Move unnecessary files out of home directory

This commit is contained in:
Graham Triggs 2015-11-25 13:58:02 +00:00
parent 307787b316
commit af77804dfe
7 changed files with 0 additions and 0 deletions

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# -----------------------------------------------------------------------------
#
# Vitro build properties
#
# This file is provided as example.build.properties.
#
# Save a copy of this file as build.properties, and edit the properties as
# needed for your installation.
#
# -----------------------------------------------------------------------------
#
# The base install directory for your Tomcat server. The Vitro application
# will be deployed in the /webapps directory below this base.
#
tomcat.home = /usr/local/tomcat
#
# The name of the Vitro application. This will be used as the name of the
# subdirectory within your Tomcat server's /webapps directory. It also appears
# in the URL for the application. For example, http://my.vitro.server/vitro
#
webapp.name = vitro
#
# The location where the Vitro application will store the data that it creates.
# This includes uploaded files (usually images) and the search index.
#
vitro.home = /usr/local/vitro/home
#
# Additional languages to be built into your VIVO site. The locales specified
# here must appear as sub-directories of [vivo]/languages in the distribution.
# Find more information on the VIVO Wiki (https://wiki.duraspace.org/display/VIVO).
#
#languages.addToBuild =

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# -----------------------------------------------------------------------------
