From 390404bd8c90da3571a65a26d1e710625422de92 Mon Sep 17 00:00:00 2001
From: Tim Eilers <tim.eilers@kps.com>
Date: Wed, 6 May 2020 16:00:55 +0200
Subject: [PATCH] Adapting templates to state if 8.7.1 tarball, while keeping
 required modifications in place. Fixes #300.

---
 templates/check-java.sh.erb | 64 +++++++++++++++++++++++++++----------
 templates/server.xml.erb    | 22 ++-----------
 templates/setenv.sh.erb     | 51 +++++++++++++++++------------
 3 files changed, 82 insertions(+), 55 deletions(-)

diff --git a/templates/check-java.sh.erb b/templates/check-java.sh.erb
index a516d40e..9181f500 100644
--- a/templates/check-java.sh.erb
+++ b/templates/check-java.sh.erb
@@ -1,26 +1,58 @@
 #!/bin/sh
 # This file is managed by Puppet
 
-# This file should be identical to 'check-java.sh' in the Jira 7.0.4 standalone
+# This file should be identical to 'check-java.sh' in the Jira 8.7.1 standalone
 # tarball.
 
-_EXPECTED_JAVA_VERSION="8"
-
 #
 # check for correct java version by parsing out put of java -version
-# we expect first line to be in format 'java version "1.8.0_40"' and assert that minor version number will be 8 or higher
+# we expect first line to be in format 'java version "1.8.0_161"' or 'java version "10.0.1" 2018-04-17'
+# or 'openjdk version "11-ea" 2018-09-25' and assert that version number will be 8 or 11 (if enabled)
+# or sth like 'Picked up JDK_JAVA_OPTIONS:' (which we need to skip)
 #
 
-"$_RUNJAVA" -version 2>&1 | grep "java version" | (
-        IFS=. read ignore1 version ignore2
-        if [ ! ${version:-0} -ge "$_EXPECTED_JAVA_VERSION" ]
-        then
-           echo "*************************************************************************************************************************************"
-           echo "**********     Wrong JVM version! You are running with "$ignore1"."$version"."$ignore2" but JIRA requires at least 1.8 to run.      **********"
-           echo "*************************************************************************************************************************************"
-           exit 1
-        fi
-    )
-if [ $? -ne 0 ] ; then
-   exit 1
+java_raw_version=`echo "$($_RUNJAVA -version 2>&1)" | grep -v "JDK_JAVA_OPTIONS" | grep "version" | awk '{ print substr($3, 2, length($3)-2); }'`
+java_version=0
+
+if [[ $java_raw_version = *-ea* ]]
+then
+	# early access format e.g 11-ea
+    IFS='-' read -a values <<< "$java_raw_version"
+    java_version=${values[0]}
+else
+	if [[ $java_raw_version = 1.* ]]
+	then
+		# old format e.g. 1.8.0_161
+	    IFS='.' read -a values <<< "$java_raw_version"
+		java_version=${values[1]}
+	else
+		# new format e.g. 10.0.1
+		IFS='.' read -a values <<< "$java_raw_version"
+		java_version=${values[0]}
+	fi
+fi
+
+if [ $java_version -ne 8 ] && [ $java_version -ne 11 ]
+then
+    echo "****************************************************************************"
+    echo "*******      Wrong JVM version! Jira requires 1.8 or 11 to run.      *******"
+    echo "****************************************************************************"
+    echo "***"
+    echo "*** Output of java -version command is:"
+    $_RUNJAVA -version 2>&1
+    echo "*** (End of output) ***"
+    echo "***"
+    if [ "$ignore_jvm_version" = "true" ]
+    then
+        echo "*** Environment variable 'ignore_jvm_version' is set to 'true'"
+        echo "*** Jira is going to bypass restriction and run using existing JVM version"
+        echo "***"
+        echo "****************************************************************************"
+    else
+        echo "*** If you want Jira to start using this JVM"
+        echo "*** set environment variable 'ignore_jvm_version' to 'true'"
+        echo "***"
+        echo "****************************************************************************"
+        exit 1
+    fi
 fi
diff --git a/templates/server.xml.erb b/templates/server.xml.erb
index e7ecf54d..8cc5b8bc 100644
--- a/templates/server.xml.erb
+++ b/templates/server.xml.erb
@@ -1,16 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<!--
-   ====================================================================================
-
-   Atlassian JIRA Standalone Edition Tomcat Configuration.
-
 
