Everything patched/upgraded except Flywaydb

pom.xml

@@ -5,7 +5,7 @@
   <groupId>no.nibio.vips.model.</groupId>
   <artifactId>VIPSCoreManager</artifactId>
   <packaging>war</packaging>
-  <version>1.0-SNAPSHOT</version>
+  <version>2022.1</version>
 
   <name>VIPSCoreManager</name>
   <url>http://maven.apache.org</url>
@@ -14,48 +14,48 @@
      <dependency>
       <groupId>javax</groupId>
       <artifactId>javaee-web-api</artifactId>
-      <version>8.0</version>
+      <version>8.0.1</version>
       <type>jar</type>
       <scope>provided</scope>
   </dependency>
     <dependency>
       <groupId>org.jboss.resteasy</groupId>
       <artifactId>resteasy-jaxrs</artifactId>
-      <version>3.6.3.Final</version>
+      <version>3.15.3.Final</version>
       <scope>provided</scope> 
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-core</artifactId>
-      <version>2.11.3</version>
+      <version>2.13.1</version>
       <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-annotations</artifactId>
-      <version>2.11.3</version>
+      <version>2.13.1</version>
       <scope>provided</scope>
     </dependency>
     <dependency>
             <groupId>com.fasterxml.jackson.datatype</groupId>
             <artifactId>jackson-datatype-jsr310</artifactId>
-            <version>2.11.3</version>
+            <version>2.13.1</version>
             <type>jar</type>
         </dependency>
      <dependency>
       <groupId>no.nibio.vips.common</groupId>
       <artifactId>VIPSCommon</artifactId>
-      <version>1.0-SNAPSHOT</version>
+      <version>2022.1</version>
     </dependency>
     <dependency>
       <groupId>com.thetransactioncompany</groupId>
       <artifactId>cors-filter</artifactId>
-      <version>1.7.1</version>
+      <version>2.10</version>
     </dependency>
     <dependency>
       <groupId>org.jboss.resteasy</groupId>
       <artifactId>resteasy-client</artifactId>
-      <version>3.6.3.Final</version>
+      <version>5.0.1.Final</version>
       <scope>provided</scope>
     </dependency>
     <dependency>
@@ -66,7 +66,7 @@
     <dependency>
         <groupId>com.bedatadriven</groupId>
         <artifactId>jackson-datatype-jts</artifactId>
-        <version>2.2</version>
+        <version>2.4</version>
       </dependency>
   </dependencies>
 
@@ -75,16 +75,16 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-compiler-plugin</artifactId>
-        <version>2.0.2</version>
+        <version>3.8.1</version>
         <configuration>
-          <source>10</source>
-          <target>10</target>
+          <source>11</source>
+          <target>11</target>
         </configuration>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-javadoc-plugin</artifactId>
-        <version>2.9.1</version>
+        <version>3.3.1</version>
         <configuration>
           <tags>
             <tag>

src/main/java/no/nibio/vips/coremanager/service/ManagerResourceImpl.java

@@ -29,6 +29,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import javax.ejb.EJB;
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.Consumes;
@@ -45,10 +46,10 @@ import javax.ws.rs.core.Context;
 import javax.ws.rs.core.Response;
 import no.nibio.vips.core.service.ModelResource;
 import no.nibio.vips.coremanager.config.JacksonConfig;
-import no.nibio.vips.coremanager.session.ControllerGetter;
 import no.nibio.vips.coremanager.entity.ModelUsageLog;
 import no.nibio.vips.coremanager.entity.VIPSCoreCredentials;
 import no.nibio.vips.coremanager.entity.VipsCoreUser;
+import no.nibio.vips.coremanager.session.UserController;
 import no.nibio.vips.entity.ModelConfiguration;
 import no.nibio.vips.entity.ModelRunRequest;
 import no.nibio.vips.ipmdecisions.IPMDecisionsModelConfiguration;
@@ -74,6 +75,8 @@ public class ManagerResourceImpl implements ManagerResource{
     @Context
     HttpServletRequest servletRequest;
     