#
# Vitro runtime properties
#
# This file is provided as example.runtime.properties.
#
# Save a copy of this file as runtime.properties in your Vitro home directory,
# and edit the properties as needed for your installation.
#
# -----------------------------------------------------------------------------
#
# This namespace will be used when generating URIs for objects created in the
# editor. In order to serve linked data, the default namespace must be composed
# as follows (optional elements in parentheses):
#
# scheme + server_name (+ port) (+ servlet_context) + "/individual/"
#
# For example, Cornell's default namespace is:
#
# http://vivo.cornell.edu/individual/
#
Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
#
# URL of Solr context used in local Vitro search. This will usually consist of:
# scheme + server_name + port + vitro_webapp_name + "solr"
# In the standard installation, the Solr context will be on the same server as Vitro,
# and in the same Tomcat instance. The path will be the Vitro webapp.name (specified
# above) + "solr"
# Example:
# vitro.local.solr.url = http://localhost:8080/vitrosolr
vitro.local.solr.url = http://localhost:8080/vitrosolr
#
# Email parameters which VIVO can use to send mail. If these are left empty,
# the "Contact Us" form will be disabled and users will not be notified of
# changes to their accounts.
#
email.smtpHost = smtp.my.domain.edu
email.replyTo = vivoAdmin@my.domain.edu
#
# The basic parameters for a MySQL database connection. Change the end of the
# URL to reflect your database name (if it is not "vitro"). Change the username
# and password to match the authorized user you created in MySQL.
#
VitroConnection.DataSource.url = jdbc:mysql://localhost/vitro
VitroConnection.DataSource.username = vitroweb
VitroConnection.DataSource.password = vitrovitro
#
# The maximum number of active connections in the database connection pool.
# Increase this value to support a greater number of concurrent page requests.
#
VitroConnection.DataSource.pool.maxActive = 40
#
# The maximum number of database connections that will be allowed
# to remain idle in the connection pool. Default is 25%
# of the maximum number of active connections.
#
VitroConnection.DataSource.pool.maxIdle = 10
#
# Parameters to change in order to use VIVO with a database other than
# MySQL.
#
VitroConnection.DataSource.dbtype = MySQL
VitroConnection.DataSource.driver = com.mysql.jdbc.Driver
VitroConnection.DataSource.validationQuery = SELECT 1
#
# The email address of the root user for the VIVO application. The password
# for this user is initially set to "rootPassword", but you will be asked to
# change the password the first time you log in.
#
rootUser.emailAddress = root@myDomain.com
#
# How is a logged-in user associated with a particular Individual? One way is
# for the Individual to have a property whose value is the username of the user.
# This is the name of that property.
#
selfEditing.idMatchingProperty = http://vitro.mydomain.edu/ns#networkId
#
# If an external authentication system like Shibboleth or CUWebAuth is to be
# used, these properties say how the login button should be labeled, and which
# HTTP header will contain the user ID from the authentication system. If such
# as system is not to be used, leave these commented out. Consult the
# installation instructions for more details.
#
#externalAuth.buttonText = Log in using BearCat Shibboleth
#externalAuth.netIdHeaderName = remote_userID
#
# Types of individual for which we can create proxy editors.
# If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing
proxy.eligibleTypeList = http://www.w3.org/2002/07/owl#Thing
#
# Show only the most appropriate data values based on the Accept-Language
# header supplied by the browser. Default is false if not set.
#
# RDFService.languageFilter = true
#
# Tell VIVO to generate HTTP headers on its responses to facilitate caching the
# profile pages that it creates.
#
# For more information, see
# https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance
#
# Developers will likely want to leave caching disabled, since a change to a
# Freemarker template or to a Java class would not cause the page to be
# considered stale.
#
# http.createCacheHeaders = true
#
# Force VIVO to use a specific language or Locale instead of those
# specified by the browser. This affects RDF data retrieved from the model,
# if RDFService.languageFilter is true. This also affects the text of pages
# that have been modified to support multiple languages.
#
# languages.forceLocale = en_US
#
# A list of supported languages or Locales that the user may choose to
# use instead of the one specified by the browser. Selection images must
# be available in the i18n/images directory of the theme. This affects
# RDF data retrieved from the model, if RDFService.languageFilter is true.
# This also affects the text of pages that have been modified to support
# multiple languages.
#
# This should not be used with languages.forceLocale, which will override it.
#
# languages.selectableLocales = en, es, fr

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#
# A list of JARs that we know to be required by the source code (and notes on where they are required).
#
# The "jarlist" target of the build script will work on the assumption that these JARs and any JARs
# that they depend on are required by the app.
#
# For example, the JDBC drivers are never explicitly included, but instead are invoked using Class.forName(),
# so they are required even though the "jarlist" target won't find any such requirement.
#
# JDBC drivers that we want to include.
# Oracle and MySQL
ojdbc14_g.jar
mysql-connector-java-5.1.16-bin.jar
# Don't know who requires the Commons Logging package - Maybe JENA?
commons-logging-1.1.1.jar
# Needed by a variety of JSPs
# datapropertyBackButtonProblems.jsp
# n3Delete.jsp
# processDatapropRdfForm.jsp
# processRdfForm2.jsp
xstream-1.2.2.jar
# Used in error.jsp, which should probably go away.
cos.jar

