Move code to jakarta namespace and update dependencies to use Jakarta…

… EE 9.1

MetFragWeb/pom.xml

@@ -54,13 +54,10 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-email</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>commons-fileupload</groupId>
-			<artifactId>commons-fileupload</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.primefaces</groupId>
 			<artifactId>primefaces</artifactId>
+			<classifier>jakarta</classifier>
 		</dependency>
 		<dependency>
 			<groupId>org.primefaces.themes</groupId>

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragWebBean.java

@@ -6,17 +6,17 @@
 import java.net.UnknownHostException;
 import java.util.List;
 
-import javax.annotation.PostConstruct;
-import javax.faces.application.FacesMessage;
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.SessionScoped;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.model.SelectItem;
+import jakarta.annotation.PostConstruct;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.bean.ManagedBean;
+import jakarta.faces.bean.SessionScoped;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.model.SelectItem;
 import javax.imageio.ImageIO;
-import javax.servlet.ServletContext;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
+import jakarta.servlet.ServletContext;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpSession;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.mail.EmailAttachment;
@@ -277,7 +277,7 @@ public void parametersUploadListener(org.primefaces.event.FileUploadEvent event)
 	/*
 	 * database search settings
 	 */
-	public java.util.List<javax.faces.model.SelectItem> getAvailableDatabases() {
+	public java.util.List<jakarta.faces.model.SelectItem> getAvailableDatabases() {
 		return this.beanSettingsContainer.getAvailableParameters().getDatabases();
 	}
 
@@ -908,7 +908,7 @@ public void setExcludedElements(String excludedFilterElements) {
 	}
 
 	//SMARTS inclusion
-	public java.util.List<javax.faces.model.SelectItem> getAvailableSubstructureSmarts() {
+	public java.util.List<jakarta.faces.model.SelectItem> getAvailableSubstructureSmarts() {
 		return this.beanSettingsContainer.getAvailableParameters().getSubstructureSmarts();
 	}
 
@@ -1070,7 +1070,7 @@ public void setSelectedInformationSmarts(String selectedSmarts) {
 		this.beanSettingsContainer.setSelectedInformationSmarts(selectedSmarts);
 	}
 
-	public java.util.List<javax.faces.model.SelectItem> getAvailableSubstructureInformationSmarts() {
+	public java.util.List<jakarta.faces.model.SelectItem> getAvailableSubstructureInformationSmarts() {
 		return this.beanSettingsContainer.getAvailableParameters().getSubstructureInformationSmarts();
 	}
 
@@ -1814,11 +1814,11 @@ private boolean checkScoreSettings() {
 	/*
 	 * fragmenter settings
 	 */	
-	public java.util.List<javax.faces.model.SelectItem> getPrecursorModes() {
+	public java.util.List<jakarta.faces.model.SelectItem> getPrecursorModes() {
 		return this.beanSettingsContainer.getAvailableParameters().getPrecursorModes();
 	}
 
-	public java.util.List<javax.faces.model.SelectItem> getTreeDepths() {
+	public java.util.List<jakarta.faces.model.SelectItem> getTreeDepths() {
 		return this.beanSettingsContainer.getAvailableParameters().getTreeDepths();
 	}
 
@@ -3014,7 +3014,7 @@ public void viewExpiredListener() {
 		System.out.println("session expired " + this.beanSettingsContainer.getRootSessionFolder());
 		FacesContext fc = FacesContext.getCurrentInstance();
         java.util.Map<String, Object> requestMap = fc.getExternalContext().getRequestMap();
-        javax.faces.application.NavigationHandler nav =
+		jakarta.faces.application.NavigationHandler nav =
                 fc.getApplication().getNavigationHandler();
         // Push some useful stuff to the request scope for
         // use in the page

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/exception/ViewExpiredExceptionExceptionHandler.java

@@ -3,14 +3,14 @@
 import java.util.Iterator;
 import java.util.Map;
 
-import javax.faces.FacesException;
-import javax.faces.application.NavigationHandler;
-import javax.faces.application.ViewExpiredException;
-import javax.faces.context.ExceptionHandler;
-import javax.faces.context.ExceptionHandlerWrapper;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ExceptionQueuedEvent;
-import javax.faces.event.ExceptionQueuedEventContext;
+import jakarta.faces.FacesException;
+import jakarta.faces.application.NavigationHandler;
+import jakarta.faces.application.ViewExpiredException;
+import jakarta.faces.context.ExceptionHandler;
+import jakarta.faces.context.ExceptionHandlerWrapper;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ExceptionQueuedEvent;
+import jakarta.faces.event.ExceptionQueuedEventContext;
 
 import org.primefaces.PrimeFaces;
 

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/exception/ViewExpiredExceptionExceptionHandlerFactory.java

@@ -1,7 +1,7 @@
 package de.ipbhalle.metfragweb.exception;
 
-import javax.faces.context.ExceptionHandler;
-import javax.faces.context.ExceptionHandlerFactory;
+import jakarta.faces.context.ExceptionHandler;
+import jakarta.faces.context.ExceptionHandlerFactory;
 import de.ipbhalle.metfragweb.exception.ViewExpiredExceptionExceptionHandler;
 
 public class ViewExpiredExceptionExceptionHandlerFactory extends ExceptionHandlerFactory {

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/helper/ProcessCompoundsThreadRunner.java

