WIP Replacing SpringBoot 2 by SpringBoot 3, handling Hibernate changes as well, fixing tests.

Author: kinow

README.md

@@ -30,19 +30,19 @@ Then run the following commands to clone the project in your local system.
 
 In the project directory, to start CWLViewer exposed on port `8080`, run:
 
-    docker-compose up
+    docker compose up
 
 The web server will connect to a local host, you'll see the message saying "Tomcat started on port(s):8080".
 
 To see the locally running CWL Viewer app, visit http://localhost:8080/ in your web browser.
 
 To stop and remove:
 
-    docker-compose down
+    docker compose down
 
 
 If you change the source code, then use this `docker-compose.override.yml` and
-re-build with `docker-compose build`:
+re-build with `docker compose build`:
 
 ```yaml
 version: '3.9'
@@ -75,7 +75,7 @@ services:
 Then start the containers:
 
 ```
-docker-compose up
+docker compose up
 ```
 
 Then start Spring Boot locally:
@@ -91,7 +91,7 @@ Now you can connect to http://localhost:7999 in your browser.
 To completely reset the state, you must delete the data volumes:
 
 ```
-docker-compose down
+docker compose down
 docker volume rm  cwlviewer_bundle cwlviewer_git cwlviewer_graphviz cwlviewer_postgres cwlviewer_sparql
 ```
 

docker-compose.yml

@@ -1,4 +1,4 @@
-version: '3.9'
+version: '3.2'
 networks:
   postgres:
   sparql:
@@ -77,4 +77,4 @@ services:
       nofile:
         soft: 65536
         hard: 65536
-    command: "/start-jena.sh"
+    command: "/start-jena.sh"

pom.xml

@@ -15,7 +15,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.7.18</version>
+    <version>3.1.4</version>
     <relativePath/>
   </parent>
 
@@ -68,12 +68,20 @@
     <dependency>
       <groupId>org.springframework.data</groupId>
       <artifactId>spring-data-commons</artifactId>
-      <version>2.7.18</version>
     </dependency>
     <dependency>
-      <groupId>com.vladmihalcea</groupId>
-      <artifactId>hibernate-types-55</artifactId>
-      <version>2.21.1</version>
+      <groupId>org.springframework.data</groupId>
+      <artifactId>spring-data-jpa</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>jakarta.persistence</groupId>
+      <artifactId>jakarta.persistence-api</artifactId>
+      <version>3.1.0</version>
+    </dependency>
+    <dependency>
+      <groupId>io.hypersistence</groupId>
+      <artifactId>hypersistence-utils-hibernate-62</artifactId>
+      <version>3.5.2</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

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

@@ -21,12 +21,14 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.EnableScheduling;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 @SpringBootApplication
 @EnableAsync
+@EnableJpaRepositories
 @EnableScheduling
 @EnableTransactionManagement
 public class CwlViewerApplication {

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

@@ -19,7 +19,7 @@
 
 package org.commonwl.view.cwl;
 
-import javax.validation.ValidationException;
+import jakarta.validation.ValidationException;
 
 /** Exception thrown when a workflow failed CWLTool validation */
 public class CWLValidationException extends ValidationException {

src/main/java/org/commonwl/view/git/GitDetails.java

@@ -19,6 +19,8 @@
 
 package org.commonwl.view.git;
 
+import com.fasterxml.jackson.annotation.JsonAutoDetect;
+import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -28,13 +30,14 @@
 import java.net.URISyntaxException;
 import java.nio.file.Path;
 import java.util.Objects;
+
 import org.commonwl.view.util.LicenseUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /** Represents all the parameters necessary to access a file/directory with Git */
 @JsonIgnoreProperties(
-    value = {"internalUrl"},
+    value = {"internalUrl", "logger"},
     ignoreUnknown = true)
 public class GitDetails implements Serializable {
 
@@ -45,6 +48,7 @@ public class GitDetails implements Serializable {
   private String path;
