Merge pull request #66 from protegeproject/upgrade-spring-boot

Upgrade spring boot to 3.4.1
protegeproject · Jan 17, 2025 · 0f01a7e · 0f01a7e
2 parents 88810c5 + ddc5485
commit 0f01a7e
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Showing 914 changed files with 3,989 additions and 4,037 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.5.3</version>
+        <version>3.4.1</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
 
@@ -65,7 +65,7 @@
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-common</artifactId>
-            <version>0.9.4</version>
+            <version>0.9.8</version>
         </dependency>
         <dependency>
             <groupId>edu.stanford.protege</groupId>
@@ -91,27 +91,27 @@
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-entity-frames</artifactId>
-            <version>0.9.2</version>
+            <version>0.9.3</version>
         </dependency>
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-ipc</artifactId>
-            <version>1.0.4</version>
+            <version>1.0.10</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-amqp</artifactId>
-            <version>3.0.8</version>
+            <version>3.2.1</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.amqp</groupId>
             <artifactId>spring-rabbit</artifactId>
-            <version>3.0.8</version>
+            <version>3.2.1</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.amqp</groupId>
             <artifactId>spring-amqp</artifactId>
-            <version>3.0.8</version>
+            <version>3.2.1</version>
         </dependency>
 
         <dependency>
@@ -126,26 +126,9 @@
         </dependency>
 
         <dependency>
-            <groupId>org.glassfish</groupId>
-            <artifactId>javax.json</artifactId>
-            <version>1.0.4</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.glassfish.jersey.containers</groupId>
-            <artifactId>jersey-container-servlet</artifactId>
-            <version>2.27</version>
-        </dependency>
-        <dependency>
-            <groupId>org.glassfish.jersey.inject</groupId>
-            <artifactId>jersey-hk2</artifactId>
-            <version>2.27</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.glassfish.jersey.media</groupId>
-            <artifactId>jersey-media-json-jackson</artifactId>
-            <version>2.26</version>
+            <groupId>jakarta.inject</groupId>
+            <artifactId>jakarta.inject-api</artifactId>
+            <version>2.0.1</version>
         </dependency>
 
         <dependency>
@@ -155,12 +138,6 @@
             <scope>test</scope>
         </dependency>
 
-        <dependency>
-            <groupId>javax.inject</groupId>
-            <artifactId>javax.inject</artifactId>
-            <version>1</version>
-        </dependency>
-
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
@@ -174,14 +151,14 @@
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-jackson</artifactId>
-            <version>0.9.0</version>
+            <version>0.9.3</version>
         </dependency>
 
 
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-revision-manager</artifactId>
-            <version>0.9.0</version>
+            <version>0.9.2</version>
         </dependency>
 
         <dependency>
@@ -203,11 +180,6 @@
             <version>4.11.0</version>
         </dependency>
 
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-            <version>2.6</version>
-        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
@@ -219,12 +191,6 @@
             <version>4.5.1</version>
         </dependency>
 
-        <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
-            <version>2.6</version>
-        </dependency>
-
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-apibinding</artifactId>
@@ -350,29 +316,23 @@
             <version>${autovalue.version}</version>
         </dependency>
 
-        <dependency>
-            <groupId>org.junit.vintage</groupId>
-            <artifactId>junit-vintage-engine</artifactId>
-            <version>5.6.3</version>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
-            <version>1.18.1</version>
+            <version>1.20.4</version>
             <scope>test</scope>
         </dependency>
 
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>rabbitmq</artifactId>
             <scope>test</scope>
+            <version>1.20.4</version>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>mongodb</artifactId>
-            <version>1.18.1</version>
+            <version>1.20.4</version>
         </dependency>
 
     </dependencies>

diff --git a/src/main/java/edu/stanford/protege/webprotege/ApplicationBeansConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/ApplicationBeansConfiguration.java
@@ -65,8 +65,8 @@
 import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
 import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
 
-import javax.inject.Provider;
-import javax.inject.Singleton;
+import jakarta.inject.Provider;
+import jakarta.inject.Singleton;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Properties;
@@ -115,11 +115,6 @@ public TempFileFactoryImpl provideTempFileFactory() {
         return new TempFileFactoryImpl();
     }
 
