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fix log4j config logic #166

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Merged
labkey-willm merged 2 commits into from
Jan 28, 2026
Merged

fix log4j config logic #166

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00cc86a
fix log4j config logic to not break when not using json; remove comme…
labkey-willm Jan 27, 2026
3805fdb
remove rest of legacy logging options from application.properties
labkey-willm Jan 28, 2026
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62 changes: 0 additions & 62 deletions application.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -12,68 +12,6 @@ spring.main.banner-mode=off
spring.application.name=labkey
server.servlet.application-display-name=labkey

# logging.pattern.console=
logging.pattern.console=%clr(%d{yyyy-MM-dd HH:mm:ss.SSS}){faint} E %clr(%-5.5p) %clr(%5.5replace(%p){'.+', ${PID:-}}){magenta} %clr(---){faint} %clr([%15.15t]){faint} %clr(${LOGGER_PATTERN:-%-40.40logger{39}}){cyan} %clr(:){faint} %m%n%wEx

logging.level.root=WARN

# custom tomcat group
logging.group.tomcat=org.apache.catalina, org.apache.coyote, org.apache.tomcat
logging.level.tomcat=${LOG_LEVEL_TOMCAT}

logging.level.org.apache.coyote.http2=OFF

# default groups
logging.level.web=${LOG_LEVEL_SPRING_WEB}
logging.level.sql=${LOG_LEVEL_SQL}

logging.level.net.sf.ehcache=ERROR

# logging.level.org.apache=TRACE
# logging.level.org.apache.catalina.core.Catalina=TRACE
logging.level.org.apache.catalina.core.ContainerBase.[Tomcat].[localhost]=TRACE
# logging.level.org.apache.catalina.core=TRACE
# logging.level.org.apache.catalina.LifecycleException=TRACE
logging.level.org.apache.catalina.loader.WebappClassLoaderBase=OFF
# logging.level.org.apache.catalina.session=TRACE
# logging.level.org.apache.catalina.startup.ContextConfig=OFF
# logging.level.org.apache.catalina.util.LifecycleBase=TRACE
# logging.level.org.apache.catalina.util=TRACE
# logging.level.org.apache.catalina=TRACE
# logging.level.org.apache.coyote=TRACE
# logging.level.org.apache.logging.log4j.core.net=TRACE
# logging.level.org.apache.naming=OFF
logging.level.org.apache.tomcat.util.IntrospectionUtils=OFF
# logging.level.org.apache.tomcat.util.net=TRACE
logging.level.org.apache.tomcat.util.scan=OFF
# logging.level.org.apache.tomcat.util=TRACE
logging.level.org.labkey.embedded.LabKeyServer=DEBUG
logging.level.org.springframework.boot.autoconfigure.logging.ConditionEvaluationReportLoggingListener=OFF
# logging.level.org.springframework.boot.autoconfigure=OFF
# logging.level.org.springframework.boot.context.embedded.tomcat.TomcatEmbeddedServletContainer=TRACE
# logging.level.org.springframework.boot.web.embedded.tomcat.TomcatWebServer=TRACE
# logging.level.org.springframework.boot.web.servlet.context=TRACE
# logging.level.org.springframework.boot.web.servlet=WARN
#logging.level.org.springframework.boot=INFO

logging.level.org.springframework.jdbc.core=WARN
logging.level.org.hibernate.SQL=WARN
logging.level.org.jooq.tools.LoggerListener=WARN
logging.level.org.springframework.core.codec=WARN
logging.level.org.springframework.http=WARN
logging.level.org.springframework.web=WARN
logging.level.org.springframework.boot.actuate.endpoint.web=WARN
logging.level.org.springframework.boot.web.servlet.ServletContextInitializerBeans=WARN
logging.level.org.springframework.boot=WARN

# logging.level.org.apache.catalina.loader.WebappClassLoaderBase=INFO
logging.level.org.apache.jasper.servlet.TldScanner=WARN
logging.level.org.apache.tomcat.util.digester.Digester=INFO

