Firefly 1836 tomcat upgrade

README.md

@@ -71,7 +71,7 @@ There are several branches in the repository.  Here are the ones that you should
  -  [Gradle 8.10] (https://gradle.org/install/)
     Gradle is an open source build automation system.
 
- -  [Tomcat 9] (https://tomcat.apache.org/download-90.cgi)
+ -  [Tomcat 11] (https://tomcat.apache.org/download-11.cgi)
     Apache Tomcat is an open source software implementation of the Java Servlet and JavaServer Pages technologies.
 
  -  [Node v18] (https://nodejs.org/)

build.gradle

@@ -1,24 +1,8 @@
 ext.fireflyPath = rootDir.path
-
-allprojects {
-  defaultTasks 'preselect'
-}
+apply from: "$fireflyPath/buildScript/base.gincl"
 
 subprojects {
   apply plugin: "java"
   apply from: "$fireflyPath/buildScript/global.gincl"
   apply from: "$fireflyPath/buildScript/tasks.gincl"
 }
-
-task purge {
-  description= 'Remove all build files from this project, including node_module.'
-
-  doLast {
-    println('Removes all firefly build directories.')
-    delete "${fireflyPath}/build", "${fireflyPath}/jars/build", "${fireflyPath}/node_modules"
-  }
-}
-
-task preselect {
-  description= 'A placeholder task to designate the task to run for each project.  Similar to defaultTasks.'
-}

buildScript/base.gincl

@@ -0,0 +1,48 @@
+import java.nio.file.Path
+import java.nio.file.Paths
+import java.nio.file.Files
+
+def deleteLink(String filePath) {
+    Path path = Paths.get(filePath)
+    if (Files.exists(path) && Files.isSymbolicLink(path)) {
+            println("Deleting symlink: $filePath")
+            Files.delete(path)   // deletes symlink only
+    }
+}
+
+allprojects {
+    defaultTasks 'preselect'
+}
+
+task preselect {
+    description= 'A placeholder task to designate the task to run for each project.  Similar to defaultTasks.'
+}
+
+task purge {
+    description = 'Removes all build files from this project, including node_modules, Maven cache, and Gradle cache.'
+
+    doLast {
+        println('Removing build directories, including node_modules, Maven cache, and Gradle cache.')
+        delete "${rootDir}/build",
+                "${rootDir}/jars/build",
+                "${rootDir}/node_modules",
+                "${rootDir}/.gradle"
+
+        println('Removing Maven and Gradle caches...')
+        delete "${System.getProperty('user.home')}/.m2/repository",
+                "${System.getProperty('user.home')}/.gradle/caches"
+
+        deleteLink("${rootDir}/yarn.lock")
+        deleteLink("${rootDir}/package.json")
+        deleteLink("${rootDir}/config/test")
+
+    }
+}
+
+task clean {
+    description= 'Removes all build files except installed libraries, e.g. node_modules, Maven cache.'
+    doLast {
+        println('Removing all build directories.')
+        delete "${rootDir}/build", "${rootDir}/jars/build"
+    }
+}

buildScript/dependencies.gradle

@@ -7,15 +7,18 @@ def libPath = "$fireflyPath/jars"
 //project.ext.properties.each{ k, v -> println "${k}:${v}\n" }
 
 repositories {
-    mavenCentral()
     maven {
         url "https://maven.repository.redhat.com/ga/"
+        content {
+            includeGroup "org.josso"
+        }
     }
     flatDir {
         name 'firefly_repo'
         dirs  "$libPath/build",
               "$libPath/starlink"
     }
+    mavenCentral()
 }
 
 configurations {
@@ -35,7 +38,7 @@ dependencies {
     // ============== from maven central ===============
 
     // apache commons
-    implementation 'commons-fileupload:commons-fileupload:1.2.2', 'commons-io:commons-io:2.4', 'commons-lang:commons-lang:2.2', 'org.apache.commons:commons-csv:1.0', 'org.apache.commons:commons-compress:1.28.0'
+    implementation 'commons-io:commons-io:2.4', 'commons-lang:commons-lang:2.2', 'org.apache.commons:commons-csv:1.0', 'org.apache.commons:commons-compress:1.28.0'
 
     // axis  Web Services SOAP
     implementation 'axis:axis:1.4'
@@ -78,7 +81,10 @@ dependencies {
     implementation 'org.reflections:reflections:0.9.11'
 
     // servlet API
-    implementation 'javax.servlet:javax.servlet-api:3.1.0'
+    implementation 'jakarta.servlet:jakarta.servlet-api:6.1.0'
+
+    // FileUpload Jakarta fork for servlet api 6.0+
+    implementation 'org.apache.commons:commons-fileupload2-jakarta:2.0.0-M1'
 