-    @Bean
-    public DefaultMustacheFactory providesMustacheFactory() {
-        return new DefaultMustacheFactory();
-    }
-
     @Bean
     DataDirectoryProvider getDataDirectoryProvider() {
         return new DataDirectoryProvider();

diff --git a/src/main/java/edu/stanford/protege/webprotege/EntityMatcherBeansConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/EntityMatcherBeansConfiguration.java
@@ -7,8 +7,9 @@
 import edu.stanford.protege.webprotege.match.*;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Scope;
 
-import javax.inject.Provider;
+import jakarta.inject.Provider;
 
 /**
  * Matthew Horridge
@@ -18,63 +19,63 @@
 public class EntityMatcherBeansConfiguration {
 
     @Bean
-    SubClassOfMatcherFactory subClassOfMatcherFactory(Provider<ClassHierarchyProvider> p1) {
+    SubClassOfMatcherFactory subClassOfMatcherFactory(ClassHierarchyProvider p1) {
         return new SubClassOfMatcherFactory(p1);
     }
 
     @Bean
-    LeafClassMatcherFactory leafClassMatcherFactory(Provider<ClassHierarchyProvider> p1) {
+    LeafClassMatcherFactory leafClassMatcherFactory(ClassHierarchyProvider p1) {
         return new LeafClassMatcherFactory(p1);
     }
 
     @Bean
-    NotSubClassOfMatcherFactory notSubClassOfMatcherFactory(Provider<ClassHierarchyProvider> p1) {
+    NotSubClassOfMatcherFactory notSubClassOfMatcherFactory(ClassHierarchyProvider p1) {
         return new NotSubClassOfMatcherFactory(p1);
     }
 
     @Bean
-    InstanceOfMatcherFactory instanceOfMatcherFactory(Provider<ClassHierarchyProvider> p1,
-                                                      Provider<ProjectOntologiesIndex> p2,
-                                                      Provider<ClassAssertionAxiomsByClassIndex> p3,
-                                                      Provider<ProjectSignatureByTypeIndex> p4) {
+    InstanceOfMatcherFactory instanceOfMatcherFactory(ClassHierarchyProvider p1,
+                                                      ProjectOntologiesIndex p2,
+                                                      ClassAssertionAxiomsByClassIndex p3,
+                                                      ProjectSignatureByTypeIndex p4) {
         return new InstanceOfMatcherFactory(p1, p2, p3, p4);
     }
 
     @Bean
-    ConflictingBooleanValuesMatcherFactory conflictingBooleanValuesMatcherFactory(Provider<AnnotationAssertionAxiomsIndex> p1) {
+    ConflictingBooleanValuesMatcherFactory conflictingBooleanValuesMatcherFactory(AnnotationAssertionAxiomsIndex p1) {
         return new ConflictingBooleanValuesMatcherFactory(p1);
     }
 
     @Bean
-    EntityIsDeprecatedMatcherFactory entityIsDeprecatedMatcherFactory(Provider<AnnotationAssertionAxiomsIndex> p1) {
+    EntityIsDeprecatedMatcherFactory entityIsDeprecatedMatcherFactory(AnnotationAssertionAxiomsIndex p1) {
         return new EntityIsDeprecatedMatcherFactory(p1);
     }
 
     @Bean
-    AnnotationValuesAreNotDisjointMatcherFactory annotationValuesAreNotDisjointMatcherFactory(Provider<AnnotationAssertionAxiomsIndex> p1) {
+    AnnotationValuesAreNotDisjointMatcherFactory annotationValuesAreNotDisjointMatcherFactory(AnnotationAssertionAxiomsIndex p1) {
         return new AnnotationValuesAreNotDisjointMatcherFactory(p1);
     }
 
     @Bean
-    NonUniqueLangTagsMatcherFactory nonUniqueLangTagsMatcherFactory(Provider<AnnotationAssertionAxiomsIndex> p1) {
+    NonUniqueLangTagsMatcherFactory nonUniqueLangTagsMatcherFactory(AnnotationAssertionAxiomsIndex p1) {
         return new NonUniqueLangTagsMatcherFactory(p1);
     }
 
