enable optional JSON logging to console

application.properties

@@ -18,7 +18,7 @@ logging.pattern.console=%clr(%d{yyyy-MM-dd HH:mm:ss.SSS}){faint} E %clr(%-5.5p)
 logging.level.root=WARN
 
 # custom tomcat group
-logging.group.tomcat=org.apache.catalina,org.apache.coyote,org.apache.tomcat
+logging.group.tomcat=org.apache.catalina, org.apache.coyote, org.apache.tomcat
 logging.level.tomcat=${LOG_LEVEL_TOMCAT:OFF}
 
 logging.level.org.apache.coyote.http2=OFF
@@ -97,20 +97,21 @@ context.validationQuery[0]=${POSTGRES_VALIDATION_QUERY:-SELECT 1}
 # context.username[1]=@@extraJdbcUser@@
 # context.password[1]=@@extraJdbcPassword@@
 
-# TODO: console access logs w/o symlink
-# server.tomcat.accesslog.enabled=true
-# server.tomcat.accesslog.directory=/dev
-# server.tomcat.accesslog.prefix=stdout
-# server.tomcat.accesslog.buffered=false
-# server.tomcat.accesslog.suffix=
-# server.tomcat.accesslog.pattern=%{org.apache.catalina.AccessLog.RemoteAddr}r %l %u %t "%r" %s %b %D %S "%{Referer}i" "%{User-Agent}i" %{LABKEY.username}s %q
-
-server.tomcat.accesslog.directory=/tmp
+# send access logs to stdout:
 server.tomcat.accesslog.enabled=true
-server.tomcat.accesslog.prefix=access
-server.tomcat.accesslog.suffix=.log
-server.tomcat.accesslog.rotate=false
-server.tomcat.accesslog.pattern=%{org.apache.catalina.AccessLog.RemoteAddr}r %l %u %t "%r" %s %b %D %S "%{Referer}i" "%{User-Agent}i" %{LABKEY.username}s %q
+server.tomcat.accesslog.directory=/dev
+server.tomcat.accesslog.prefix=stdout
+server.tomcat.accesslog.buffered=false
+server.tomcat.accesslog.suffix=
+server.tomcat.accesslog.file-date-format=
+
+# send access logs to file:
+# server.tomcat.accesslog.directory=/tmp
+# server.tomcat.accesslog.enabled=true
+# server.tomcat.accesslog.prefix=access
+# server.tomcat.accesslog.suffix=.log
+# server.tomcat.accesslog.rotate=false
+# # server.tomcat.accesslog.pattern=%{org.apache.catalina.AccessLog.RemoteAddr}r %l %u %t "%r" %s %b %D %S "%{Referer}i" "%{User-Agent}i" %{LABKEY.username}s %q
 
 server.http2.enabled=true
 

docker-compose.yml

@@ -81,6 +81,8 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - JSON_OUTPUT=${JSON_OUTPUT-false}      
       - SLEEP=${SLEEP:-0}
 
   pg-community:
@@ -189,6 +191,8 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - JSON_OUTPUT=${JSON_OUTPUT-false}      
       - SLEEP=${SLEEP:-0}
 
   pg-allpg:
@@ -295,6 +299,8 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - JSON_OUTPUT=${JSON_OUTPUT-false}      
       - SLEEP=${SLEEP:-0}
 
   pg-enterprise:
@@ -401,6 +407,8 @@ services:
 
       - LABKEY_CUSTOM_PROPERTIES_S3_URI=${LABKEY_CUSTOM_PROPERTIES_S3_URI}
       - LABKEY_DEFAULT_PROPERTIES_S3_URI=${LABKEY_DEFAULT_PROPERTIES_S3_URI}
+      - LOG4J_CONFIG_FILE=${LOG4J_CONFIG_FILE-log4j2.xml}
+      - JSON_OUTPUT=${JSON_OUTPUT-false}
       - SLEEP=${SLEEP:-0}
 
   pg-lims_starter:

entrypoint.sh

@@ -13,6 +13,13 @@ keystore_format="${TOMCAT_KEYSTORE_FORMAT:-}"
 