-   See the following for more information
-
-   http://confluence.atlassian.com/display/JIRA/Configuring+JIRA+Standalone
-
-   ====================================================================================
- -->
 <!--
   Licensed to the Apache Software Foundation (ASF) under one or more
   contributor license agreements.  See the NOTICE file distributed with
@@ -28,21 +17,14 @@
   limitations under the License.
 -->
 <Server port="<%= @tomcat_shutdown_port %>" shutdown="SHUTDOWN">
-
-    <!--APR library loader. Documentation at /docs/apr.html -->
     <Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" />
+    <Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener"/>
     <Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener"/>
 <%- if scope.function_versioncmp([@version, '6.4.14']) <= 0 && @product =~ /^jira/ -%>
     <Listener className="org.apache.catalina.core.JasperListener"/>
 <% else -%>
     <Listener className="org.apache.catalina.startup.VersionLoggerListener" />
 <%- end -%>
-    <!-- Security listener. Documentation at /docs/config/listeners.html
-    <Listener className="org.apache.catalina.security.SecurityListener" />
-    -->
-    <!-- Prevent memory leaks due to use of particular java/javax APIs-->
-    <Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener" />
-    <Listener className="org.apache.catalina.core.ThreadLocalLeakPreventionListener" />
 
     <Service name="Catalina">
         <Connector port="<%= @tomcat_port %>"
@@ -62,6 +44,7 @@
                    useBodyEncodingForURI="<%= @tomcat_use_body_encoding_for_uri %>"
                    acceptCount="<%= @tomcat_accept_count %>"
                    disableUploadTimeout="<%= @tomcat_disable_upload_timeout %>"
+                   bindOnInit="false"
 <% if @tomcat_native_ssl && @tomcat_redirect_https_port -%>
                    redirectPort="<%= @tomcat_redirect_https_port %>"
 <% else -%>
@@ -128,6 +111,7 @@
                               factory="org.objectweb.jotm.UserTransactionFactory" jotm.timeout="60"/>
                     <Manager pathname=""/>
                     <JarScanner scanManifest="false"/>
+                    <Valve className="org.apache.catalina.valves.StuckThreadDetectionValve" threshold="120" />
                 </Context>
 
             </Host>
diff --git a/templates/setenv.sh.erb b/templates/setenv.sh.erb
index 80788a7f..d6a71901 100755
--- a/templates/setenv.sh.erb
+++ b/templates/setenv.sh.erb
@@ -1,3 +1,8 @@
+#
+# If the limit of files that Jira can open is too low, it will be set to this value.
+#
+MIN_NOFILES_LIMIT=16384
+
 #
 # One way to set the JIRA HOME path is here via this variable.  Simply uncomment it and set a valid path like /jira/home.  You can of course set it outside in the command terminal.  That will also work.
 #
@@ -17,17 +22,29 @@ CATALINA_OPTS="<%= scope.lookupvar('jira::catalina_opts') %> $CATALINA_OPTS"
 #
 JVM_SUPPORT_RECOMMENDED_ARGS="<%= scope.lookupvar('jira::jvm_optional') %>"
 
+#
+#  You can use variable below to modify garbage collector settings.
+#  For Java 8 we recommend default settings
+#  For Java 11 and relatively small heaps we recommend: -XX:+UseParallelGC
+#  For Java 11 and larger heaps we recommend: -XX:+UseG1GC -XX:+ExplicitGCInvokesConcurrent
+#
+JVM_GC_ARGS="-XX:+ExplicitGCInvokesConcurrent"
+
 #
 # The following 2 settings control the minimum and maximum given to the JIRA Java virtual machine.  In larger JIRA instances, the maximum amount will need to be increased.
 #
 JVM_MINIMUM_MEMORY="<%= scope.lookupvar('jira::jvm_xms') %>"
 JVM_MAXIMUM_MEMORY="<%= scope.lookupvar('jira::jvm_xmx') %>"
-JVM_PERMGEN_MEMORY="<%= scope.lookupvar('jira::jvm_permgen') %>"
+
+#
+# The following setting configures the size of JVM code cache.  A high value of reserved size allows Jira to work with more installed apps.
+#
+JVM_CODE_CACHE_ARGS='-XX:InitialCodeCacheSize=32m -XX:ReservedCodeCacheSize=512m'
 