   private String packedId;
 
+  @JsonCreator
   public GitDetails(String repoUrl, String branch, String path) {
     this.repoUrl = repoUrl;
 
@@ -110,16 +114,12 @@ public GitType getType() {
       if (domain.startsWith("www.")) {
         domain = domain.substring(4);
       }
-      switch (domain) {
-        case "github.com":
-          return GitType.GITHUB;
-        case "gitlab.com":
-          return GitType.GITLAB;
-        case "bitbucket.org":
-          return GitType.BITBUCKET;
-        default:
-          return GitType.GENERIC;
-      }
+      return switch (domain) {
+        case "github.com" -> GitType.GITHUB;
+        case "gitlab.com" -> GitType.GITLAB;
+        case "bitbucket.org" -> GitType.BITBUCKET;
+        default -> GitType.GENERIC;
+      };
     } catch (URISyntaxException ex) {
       return GitType.GENERIC;
     }
@@ -133,27 +133,23 @@ public GitType getType() {
    */
   public String getUrl(String branchOverride) {
     String packedPart = packedId == null ? "" : "#" + packedId;
-    switch (getType()) {
-      case GITHUB:
-      case GITLAB:
-        return "https://"
-            + normaliseUrl(repoUrl).replace(".git", "")
-            + "/blob/"
-            + branchOverride
-            + "/"
-            + path
-            + packedPart;
-      case BITBUCKET:
-        return "https://"
-            + normaliseUrl(repoUrl).replace(".git", "")
-            + "/src/"
-            + branchOverride
-            + "/"
-            + path
-            + packedPart;
-      default:
-        return repoUrl;
-    }
+    return switch (getType()) {
+      case GITHUB, GITLAB -> "https://"
+              + normaliseUrl(repoUrl).replace(".git", "")
+              + "/blob/"
+              + branchOverride
+              + "/"
+              + path
+              + packedPart;
+      case BITBUCKET -> "https://"
+              + normaliseUrl(repoUrl).replace(".git", "")
+              + "/src/"
+              + branchOverride
+              + "/"
+              + path
+              + packedPart;
+      default -> repoUrl;
+    };
   }
 
   /**
@@ -174,18 +170,15 @@ public String getUrl() {
   public String getInternalUrl(String branchOverride) {
     String packedPart = packedId == null ? "" : "%23" + packedId;
     String pathPart = path.equals("/") ? "" : "/" + path;
-    switch (getType()) {
-      case GITHUB:
-      case GITLAB:
-        return "/workflows/"
-            + normaliseUrl(repoUrl).replace(".git", "")
-            + "/blob/"
-            + branchOverride
-            + pathPart
-            + packedPart;
-      default:
-        return "/workflows/" + normaliseUrl(repoUrl) + "/" + branchOverride + pathPart + packedPart;
-    }
+    return switch (getType()) {
+      case GITHUB, GITLAB -> "/workflows/"
+              + normaliseUrl(repoUrl).replace(".git", "")
+              + "/blob/"
+              + branchOverride
+              + pathPart
+              + packedPart;
+      default -> "/workflows/" + normaliseUrl(repoUrl) + "/" + branchOverride + pathPart + packedPart;
+    };
   }
 
   /**
@@ -211,25 +204,21 @@ public String getRawUrl(String branchOverride, String pathOverride) {
     if (pathOverride == null) {
       pathOverride = path;
     }
-    switch (getType()) {
-      case GITHUB:
-        return "https://raw.githubusercontent.com/"
-            + normaliseUrl(repoUrl).replace("github.com/", "").replace(".git", "")
-            + "/"
-            + branchOverride
-            + "/"
-            + pathOverride;
-      case GITLAB:
-      case BITBUCKET:
-        return "https://"
-            + normaliseUrl(repoUrl).replace(".git", "")
-            + "/raw/"
-            + branchOverride
-            + "/"
-            + pathOverride;
-      default:
-        return repoUrl;
-    }
+    return switch (getType()) {
+      case GITHUB -> "https://raw.githubusercontent.com/"