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#
# A list of files and directories that are known exceptions to the
# license-insertion process.
#
# Files will only be altered if they contain a "magic" license place-holder,
# but if they match one of the file-matchers and don't contain a place-holder,
# the process will write a warning.
#
# File-matchers are:
# '*.java', '*.jsp', '*.tld', '*.xsl', '*.xslt', '*.css', '*.js', 'build.xml'
#
# Known exceptions listed here produce no warnings.
#
# Any files added to this list should include a comment, so we know where they
# came from, or why they don't require a license statement.
#
# The AI ingest files are exceptions -- until we decide otherwise.
utilities/ingest/**/*
# PROBLEM: Can't find any info on licensing.
webapp/web/templates/freemarker/page/partials/doctype.html
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/src/edu/cornell/mannlib/vitro/webapp/web/ContentType.java
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/src/org/json/*
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/JsonToFmModel.java
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/tiny_mce/*
webapp/web/js/tiny_mce/**/*
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/jquery.js
webapp/web/js/jquery-ui/*
webapp/web/js/jquery_plugins/*
webapp/web/js/jquery.fix.clone.js
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/dojo.js
webapp/web/src/AdapterRegistry.js
webapp/web/src/animation/*
webapp/web/src/animation.js
webapp/web/src/behavior.js
webapp/web/src/bootstrap1.js
webapp/web/src/bootstrap2.js
webapp/web/src/browser_debug.js
webapp/web/src/collections/*
webapp/web/src/compat/*
webapp/web/src/data/*
webapp/web/src/data.js
webapp/web/src/date.js
webapp/web/src/debug/*
webapp/web/src/debug.js
webapp/web/src/Deferred.js
webapp/web/src/dnd/*
webapp/web/src/doc.js
webapp/web/src/dom.js
webapp/web/src/event/*
webapp/web/src/event.js
webapp/web/src/experimental.js
webapp/web/src/flash.js
webapp/web/src/fx/*
webapp/web/src/graphics/*
webapp/web/src/hostenv_adobesvg.js
webapp/web/src/hostenv_browser.js
webapp/web/src/hostenv_dashboard.js
webapp/web/src/hostenv_jsc.js
webapp/web/src/hostenv_rhino.js
webapp/web/src/hostenv_spidermonkey.js
webapp/web/src/hostenv_svg.js
webapp/web/src/hostenv_wsh.js
webapp/web/src/html/*
webapp/web/src/html.js
webapp/web/src/i18n/*
webapp/web/src/iCalendar.js
webapp/web/src/io/*
webapp/web/src/io.js
webapp/web/src/json.js
webapp/web/src/lang/*
webapp/web/src/lang.js
webapp/web/src/lfx/*
webapp/web/src/loader.js
webapp/web/src/loader_xd.js
webapp/web/src/logging/*
webapp/web/src/math/*
webapp/web/src/math.js
webapp/web/src/profile.js
webapp/web/src/reflect/*
webapp/web/src/regexp.js
webapp/web/src/rpc/*
webapp/web/src/selection/*
webapp/web/src/storage/*
webapp/web/src/storage.js
webapp/web/src/string/*
webapp/web/src/string.js
webapp/web/src/style.js
webapp/web/src/svg.js
webapp/web/src/text/*
webapp/web/src/undo/*
webapp/web/src/uri/*
webapp/web/src/uuid/*
webapp/web/src/validate/*
webapp/web/src/validate.js
webapp/web/src/widget/*
webapp/web/src/widget/**/*
webapp/web/src/xml/*
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/templates/freemarker/page/partials/googleAnalytics.ftl
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/WEB-INF/tlds/sparqltag.tld
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/WEB-INF/tlds/c.tld
webapp/web/WEB-INF/tlds/fn.tld
# PROBLEM: Can't find any info on licensing.
webapp/web/WEB-INF/tlds/database.tld
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/WEB-INF/tlds/taglibs-mailer.tld
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/WEB-INF/tlds/taglibs-random.tld
webapp/web/WEB-INF/tlds/taglibs-string.tld
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/themes/enhanced/css/blueprint/grid.css
webapp/web/themes/enhanced/css/blueprint/ie.css
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/css/jquery_plugins/jquery.realperson.css
