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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

Build all modules with "mvn clean install" at the top level - either through Eclipse or via the command line.

Step 3

  Stock setup for Windows

  • Create a directory to hold your admin, 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)
  • Unpack the config/windows-dev/target/term-server-config-windows-dev.*.zip file into your data directory (e.g. c:/data)

  Stock setup for Unix/Linux/Mac

  • Create a directory to hold your admin, configuration and data files (e.g. ~/data)
  • Copy the term-server-config/src/main/resources/data/snomedct-20140131-mini folder to your data directory (e.g. ~/data).
  • Copy the term-server-config/src/main/resources/data/icd9cm-2013.xml file into your data directory (e.g. ~/data)
  • Unpack the config/prod/target/term-server-config-prod.*.zip file into a directory (e.g. ~/)

Step 4

Edit the configuration file (now in config.properties in your data directory) 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)
  • ihtsdo.security.activated (set to false for dev environment)

Step 5

Set up environment:

  • Make sure the "mvn" executable for your local maven installation is in the path
    • On Windows this means adding to the PATH variable so that it runs in a "cmd" shell without fully qualified path.

Step 6

Create a MySQL UTF8 database. e.g.

  • CREATE database tsdb CHARACTER SET utf8 default collate utf8_unicode_ci;


Step 7

Run the corresponding load script for your environment;.

  • Step 3 creates a bin directory in the chosen data directory.  There is a "load" script that can be used with the setup at this point to create a default development instance of the application
    • For Windows: run load.bat (e.g. c:/data/bin/load.bat)
    • For Unix/Linux/Mac: run load.csh (e.g. ~/bin/load.bat)
  • NOTE: if re-running this, you first have to run the sql in "truncate_all.sql" to clear your database of tables (Recommend using MySQL Workbench for this in the dev environment).

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 for Tomcat.
  • 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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