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
App Development¶
Guidelines for developing internal SODAR Core apps (ones included when installing the django-sodar-core package) are detailed in this section.
REST API Views¶
For internal SODAR Core apps, you need to use core counterparts to the mixins
than provided for SODAR Core using sites. The counterparts use different media
type and versioning from views to be implemented on external sites. This is to
prevent version number clashes requiring changes in external APIs. The classes
can be found in projectroles.views_api
and are as follows:
CoreAPIVersioning
CoreAPIRenderer
CoreAPIBaseMixin
CoreAPIBaseProjectMixin
CoreAPIGenericProjectMixin
For detailed API descriptions, see docstrings in the view_api
module. The
media type and versioning for these views are hardcoded and should not be
changed, except version information upon a new release of SODAR Core.
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