mechanism to pre-load (or dynamically load) the terminology code-system data modules.

[barabo]

The module/terminology/code-system directory structure needs a way to be populated.

One idea would be to update the fhir-jq shell function to inspect the jq exit code. It could look for code 32 (code-system unknown) or code 42 (concept_code unknown in a known code-system), and emit a hint for the user suggesting how the missing data should be added.

If a terminology database is available, the missing systems and concept fields could be automatically added. If users were instructed to download terminology from Athena to populate tables in a sqlite database, it would be easy to have the shell function parse the error message for the missing code-system / concept_code, create missing directories, and inject the codes that are failing.

A configuration option could suggest whether the whole set of codes is loaded when a new code-system is added, or whether new codes are added as they are needed.

Example

The current instructions have users define the following in their shell .rc file:

# The fhir-jq installation directory.
export FHIR_JQ="${HOME}/.jq/fhir"
mkdir -p "${FHIR_JQ}"

##
# fhir-jq is used just like jq, but it injects the path to the fhir-jq
# module when invoked.  All other `jq` args are passed along to jq.
#
function fhir-jq() {
  jq -L "${FHIR_JQ}" "${@}"
}

The shell function could be updated to look more like this:

##
# fhir-jq is used just like jq, but it injects the path to the fhir-jq
# module when invoked.  All other `jq` args are passed along to jq.
#
function fhir-jq() {
  jq -L "${FHIR_JQ}" "${@}"
  local jq_exit_code=${?}

  # Hint when a code is missing from a known code-system.
  if (( jq_exit_code == 42 )); then
    local fixer="${FHIR_JQ}/terminology/bin/add-concept-code.sh"
    cat <<EOM
To add the missing concept_code in the error above, run: ${fixer}
EOM

  # Hint when a code-system is missing.
  elif (( jq_exit_code == 32 )); then
    local fixer="${FHIR_JQ}/terminology/bin/add-code-system.sh"
    cat <<EOM
To add the missing code-system in the error above, run: ${fixer}
EOM

  # Hint when a generic error is detected.
  elif (( jq_exit_code != 0 )); then
    # etc...

  else
    # Default.
  fi

  # Return the original exit code.
  return ${jq_exit_code}
}