Upgrade to tommee 9, move to jakarta namespace, add deprecated aristo…

… theme to primefaces, remove incompatible commons-fileupload, upgrade required dependencies.
ipb-halle · Oct 18, 2024 · 56b72d7 · 56b72d7
1 parent 2183a4d
commit 56b72d7
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diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -2,30 +2,43 @@ name: Docker Image
 
 on:
   push:
-    branches: [ master ]
+    branches:
+      - 'master'
+      - 'dev'
+    tags:
+      - 'v*'
 
 jobs:
   docker:
-
     runs-on: ubuntu-latest
 
     steps:
+      - name: Checkout
+        uses: actions/checkout@v4
       - name: Log in to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v3
+        uses: docker/metadata-action@v5
         with:
           images: ipbhalle/metfragweb
+          tags: |
+            # tag event
+            type=ref,event=tag
+            # set latest tag for main branch and tags
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/') }}
+            # set dev tag for dev branch
+            type=raw,value=dev,enable=${{ github.ref == 'refs/heads/dev'}}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
-          push: true
-          tags: ipbhalle/metfragweb:latest
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=registry,ref=ipbhalle/metfragweb:latest
           cache-to: type=inline
diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,7 @@ LocalDatabasesFolderForWeb = /vol/file_databases' > /MetFragRelaunched/MetFragWe
 RUN mvn -Dhttps.protocols=TLSv1.2 -f MetFragRelaunched clean package -pl MetFragLib -pl MetFragWeb -am -DskipTests
 
 
-FROM tomee:8.0.15
+FROM tomee:9
 
 RUN set -eux; \
 	apt-get update; \

diff --git a/MetFragLib/pom.xml b/MetFragLib/pom.xml
@@ -74,10 +74,6 @@
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
 		</dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-core</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.openjdk.nashorn</groupId>
             <artifactId>nashorn-core</artifactId>

diff --git a/MetFragLib/src/main/java/de/ipbhalle/metfraglib/settings/MetFragGlobalSettings.java b/MetFragLib/src/main/java/de/ipbhalle/metfraglib/settings/MetFragGlobalSettings.java
@@ -167,7 +167,8 @@ public static MetFragGlobalSettings readSettings(java.io.File parameterFile, Log
 			 * check whether the current parameter has already been defined
 			 */
 			if (setParameters.contains(tmp[0].trim())) {
-				logger.error(tmp[0].trim() + " was already defined in the parameter file.");
+				if (logger != null)
+                	logger.error(tmp[0].trim() + " was already defined in the parameter file.");
 				parameterFileReader.close();
 				throw new Exception();
 			}
@@ -181,7 +182,8 @@ public static MetFragGlobalSettings readSettings(java.io.File parameterFile, Log
 				settings.set(tmp[0].trim(), ParameterDataTypes.getParameter(valueString.trim(), tmp[0].trim()));
 			}
 			catch(Exception e) {
-				logger.error("Error in parameter file at \"" + line + " \"");
+				if (logger != null)
+					logger.error("Error in parameter file at \"" + line + " \"");
 				parameterFileReader.close();
 				throw new Exception("Error in parameter file at \"" + line + " \"");
 			}

diff --git a/MetFragWeb/pom.xml b/MetFragWeb/pom.xml
@@ -21,7 +21,7 @@
 				<version>1.9.13</version>
 				<configuration>
 					<container>
-						<containerId>tomee8x</containerId>
+						<containerId>tomee9x</containerId>
 					</container>
 					<deployables>
 						<deployable>
@@ -54,13 +54,14 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-email</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>commons-fileupload</groupId>
-			<artifactId>commons-fileupload</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>jakarta.platform</groupId>
@@ -74,5 +75,10 @@
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.primefaces.themes</groupId>
+			<artifactId>aristo</artifactId>
+			<version>1.1.0</version>
+		</dependency>
 	</dependencies>
 </project>
diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/container/AvailableParameters.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/container/AvailableParameters.java
@@ -7,8 +7,8 @@
 import java.util.Comparator;
 import java.util.Hashtable;
 
-import javax.faces.model.SelectItem;
-import javax.faces.model.SelectItemGroup;
+import jakarta.faces.model.SelectItem;
+import jakarta.faces.model.SelectItemGroup;
 
 import de.ipbhalle.metfraglib.parameter.ClassNames;
 import de.ipbhalle.metfraglib.parameter.Constants;

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/container/BeanSettingsContainer.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/container/BeanSettingsContainer.java
@@ -6,9 +6,9 @@
 import java.util.HashMap;
 import java.util.List;
 
-import javax.faces.context.FacesContext;
-import javax.faces.model.SelectItem;
-import javax.servlet.ServletContext;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.model.SelectItem;
+import jakarta.servlet.ServletContext;
 
 import org.apache.log4j.Level;
 import org.primefaces.model.chart.AxisType;

