relis

ReLiS

ReLiS is a tool for conducting systematic reviews.

Systematic review is a technique used to search for evidence in scientific literature that is conducted in a formal manner, following a well-defined process, according to a previously elaborated protocol. Conducting a systematic reviews involves many steps over a long period of time, and is often laborious and repetitive. This is why we have created ReLiS which provides essential software support to reviewers in conducting high quality systematic reviews. With ReLiS, you can plan, conduct, and report your review.

Unlike other systematic review tools, ReLiS is an online tool that automatically installs and configures your projects. You conduct reviews collaboratively and iteratively on the cloud. ReLiS is engineered following a model-driven development approach. It features a domain-specific modeling editor and an architecture that enables on-the-fly installation and (re)configuration of multiple concurrently running projects.

You can use a publicly available instance of ReLiS at http://relis.iro.umontreal.ca/. This GitHub repository allows you to install ReLiS on your servers.

Features

High-level features supported:

• Collaboration support
• Protocol development and modification iteratively
• Traceability
• Decision tracking
• Support inclusion and exculsion
• Support quality assessment
• Data extraction form
• Data management
• Data maintenance
• Basic statistical analysis
• Report preparation
• Data sharing
• Visualization
• Export studies and data
• Storage of studies (all but PDF)

Installation

The project can be installed locally using docker. Make sure to follow the pre-requisite steps to have an up and running docker environment.

Pre-requisite:

• Install docker on your local environment (download at: https://www.docker.com/products/docker-desktop)
• Install docker-compose on your local environment (it comes by default with docker on mac and windows)
• Run command “docker-compose” to check that docker is correctly installed
• For Windows users, if Docker cannot start with the following error : “Hardware assisted virtualization and data execution protection must be enabled in the BIOS” then excute following steps:
  • Enable features : Virtual Machine Platform, Windows Subsystem for Linux and Hyper-V using “Windows Features” (See https://docs.docker.com/docker-for-windows/troubleshoot/#virtualization for more information)
  • Restart you system and press esc key or any correspondent key to enter the BIOS settings in windows
  • Press f10 or other key to enter BIOS Setup
  • Go to System Configuration then Device Configuration
  • Enable Virtualization
  • Restart your system If Docker still not start with the error “Docker.ApiServices.WSL2.WslKernet NotInstalledException” then excute following steps:
  • use the link https://docs.microsoft.com/en-us/windows/wsl/install-win10#step-4---download-the-linux-kernel-update-package to download and intall linux kernal update
  • Restart you system if Docker not start

Build and run the application:

1. Clone the project from GitHub (git clone https://github.com/geodes-sms/relis.git)

2. On Windows, ensure the end-of-line encoding for the files deployment/entrypoint.sh and deployment/tomcat/entrypoint.sh use UNIX LF (not CR LF).

3. Run following command from the directory deployment/

   docker-compose build

4. Run following command from the directory deployment/

   docker-compose up -d

5. From your browser go to url localhost:8083 to access the application. Default credentials are: Username: admin Password: 123

6. For test purpose you can also access the database using PHPMyAdmin on localhost:8083/phpmyadmin. Default credentials are: Username: root Password:

   No password required (You should use this feature only on the local environment).

7. If you get the error “Incorrect permissions on the configuration file, it should not be write to everyone!” then add the statement $cfg['CheckConfigurationPermissions'] = false; to the phpmyadmin config file: relis-docker-implementation\phpmyadmin\config.inc.php

Useful command

To connect inside your docker container run the following command from the directory relis_deployment/

docker-compose exec relis-application bash

Make sure the user has the rights to access and edit the workspace/ folder. For example, run

chmod -R 755 workspace

Make sure the user has the rights to access and edit the export_r/ folder. For example, run

chmod -R 777 cside/export_r/

PHP Container Debug with Xdebug and PhpStorm

1. Update relis_deployment/docker/Dockerfile by adding: RUN pecl install xdebug-2.6.0

2. Add xdebug setting to relis_deploymant\php\conf\50_xdebug.ini :

[xdebug]
xdebug.mode=debug
xdebug.remote_handler = dbgp
xdebug.client_host = host.docker.internal
xdebug.client_port = 9000
xdebug.start_with_request = yes
xdebug.discover_client_host = true
xdebug.idekey = VSCODE

3. Configure server in PhpStorm: In File -> Setting -> PHP ->Server. Add a new server using + icon, and configure it like on the following screenshot

Note: Make sure to check “Use path mappings” and map your implementation folder (for example: D:\Projects\ReLiSProject\relis-docker-implementation) to /u/relis/public_html

You can also check debug setting, Debug port : 9000

4. Configure Php remote debugger in PhpStorm: In Run -> Edit configurations -> PHP Remote Debug. Add a new configuration and give it values like on the following screenshot:

5. Build ReLiS docker image and Run ReLiS

   • Run following command from the directory relis_deployment/

   docker-compose build

   • Run following command from the directory relis_deployment/

   docker-compose up -d

6. Debugging: To debug click on Run and choose “docker” then you will notice that the debugger is waiting for incoming connection with ide key ‘docker’.

Application structure on GIT

Branch naming convention:

• prod: is the branch that is used in production
• prod-testing: is the branch used for final testing
• main: is the branch on which we develop
• feature-X (feature branch): X represents the feature we are working on (the number of the ticket if the feature is a task in github or a keyword for the task).

Development process:

1. Create new task : For any new task create a feature branch from develop before getting the last version of develop:

   git checkout main

   git pull origin main

   git checkout -b feature-taskNumber

2. Add your code: Add all changes needed in your feature branch
3. Update documentation: Go to initial_db.sql by updating or inserting the text in the info table (starting at line 141).
4. Create a pull request(PR) to the branch main: When the code is ready to be merged, create a pull request to the main branch. To avoid conficts while merging the code, make sure to pull the last version of develop in the feature branch before creating an PR.
5. Quality assurance: upon a PR on the main branch, a suite of unit tests verify the integrity of the new code. When the tests pass (see Github Actions), you can merge the feature-X branch and delete it.
6. Repeat steps 1 to 3 for each new task.

Deployment process:

1. Deploy to prod-testing: when the code is ready to be fully tested the code from main is moved to prod-testing branch. This branch is deployed on the test server for further testing.
2. Deploy the prod-testing branch to prod branch on a test server and proceed with testing. This branch is deployed on the production server to be available to the public.
3. Tag and release: create a tag from prod and create a release by increasing the version number.

Distribution

Source code

To compile the source code, you need the following dependencies:

The source code is licensed under a GNU GENERAL PUBLIC LICENSE 3

Change log

Version 1.2

Bug fixes prior to docker version

Version 1.1

Some preliminary bug fixes

Version 1.0

Initial version of ReLiS with CodeIgnitier