     // spring jdbc
     implementation 'org.springframework:spring-jdbc:2.5.5'
@@ -91,7 +97,7 @@ dependencies {
     implementation 'javax.validation:validation-api:1.1.0.Final'
 
     // websocket
-    implementation 'javax.websocket:javax.websocket-api:1.1'
+    implementation 'jakarta.platform:jakarta.jakartaee-web-api:10.0.0'
 
     // junit for java test
     implementation 'junit:junit:4.12'

config/web.xml

@@ -27,23 +27,6 @@
         <url-pattern>/firefly_loader.js</url-pattern>
     </filter-mapping>
 
-    <!--GZipFilter-->
-    <filter>
-        <filter-name>GZipFilter</filter-name>
-        <filter-class>net.sf.ehcache.constructs.web.filter.GzipFilter</filter-class>
-    </filter>
-    <filter-mapping>
-        <filter-name>GZipFilter</filter-name>
-        <url-pattern>*.html</url-pattern>
-        <url-pattern>*.css</url-pattern>
-        <url-pattern>*.js</url-pattern>
-        <url-pattern>/sticky/CmdSrv</url-pattern>
-        <url-pattern>/CmdSrv/sync</url-pattern>
-        <url-pattern>/CmdSrv/async</url-pattern>
-        <url-pattern>/CmdSrv/async/*</url-pattern>
-        <url-pattern>/sticky/firefly/events</url-pattern>
-    </filter-mapping>
-
     <!--CORS Filter-->
     <filter>
         <filter-name>CorsFilter</filter-name>

docker/Dockerfile

@@ -38,7 +38,7 @@ RUN apt-get update \
 # cleanup
     && rm -rf /var/lib/apt/lists/*;
 
-COPY --from=tomcat:9.0-jre21-temurin-jammy /usr/local/tomcat /usr/local/tomcat
+COPY --from=tomcat:11.0.11-jre21-temurin-jammy /usr/local/tomcat /usr/local/tomcat
 
 
 ENV CATALINA_HOME=/usr/local/tomcat \
@@ -106,7 +106,7 @@ RUN gradle -Penv=${env} -PBranchOverride=${BranchOverride} ${target}
 # /external                 : default external data directory visible to Firefly
 
 
-FROM tomcat:9.0-jre21-temurin-jammy
+FROM tomcat:11.0.11-jre21-temurin-jammy
 
 ARG build_dir
 ARG user=tomcat
@@ -164,6 +164,13 @@ COPY firefly/docker/local.xml conf/Catalina/localhost
 #copy all wars, typically there should only be one
 COPY --from=builder /opt/work/${build_dir}/build/dist/*.war ${CATALINA_HOME}/webapps-ref/
 
+# Turn on GZIP compression by adding these attributes to the Tomcat connector:
+# - compression="on" → turn on response compression
+# - useSendfile="false" →  avoids bypassing compression for static files
+# - compressibleMimeType → list of text-based formats to compress (HTML, CSS, JS, JSON, VOTable, XML, CSV, SVG, Fonts)
+RUN sed -i 's/<Connector port="8080" protocol="HTTP\/1.1"/<Connector port="8080" protocol="HTTP\/1.1" compression="on" useSendfile="false" compressibleMimeType="text\/html,text\/plain,text\/css,text\/javascript,application\/javascript,application\/json,application\/xml,text\/xml,application\/x-votable+xml,application\/x-yaml,application\/ld+json,image\/svg+xml,text\/csv,application\/xhtml+xml,application\/rss+xml,application\/atom+xml,application\/x-font-ttf,font\/otf,font\/woff,font\/woff2"/' \
+    $CATALINA_HOME/conf/server.xml
+
 # preinstall DuckDB extensions; remember to update version when DuckDB is updated
 ARG DUCKDB_TARGET=v1.1.3/linux_amd64_gcc4
 RUN mkdir -p temp/$DUCKDB_TARGET \

gradle.properties

@@ -1 +1,2 @@
 org.gradle.jvmargs=-Xms256m -Xmx8048m
+org.gradle.daemon=false

src/firefly/java/edu/caltech/ipac/firefly/api/Async.java

@@ -15,9 +15,9 @@
 import edu.caltech.ipac.firefly.core.background.JobInfo;
 import edu.caltech.ipac.firefly.core.background.JobManager;
 
