Basic ArcadeDB server implementation

BioDWH2 · Dec 7, 2021 · b16d55e · b16d55e
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "maven"
+    directory: "/src/"
+    target-branch: "develop"
+    schedule:
+      interval: "daily"
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,45 @@
+name: Create release on version tag and publish core package
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+jobs:
+  build:
+    name: Create Release
+    runs-on: ubuntu-latest
+    if: github.repository == 'BioDWH2/BioDWH2-ArcadeDB-Server' # Only run on main repository and not forks
+    steps:
+      - name: Retrieve tag name
+        id: tag_name
+        uses: little-core-labs/[email protected]
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ steps.tag_name.outputs.tag }}
+          release_name: Release ${{ steps.tag_name.outputs.tag }}
+          draft: false
+          prerelease: false
+      - uses: actions/setup-java@v1
+        with:
+          java-version: 11
+      - name: Build with Maven
+        env:
+          USENAME: ${{ github.actor }}
+          PASSWORD: ${{ secrets.GITHUB_TOKEN }}
+        run: mvn package -DskipTests --file src/pom.xml --settings src/settings.xml
+      - name: Upload Release Asset
+        id: upload-release-asset 
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./src/target/BioDWH2-ArcadeDB-Server-${{ steps.tag_name.outputs.tag }}.jar
+          asset_name: BioDWH2-ArcadeDB-Server-${{ steps.tag_name.outputs.tag }}.jar
+          asset_content_type: application/java-archive
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -0,0 +1,16 @@
+name: Java CI
+on: [push]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 11
+      uses: actions/setup-java@v1
+      with:
+        java-version: 11
+    - name: Build with Maven
+      env:
+        USENAME: ${{ github.actor }}
+        PASSWORD: ${{ secrets.GITHUB_TOKEN }}
+      run: mvn package --file src/pom.xml --settings src/settings.xml
diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@ This repository contains the **BioDWH2-ArcadeDB-Server** utility which can be us
 The latest release version of **BioDWH2-ArcadeDB-Server** can be downloaded [here](https://github.com/BioDWH2/BioDWH2-ArcadeDB-Server/releases/latest).
 
 ## Usage
-BioDWH2-ArcadeDB-Server requires the Java Runtime Environment. The JRE 8 is available [here](https://www.oracle.com/java/technologies/javase-jre8-downloads.html).
+BioDWH2-ArcadeDB-Server requires the Java Runtime Environment 11+. The JRE 11 archive is available [here](https://www.oracle.com/java/technologies/javase/jdk11-archive-downloads.html).
 
 Creating a database from any workspace is done using the following command. Every time the workspace is updated or changed, the create command has to be executed again.
 ~~~BASH
@@ -29,6 +29,5 @@ Usage: BioDWH2-ArcadeDB-Server.jar [-h] [-c <workspacePath>] [-cs <workspacePath
   -s, --start <workspacePath>           Start an ArcadeDB server for the workspace
   -c, --create <workspacePath>          Create an ArcadeDB database from the workspace graph
   -cs, --create-start <workspacePath>   Create and start an ArcadeDB database from the workspace graph
-  -p, --port <port>                     Specifies the ArcadeDB server port(-range) (default 2424-2430)
-  -sp, --studio-port <studioPort>       Specifies the ArcadeDB Studio port(-range) (default 2480-2490)
+  -p, --port <port>                     Specifies the ArcadeDB server port(-range) (default 2480-2489)
 ~~~
diff --git a/src/pom.xml b/src/pom.xml
@@ -0,0 +1,117 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>de.unibi.agbi.biodwh2.arcadedb.server</groupId>
+    <artifactId>BioDWH2-ArcadeDB-Server</artifactId>
+    <version>1.0.0</version>
+
+    <build>
+        <finalName>BioDWH2-ArcadeDB-Server-v${project.version}</finalName>
+        <plugins>
+            <plugin>
+                <groupId>com.github.jinnovations</groupId>
+                <artifactId>attribution-maven-plugin</artifactId>
+                <version>0.9.8</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>generate-attribution-file</goal>
+                        </goals>
+                        <phase>generate-resources</phase>
+                    </execution>
+                </executions>
+                <configuration>
+                    <outputFile>${project.build.directory}/attribution.xml</outputFile>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.2.4</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <transformers>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>de.unibi.agbi.biodwh2.arcadedb.server.ArcadeDBServer</mainClass>
+                                    <manifestEntries>
+                                        <BioDWH2-version>${project.version}</BioDWH2-version>
