Bump org.springframework.boot:spring-boot-starter-parent from 3.1.4 to 4.1.0-RC1

.github/workflows/ci-build.yml

@@ -30,7 +30,7 @@ jobs:
         uses: actions/setup-java@v5
         with:
           distribution: 'adopt'
-          java-version: '17'
+          java-version: '25'
 
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1

.github/workflows/codeql-analysis.yml

@@ -21,7 +21,7 @@ jobs:
       uses: actions/setup-java@v5
       with:
         distribution: 'adopt'
-        java-version: '17'
+        java-version: '25'
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

Dockerfile

@@ -1,4 +1,4 @@
-FROM docker.io/library/maven:3-eclipse-temurin-17-alpine AS build-licensee
+FROM docker.io/library/maven:3-eclipse-temurin-25-alpine AS build-licensee
 
 RUN apk add --update \
   alpine-sdk \
@@ -10,7 +10,7 @@ RUN apk add --update \
 RUN gem install licensee
 
 
-FROM docker.io/library/maven:3-eclipse-temurin-17-alpine
+FROM docker.io/library/maven:3-eclipse-temurin-25-alpine
 MAINTAINER Stian Soiland-Reyes <stain@apache.org>
 
 # Build-time metadata as defined at https://github.com/opencontainers/image-spec/blob/main/annotations.md

README.md

@@ -1,16 +1,21 @@
 # CWL Viewer
 
-This is a [Spring Boot](http://projects.spring.io/spring-boot/) MVC application which fetches [Common Workflow Language](http://www.commonwl.org/) files from a Github repository and creates a page for it detailing the main workflow and its inputs, outputs and steps.
+This is a [Spring Boot](http://projects.spring.io/spring-boot/) MVC application which fetches [Common Workflow Language](http://www.commonwl.org/) files
+from a GitHub repository and creates a page for it detailing the main workflow and its inputs, outputs and steps.
 
 [![Build Status](https://github.com/common-workflow-language/cwlviewer/workflows/CWL%20Viewer%20Build/badge.svg?branch=main)](https://github.com/common-workflow-language/cwlviewer/actions?query=workflow%3A%22CWL%20Viewer%20Build%22) [![Coverage Status](https://coveralls.io/repos/github/common-workflow-language/cwlviewer/badge.svg)](https://coveralls.io/github/common-workflow-language/cwlviewer) [![Gitter](https://img.shields.io/gitter/room/gitterHQ/gitter.svg)](https://gitter.im/common-workflow-language/cwlviewer?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![](https://images.microbadger.com/badges/image/commonworkflowlanguage/cwlviewer.svg)](https://microbadger.com/images/commonworkflowlanguage/cwlviewer "MicroBadger commonworkflowlanguage/cwlviewer") [![Docker image commonworkflowlanguage/cwlviewer](https://images.microbadger.com/badges/version/commonworkflowlanguage/cwlviewer.svg)](https://hub.docker.com/r/commonworkflowlanguage/cwlviewer/ "Docker Hub commonworkflowlanguage/cwlviewer")
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.823534.svg)](https://doi.org/10.5281/zenodo.823534)
 
 # Using CWL Viewer
 
-You are recommended to use the **production instance** of CWL Viewer at https://view.commonwl.org/ which runs the latest [release](https://github.com/common-workflow-language/cwlviewer/releases). Any downtime should be reported on the [gitter chat for cwlviewer](https://gitter.im/common-workflow-language/cwlviewer).
+You are recommended to use the **production instance** of CWL Viewer at https://view.commonwl.org/ which runs
+the latest [release](https://github.com/common-workflow-language/cwlviewer/releases). Any downtime should be reported on the [gitter chat for cwlviewer](https://gitter.im/common-workflow-language/cwlviewer).
 
-<!--- I don't think this is a thing any more.
-The **dev instance** at http://view.commonwl.org:8082/ corresponds to the current `master` branch, and is updated every 6 minutes to run the latest [commonworkflowlanguage/cwlviewer docker image](https://hub.docker.com/r/commonworkflowlanguage/cwlviewer/builds/). Note that this instance is NOT secured and might break at any time.
+<!--- I don't think this is a thing anymore.
+The **dev instance** at http://view.commonwl.org:8082/ corresponds to the current `master` branch,
+and is updated every 6 minutes to run the latest
+[commonworkflowlanguage/cwlviewer docker image](https://hub.docker.com/r/commonworkflowlanguage/cwlviewer/builds/).
+Note that this instance is NOT secured and might break at any time.
 -->
 
 # Running
@@ -19,7 +24,8 @@ If you are a developer, or you want to use the CWL Viewer in a closed environmen
 
 ## Recommended - Running with Docker
 
-This application can be started with [Docker](https://www.docker.com/) and [Docker Compose](https://docs.docker.com/compose/install/) and Docker Compose is the recommended method of running or developing this codebase.
+This application can be started with [Docker](https://www.docker.com/) and [Docker Compose](https://docs.docker.com/compose/install/) and Docker Compose is the recommended
+method of running or developing this codebase.
 
