BCO Portal Local Deployment
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Configuration
In order to work with BCO API locally on a Mac OS, please follow the following steps to set up:
BCO_API
- Clone the GitHub Repository
- Open Terminal, enter the following commands:
git clone https://github.com/biocompute-objects/bco_api
cd bco_api
- Open Terminal, enter the following commands:
- Switch to the latest release branch:
git switch 22.10
- Enter the repository, create a virtual environment, and install the required packages:
pyenv local 3.9.4
(Note: will show as pyenv: command not found if already installed)python3.9 -m venv env
source env/bin/activate
(activated virtual environment by showing (env) (base) MacBook-Pro-3:bco_api)python -m pip install -r requirements.txt
(if installation failed, make sure you are in the correct path: /Users/Username/bco_api)
- Modify Configuration file
- Once in the virtual environment, make sure you are on the path:/Users/Username/bco_api
- Edit the server.conf file:
vim bco_api/bco_api/server.conf
- Quick check to make sure the server can run
cd bco_api/bco_api
(Note after this command, should under path /Users/Username/bco_api/bco_api)- Make migrations:
python3.9 manage.py migrate
- If run successfully, should observe the following:
- Create a super user for the API:
python3.9 manage.py createsuperuser
- Follow the prompts
python3.9 manage.py runserver 8000:
- Once see the messages as shown in the figure above, go to http://localhost:8000/api/admin/ on the local browser to see if BCO API is set up successfully
UserDB
- Clone the GitHub Repository
- Open Terminal, enter the following commands:
git clone https://github.com/biocompute-objects/userdb
cd userdb/
- Open Terminal, enter the following commands:
- Switch to the desired branch: e.g.
git switch 22.10
- Enter the repository, create a virtual environment, and install the required packages:
pyenv local 3.9.4
python3.9 -m venv env
source env/bin/activate
python -m pip install -r requirements.txt
- Modify the Config file:
vim portalusers/settings.py
- Make migrations:
python3.9 manage.py migrate
- Create a super user for the API:
python3.9 manage.py createsuperuser
(Note: this step can be skipped if a superuser is already created or not superuser account is not necessary) - Run server:
python3.9 manage.py runserver 8181
- If ran successfully, you should observe as shown in the following figure:
- Once see the messages as shown in the figure above, go to http://localhost:8181/users/admin/ on the local browser to see if BCO API is set up successfully (Note: If it worked you should be able to login using the SuperUser credentials you created above)
Portal Deployment Instructions
- Clone the repository
- git clone https://github.com/biocompute-objects/portal
- cd portal/
- Switch to the desired branch: e.g.
git switch 22.10
- Install packages with either of the following commands:
npm install
npm install --legacy-peer-deps
- Edit /portal/src/App.js line 87 based on your need :
- For local,
sending = hostnames.local
- For the test site,
sending = hostnames.test
- For the production site,
sending = hostnames.production
- For local,
- Start running:
npm run start
Production Portal Deployment
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, then perform a few administrative steps to start the API.
- Connect to 'go.vpn.gwu.edu/SMHS_BIOC' VPN first.
- Enter test/production server via:
ssh USERNAME@test.portal.biochemistry.gwu.edu
(for test server)/ssh USERNAME@portal.biochemistry.gwu.edu
(for production server) (Note: /home and /etc are shared between the two servers) - Backup and archive DB:
cd /var/www/bcoeditor/db_backups
cp ../bco_api/bco_api/db.sqlite3 db.sqlite3.bak.api.[TODAY'S DATE] (e.g. cp ../bco_api/bco_api/db.sqlite3 db.sqlite3.bak.api.22.10.25)
cp ../userdb/db.sqlite3 db.sqlite3.bak.udb.[TODAY'S DATE]
cp ../bco_api/bco_api/server.conf server.conf.bak.[TODAY'S DATE]
- Pull the repository
cd /var/www/bcoeditor/bco_api
git clone https://github.com/biocompute-objects/bco_api
(if cloned already, step not needed)
- Enter the repository, create a virtual environment and install the required packages:
- First switch to the proper user account via
su - bco_api_user
(If you need to use this account, please contact the BCO team for the password) - Switch to the desired branch:
git switch 22.11
source env/bin/activate
pip3.9 install -r requirements.txt
