Configuring the CEDAR microservices¶
Some CEDAR microservices must be configured to allow them to access external resources.
This configuration information is stored in environment variables that are assigned by the
set-env-external.sh script, which is located at the base of your CEDAR installation directory.
You will have created this file earlier in the CEDAR installation process.
Terminology microservice configuration¶
CEDAR is supplied with controlled terminologies via a BioPortal or OntoPortal service, which may be running locally or remotely.
All access to a BioPortal or OntoPortal service is routed through the CEDAR terminology microservice.
This microservice is configured using two environment variables:
||Specifies an API key for accessing BioPortal or OntoPortal REST services|
||Specifies the base URL of the REST APIs for a BioPortal or OntoPortal service|
Instructions for obtaining a BioPortal or OntoPortal API key can be found here. If you want information on installing your own OntoPortal service (OntoPortal is the name we give the BioPortal software distribution that is used for external deployments) you can see the OntoPortal Administration Documentation.
CEDAR_BIOPORTAL_REST_BASE value is
https://data.bioontology.org/, which is the public BioPortal service.
If you wish to use this service, you can create an account there and immediately obtain the BioPortal API key associated with that account.
After obtaining an API key and determining the base REST endpoint URL, edit your
set-env-internal.sh file to set these variables.
These variables are read at microservice startup, so you will need to stop and restart the terminology microservice if it is aready running (using the commands,
startterminology, respectively) so that it picks up updated values.