BCO Portal Local Deployment - Revision history

Twang9: /* Manual Account Creation */

2022-11-01T15:10:30Z

Manual Account Creation

← Older revision		Revision as of 15:10, 1 November 2022
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	== '''Manual Account Creation'''==		== '''Manual Account Creation'''==
	# Clear the dbs (rdb.sh) and sign up for an account: <code>sudo journalctl -u bco_api \| tail -n 30</code>		# Clear the dbs (rdb.sh) and sign up for an account: <code>sudo journalctl -u bco_api \| tail -n 30</code>
	# Take token and email and enter as follows:<code>[HOSTNAME]/api/accounts/activate/[EMAIL with @ escaped(%40)]/[TempID]		# Take token and email and enter as follows:<code>[HOSTNAME]/api/accounts/activate/[EMAIL with @ escaped(%40)]/[TempID]['email', 'temp_identifier', 'hostname', 'token']
	['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</code>		{'email': 'hadley_king@gwu.edu', 'temp_identifier': 'a20b90c7eec1447a9829071d60394951', 'hostname': 'https://portal.biochemistry.gwu.edu/users/add_api/', 'token': 'eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJ1c2VyX2lkIjoxLCJ1c2VybmFtZSI6ImhhZGxleWtpbmci</code>

Twang9 at 15:09, 1 November 2022

2022-11-01T15:09:49Z

← Older revision		Revision as of 15:09, 1 November 2022
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	# <code>npm install</code> or <code>npm install --legacy-peer-deps</code>		# <code>npm install</code> or <code>npm install --legacy-peer-deps</code>
	# Edit /var/www/bcoeditor/portal/src/App.js based on need. For example, when working on the test portal, make sure <code>const sending = hostnames.test</code>, also update the versions under <code>const versions</code>		# Edit /var/www/bcoeditor/portal/src/App.js based on need. For example, when working on the test portal, make sure <code>const sending = hostnames.test</code>, also update the versions under <code>const versions</code>

			== '''Manual Account Creation'''==
			# Clear the dbs (rdb.sh) and sign up for an account: <code>sudo journalctl -u bco_api \| tail -n 30</code>
			# Take token and email and enter as follows:<code>[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</code>

Twang9 at 20:45, 31 October 2022

2022-10-31T20:45:44Z

← Older revision		Revision as of 20:45, 31 October 2022
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	## Restart the server:<code>sudo systemctl restart nginx</code>		## Restart the server:<code>sudo systemctl restart nginx</code>
	## Make sure API is accessible via web browser. (EX: https://portal.biochemistry.gwu.edu/users/admin/. Log in using the superuser credential created)		## Make sure API is accessible via web browser. (EX: https://portal.biochemistry.gwu.edu/users/admin/. Log in using the superuser credential created)

			== '''Portal Deployment''' ==
			# Pull the repository: <code>cd /var/www/bcoeditor/portal</code>
			# Switch branch:<code>git switch --detach 22.01(any branch name) -f</code>
			# <code>npm install</code> or <code>npm install --legacy-peer-deps</code>
			# Edit /var/www/bcoeditor/portal/src/App.js based on need. For example, when working on the test portal, make sure <code>const sending = hostnames.test</code>, also update the versions under <code>const versions</code>

Twang9: /* UserDB Production Portal Deployment */

2022-10-28T22:00:05Z

UserDB Production Portal Deployment

← Older revision		Revision as of 22:00, 28 October 2022
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	### Start the service: <code>sudo systemctl start bco_api</code>		### Start the service: <code>sudo systemctl start bco_api</code>
	## Make sure the service is running: <code>sudo systemctl status bco_api</code>		## Make sure the service is running: <code>sudo systemctl status bco_api</code>
			## Restart the server:<code>sudo systemctl restart nginx</code>
			## Make sure API is accessible via web browser. (EX: https://portal.biochemistry.gwu.edu/users/admin/. Log in using the superuser credential created)

Twang9 at 21:57, 28 October 2022

2022-10-28T21:57:35Z

← Older revision		Revision as of 21:57, 28 October 2022
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	## Deactivate virtual environment: <code>deactivate</code>		## Deactivate virtual environment: <code>deactivate</code>
	## 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/		## 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/