 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 'server/labkeywebapp/WEB-INF/classes/log4j2.xml' to use embedded tomcat version
+LOG4J_CONFIG_FILE="${LOG4J_CONFIG_FILE:='log4j2.xml'}"
+
+# below assumes using local log4j2.xml file, as the embedded version is not available for edits until after server is running
+JSON_OUTPUT="${JSON_OUTPUT:-false}"
+
 SLEEP="${SLEEP:=0}"
 
 main() {
@@ -134,8 +141,8 @@ main() {
   # rm -rf awsclibin aws-cli
   unset AWS_ACCESS_KEY_ID AWS_SECRET_ACCESS_KEY AWS_SESSION_TOKEN
 
-  echo "sleeping for $SLEEP seconds..."
-  sleep $SLEEP
+  # echo "sleeping for $SLEEP seconds..."
+  # sleep $SLEEP
 
   for prop_file in server/startup/*.properties; do
     envsubst < "$prop_file" > "${prop_file}.tmp" \
@@ -146,6 +153,7 @@ main() {
     keystore_pass="$(random_string 64)"
   fi
 
+  # below only works if server.tomcat.accesslog settings in application.properties are set to go to file instead of stdout
   if [ -n "$TOMCAT_ENABLE_ACCESS_LOG" ]; then
     ln -sfv /proc/1/fd/1 /tmp/access.log
   fi
@@ -209,6 +217,15 @@ main() {
   unset LABKEY_CREATE_INITIAL_USER LABKEY_CREATE_INITIAL_USER_APIKEY LABKEY_INITIAL_USER_APIKEY LABKEY_INITIAL_USER_EMAIL LABKEY_INITIAL_USER_GROUP LABKEY_INITIAL_USER_ROLE
   unset LABKEY_EK SLEEP
 
+  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" \/>/' $LOG4J_CONFIG_FILE
+    sed -i 's/^logging.pattern.console/# logging.pattern.console/' config/application.properties
+  else
+    echo "saw JSON_OUTPUT=$JSON_OUTPUT and LOG4J_CONFIG_FILE=$LOG4J_CONFIG_FILE"
+  fi
+
   # shellcheck disable=SC2086
   exec java \
     \
@@ -237,7 +254,7 @@ main() {
     -Dlogback.debug="$debug_string" \
     \
     -Dlog4j.debug="$debug_string" \
-    -Dlog4j.configurationFile=log4j2.xml \
+    -Dlog4j.configurationFile="$LOG4J_CONFIG_FILE" \
     \
     -Dorg.apache.catalina.startup.EXIT_ON_INIT_FAILURE=true \
     \

log4j2.xml

@@ -1,11 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
 <Configuration packages="org.labkey.api.util">
+
     <Appenders>
         <Console name="CONSOLE" target="SYSTEM_OUT">
-            <PatternLayout
-                pattern="%d{yyyy-MM-dd HH:mm:ss.SSS} I %-5.5p %5.5L --- [%15.15t] ${env:LOGGER_PATTERN} : %m%n%xEx"
-            />
+            <!-- p=priority c=category d=datetime t=thread m=message n=newline -->
+            <PatternLayout pattern="%-5p %-24.24c{1} %d{ISO8601} %24.24t : %m%n" />
+
+            <!-- <JSONLayout compact="true" eventEol="true" properties="true" stacktraceAsString="true" /> -->
+
         </Console>
 
         <RollingFile name="ERRORS"
@@ -139,20 +142,108 @@
 
     <Loggers>
 
-        <Logger name="org.apache" level="${env:LOG_LEVEL_TOMCAT:-OFF}"/>
-
-        <Logger name="org.springframework.web" level="${env:LOG_LEVEL_SPRING_WEB:-OFF}"/>
-
         <!-- category for server side script messages -->
         <Logger name="org.labkey.api.script.ScriptService.Console" level="${env:LOG_LEVEL_API_SETTINGS:-INFO}">
             <AppenderRef ref="SessionAppender"/>
         </Logger>
 
