tranSMART

This is the repository containing the core components and documentation of the tranSMART platform, an open source data sharing and analytics platform for translational biomedical research. tranSMART is maintained by the tranSMART Foundation. Official releases can be found on the tranSMART Foundation website, and the tranSMART Foundation's development repositories can be found at https://github.com/transmart/.

Overview

The platform provides an API, which is available under transmart-rest-api. Its v1 endpoints are documented there, the v2 endpoints are documented using Swagger in open-api. There is a main application transmart-server, exposing the API and extended by multiple plugins. As an user interface there is a frontend application transmartApp built as a "web" profiled Grails platform plugin, and an Angular4 based front end named glowing bear is being developed. The OAuth2 authentication of the API is managed by transmart-oauth plugin.

Database definitions and installation instructions are in transmart-data. A data loading tool based on Spring Batch is available as transmart-batch.

Relation to other transmart repositories

Before version 17.1, the tranSMART source code was split over a number of different repositories with names such as transmartApp, transmart-core-api, transmart-core-db, transmart-rest-api, RModules, etc. As of version 17.1 the components that make up the core server have been merged into a single repository. If you want the source for tranSMART 16.x or older, look at the separate repositores, if you want the sources for version 17+, you will want this repository.

Build and run

The project is built using gradle. Any version > 2.12 and < 2.3 should suffice (version 2.13 is recommended). Other versions may cause some build issues. To build the project, run:

gradle :transmart-server:bootRepackage

This should create the file transmart-server/build/libs/transmart-server-17.1-SNAPSHOT.war. Run it with:

java -jar transmart-server/build/libs/transmart-server-17.1-SNAPSHOT.war

The application expects configuration in ~/.grails/transmartConfig. Check transmart-data on how to set up the database and generate the required configuration files.

Deployment

Deployment artefacts are published to the Nexus repository of The Hyve.

Fetch and run transmart-server:

# Fetch artefacts using Maven 
mvn dependency:get -Dartifact=org.transmartproject:transmart-server:17.1-SNAPSHOT:war -DremoteRepositories=https://repo.thehyve.nl/content/repositories/snapshots/,https://repo.grails.org/grails/core
mvn dependency:copy -Dartifact=org.transmartproject:transmart-server:17.1-SNAPSHOT:war -DoutputDirectory=.
# Start the web application
java -jar transmart-server-17.1-SNAPSHOT.war

Fetch transmart-data, configure, start services

tranSMART also requires a configuration file to be generated in ~/.grails/transmartConfig and Rserve and Solr to run. Scripts to generate the configuration and to start Rserve and Solr are shipped with transmart-data.

Fetch transmart-data:

mvn dependency:get -Dartifact=org.transmartproject:transmart-data:17.1-SNAPSHOT:tar -DremoteRepositories=https://repo.thehyve.nl/content/repositories/snapshots/
mvn dependency:unpack -Dartifact=org.transmartproject:transmart-data:17.1-SNAPSHOT:tar -DoutputDirectory=.

To generate the configuration, please consult the documentation of transmart-data. Once a correct vars file has been created, the configuration can be generated and installed with these commands (requires php):

pushd transmart-data-17.1-SNAPSHOT
source vars
make -C config install
popd

Start Solr:

pushd transmart-data-17.1-SNAPSHOT/solr
java -jar start.jar &
popd

Rserve can be fetched and installed using apt (for debian or ubuntu) or yum (for redhat or centos). For apt, use:

# Using apt
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 79cbff36340878cfb6a09bbecf5b7bd93375da21
sudo add-apt-repository "deb http://apt.thehyve.net/internal/ xenial main"
sudo apt-get update
sudo apt-get install transmart-r

For yum, use the following repository url with gpgcheck=0: https://repo.thehyve.nl/content/repositories/releases.

Git history

This repository is a merge of several, previously separated, repositories from github.com/transmart. The history of those repositories is merged in as well (branch transmart-history), but the current master branch is disconnected from these histories. The master branch can locally be connected to the history with git replace.

# replace the master-base object with transmart-history
git replace 58a48ff dd57ce1

License

Copyright © 2008-2017 See the COPYRIGHT file.

tranSMART is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Some subprojects may have more permissive licenses. Check the individual projects and files for details.