CTS2-LE Installation and Deployment

This section describes how to install and deploy a CTS2-LE server instance along with the navigator front-end. It has to be ensured that the system fulfils the defined prerequisites. The following steps are aligned to the recommended system environment and hence offer commands on the basis of an Ubuntu-like OS.

General settings

Configure roles and users

Since the web application can be managed by means of the tomcat manager interface, it is useful to configure a role and a user. In /var/lib/tomcat7/conf/tomcat-users.xml add a role manager-gui and assign it to a user in the following manner:

<role rolename="manager-gui"/>
<user username="user" password="password" roles="manager-gui"/>

Encoding

Make sure, the correct encoding for requests and responses is set. In /var/lib/tomcat7/conf/server.xml check the attribute URIEncoding in the connector tag.

<Connector connectionTimeout="20000" port="8080" protocol="HTTP/1.1" redirectPort="8443" URIEncoding="UTF-8"/>

Increasing Java heap space

Experience has shown that increasing the heap space for tomcat positively influences the servers efficiency. Therefore, it is recommended to permanently set the environment variable CATALINA_OPTS.

CATALINA_OPTS="-Xms512m -Xmx900m"

Setting the resource root

Select a directory where the terminology store instances will be located. The directory has to be specified by setting an environment variable called CTS2LE_RESOURCE_ROOT.

Since the resource root is one of the building blocks of CTS2-LE, no arbitrary manipulation of the files within the directory should be done. Only apply changes to the files which are described in this section.

Extract the delivered start-up directory to the defined destination and set access rights recursively.

sudo chmod -R 777 $CTS2LE_RESOURCE_ROOT

Delivered artifacts

You will be receiving a zip-compressed archive that combines several artifacts that allow for a fast and clean installation of CTS2-LE. The archive file has to be unzipped in the $CTS2LE_RESOURCE_ROOT directory and then shows the following structure:

/bin
    WebCts2LE.war 
    WebCts2LEStarter.sh 
/signatures
/queries
/load-vocabs
/jdbm2
cts2_conf.xml
grouping.json
setting.json

You should leave most of the directories untouched. Only adapt or execute the highlighted files as described in the section.

cts2_conf.xml

All standard terminological resources (ICD-10, LOINC, HL7v3, FHIR etc.) require the user to obtain an individual license. Therefore such terminologies are not part of the CTS2-LE distribution but have to be licenced and loaded by the CTS2-LE customer. To ease this process, the CTS2-LE distribution includes a set of "terminology loaders" which allow for an automatic integration of the most common standard terminologies into CTS2-LE. This section describes how these loaders can be activated for loading standard terminologies and value sets into CTS2-LE.

When receiving a CTS2-LE distribution, this file will comprise a reference to any terminology for which the user has obtained a license. The XML-structured file lists the available terminologies under the element vocabularies. A specific vocabulary is defined by a friendly-name and a resourceID, for example the Example code system will appear as the following line:

<conf>	
	<vocabularies loadAll="false">
		<vocabulary load="true" friendly-name="Example code system" resourceID="exa"/>
	</vocabularies>
</conf>

The friendly name is a human readable name for a terminology and may be modified by the user if he prefers a different designation. However, the attribute resourceID must not be changed as it is a system intern identifier for the terminology.

To load a vocabulary, the attribute load has to be set to true.

Mark any desired vocabulary by following this strategy (or load all terminologies by enabling loadAll in the <vocabularies> element) and save the file. There are no restrictions concerning the amount of terminologies that can be loaded in one run, thus a user might enable any available resource before saving the file.

WebCts2LE.war and WebCts2LEStarter.sh

1. a web application archive (WebCts2LE.war) which will be deployed in a servlet container
2. a script (WebCts2LEStarter) for loading the store content

Deployment

The delivered script WebCts2LEStarter.sh serves 2 use cases:

1. it automatically deploys the war-file
2. it faciliates the process of loading core terminologies

Before starting the script, check the value of the tomcat version and tomcat home-directory.

NAME=tomcat7
CATALINA_BASE=/var/lib/$NAME

Ensure that the script is executable by running the following command:

chmod +x WebCts2LEStarter.sh

Finally, start the script by appending the war-file as an argument.

./WebCts2LEStarter.sh WebCts2LE.war

Troubleshooting

• Do not run the starter script with root privileges.