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Overview

Documents setting up code, config, and data in a development environment using Eclipse.

Prerequisites

  • Git client
  • Java 7 installed
  • Mysql 5.5 or 5.6 installed
  • Maven 3.2.+ installed
  • Tomcat 7 installed and configured

Details

Step 1

Clone the Github repository to a local directory (e.g. c:/workspace/SNOMED-Terminology-Server)

Step 2

  • Create a directory to hold your configuration and data files (e.g. c:/data)
  • Copy the term-server-config/src/main/resources/data/snomedct-20140131-mini folder to your data directory (e.g. c:/data).
  • Copy the term-server-config/src/main/resources/data/icd9cm-2013.xml file into your data directory (e.g. c:/data)
  • Copy the term-server-config/src/main/resources/config.properties.dev to your data directory (e.g. c:/data) and rename it to "config.properties"

Step 3

Edit the configuration file to set correctly for your environment.  In particular, edit these:

  • javax.persistence.jdbc.url
  • javax.persistence.jdbc.user
  • javax.persistence.jdbc.password
  • hibernate.search.default.indexBase  ( recommend choosing something below your data dir, e.g. c:/data/indexes)
  • loader.SNOMEDCT.input.data (set to the path of your SNOMED data, e.g. c:/data/snomedct-20140131-mini)
  • loader.ICD9CM.input.data (set to the path of your ICD9CM data, e.g. c:/data/icd9cm-2013.xml)
  • ihtsdo.security.activated (set to false for dev environment)

Step 4

Set three environment variables:

  • MVN_HOME - path to mvn installation (so bin/mvn is accessible from there)
    • Only needed on Windows, assume "mvn" is in path on Linux
  • SERVER_CONFIG - path to the configuration file (e.g. c:/data/config.properties).
  • SERVER_HOME - path to where the code is installed, (e.g. c:/workspace/SNOMED-Terminology-Server)

Step 5

Create a MySQL UTF8 database. e.g.

  • CREATE database tsdb CHARACTER SET utf8 default collate utf8_unicode_ci;


Step 6

Run the admin loader script for your platform.  See term-server-admin/loader/src/main/resources/scripts

  • load.bat - for Windows
  • load.sh - for Linux

NOTE: if re-running this, you first have to run the sql in "truncate_all.sql" to clear your database of tables.

Step 7

Build all modules with "mvn clean install" at the top level - either through Eclipse or via the command line.  Among other things, this will produce a term-server-rest.war file that can be deployed.

Step 8

Deploy the term-server-rest.war file to a Tomcat server - either through Eclipse or a standalone tomcat installation.

Setting up Tomcat in Eclipse is very easy, you follow these steps.

  • Download and install apache tomcat 7 in c:/apache-tomcat-XXXX
  • In Eclipse use the J2EE perspective and click on the "Servers" tab.
  • From here, you can add a server which simply involves pointing Eclipse to the install directory.
  • You can right-click on term-server-rest.war file and use "Run As->Run on Server" to deploy to Tomcat.
    • NOTE: sometimes in Eclipse this doesn't work and the tomcat does not properly recognize or deploy the app.
    • In this event, double-click on the tomcat server installation in the servers tab.
    • In the configuration screen click "Open launch configuration"

    • There, look on the Arguments tab and find the -D setting for "catalina.base", e.g.

      -Dcatalina.base="C:\Users\Brian Carlsen\workspace-luna\.metadata\.plugins\org.eclipse.wst.server.core\tmp0"
    •  If you open this directory you'll see a "webapps" folder.  To deploy you simply build and copy term-server-rest.war to that directory and launch the server in Eclipse.

  • The Tomcat server needs to be able to find the run configuration. Double-click on the Tomcat server you installed, open the launch configuration and add this setting:

    -Drun.config=/path/to/your/config.properties

Step 9

Check that it all works by going to

http://localhost:8080/term-server-rest/index.html

This should be a "swagger" Api documenting the current state of the API.  You should be able to test services by using "guest" as the authToken parameter.

 

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