From 12439166aad6a7dad047b00187369387baacfbf1 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Tue, 14 Apr 2020 12:04:16 +0200
Subject: [PATCH 1/4] Upgrade to Jakarta EE 8, including Mojarra (JSF) 2.3
 dependency upgrade. #4260

---
 pom.xml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/pom.xml b/pom.xml
index 91eaac30544..bb66b9bb293 100644
--- a/pom.xml
+++ b/pom.xml
@@ -24,6 +24,10 @@
         -->
         <argLine>-Duser.timezone=${project.timezone} -Dfile.encoding=${project.build.sourceEncoding} -Duser.language=${project.language} -Duser.region=${project.region}</argLine>
         <skipUnitTests>false</skipUnitTests>
+        
+        <jakartaee-api.version>8.0.0</jakartaee-api.version>
+        <!-- Make this correspond to the version used in Payara: 5.201 uses (patched) 2.3.14 -->
+        <mojarra.version>2.3.14</mojarra.version>
         <aws.version>1.11.172</aws.version>
         <jackson.version>2.9.6</jackson.version>
         <commons.logging.version>1.2</commons.logging.version>
@@ -289,15 +293,15 @@
             <type>jar</type>
         </dependency>
         <dependency>
-            <groupId>javax</groupId>
-            <artifactId>javaee-api</artifactId>
-            <version>7.0</version>
+            <groupId>jakarta.platform</groupId>
+            <artifactId>jakarta.jakartaee-api</artifactId>
+            <version>${jakartaee-api.version}</version>
             <scope>provided</scope>
         </dependency>
         <dependency>
-            <groupId>javax</groupId>
-            <artifactId>javaee-web-api</artifactId>
-            <version>7.0</version>
+            <groupId>org.glassfish</groupId>
+            <artifactId>jakarta.faces</artifactId>
+            <version>${mojarra.version}</version>
             <scope>provided</scope>
         </dependency>
         <dependency>

From 38166cd8b58fc5d9f0df4124b09a9e220b60268a Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Tue, 14 Apr 2020 12:16:39 +0200
Subject: [PATCH 2/4] Move all testing related dependencies into ONE place in
 pom.xml.

---
 pom.xml | 108 +++++++++++++++++++++++++++++---------------------------
 1 file changed, 56 insertions(+), 52 deletions(-)

diff --git a/pom.xml b/pom.xml
index bb66b9bb293..75934b90aa4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -138,40 +138,6 @@
             <artifactId>passay</artifactId>
             <version>1.1.0</version>
         </dependency>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter</artifactId>
-            <version>${junit.jupiter.version}</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>${junit.version}</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.junit.vintage</groupId>
-            <artifactId>junit-vintage-engine</artifactId>
-            <version>${junit.vintage.version}</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-library</artifactId>
-            <version>2.2</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.testcontainers</groupId>
-            <artifactId>testcontainers</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.testcontainers</groupId>
-            <artifactId>junit-jupiter</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.glassfish</groupId>
             <artifactId>javax.json</artifactId>
@@ -447,12 +413,6 @@
             <artifactId>jsoup</artifactId>
             <version>1.11.3</version>
         </dependency>
-        <dependency>
-            <groupId>com.jayway.restassured</groupId>
-            <artifactId>rest-assured</artifactId>
-            <version>2.4.0</version>
-            <scope>test</scope>
-        </dependency>
         <!-- Added specific versionf of SLF4J jars; otherwise we end up with
         conflicting versions of slf4j-api and slf4j-log4j12, loaded as
         dependencies for different packages; which was causing some incompatibility
@@ -467,18 +427,6 @@
             <artifactId>slf4j-log4j12</artifactId>
             <version>1.7.7</version>
         </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-core</artifactId>
-            <version>${mockito.version}</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-junit-jupiter</artifactId>
-            <version>${mockito.version}</version>
-            <scope>test</scope>
-        </dependency>
         <!-- Added for DataCite -->
         <!--dependency>
             <groupId>org.slf4j</groupId>
@@ -631,6 +579,62 @@
             <artifactId>opennlp-tools</artifactId>
             <version>1.9.1</version>
         </dependency>
+        
+        
+        <!-- TESTING DEPENDENCIES -->
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>${junit.jupiter.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>${junit.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.vintage</groupId>
+            <artifactId>junit-vintage-engine</artifactId>
+            <version>${junit.vintage.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-library</artifactId>
+            <version>2.2</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.jayway.restassured</groupId>
+            <artifactId>rest-assured</artifactId>
+            <version>2.4.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>testcontainers</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
+            <version>${mockito.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-junit-jupiter</artifactId>
+            <version>${mockito.version}</version>
+            <scope>test</scope>
+        </dependency>
+        
     </dependencies>
     <build>
         <!--        <testResources>

From a30040692a0dc8ccc4160abb57614cf6f006e340 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Tue, 14 Apr 2020 12:54:58 +0200
Subject: [PATCH 3/4] Primefaces removed Atmoshphere used by Push with PF6.2+.

See also https://www.primefaces.org/primefaces-6-2-roadmap
and https://github.com/primefaces/primefaces/issues/3385

Removing this completely unused dependency.
---
 pom.xml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/pom.xml b/pom.xml
index 75934b90aa4..131e5ceab3f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -280,11 +280,6 @@
             <artifactId>all-themes</artifactId>
             <version>1.0.10</version>
         </dependency>
-        <dependency>
-            <groupId>org.atmosphere</groupId>
-            <artifactId>atmosphere-runtime</artifactId>
-            <version>2.4.2</version>
-        </dependency>
         <dependency>
             <groupId>org.omnifaces</groupId>
             <artifactId>omnifaces</artifactId>

From c0d24b0ed3d5040de376ee223d552ffeab5edd62 Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Fri, 17 Apr 2020 15:39:49 +0200
Subject: [PATCH 4/4] Refactor deprecated javax.faces.bean usages. #4260

---
 .../java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java   | 2 +-
 .../iq/dataverse/harvest/client/HarvesterServiceBean.java       | 2 --
 .../java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java | 2 --
 3 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java b/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java
index 121a1bd79d6..2f987dde82b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java
@@ -6,7 +6,7 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
-import javax.faces.bean.SessionScoped;
+import javax.enterprise.context.SessionScoped;
 import javax.faces.context.FacesContext;
 import javax.inject.Named;
 import javax.json.JsonObject;
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
index 9d0ee40d9d3..0d15c900ba3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
@@ -27,7 +27,6 @@
 import javax.ejb.EJBException;
 import javax.ejb.Stateless;
 import javax.ejb.Timer;
-import javax.faces.bean.ManagedBean;
 import javax.inject.Named;
 //import javax.xml.bind.Unmarshaller;
 import javax.xml.parsers.ParserConfigurationException;
@@ -54,7 +53,6 @@
  */
 @Stateless(name = "harvesterService")
 @Named
-@ManagedBean
 public class HarvesterServiceBean {
     @PersistenceContext(unitName="VDCNet-ejbPU")
     private EntityManager em;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
index 6c2e9944b1a..6743c19875a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
@@ -110,7 +110,6 @@
 import javax.jms.QueueSender;
 import javax.jms.QueueSession;
 import javax.jms.Message;
-import javax.faces.bean.ManagedBean;
 import javax.faces.application.FacesMessage;
 
 /**
@@ -122,7 +121,6 @@
  */
 @Stateless
 @Named
-@ManagedBean
 public class IngestServiceBean {
     private static final Logger logger = Logger.getLogger(IngestServiceBean.class.getCanonicalName());
     @EJB