EHR-QC-Preprocess
=================

Follow the below steps to install EHR-QC-Preprocess in your computer.


Login
------

Upon login to a system and opening a terminal, the following prompt should appear, where the ``user`` is the user name and the ``hostname`` is the hostname of the system.

.. code-block:: console

   user@hostname:~$


Change directory
----------------

From the home directory which will be open by default, change to a suitable directory on your computer where the utility needs to be installed. For example, in this tutorial we have changed to ``workspace`` directory.

.. code-block:: console

   user@hostname:~$ cd workspace


Clone
-----

In the destination folder, clone the current version of EHR-QC repository from the GitHub.

.. code-block:: console

   user@hostname:~/workspace$ git clone <Add GitLab repo link here>


Open EHR-QC
-----------

Open the ``EHR-QC-Preprocess`` directory that is downloaded from GitHub after cloning.

.. code-block:: console

   user@hostname:~/workspace$ cd EHR-QC-Preprocess


Python virtual environment
--------------------------

The Python virtual environment encaptulates all the libraries required for the EHR-QC-Preprocess. All the necessary libraries listed in a requirements.txt file that can be found at the root of the repository. Below are the instructions to create and install dependancies in the Python virtual environment.

.. note::
   ``EHR-QC-Preprocess`` requires ``Python version 3.9`` or higher. For installing Python, please refer the below link: https://www.python.org/downloads/


Create virtual environment
~~~~~~~~~~~~~~~~~~~~~~~~~~

Inside the ``EHR-QC-Preprocess`` directory, create a new Python virtual enviroment to conveniently manage all the dependencies required for the utility.

.. code-block:: console

   user@hostname:~/workspace/EHR-QC-Preprocess$ python3 -m venv .venv


Activate virtual environment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

After creating the Python virtual enviroment, activate the virtual enviroment to start using it for subsequent commands. The prompt will change with ``(.venv)`` appearing in front of it as shown below;

.. code-block:: console

   user@hostname:~/workspace/EHR-QC-Preprocess$ source .venv/bin/activate
   (.venv) user@hostname:~/workspace/EHR-QC-Preprocess$


Install dependencies
~~~~~~~~~~~~~~~~~~~~

Install all the required dependencies listed in the requirements.txt file in the newly created Python virtual environment.

.. code-block:: console

   (.venv) user@hostname:~/workspace/EHR-QC-Preprocess$ pip install -r requirements.txt


Verify
~~~~~~

Verify the installation by running the following command. The expected output should contain ``EHR-QC <version number>``.

.. code-block:: console

   (.venv) user@hostname:~/workspace/EHR-QC-Preprocess$ python -m EHR-QC -v
   EHR-QC 1.0