+                                        <BioDWH2-build-date>${maven.build.timestamp}</BioDWH2-build-date>
+                                    </manifestEntries>
+                                </transformer>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.IncludeResourceTransformer">
+                                    <resource>META-INF/attribution.xml</resource>
+                                    <file>${project.build.directory}/attribution.xml</file>
+                                </transformer>
+                            </transformers>
+                            <filters>
+                                <filter>
+                                    <artifact>*:*</artifact>
+                                    <excludes>
+                                        <exclude>about.html</exclude>
+                                        <exclude>META-INF/maven/</exclude>
+                                        <exclude>META-INF/native/</exclude>
+                                        <exclude>META-INF/native-image/</exclude>
+                                        <exclude>META-INF/proguard/</exclude>
+                                        <exclude>META-INF/versions/</exclude>
+                                        <exclude>META-INF/*.SF</exclude>
+                                        <exclude>META-INF/*.DSA</exclude>
+                                        <exclude>META-INF/*.RSA</exclude>
+                                        <exclude>META-INF/MANIFEST.MF</exclude>
+                                        <exclude>META-INF/README*</exclude>
+                                        <exclude>META-INF/CHANGES*</exclude>
+                                        <exclude>META-INF/LICENSE*</exclude>
+                                        <exclude>META-INF/NOTICE*</exclude>
+                                        <exclude>META-INF/*.kotlin_module</exclude>
+                                        <exclude>META-INF/io.netty.versions.properties</exclude>
+                                    </excludes>
+                                </filter>
+                            </filters>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>de.unibi.agbi.biodwh2</groupId>
+            <artifactId>biodwh2-core</artifactId>
+            <version>0.4.1</version>
+        </dependency>
+        <dependency>
+            <groupId>info.picocli</groupId>
+            <artifactId>picocli</artifactId>
+            <version>4.6.2</version>
+        </dependency>
+        <dependency>
+            <groupId>commons-codec</groupId>
+            <artifactId>commons-codec</artifactId>
+            <version>1.15</version>
+        </dependency>
+        <dependency>
+            <groupId>com.arcadedb</groupId>
+            <artifactId>arcadedb-server</artifactId>
+            <version>21.11.1</version>
+        </dependency>
+    </dependencies>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+        <argLine>-XX:MaxDirectMemorySize=512g</argLine>
+    </properties>
+</project>
diff --git a/src/settings.xml b/src/settings.xml
@@ -0,0 +1,38 @@
+<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
+                      http://maven.apache.org/xsd/settings-1.0.0.xsd">
+
+  <activeProfiles>
+    <activeProfile>github</activeProfile>
+  </activeProfiles>
+
+  <profiles>
+    <profile>
+      <id>github</id>
+      <repositories>
+        <repository>
+          <id>central</id>
+          <url>https://repo1.maven.org/maven2</url>
+          <releases><enabled>true</enabled></releases>
+          <snapshots><enabled>true</enabled></snapshots>
+        </repository>
+        <repository>
+          <id>BioDWH2 github</id>
+          <name>GitHub Apache Maven Packages</name>
+          <url>https://maven.pkg.github.com/biodwh2/biodwh2</url>
+          <releases><enabled>true</enabled></releases>
+          <snapshots><enabled>true</enabled></snapshots>
+        </repository>
+      </repositories>
+    </profile>
+  </profiles>
+
+  <servers>
+    <server>
+      <id>BioDWH2 github</id>
+      <username>${env.USERNAME}</username>
+      <password>${env.PASSWORD}</password>
+    </server>
+  </servers>
+</settings>
diff --git a/src/src/main/java/de/unibi/agbi/biodwh2/arcadedb/server/ArcadeDBServer.java b/src/src/main/java/de/unibi/agbi/biodwh2/arcadedb/server/ArcadeDBServer.java
@@ -0,0 +1,134 @@
+package de.unibi.agbi.biodwh2.arcadedb.server;
+
+import de.unibi.agbi.biodwh2.core.net.BioDWH2Updater;
+import de.unibi.agbi.biodwh2.arcadedb.server.model.CmdArgs;
+import org.apache.commons.lang3.StringUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class ArcadeDBServer {
+    private static final Logger LOGGER = LoggerFactory.getLogger(ArcadeDBServer.class);
+
+    private ArcadeDBServer() {
+    }
+
+    public static void main(final String... args) {
