Issue 464: Prevent multiple versions of jars getting into distributions & Issue 1015 (special treatment for some classifier versions)

README.md

@@ -12,6 +12,14 @@ If you are making changes to the plugins, please see the [internal docs](https:/
 on how to do that, including how to develop and test locally and the versioning information.
 
 ## Release Notes
+### TBD
+*Released*: TBD
+(Earliest compatible LabKey version: 25.10)
+- [GitHub Issue 464](https://github.com/LabKey/internal-issues/issues/464) Update `Distribution.substituteModuleDependencies` (moved from `BuildUtils`) to incorporate variant usage so it will pick up the module file
+- Update to Gradle 9.4.1
+- Update various dependency versions
+- [Github Issue 1015](https://github.com/LabKey/internal-issues/issues/1015) Update `CheckForVersionConflicts` to account for using some jars that differ by classifier only but should not coexist.
+
 ### 7.3.1
 *Released* 11 February 2026
 (Earliest compatible LabKey version: 25.10)

build.gradle

@@ -35,15 +35,15 @@ dependencies {
     api "org.apache.commons:commons-text:${commonsTextVersion}"
     api "commons-io:commons-io:${commonsIoVersion}"
     api "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}"
-    implementation "org.apache.httpcomponents.core5:httpcore5:${httpcoreVersion}"
-    api "org.apache.httpcomponents.client5:httpclient5:${httpclientVersion}"
+    implementation "org.apache.httpcomponents.core5:httpcore5:${httpcore5Version}"
+    api "org.apache.httpcomponents.client5:httpclient5:${httpclient5Version}"
     api "org.json:json:${jsonVersion}"
     implementation "com.graphql-java:graphql-java:${graphqlJavaVersion}"
     api "org.ajoberstar.grgit:grgit-gradle:${grgitGradleVersion}"
 }
 
 group = 'org.labkey.build'
-project.version = "7.4.0-SNAPSHOT"
+project.version = "7.4.0-dependencySub-SNAPSHOT"
 
 gradlePlugin {
     plugins {

gradle.properties

@@ -1,18 +1,18 @@
 artifactory_contextUrl=https://labkey.jfrog.io/artifactory
 
-artifactoryPluginVersion=6.0.0
+artifactoryPluginVersion=6.0.4
 
-commonsIoVersion=2.20.0
-commonsLang3Version=3.18.0
-commonsTextVersion=1.14.0
+commonsIoVersion=2.21.0
+commonsLang3Version=3.20.0
+commonsTextVersion=1.15.0
 
-grgitGradleVersion=5.3.2
-graphqlJavaVersion=24.2
+grgitGradleVersion=5.3.3
+graphqlJavaVersion=25.0
 
-groovySqlVersion=4.0.27
+groovySqlVersion=5.0.4
 
-httpclientVersion=5.5
-httpcoreVersion=5.3.4
+httpclient5Version=5.6
+httpcore5Version=5.4.2
 
-jacksonVersion=2.19.2
-jsonVersion=20250517
+jacksonVersion=2.21.2
+jsonVersion=20251224

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-9.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.4.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/groovy/org/labkey/gradle/plugin/Api.groovy

@@ -17,6 +17,7 @@ package org.labkey.gradle.plugin
 
 import org.gradle.api.Plugin
 import org.gradle.api.Project
+import org.gradle.api.attributes.Usage
 import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.tasks.Copy
 import org.gradle.api.tasks.bundling.Jar
@@ -52,7 +53,14 @@ class Api implements Plugin<Project>
     private void addConfigurations(Project project)
     {
         project.configurations {
-            apiJarFile // used by other project to declare dependencies to this project api jar
+            apiJarFile { // used by other project to declare dependencies to this project's api jar
+                canBeConsumed = true
+                canBeResolved = false
+                attributes.attribute(Usage.USAGE_ATTRIBUTE, project.objects.named(Usage, Usage.JAVA_RUNTIME))
+                // The second attribute is needed to be able to distinguish from the module jar file when doing dependency substitution for distributions
+                attributes.attribute(FileModule.ARTIFACT_TYPE, FileModule.API_JAR_ARTIFACT_TYPE)
+            }
+
         }
         project.configurations.apiJarFile.setDescription("Configuration that depends on the task that generates the api jar file.  Projects that depend on this project's api jar file should use this configuration in their dependency declaration.")
     }

src/main/groovy/org/labkey/gradle/plugin/Distribution.groovy

@@ -18,7 +18,10 @@ package org.labkey.gradle.plugin
 import org.gradle.api.Plugin
 import org.gradle.api.Project
 import org.gradle.api.Task
+import org.gradle.api.UnknownDomainObjectException
+import org.gradle.api.artifacts.Configuration
 import org.gradle.api.artifacts.Dependency
+import org.gradle.api.artifacts.DependencySubstitutions
 import org.gradle.api.artifacts.ModuleDependency
 import org.gradle.api.artifacts.ProjectDependency
 import org.gradle.api.file.DeleteSpec
@@ -95,7 +98,7 @@ class Distribution implements Plugin<Project>
 
