SNOMED CT Refset Management & Translation Tooling

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Overview

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

Prerequisites

Details

Step 1 - Create directories

  Setup for Windows

  • Create a data directory to hold your data files (e.g. c:/refset/data)
  • Create a config directory to hold your config files (e.g. c:/refset/config)
  • Create a code directory to hold the code (e.g. c:/workspace/ihtsdo-refset-tool)
  • 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.

  Setup for Unix/Linux/Mac

  • Create a data directory to hold your data files (e.g. ~/data)
  • Create a config directory to hold your config files (e.g. ~/config)
  • Create a code directory to hold the code (e.g. ~/code)
  • Make sure the "mvn" executable for your local maven installation is in the path

Step 2 - Clone repository

Clone the Github repository to the directory created to hold the code.

Step 3 - Build project

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

  • NOTE: this uses the standard "dev-windows" configuration by default.  To use a different configuration artifact pass the following three parameters (this is not commonly needed):
    • -Dconfig.groupId=...
    • -Dconfig.artifactId=...
    • -Dconfig.version=...
  • For most dev deployments, the default build is fine because the only setting really used for the rest/webapp packages is the "base.url" which by default is set to http://localhost:8080/refset-rest 
  • For a production deployment, you would want to use a different setting.  For example, see PROD Deploy Instructions

Step 4 - Setup Configuration

Choose a "dev-windows" or "prod" config project target and unzip it into the directory created to hold your config files.

  • config/dev-windows/target/refset-config-dev-windows.*.zip (e.g. unzip to c:/refset/config)
  • config/prod/target/refset-config-prod.*.zip (e.g. unzip to ~/refset/config)

Unzip the config/target/refset-config.*.zip file into the directory created to hold your data files (these are the sample data artifacts).  For example, unzip to c:/refset/data when building a dev environment on Windows.

Step 5 - Edit configuration

Edit the "config.properties" file in your config files directory to set correctly for your environment.  In particular, edit these:

  • javax.persistence.jdbc.url (contains the database name)
  • javax.persistence.jdbc.user
  • javax.persistence.jdbc.password
  • hibernate.search.default.indexBase  ( recommend choosing something in your data dir, e.g. c:/refset/data/indexes or ~/refset/indexes)
  • mail.smtp.* (list for automated system emails)
  • identifier.assignment.handler.
    • If you have a Snomed-provided IMS account, you can put your name and password below to access the Snomed identifier service:
    • If you do NOT have a Snomed-provided IMS account, you can use the provided simple identifier handler:
      • identifier.assignment.handler=DEFAULT
        identifier.assignment.handler.DEFAULT.class=org.ihtsdo.otf.refset.jpa.services.handlers.DummyComponentIdentifierServiceHandler
        #identifier.assignment.handler.DEFAULT.class=org.ihtsdo.otf.refset.jpa.services.handlers.IhtsdoComponentIdentifierServiceHandler
        #identifier.assignment.handler.DEFAULT.url=https://cis.ihtsdotools.org/api
        #identifier.assignment.handler.DEFAULT.userName=EDIT_THIS
        #identifier.assignment.handler.DEFAULT.password=EDIT_THIS
  • terminology.handler, e.g.

    • terminology.handler=BROWSER,SNOWOWL,SNOWOWL-SE
      terminology.handler.BROWSER.class=org.ihtsdo.otf.refset.jpa.services.handlers.BrowserTerminologyHandler
      terminology.handler.BROWSER.defaultUrl=https://sct-rest.ihtsdotools.org/api
      terminology.handler.BROWSER.apiKey=EDIT_THIS
      terminology.handler.SNOWOWL.class=org.ihtsdo.otf.refset.jpa.services.handlers.SnowowlTerminologyHandler
      terminology.handler.SNOWOWL.defaultUrl=https://authoring.ihtsdotools.org/snowowl/snomed-ct/v2
      terminology.handler.SNOWOWL.authHeader=Basic EDIT_THIS
      terminology.handler.SNOWOWL.apiKey=EDIT_THIS
      terminology.handler.SNOWOWL-SE.class=org.ihtsdo.otf.refset.jpa.services.handlers.SnowowlTerminologyHandler
      terminology.handler.SNOWOWL-SE.defaultUrl=https://se-authoring.ihtsdotools.org/snowowl/snomed-ct/v2
      terminology.handler.SNOWOWL-SE.apiKey=EDIT_THIS

  • base.url=EDIT_THIS (e.g. http://localhost:8080/refset-rest)

  • logout.url=EDIT_THIS (e.g. http://localhost:8080/refset-rest/index.html)

Step 6 - Create database

Create a MySQL UTF8 database. e.g.

  • CREATE database refsetdb CHARACTER SET utf8 default collate utf8_unicode_ci;


Step 7 - Generate sample data

Run the admin tool for generating sample data.  Here is a sample command line invocation that clears the database and indexes, then loads the sample data.  It assumes the config.properties file has been properly edited as described above.   


# from top-level code directory
cd admin
mvn install -PSample -Drefset.config=/home/ihtsdo/config/config.properties -Dmode=create >&! mvn.log

Following is a sample Eclipse run configuration for the same thing.


Step 8 - Deploy application, Launch Server

Deploy the refset-rest.war file to a Tomcat server - either through Eclipse or a standalone tomcat installation.  NOTE: It should also be deployable to a simple Jetty container as an alternative.

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

  • Download and install apache tomcat 7 (or higher) 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 refset-rest.war file and use "Run As->Run on Server" to deploy to Tomcat.

  • 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:


    -Drefset.config=c:/refset/config/config.properties

Setting up Jetty in Eclipse is also very easy.  Follow these steps:


Step 9 - Test application

Check that it all works by going to

http://localhost:8080/refset-rest/index.html


This should be a demo app that contains a basic terminology browser and (in the header) a link to a  "swagger" Api documenting the service calls available. You should be able to log in to either the application or the Swagger services by authenticating with "guest" username and "guest" password.  

NOTE: in the Eclipse dev environment, the swagger API does not load properly because Eclipse m2e is unable to handle the maven plugin executions that handle the interpolation of ${base.url} in the swagger files.  Building and deploying the actual umls-server-rest.war file is needed for this to work properly.


Step 10 - Run the Examples

See the examples project for some sample code on using the REST APIs in a variety of different ways.  You can run the examples against the standard dev database load through Maven. 


cd /path/to/examples/
mvn install -DskipTests=false -Drefset.config=/path/to/config.properties

NOTE: the examples require the server to be running, they do not access the database directly.


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