Upgrade Spring Framework to 5.3.18

oai-pmh_data_provider/data_provider_web/pom.xml

@@ -301,6 +301,12 @@
       <artifactId>velocity-tools-view</artifactId>
       <version>1.1</version>
 	</dependency>
+	<!-- Apache Velocity Engine for Spring 5.x compatibility -->
+	<dependency>
+		<groupId>org.apache.velocity</groupId>
+		<artifactId>velocity-engine-core</artifactId>
+		<version>2.3</version>
+	</dependency>
 	<dependency>
       <groupId>org.cipres.treebase</groupId>
       <artifactId>treebase-core</artifactId>

oai-pmh_data_provider/data_provider_web/src/main/java/org/springframework/web/servlet/view/velocity/VelocityConfigurer.java

@@ -0,0 +1,95 @@
+package org.springframework.web.servlet.view.velocity;
+
+import java.io.IOException;
+import java.util.Properties;
+
+import org.apache.velocity.app.VelocityEngine;
+import org.apache.velocity.exception.VelocityException;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.context.ResourceLoaderAware;
+import org.springframework.core.io.ResourceLoader;
+import org.springframework.web.context.ServletContextAware;
+
+import javax.servlet.ServletContext;
+
+/**
+ * Custom VelocityConfigurer for Spring 5.x compatibility.
+ * This class provides Velocity template engine configuration that was removed from Spring 5.x.
+ */
+public class VelocityConfigurer implements InitializingBean, ResourceLoaderAware, ServletContextAware {
+
+    private VelocityEngine velocityEngine;
+    private String resourceLoaderPath;
+    private Properties velocityProperties;
+    private ResourceLoader resourceLoader;
+    private ServletContext servletContext;
+
+    public void setResourceLoaderPath(String resourceLoaderPath) {
+        this.resourceLoaderPath = resourceLoaderPath;
+    }
+
+    public void setVelocityProperties(Properties velocityProperties) {
+        this.velocityProperties = velocityProperties;
+    }
+
+    @Override
+    public void setResourceLoader(ResourceLoader resourceLoader) {
+        this.resourceLoader = resourceLoader;
+    }
+
+    @Override
+    public void setServletContext(ServletContext servletContext) {
+        this.servletContext = servletContext;
+    }
+
+    public VelocityEngine getVelocityEngine() {
+        return this.velocityEngine;
+    }
+
+    @Override
+    public void afterPropertiesSet() throws Exception {
+        this.velocityEngine = createVelocityEngine();
+    }
+
+    protected VelocityEngine createVelocityEngine() throws Exception {
+        VelocityEngine velocityEngine = new VelocityEngine();
+
+        Properties props = new Properties();
+
+        // Determine loader type and path
+        String loaderType = "classpath";
+        String loaderClass = "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader";
+        String loaderPath = null;
+
+        if (resourceLoaderPath != null) {
+            String path = resourceLoaderPath;
+            if (servletContext != null) {
+                if (!path.startsWith("/")) {
+                    path = "/" + path;
+                }
+                String realPath = servletContext.getRealPath(path);
+                // Use file loader if real path is available
+                if (realPath != null) {
+                    loaderType = "file";
+                    loaderClass = "org.apache.velocity.runtime.resource.loader.FileResourceLoader";
+                    loaderPath = realPath;
+                }
+            }
+        }
+
+        // Set loader configuration
+        props.setProperty("resource.loaders", loaderType);
+        props.setProperty("resource.loader." + loaderType + ".class", loaderClass);
+        if (loaderPath != null) {
+            props.setProperty("resource.loader." + loaderType + ".path", loaderPath);
+        }
+
+        // Add any custom properties
+        if (velocityProperties != null) {
+            props.putAll(velocityProperties);
+        }
+
+        velocityEngine.init(props);
+        return velocityEngine;
+    }
+}

oai-pmh_data_provider/data_provider_web/src/main/java/org/springframework/web/servlet/view/velocity/VelocityViewResolver.java

