Install and Run

Install

Follow the below steps to install Pathogene-on-FHIR in your computer.

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.

user@hostname:~$ cd workspace

Clone

In a destination folder, clone current version of the Pathogene-on-FHIR repository from the GitHub.

user@hostname:~/workspace$ git clone https://github.com/ryashpal/Pathogene-on-FHIR.git

Open Pathogene-on-FHIR

Open the Pathogene-on-FHIR directory that is downloaded from GitHub after cloning.

user@hostname:~/workspace$ cd Pathogene-on-FHIR

Create Python virtual environment

The Python virtual environment encaptulates all the libraries required for the Pathogene-on-FHIR. 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

Pathogene-on-FHIR 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 Pathogene-on-FHIR directory, create a new Python virtual enviroment to conveniently manage all the dependencies required for the utility.

user@hostname:~/workspace/Pathogene-on-FHIR$ 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;

user@hostname:~/workspace/Pathogene-on-FHIR$ source .venv/bin/activate
(.venv) user@hostname:~/workspace/Pathogene-on-FHIR$

Install dependencies

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

(.venv) user@hostname:~/workspace/Pathogene-on-FHIR$ pip install -r requirements.txt

Verify

Verify the installation by running the following command. The expected output should contain Pathogene-on-FHIR <version number>.

(.venv) user@hostname:~/workspace/Pathogene-on-FHIR$ python -m Pathogene-on-FHIR -v
Pathogene-on-FHIR 1.0

Run

Use the below command to run the Pathogene-on-FHIR utility. This will run the utility according to the instructions provided in the configuration file.

For instructions on seting up configuration files, please refer to this `link https://ehr-int-tutorial.readthedocs.io/en/latest/configurations.html`_

(.venv) user@hostname:~/workspace/Pathogene-on-FHIR$ python src/Run.py