+    @EJB
+    private UserController userController;
     
     private InputStream getStaticFileAsInputStream(ServletContext servletContext, String filePath)
     {
@@ -282,7 +285,7 @@ public class ManagerResourceImpl implements ManagerResource{
             Map<String,String> loginInfo  = new HashMap<>();
             loginInfo.put("username", (String)input.get("username"));
             loginInfo.put("password", (String)input.get("password"));
-            VIPSCoreCredentials credentials = ControllerGetter.getUserController().getVIPSCoreCredentials(loginInfo);
+            VIPSCoreCredentials credentials = userController.getVIPSCoreCredentials(loginInfo);
             if(credentials == null)
             {
                 throw new WebApplicationException(Response.status(Response.Status.UNAUTHORIZED).entity("Not accepted!").build());
@@ -307,7 +310,7 @@ public class ManagerResourceImpl implements ManagerResource{
     @Override
     public Response getUsersForOrganization(@PathParam("organizationId") Integer organizationId)
     {
-        List<VipsCoreUser> users = ControllerGetter.getUserController().getVipsCoreUserForOrganization(organizationId);
+        List<VipsCoreUser> users = userController.getVipsCoreUserForOrganization(organizationId);
         return Response.ok().entity(users).build();
     }
     
@@ -328,7 +331,7 @@ public class ManagerResourceImpl implements ManagerResource{
         try
         {
             // First, we authenticate
-            VIPSCoreCredentials credentials = ControllerGetter.getUserController().getVIPSCoreCredentials(request.getLoginInfo());
+            VIPSCoreCredentials credentials = userController.getVIPSCoreCredentials(request.getLoginInfo());
             if(credentials == null)
             {
                 throw new WebApplicationException(Response.status(Response.Status.UNAUTHORIZED).entity("Credentials not accepted").build());
@@ -354,7 +357,7 @@ public class ManagerResourceImpl implements ManagerResource{
                 {
                     throw new WebApplicationException(Response.status(Response.Status.UNAUTHORIZED).entity("Invalid IP address").build());
                 }
-                user = ControllerGetter.getUserController().getVipsCoreUser(request.getVipsCoreUserId());
+                user = userController.getVipsCoreUser(request.getVipsCoreUserId());
             }
             
             ModelUsageLog log = new ModelUsageLog();
@@ -383,13 +386,13 @@ public class ManagerResourceImpl implements ManagerResource{
                 // Log it
                 Integer substrEnd = Math.min(2047, res.length());
                 log.setMessage(res.substring(0,substrEnd));
-                ControllerGetter.getUserController().storeModelUsageLog(log);
+                userController.storeModelUsageLog(log);
                 // Send exception
                 throw new WebApplicationException(Response.status(resp.getStatus()).entity(res).build());
             }
             else
             {
-                ControllerGetter.getUserController().storeModelUsageLog(log);
+                userController.storeModelUsageLog(log);
                 // Assuming that String is the quickest way of forwarding this
                 String resultAsString = resp.readEntity(String.class);
                 return Response.ok().entity(resultAsString).build();

src/main/java/no/nibio/vips/coremanager/session/ControllerGetter.java

-/*
- * Copyright (c) 2014 NIBIO <http://www.nibio.no/>. 
- * 
- * This file is part of VIPSCoreManager.
- * VIPSCoreManager is free software: you can redistribute it and/or modify
- * it under the terms of the NIBIO Open Source License as published by 
- * NIBIO, either version 1 of the License, or (at your option) any
- * later version.
- * 
- * VIPSCoreManager is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * NIBIO Open Source License for more details.
- * 
- * You should have received a copy of the NIBIO Open Source License
- * along with VIPSCoreManager.  If not, see <http://www.nibio.no/licenses/>.
- * 
- */
-
-package no.nibio.vips.coremanager.session;
-
-import javax.naming.InitialContext;
-import javax.naming.NamingException;
-
-/**
- * @copyright 2013 <a href="http://www.nibio.no/">NIBIO</a>
- * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
- */
-public class ControllerGetter {
-    
-    private static final String JNDI_PATH = "java:global/VIPSCoreManager-1.0-SNAPSHOT/";
-
-    public static UserController getUserController()
-    {
-        try
-        {
-            InitialContext ic = new InitialContext();
-            UserController retVal = (UserController) ic.lookup(ControllerGetter.getJndiPath(UserController.class));
-
-            return retVal;
-        }catch(NamingException ne)
-        {
-            System.out.println("Kunne ikke finne " + UserController.class.getSimpleName());
-            return null;
-        }
-    }
-    
-    private static String getJndiPath(Class obj)
-    {
-        String retVal = ControllerGetter.JNDI_PATH + obj.getSimpleName();
-        //System.out.println("JNDI-path=" + retVal);
-        return retVal;
-    }
-}