# PROBLEM: Can't find any info on licensing.
webapp/web/themes/enhanced/css/blueprint/liquid.css
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/betterDateInput.js
# PROBLEM: Can't find any info on licensing.
webapp/web/js/detect.js
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/toggle.js
webapp/web/js/toggle.js
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/html5.js
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/selectivizr.js
# PROBLEM: Can't find any info on licensing.
webapp/web/js/jquery_plugins/supersleight.js
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/raphael/*
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/sparql/prototype.js
# See /doc/3rd-party-licenses.txt for LICENSE file
webapp/web/js/amplify/amplify.store.min.js
# Apache Solr search platform. See /doc/3rd-party-licenses.txt for LICENSE file
solr/**/*
solr/*
# OWASP AntiSamy Project. See /doc/3rd-party-licenses.txt for LICENSE file
webapp/src/edu/cornell/mannlib/vitro/webapp/web/antisamy-vitro-1.4.4.xml
# A kluge class derived from JarJar code. See /doc/3rd-party-licenses.txt for LICENSE file
utilities/buildutils/src/com/tonicsystems/jarjar/KlugedDepFind.java
#Public Domain
webapp/web/js/json2.js
# Part of the OpenSocial integration - What license should apply here?
webapp/src/edu/ucsf/vitro/opensocial/GadgetController.java
webapp/src/edu/ucsf/vitro/opensocial/GadgetSpec.java
webapp/src/edu/ucsf/vitro/opensocial/GadgetViewRequirements.java
webapp/src/edu/ucsf/vitro/opensocial/OpenSocialManager.java
webapp/src/edu/ucsf/vitro/opensocial/PreparedGadget.java
webapp/web/js/openSocial/shindig.js
opensocial/sample-gadgets/SearchExample.xml
opensocial/sample-gadgets/ProfileListTool.xml
opensocial/sample-gadgets/SlideShare.xml
opensocial/sample-gadgets/Twitter.xml
opensocial/sample-gadgets/RDFTest.xml
opensocial/sample-gadgets/WEB-INF/web.xml
opensocial/sample-gadgets/Mentor.xml
opensocial/sample-gadgets/Links.xml

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# --------------------------------------------------------------------------
# Properties for running the licenser utility in Vitro core.
# --------------------------------------------------------------------------
# The path to the top level directory to be scanned or copied
# (if relative, then relative to this file)
source_dir = ../../../
# The path to the top level directory to copy into (ignored if only scanning)
# (if relative, then relative to this file)
target_dir =
# A list of filename globs that match the files we want to license,
# delimited by commas with optional white-space.
file_matchers = *.java, *.jsp, *.tld, *.xsl, *.xslt, *.css, *.js, *.ftl, *.xml
# "globs" that describe paths that we won't follow for scanning OR FOR COPYING.
# (relative to the source_dir)
skip_directories = ./bin, ./.svn, ./**/.svn, ./webapp/.build
# The path to a file containing filename/path globs that match the files that
# we know should have no license tags in them.
# The file contains one glob per line; blank lines and comments ("#") are ignored.
# (if relative, then relative to the source directory)
known_exceptions = webapp/config/licenser/known_exceptions.txt
# The path to the text of the license agreement (ignored if only scanning)
# If the agreement contains a ${year} token, the current year will be substituted.
# (if relative, then relative to the source directory)
license_file = doc/license.txt
# Set to 'full' for a full report, 'short' for a brief statment, or to anything
# else for a medium-length summary.
report_level = short

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#
# This file sets the log levels for the Vitro webapp.
#
# There are 8 principal logging levels, as follows:
# <-- more messages ALL TRACE DEBUG INFO WARN ERROR FATAL OFF fewer messages -->
#
# The default logging level is specified on the rootLogger. Other levels can be
# set for individual classes or packages as desired.
#
# Examples of setting levels:
# log4j.logger.edu.cornell.mannlib.vitro.webapp.ConfigurationProperties=INFO
# -- sets INFO level for this one class
# log4j.logger.org.apache.catalina=INFO
# -- sets INFO level for all classes in "org.apache.catalina" package
# and any sub-packages.
#
# Documentation for this file can be found here:
# http://logging.apache.org/log4j/1.2/apidocs/org/apache/log4j/PropertyConfigurator.html#doConfigure(java.lang.String,%20org.apache.log4j.spi.LoggerRepository)