 Then run the following commands to clone the project in your local system.
 
@@ -134,7 +140,8 @@ To compile you will need [Java 17](https://www.oracle.com/java/technologies/down
 (e.g. [Eclipse Adoptium](https://projects.eclipse.org/projects/adoptium)) and version, as well as
 [Apache Maven 3](https://maven.apache.org/download.cgi) (`apt install maven`).
 
-Spring Boot uses an embedded HTTP server. The Spring Boot Maven plugin includes a run goal which can be used to quickly compile and run it:
+Spring Boot uses an embedded HTTP server. The Spring Boot Maven plugin includes a run goal which can be used to
+quickly compile and run it:
 
 ```
 $ mvn spring-boot:run
@@ -166,9 +173,11 @@ Now check out http://localhost:8080/ to access CWL Viewer.
 
 ## Configuration
 
-There are a variety of configuration options detailed in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) which can be adjusted.
+There are a variety of configuration options detailed in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) which can
+be adjusted.
 
-When deploying with docker, these can be overridden externally by creating/modifying `docker-compose.override.yml` as follows:
+When deploying with docker, these can be overridden externally by creating/modifying `docker-compose.override.yml`
+as follows:
 
 ```yaml
 version: '3.9'

pom.xml

@@ -15,18 +15,17 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.1.4</version>
+    <version>4.1.0-RC1</version>
     <relativePath/>
   </parent>
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-    <java.version>17</java.version>
+    <java.version>25</java.version>
     <jena.version>6.1.0</jena.version>
     <!-- BEGIN should correspond to https://repo1.maven.org/maven2/org/apache/jena/jena/3.9.0/jena-3.9.0.pom -->
     <ver.jsonldjava>0.13.6</ver.jsonldjava>
-    <ver.jackson>2.21.3</ver.jackson>
     <!-- END -->
     <log4j2.version>2.17.0</log4j2.version>
   </properties>
@@ -65,24 +64,6 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-data-jpa</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.springframework.data</groupId>
-      <artifactId>spring-data-commons</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.springframework.data</groupId>
-      <artifactId>spring-data-jpa</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>io.hypersistence</groupId>
-      <artifactId>hypersistence-utils-hibernate-62</artifactId>
-      <version>3.9.4</version>
-    </dependency>
-    <dependency>
-      <groupId>com.fasterxml.jackson.module</groupId>
-      <artifactId>jackson-module-jakarta-xmlbind-annotations</artifactId>
-      <version>2.21.3</version>
-    </dependency>
     <!-- Liquibase; note that Flyway, while probably having more documentation and users,
          changed its license model. Similarly to mongo, we prefer an open license that
          won't lock users or developers from updating or modifying the code if necessary.
@@ -124,12 +105,6 @@
         </exclusion>
       </exclusions>
     </dependency>
-    <!-- JSON parsing -->
-    <dependency>
-      <groupId>com.fasterxml.jackson.core</groupId>
-      <artifactId>jackson-core</artifactId>
-      <version>${ver.jackson}</version>
-    </dependency>
     <!-- Jena, turtle -->
     <dependency>
       <groupId>org.apache.jena</groupId>
@@ -184,14 +159,13 @@
     </dependency>
     <dependency>
       <groupId>org.testcontainers</groupId>
-      <artifactId>junit-jupiter</artifactId>
+      <artifactId>postgresql</artifactId>
       <version>1.21.4</version>
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>org.testcontainers</groupId>
-      <artifactId>postgresql</artifactId>
-      <version>1.21.4</version>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-data-jpa-test</artifactId>
       <scope>test</scope>
     </dependency>
     <!-- We use mockito-inline as it supports mocking static methods -->

src/main/java/org/commonwl/view/CwlViewerApplication.java

@@ -33,7 +33,7 @@
 @EnableTransactionManagement
 public class CwlViewerApplication {
 
