From 331c91bcb3958289f5f9e70efd47b559cfe958ca Mon Sep 17 00:00:00 2001
From: Ryan Doherty <tech@conical.org>
Date: Mon, 11 Nov 2024 00:30:50 -0500
Subject: [PATCH 1/3] Comment out JBrowse build

---
 build.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build.xml b/build.xml
index 6d85c830c..ab750d7c9 100644
--- a/build.xml
+++ b/build.xml
@@ -14,7 +14,6 @@
 
   <target name="ApiCommonWebsite-Installation" depends="EbrcWebSvcCommon-Installation,
                                                         ApiCommonModel-Installation,
-                                                        JBrowse-Installation,
                                                         ApiCommonWebsite/Model-Installation,
                                                         ApiCommonWebsite/View-Installation,
                                                         ApiCommonWebsite/Site-Installation,

From 9a5a64f18aa38b7f86c28f0881d5e4c25ef80e05 Mon Sep 17 00:00:00 2001
From: Ryan Doherty <tech@conical.org>
Date: Mon, 11 Nov 2024 00:38:04 -0500
Subject: [PATCH 2/3] Remove more JBrowse

---
 build.xml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/build.xml b/build.xml
index ab750d7c9..fcffe3690 100644
--- a/build.xml
+++ b/build.xml
@@ -5,7 +5,6 @@
   <!-- oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo -->
 
   <import file="${projectsDir}/EbrcWebSvcCommon/build.xml" />
-  <import file="${projectsDir}/JBrowse/build.xml" />
   <import file="${projectsDir}/ApiCommonModel/build.xml" />
 
   <!-- oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo -->
@@ -87,7 +86,6 @@
   <!-- oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo -->
 
   <target name="ApiCommonWebsite-WebInstallation" depends="EbrcWebSvcCommon-WebInstallation,
-                                                           JBrowse-WebInstallation,
                                                            ApiCommonWebsite-Installation,
                                                            ApiCommonWebsite/View-WebInstallation,
                                                            ApiCommonWebsite/Site-WebInstallation">

From 1e38413e2f73720710d96982bbd0717db7947041 Mon Sep 17 00:00:00 2001
From: Ryan Doherty <tech@conical.org>
Date: Tue, 7 Jan 2025 16:51:31 -0500
Subject: [PATCH 3/3] Changes for Servlet 4.0/Tomcat 9

---
 Model/pom.xml               |  2 +-
 Service/pom.xml             |  7 +------
 Site/webapp/WEB-INF/web.xml | 11 +++--------
 3 files changed, 5 insertions(+), 15 deletions(-)

diff --git a/Model/pom.xml b/Model/pom.xml
index c216d7981..01a23cfca 100644
--- a/Model/pom.xml
+++ b/Model/pom.xml
@@ -91,7 +91,7 @@
 
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
     </dependency>
 
     <dependency>
diff --git a/Service/pom.xml b/Service/pom.xml
index adf94e8c9..4a255eced 100644
--- a/Service/pom.xml
+++ b/Service/pom.xml
@@ -72,7 +72,7 @@
 
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
       <scope>provided</scope>
     </dependency>
 
@@ -86,11 +86,6 @@
       <artifactId>jersey-media-multipart</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>org.glassfish.jersey.core</groupId>
-      <artifactId>jersey-server</artifactId>
-    </dependency>
-
     <dependency>
       <groupId>commons-io</groupId>
       <artifactId>commons-io</artifactId>
diff --git a/Site/webapp/WEB-INF/web.xml b/Site/webapp/WEB-INF/web.xml
index aa5ab0d6c..3f5280146 100644
--- a/Site/webapp/WEB-INF/web.xml
+++ b/Site/webapp/WEB-INF/web.xml
@@ -1,9 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<web-app version="2.4"
-    xmlns="http://java.sun.com/xml/ns/j2ee"
-    xmlns:web="http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+<web-app version="4.0"
+    xmlns="http://xmlns.jcp.org/xml/ns/javaee"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd">
+    xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-app_4_0.xsd">
 
   <context-param>
     <param-name>GUS_HOME</param-name>
@@ -16,10 +15,6 @@
     <param-value>/service</param-value>
   </context-param>
 
-  <listener>
-    <listener-class>se.jiderhamn.classloader.leak.prevention.ClassLoaderLeakPreventorListener</listener-class>
-  </listener>
-
   <listener>
     <listener-class>org.apidb.apicommon.controller.ApplicationInitListener</listener-class>
   </listener>