Added documentation related to local code deployment

docs/developers-docs/deploying_local_code.md

@@ -0,0 +1,91 @@
+---
+title: Deploying local code
+layout: default
+summary: The procedure to deploy your own code onto the appliance
+status: Draft
+parent: Developer Guide
+nav_order: 5
+---
+# Deploying local code
+The procedure to deploy your own code in the appliance
+{: .fs-6 .fw-300 }
+
+You may want to use your own code in the appliance. In that case you will need to modify a few configuration files in order to use your repository instead of the NCBO one. There is no fixed procedure yet since it relies on the dependencies and the appliance version you are using.
+
+## Deploying a fork of AgroPortal into a 3.1 appliance (10-10-2023)
+
+Deploying the API code.
+```
+# Edit the deploy.rb file
+nano /srv/ontoportal/ontologies_api/current/config/deploy.rb
+# Replace the NCBO repo with your repository
+
+# Copy configuration files
+cp -r /srv/ontoportal/virtual_appliance/appliance_config/ontologies_api/config /srv/ontoportal/ontologies_api/shared/config
+
+# Install required gems and deploy the API using Capistrano
+cd /srv/ontoportal/ontologies_api/current
+bundle install --with development
+bundle exec cap appliance deploy
+```
+
+Deploying the UI code and update the dependencies.
+This procedure does not include Github actions to automatize the deployment so you will be running a few bundle commands to manually update the appliance with your latest code.
+```
+# Install Ruby 2.7
+rbenv local 2.7.6
+sudo su - ontoportal
+echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile
+echo 'eval "$(rbenv init -)"' >> ~/.bash_profile
+bash
+
+# Install Node.js 14
+# (as centos user)
+curl -sL https://rpm.nodesource.com/setup_14.x | sudo bash -
+sudo yum clean all && sudo yum makecache fast
+sudo yum install -y gcc-c++ make
+sudo yum install -y nodejs
+
+# Install required gem
+sudo /usr/local/rbenv/shims/gem install --default uri --version 0.12.0
+
+# Copy UI configuration files
+cp -r /srv/ontoportal/virtual_appliance/appliance_config/bioportal_web_ui/config /srv/ontoportal/bioportal_web_ui/shared/config
+cp -r /srv/ontoportal/bioportal_web_ui /srv/ontoportal/ontoportal_web_ui
+
+# Edit Rails credentials
+cd /srv/ontoportal/ontoportal_web_ui/current
+RAILS_ENV=appliance EDITOR="nano" bin/rails credentials:edit --environment appliance
+
+# Create a directory for credentials and copy them
+mkdir /srv/ontoportal/ontoportal_web_ui/shared/config/credentials
+cp config/credentials/* /srv/ontoportal/ontoportal_web_ui/shared/config/credentials/
+
+# Modify deploy.rb
+# (Append the listed linked files and directories)
+# Example:
+# append :linked_files, 'config/database.yml', 'config/bioportal_config_appliance.rb'
+# append :linked_dirs, 'log', 'tmp', '.bundle', 'config/locales'
+# append :linked_files, 'config/secrets.yml', 'config/site_config.rb', 'config/newrelic.yml','config/credentials/appliance.key', 'config/credentials/appliance.yml.enc
+
+# Upload newrelic.yml (if needed)
+# Copy database.yml
+cp config/database.yml /srv/ontoportal/ontoportal_web_ui/shared/config
+
+# Copy UI configuration
+cp -r /srv/ontoportal/virtual_appliance/appliance_config/bioportal_web_ui/ /srv/ontoportal/virtual_appliance/appliance_config/ontoportal_web_ui
+
+# Modify bioportal_config_appliance.rb with updated config
+
+# Install Capistrano and deploy. This is the set of commands you will use every time you want to update the appliance with the latest code
+bundle install --with development
+bundle config unset with
+bundle exec cap appliance deploy
+
+# Update Apache configuration if necessary
+sudo nano /etc/httpd/conf.d/10-appliance...
+# Change "bioportal" to "ontoportal" if the repo name is different from the original
+
+# Restart the server
+sudo oprestart
+```