Lift and Shift Combined Updates

[jonrandahl]

This PR resolves or updates the following tickets:

• https://github.com/epimorphics/hmlr-linked-data/issues/114
• https://github.com/epimorphics/hmlr-linked-data/issues/117
• https://github.com/epimorphics/hmlr-linked-data/issues/124

Additional Changes:

• Updated the README to include the API_SERVICE_URL variable to ensure the local standard_reports_manager instance is used in the test environment.
• Ensures we're using the latest version of json_rails_logger as well as other minor and patch updated gems, please see Gemfile.lock for specific updates.