			== '''UserDB Production Portal Deployment''' ==
			# Connect to 'go.vpn.gwu.edu/SMHS_BIOC' VPN first.
			# Enter test/production server via <code>ssh USERNAME@test.portal.biochemistry.gwu.edu</code> (for test server)/<code>ssh USERNAME@portal.biochemistry.gwu.edu</code> (for production server) (Note: /home and /etc are shared between the two servers)
			# Enter the repository: <code>cd /var/www/bcoeditor/userdb</code>
			# Clone the repository: <code>git clone https://github.com/biocompute-objects/bco_api</code>
			# Change directory: <code>cd /var/www/bcoeditor/userdb/bco_api</code>
			# Go to the desired branch/tag: <code>git switch 22.11(this number should be whatever branch you want to go to)</code>
			# Create a virtual environment: <code>source env/bin/activate</code>
			# Install the required packages: <code>pip3.9 install -r requirements.txt</code>
			# Modify the Configuration file: <code>vim /var/www/bcoeditor/userdb/portalusers/settings.py</code>
			# Make sure the server runs properly: <code>cd /var/www/bcoeditor/userdb</code>
			## Make migrations: <code>python3.9 manage.py migrate</code> followed by <code>python3.9 manage.py collectstatic</code>
			## Create a super user for the API: <code>python3.9 manage.py createsuperuser</code>
			## Run server: <code>python3.9 manage.py runserver 8080</code>
			## Ctrl+C to exit the running server
			# Deactivate the virtual environment
			#sudo Steps:
			## Gunicorn (only if userdb.service OR userdb.socket IS MODIFIED): <code>cd admin_onlu</code>
			### Copy the system service files over:
			#### <code>sudo cp /var/www/bcoeditor/userdb/admin_only/userdb.service /etc/systemd/system/</code>
			#### <code>sudo cp /var/www/bcoeditor/userdb/admin_only/userdb.socket /etc/systemd/system/</code>
			### Enable files: <code>sudo systemctl enable bco_api</code>
			### Start the service: <code>sudo systemctl start bco_api</code>
			## Make sure the service is running: <code>sudo systemctl status bco_api</code>

Twang9: /* Production Portal Deployment */

2022-10-28T20:35:23Z

Production Portal Deployment

← Older revision		Revision as of 20:35, 28 October 2022
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	## Restart the server: <code>sudo systemctl restart nginx</code>		## Restart the server: <code>sudo systemctl restart nginx</code>
	## Deactivate virtual environment: <code>deactivate</code>		## Deactivate virtual environment: <code>deactivate</code>
	## Check the server by going to either ~~sites~~ on the web browser: https://biocomputeobject.org/api/admin/(login using the SuperUser credential just created) or https://biocomputeobject.org/api/docs/		## 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/

