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BioCompute Portal Local Deployment Instructions/notes

This README provides instructions to deploy the BioCompute Portal Locally

Prerequisites

Before starting, ensure you have the following installed:

BCO Portal Client deployment (portal_userdb/client)

  • For HTTPS access:

git clone https://github.com/biocompute-objects/portal_userdb

  • For SSH access*(RECCOMENDED)*:

git@github.com:biocompute-objects/portal_userdb.git

Then

cd portal_userdb/

Make sure you are on the desired branch:

git switch <BRANCH NAME> (24.06.27 Reccomended)

Stash Any Local Changes

git stash git stash drop

Enter the repository, create a environment file, and install the required packages

cd portal_userdb/client/

For Windows:

cd portal_userdb/client/

Install Node packages via Node Package Manager (NPM)

npm install

Set up the environment file

cp .env.example .env

Then you will have to add values for the following:

REACT_APP_USERDB_URL=http://localhost:8080/users/
REACT_APP_BCOAPI_URL=http://127.0.0.1:8000/api/
REACT_APP_GOOGLE_CLIENT_ID=******************************************
REACT_APP_ORCID_URL=https://sandbox.orcid.org
REACT_APP_ORCID_CLIENT_ID==******************************************
REACT_APP_ORCID_CLIENT_SECRET==******************************************
REACT_APP_SERVER_URL=http://localhost:3000
REACT_APP_BCOAPI_TOKEN=*****************

Verify you are still in the right directory and install client dependencies

cd client

npm install

Start service

npm run start

This will open http://localhost:3000/ in your default web browser if everything went according to plan. See the troubleshooting tips if not.

This terminal will be serving the React frontend.

BCO Portal Server deployment (portal_userdb/server)

Open a new terminal and return to the project root

cd PATH/TO/PROJECT/portal_userdb

Enter the server directory, create a virtual environment, and install the required packages

For Mac/Linux:

cd server

pyenv local 3.10.6 (optional)

python3 -m venv env

source env/bin/activate

pip3.9 install -r requirements.txt

For Windows:

cd server

python -m venv env

source env/Scripts/activate

pip install -r requirements.txt

If Given the Error Failed Building Wheel For Ruamel.Yaml.Clib Run These Commands

pyenv local (if pyenv was installed)

pyenv versions (if pyenv was installed)

pyenv local 3.10.6 (if pyenv was installed)

source ~/.zshrc (or specified terminal)

pip install --upgrade pip

Rerun Installation of Requirements.txt

pip install -r requirements.txt

Generate the secrets file

  • Copy the .secrets.example to .secrets

    cp .secrets.example .secrets

  • On linux (or MAC) generate a 32-bytes long PSK key using the openssl command for the DJANO_KEY:

openssl rand -base64 32

  • On Windows, generate a 32-bytes long PSK key using the PowerShell command for the DJANGO_KEY:

[Convert]::ToBase64String((1..32 | ForEach-Object { Get-Random -Minimum 0 -Maximum 256 }) -as [byte[]])

  • Update the .secrets file with the required keys:
[GOOGLE_KEYS]
DJANGO_GOOGLE_OAUTH2_CLIENT_ID=<your-client-id-here>
DJANGO_GOOGLE_OAUTH2_CLIENT_SECRET=<your-client-secret-here>

[DJANGO_KEYS]
SECRET_KEY=<your-Django-secret-key--here>

[ORCID_KEYS]
DJANGO_ORCID_OAUTH2_CLIENT_URL=http://localhost:3000
DJANGO_ORCID_OAUTH2_CLIENT_ID=<your-orcid-id-here>
DJANGO_ORCID_OAUTH2_CLIENT_SECRET=<your-orcid-secret-here>
DJANGO_ORCID_OAUTH2_URL=https://sandbox.orcid.org

[SERVER]
SERVER_VERSION=24.04
SERVER_URL=http://localhost:3000
SERVER_DB_URL=http://127.0.0.1:8000
#DATABASE=/Users/hadley_king/Data/userdb/db.sqlite3
DATABASE=db.sqlite3

Set up DB

Option #1: Use existing DB

cp admin/db.sqlite3 .

python3 manage.py migrate

superusername: bco_api_user
password: testing123
Option #2: Create a new DB with test data

Create a DB:

python3 manage.py migrate

Load the DB with test data:

python manage.py loaddata config/fixtures/local_data/json

Run Server

python3 manage.py runserver 8080

Make sure API is accessible via web browser. EX:

http://localhost:8080/users/admin/

If it worked you should be able to see the API Documentation site at:

http://localhost:8080/users/docs/

BCO_API

The BCO API repository contains a top-level folder “admin_only” which contains service definitions for gunicorn and django. Thus, we can first clone the repository (only necessary to clone once since we can use the shell scripts in the repository after the initial cloning to administer the application), then we can perform a few administrative steps to start the API.

Clone the repository

git clone https://github.com/biocompute-objects/bco_api

cd bco_api

Make sure you are on the desired branch (Check for latest branch):

git switch 24.06.27

Enter the repository, create a virtual environment, and install the required packages

pyenv local 3.10.6

python3 -m venv env

source env/bin/activate

python -m pip install -r requirements.txt

(You can use python3.9 if you’d like, but since you’re in the virtual environment you created python points to python3.9)

Modify the .Secrets file:

Check/Edit the .secrets file

This is the main server configuration file for the BCO API. (most of these values will NOT need to be changed for local deployment)

nano .secrets

**Add Given Fields and Contact Admin for Keys

[DJANGO_KEYS]
SECRET_KEY=***************
ANON_KEY=******************************
[SERVER]
PRODUCTION=False
DEBUG=True
ALLOWED_HOSTS=*
SERVER_VERSION=24.06.13
HOSTNAME=127.0.0.1:8000
HUMAN_READABLE_HOSTNAME=DEV BCODB
PUBLIC_HOSTNAME=http://127.0.0.1:8000
SERVER_URL=http://localhost:3000
DATABASE=db.sqlite3
EMAIL_BACKEND=django.core.mail.backends.console.EmailBackend

Set up DB

cd bco_api/bco_api

Option #1: Use existing DB

Copy the dev db

cp ../admin_only/db.sqlite3.dev db.sqlite3

superusername: bco_api_user
password: testing123

Make Migrations

python3 manage.py migrate

Option #2: Create a new DB

Make Migrations

python3 manage.py migrate

Create a super user for the API:

python3 manage.py createsuperuser

Then follow the prompts

Then: Do a quick check to make sure the server can run

Start the server

python3 manage.py runserver 8000

Make sure API is accessible via web browser.

[YOU WEB HOST HERE]/api/admin/

EX: http://localhost:8000/api/admin/

If it worked you should be able to login using the SuperUser credentials you created above

Log in with the superuser credentials you created or imported

If you copied over the existing dbs you should be able to log in with any of the crednetials listed in /portal_userdb/server/admin/users.tsv

Otherwise you will have to register a new user.