Use picocli. Static link Linux binaries.

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
   linux-image:
     name: Linux
     runs-on: ubuntu-latest
-    container: debian:stretch
+    container: public.ecr.aws/seqera-labs/graalvm-static:latest
     timeout-minutes: 90
 
     steps:
@@ -49,7 +49,7 @@ jobs:
           path: build/reports/tests/test/
 
       - name: Build Native Image
-        run: ./gradlew nativeBuild
+        run: ./gradlew nativeCompile
 
       - name: Upload linux native image artifact
         uses: actions/upload-artifact@v2
@@ -92,7 +92,7 @@ jobs:
           path: build/reports/tests/test/
 
       - name: Build Native Image
-        run: ./gradlew nativeBuild
+        run: ./gradlew nativeCompile
 
       - name: Upload Mac native image artifact
         uses: actions/upload-artifact@v2
@@ -141,7 +141,7 @@ jobs:
           path: build/reports/tests/test/
 
       - name: Build Native Image
-        run: ./gradlew nativeBuild
+        run: ./gradlew nativeCompile
 
       - name: Upload Windows native image artifact
         uses: actions/upload-artifact@v2

.gitignore

@@ -12,3 +12,4 @@ out/
 .settings
 .classpath
 .factorypath
+**/build-info.properties

VERSION

@@ -0,0 +1 @@
+0.1

VERSION-API

@@ -0,0 +1 @@
+1.6

build.gradle

@@ -24,13 +24,16 @@ def junitVersion = providers.gradleProperty('junit.jupiter.version')
         .get()
 
 dependencies {
+    annotationProcessor("info.picocli:picocli-codegen")
     annotationProcessor("io.micronaut:micronaut-http-validation")
     annotationProcessor("io.micronaut:micronaut-inject-java")
     annotationProcessor("io.micronaut:micronaut-graal")
     implementation("io.micronaut:micronaut-http-client")
     implementation("io.micronaut:micronaut-runtime")
+    implementation("io.micronaut.picocli:micronaut-picocli")
     implementation("io.micronaut.rxjava2:micronaut-rxjava2")
     implementation("io.micronaut.rxjava2:micronaut-rxjava2-http-client")
+    implementation("info.picocli:picocli")
     implementation("javax.annotation:javax.annotation-api")
     implementation("javax.inject:javax.inject:1")
     runtimeOnly("ch.qos.logback:logback-classic")
@@ -46,21 +49,46 @@ application {
     mainClass.set("io.seqera.tower.agent.Agent")
 }
 
-java {
+String gitVersion() {
+    def p = new ProcessBuilder().command('sh', '-c', 'git rev-parse --short HEAD').start()
+    def r = p.waitFor()
+    return r == 0 ? p.text.trim() : '(unknown)'
+}
+
+task buildInfo {
+    doLast {
+        def version = rootProject.file('VERSION').text.trim()
+        def versionApi = rootProject.file('VERSION-API').text.trim()
+        def commitId = gitVersion().trim()
+        def info = """\
+                    version=${version}
+                    versionApi=${versionApi}
+                    commitId=${commitId}
+                """.stripIndent().toString()
+        def f = file("src/main/resources/META-INF/build-info.properties")
+        f.parentFile.mkdirs()
+        f.text = info
+    }
+}
+
+compileJava {
     sourceCompatibility = JavaVersion.toVersion("11")
     targetCompatibility = JavaVersion.toVersion("11")
+    options.compilerArgs += ["-Aproject=${project.name}"]
+    dependsOn buildInfo
 }
 
 test {
     useJUnitPlatform()
 }
 
-
 graalvmNative {
     binaries {
         main {
             imageName = 'towr-agent'
             mainClass = 'io.seqera.tower.agent.Agent'
+            buildArgs.add('--static')
+            buildArgs.add('--libc=musl')
         }
 