#
# More information can be found here:
# http://logging.apache.org/log4j/1.2/manual.html
#
# The "production" version of this file is log4j.properties.
# debug.log4j.properties exists will be used instead, if it exists, but is not stored in Subversion.
log4j.appender.AllAppender=org.apache.log4j.RollingFileAppender
log4j.appender.AllAppender.File= $${catalina.home}/logs/${webapp.name}.all.log
log4j.appender.AllAppender.MaxFileSize=10MB
log4j.appender.AllAppender.MaxBackupIndex=10
log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout
log4j.appender.AllAppender.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss,SSS} %-5p [%c{1}] %m%n
log4j.rootLogger=INFO, AllAppender
# These classes are too chatty to display INFO messages.
log4j.logger.edu.cornell.mannlib.vitro.webapp.startup.StartupStatus=WARN
log4j.logger.edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase=WARN
log4j.logger.org.semanticweb.owlapi.rdf.rdfxml.parser=WARN
# Spring as a whole is too chatty to display INFO messages.
log4j.logger.org.springframework=WARN
# suppress odd warnings from libraries
log4j.logger.com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes=FATAL
log4j.logger.com.hp.hpl.jena.sdb.sql.SDBConnection=ERROR
log4j.logger.org.openjena.riot=FATAL
log4j.logger.org.apache.jena.riot=FATAL
log4j.logger.org.directwebremoting=FATAL

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JAVA_HOME=/usr/local/java/jdk1.5.0_06
TOMCAT_HOME=/usr/local/tomcat
CATALINA_HOME=/usr/local/tomcat
#these are for options that are only set at start time
# useful for jmx or remote debugging.
START_OPTS=""
# the gc log and the jvm options are saved in the logs directory
DATESTR=`date +%Y%m%d.%H%M`
GCFILE=$CATALINA_HOME/logs/gc$DATESTR.txt
OPT_FILE=$CATALINA_HOME/logs/opts$DATESTR.txt
# This is an example of the setenv.sh file from
# cugir-tng.mannlib.cornell.edu
# To use this file copy it to /usr/local/tomcat/bin/setenv.sh
# When catalina.sh is called this file will be used to
# set the environmental variables that are
# in effect when starting the JVM for tomcat.
# java memory tools:
# jconsole is useful to watch the survivor, Edan, tenured and
# perm spaces. gcviewer is useful for statistics.
#An acceptable group of settings, use this as a starting point
# CATALINA_OPTS=" -Xms1024m -Xmx1024m -XX:MaxPermSize=128m \
# -XX:+UseParallelGC \
# -Dfile.encoding=UTF-8 \
# -Xloggc:$GCFILE -XX:+PrintGCDetails -XX:+PrintGCTimeStamps "
# attempting a low GCTimeRatio,
# GCTimeRatio indicates how much time to spend in gc vs. application
# app time / gc time = 1 / (1+ GCTimeRatio)
# GCTimeRatio of 11 is aprox %8 of the time in GC
#
# Result: best so far. After about 12 hours the heap is
# hovering around 100mb. This is the first group of settings
# that seem like they will be stable for a long period of time.
# throughput is 98.79%
# This is a log for these settings: /usr/local/tomcat/logs/gc20060809.1638.txt
CATALINA_OPTS=" -Xms1024m -Xmx1024m -XX:MaxPermSize=128m \
-XX:+UseParallelGC -XX:GCTimeRatio=11 -XX:+UseAdaptiveSizePolicy \
-Dfile.encoding=UTF-8 \
-Xloggc:$GCFILE -XX:+PrintGCDetails -XX:+PrintGCTimeStamps "
