Consider transitives when identifying project dependencies

Previously, when building a layered jar, the Gradle plugin only
considered a configuration's direct dependencies when identifying
project dependencies. This resulted in transitive project dependencies
being missed when deciding which dependencies belong in the
application layer.

This commit updates ResolvedDependencies to consider all projects
from the root project when collecting the IDs of local projects. This
ensures that any project dependency, no matter where it appears in the
dependency graph, is successfully identified.

Fixes gh-25163

Author: wilkinsona

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/BootJar.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2020 the original author or authors.
+ * Copyright 2012-2021 the original author or authors.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -74,15 +74,16 @@ public class BootJar extends Jar implements BootArchive {
 	 */
 	public BootJar() {
 		this.support = new BootArchiveSupport(LAUNCHER, new LibrarySpec(), new ZipCompressionResolver());
-		this.bootInfSpec = getProject().copySpec().into("BOOT-INF");
-		this.mainClass = getProject().getObjects().property(String.class);
+		Project project = getProject();
+		this.bootInfSpec = project.copySpec().into("BOOT-INF");
+		this.mainClass = project.getObjects().property(String.class);
 		configureBootInfSpec(this.bootInfSpec);
 		getMainSpec().with(this.bootInfSpec);
-		getProject().getConfigurations().all((configuration) -> {
+		project.getConfigurations().all((configuration) -> {
 			ResolvableDependencies incoming = configuration.getIncoming();
 			incoming.afterResolve((resolvableDependencies) -> {
 				if (resolvableDependencies == incoming) {
-					this.resolvedDependencies.processConfiguration(configuration);
+					this.resolvedDependencies.processConfiguration(project, configuration);
 				}
 			});
 		});

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/ResolvedDependencies.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2020 the original author or authors.
+ * Copyright 2012-2021 the original author or authors.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -22,9 +22,9 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import org.gradle.api.Project;
 import org.gradle.api.artifacts.Configuration;
 import org.gradle.api.artifacts.ModuleVersionIdentifier;
-import org.gradle.api.artifacts.ProjectDependency;
 import org.gradle.api.artifacts.ResolvedArtifact;
 import org.gradle.api.artifacts.ResolvedConfiguration;
 
@@ -44,13 +44,15 @@ class ResolvedDependencies {
 
 	private final Map<Configuration, ResolvedConfigurationDependencies> configurationDependencies = new LinkedHashMap<>();
 
-	void processConfiguration(Configuration configuration) {
-		Set<String> projectDependencyIds = configuration.getAllDependencies().withType(ProjectDependency.class).stream()
-				.map((projectDependency) -> projectDependency.getGroup() + ":" + projectDependency.getName() + ":"
-						+ projectDependency.getVersion())
+	private String projectId(Project project) {
+		return project.getGroup() + ":" + project.getName() + ":" + project.getVersion();
+	}
+
+	void processConfiguration(Project project, Configuration configuration) {
+		Set<String> localProjectIds = project.getRootProject().getAllprojects().stream().map(this::projectId)
 				.collect(Collectors.toSet());
 		this.configurationDependencies.put(configuration,
-				new ResolvedConfigurationDependencies(projectDependencyIds, configuration.getResolvedConfiguration()));
+				new ResolvedConfigurationDependencies(localProjectIds, configuration.getResolvedConfiguration()));
 	}
 