         test {
@@ -70,3 +98,5 @@ graalvmNative {
     }
 }
 
+
+

graalvm-static/Dockerfile

@@ -0,0 +1,40 @@
+FROM debian:bullseye
+RUN DEBIAN_FRONTEND=noninteractive apt update && apt install --assume-yes --no-install-recommends build-essential zlib1g-dev wget ca-certificates && rm -rf /var/lib/apt/lists/*
+RUN mkdir /libs
+RUN mkdir /downloads
+
+# Musl
+RUN cd /downloads && wget https://musl.libc.org/releases/musl-1.2.2.tar.gz && tar xvzf musl-1.2.2.tar.gz && rm musl-1.2.2.tar.gz
+RUN cd /downloads/musl-1.2.2 && ./configure --disable-shared --prefix=/libs && make && make install
+
+# zlib
+ENV PATH="/libs/bin:${PATH}"
+RUN cd /downloads && wget https://zlib.net/zlib-1.2.11.tar.gz && tar xvzf zlib-1.2.11.tar.gz && rm zlib-1.2.11.tar.gz
+RUN cd /downloads/zlib-1.2.11 && CC=musl-gcc ./configure --static --prefix=/libs && make && make install
+
+# libstdc++
+RUN cp /usr/lib/gcc/x86_64-linux-gnu/10/libstdc++.a /libs/lib/
+
+
+#
+# tar xvzf musl-1.2.2.tar.gz
+# cd musl-1.2.2
+
+# ./configure --disable-shared --prefix=/libs
+# make
+# make install
+
+# cd ..
+# wget https://zlib.net/zlib-1.2.11.tar.gz
+# tar xvzf zlib-1.2.11.tar.gz
+# cd zlib-1.2.11
+
+# export PATH=/libs/bin:$PATH
+# export CC=musl-gcc
+# ./configure --static --prefix=/libs
+
+# cp /usr/lib/gcc/x86_64-linux-gnu/10/libstdc++.a /libs/lib/
+
+# apt install wget
+# wget https://github.com/graalvm/graalvm-ce-builds/releases/download/vm-21.2.0/graalvm-ce-java11-linux-amd64-21.2.0.tar.gz
+# tar xvzf

micronaut-cli.yml

@@ -3,4 +3,4 @@ defaultPackage: io.seqera.tower.agent
 testFramework: junit
 sourceLanguage: java
 buildTool: gradle
-features: [annotation-api, app-name, graalvm, gradle, http-client, java, java-application, junit, logback, netty-server, readme, shade, yaml]
+features: [annotation-api, app-name, graalvm, gradle, http-client, java, java-application, junit, logback, netty-server, picocli, picocli-java-application, picocli-junit, readme, shade, yaml]

src/main/java/io/seqera/tower/agent/Agent.java

@@ -1,48 +1,81 @@
 package io.seqera.tower.agent;
 
+import io.micronaut.configuration.picocli.PicocliRunner;
 import io.micronaut.context.ApplicationContext;
 import io.micronaut.http.HttpRequest;
 import io.micronaut.http.MutableHttpRequest;
 import io.micronaut.rxjava2.http.client.websockets.RxWebSocketClient;
 import io.micronaut.scheduling.TaskScheduler;
+import io.micronaut.websocket.exceptions.WebSocketClientException;
 import io.seqera.tower.agent.exchange.CommandResponse;
 
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.time.Duration;
-import java.util.Map;
 
-public class Agent {
+import io.seqera.tower.agent.utils.VersionProvider;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+import picocli.CommandLine.Command;
 
+@Command(
+        name = "towr-agent",
+        description = "Nextflow Tower anywhere agent",
+        headerHeading = "%n",
+        versionProvider = VersionProvider.class,
+        mixinStandardHelpOptions = true,
+        sortOptions = false,
+        abbreviateSynopsis = true,
+        descriptionHeading = "%n",
+        commandListHeading = "%nCommands:%n",
+        requiredOptionMarker = '*',
+        usageHelpWidth = 160,
+        parameterListHeading = "%nParameters:%n",
+        optionListHeading = "%nOptions:%n"
+)
+public class Agent implements Runnable {
+    private static Logger logger = LoggerFactory.getLogger(Agent.class);
     private ApplicationContext ctx;
-    private Map<String,String> env;
-    private String hostName;
-    private String accessToken;
-    private String towerUrl;
+
+    @Parameters(index = "0", paramLabel = "AGENT_KEY", description = "Agent key to identify this agent", arity = "1")
+    String agentKey;
+
+    @Option(names = {"-t", "--access-token"}, description = "Tower personal access token (TOWER_ACCESS_TOKEN)", defaultValue = "${TOWER_ACCESS_TOKEN}")
+    String token;
+
+    @Option(names = {"-u", "--url"}, description = "Tower server API endpoint URL. Defaults to tower.nf (TOWER_API_ENDPOINT)", defaultValue = "${TOWER_API_ENDPOINT:-https://api.tower.nf}", required = true)
+    public String url;
 
     private AgentClientSocket agentClient;
 
