Update deployment scripts to use CI/CD

[syphax-bouazzouni]

Context

Currently, we are using our own scripts to do our deployments, the source code can be found here https://gite.lirmm.fr/jonquetlab/ontoportal_deploy_scripts.

Why do we don't use the original scripts in the appliance? the problem was that they were working only if we use the source code of NCBO and use the configuration files that are inside the appliance.

In September 2022, Alex from Stanford did pull requests to add GitHub actions to deploy our code each time we push code to GitHub.

• https://github.com/ncbo/bioportal_web_ui/pull/222
• https://github.com/ncbo/ontologies_api/commit/8875ec5ebd59b1c4a4d30baf771f333fbc4510b7
• not done for cron

Requirements

• [ ] See how it works and add developer documentation for it at https://ontoportal.github.io/administration/
• [x] #400
• [ ] We need to make it possible to start the action on demand not only on branch push
• [ ] Add branch stage and configure the action to deploy to Stageportal
• [ ] Configure the action to deploy the branch development to Testportal
• [ ] Configure the action to deploy the branch master to SIFR Bioportal and Agroportal

[syphax-bouazzouni]

Documentation from https://github.com/ncbo/bioportal_web_ui/blob/08f4ce636893e32dc3435042f28ad293bf5aed11/.github/workflows/deploy.yml

# Workflow to deploy OntoPortal UI to stage/prod systems
#
# Required github secrets:
#
# CONFIG_REPO - github repo containing config and customizations for UI. Format 'author/private_config_repo'
# it is used for getting capistrano deployment configuration for stages on the github actions runner and
# PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the UI hosts for pulling configs.
#
# GH_PAT - github Personal Access Token for accessing private config repo
#
# SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if UI nodes live on private network.
#
# DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/
# this SSH key is used for accessing jump host, UI nodes, and private github repo.

[syphax-bouazzouni]

Docs: https://stageportal.notion.site/How-to-deploy-our-code-4715f02dab9e4f16bb3312b93e13e9f6