Edge Module API

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This repository contains the backend of the edge-module. It's intended to be deployed locally at the edge of the MES-CoBraD platform.

Such set of APIs allows the communications between the Edge module UI (Deployed within the MES-CoBraD platform) and the edge module functionalities.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

• Python 3.7
• Git

Installing

A step by step series of examples that tell you how to get a development env running

Install docker on you dev machine

https://docs.docker.com/get-docker/

Run the following command to initializate a Python 3.7 environment

docker run --name python-dev --env-file dev.env -v "$(pwd)/src:/usr/src/" -d python:3.7-slim tail -f /dev/null && docker exec -it python-dev /bin/sh

Install Git

apt-get update
apt-get install git

Install Dependencies

pip3 install --no-cache-dir -r requirements.txt

Deployment

1. Open terminal (Find a launcher for the terminal by clicking on the Activities item at the top left of the screen, then type 'terminal'. If you can't find the launcher you can try keyboard shortcut to start it: Ctrl-Alt-T)

2. Next step is installing Docker. Type next commands one by one in terminal:

   wget https://get.docker.com
   

   mv index.html get-docker.sh && chmod a+x get-docker.sh
   

   DRY_RUN=1 sudo sh ./get-docker.sh
   

   DRY_RUN=0 sudo sh ./get-docker.sh
   

3. Next step is creating folder where all the needed files will be stored and download files. Follow next steps, one by one:

   mkdir mescobrad-edge
   

   cd mescobrad-edge
   

   wget https://raw.githubusercontent.com/mescobrad-project/edge-module-api/main/docker/docker-compose.yml
   

   wget https://raw.githubusercontent.com/mescobrad-project/edge-module-api/main/docker/edge_module.config
   

4. Set credentials for local instance of the MinIO in the downloaded docker-compose.yml file:

   • First open docker-compose.yml file:

     nano docker-compose.yml
     

   • Instead of empty string, type your credentials for next variables in the open file. Take care that min length of characters for user is 5 and for password is 8:

     MINIO_ROOT_USER: ""
     

     MINIO_ROOT_PASSWORD: ""
     

5. Customize edge_module.config file.

   • First open edge_module.config file:

     nano edge_module.config
     

   • Set the following variables in the opened file:

     OBJ_STORAGE_URL_LOCAL=http://mescobrad-edge_minio_1:9000
     

     OBJ_STORAGE_ACCESS_ID_LOCAL - the same username you have chosen in previous step (value of *MINIO_ROOR_USER* from the previous step)
     

     OBJ_STORAGE_ACCESS_SECRET_LOCAL - the same password you have chosen in previous step (value of *MINIO_ROOT_PASSWORD* from the previous step)
     

     OBJ_STORAGE_BUCKET_LOCAL - a bucket name of your choice
     

6. Run the docker-compose.yml:

   • First login into registry.opsilab.eng.it

     docker login registry.opsilab.eng.it
     

   • Run the following command

     docker-compose -f docker-compose.yml up -d
     

7. Run Swagger UI:

   • First download swagger.yaml file:

     wget https://raw.githubusercontent.com/mescobrad-project/edge-module-api/main/src/mescobrad_edge/swagger/swagger.yaml
     

   • Open https://editor.swagger.io/ in the browser
   • Import the swagger.yaml file downloaded in the previous step. Open File tab within main menu, and choose Import file, and then choose swagger.yaml file
   • Be sure that the schemes are set to HTTP. From the drop down menu schemes choose HTTP.
   • Within authorize tab put 'abc' as a token
   • Run plugins/install_plugin providing following urls to install. Choose the ones which you need and install each, one by one.

     • Plugins needed to install for using questionnaires anonymisation plugin:

       • https://github.com/mescobrad-project/edge_plugin_upload.git
       • https://github.com/mescobrad-project/edge_plugin_download.git
       • https://github.com/mescobrad-project/questionnaire_anonymisation_plugin.git

     • MRI anonymisation plugin:

       • https://github.com/mescobrad-project/mri_anonymisation_plugin.git

     • EDF anonymisation plugin:

       • https://github.com/mescobrad-project/edf_anonymisation_plugin.git

8. Navigate to each plugin folder under /var/lib/docker/volumes/plugins and change data within plugin.config file. For example:

   cd var/lib/docker/volumes/plugins/mri_anonymisation_plugin
   

   nano plugin.config
   

   When file is updated, save and close file. Continue in the same way for all the others installed plugins.

Note: All the variables which contain LOCAL within name, reference to the local instance of MinIO, otherwise reference to the data lake instance

Built With

• Connexion - a framework built on top of Flask that automagically handles HTTP requests based on OpenAPI Specification
• Pip - Dependency Management

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Danilo Trombino - SW & Data Engineer - trowdan

See also the list of contributors who participated in this project.