@@ -0,0 +1,149 @@
+package org.springframework.web.servlet.view.velocity;
+
+import java.io.StringWriter;
+import java.util.Locale;
+import java.util.Map;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.velocity.VelocityContext;
+import org.apache.velocity.app.VelocityEngine;
+import org.apache.velocity.context.Context;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.web.servlet.View;
+import org.springframework.web.servlet.ViewResolver;
+import org.springframework.web.servlet.view.AbstractUrlBasedView;
+
+/**
+ * Custom VelocityViewResolver for Spring 5.x compatibility.
+ * This class provides Velocity view resolution that was removed from Spring 5.x.
+ */
+public class VelocityViewResolver implements ViewResolver, InitializingBean, ApplicationContextAware {
+
+    private VelocityEngine velocityEngine;
+    private String prefix = "";
+    private String suffix = ".vm";
+    private String contentType = "text/html;charset=UTF-8";
+    private String encoding = "UTF-8";
+    private boolean exposeRequestAttributes = false;
+    private boolean exposeSessionAttributes = false;
+    private ApplicationContext applicationContext;
+
+    public void setVelocityEngine(VelocityEngine velocityEngine) {
+        this.velocityEngine = velocityEngine;
+    }
+
+    public void setPrefix(String prefix) {
+        this.prefix = (prefix != null ? prefix : "");
+    }
+
+    public void setSuffix(String suffix) {
+        this.suffix = (suffix != null ? suffix : "");
+    }
+
+    public void setContentType(String contentType) {
+        this.contentType = contentType;
+    }
+
+    public void setEncoding(String encoding) {
+        this.encoding = encoding;
+    }
+
+    public void setExposeRequestAttributes(boolean exposeRequestAttributes) {
+        this.exposeRequestAttributes = exposeRequestAttributes;
+    }
+
+    public void setExposeSessionAttributes(boolean exposeSessionAttributes) {
+        this.exposeSessionAttributes = exposeSessionAttributes;
+    }
+
+    @Override
+    public void setApplicationContext(ApplicationContext applicationContext) {
+        this.applicationContext = applicationContext;
+    }
+
+    @Override
+    public void afterPropertiesSet() throws Exception {
+        // If velocityEngine is not set, try to get it from VelocityConfigurer
+        if (this.velocityEngine == null && this.applicationContext != null) {
+            try {
+                VelocityConfigurer configurer = this.applicationContext.getBean(VelocityConfigurer.class);
+                this.velocityEngine = configurer.getVelocityEngine();
+            } catch (Exception e) {
+                // VelocityConfigurer bean not found or error getting engine
+            }
+        }
+
+        if (this.velocityEngine == null) {
+            throw new IllegalArgumentException("Property 'velocityEngine' is required");
+        }
+    }
+
+    @Override
+    public View resolveViewName(String viewName, Locale locale) throws Exception {
+        return new VelocityView(prefix + viewName + suffix);
+    }
+
+    private class VelocityView implements View {
+        private final String templatePath;
+
+        public VelocityView(String templatePath) {
+            this.templatePath = templatePath;
+        }
+
+        @Override
+        public String getContentType() {
+            return contentType;
+        }
+
+        @Override
+        public void render(Map<String, ?> model, HttpServletRequest request, HttpServletResponse response)
+                throws Exception {
+
+            response.setContentType(getContentType());
+
+            Context velocityContext = new VelocityContext();
+
+            // Add model attributes to Velocity context
+            if (model != null) {
+                for (Map.Entry<String, ?> entry : model.entrySet()) {
+                    velocityContext.put(entry.getKey(), entry.getValue());
+                }
+            }
+
+            // Add request attributes if configured
+            if (exposeRequestAttributes && request != null) {
+                java.util.Enumeration<String> attrNames = request.getAttributeNames();
+                while (attrNames.hasMoreElements()) {
+                    String attrName = attrNames.nextElement();
+                    velocityContext.put(attrName, request.getAttribute(attrName));
+                }
+            }
+
+            // Add session attributes if configured
+            if (exposeSessionAttributes && request != null && request.getSession(false) != null) {
+                java.util.Enumeration<String> attrNames = request.getSession().getAttributeNames();
+                while (attrNames.hasMoreElements()) {
+                    String attrName = attrNames.nextElement();
+                    velocityContext.put(attrName, request.getSession().getAttribute(attrName));
+                }
+            }
+
+            // Add request, response, and session to context for compatibility
+            velocityContext.put("request", request);
+            velocityContext.put("response", response);
+            if (request.getSession(false) != null) {
+                velocityContext.put("session", request.getSession());
+            }
+
+            // Merge template
+            StringWriter writer = new StringWriter();
+            velocityEngine.mergeTemplate(templatePath, encoding, velocityContext, writer);
+
+            response.getWriter().write(writer.toString());
+        }
+    }
+}

oai-pmh_data_provider/pom.xml

@@ -39,31 +39,31 @@
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-core</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-beans</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-context</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-webmvc</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-test</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
       <scope>test</scope>
     </dependency>
 

pom.xml

@@ -75,55 +75,55 @@
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-core</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-beans</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-context</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-jdbc</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-orm</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-tx</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-webmvc</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-context-support</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
     </dependency>
 
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-test</artifactId>
-      <version>4.3.30.RELEASE</version>
+      <version>5.3.18</version>
       <scope>test</scope>
     </dependency>
 

treebase-core/src/test/java/org/cipres/treebase/dao/AbstractDAOTest.java

@@ -18,7 +18,6 @@
 import org.springframework.orm.hibernate5.HibernateTemplate;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.context.transaction.TransactionConfiguration;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.DefaultTransactionDefinition;
@@ -39,7 +38,6 @@
 	"classpath:applicationContext-dao.xml",
 	"classpath:applicationContext-service.xml"
 })
-@TransactionConfiguration(defaultRollback = true)
 @Transactional
 public abstract class AbstractDAOTest {
 

treebase-core/src/test/java/org/cipres/treebase/service/AbstractServiceTest.java

@@ -5,7 +5,6 @@
 import org.junit.runner.RunWith;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.test.context.transaction.TransactionConfiguration;
 import org.springframework.transaction.annotation.Transactional;
 
 /**
@@ -23,7 +22,6 @@
 	"classpath:applicationContext-dao.xml",
 	"classpath:applicationContext-service.xml"
 })
-@TransactionConfiguration(defaultRollback = true)
 @Transactional
 public abstract class AbstractServiceTest {