About InjectTool
================

Introduction
------------

The IMAGE InjectTool is a tool which makes it easier to archive genebank data into BioSamples
from the user point of view. InjectTool is structured as a web application and runs inside
a web server. Users can register into website in order to upload their data in a
private space, they can validate their data against `IMAGE-metadata`_ and can fix
or update data using the application. If data are compliant with `IMAGE-metadata`_
standards, they could upload their data into `BioSamples`_ using and use this
application even to maintain and update data from InjectTool to `BioSamples`_.
InjectTool site is available `here <https://inject.image2020genebank.eu/>`_,
while its code is available from `github <https://github.com/cnr-ibba/IMAGE-InjectTool>`_

.. image:: ../_static/use_case-injecttool.png


InjectTool composed image
-------------------------

InjectTool is a docker-compose application running Django, NGINX, PostgreSQL, redis
and Celery. The application is mainly developed in python, and structured in a
django project. Each docker container is structured in order to do specific stuff,
and they are linked through docker-composed `configuration file`_.

Here is a graphical presentation of InjectTool system:

.. image:: ../_static/docker-images.png

The container componing InjectTool are the followings:

- **nginx**: is the frontend layer to InjectTool. It runs a NGINX instance and it exposes ``26080`` port.
  It serves InjectTool application to users. It provide the static content of the site and forwards
  all the dynamic requests to the **uwsgi** container. The configuration files are
  inside the `nginx`_ folder of InjectTool project.

- **db**: is a PostgreSQL instance in which all InjectTool data are stored. The
  :ref:`UID <The Unified Internal Database>`
  is inside this image. All the configuration files are inside the `postgres`_
  folder, while data will be stored persistently inside the InjectTool working
  directory inside *postgres_data* folder

- **redis**: is a redis instance of InjectTool backend. It is required by Celery
  to store and retrive information for its tasks. It stores temporary data useful
  for the InjectTool application. It doesn't store anything outside its container
  environment, so all its data need to be considered as temporary

- **uwsgi**: is part of the backend layer. It manages django codes, it receives request
  from NGINX and replies with dynamic content. The configuration files are inside
  `uwsgi`_ folder of InjectTool project, while django code is stored inside and
  specific InjectTool configuration files are stored in `django_data`_ folder

- **asgi**: is part of backend layer. It manages real time message for real time
  updates (ie status update, messages updates) without reloading pages.

In addtion, we have three container based on *uwsgi* container which run different
celery operations:

- **celery-worker**: The first of the three containers running Celery. It relies on
  *uwsgi* container, since it share the same django code of *uwsgi*. It performs
  :ref:`InjectTool time consuming tasks <Asynchronous Tasks>` asynchronously, like
  data import, validation and data submission to BioSamples. It consumes task
  stored in *redis* by **celery-beat** or by the user while doing stuff,
  and has access to *postgres* database in order to store data persistently.

- **celery-beat**: The second of the three containers running celery. It send
  :ref:`routine tasks <Routine Tasks>` or tasks on regular timing to
  **celery-worker**. This operates without user intervention

- **celery-flower**: is a monitoring instance of celery workers. It displays information
  regarding tasks. Its contents are rendered in HTML and reached through ``5555`` port.
  This container is available only using ``docker-compose-devel.yml`` configuration
  file.

.. _`configuration file`: https://github.com/cnr-ibba/IMAGE-InjectTool/blob/master/docker-compose.yml
.. _`nginx`: https://github.com/cnr-ibba/IMAGE-InjectTool/tree/master/nginx
.. _`postgres`: https://github.com/cnr-ibba/IMAGE-InjectTool/tree/master/postgres
.. _`uwsgi`: https://github.com/cnr-ibba/IMAGE-InjectTool/tree/master/uwsgi
.. _`django_data`: https://github.com/cnr-ibba/IMAGE-InjectTool/tree/master/django-data
.. _`IMAGE-metadata`: https://github.com/cnr-ibba/IMAGE-metadata
.. _`BioSamples`: https://www.ebi.ac.uk/biosamples/