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thehyve / transmart-core

Core components and documentation of the tranSMART platform. https://i2b2transmart.org/
GNU General Public License v3.0
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data-warehouse open-source transmart

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tranSMART

Build Status

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 i2b2 tranSMART Foundation. Official releases can be found on the Foundation website, and the Foundation's development repositories can be found at https://github.com/transmart/.

All the instructions on how to install, build and run a private instance of tranSMART, get set up for developing or upgrade to the latest version of tranSMART from an older version are available in the installation documentation.

For details on contributing code changes via pull requests, see the Contributing document.

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. The main application is transmart-api-server, exposing the API.

As user interface, the modern cohort selector Glowing Bear is available.

The database schema is described in the data model documentation. The schema is created using Liquibase at application startup, when it is configured to do so (see Setup database). This is only tested with PostgreSQL. The transmart-copy tool can be used to load data into the database. Legacy database definitions and installation instructions are in transmart-data, tested with both PostgreSQL and Oracle databases.

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.

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

Further reading

License

Copyright © 2008-2018 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.