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use jar-base log4j2.xml unless otherwise specified #134

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use jar-base log4j2.xml unless otherwise specified #134

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8 changes: 4 additions & 4 deletions docker-compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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}
Expand Down Expand Up @@ -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}
Expand Down Expand Up @@ -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}
Expand Down Expand Up @@ -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=${SLEEP:-0}
Expand Down
11 changes: 8 additions & 3 deletions entrypoint.sh
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Expand Up @@ -15,7 +15,7 @@ LABKEY_CUSTOM_PROPERTIES_S3_URI="${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}"
Expand Down Expand Up @@ -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=""
Expand Down Expand Up @@ -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 \
\
Expand Down