Fix loose app generation for jar project dependencies in war projects

src/main/groovy/io/openliberty/tools/gradle/tasks/DeployTask.groovy

@@ -1,5 +1,5 @@
 /**
- * (C) Copyright IBM Corporation 2014, 2021.
+ * (C) Copyright IBM Corporation 2014, 2023.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -347,26 +347,39 @@ class DeployTask extends AbstractServerTask {
 
     private void addWarEmbeddedLib(Element parent, LooseWarApplication looseApp, Task task) throws Exception {
         ArrayList<File> deps = new ArrayList<File>();
-        task.classpath.each {deps.add(it)}
+        task.classpath.each {
+            deps.add(it)
+        }
         //Removes WEB-INF/lib/main directory since it is not rquired in the xml
-        if(deps != null && !deps.isEmpty()) {
+        if (deps != null && !deps.isEmpty()) {
             deps.remove(0)
         }
         File parentProjectDir = new File(task.getProject().getRootProject().rootDir.getAbsolutePath())
         for (File dep: deps) {
-            String dependentProjectName = "project ':"+getProjectPath(parentProjectDir, dep)+"'"
-            Project siblingProject = project.getRootProject().findProject(dependentProjectName)
-            boolean isCurrentProject = ((task.getProject().toString()).equals(dependentProjectName))
-            if (!isCurrentProject && siblingProject != null){
-                Element archive = looseApp.addArchive(parent, "/WEB-INF/lib/"+ dep.getName());
-                looseApp.addOutputDirectory(archive, siblingProject, "/");
-                Task resourceTask = siblingProject.getTasks().findByPath(":"+dependentProjectName+":processResources");
-                if (resourceTask.getDestinationDir() != null){
+            String dependencyProjectName = getProjectPath(parentProjectDir, dep)
+            String projectDependencyString = "project ':" + dependencyProjectName + "'"
+            Project siblingProject = project.getRootProject().findProject(dependencyProjectName)
+            boolean isCurrentProject = ((task.getProject().toString()).equals(projectDependencyString))
+            if (!isCurrentProject && siblingProject != null) {
+                Element archive = looseApp.addArchive(parent, "/WEB-INF/lib/" + dep.getName());
+                //Add sibling project class directories to <archive/> as <dir>
+                siblingProject.sourceSets.main.getOutput().getClassesDirs().each {
+                    looseApp.getConfig().addDir(archive, it, "/");
+                }
+                Task resourceTask = siblingProject.getTasks().findByPath(":" + projectDependencyString + ":processResources");
+                if (resourceTask != null && resourceTask.getDestinationDir() != null) {
                     looseApp.addOutputDir(archive, resourceTask.getDestinationDir(), "/");
                 }
-                File manifestFile = project.sourceSets.main.getOutput().getResourcesDir().getParentFile()
-                looseApp.addManifestFileWithParent(archive, manifestFile);
-            } else if(FilenameUtils.getExtension(dep.getAbsolutePath()).equalsIgnoreCase("jar")){
+                File resourceDir = siblingProject.sourceSets.main.getOutput().getResourcesDir()
+                File manifestFile = null
+                if (resourceDir.exists() && resourceDir.listFiles().length > 0) {
+                    File metaInfDir = new File(resourceDir, "META-INF")
+                    if (metaInfDir.exists() && metaInfDir.listFiles().length > 0) {
+                        manifestFile = new File(metaInfDir, "MANIFEST.MF")
+                    }
+                }
+                looseApp.addManifestFileWithParent(archive, manifestFile, resourceDir.getParentFile().getCanonicalPath());
+            } else if (FilenameUtils.getExtension(dep.getAbsolutePath()).equalsIgnoreCase("jar")) {
                 addLibrary(parent, looseApp, "/WEB-INF/lib/", dep);
             } else {
                 looseApp.addOutputDir(looseApp.getDocumentRoot(), dep , "/WEB-INF/classes/");