@@ -4,7 +4,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 
-import javax.faces.model.SelectItem;
+import jakarta.faces.model.SelectItem;
 import javax.imageio.ImageIO;
 
 import org.apache.commons.io.FileUtils;

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/validator/PeakListValidator.java

@@ -1,10 +1,10 @@
 package de.ipbhalle.metfragweb.validator;
 
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
 
 import de.ipbhalle.metfraglib.list.DefaultPeakList;
 import de.ipbhalle.metfraglib.peak.TandemMassPeak;

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/validator/PositiveDoubleValueValidator.java

@@ -1,10 +1,10 @@
 package de.ipbhalle.metfragweb.validator;
 
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
 
 public class PositiveDoubleValueValidator implements Validator {
 

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/validator/SearchPPMValidator.java

@@ -1,11 +1,11 @@
 package de.ipbhalle.metfragweb.validator;
 
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
 
 public class SearchPPMValidator implements Validator {
 

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/validator/SmartsExpressionValidator.java

@@ -1,10 +1,10 @@
 package de.ipbhalle.metfragweb.validator;
 
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
 import javax.script.ScriptEngineManager;
 import javax.script.ScriptException;
 

MetFragWeb/src/main/java/de/ipbhalle/metfragweb/validator/SmartsValidator.java

@@ -1,10 +1,10 @@
 package de.ipbhalle.metfragweb.validator;
 
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
 
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;

MetFragWeb/src/main/webapp/WEB-INF/web.xml

@@ -16,16 +16,16 @@
 		<mime-type>application/xml</mime-type>
 	</mime-mapping>
 	<context-param>
-		<param-name>javax.faces.FACELETS_BUFFER_SIZE</param-name>
-		<param-value>65535</param-value>
+		<param-name>jakarta.faces.FACELETS_BUFFER_SIZE</param-name>
+		<param-value>65535</param-value> <!-- 64KB -->
 	</context-param>
 	<context-param>
 		<description>State saving method: 'client' or 'server' (=default). See JSF Specification 2.5.2</description>
-		<param-name>javax.faces.STATE_SAVING_METHOD</param-name>
+		<param-name>jakarta.faces.STATE_SAVING_METHOD</param-name>
 		<param-value>server</param-value>
 	</context-param>
-	<context-param>
-		<param-name>javax.servlet.jsp.jstl.fmt.localizationContext</param-name>
+		<context-param>
+		<param-name>jakarta.servlet.jsp.jstl.fmt.LocalizationContext</param-name>
 		<param-value>resources.application</param-value>
 	</context-param>
 	<context-param>
@@ -34,7 +34,7 @@
 	</context-param>
 	<servlet>
 		<servlet-name>Faces Servlet</servlet-name>
-		<servlet-class>javax.faces.webapp.FacesServlet</servlet-class>
+		<servlet-class>jakarta.faces.webapp.FacesServlet</servlet-class>
 		<load-on-startup>1</load-on-startup>
 	</servlet>
 	<servlet-mapping>
@@ -45,28 +45,16 @@
 		<servlet-name>Faces Servlet</servlet-name>
 		<url-pattern>*.xhtml</url-pattern>
 	</servlet-mapping>
+<!-- 	<context-param> -->
+<!-- 		<param-name>com.sun.faces.expressionFactory</param-name> -->
+<!-- 		<param-value>com.sun.el.ExpressionFactoryImpl</param-value> -->
+<!-- 	</context-param> -->
 	<context-param>
-		<param-name>com.sun.faces.expressionFactory</param-name>
-		<param-value>com.sun.el.ExpressionFactoryImpl</param-value>
-	</context-param>
-	<context-param>
-		<param-name>primefaces.UPLOADER</param-name>
-		<param-value>commons</param-value>
-	</context-param>
-	<context-param>
-		<param-name>facelets.SKIP_COMMENTS</param-name>
+		<param-name>jakarta.faces.FACELETS_SKIP_COMMENTS</param-name>
 		<param-value>true</param-value>
 	</context-param>
-	<filter>
-		<filter-name>PrimeFaces FileUpload Filter</filter-name>
-		<filter-class>org.primefaces.webapp.filter.FileUploadFilter</filter-class>
-	</filter>
-	<filter-mapping>
-		<filter-name>PrimeFaces FileUpload Filter</filter-name>
-		<servlet-name>Faces Servlet</servlet-name>
-	</filter-mapping>
 	<error-page>
-		<exception-type>javax.faces.application.ViewExpiredException</exception-type>
+		<exception-type>jakarta.faces.application.ViewExpiredException</exception-type>
 		<location>/includes/errorpages/viewExpired.xhtml</location>
 	</error-page>
 </web-app>

pom.xml

@@ -113,7 +113,7 @@
 			<dependency>
 				<groupId>org.omnifaces</groupId>
 				<artifactId>omnifaces</artifactId>
-				<version>3.14.6</version>
+				<version>4.5.1</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.commons</groupId>
@@ -129,6 +129,7 @@
 				<groupId>org.primefaces</groupId>
 				<artifactId>primefaces</artifactId>
 				<version>10.0.0</version>
+				<classifier>jakarta</classifier>
 			</dependency>
 			<dependency>
 				<groupId>org.primefaces.themes</groupId>
@@ -138,7 +139,7 @@
 			<dependency>
 				<groupId>jakarta.platform</groupId>
 				<artifactId>jakarta.jakartaee-api</artifactId>
-				<version>8.0.0</version>
+				<version>9.1.0</version>
 				<scope>provided</scope>
 			</dependency>