-  public static void main(String[] args) {
+  static void main(String[] args) {
     SpringApplication.run(CwlViewerApplication.class, args);
   }
 }

src/main/java/org/commonwl/view/Scheduler.java

@@ -1,3 +1,22 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
 package org.commonwl.view;
 
 import java.io.File;
@@ -63,14 +82,13 @@ public void removeOldQueuedWorkflowEntries() {
     calendar.add(Calendar.HOUR, -QUEUED_WORKFLOW_AGE_LIMIT_HOURS);
     Date removeTime = calendar.getTime();
 
-    logger.info("The time is " + now);
-    logger.info(
-        "Delete time interval is : OLDER THAN " + QUEUED_WORKFLOW_AGE_LIMIT_HOURS + " HOURS");
-    logger.info("Deleting queued workflows older than or equal to " + removeTime);
+    logger.info("The time is {}", now);
+    logger.info("Delete time interval is : OLDER THAN {} HOURS", QUEUED_WORKFLOW_AGE_LIMIT_HOURS);
+    logger.info("Deleting queued workflows older than or equal to {}", removeTime);
 
     logger.info(
-        queuedWorkflowRepository.deleteByTempRepresentation_RetrievedOnLessThanEqual(removeTime)
-            + " Old queued workflows removed");
+        "{} Old queued workflows removed",
+        queuedWorkflowRepository.deleteByTempRepresentation_RetrievedOnLessThanEqual(removeTime));
   }
 
   /**
@@ -79,9 +97,9 @@ public void removeOldQueuedWorkflowEntries() {
    * <p>Will scan each temporary directory (graphviz, RO, git), searching for files exceeding a
    * specified threshold.
    *
-   * <p>It scans the first level directories, i.e. it does not recursively scans directories. So it
+   * <p>It scans the first level directories, i.e. it does not recursively scan directories. So it
    * will delete any RO or Git repository directories that exceed the threshold. Similarly, it will
-   * delete any graph (svg, png, etc) that also exceed it.
+   * delete any graph (svg, png, etc.) that also exceeds it.
    *
    * <p>Errors logged through Logger. Settings in Spring application properties file.
    *
@@ -110,7 +128,7 @@ private void clearDirectory(String temporaryDirectory) {
     File temporaryDirectoryFile = new File(temporaryDirectory);
     String[] files = temporaryDirectoryFile.list(new AgeFileFilter(Date.from(cutoff)));
 
-    if (files != null && files.length > 0) {
+    if (files != null) {
       for (String fileName : files) {
         File fileToDelete = new File(temporaryDirectoryFile, fileName);
         try {
@@ -122,9 +140,9 @@ private void clearDirectory(String temporaryDirectory) {
           // expected and
           // must be treated as errors.
           logger.error(
-              String.format(
-                  "Failed to delete old temporary file or directory [%s]: %s",
-                  fileToDelete.getAbsolutePath(), e.getMessage()),
+              "Failed to delete old temporary file or directory [{}]: {}",
+              fileToDelete.getAbsolutePath(),
+              e.getMessage(),
               e);
         }
       }

src/main/java/org/commonwl/view/WebConfig.java

@@ -38,7 +38,7 @@ public class WebConfig implements WebMvcConfigurer {
    * @see Workflow#getPermalink(Format)
    * @see WorkflowPermalinkController
    */
-  public static enum Format {
+  public enum Format {
     // Browser
     html(MediaType.TEXT_HTML),
     // API

src/main/java/org/commonwl/view/cwl/CWLElement.java

@@ -20,23 +20,22 @@
 package org.commonwl.view.cwl;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
 /** Represents the input/output of a workflow/tool */
 @JsonInclude(JsonInclude.Include.NON_EMPTY)
-public class CWLElement {
+public class CWLElement implements Serializable {
 
   private String label;
   private String doc;
   private String type;
   private String format;
-  private List<String> sourceID;
+  private final List<String> sourceID = new ArrayList<>();
   private String defaultVal;
 
-  public CWLElement() {
-    this.sourceID = new ArrayList<>();
-  }
+  public CWLElement() {}
 
   public String getLabel() {
     return label;

src/main/java/org/commonwl/view/cwl/CWLNotAWorkflowException.java

@@ -20,6 +20,7 @@
 package org.commonwl.view.cwl;
 
 /** Exception thrown when the provided CWL document is not a Workflow. */
+@SuppressWarnings("unused")
 public class CWLNotAWorkflowException extends CWLValidationException {
 
   public CWLNotAWorkflowException(String message) {