         BuildUtils.addLabKeyDependency(project: project, config: "embedded", depProjectPath: BuildUtils.getEmbeddedProjectPath(project.gradle), depVersion: project.labkeyVersion, depProjectConfig: "embedded", transitive: false)
         TaskUtils.configureTaskIfPresent(project, 'artifactoryDeploy', { dependsOn(project.tasks.distribution) })
-
+        substituteModuleDependencies(project, "distribution")
     }
 
     private static void addTasks(Project project)
@@ -161,6 +164,40 @@ class Distribution implements Plugin<Project>
                     project.dependencies.add("distribution", dep)
         }
     }
+
+    // See GH Issue 464
+    static void substituteModuleDependencies(Project project, String configName)
+    {
+        try {
+            project.configurations.named(configName) { Configuration config ->
+                config.resolutionStrategy.dependencySubstitution { DependencySubstitutions ds ->
+                    project.rootProject.subprojects {
+                        Project p ->
+                            {
+                                p.logger.debug("Considering substitution for ${p.path}.")
+                                if (BuildUtils.shouldBuildFromSource(p)) {
+                                    if (p.plugins.hasPlugin('org.labkey.build.module') ||
+                                            p.plugins.hasPlugin('org.labkey.build.fileModule') ||
+                                            p.plugins.hasPlugin('org.labkey.build.javaModule')
+                                    ) {
+                                        ds.substitute(ds.module("org.labkey.module:${p.name}"))
+                                                .using(variant(ds.project(p.path)) {
+                                                    attributes {
+                                                        attribute(FileModule.ARTIFACT_TYPE, FileModule.MODULE_ARTIFACT_TYPE)
+                                                    }
+                                                })
+
+                                        p.logger.info("Substituting org.labkey.module:${p.name} with ${p.path} module file")
+                                    }
+                                }
+                            }
+                    }
+                }
+            }
+        } catch (UnknownDomainObjectException ignore) {
+            project.logger.debug("No ${configName} configuration found for ${project.path}.")
+        }
+    }
 }
 
 

src/main/groovy/org/labkey/gradle/plugin/FileModule.groovy

@@ -23,6 +23,8 @@ import org.gradle.api.UnknownDomainObjectException
 import org.gradle.api.artifacts.Configuration
 import org.gradle.api.artifacts.Dependency
 import org.gradle.api.artifacts.ProjectDependency
+import org.gradle.api.attributes.Attribute
+import org.gradle.api.attributes.Usage
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.java.archives.Manifest
@@ -44,6 +46,10 @@ import org.labkey.gradle.util.TaskUtils
  */
 class FileModule implements Plugin<Project>
 {
+    public static final Attribute ARTIFACT_TYPE = Attribute.of('artifactType', String)
+    public static final String MODULE_ARTIFACT_TYPE = "module"
+    public static final String API_JAR_ARTIFACT_TYPE = "apiJar"
+
     static boolean shouldDoBuild(Project project, boolean logMessages)
     {
         List<String> indicators = new ArrayList<>()
@@ -115,7 +121,13 @@ class FileModule implements Plugin<Project>
     {
         project.configurations
                 {
-                    published
+                    published {
+                        canBeConsumed = true
+                        canBeResolved = false
+                        attributes.attribute(Usage.USAGE_ATTRIBUTE, project.objects.named(Usage, Usage.JAVA_RUNTIME))
+                        // The second attribute is needed to be able to distinguish from the API jar file when doing dependency substitution for distributions
+                        attributes.attribute(ARTIFACT_TYPE, MODULE_ARTIFACT_TYPE)
+                    }
                 }
     }
 
@@ -168,8 +180,7 @@ class FileModule implements Plugin<Project>
 
         project.artifacts
                 {
-                    // TODO: Figure out how to add this artifact without resolving 'module' task
-                    published moduleTask.get()
+                    published(moduleTask)
                 }
 
         project.tasks.register('deployModule')

src/main/groovy/org/labkey/gradle/plugin/ServerDeploy.groovy

@@ -16,18 +16,19 @@
 package org.labkey.gradle.plugin
 
 import org.apache.commons.lang3.SystemUtils
-import org.gradle.api.file.DuplicatesStrategy
-import org.gradle.api.DefaultTask
 import org.gradle.api.Plugin
 import org.gradle.api.Project
 import org.gradle.api.Task
-import org.gradle.api.artifacts.Configuration
-import org.gradle.api.file.CopySpec
 import org.gradle.api.file.DeleteSpec
 import org.gradle.api.file.FileCollection
 import org.gradle.api.tasks.Delete
 import org.labkey.gradle.plugin.extension.ServerDeployExtension
-import org.labkey.gradle.task.*
+import org.labkey.gradle.task.CheckForVersionConflicts
+import org.labkey.gradle.task.DeployApp
+import org.labkey.gradle.task.DeployDistribution
+import org.labkey.gradle.task.StageDistribution
+import org.labkey.gradle.task.StageModules
+import org.labkey.gradle.task.UndeployModules
 import org.labkey.gradle.util.BuildUtils
 import org.labkey.gradle.util.GroupNames
 import org.labkey.gradle.util.TaskUtils

src/main/groovy/org/labkey/gradle/task/CheckForVersionConflicts.groovy

@@ -34,6 +34,40 @@ class CheckForVersionConflicts  extends DefaultTask
     @Input
     Set<String> MULTIPLE_VERSIONS_ALLOWED = Set.of("jackson-core", "jackson-databind")
 
