Update Build and Deployment Documentation

[martinjoconnor]

Documentation needs to be updated in several places.

Some notes from Alex:

CEDAR Documentation instructs to start frontend service with “gulp” or “starteditor” command; however that is not necessary since nginx can serve frontend content directly as long as  etc/nginx/cedar/frontend-cedar.inc.conf configured something like this:
 

server {

    listen          80;

    server_name     cedar.metadatacenter.orgx;

    return          301 https://cedar.metadatacenter.orgx$request_uri;

}

 

server {

    listen          443 ssl;

    server_name     cedar.metadatacenter.orgx;

    include         cedar/include-ssl.conf;

    root              /home/cedar/CEAR/cedar-template-editor/app/;

    try_files       $uri /index.html;

    error_log       /home/cedar/CEDAR/log/cedar-frontend-editor/nginx-error.log warn;

    access_log      /home/cedar/CEDAR/log/cedar-frontend-editor/nginx-access.log combined if=$loggable;

}

 

When changing CEDAR_BIOPORTAL_REST_BASE it is a good idea to do the following in order to avoid odd inconsistencies:
clear browser cache
clear terminology server cache.  Terminology service caches the full list of ontologies and value sets (just their general description). It’s regenerated every 2 hours I believe. To force regeneration do: stopterminology, delete the {$CEDAR_HOME}/cache/terminology folder, startterminology, and wait for the cache to be regenerated (it will take around 5 minutes). The console output will tell you once it’s done
 
My previous recommendation to add  CEDAR_BIOPORTAL_API_KEY and CEDAR_BIOPORTAL_REST_BASE environmental variables to  ~/.bash_profile turned out to be counterproductive and it is better to set them only in one place (set-env-external.sh)