Rename to transmart-core.

CONTRIBUTING.md

@@ -15,7 +15,7 @@ Are you ready to contribute to TranSMART? We'd love to have you on board, and we
 ### Submitting a Pull Request
 Before you submit your pull request consider the following guidelines:
 
-* Search the [tranSMART](https://github.com/thehyve/transmart-upgrade/pulls) repository for an open or closed Pull Request
+* Search the [tranSMART](https://github.com/thehyve/transmart-core/pulls) repository for an open or closed Pull Request
   that relates to your submission.
 * Make your changes in a new git branch
 
@@ -40,7 +40,7 @@ Before you submit your pull request consider the following guidelines:
     git push origin [name_of_your_new_branch]
     ```
 
-* In GitHub, send a pull request to `transmart-upgrade:master`.
+* In GitHub, send a pull request to `transmart-core:master`.
 * If we suggest changes then
   * Make the required updates.
   * Re-run the tests on the project and ensure tests are still passing.
@@ -113,7 +113,7 @@ After your pull request is merged, you have to delete your branch (if it was not
     ```
 
 ## <a name="test-travis"></a> Automated tests on Travis CI
-All Pull Requests are automatically tested on [Travis CI](https://travis-ci.org/thehyve/transmart-upgrade). Currently there is a set of tests for the core modules:
+All Pull Requests are automatically tested on [Travis CI](https://travis-ci.org/thehyve/transmart-core). Currently there is a set of tests for the core modules:
 * Tests for transmart-core-db module against H2 database, 
 * Tests for transmart-rest-api module, 
 * Tests for transmart-core-db module against Postgres database,
@@ -175,4 +175,4 @@ Fix #1234
 ```
 ## <a name="additional-resources"></a>Additional Resources
 * [General GitHub documentation](http://help.github.com/)
-* [GitHub pull request documentation](http://help.github.com/send-pull-requests/)
+* [GitHub pull request documentation](http://help.github.com/send-pull-requests/)

README.md

@@ -1,5 +1,5 @@
 # tranSMART
-[![Build Status](https://travis-ci.org/thehyve/transmart-upgrade.svg?branch=master)](https://travis-ci.org/thehyve/transmart-upgrade/branches)
+[![Build Status](https://travis-ci.org/thehyve/transmart-core.svg?branch=master)](https://travis-ci.org/thehyve/transmart-core/branches)
 
 Repository containing the core components and documentation of the _tranSMART_ platform,
 an open source data sharing and analytics platform for translational biomedical research, maintained

contributors.md

@@ -1,11 +1,11 @@
-# transmart-upgrade contributers
+# transmart-core contributers
 Thank you for contributing to TranSmart
-[gijskant](https://github.com/gijskant)
-[JanKanis](https://github.com/JanKanis)
-[forus](https://github.com/forus)
-[ewelinagr](https://github.com/ewelinagr)
-[PiotrZakrzewski](https://github.com/PiotrZakrzewski)
-[BarteldKlasens](https://github.com/BarteldKlasens)
-[OlafMeuwese](https://github.com/OlafMeuwese)
-[rnugraha](https://github.com/rnugraha)
-[Jarvanerp](https://github.com/Jarvanerp)
+- [gijskant](https://github.com/gijskant)
+- [JanKanis](https://github.com/JanKanis)
+- [forus](https://github.com/forus)
+- [ewelinagr](https://github.com/ewelinagr)
+- [PiotrZakrzewski](https://github.com/PiotrZakrzewski)
+- [BarteldKlasens](https://github.com/BarteldKlasens)
+- [OlafMeuwese](https://github.com/OlafMeuwese)
+- [rnugraha](https://github.com/rnugraha)
+- [Jarvanerp](https://github.com/Jarvanerp)

docker/tm_test_db/Dockerfile

@@ -17,13 +17,13 @@ RUN curl -s "https://get.sdkman.io" | bash && \
 ENV BRANCH master
 # change this to use a different branch of transmart-upgrade
 
-RUN git clone -b $BRANCH --depth 1 https://github.com/thehyve/transmart-upgrade.git /tmp/transmart-upgrade
+RUN git clone -b $BRANCH --depth 1 https://github.com/thehyve/transmart-core.git /tmp/transmart-core
 
 ENV POSTGRES_PASSWORD ''
 
 RUN ln -snf /root/.sdkman/candidates/groovy/current/bin/groovy /bin/groovy
-RUN echo "cd /tmp/transmart-upgrade/transmart-data && \
+RUN echo "cd /tmp/transmart-core/transmart-data && \
  mkdir -p /var/lib/postgresql/tablespaces/{biomart,deapp,indx,search_app,transmart} && \
  chown -R postgres:postgres /var/lib/postgresql && \
- make -C env ../vars && source /tmp/transmart-upgrade/transmart-data/vars && \
+ make -C env ../vars && source /tmp/transmart-core/transmart-data/vars && \
  make postgres_test" >> /docker-entrypoint-initdb.d/01-create.sh

transmart-batch/README.md

@@ -62,8 +62,8 @@ The script `transmart-batch.sh` executes the generated `.jar` by running `java -
 These are the required commands:
 ```bash
     # fetch the source code
-    git clone https://github.com/thehyve/transmart-upgrade/
-    cd transmart-upgrade/transmart-batch
+    git clone https://github.com/thehyve/transmart-core
+    cd transmart-core/transmart-batch
     # build transmart-batch
     gradle shadowJar
     # run transmart-batch

transmart-java/contributors.md

@@ -1,7 +1,7 @@
-# transmart-upgrade contributers
+# transmart-java contributers
 Thank you for contributing to TranSmart
-[gijskant](https://github.com/gijskant)
-[JanKanis](https://github.com/JanKanis)
-[forus](https://github.com/forus)
-[ewelinagr](https://github.com/ewelinagr)
-[PiotrZakrzewski](https://github.com/PiotrZakrzewski)
+- [gijskant](https://github.com/gijskant)
+- [JanKanis](https://github.com/JanKanis)
+- [forus](https://github.com/forus)
+- [ewelinagr](https://github.com/ewelinagr)
+- [PiotrZakrzewski](https://github.com/PiotrZakrzewski)