# logging.level.org.apache.tomcat.util.scan.StandardJarScanner=INFO
# logging.level.org.springframework.boot.autoconfigure.condition=INFO
# logging.level.org.springframework.core.env.PropertySourcesPropertyResolver=INFO

context.resources.jdbc.labkeyDataSource.type=javax.sql.DataSource
context.resources.jdbc.labkeyDataSource.driverClassName=org.postgresql.Driver
# context.resources.jdbc.labkeyDataSource.url=jdbc:postgresql://${POSTGRES_HOST:-localhost}:${POSTGRES_PORT:-5432}/${POSTGRES_DB:-${POSTGRES_USER}}${POSTGRES_PARAMETERS:-}
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17 changes: 9 additions & 8 deletions entrypoint.sh
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Expand Up @@ -15,7 +15,6 @@ LABKEY_CUSTOM_PROPERTIES_S3_URI="${LABKEY_CUSTOM_PROPERTIES_S3_URI:=none}"
LABKEY_OPTIONAL_APP_PROPERTIES_S3_URI="${LABKEY_OPTIONAL_APP_PROPERTIES_S3_URI:=none}"
LABKEY_DEFAULT_PROPERTIES_S3_URI="${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}"

# below assumes using local log4j2.xml file, as the embedded version is not available for edits until after server is running
Expand Down Expand Up @@ -226,20 +225,22 @@ main() {

sed -i "s/@@encryptionKey@@/${LABKEY_EK}/" config/application.properties

# Check if we want JSON output, we are using the base log4j2.xml config
# Check if we want JSON output, and/or if we are using the base log4j2.xml config
export LOG4J_CONFIG_OPTION=""
if [ "${JSON_OUTPUT}" = "true" ] && [ "${LOG4J_CONFIG_FILE}" = "log4j2.xml" ]; then
echo "JSON_OUTPUT==true && LOG4J_CONFIG_FILE==log4j2.xml, so using the base log4j2.xml with labkey.log4j2.xml overrides, to send JSON output to console"
LOG4J_CONFIG_FILE="log4j2.xml, config/labkey.log4j2.xml"
echo "Log4j configuration files: $LOG4J_CONFIG_FILE"
export LOG4J_CONFIG_OPTION="-Dlog4j.configurationFile=log4j2.xml,config/labkey.log4j2.xml"
# if the override file exists and isn't empty, use that to override whatever was set in LOG4J_CONFIG_FILE (which might still be server default of log4j2.xml)
elif [ -f "config/${LOG4J_CONFIG_OVERRIDE}" ] && [ -s "config/${LOG4J_CONFIG_OVERRIDE}" ]; then
echo "LOG4J_CONFIG_OVERRIDE==${LOG4J_CONFIG_OVERRIDE}, so using that to override default settings in LOG4J_CONFIG_FILE (${LOG4J_CONFIG_FILE})"
LOG4J_CONFIG_FILE="${LOG4J_CONFIG_FILE:=log4j2.xml},config/${LOG4J_CONFIG_OVERRIDE}"
echo "Log4j configuration files: $LOG4J_CONFIG_FILE"
else
export LOG4J_CONFIG_OPTION="-Dlog4j.configurationFile=${LOG4J_CONFIG_FILE:=log4j2.xml},config/${LOG4J_CONFIG_OVERRIDE}"
elif [ "${LOG4J_CONFIG_FILE}" = "log4j2.xml" ]; then
echo "saw JSON_OUTPUT=$JSON_OUTPUT and LOG4J_CONFIG_FILE=$LOG4J_CONFIG_FILE and LOG4J_CONFIG_OVERRIDE=$LOG4J_CONFIG_OVERRIDE (which, if defined, was empty)"
echo "... so configuring nothing for LOG4J_CONFIG_OPTION"
fi

echo "Log4j configuration option(s): $LOG4J_CONFIG_OPTION"

export DD_JAVA_AGENT=""
export DD_JMX=""
if [ "$DD_COLLECT_APM" = "true" ]; then
Expand Down Expand Up @@ -315,7 +316,7 @@ main() {
-Dlogback.debug="$debug_string" \
\
-Dlog4j.debug="$debug_string" \
-Dlog4j.configurationFile="$LOG4J_CONFIG_FILE" \
${LOG4J_CONFIG_OPTION} \
\
-Dorg.apache.catalina.startup.EXIT_ON_INIT_FAILURE=true \
\
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2 changes: 1 addition & 1 deletion quickstart_envs.sh
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Expand Up @@ -3,7 +3,7 @@
# example minimal set of environment variables to get started - see readme for additional envs you may wish to set

# embedded tomcat LabKey .jar version to build container with
export LABKEY_VERSION="26.1"
export LABKEY_VERSION="26.2"

# minimal SMTP settings
export SMTP_HOST="localhost"
Expand Down