Set Up COPO Project on Linux

Note

If you are using a different OS other than Ubuntu, you can skip this step. See COPO project guidelines for Windows users if Windows is your preferred OS.

Install Python

sudo apt -y install software-properties-common
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt update
sudo apt -y install python3.8

Install Python Development Tools

sudo apt -y install python3.8-distutils
sudo apt -y install build-essential libssl-dev libffi-dev
sudo apt -y install libxml2-dev libxslt1-dev python3-django
sudo apt update && sudo apt install -y default-jre rsync git nano libxml2-dev python build-essential make gcc python3-dev locales python3-pip ruby-dev rubygems poppler-utils

Install Required Packages

Install required packages and enable the databases to start on boot

sudo apt -y install supervisor
sudo gem install sass
sudo apt -y install redis mongodb postgresql
sudo systemctl enable mongodb
sudo systemctl enable postgresql
sudo systemctl enable redis

Install MongoDB on your local machine

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 7F0CEB10
echo "deb http://repo.mongodb.org/apt/ubuntu "$(lsb_release -sc)"/mongodb-org/3.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.0.list
sudo apt update
sudo apt -y install mongodb-org

Install Integrated Development Environment (IDE)

Any IDE can be used to work on the project. However, we recommend using one of the following IDEs:

PyCharm Professional

A cross-platform IDE that provides consistent experience on the Windows, macOS, and Linux operating systems.

sudo snap install pycharm-professional --classic

OR

Visit PyCharm website to download an appropriate version for your OS or download it from the Ubuntu Software Center.

Visual Studio Code

VSCode is a lightweight but powerful source code editor which runs on your desktop and is available on Windows, macOS and Linux.

It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages (such as C++, C#, Java, Python, PHP, Go) and runtimes (such as .NET and Unity).

Visit VSCode website to download an appropriate version for your OS or download it from the Ubuntu Software Center

Configure IDE

PyCharm

Note

If using VSCode IDE, you can skip this step.

Warning

If you encounter the error, Error: Please enable Django support for the project, navigate to File->Settings->Languages & Frameworks->Django->Enable Django to enable Django support for the project.

If using PyCharm IDE, add a new configuration by following the steps below: #. Navigate to Add New Configuration #. Select Django server #. Click Save

Visit Run/debug configurations to learn how to create a configuration in PyCharm.

VSCode

If using VSCode IDE, add a new configuration by following the steps below: #. Navigate to Run -> Add Configuration #. Edit the launch.json file that is created with the following file contents:

VSCode launch.json configuration file contents

{
	"version": "0.2.0",
	"configurations": [
   	 
    	{
        	"name": "Python: Django",
        	"type": "python",
        	"request": "launch",
        	"program": "${workspaceFolder}/manage.py",    
        	"env" : {
            	"PYTHONPATH1" : "${workspaceFolder}/lib:${PYTHONPATH}"
        	}, 	 
        	"args": [
            	"runserver",
            	"0.0.0.0:8000"
        	],
        	"django": true,
        	"justMyCode": false
    	}, 	 
    	{
        	"name": "Python: Django makemigration",
        	"type": "python",
        	"request": "launch",
        	"program": "${workspaceFolder}/manage.py",    
        	"env" : {
            	"PYTHONPATH" : "${workspaceFolder}/lib:${PYTHONPATH}"
        	}, 	 
        	"args": [
            	"makemigration"
        	],
        	"django": true,
        	"justMyCode": false
    	},           	 
    	{
        	"name": "Python: Celery Workers",
        	"type": "python",
        	"request": "launch",
        	"module": "celery",
        	"console": "integratedTerminal",
        	"env" : {
            	"GEVENT_SUPPORT": "True"
        	},
        	"args": ["-A", "web", "worker", "-l", "debug", "-P", "gevent", "--concurrency" , "10", "-Q", "celery",  "-E"],
        	"justMyCode": true
    	},
    	{
        	"name": "Python: Celery Beat",
        	"type": "python",
        	"request": "launch",
        	"module": "celery",
        	"console": "integratedTerminal",
        	"args": ["-A", "web", "beat", "-l", "debug"]
     	}    
	]
}

Declare Environment Variables

Set secrets in the environment variables in your .bashrc file. Activate .bashrc file by running the command: source .bashrc

If using PyCharm IDE, declare the environment variables in the following places: * Edit Configurations > Environment variables * File->Settings->Build, Execution, Deployment->Console->Python console * File->Settings->Build, Execution, Deployment->Console->Django console * File->Settings->Languages & Frameworks->Django->Enable Django

Set up Python virtual environment

Run the following commands within the project directory to set up a Python virtual environment for the project

Alternatively, you can create a virtual environment for the project with the command: python3 -m venv venv

Install packages with pip3 and Python3

 sudo apt install -y python3-virtualenv
 source venv/bin/activate
 pip3 install -r requirements/base.txt
 pip3 install celery
 python manage.py migrate && python manage.py social_accounts && python manage.py setup_groups && python manage.py setup_schemas && python manage.py createcachetable && supervisord -c celery.conf && supervisorctl -c celery.conf start all
 python manage.py createsuperuser

Warning

Here are solutions to possible errors that you might encounter after having ran the above commands:

Possible error #1: TypeError: ‘Collection’ object is not callable. If you meant to call the ‘authenticate’ method on a ‘Database’ object it is failing because no such method exists.

Solution #1: Run the command: $ pip3 install pymongo==3.11.4 Reason: pymongo versions >4 is incompatible with the COPO project
Possible error #2: Issues related to importlib, rdlib, lxml, numpy, pandas and cffi Python packages

Solution #2: #. In the requirements/base.txt file located in the project directory, change the version numbers for the following packages so that all packages can be compatible with each other
- asgiref==3.7.2
- cffi==1.15.1
- importlib-metadata==1.6.1
- lxml==4.9.3
- numpy==1.20.0
- pandas==1.2.2
1. Change line 12 in wizard_helper.py file from pandas.io.json import json_normalize to from pandas import json_normalize
2. Run the command: pip3 install -r requirements/base.txt again to install the packages
Possible error #2: text index required for $text query

Solution #3: Create an index in the SampleCollection in mongoDB: db.SampleCollection.createIndex( { "$**": "text" } )

Set Up Mongo Database in COPO Project

Note

Replace the username and password for MongoDB with your own username and password

Run the 4_mongo_setup.sh MongoDB set up script to configure the MongoDB database on your machine

Set up MongoDB in Studio3T

Note

Replace the <username> and <password> for MongoDB with your MongoDB username and password By default, the username for MongoDB is copo_user. The hostname,``localhost``,, can also be substituted with the IP address of 127.0.0.1

Create a new MongoDB connection manually with the following details: * Connection Name: copo_mongo * Connection Type: Standalone Connection * Hostname: localhost * Port: 27017 * Authentication: Username and Password * Username: copo_user * Password: <password> * Authentication Database: admin

OR

MongoDB URI: mongodb://copo_user:password@localhost:27017/copo_mongo?retryWrites=true&connectTimeoutMS=10000&authSource=admin&authMechanism=SCRAM-SHA-1

Set Up PostgreSQL Database in COPO Project

Note

Replace the username and password of PostgreSQL with your own username and password

Run the 3_db_setup.sh PostgreSQL set up script to configure the PostgreSQL database on your machine

Launch COPO Website

Launch COPO website using the following command

python manage.py runserver

Alternatively, click on the Run button (i.e the green play button) on the top-right corner of the PyCharm IDE to launch the website.