# bdc34 2006-08-08
# Trying adaptiveSizePolicy with parallel GC.
# Result: This did an out of memory when a crawler came along
# but even before that it looked bad.
# CATALINA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=128m \
# -XX:NewSize=512m \
# -XX:+UseParallelGC -XX:+UseAdaptiveSizePolicy \
# -Dfile.encoding=UTF-8 \
# -XX:+PrintGCDetails -XX:+PrintGCTimeStamps \
# -Xloggc:$GCFILE "
# bdc34 2006-08-08
# Trying the concurrent gc
# Result: after 10min it seems odd. The survivor space doesn't get
# used at all. It is always showing up in jconsole as zero mb. So
# objects are going directly from the edan space to the tenured space?
#
# Result: sort of rapid growth of heap with odd paterns of collection.
# doesn't seem useful
# CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=256m \
# -XX:+UseConcMarkSweepGC \
# -XX:+UseAdaptiveSizePolicy \
# -XX:-TraceClassUnloading \
# -Dfile.encoding=UTF-8 \
# -XX:+PrintGCDetails -XX:+PrintGCTimeStamps \
# -Xloggc:/usr/local/tomcat/logs/gc.txt "
# bdc34 2006-08-07
# Attempting to increase the PermGen Size. Notice
# that PermGen size is in addition to the heap
# size specified in -Xmx.
#
# Also removing GCTimeRatio to allow for
# a lot of garbage collecting. I don't want
# any bound on GC, time or throughput. I don't
# know if not specifying a value will achieve this.
#
# Logging gc to /usr/local/tomcat/logs/gc.txt
# so I can look at it with http://www.tagtraum.com/gcviewer.html
#
# Setting max heap to initial heap to avoid growing the
# heap and associated gc cycles.
#
# Result: I ran this for two days and it seemed to work well.
# It would do minor collections for about 20h. The heap would
# get to around 1G and then the jvm would do
# a full colleciton that would drop the heap down to 50m.
# It seems that having the heap at 1G only buys time and
# that the application could live in 128-256mb.
# gcviewer was reporting 99.0% collection rates.
# It seems that these settings would work but might need to
# be restarted about once a week.
#
# Increasing the MaxPermSize seems to be important.
# The permGen includes things like classes and code. This is
# a problem since JSPs are classes and code so reloading a JSP
# adds to the permGen. The documentation weakly indicates that
# the permGen gets collected in full collections. I have not
# seen evidence that this it does when watching jconsole.
# Sun's JVM seperates the heap and classes but IBM and BEA do not.
#
# CATALINA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=256m \
# -XX:+UseParallelGC \
# -Dfile.encoding=UTF-8 \
# -XX:+PrintGCDetails -XX:+PrintGCTimeStamps \
# -Xloggc:/usr/local/tomcat/logs/gc.txt "
#bdc 2005-10-18
# CATALINA_OPTS="-server -Xms512m -Xmx1024m \
# -XX:+UseParallelGC \
# -XX:ParallelGCThreads=8 -XX:-PrintTenuringDistribution \
# -XX:MaxPermSize=256 \
# -XX:NewRatio=5 -XX:GCTimeRatio=19 -XX:SurvivorRatio=32 \
# -Dfile.encoding=UTF-8 \
# -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Xloggc:/usr/local/tomcat/log/gc.txt \
# -verbose:gc "
#These are the java command args needed to allow remote jmx
JMXREMOTE=" -Dcom.sun.management.jmxremote.port=8022 "
#we only what jmxremote when we start, not on stop since the
#port will be in use. This also could be done with jpda
START_OPTS="$JMXREMOTE"
# we want to allow access to files created by tomcat by the mannit group
umask 002
# this makes a link from the current gc log to a place were we can get it over http
# those '&& true' are just to force success so we don't exit
rm -f /usr/local/apache/htdocs/private/tmp/gc.txt && true
ln -f -s $GCFILE /usr/local/apache/htdocs/private/tmp/gc.txt && true
#We want a record of the JVM options to compare with the gc log.
echo "CATALINA_OPTS: $CATALINA_OPTS" > $OPT_FILE
echo "START_OPTS: $START_OPTS" >> $OPT_FILE
# We need to export any variables that are to be used outside of script:
export JAVA_HOME CATALINA_OPTS TOMCAT_HOME CATALINA_HOME
export START_OPTS
# displays a note about what parameters will be used:
#echo "Using CATALINA Opts from tomcat/bin/setenv.sh: "
#echo " $CATALINA_OPTS"