Merge pull request thehyve#162 from thehyve/readme-license

Replace README, add license file.

COPYRIGHT

@@ -0,0 +1,2 @@
+TODO
+

LICENSE

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+tranSMART platform.
+Copyright (C) 2008-2017  The tranSMART developers.
+See the COPYRIGHT file at the top-level directory of this distribution.
+
+This program 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 (see <gpl-3.0.txt>).  If not, see
+<http://www.gnu.org/licenses/>.
+

README.md

@@ -1,30 +1,50 @@
-# transmart-upgrade
+# tranSMART
 [![Build Status](https://travis-ci.org/thehyve/transmart-upgrade.svg?branch=master)](https://travis-ci.org/thehyve/transmart-upgrade/branches)
 
-Temporary repo for sharing work on transmart upgrade to grails 3.1.10
-
-## To do
-### Repository
-- [x] Adapt `.travis.yml`
-- [ ] Migrate selected repositories after upgrade to a single one called `transmart`
-- [ ] Move in git history of originating repositories
-
-### Files, configuration
-- [x] Apply gradle modules architecture to the project
-- [x] Migrate `BuildConfig.groovy` to `build.gradle`
-- [x] Merge `DataSource.groovy` and `config.groovy` into application.groovy inside `grails-app/conf/`
-- [ ] (maybe) move ``*/src/main/resources/*` to `*/src/main/resources/public/*`, I'm not sure if that is needed or not, see https://github.com/grails/grails-core/releases/tag/v3.0.12
-	I think this is only needed if the resources in question are to be served under the `/static` path in the web application, but not sure.
-- [ ] Replace `WEB-INF/applicationContext.xml` and `sitemesh.xml`. Beans from applicationContext are now defined in `grails-app/conf/spring/resources.groovy`, sitemesh functionality is gone (so we'll need to see if it's needed and if so figure out a replacement)
-- [x] Move version from ``*GrailsPlugin.groovy` to `build.gradle`
-
-### Fix code
-- [x] Replace audit metric before and after with interceptors
-- [x] Move in fixes for change in hibernate classes paths
-
-### Tests
-- [x] transmart-core-db-tests
-- [x] transmart-rest-api
-    - Added `@Ignore` to `StudyLoadingServiceSpec`
-- [ ] transmartApp:
-    - all failing
+Repository containing the core components and documentation of the _tranSMART_ platform,
+an open source data sharing and analytics platform for translational biomedical research, maintained
+by the [tranSMART Foundation](http://transmartfoundation.org).
+
+## Overview
+
+The platform provides an API, which is available under [transmart-rest-api](transmart-rest-api).
+Its `v1` endpoints are documented there, the `v2` endpoints are documented using Swagger in [open-api](open-api).
+There is a frontend application [transmartApp](transmartApp) built on Grails, and an Angular based
+front end named [glowing bear](https://github.com/thehyve/transmart-base-ui) is being developed.
+The OAuth2 authentication of the API is currently also part of `transmartApp`.
+
+Database definitions and installation instructions are in [transmart-data](transmart-data).
+A data loading tool based on Spring Batch is available as [transmart-batch](transmart-batch).
+
+## Build and run
+
+The project is built using [gradle](https://gradle.org/). Any version `> 2.12` should suffice.
+To build the project, run:
+```
+gradle :transmartApp:bootRepackage
+```
+This should create the file `transmartApp/build/libs/transmartApp-17.1.war`.
+Run it with:
+```
+java -jar transmartApp/build/libs/transmartApp-17.1.war
+```
+
+The application expects configuration in `~/.grails/transmartConfig`. Check [transmart-data](transmart-data) on how to set up the database and generate the required configuration files.
+
+## License
+
+Copyright © 2008-2017  The tranSMART developers.
+See the [COPYRIGHT](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](gpl-3.0.txt) 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.
+