- First switch to the proper user account via
- Check the Configuration files:
- Edit the server.conf file:
vim /var/www/bcoeditor/bco_api/bco_api/server.conf
- Change the version number to match the version you are modifying
- Edit the server.conf file:
- Make sure the server can run and Make Migrations:
cd /var/www/bcoeditor/bco_api/bco_api
python3.9 manage.py migrate
python3.9 manage.py collectstatic
python3.9 manage.py runserver 8000
- Go to https://test.portal.biochemistry.gwu.edu/api/admin/ to check if the server runs properly
- Ctrl+C to exit the running server
- sudo Steps:
- nGinx (only if bco_api.conf was modified):
sudo cp /var/www/bcoeditor/bco_api/admin_only/bco_api.conf /etc/nginx/conf.d/
- Gunicorn (only if bco_api.conf was modified):
- Copy the system service files over:
sudo cp /var/www/bcoeditor/bco_api/admin_only/bco_api.service /etc/systemd/system/bco_api.service
sudo cp /var/www/bcoeditor/bco_api/admin_only/bco_api.socket /etc/systemd/system/bco_api.socket
- Enable files:
sudo systemctl enable bco_api
- Start the service:
sudo systemctl start bco_api
- Copy the system service files over:
- Make sure the service is running:
sudo systemctl status bco_api
- nGinx (only if bco_api.conf was modified):
- Access API via web browser:
- Restart the server:
sudo systemctl restart nginx
- Deactivate virtual environment:
deactivate
- Check the server by going to either site on the web browser: https://biocomputeobject.org/api/admin/ (login using the SuperUser credential just created) or https://biocomputeobject.org/api/docs/
- Restart the server:
UserDB Production Portal Deployment
- Connect to 'go.vpn.gwu.edu/SMHS_BIOC' VPN first.
- Enter test/production server via
ssh USERNAME@test.portal.biochemistry.gwu.edu
(for test server)/ssh USERNAME@portal.biochemistry.gwu.edu
(for production server) (Note: /home and /etc are shared between the two servers) - Enter the repository:
cd /var/www/bcoeditor/userdb
- Clone the repository:
git clone https://github.com/biocompute-objects/bco_api
- Change directory:
cd /var/www/bcoeditor/userdb/bco_api
- Go to the desired branch/tag:
git switch 22.11(this number should be whatever branch you want to go to)
- Create a virtual environment:
source env/bin/activate
- Install the required packages:
pip3.9 install -r requirements.txt
- Modify the Configuration file:
vim /var/www/bcoeditor/userdb/portalusers/settings.py
- Make sure the server runs properly:
cd /var/www/bcoeditor/userdb
- Make migrations:
python3.9 manage.py migrate
followed bypython3.9 manage.py collectstatic
- Create a super user for the API:
python3.9 manage.py createsuperuser
- Run server:
python3.9 manage.py runserver 8080
- Ctrl+C to exit the running server
- Make migrations:
- Deactivate the virtual environment
- sudo Steps:
- Gunicorn (only if userdb.service OR userdb.socket IS MODIFIED):
cd admin_onlu
- Copy the system service files over:
sudo cp /var/www/bcoeditor/userdb/admin_only/userdb.service /etc/systemd/system/
sudo cp /var/www/bcoeditor/userdb/admin_only/userdb.socket /etc/systemd/system/
- Enable files:
sudo systemctl enable bco_api
- Start the service:
sudo systemctl start bco_api
- Copy the system service files over:
- Make sure the service is running:
sudo systemctl status bco_api
- Restart the server:
sudo systemctl restart nginx
- Make sure API is accessible via web browser. (EX: https://portal.biochemistry.gwu.edu/users/admin/. Log in using the superuser credential created)
- Gunicorn (only if userdb.service OR userdb.socket IS MODIFIED):
Portal Deployment
- Pull the repository:
cd /var/www/bcoeditor/portal
- Switch branch:
git switch --detach 22.01(any branch name) -f
npm install
ornpm install --legacy-peer-deps
- Edit /var/www/bcoeditor/portal/src/App.js based on need. For example, when working on the test portal, make sure
const sending = hostnames.test
, also update the versions underconst versions
Manual Account Creation
- Clear the dbs (rdb.sh) and sign up for an account:
sudo journalctl -u bco_api | tail -n 30
- Take token and email and enter as follows:
[HOSTNAME]/api/accounts/activate/[EMAIL with @ escaped(%40)]/[TempID]['email', 'temp_identifier', 'hostname', 'token']
{'email': 'hadley_king@gwu.edu', 'temp_identifier': 'a20b90c7eec1447a9829071d60394951', 'hostname': 'https://portal.biochemistry.gwu.edu/users/add_api/', 'token': 'eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJ1c2VyX2lkIjoxLCJ1c2VybmFtZSI6ImhhZGxleWtpbmci