
 public interface ObjectPersistentStore {
-    /**
-     * Get a snapshot of the persistent store.
-     * @return a snapshot of the persistent store
-     */
     Snapshot<JObjectKey, ByteBuffer> getSnapshot();
 
-    /**
-     * Commit a transaction to the persistent store.
-     * @param names the transaction manifest
-     * @param txId the transaction ID
-     */
-    void commitTx(TxManifestRaw names, long txId);
+    Runnable prepareTx(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

@@ -5,22 +5,15 @@ import com.usatiuk.objects.JDataVersionedWrapperSerializer;
 import com.usatiuk.objects.JObjectKey;
 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
@@ -29,22 +22,14 @@ 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 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())));
+            public Stream<CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>> getIterator(IteratorStart start, JObjectKey key) {
+                return _backing.getIterator(start, key).map(i -> new MappingKvIterator<JObjectKey, MaybeTombstone<ByteBuffer>, MaybeTombstone<JDataVersionedWrapper>>(i,
+                        d -> serializer.deserialize(((DataWrapper<ByteBuffer>) d).value())));
             }
 
             @Nonnull
@@ -66,12 +51,6 @@ 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()
@@ -80,12 +59,7 @@ public class SerializingObjectPersistentStore {
                 , objs.deleted());
     }
 
-    /**
-     * 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);
+    Runnable prepareTx(TxManifestObj<? extends JDataVersionedWrapper> objects, long txId) {
+        return delegateStore.prepareTx(prepareManifest(objects), txId);
     }
 }

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

@@ -6,6 +6,7 @@ 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

@@ -7,6 +7,7 @@ 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 {
 }