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.time.Instant;
 import java.util.Comparator;
 import java.util.List;

src/firefly/java/edu/caltech/ipac/firefly/server/RequestAgent.java

@@ -6,9 +6,9 @@
 import edu.caltech.ipac.firefly.server.util.Logger;
 import edu.caltech.ipac.util.StringUtils;
 
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.Cookie;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;

src/firefly/java/edu/caltech/ipac/firefly/server/RequestOwner.java

@@ -13,7 +13,7 @@
 import edu.caltech.ipac.util.AppProperties;
 import edu.caltech.ipac.util.cache.StringKey;
 
-import javax.servlet.http.Cookie;
+import jakarta.servlet.http.Cookie;
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;

src/firefly/java/edu/caltech/ipac/firefly/server/ServCommand.java

@@ -6,9 +6,9 @@
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import edu.caltech.ipac.firefly.server.util.Logger;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 /**
  * Date: 10/24/16

src/firefly/java/edu/caltech/ipac/firefly/server/ServerCommandAccess.java

@@ -19,8 +19,8 @@
 import edu.caltech.ipac.firefly.server.ws.WsServerCommands;
 import edu.caltech.ipac.firefly.core.background.Job;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.util.HashMap;
 import java.util.Map;
 

src/firefly/java/edu/caltech/ipac/firefly/server/ServerContext.java

@@ -19,14 +19,13 @@
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 
-import javax.servlet.ServletContext;
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-import javax.servlet.annotation.WebListener;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import javax.websocket.HandshakeResponse;
-import javax.websocket.server.HandshakeRequest;
+import jakarta.servlet.ServletContext;
+import jakarta.servlet.ServletContextEvent;
+import jakarta.servlet.ServletContextListener;
+import jakarta.servlet.annotation.WebListener;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.websocket.server.HandshakeRequest;
 import java.io.File;
 import java.io.IOException;
 import java.lang.management.ManagementFactory;
@@ -401,15 +400,6 @@ public static RequestAgent getHttpRequestAgent(HttpServletRequest request, HttpS
         return new RequestAgent.HTTP(request, response);
     }
 
-    public static RequestAgent getWsRequestAgent(HandshakeRequest request, HandshakeResponse response) {
-        // this is an abstraction point.  this class can be loaded from configuration.
-        if (request instanceof HttpServletRequest) {
-            return new RequestAgent.HTTP((HttpServletRequest) request, (HttpServletResponse) response);
-        } else {
-            return null;
-        }
-    }
-
     //====================================================================
     //
     //====================================================================

src/firefly/java/edu/caltech/ipac/firefly/server/events/WebsocketConnector.java

@@ -9,13 +9,13 @@
 import edu.caltech.ipac.firefly.server.util.Logger;
 import edu.caltech.ipac.firefly.util.event.Name;
 
-import javax.websocket.CloseReason;
-import javax.websocket.OnClose;
-import javax.websocket.OnError;
-import javax.websocket.OnMessage;
-import javax.websocket.OnOpen;
-import javax.websocket.Session;
-import javax.websocket.server.ServerEndpoint;
+import jakarta.websocket.CloseReason;
+import jakarta.websocket.OnClose;
+import jakarta.websocket.OnError;
+import jakarta.websocket.OnMessage;
+import jakarta.websocket.OnOpen;
+import jakarta.websocket.Session;
+import jakarta.websocket.server.ServerEndpoint;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;

src/firefly/java/edu/caltech/ipac/firefly/server/filters/CommonFilter.java

@@ -10,9 +10,9 @@
 import edu.caltech.ipac.firefly.server.util.StopWatch;
 import edu.caltech.ipac.util.cache.CacheManager;
 
-import javax.servlet.*;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.*;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 

src/firefly/java/edu/caltech/ipac/firefly/server/filters/CorsFilter.java

@@ -3,14 +3,14 @@
  */
 package edu.caltech.ipac.firefly.server.filters;
 
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.Filter;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.FilterConfig;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
 

src/firefly/java/edu/caltech/ipac/firefly/server/filters/NoCacheFilter.java

@@ -3,13 +3,13 @@
  */
 package edu.caltech.ipac.firefly.server.filters;
 
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.Filter;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.FilterConfig;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.util.Date;
 

src/firefly/java/edu/caltech/ipac/firefly/server/query/SearchServerCommands.java

@@ -38,8 +38,8 @@
 import edu.caltech.ipac.util.StringUtils;
 import org.json.simple.JSONObject;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.math.BigInteger;

src/firefly/java/edu/caltech/ipac/firefly/server/rpc/VisServerCommands.java

@@ -21,8 +21,8 @@
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;