+        final CmdArgs commandLine = parseCommandLine(args);
+        new ArcadeDBServer().run(commandLine);
+    }
+
+    private static CmdArgs parseCommandLine(final String... args) {
+        final CmdArgs result = new CmdArgs();
+        final CommandLine cmd = new CommandLine(result);
+        cmd.parseArgs(args);
+        return result;
+    }
+
+    private void run(final CmdArgs commandLine) {
+        BioDWH2Updater.checkForUpdate("BioDWH2-ArcadeDB-Server",
+                                      "https://api.github.com/repos/BioDWH2/BioDWH2-ArcadeDB-Server/releases");
+        if (commandLine.createStart != null)
+            createAndStartWorkspaceServer(commandLine);
+        else if (commandLine.start != null)
+            startWorkspaceServer(commandLine);
+        else if (commandLine.create != null)
+            createWorkspaceDatabase(commandLine);
+        else
+            printHelp(commandLine);
+    }
+
+    private void createAndStartWorkspaceServer(final CmdArgs commandLine) {
+        final String workspacePath = commandLine.createStart;
+        if (!verifyWorkspaceExists(workspacePath)) {
+            printHelp(commandLine);
+            return;
+        }
+        final ArcadeDBService service = new ArcadeDBService(workspacePath);
+        service.deleteOldDatabase();
+        service.startArcadeDBService(commandLine.port);
+        service.createDatabase();
+        storeWorkspaceHash(workspacePath);
+        service.openBrowser();
+    }
+
+    private boolean verifyWorkspaceExists(final String workspacePath) {
+        if (StringUtils.isEmpty(workspacePath) || !Paths.get(workspacePath).toFile().exists()) {
+            if (LOGGER.isErrorEnabled())
+                LOGGER.error("Workspace path '" + workspacePath + "' was not found");
+            return false;
+        }
+        if (LOGGER.isInfoEnabled())
+            LOGGER.info("Using workspace directory '" + workspacePath + "'");
+        return true;
+    }
+
+    private void printHelp(final CmdArgs commandLine) {
+        CommandLine.usage(commandLine, System.out);
+    }
+
+    private void storeWorkspaceHash(final String workspacePath) {
+        if (LOGGER.isInfoEnabled())
+            LOGGER.info("Updating workspace ArcadeDB cache checksum...");
+        final Path hashFilePath = Paths.get(workspacePath, "arcadedb/checksum.txt");
+        try {
+            final String hash = HashUtils.getFastPseudoHashFromFile(
+                    Paths.get(workspacePath, "sources/mapped.db").toString());
+            final FileWriter writer = new FileWriter(hashFilePath.toFile());
+            writer.write(hash);
+            writer.close();
+        } catch (IOException e) {
+            if (LOGGER.isErrorEnabled())
+                LOGGER.error("Failed to store hash of workspace mapped graph", e);
+        }
+    }
+
+    private void startWorkspaceServer(final CmdArgs commandLine) {
+        final String workspacePath = commandLine.start;
+        if (!verifyWorkspaceExists(workspacePath)) {
+            printHelp(commandLine);
+            return;
+        }
+        if (!checkArcadeDBDatabaseMatchesWorkspace(workspacePath) && LOGGER.isInfoEnabled())
+            LOGGER.warn("The ArcadeDB database is out-of-date and should be recreated with the --create command");
+        final ArcadeDBService service = new ArcadeDBService(workspacePath);
+        service.startArcadeDBService(commandLine.port);
+        service.openBrowser();
+    }
+
+    private boolean checkArcadeDBDatabaseMatchesWorkspace(final String workspacePath) {
+        try {
+            final String hash = HashUtils.getFastPseudoHashFromFile(
+                    Paths.get(workspacePath, "sources/mapped.db").toString());
+            final Path hashFilePath = Paths.get(workspacePath, "arcadedb/checksum.txt");
+            if (Files.exists(hashFilePath)) {
+                final String storedHash = new String(Files.readAllBytes(hashFilePath)).trim();
+                return hash.equals(storedHash);
+            }
+        } catch (IOException e) {
+            if (LOGGER.isWarnEnabled())
+                LOGGER.warn("Failed to check hash of workspace mapped graph", e);
+        }
+        return false;
+    }
+
+    private void createWorkspaceDatabase(final CmdArgs commandLine) {
+        final String workspacePath = commandLine.create;
+        if (!verifyWorkspaceExists(workspacePath)) {
+            printHelp(commandLine);
+            return;
+        }
+        final ArcadeDBService service = new ArcadeDBService(workspacePath);
+        service.deleteOldDatabase();
+        service.startArcadeDBService(commandLine.port);
+        service.createDatabase();
+        storeWorkspaceHash(workspacePath);
+        service.stopArcadeDBService();
+    }
+}