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/CompareSpectraD3JSBean.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/CompareSpectraD3JSBean.java
@@ -4,14 +4,14 @@
 import java.io.IOException;
 import java.util.Random;
 
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.SessionScoped;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
+import jakarta.faces.bean.ManagedBean;
+import jakarta.faces.bean.SessionScoped;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
 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.openscience.cdk.exception.CDKException;

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragLandingBean.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragLandingBean.java
@@ -1,15 +1,15 @@
 package de.ipbhalle.metfragweb.controller;
 
-import javax.annotation.PostConstruct;
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.RequestScoped;
-import javax.faces.context.FacesContext;
+import jakarta.annotation.PostConstruct;
+import jakarta.faces.bean.ManagedBean;
+import jakarta.faces.bean.RequestScoped;
+import jakarta.faces.context.FacesContext;
 
 import de.ipbhalle.metfraglib.parameter.Constants;
 import de.ipbhalle.metfraglib.parameter.VariableNames;
 import de.ipbhalle.metfragweb.datatype.Parameter;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import org.primefaces.PrimeFaces;
 

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragWebBean.java b/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;
@@ -31,6 +31,7 @@
 import org.primefaces.event.organigram.OrganigramNodeSelectEvent;
 import org.primefaces.model.OrganigramNode;
 import org.primefaces.model.StreamedContent;
+import org.primefaces.model.DefaultStreamedContent;
 import org.primefaces.model.chart.AxisType;
 import org.primefaces.model.chart.LineChartModel;
 import org.primefaces.model.chart.LineChartSeries;
@@ -276,7 +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();
 	}
 
@@ -907,7 +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();
 	}
 
@@ -1069,7 +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();
 	}
 
@@ -1813,11 +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();
 	}
 
@@ -2013,7 +2014,7 @@ public org.primefaces.model.StreamedContent getDownloadParameters() {
 		try {
 			resource = this.beanSettingsContainer.getUserOutputDataHandler().getDownloadParameters(this.errorMessages, pathToProperties);
 		} catch(Exception e) {
-			resource = new org.primefaces.model.DefaultStreamedContent(System.in, "application/zip", "MetFragWeb_Parameters.zip");
+			resource = DefaultStreamedContent.builder().contentType("application/zip").name("MetFragWeb_Parameters.zip").stream(() -> System.in).build();
 		}
 		return resource;
 	}
@@ -2702,7 +2703,7 @@ public void closeScoresView() {
 	 * @return
 	 */
 	public org.primefaces.model.StreamedContent generateCandidateDownloadFile() {
-		org.primefaces.model.StreamedContent resource = new org.primefaces.model.DefaultStreamedContent(System.in, "application/vnd.ms-excel", "MetFragWeb_Candidate.xls" );
+		org.primefaces.model.StreamedContent resource = DefaultStreamedContent.builder().contentType("application/vnd.ms-excel").name("MetFragWeb_Candidate.xls").stream(() -> System.in).build();
 		try {
 			resource = this.beanSettingsContainer.getUserOutputDataHandler().generatedCandidateDownloadFile(this.currentScoreCandidate, this.beanSettingsContainer.getMetFragSettings());
 		} catch (Exception e1) {
@@ -3005,7 +3006,7 @@ 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

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/datatype/AvailableScore.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/datatype/AvailableScore.java
@@ -2,7 +2,7 @@
 
 import java.io.Serializable;
 
-import javax.faces.model.SelectItem;
+import jakarta.faces.model.SelectItem;
 
 public class AvailableScore extends SelectItem implements Serializable, Comparable<AvailableScore> {
 

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/datatype/CandidateStatistics.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/datatype/CandidateStatistics.java
@@ -2,7 +2,7 @@
 
 import java.util.List;
 
-import javax.faces.model.SelectItem;
+import jakarta.faces.model.SelectItem;
 
 import org.primefaces.model.chart.AxisType;
 import org.primefaces.model.chart.LineChartModel;

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/datatype/DownloadResource.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/datatype/DownloadResource.java
@@ -7,8 +7,8 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.faces.application.Resource;
-import javax.faces.context.FacesContext;
+import jakarta.faces.application.Resource;
+import jakarta.faces.context.FacesContext;
 
 public class DownloadResource extends Resource implements java.io.Serializable {
 

diff --git a/.../src/main/java/de/ipbhalle/metfragweb/exception/ViewExpiredExceptionExceptionHandler.java b/.../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;
 

diff --git a/...in/java/de/ipbhalle/metfragweb/exception/ViewExpiredExceptionExceptionHandlerFactory.java b/...in/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 {

diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/helper/ProcessCompoundsThreadRunner.java b/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;