Overview
Documents setting up code, config, and data in a development environment using Eclipse.
Prerequisites
- 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.
References/Links
- loader.SNOMEDCT.input.data (set to the path of your SNOMED data, e.g. c:/data/snomedct-20140131-mini)