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DEPLOYING.md

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Deployment

The TreeBASE web application needs to be deployed in a 'servlet container', i.e. a web server that can invoke Java functionality. This document describes the steps and gotchas involved in this process. It is assumed that you meet the following requirements:

  • the database has been loaded
  • the WAR for the OAI-PMH web service interface
  • the WAR web application has been compiled and bundled such that it contains a context.xml with the credentials for the database and a plausible location for headless mesquite
  • the required Apple JARs (described here) that headless mesquite needs
  • headless mesquite itself

Except for the database loading, all of these requirements are met for the specific deployment at Naturalis in the treebase-artifacts repository. The following steps are geared towards that specific deployment. The assumption is that we are working with Tomcat 7. This version is more strict with certain constructs than previous versions, such that certain code fixes have been necessary, and an additional command line argument needs to be passed to Tomcat to reduce its severity (see below).

Installing the requirements

$ sudo su
# cd /usr/local/src
# git clone https://github.com/naturalis/treebase-artifact

By cloning in this location, the following is accomplished:

  • the Apple JARs end up in /usr/local/src/treebase-artifact/mesquite/apple
  • headless mesquite ends up in /usr/local/src/treebase-artifact/mesquite/, which is what the JNDI variable tb2/MesquiteFolder is set to in the context.xml
  • the WAR files for treebase and for the OAI-PMH service are ready to be deployed

What needs to happen next is that the WAR files are copied into the webapps folder of the servlet container. On Ubuntu 16.04LTS with tomcat v.7, the paths go like this:

# cp /usr/local/src/treebase-artifact/treebase-web.war /var/lib/tomcat7/webapps/
# cp /usr/local/src/treebase-artifact/data_provider_web.war /var/lib/tomcat7/webapps/

In addition, it is necessary to place the right JDBC driver jar for PostgreSQL in the library folder of Tomcat itself. Like so:

# cd /usr/share/tomcat7/lib && wget https://jdbc.postgresql.org/download/postgresql-42.1.3.jar

Launching the server

The invocation of the tomcat server has a couple of additional parameters that must not be forgotten:

  • The Apple JARs that mesquite needs (MRJToolkit.jar and ui.jar) must be added to the class path, note the argument -classpath below.
  • The web application uses certain JSP constructs that Tomcat v.7, which is more strict than previous versions, doesn't like. This strictness is turned off using the -Dorg.apache.el.parser.SKIP_IDENTIFIER_CHECK=true.
  • The web application needs more memory than is assigned by default. In the argument list below the memory usage has been incremented fourfold from -Xmx128m to -Xmx512m.

In the invocation below, all other arguments are default:

TOM=/usr/share/tomcat7/bin
APPLE=/usr/local/src/treebase-artifact/mesquite/apple
/usr/lib/jvm/default-java/bin/java \
    -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties \
    -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager \
    -Djava.awt.headless=true -Xmx512m -XX:+UseConcMarkSweepGC \
    -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed \
    -classpath $TOM/bootstrap.jar:$TOM/tomcat-juli.jar:$APPLE/MRJToolkit.jar:$APPLE/ui.jar \
    -Dcatalina.base=/var/lib/tomcat7 \
    -Dcatalina.home=/usr/share/tomcat7 \
    -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp \
    -Dorg.apache.el.parser.SKIP_IDENTIFIER_CHECK=true \
    org.apache.catalina.startup.Bootstrap start

Successful deployment should result in a functioning website, e.g. at http://145.136.242.33/treebase-web