Add license headers and plugin to check always on tests. Minor format…

…ing changes.

.github/workflows/build.yml

@@ -153,7 +153,7 @@ jobs:
   release:
     name: Release
     if: "contains(github.event.head_commit.message, '[release]') && github.event.ref=='refs/heads/master'"
-    needs: [linux-image, mac-image, windows-image]
+    needs: [ linux-image, mac-image, windows-image ]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository

HEADER.txt

@@ -0,0 +1,8 @@
+Copyright (c) ${year}, ${name}.
+
+This Source Code Form is subject to the terms of the Mozilla Public
+License, v. 2.0. If a copy of the MPL was not distributed with this
+file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+This Source Code Form is "Incompatible With Secondary Licenses", as
+defined by the Mozilla Public License, v. 2.0.

README.md

@@ -1,12 +1,9 @@
 # Tower Agent
 
-Tower Agent allows Tower to launch pipelines on HPC clusters that do not allow 
-direct access throw an SSH client. 
+Tower Agent allows Tower to launch pipelines on HPC clusters that do not allow direct access throw an SSH client.
 
-Tower Agent it's a standalone process that when executed in a node that can submit 
-jobs to the cluster (i.e. the login node) it establishes an authenticated secure 
-reverse connection with Tower, allowing Tower to submit and monitor new jobs. The 
-jobs are submitted on behalf of the same user that it's running the agent process.
+Tower Agent it's a standalone process that when executed in a node that can submit jobs to the cluster (i.e. the login node) it establishes an authenticated secure reverse connection with Tower, allowing Tower to submit and monitor new
+jobs. The jobs are submitted on behalf of the same user that it's running the agent process.
 
 ## Build binary version
 

build.gradle

@@ -1,6 +1,18 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ *  This Source Code Form is subject to the terms of the Mozilla Public
+ *  License, v. 2.0. If a copy of the MPL was not distributed with this
+ *  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ *  This Source Code Form is "Incompatible With Secondary Licenses", as
+ *  defined by the Mozilla Public License, v. 2.0.
+ */
+
 import org.gradle.nativeplatform.platform.internal.DefaultNativePlatform
 
 plugins {
+    id 'org.cadixdev.licenser' version '0.6.1'
     id 'org.graalvm.buildtools.native'
     id("io.micronaut.application") version "2.0.6"
 }
@@ -47,6 +59,16 @@ dependencies {
     testImplementation('org.junit.jupiter:junit-jupiter')
 }
 
+license {
+    header = project.file('HEADER.txt')
+    properties {
+        name = 'Seqera Labs'
+        year = 2021
+    }
+    exclude '**/*.properties'
+    exclude 'gradlew'
+}
+
 application {
     mainClass.set("io.seqera.tower.agent.Agent")
 }
@@ -82,6 +104,7 @@ compileJava {
 
 test {
     useJUnitPlatform()
+    dependsOn checkLicenses
 }
 
 
@@ -102,3 +125,4 @@ graalvmNative {
 
 
 
+

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, picocli, picocli-java-application, picocli-junit, 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 ]

settings.gradle

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ *  This Source Code Form is subject to the terms of the Mozilla Public
+ *  License, v. 2.0. If a copy of the MPL was not distributed with this
+ *  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ *  This Source Code Form is "Incompatible With Secondary Licenses", as
+ *  defined by the Mozilla Public License, v. 2.0.
+ */
+
 pluginManagement {
     plugins {
         id 'org.graalvm.buildtools.native' version getProperty('native.gradle.plugin.version')
@@ -8,4 +19,4 @@ pluginManagement {
     }
 }
 
-rootProject.name="tower-agent"
+rootProject.name = "tower-agent"

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

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent;
 
 import io.micronaut.configuration.picocli.PicocliRunner;
@@ -7,18 +18,17 @@
 import io.micronaut.rxjava2.http.client.websockets.RxWebSocketClient;
 import io.micronaut.scheduling.TaskScheduler;
 import io.micronaut.websocket.exceptions.WebSocketClientException;
-
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.time.Duration;
-
 import io.seqera.tower.agent.exchange.HeartbeatMessage;
 import io.seqera.tower.agent.utils.VersionProvider;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
-import picocli.CommandLine.Command;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.time.Duration;
 
 @Command(
         name = "tw-agent",
@@ -37,7 +47,6 @@
 )
 public class Agent implements Runnable {
     private static Logger logger = LoggerFactory.getLogger(Agent.class);
-    private ApplicationContext ctx;
 
     @Parameters(index = "0", paramLabel = "AGENT_CONNECTION_ID", description = "Agent connection ID to identify this agent", arity = "1")
     String agentKey;
@@ -46,14 +55,19 @@ public class Agent implements Runnable {
     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;
+    String url;
 