     Agent() {
-        env =  System.getenv();
         ctx = ApplicationContext.run();
     }
 
-    public void run() throws Exception {
-        hostName = env.get("TOWER_AGENT_HOSTNAME");
-        if (hostName == null) throw new IllegalStateException("TOWER_AGENT_HOSTNAME not set");
-
-        accessToken = env.get("TOWER_ACCESS_TOKEN");
-        if (accessToken == null) throw new IllegalStateException("TOWER_ACCESS_TOKEN not set");
-
-        towerUrl = env.get("TOWER_API_ENDPOINT");
-        if (towerUrl == null) throw new IllegalStateException("TOWER_API_ENDPOINT not set");
+    @Override
+    public void run() {
 
-        final URI uri = new URI(towerUrl + "/agent/" + hostName + "/connect");
-        final MutableHttpRequest<?> req = HttpRequest.GET(uri).bearerAuth(accessToken);
-        final RxWebSocketClient webSocketClient = ctx.getBean(RxWebSocketClient.class);
-        agentClient = webSocketClient.connect(AgentClientSocket.class, req).blockingFirst();
+        final URI uri;
+        try {
+            uri = new URI(url + "/agent/" + agentKey + "/connect");
+            final MutableHttpRequest<?> req = HttpRequest.GET(uri).bearerAuth(token);
+            final RxWebSocketClient webSocketClient = ctx.getBean(RxWebSocketClient.class);
+            agentClient = webSocketClient.connect(AgentClientSocket.class, req).blockingFirst();
+            logger.info("Connected");
 
-        System.out.println("Connected");
-        sendPeriodicHeartbeat();
+            sendPeriodicHeartbeat();
+        } catch (URISyntaxException e) {
+            logger.error(String.format("Invalid URI: %s/agent/%s/connect - %s", url, agentKey, e.getMessage()));
+            System.exit(-1);
+        } catch (WebSocketClientException e) {
+            logger.error(String.format("Connection error - %s", e.getMessage()));
+            System.exit(-1);
+        } catch (Throwable e) {
+            e.printStackTrace();
+            System.exit(-1);
+        }
     }
 
     /**
@@ -58,6 +91,6 @@ private void sendPeriodicHeartbeat() {
     }
 
     public static void main(String[] args) throws Exception {
-        new Agent().run();
+        PicocliRunner.run(Agent.class, args);
     }
 }

src/main/java/io/seqera/tower/agent/AgentClientSocket.java

@@ -70,7 +70,9 @@ void onMessage(CommandRequest message) {
 
     @OnClose
     void onClose() {
-        System.out.println("Closed after " + Duration.between(openingTime, Instant.now()));
+        if (openingTime != null) {
+            System.out.println("Closed after " + Duration.between(openingTime, Instant.now()));
+        }
     }
 
     abstract void send(CommandResponse response);

src/main/java/io/seqera/tower/agent/utils/VersionProvider.java

@@ -0,0 +1,15 @@
+package io.seqera.tower.agent.utils;
+
+import picocli.CommandLine;
+
+import java.util.Properties;
+
+public class VersionProvider implements CommandLine.IVersionProvider {
+
+    @Override
+    public String[] getVersion() throws Exception {
+        Properties properties = new Properties();
+        properties.load(this.getClass().getResourceAsStream("/META-INF/build-info.properties"));
+        return new String[]{String.format("@|yellow Tower Agent version %s (build %s)|@", properties.get("version"), properties.get("commitId"))};
+    }
+}

towr-agent

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+
+bash -c "./gradlew run -q --args=\"${*@Q}\""
+