 	DependencyDescriptor find(File file) {

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests.java

@@ -149,6 +149,7 @@ void multiModuleImplicitLayers() throws IOException {
 			assertThat(jarFile.getEntry(layerToolsJar)).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/alpha-1.2.3.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/bravo-1.2.3.jar")).isNotNull();
+			assertThat(jarFile.getEntry("BOOT-INF/lib/charlie-1.2.3.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/commons-lang3-3.9.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/spring-core-5.2.5.RELEASE.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/spring-jcl-5.2.5.RELEASE.jar")).isNotNull();
@@ -171,7 +172,8 @@ void multiModuleImplicitLayers() throws IOException {
 		assertThat(indexedLayers.get("spring-boot-loader")).containsExactly("org/");
 		assertThat(indexedLayers.get("snapshot-dependencies")).containsExactlyElementsOf(expectedSnapshotDependencies);
 		assertThat(indexedLayers.get("application")).containsExactly("BOOT-INF/classes/", "BOOT-INF/classpath.idx",
-				"BOOT-INF/layers.idx", "BOOT-INF/lib/alpha-1.2.3.jar", "BOOT-INF/lib/bravo-1.2.3.jar", "META-INF/");
+				"BOOT-INF/layers.idx", "BOOT-INF/lib/alpha-1.2.3.jar", "BOOT-INF/lib/bravo-1.2.3.jar",
+				"BOOT-INF/lib/charlie-1.2.3.jar", "META-INF/");
 		BuildResult listLayers = this.gradleBuild.build("listLayers");
 		assertThat(listLayers.task(":listLayers").getOutcome()).isEqualTo(TaskOutcome.SUCCESS);
 		String listLayersOutput = listLayers.getOutput();
@@ -244,6 +246,7 @@ void multiModuleCustomLayers() throws IOException {
 			assertThat(jarFile.getEntry(layerToolsJar)).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/alpha-1.2.3.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/bravo-1.2.3.jar")).isNotNull();
+			assertThat(jarFile.getEntry("BOOT-INF/lib/charlie-1.2.3.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/commons-lang3-3.9.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/spring-core-5.2.5.RELEASE.jar")).isNotNull();
 			assertThat(jarFile.getEntry("BOOT-INF/lib/spring-jcl-5.2.5.RELEASE.jar")).isNotNull();
@@ -259,6 +262,7 @@ void multiModuleCustomLayers() throws IOException {
 		Set<String> expectedSubprojectDependencies = new TreeSet<>();
 		expectedSubprojectDependencies.add("BOOT-INF/lib/alpha-1.2.3.jar");
 		expectedSubprojectDependencies.add("BOOT-INF/lib/bravo-1.2.3.jar");
+		expectedSubprojectDependencies.add("BOOT-INF/lib/charlie-1.2.3.jar");
 		Set<String> expectedDependencies = new TreeSet<>();
 		expectedDependencies.add("BOOT-INF/lib/spring-core-5.2.5.RELEASE.jar");
 		expectedDependencies.add("BOOT-INF/lib/spring-jcl-5.2.5.RELEASE.jar");
@@ -348,7 +352,7 @@ private boolean isInIndex(List<String> index, String file) {
 	private void writeSettingsGradle() {
 		try (PrintWriter writer = new PrintWriter(
 				new FileWriter(new File(this.gradleBuild.getProjectDir(), "settings.gradle")))) {
-			writer.println("include 'alpha', 'bravo'");
+			writer.println("include 'alpha', 'bravo', 'charlie'");
 		}
 		catch (IOException ex) {
 			throw new RuntimeException(ex);

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootJarTests.java

@@ -323,7 +323,7 @@ private void addContent() throws IOException {
 			return null;
 		}).given(resolvableDependencies).afterResolve(any(Action.class));
 		given(configuration.getIncoming()).willReturn(resolvableDependencies);
-		bootJar.getResolvedDependencies().processConfiguration(configuration);
+		bootJar.getResolvedDependencies().processConfiguration(bootJar.getProject(), configuration);
 	}
 
 	private ResolvedArtifact mockLibraryArtifact(String fileName, String group, String module, String version) {

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests-multiModuleCustomLayers.gradle

@@ -7,6 +7,11 @@ subprojects {
 	apply plugin: 'java'
 	group = 'org.example.projects'
 	version = '1.2.3'
+	if (it.name == 'bravo') {
+		dependencies {
+			implementation(project(':charlie'))
+		}
+	}
 }
 
 bootJar {

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/tasks/bundling/BootJarIntegrationTests-multiModuleImplicitLayers.gradle

@@ -7,6 +7,11 @@ subprojects {
 	apply plugin: 'java'
 	group = 'org.example.projects'
 	version = '1.2.3'
+	if (it.name == 'bravo') {
+		dependencies {
+			implementation(project(':charlie'))
+		}
+	}
 }
 
 bootJar {