src/test/groovy/io/openliberty/tools/gradle/TestLooseWarWithLooseJar.groovy

@@ -0,0 +1,135 @@
+package io.openliberty.tools.gradle;
+
+import org.junit.AfterClass
+import org.junit.BeforeClass
+import org.junit.Test
+
+import java.io.File;
+import java.io.FileInputStream;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathFactory;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+
+public class TestLooseWarWithLooseJar extends AbstractIntegrationTest{
+    static File resourceDir = new File("build/resources/test/loose-war-with-loose-jar")
+    static File buildDir = new File(integTestDir, "/loose-war-with-loose-jar")
+    static String buildFilename = "build.gradle"
+
+    @BeforeClass
+    public static void setup() {
+        createDir(buildDir)
+        createTestProject(buildDir, resourceDir, buildFilename)
+    }
+
+    @Test
+    public void test_loose_config_file_exists() {
+        try {
+            runTasks(buildDir, 'deploy')
+        } catch (Exception e) {
+            throw new AssertionError ("Fail on task deploy. " + e)
+        }
+        assert new File('build/testBuilds/loose-war-with-loose-jar/ejb-war/build/wlp/usr/servers/testServer/apps/ejb-war.war.xml').exists() : 'looseApplication config file was not copied over to the liberty runtime'
+    }
+
+    /*
+        Expected output to the XML
+        <?xml version="1.0" encoding="UTF-8"?>
+        <archive>
+            <dir sourceOnDisk="/Users/../../ci.gradle/build/testBuilds/loose-war-with-loose-jar/ejb-war/src/main/webapp" targetInArchive="/"/>
+            <dir sourceOnDisk="/Users/../../ci.gradle/build/testBuilds/loose-war-with-loose-jar/build/classes/java/main" targetInArchive="/WEB-INF/classes/"/>
+            <archive targetInArchive="/WEB-INF/lib/ejb-ejb.jar">
+                <dir sourceOnDisk="/Users/../../ci.gradle/build/testBuilds/loose-war-with-loose-jar/ejb-ejb/build/classes/java/main" targetInArchive="/"/>
+                <file sourceOnDisk="/Users/../../ci.gradle/build/testBuilds/loose-war-with-loose-jar/ejb-ejb/build/resources/tmp/META-INF/MANIFEST.MF" targetInArchive="/META-INF/MANIFEST.MF"/>
+            </archive>
+            <file sourceOnDisk="/Users/../.gradle/caches/modules-2/files-2.1/javax/javaee-api/7.0/51399f902cc27a808122edcbebfaa1ad989954ba/javaee-api-7.0.jar" targetInArchive="/WEB-INF/lib/javaee-api-7.0.jar"/>
+            <file sourceOnDisk="/Users/../.gradle/caches/modules-2/files-2.1/com.sun.mail/javax.mail/1.5.0/ec2410fdf7e0a3022e7c2a2e6241039d1abc1e98/javax.mail-1.5.0.jar" targetInArchive="/WEB-INF/lib/javax.mail-1.5.0.jar"/>
+            <file sourceOnDisk="/Users/../.m2/repository/javax/activation/activation/1.1/activation-1.1.jar" targetInArchive="/WEB-INF/lib/activation-1.1.jar"/>
+            <file sourceOnDisk="/Users/../../ci.gradle/build/testBuilds/loose-war-with-loose-jar/ejb-war/build/tmp/META-INF/MANIFEST.MF" targetInArchive="/META-INF/MANIFEST.MF"/>
+        </archive>
+    */
+    @Test
+    public void test_loose_config_file_contents_are_correct() {
+        File on = new File("build/testBuilds/loose-war-with-loose-jar/ejb-war/build/wlp/usr/servers/testServer/apps/ejb-war.war.xml");
+        FileInputStream input = new FileInputStream(on);
+
+        // get input XML Document
+        DocumentBuilderFactory inputBuilderFactory = DocumentBuilderFactory.newInstance();
+        inputBuilderFactory.setIgnoringComments(true);
+        inputBuilderFactory.setCoalescing(true);
+        inputBuilderFactory.setIgnoringElementContentWhitespace(true);
+        inputBuilderFactory.setValidating(false);
+        DocumentBuilder inputBuilder = inputBuilderFactory.newDocumentBuilder();
+        Document inputDoc=inputBuilder.parse(input);
+
+        // parse input XML Document
+        XPath xPath = XPathFactory.newInstance().newXPath();
+
+        //Check for correct number of dir elements in loose war
+        String expression = "/archive/dir";
+        NodeList nodes = (NodeList) xPath.compile(expression).evaluate(inputDoc, XPathConstants.NODESET);
+        Assert.assertEquals("Number of <dir/> element ==>", 2, nodes.getLength());