+
+        <!-- category for Mule messages -->
+        <Logger name="org.mule.MuleManager" level="info"/>
+
+        <!--
+            <Logger name="org.labkey.pipeline.mule.transformers" level="debug"/>
+         -->
+
+        <!-- category for jasper messages -->
+        <Logger name="org.apache.jasper" level="warn"/>
+
+        <!-- application classes -->
+        <Logger name="org.fhcrc" level="info"/>
+
+
         <Logger name="org.labkey" level="${env:LOG_LEVEL_LABKEY_DEFAULT:-INFO}">
             <AppenderRef ref="CONSOLE"/>
             <AppenderRef ref="LABKEY"/>
         </Logger>
 
+        <!-- uncomment to enable 'DEBUG' level on external SAML libraries to troubleshoot.
+        Note: you will also have to set dependency on slf4j lib in saml/build.gradle - uncomment 'slf4j' external libraries and build
+        <Logger name="org.opensaml" level="DEBUG">
+            <AppenderRef ref="CONSOLE"/>
+            <AppenderRef ref="LABKEY"/>
+        </Logger>
+
+        <Logger name="org.apache.xml.security" level="DEBUG">
+            <AppenderRef ref="CONSOLE"/>
+            <AppenderRef ref="LABKEY"/>
+        </Logger> -->
+
+        <Logger name="mondrian." level="info" />
+
+        <!--
+            <Logger name="org.labkey.wiki" level="debug"/>
+        -->
+
+        <!--
+            <Logger name="org.labkey.api.action.SpringActionController" level="debug"/>
+        -->
+
+        <!-- only show errors from PipelineJob output -->
+        <Logger name="org.labkey.api.pipeline.PipelineJob" level="error">
+            <AppenderRef ref="CONSOLE"/>
+        </Logger>
+
+        <!-- don't need to log PDFBox errors (e.g., FlateFilter, PDCIDFontType2) -->
+        <Logger name="org.apache.pdfbox" level="fatal"/>
+
+        <!-- this is a very verbose logger for security/permissions checking -->
+        <!--
+            <Logger name="org.labkey.api.security.SecurityManager" level="debug"/>
+        -->
+
+        <!-- Add specific module packages or classes to get debug information about
+         features you are working on. -->
+
+        <!--
+            <Logger name="org.labkey.api.data.Table" level="debug"/>
+        -->
+
+        <Logger name="org.labkey.api.data"/>
+
+        <Logger name="org.labkey.api.dataiterator"/>
+
+        <Logger name="org.labkey.docker">
+            <level value="info"/>
+        </Logger>
+
+        <Logger name="org.labkey.rstudio" level="info"/>
+
+
+        <!--
+            <Logger name="org.labkey.api.cache" level="debug"/>
+        -->
+
+        <!--
+            <Logger name="org.labkey.api.data.TempTableTracker" level="debug"/>
+        -->
+
+        <!--
+            <Logger name="org.labkey.query" level="debug"/>
+        -->
+
+        <!--
+            <Logger name="org.labkey.pipeline.mule" level="debug"/>
+        -->
+
+        <!--
+            <Logger name="org.labkey.search" level="debug"/>
+        -->
+
+        <!--
+            <Logger name="org.labkey.search.model.LuceneSearchServiceImpl" level="debug"/>
+        -->
+
         <Logger name="org.labkey.api.util.MemTracker" additivity="false" level="${env:LOG_LEVEL_LABKEY_DEFAULT:-DEBUG}">
             <AppenderRef ref="LABKEYMemory"/>
         </Logger>
@@ -161,18 +252,15 @@
             <AppenderRef ref="THREAD_DUMP"/>
         </Logger>
 
-
-
         <!--
-            set to DEBUG for startup property messages set to TRACE for values
+            <Logger name="org.labkey.api.view.ViewServlet" additivity="false" level="debug"/>
         -->
-        <Logger name="org.labkey.api.module.ModuleLoader"
-                level="${env:LOG_LEVEL_API_MODULELOADER:-WARN}"
-        />
 
