From e8220359acbb0a3f7371f60e245949e4957ec49b Mon Sep 17 00:00:00 2001
From: Will Mooreston <willm@labkey.com>
Date: Wed, 29 Jan 2025 16:28:01 -0800
Subject: [PATCH] WIP: use jar-base log4j2.xml unless otherwise specified

---
 docker-compose.yml |  8 ++++----
 entrypoint.sh      | 11 ++++++++---
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index eece112..a570a5e 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -81,7 +81,7 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
-      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE}
       - JSON_OUTPUT=${JSON_OUTPUT-false}
       - DD_COLLECT_APM=${DD_COLLECT_APM-false}      
       - SLEEP=${SLEEP:-0}
@@ -193,7 +193,7 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
-      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE}
       - JSON_OUTPUT=${JSON_OUTPUT-false}
       - DD_COLLECT_APM=${DD_COLLECT_APM-false}
       - SLEEP=${SLEEP:-0}
@@ -303,7 +303,7 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
-      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE}
       - JSON_OUTPUT=${JSON_OUTPUT-false}
       - DD_COLLECT_APM=${DD_COLLECT_APM-false}
       - SLEEP=${SLEEP:-0}
@@ -417,7 +417,7 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
-      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE}
       - JSON_OUTPUT=${JSON_OUTPUT-false}
       - DD_COLLECT_APM=${DD_COLLECT_APM-false}
       - SLEEP=${SLEEP:-0}
diff --git a/entrypoint.sh b/entrypoint.sh
index 4cd9b57..41d677f 100755
--- a/entrypoint.sh
+++ b/entrypoint.sh
@@ -15,7 +15,7 @@ LABKEY_CUSTOM_PROPERTIES_S3_URI="${LABKEY_CUSTOM_PROPERTIES_S3_URI:=none}"
 LABKEY_DEFAULT_PROPERTIES_S3_URI="${LABKEY_DEFAULT_PROPERTIES_S3_URI:=none}"
 
 # set below to 'labkeywebapp/WEB-INF/classes/log4j2.xml' to use embedded tomcat version from the built .jar
-LOG4J_CONFIG_FILE="${LOG4J_CONFIG_FILE:=log4j2.xml}"
+LOG4J_CONFIG_FILE="${LOG4J_CONFIG_FILE}"
 
 # below assumes using local log4j2.xml file, as the embedded version is not available for edits until after server is running
 JSON_OUTPUT="${JSON_OUTPUT:-false}"
@@ -231,13 +231,18 @@ main() {
 
   sed -i "s/@@encryptionKey@@/${LABKEY_EK}/" config/application.properties
 
+  export LOG4J_JAVA_OPTION="-Dlog4j.configurationFile=$LOG4J_CONFIG_FILE"
   if [ "$JSON_OUTPUT" = "true" ] && [ "$LOG4J_CONFIG_FILE" = "log4j2.xml" ]; then
     echo "JSON_OUTPUT==true && LOG4J_CONFIG_FILE==log4j2.xml, so updating application.properties and log4j2.xml to output JSON to console"
     sed -i '/<!-- p=priority c=category d=datetime t=thread m=message n=newline -->/d' $LOG4J_CONFIG_FILE
     sed -i 's/<PatternLayout.*\/>/<JSONLayout compact="true" eventEol="true" properties="true" stacktraceAsString="true" \/>/' $LOG4J_CONFIG_FILE
     sed -i 's/^logging.pattern.console/# logging.pattern.console/' config/application.properties
-  else
+  elif [ -n "$LOG4J_CONFIG_FILE" ]; then
     echo "saw JSON_OUTPUT=$JSON_OUTPUT and LOG4J_CONFIG_FILE=$LOG4J_CONFIG_FILE"
+  else
+    # if LOG4J_CONFIG_FILE isn't defined, clear the option so the version included in the jar is used
+    echo "saw JSON_OUTPUT=$JSON_OUTPUT and LOG4J_CONFIG_FILE is undefined, so using jar-based config"
+    export LOG4J_JAVA_OPTION=""
   fi
 
   export DD_JAVA_AGENT=""
@@ -303,7 +308,7 @@ main() {
     -Dlogback.debug="$debug_string" \
     \
     -Dlog4j.debug="$debug_string" \
-    -Dlog4j.configurationFile="$LOG4J_CONFIG_FILE" \
+    ${LOG4J_JAVA_OPTION} \
     \
     -Dorg.apache.catalina.startup.EXIT_ON_INIT_FAILURE=true \
     \