+    private ApplicationContext ctx;
     private AgentClientSocket agentClient;
 
     Agent() {
         ctx = ApplicationContext.run();
     }
 
+    public static void main(String[] args) throws Exception {
+        PicocliRunner.run(Agent.class, args);
+    }
+
     @Override
     public void run() {
 
@@ -89,8 +103,4 @@ private void sendPeriodicHeartbeat() {
             agentClient.send(new HeartbeatMessage());
         });
     }
-
-    public static void main(String[] args) throws Exception {
-        PicocliRunner.run(Agent.class, args);
-    }
 }

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

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent;
 
 import io.micronaut.http.HttpRequest;
@@ -58,13 +69,13 @@ void onClose() {
     private void execCommand(CommandRequest message) {
         try {
             System.out.println("Execute command: " + message.getCommand());
-            Process process = new ProcessBuilder().command("sh","-c", message.getCommand()).start();
+            Process process = new ProcessBuilder().command("sh", "-c", message.getCommand()).start();
             int exitStatus = process.waitFor();
             // read the stdout
             BufferedReader reader = new BufferedReader(new InputStreamReader(process.getInputStream()));
             StringBuilder builder = new StringBuilder();
-            String line=null;
-            while ( (line = reader.readLine()) != null) {
+            String line = null;
+            while ((line = reader.readLine()) != null) {
                 builder.append(line);
                 builder.append("\n");
             }
@@ -75,8 +86,7 @@ private void execCommand(CommandRequest message) {
             System.out.println("Sending response --> " + response);
             session.sendSync(response);
             System.out.println("Response sent");
-        }
-        catch ( Throwable e ){
+        } catch (Throwable e) {
             // send result
             CommandResponse response = new CommandResponse(message.getId(), e.getMessage().getBytes(), -1);
             session.sendSync(response);

src/main/java/io/seqera/tower/agent/exchange/AgentMessage.java

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent.exchange;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
@@ -13,4 +24,5 @@
         @JsonSubTypes.Type(value = CommandResponse.class, name = "command-response"),
         @JsonSubTypes.Type(value = HeartbeatMessage.class, name = "heartbeat")
 })
-public abstract class AgentMessage implements Serializable {}
+public abstract class AgentMessage implements Serializable {
+}

src/main/java/io/seqera/tower/agent/exchange/CommandRequest.java

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent.exchange;
 
 import io.micronaut.core.annotation.ReflectiveAccess;

src/main/java/io/seqera/tower/agent/exchange/CommandResponse.java

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent.exchange;
 
 import io.micronaut.core.annotation.ReflectiveAccess;

src/main/java/io/seqera/tower/agent/exchange/HeartbeatMessage.java

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent.exchange;
 
 import io.micronaut.core.annotation.ReflectiveAccess;

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

@@ -1,3 +1,14 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent.utils;
 
 import picocli.CommandLine;

src/main/resources/application.yml

@@ -1,3 +1,14 @@
+#
+# Copyright (c) 2021, Seqera Labs.
+#
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+#
+# This Source Code Form is "Incompatible With Secondary Licenses", as
+# defined by the Mozilla Public License, v. 2.0.
+#
+
 micronaut:
   application:
     name: towerAgent

src/main/resources/logback.xml

@@ -1,3 +1,14 @@
+<!--
+    Copyright (c) 2021, Seqera Labs.
+
+    This Source Code Form is subject to the terms of the Mozilla Public
+    License, v. 2.0. If a copy of the MPL was not distributed with this
+    file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+    This Source Code Form is "Incompatible With Secondary Licenses", as
+    defined by the Mozilla Public License, v. 2.0.
+-->
+
 <configuration>
 
     <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
@@ -10,6 +21,6 @@
     </appender>
 
     <root level="info">
-        <appender-ref ref="STDOUT" />
+        <appender-ref ref="STDOUT"/>
     </root>
 </configuration>

src/test/java/io/seqera/tower/agent/AgentTest.java

@@ -1,11 +1,21 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
 package io.seqera.tower.agent;
 
 import io.micronaut.runtime.EmbeddedApplication;
 import io.micronaut.test.extensions.junit5.annotation.MicronautTest;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.Assertions;
-
 import jakarta.inject.Inject;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
 
 @MicronautTest
 class AgentTest {

tw-agent

@@ -1,5 +1,16 @@
 #!/bin/bash
 
 
+#
+# Copyright (c) 2021, Seqera Labs.
+#
+#  This Source Code Form is subject to the terms of the Mozilla Public
+#  License, v. 2.0. If a copy of the MPL was not distributed with this
+#  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+#
+#  This Source Code Form is "Incompatible With Secondary Licenses", as
+#  defined by the Mozilla Public License, v. 2.0.
+#
+
 bash -c "./gradlew run -q --args=\"${*@Q}\""