+              + normaliseUrl(repoUrl).replace("github.com/", "").replace(".git", "")
+              + "/"
+              + branchOverride
+              + "/"
+              + pathOverride;
+      case GITLAB, BITBUCKET -> "https://"
+              + normaliseUrl(repoUrl).replace(".git", "")
+              + "/raw/"
+              + branchOverride
+              + "/"
+              + pathOverride;
+      default -> repoUrl;
+    };
   }
 
   /**

src/main/java/org/commonwl/view/git/GitLicenseException.java

@@ -1,6 +1,6 @@
 package org.commonwl.view.git;
 
-import javax.validation.ValidationException;
+import jakarta.validation.ValidationException;
 
 public class GitLicenseException extends ValidationException {
 

src/main/java/org/commonwl/view/util/BaseEntity.java

@@ -1,10 +1,6 @@
 package org.commonwl.view.util;
 
-import com.vladmihalcea.hibernate.type.json.JsonBinaryType;
-import javax.persistence.MappedSuperclass;
-import org.hibernate.annotations.TypeDef;
-import org.hibernate.annotations.TypeDefs;
+import jakarta.persistence.MappedSuperclass;
 
-@TypeDefs({@TypeDef(name = "json", typeClass = JsonBinaryType.class)})
 @MappedSuperclass
 public class BaseEntity {}

src/main/java/org/commonwl/view/workflow/QueuedWorkflow.java

@@ -1,28 +1,27 @@
 package org.commonwl.view.workflow;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
+import io.hypersistence.utils.hibernate.type.json.JsonType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Convert;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Table;
 import java.io.Serializable;
 import java.util.List;
 import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Convert;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Table;
 import org.commonwl.view.cwl.CWLToolStatus;
 import org.commonwl.view.util.BaseEntity;
 import org.hibernate.annotations.GenericGenerator;
 import org.hibernate.annotations.Type;
 
 /** A workflow pending completion of cwltool */
-@JsonIgnoreProperties(value = {"id", "tempRepresentation", "workflowList"})
+// JsonIgnoreProperties(value = {"id", "tempRepresentation", "workflowList"})
 @JsonInclude(JsonInclude.Include.NON_EMPTY)
 @Entity
 @Table(name = "queued_workflow")
-@SuppressWarnings("JpaAttributeTypeInspection")
 public class QueuedWorkflow extends BaseEntity implements Serializable {
 
   // ID for database
@@ -34,20 +33,20 @@ public class QueuedWorkflow extends BaseEntity implements Serializable {
 
   // Very barebones workflow to build loading thumbnail and overview
   @Column(columnDefinition = "jsonb")
-  @Type(type = "json")
+  @Type(value = JsonType.class)
   @Convert(disableConversion = true)
   private Workflow tempRepresentation;
 
   // List of packed workflows for packed workflows
   // TODO: Refactor so this is not necessary
   @Column(columnDefinition = "jsonb")
-  @Type(type = "json")
+  @Type(value = JsonType.class)
   @Convert(disableConversion = true)
   private List<WorkflowOverview> workflowList;
 
   // Cwltool details
   @Column(columnDefinition = "jsonb")
-  @Type(type = "json")
+  @Type(value = JsonType.class)
   @Convert(disableConversion = true)
   private CWLToolStatus cwltoolStatus = CWLToolStatus.RUNNING;
 

src/main/java/org/commonwl/view/workflow/QueuedWorkflowRepository.java

@@ -5,6 +5,7 @@
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
+import org.springframework.stereotype.Repository;
 import org.springframework.transaction.annotation.Transactional;
 
 /**
@@ -13,8 +14,8 @@
  * <p>Use only queries without objects and JSON here. For other methods use the Impl class to avoid
  * issues with serialization.
  */
-public interface QueuedWorkflowRepository
-    extends JpaRepository<QueuedWorkflow, String>, QueuedWorkflowRepositoryCustom {
+@Repository
+public interface QueuedWorkflowRepository extends JpaRepository<QueuedWorkflow, String>, QueuedWorkflowRepositoryCustom {
 
   /**
    * Deletes all queued workflows with date retrieved on older or equal to the Date argument passed.