thehyve/transmart-core

Name: transmart-core

Owner: The Hyve

Description: Core components and documentation of the tranSMART platform. http://transmartfoundation.org

Created: 2017-04-05 08:07:13.0

Updated: 2017-10-20 16:04:20.0

Pushed: 2018-01-11 10:09:31.0

Homepage: null

Size: 348162

Language: JavaScript

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README

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 and Git history

This repository is a merge of several, previously separated, repositories from github.com/transmart, 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 this repository. If you want the source for tranSMART 16.x or older, look at the separate repositores.

The history of those repositories is merged into this one 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.

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

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:

le :transmart-server:bootRepackage

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

 -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:

tch artefacts using Maven 
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
dependency:copy -Dartifact=org.transmartproject:transmart-server:17.1-SNAPSHOT:war -DoutputDirectory=.
art the web application
 -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:

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

d transmart-data-17.1-SNAPSHOT
ce vars
 -C config install

Start Solr:

d transmart-data-17.1-SNAPSHOT/solr
 -jar start.jar &

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

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

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

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.