 #
 # The following are the required arguments for JIRA.
 #
-JVM_REQUIRED_ARGS="-Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true"
+JVM_REQUIRED_ARGS='-Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory'
 
 # Uncomment this setting if you want to import data without notifications
 #
@@ -44,10 +61,14 @@ DISABLE_NOTIFICATIONS=" -Datlassian.mail.senddisabled=true -Datlassian.mail.fetc
 #-----------------------------------------------------------------------------------
 
 #-----------------------------------------------------------------------------------
-# This allows us to actually debug GC related issues by correlating timestamps
-# with other parts of the application logs.
+# Prevents the JVM from suppressing stack traces if a given type of exception
+# occurs frequently, which could make it harder for support to diagnose a problem.
 #-----------------------------------------------------------------------------------
-JVM_EXTRA_ARGS="-XX:+PrintGCDateStamps"
+JVM_EXTRA_ARGS="-XX:-OmitStackTraceInFastThrow -Djava.locale.providers=COMPAT"
+
+CURRENT_NOFILES_LIMIT=$( ulimit -Hn )
+ulimit -Sn $CURRENT_NOFILES_LIMIT
+ulimit -n $(( CURRENT_NOFILES_LIMIT > MIN_NOFILES_LIMIT  ? CURRENT_NOFILES_LIMIT : MIN_NOFILES_LIMIT ))
 
 PRGDIR=`dirname "$0"`
 cat "${PRGDIR}"/jirabanner.txt
@@ -65,25 +86,15 @@ if [ "$JIRA_HOME" != "" ]; then
     fi
 fi
 
-JAVA_OPTS="-Xms${JVM_MINIMUM_MEMORY} -Xmx${JVM_MAXIMUM_MEMORY} ${JAVA_OPTS} ${JVM_REQUIRED_ARGS} ${DISABLE_NOTIFICATIONS} ${JVM_SUPPORT_RECOMMENDED_ARGS} ${JVM_EXTRA_ARGS} ${JIRA_HOME_MINUSD}"
-
-# Perm Gen size needs to be increased if encountering OutOfMemoryError: PermGen problems. Specifying PermGen size is not valid on IBM JDKs
-JIRA_MAX_PERM_SIZE=${JVM_PERMGEN_MEMORY}
-if [ -f "${PRGDIR}/permgen.sh" ]; then
-    echo "Detecting JVM PermGen support..."
-    . "${PRGDIR}/permgen.sh"
-    if [ $JAVA_PERMGEN_SUPPORTED = "true" ]; then
-        echo "PermGen switch is supported. Setting to ${JIRA_MAX_PERM_SIZE}"
-        JAVA_OPTS="-XX:MaxPermSize=${JIRA_MAX_PERM_SIZE} ${JAVA_OPTS}"
-    else
-        echo "PermGen switch is NOT supported and will NOT be set automatically."
-    fi
-fi
+JAVA_OPTS="-Xms${JVM_MINIMUM_MEMORY} -Xmx${JVM_MAXIMUM_MEMORY} ${JVM_CODE_CACHE_ARGS} ${JAVA_OPTS} ${JVM_REQUIRED_ARGS} ${DISABLE_NOTIFICATIONS} ${JVM_SUPPORT_RECOMMENDED_ARGS} ${JVM_EXTRA_ARGS} ${JIRA_HOME_MINUSD} ${START_JIRA_JAVA_OPTS}"
 
 export JAVA_OPTS CATALINA_OPTS
 
+# DO NOT remove the following line
+# !INSTALLER SET JAVA_HOME
+
 echo ""
-echo "If you encounter issues starting or stopping JIRA, please see the Troubleshooting guide at http://confluence.atlassian.com/display/JIRA/Installation+Troubleshooting+Guide"
+echo "If you encounter issues starting or stopping Jira, please see the Troubleshooting guide at https://docs.atlassian.com/jira/jadm-docs-087/Troubleshooting+installation"
 echo ""
 if [ "$JIRA_HOME_MINUSD" != "" ]; then
     echo "Using JIRA_HOME:       $JIRA_HOME"