OHDSI/Olympus

Name: Olympus

Owner: Observational Health Data Sciences and Informatics

Description: [UNDER DEVELOPMENT] OLYMPUS - An OHDSI Launcher and Configurator

Created: 2015-01-28 03:22:07.0

Updated: 2016-08-31 10:08:28.0

Pushed: 2015-10-07 19:13:31.0

Homepage:

Size: 108281

Language: JavaScript

GitHub Committers

User	Most Recent Commit	# Commits
Jon Duke	2015-04-28 13:25:21.0	6
Alex Franken	2015-10-07 19:13:27.0	120
Mark Velez	2015-09-29 16:20:18.0	3

Other Committers

User	Email	Most Recent Commit	# Commits
Charity Hilton	cahilton@regenstrief.org	2015-04-30 17:02:43.0	29

README

OLYMPUS - An OHDSI Launcher and Configurator

[UNDER DEVELOPMENT - TESTING PURPOSES ONLY]

Introduction

OLYMPUS (OHDSI Loaded on Your Computers to Perform Ultimate Science) is a package designed to simplify the configuration of CDM-based research environments and the usage of OHDSI tools.

Non-developers should download builds directly at http://www.ohdsi.org/analytic-tools/olympus-a-unified-platform-for-ohdsi-web-applications

Features

• Unified installation of the WebAPI server and a set of OHDSI applications
• A dashboard for app launching
• A configuration page for setting up WebAPI
• A job viewer
• Security

Technology

• Java
• Spring
• Jetty
• HTML5 / JS

System Requirements

• JRE >= 1.7 (Java 8 recommended due to a known issue with Java 7 when connected to VPNs & perm gen exhaustion)

Dependencies

• OMOP V5 CDM running an OHDSI supported dialect

Getting Started Building & Packaging

Olympus : By default, all vendor jdbc drivers are dependencies. If you wish to package with a single or subset, consider the vendor-specific db profiles mvn clean package -Polympus-oracle or package will all drivers mvn clean package . The default requires all dependencies to be accessible in an artifact repository.

Olympus packages the following applications. If you wish to build Olympus and change the applications, consider the following.

WebAPI (package using defaults mvn clean package)

• Add WebAPI.war to Olympus/src/main/webapp/WEB-INF/applications/

Hermes, Circe, Heracles, Calypso, JobViewer

• clone github repos
• copy each application to Olympus/src/main/webapp/ (e.g. webapp/Hermes, webapp/Heracles, etc.)
• edit js config files that specify WebAPI location. (GET 'http://localhost:20000/webapi' (default) endpoint to return array of available WebApis) – js files that are modified should also go in src/main/resources/applications/ , with the same path (e.g. src/main/resources/applications/Heracles/build/js/Heracles.config.js). Both the original and the ones in src/main/applications are needed so that one can develop locally with localhost and also package and deploy to a hosted server (mvn clean package -Dolympus.local.address=http://example.com:20000). maven-war-plugin webResources and filtering is used to support the latter. This mechanism is not triggered in time for use within eclipse (when run as a java application or using spring-boot maven plugin. TODO it may be worthwhile to spend some additional effort here and see if eclipse can “run on server”. Currently, one receives a “The selection cannot be run on any server”.
• See the history/log of changes made to an application after cloning/copying git log --stat -- src/main/webapp/Achilles . Check out changes in a commit git show 360b14.

Summary of changes:

• Heracles: 1) Heracles.config.js - set ohdsi_services to array returned by Olympus. 2.) Add jquery.js import into index.html
• Achilles (Web) - git show 360b14 - 1.) Change ajax calls from referencing local 'data/X.json' to call Olympus endpoint that returns the json, read from a file location defined in Olympus (default /var/achilles/data).

Changes are maintained in Olympus/src/main/resources/applications and are filtered and copied over the top of the respective files found in Olympus/src/main/webapp See 'Copying webapp webResources' in below log snippet.

O] --- maven-war-plugin:2.1.1:war (default-war) @ Olympus ---
O] Packaging webapp
O] Assembling webapp [Olympus] in [/Users/alfranke/Documents/IDE/workspace/Olympus/target/Olympus]
O] Processing war project
O] Copying webapp webResources [/Users/alfranke/Documents/IDE/workspace/Olympus/src/main/resources/applications] to [/Users/alfranke/Documents/IDE/workspace/Olympus/target/Olympus]
O] Copying webapp resources [/Users/alfranke/Documents/IDE/workspace/Olympus/src/main/webapp]
O] Webapp assembled in [805 msecs]
O] Building war: /Users/alfranke/Documents/IDE/workspace/Olympus/target/Olympus.war

To run, with the above changes considered, you must package the war and then run according to below.

Running Olympus

java -XX:MaxPermSize=128m -jar Olympus-XXX-exec.war -XX:MaxPermSize only needed prior to jre 8

Note: if you only need to develop against local Olympus code (not dependent upon the OHDSI applications), it is most efficient to run the Olympus.class as 'Java Application' (which will use an embedded jetty). Or you can use mvn spring-boot:run.

To launch a local WebAPI (if configured), on startup, add -Dolympus.webapi.launch.enabled=true

Olympus Working Directory

Olympus will create an 'olympus' directory within the ${java.io.tmpdir} environment variable location. Look for a log statement like this (Windows example) …

-05-07 15:48:54.443 INFO main org.ohdsi.olympus.DataSourceConfig -  - Using jdbcurl: jdbc:h2:file:C:\Users\afranken\AppData\Local\Temp\olympus\dbfile

Mac Example: Mac java.io.tmdir = /var/folders/56/dfxv12_d6wb8dd4blw46j43h0000gn/T Olympus dir = /var/folders/56/dfxv12_d6wb8dd4blw46j43h0000gn/T/olympus

Olympus Database

Olympus uses an h2 file database. You can access the h2 console after starting Olympus and authenticating with a user that has the 'ADMIN' authority.

http://localhost:20000/console

TODO

Consider maven war plugin web resources to contain modified application files (e.g. Hermes config.js, etc. and src/main/webapp/Hermes would contain unmodified source. Likely easier to do upgrades/diffs.

License

Apache