+
+        //Check loose jar archive element is present
+        expression = "/archive/archive";
+        nodes = (NodeList) xPath.compile(expression).evaluate(inputDoc, XPathConstants.NODESET);
+        Assert.assertEquals("Number of <archive/> element ==>", 1, nodes.getLength());
+
+        //Check loose jar targetLocation is correct
+        Assert.assertEquals("sibling archive targetInArchive attribute value", "/WEB-INF/lib/ejb-ejb.jar",
+            nodes.item(0).getAttributes().getNamedItem("targetInArchive").getNodeValue()); 
+
+        //Check loose jar contains correct amount of dir elements
+        expression = "/archive/archive/dir";
+        nodes = (NodeList) xPath.compile(expression).evaluate(inputDoc, XPathConstants.NODESET);
+        Assert.assertEquals("Number of <dir/> element ==>", 1, nodes.getLength());
+
+        //Check loose jar classes dir location
+        String nodeValue = nodes.item(0).getAttributes().getNamedItem("sourceOnDisk").getNodeValue();
+        Assert.assertEquals("sibling archive targetInArchive attribute value", buildDir.getCanonicalPath() + "/ejb-ejb/build/classes/java/main",
+            nodes.item(0).getAttributes().getNamedItem("sourceOnDisk").getNodeValue()); 
+
+         //Check loose jar contains correct amount of file elements
+        expression = "/archive/archive/file";
+        nodes = (NodeList) xPath.compile(expression).evaluate(inputDoc, XPathConstants.NODESET);
+        Assert.assertEquals("Number of <file/> element ==>", 1, nodes.getLength());
+
+        //Check loose jar manifest file location
+        nodeValue = nodes.item(0).getAttributes().getNamedItem("sourceOnDisk").getNodeValue();
+        Assert.assertEquals("sibling archive targetInArchive attribute value", buildDir.getCanonicalPath() + "/ejb-ejb/build/resources/tmp/META-INF/MANIFEST.MF",
+            nodes.item(0).getAttributes().getNamedItem("sourceOnDisk").getNodeValue()); 
+
+        //Check correct number of additional file elements are present
+        expression = "/archive/file";
+        nodes = (NodeList) xPath.compile(expression).evaluate(inputDoc, XPathConstants.NODESET);
+        Assert.assertEquals("Number of <file/> element ==>", 4, nodes.getLength());
+
+        Assert.assertEquals("archive targetInArchive attribute value", "/WEB-INF/lib/javaee-api-7.0.jar",
+            nodes.item(0).getAttributes().getNamedItem("targetInArchive").getNodeValue());
+
+        // Check that dependencies are not located in the test build dir since copyLibsDirectory not set. They will be located in the gradle cache somewhere.
+        nodeValue = nodes.item(0).getAttributes().getNamedItem("sourceOnDisk").getNodeValue();
+        assert nodeValue.endsWith("/javaee-api-7.0.jar") && !nodeValue.contains("/loose-war-with-loose-jar/") : 'archive sourceOnDisk attribute value not correct'
+
+        Assert.assertEquals("archive targetInArchive attribute value", "/WEB-INF/lib/javax.mail-1.5.0.jar",
+            nodes.item(1).getAttributes().getNamedItem("targetInArchive").getNodeValue());
+
+        // Check that dependencies are not located in the test build dir since copyLibsDirectory not set. They will be located in the gradle cache somewhere.
+        nodeValue = nodes.item(1).getAttributes().getNamedItem("sourceOnDisk").getNodeValue();
+        assert nodeValue.endsWith("/javax.mail-1.5.0.jar") && !nodeValue.contains("/loose-war-with-loose-jar/") : 'archive sourceOnDisk attribute value not correct'
+
+        Assert.assertEquals("archive targetInArchive attribute value", "/WEB-INF/lib/activation-1.1.jar",
+            nodes.item(2).getAttributes().getNamedItem("targetInArchive").getNodeValue());
+
+        // Check that dependencies are not located in the test build dir since copyLibsDirectory not set. They will be located in the gradle cache somewhere.
+        nodeValue = nodes.item(2).getAttributes().getNamedItem("sourceOnDisk").getNodeValue();
+        assert nodeValue.endsWith("/activation-1.1.jar") && !nodeValue.contains("/loose-war-with-loose-jar/") : 'archive sourceOnDisk attribute value not correct'
+    }
+}