-        <Logger name="org.labkey.api.settings"
-                level="${env:LOG_LEVEL_API_SETTINGS:-WARN}"
-        />
+        <!--
+            <Logger name="org.labkey" level="debug">
+                <AppenderRef ref="SESSION"/>
+            </Logger>
+         -->
 
         <Logger name="org.labkey.core.admin.ActionsTsvWriter" additivity="false" level="${env:LOG_LEVEL_LABKEY_DEFAULT:-INFO}">
             <AppenderRef ref="ACTION_STATS"/>
@@ -187,38 +275,44 @@
             <AppenderRef ref="CONSOLE"/>
         </Logger>
 
+        <!--
+          Other audit event types include, but are not limited to:
+            AppPropsEvent
+            AssayPublishAuditEvent
+            AttachmentAuditEvent
+            AuthenticationProviderConfiguration
+            ClientAPIActions
+            ContainerAuditEvent
+            DatasetAuditEvent
+            DomainAuditEvent
+            ExperimentAuditEvent
+            FileSystem
+            FileSystemBatch
+            GroupAuditEvent
+            ListAuditEvent
+            LoggedQuery
+            MessageAuditEvent
+            pipelineProtocolEvent
+            QueryExportAuditEvent
+            QueryUpdateAuditEvent
+            SampleTypeAuditEvent
+            SearchAuditEvent
+            SelectQuery
+         To enable logging of all events, set the level for the org.labkey.audit.event to
+         something other than "OFF".  To enable individual audit event logging, configure the
+         individual stanza like the one shown below, where you prefix the audit event type
+         with 'org.labkey.audit.event'. Then set the level to INFO and specify the appenders.
+        -->
         <Logger name="org.labkey.audit.event.UserAuditEvent" additivity="false" level="OFF">
             <AppenderRef ref="LABKEY_AUDIT"/>
             <AppenderRef ref="CONSOLE"/>
         </Logger>
 
-
-
-        <!-- <Logger name="org.labkey.api.data.DbScope" level="WARN"/>
-        <Logger name="org.labkey.api.data.SqlScriptExecutor" level="WARN"/>
-        <Logger name="org.labkey.api.data.SqlScriptManager" level="WARN"/>
-        <Logger name="org.labkey.api.data.SqlScriptRunner" level="WARN"/>
-        <Logger name="org.labkey.api.data.JdbcCommand" level="WARN"/>
-        <Logger name="org.labkey.api.data.ConnectionWrapper" level="WARN"/>
-        <Logger name="org.labkey.api.module.ModuleLoader" level="ERROR"/>
-        <Logger name="org.labkey.api.search.SearchService" level="ERROR"/>
-        <Logger name="org.labkey.api.view.ViewServlet" level="ERROR"/>
-        <Logger name="org.labkey.api.cache.ehcache" level="WARN"/>
-        <Logger name="org.labkey.api.data.queryprofiler" level="WARN"/>
-        <Logger name="org.labkey.core.admin.ActionsTsvWriter" level="WARN"/>
-        <Logger name="org.labkey.audit" level="ERROR"/>
-        <Logger name="org.labkey.search" level="ERROR"/>
-        <Logger name="org.labkey.api.util" level="TRACE"/>
-        <Logger name="org.labkey.api.exp.xar.LsidUtils" level="WARN"/> -->
-
-        <Logger name="org.labkey.api.pipeline" level="${env:LOG_LEVEL_API_PIPELINE:-WARN}">
-            <AppenderRef ref="CONSOLE"/>
-        </Logger>
+        <Logger name="NoOpLogger" level="OFF" additivity="false"/>
 
         <Root level="${env:LOG_LEVEL_DEFAULT:-FATAL}">
             <AppenderRef ref="CONSOLE"/>
             <AppenderRef ref="ERRORS"/>
         </Root>
     </Loggers>
-
 </Configuration>