SODAR Core Development

This document details instructions and guidelines for development of the SODAR Core package.

Repository Contents

In addition to the apps which will be installed by the package, the following directories are included in the repository for development use and as examples:

  • config: Example Django site configuration

  • docs: Usage and development documentation

  • example_backend_app: Example SODAR Core compatible backend app

  • example_project_app: Example SODAR Core compatible project app

  • example_site: Example SODAR Core based Django site for development

  • example_site_app: Example SODAR Core compatible site-wide app

  • requirements: Requirements for SODAR Core and development

  • utility: Setup scripts for development

Installation

Instructions on how to install a local development version of SODAR Core are detailed here. Ubuntu 16.04 LTS (Xenial) is the supported OS at this time. Later Ubuntu versions and Centos 7 have also been proven to to work, but some system dependencies may vary for different OS versions or distributions.

Installation and development should be possible on most recent versions of Linux, Mac and Windows, but this may require extra work and your mileage may vary.

If you need to set up the accompanying example site in Docker, please see online for up-to-date Docker setup tutorials for Django related to your operating system of choice.

System Installation

First you need to install OS dependencies, PostgreSQL 9.6 and Python3.6.

$ sudo utility/install_os_dependencies.sh
$ sudo utility/install_python.sh
$ sudo utility/install_postgres.sh

Database Setup

Next you need to setup the database and postgres user. You’ll be prompted to enter a database name, a username and a password.

$ sudo utility/setup_database.sh

You have to set the database URL and credentials for Django in the environment variable DATABASE_URL. For development it is recommended to place environment variables in file .env located in your project root. To enable loading the file in Django, set DJANGO_READ_DOT_ENV_FILE=1 in your environment variables when running SODAR or any of its management commands. See config/settings/base.py for more information and the env.example file for an example environment file.

Example of the database URL variable as set within an .env file:

DATABASE_URL=postgres://sodar_core:sodar_core@127.0.0.1/sodar_core

Project Setup

Clone the repository, setup and activate the virtual environment. Once in the environment, install Python requirements for the project:

$ git clone git+https://github.com/bihealth/sodar_core.git
$ cd sodar_core
$ pip install virtualenv
$ virtualenv -p python3.6 .venv
$ source .venv/bin/activate
$ utility/install_python_dependencies.sh

LDAP Setup (Optional)

If you will be using LDAP/AD auth on your site, make sure to also run:

$ sudo utility/install_ldap_dependencies.sh
$ pip install -r requirements/ldap.txt

Final Setup

Initialize the database (this will also synchronize django-plugins):

$ ./manage.py migrate

Create a Django superuser for the example_site:

$ ./manage.py createsuperuser

Now you should be able to run the server:

$ ./run.sh

Testing

To run unit tests, you have to install the headless Chrome driver (if not yet present on your system), followed by the Python test requirements:

$ sudo utility/install_chrome.sh
$ pip install -r requirements/test.txt

Now you can run all tests with the following script:

$ ./test.sh

If you want to only run a certain subset of tests, use e.g.:

$ ./test.sh projectroles.tests.test_views

For running tests with SODAR Taskflow (not currently publicly available), you can use the supplied shortcut script:

$ ./test_taskflow.sh

Contributing

SODAR Core is currently in active development in a private BIH repository. The public GitHub repository is primarily intended for publishing stable releases. Furthermore, the issue IDs within the code and documentation point to our private issue tracker unless otherwise mentioned.