src/test/resources/loose-war-with-loose-jar/build.gradle

@@ -0,0 +1,19 @@
+allprojects  {
+    group = 'sample'
+    version = '1.0'
+}
+
+subprojects {
+    apply plugin: 'java'
+
+    sourceCompatibility = 1.8
+    targetCompatibility = 1.8
+    tasks.withType(JavaCompile) {
+        options.encoding = 'UTF-8'
+    }
+
+    repositories {
+        mavenLocal()
+        mavenCentral()
+    }
+}

src/test/resources/loose-war-with-loose-jar/ejb-ejb/build.gradle

@@ -0,0 +1,10 @@
+description = 'EJB Module'
+
+dependencies {
+    testImplementation group: 'junit', name: 'junit', version:'4.13.1'
+    implementation group: 'javax', name: 'javaee-api', version:'7.0'
+}
+
+jar {
+    archiveName = baseName + '.' + extension
+}

src/test/resources/loose-war-with-loose-jar/ejb-ejb/src/main/java/wasdev/ejb/ejb/SampleStatelessBean.java

@@ -0,0 +1,11 @@
+package wasdev.ejb.ejb;
+
+import javax.ejb.Stateless;
+
+@Stateless
+public class SampleStatelessBean {
+
+    public String hello() {
+        return "Hello EJB World.";
+    }
+}

src/test/resources/loose-war-with-loose-jar/ejb-war/build.gradle

@@ -0,0 +1,41 @@
+buildscript {
+    repositories {
+        mavenLocal()
+        mavenCentral()
+        maven {
+            name = 'Sonatype Nexus Snapshots'
+            url = 'https://oss.sonatype.org/content/repositories/snapshots/'
+        }
+    }
+    dependencies {
+        classpath "io.openliberty.tools:liberty-gradle-plugin:$lgpVersion"
+    }
+}
+
+apply plugin: 'war'
+apply plugin: 'liberty'
+
+jar.enabled = false
+description = 'WAR Module'
+dependencies {
+    testImplementation group: 'junit', name: 'junit', version:'4.13.1'
+    implementation group: 'javax', name: 'javaee-api', version:'7.0'
+    implementation project(':ejb-ejb')
+    libertyRuntime group: runtimeGroup, name: kernelArtifactId, version: runtimeVersion
+}
+
+war {
+    archiveName = baseName + '.' + extension
+}
+
+liberty {
+    server {
+        name = "testServer"
+        deploy {
+            apps = [war]
+        }
+        verifyAppStartTimeout = 30
+        looseApplication = true
+    }
+}
+

src/test/resources/loose-war-with-loose-jar/ejb-war/src/main/java/wasdev/ejb/ejb/web/EJBServlet.java

@@ -0,0 +1,34 @@
+package wasdev.ejb.ejb.web;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+
+import javax.ejb.EJB;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import wasdev.ejb.ejb.SampleStatelessBean;
+
+/**
+ * A servlet which injects a stateless EJB
+ */
+@WebServlet({"/", "/ejbServlet"})
+public class EJBServlet extends HttpServlet {
+    private static final long serialVersionUID = 1L;
+
+    @EJB
+    SampleStatelessBean statelessBean;
+
+    @Override
+    protected void doGet(HttpServletRequest request,
+                         HttpServletResponse response) throws IOException {
+        PrintWriter writer = response.getWriter();
+
+        // Call hello method on a stateless session bean
+        String message = statelessBean.hello();
+
+        writer.println(message);
+    }
+}

src/test/resources/loose-war-with-loose-jar/settings.gradle

@@ -0,0 +1,6 @@
+rootProject.name = 'ejb-war'
+include ':ejb-ejb'
+include ':ejb-war'
+
+project(':ejb-ejb').projectDir = "$rootDir/ejb-ejb" as File
+project(':ejb-war').projectDir = "$rootDir/ejb-war" as File