+    // GH Issue 1015: We are using milestone versions of spring-ai jars, which use classifiers like -M2 to distinguish the differnet versions.
+    // We want to have the later milestones replace the earlier ones, so we want to exclude the milestone classifier from the name when
+    // comparing for conflicts. This is rather sketchy and I hope it goes away soon. The list has to include all transitive dependencies as
+    // we as the direct dependencies, and since the artifacts are not released for production use they are not entirely stable, so it's entirely
+    // possible that, say, a jar with milestone M2 will not have the same name with M3 or M4 and won't get cleaned up during the conflict checking.
+    @Input
+    Set<String> USE_CLASSIFIER_IN_VERSION = Set.of(
+            "spring-ai-bom",
+            "spring-ai-starter-model-google-genai",
+            "spring-ai-anthropic",
+            "spring-ai-openai",
+            "spring-ai-client-chat",
+            "spring-ai-advisors-vector-store",
+            "spring-ai-starter-model-google-genai-embedding",
+            "spring-ai-autoconfigure-model-chat-client",
+            "spring-ai-autoconfigure-mcp-sever-common",
+            "spring-ai-autoconfigure-mcp-server-webmvc",
+            "spring-ai-autoconfigure-model-chat-memory",
+            "spring-ai-autoconfigure-model-chat-observation",
+            "spring-ai-autoconfigure-model-google-genai",
+            "spring-ai-autoconfigure-model-tool",
+            "spring-ai-autoconfigure-retry",
+            "spring-ai-commons",
+            "spring-ai-google-genai",
+            "spring-ai-google-genai-embedding",
+            "spring-ai-mcp",
+            "spring-ai-mcp-annotations",
+            "spring-ai-model",
+            "spring-ai-retry",
+            "spring-ai-starter-mcp-server-webmvc",
+            "spring-ai-template-st",
+            "spring-ai-vector-store"
+    )
+
     enum ConflictAction  {
         delete,
         fail,
@@ -87,8 +121,9 @@ class CheckForVersionConflicts  extends DefaultTask
             if (matcher.matches())
             {
                 // we support artifacts with different classifiers (e.g., activeio-core-3.1.0-tests.jar should not be in conflict with activeio-core-3.1.0.jar)
-                String nameWithClassifier = matcher.group(BuildUtils.ARTIFACT_NAME_INDEX)
-                if (matcher.group(BuildUtils.ARTIFACT_CLASSIFIER_INDEX) != null)
+                String nameWithoutClassifier = matcher.group(BuildUtils.ARTIFACT_NAME_INDEX)
+                String nameWithClassifier = nameWithoutClassifier
+                if (matcher.group(BuildUtils.ARTIFACT_CLASSIFIER_INDEX) != null && !USE_CLASSIFIER_IN_VERSION.contains(nameWithoutClassifier))
                     nameWithClassifier += matcher.group(BuildUtils.ARTIFACT_CLASSIFIER_INDEX)
                 if (nameVersionMap.containsKey(nameWithClassifier))
                 {
@@ -98,7 +133,7 @@ class CheckForVersionConflicts  extends DefaultTask
                     }
                     else
                     {
-                        haveMultiples = true
+                        haveMultiples = !USE_CLASSIFIER_IN_VERSION.contains(nameWithoutClassifier)
                         conflictMessages += "Multiple existing ${matcher.group(BuildUtils.ARTIFACT_NAME_INDEX)} ${extension} files."
                     }
                 }
@@ -114,14 +149,15 @@ class CheckForVersionConflicts  extends DefaultTask
                 }
             }
         }
+        // nameVersionMap has "spring-ai", "2.2.0-M2" in it
         collection.files.each { File f ->
             Matcher matcher = BuildUtils.VERSIONED_ARTIFACT_NAME_PATTERN.matcher(f.name)
             if (matcher.matches())
             {
                 String name = matcher.group(BuildUtils.ARTIFACT_NAME_INDEX)
-                if (matcher.group(BuildUtils.ARTIFACT_CLASSIFIER_INDEX) != null)
+                if (matcher.group(BuildUtils.ARTIFACT_CLASSIFIER_INDEX) != null && !USE_CLASSIFIER_IN_VERSION.contains(name))
                     name += matcher.group(BuildUtils.ARTIFACT_CLASSIFIER_INDEX)
-                if (nameVersionMap.containsKey(name))
+                if (nameVersionMap.containsKey(name)) // with match for spring-ai
                 {
                     String version = matcher.group(BuildUtils.ARTIFACT_VERSION_INDEX)
                     if (version != null)