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Contributing to tranSMART

This applies to pre-release of 17.1 version of tranSMART.

Are you ready to contribute to TranSMART? We'd love to have you on board, and we will help you as much as we can. Here are the guidelines we'd like you to follow so that we can be of more help:

Contributing Code Changes via a Pull Request

Submitting a Pull Request

Before you submit your pull request consider the following guidelines:

  • Search the tranSMART repository for an open or closed Pull Request that relates to your submission.

  • Make your changes in a new git branch

    git checkout -b [name_of_your_new_branch] master

  • Create your patch, including appropriate test cases.

  • Follow our Coding Rules.

  • Commit your changes using a descriptive commit message that follows our commit message conventions.

    git commit -a

    Note: the optional commit -a command line option will automatically "add" and "rm" edited files.

  • Push your branch to GitHub:

    git push origin [name_of_your_new_branch]

  • 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.

    • Rebase your branch and force push to your GitHub repository (this will update your Pull Request):

      git rebase master -i
git push -f

That's it! Thank you for your contribution!

Resolving merge conflicts ("This branch has conflicts that must be resolved")

Sometimes your PR will have merge conflicts with the upstream repository's master branch. There are several ways to solve this but if not done correctly this can end up as a true nightmare. So here is one method that works quite well.

  • First, fetch the latest information from the master

    git fetch upstream

  • Rebase your branch against the upstream/master

    git rebase upstream/master

  • Git will stop rebasing at the first merge conflict and indicate which file is in conflict. Edit the file, resolve the conflict then

    git add <the file that was in conflict>
git rebase --continue

  • The rebase will continue up to the next conflict. Repeat the previous step until all files are merged and the rebase ends successfully.

  • Re-run the tests on your project to ensure tests are still passing.

  • Force push to your GitHub repository (this will update your Pull Request)

    git push -f

After your pull request is merged

After your pull request is merged, you have to delete your branch (if it was not deleted by the person performing the merge) and pull the changes from the main (upstream) repository:

  • Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:

    git push origin --delete [name_of_your_new_branch]

  • Check out the master branch:

    git checkout master -f

  • Delete the local branch:

    git branch -D [name_of_your_new_branch]

  • Update your master with the latest upstream version:

    git pull --ff upstream master

Adding database changes

Database schemas for both Oracle and Postgres are stored in the transmart-data project. In order to add a change there, follow the steps below:

  1. Add a change to both Postgres and Oracle ddl.
  2. Add a migration script for both Postgres and Oracle in a folder with a current development version scripts.
  3. Add a short description of the change in the release folder README. See the README for 17.1 release folder.
  4. If required, change the test data.

Automated tests on Travis CI

All Pull Requests are automatically tested on Travis CI. 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,
  • Tests for transmart-api-server module,
  • Tests for transmart-batch module,
  • Tests for transmart-solr-indexing module against Postgres database,
  • Tests for transmart-copy data uploader tool against Postgres database.

Coding Rules

To ensure consistency throughout the source code, keep these rules in mind as you are working:

Git Commit Guidelines

We have rules over how our git commit messages must be formatted. Please ensure to squash unnecessary commits so that your commit history is clean.

Commit Message Format

Each commit message consists of a header, a body and a footer.

<header>
<BLANK LINE>
<body>
<BLANK LINE>
<footer>

Any line of the commit message cannot be longer 100 characters! This allows the message to be easier to read on Github as well as in various git tools.

Header

The Header contains a succinct description of the change:

  • use the imperative, present tense: "change" not "changed" nor "changes"
  • don't capitalize first letter
  • no dot (.) at the end

Body

If your change is simple, the Body is optional.

Just as in the Header, use the imperative, present tense: "change" not "changed" nor "changes". The Body should include the motivation for the change and contrast this with previous behavior.

Footer

The footer is the place to reference GitHub issues that this commit Closes.

You must use the Github keywords for automatically closing the issues referenced in your commit.

Example

For example, here is a good commit message:

upgrade to Spring Boot 1.1.7

upgrade the Maven and Gradle builds to use the new Spring Boot 1.1.7,
see http://spring.io/blog/2014/09/26/spring-boot-1-1-7-released

Fix #1234

Additional Resources