     @Bean
-    EntityAnnotationMatcherFactory entityAnnotationMatcherFactory(Provider<AnnotationAssertionAxiomsIndex> p1) {
+    EntityAnnotationMatcherFactory entityAnnotationMatcherFactory(AnnotationAssertionAxiomsIndex p1) {
         return new EntityAnnotationMatcherFactory(p1);
     }
 
     @Bean
-    IriAnnotationsMatcherFactory iriAnnotationsMatcherFactory(Provider<AnnotationAssertionAxiomsIndex> p1) {
+    IriAnnotationsMatcherFactory iriAnnotationsMatcherFactory(AnnotationAssertionAxiomsIndex p1) {
         return new IriAnnotationsMatcherFactory(p1);
     }
 
     @Bean
-    EntityRelationshipMatcherFactory entityRelationshipMatcherFactory(Provider<ProjectOntologiesIndex> p1,
-                                                                      Provider<SubClassOfAxiomsBySubClassIndex> p2,
-                                                                      Provider<PropertyAssertionAxiomsBySubjectIndex> p3,
-                                                                      Provider<AxiomPropertyValueTranslator> p4) {
+    EntityRelationshipMatcherFactory entityRelationshipMatcherFactory(ProjectOntologiesIndex p1,
+                                                                      SubClassOfAxiomsBySubClassIndex p2,
+                                                                      PropertyAssertionAxiomsBySubjectIndex p3,
+                                                                      AxiomPropertyValueTranslator p4) {
         return new EntityRelationshipMatcherFactory(p1, p2, p3, p4);
     }
 

diff --git a/src/main/java/edu/stanford/protege/webprotege/FormBeansConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/FormBeansConfiguration.java
@@ -21,7 +21,7 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Scope;
 
-import javax.inject.Provider;
+import jakarta.inject.Provider;
 
 /**
  * Matthew Horridge

diff --git a/src/main/java/edu/stanford/protege/webprotege/FormDataBuilderConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/FormDataBuilderConfiguration.java
@@ -13,7 +13,7 @@
 import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.springframework.context.annotation.Bean;
 
-import javax.inject.Provider;
+import jakarta.inject.Provider;
 
 /**
  * Matthew Horridge

diff --git a/src/main/java/edu/stanford/protege/webprotege/LuceneBeansConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/LuceneBeansConfiguration.java
@@ -25,11 +25,12 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Scope;
 
-import javax.inject.Provider;
 import java.io.IOException;
 import java.io.UncheckedIOException;
 import java.nio.file.Path;
 
+import jakarta.inject.Provider;
+
 /**
  * Matthew Horridge
  * Stanford Center for Biomedical Informatics Research

diff --git a/src/main/java/edu/stanford/protege/webprotege/ProjectActionHandlerBeansConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/ProjectActionHandlerBeansConfiguration.java
@@ -68,7 +68,7 @@
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 
-import javax.inject.Provider;
+import jakarta.inject.Provider;
 import java.util.Comparator;
 
 /**

diff --git a/src/main/java/edu/stanford/protege/webprotege/ProjectBeansConfiguration.java b/src/main/java/edu/stanford/protege/webprotege/ProjectBeansConfiguration.java
@@ -103,14 +103,15 @@
 import org.semanticweb.owlapi.util.IRIShortFormProvider;
 import org.semanticweb.owlapi.util.OntologyIRIShortFormProvider;
 import org.semanticweb.owlapi.util.ShortFormProvider;
+import org.springframework.beans.factory.ObjectProvider;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Primary;
 import org.springframework.context.annotation.Scope;
 import org.springframework.data.mongodb.core.MongoTemplate;
 
-import javax.inject.Provider;
+import jakarta.inject.Provider;
 import java.io.File;
 import java.nio.file.Path;
 import java.util.Comparator;

diff --git a/src/main/java/edu/stanford/protege/webprotege/api/ActionExecutor.java b/src/main/java/edu/stanford/protege/webprotege/api/ActionExecutor.java
@@ -14,7 +14,7 @@
 import reactor.core.publisher.Mono;
 
 import javax.annotation.Nonnull;
-import javax.inject.Inject;
+import jakarta.inject.Inject;
 
 import static com.google.common.base.Preconditions.checkNotNull;