Twang9: /* Production Portal Deployment */

2022-10-28T20:30:19Z

Production Portal Deployment

← Older revision		Revision as of 20:30, 28 October 2022
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	## <code>git clone https://github.com/biocompute-objects/bco_api</code> (if cloned already, step not needed)		## <code>git clone https://github.com/biocompute-objects/bco_api</code> (if cloned already, step not needed)
	# Enter the repository, create a virtual environment and install the required packages：		# Enter the repository, create a virtual environment and install the required packages：
	## First switch to the proper user account via <code> su - bco_api_user</code> （If need to use this account, please contact BCO team for password)		## First switch to the proper user account via <code> su - bco_api_user</code> （If you need to use this account, please contact the BCO team for the password)
	## Switch to the desired branch: <code>git switch 22.11</code>		## Switch to the desired branch: <code>git switch 22.11</code>
	## <code>source env/bin/activate</code>		## <code>source env/bin/activate</code>
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	## Edit the server.conf file: <code>vim /var/www/bcoeditor/bco_api/bco_api/server.conf</code>		## Edit the server.conf file: <code>vim /var/www/bcoeditor/bco_api/bco_api/server.conf</code>
	### Change the version number to match the version you are modifying		### Change the version number to match the version you are modifying
	# Make sure the server can run: <code>cd /var/www/bcoeditor/bco_api/bco_api</code>		# Make sure the server can run and Make Migrations:
	~~# Make Migrations:~~		## <code>cd /var/www/bcoeditor/bco_api/bco_api</code>
	## <code>python3.9 manage.py migrate</code>		## <code>python3.9 manage.py migrate</code>
	## <code>python3.9 manage.py collectstatic</code>		## <code>python3.9 manage.py collectstatic</code>
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	## Go to https://test.portal.biochemistry.gwu.edu/api/admin/ to check if the server runs properly		## Go to https://test.portal.biochemistry.gwu.edu/api/admin/ to check if the server runs properly
	## Ctrl+C to exit the running server		## Ctrl+C to exit the running server
			# sudo Steps:
			## nGinx (only if bco_api.conf was modified): <code>sudo cp /var/www/bcoeditor/bco_api/admin_only/bco_api.conf /etc/nginx/conf.d/</code>
			## Gunicorn (only if bco_api.conf was modified):
			### Copy the system service files over:
			#### <code>sudo cp /var/www/bcoeditor/bco_api/admin_only/bco_api.service /etc/systemd/system/bco_api.service</code>
			#### <code>sudo cp /var/www/bcoeditor/bco_api/admin_only/bco_api.socket /etc/systemd/system/bco_api.socket</code>
			### Enable files: <code>sudo systemctl enable bco_api</code>
			### Start the service: <code>sudo systemctl start bco_api</code>
			## Make sure the service is running: <code>sudo systemctl status bco_api</code>
			# Access API via web browser:
			## Restart the server: <code>sudo systemctl restart nginx</code>
			## Deactivate virtual environment: <code>deactivate</code>
			## Check the server by going to either sites on the web browser: https://biocomputeobject.org/api/admin/(login using the SuperUser credential just created) or https://biocomputeobject.org/api/docs/

Twang9: /* Production Portal Deployment */

2022-10-27T20:12:11Z

Production Portal Deployment

← Older revision		Revision as of 20:12, 27 October 2022
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	# Make sure the server can run: <code>cd /var/www/bcoeditor/bco_api/bco_api</code>		# Make sure the server can run: <code>cd /var/www/bcoeditor/bco_api/bco_api</code>
	# Make Migrations:		# Make Migrations:
	## python3.9 manage.py migrate		## <code>python3.9 manage.py migrate</code>
	## python3.9 manage.py collectstatic		## <code>python3.9 manage.py collectstatic</code>
	## python3.9 manage.py runserver 8000		## <code>python3.9 manage.py runserver 8000</code>
	## Go to https://test.portal.biochemistry.gwu.edu/api/admin/ to ~~make changes~~		## Go to https://test.portal.biochemistry.gwu.edu/api/admin/ to check if the server runs properly
	## Ctrl+C to exit the running server		## Ctrl+C to exit the running server

Twang9: /* Production Portal Deployment */

2022-10-27T19:30:20Z

Production Portal Deployment

← Older revision		Revision as of 19:30, 27 October 2022
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	## <code>source env/bin/activate</code>		## <code>source env/bin/activate</code>
	## <code>pip3.9 install -r requirements.txt</code>		## <code>pip3.9 install -r requirements.txt</code>
			# Check the Configuration files:
			## Edit the server.conf file: <code>vim /var/www/bcoeditor/bco_api/bco_api/server.conf</code>
			### Change the version number to match the version you are modifying
			# Make sure the server can run: <code>cd /var/www/bcoeditor/bco_api/bco_api</code>
			# Make Migrations:
			## 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 make changes
			## Ctrl+C to exit the running server

Twang9: /* Production Portal Deployment */

2022-10-25T15:41:49Z

Production Portal Deployment

← Older revision		Revision as of 15:41, 25 October 2022
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	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.		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: <code>ssh USERNAME@test.portal.biochemistry.gwu.edu</code> (for test server)/<code>ssh USERNAME@portal.biochemistry.gwu.edu</code> (for production server) (Note: /home and /etc are shared between the two servers)		# Enter test/production server via: <code>ssh USERNAME@test.portal.biochemistry.gwu.edu</code> (for test server)/<code>ssh USERNAME@portal.biochemistry.gwu.edu</code> (for production server) (Note: /home and /etc are shared between the two servers)
	# Backup and archive DB		# Backup and archive DB:
	## <code>cd /var/www/bcoeditor/db_backups</code>		## <code>cd /var/www/bcoeditor/db_backups</code>
	## <code>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)</code>		## <code>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)</code>