Allow external definitions

[abhidg]

We should be able to lookup from an external data source. Use cases for this functionality:

• Looking up names of countries from ISO codes
• Looking up latitude, longitude from name
• Mapping unique IDs from another source

[abhidg]

Detailed description

Allow external definitions in adtl. Two kinds of external definitions are supported:

• Passed on the command line as --def that will add the definition(s) to the definition map
• Included statically in include_defs section in the top-level adtl header

Example of including an external definition:

[adtl]
include_defs = ["./country.toml"]

This will add the country.toml file in the same folder to the definitions map. For example, country.toml could look like this

[countryMap.values]
1 = "ALB"
2 = "ZZZ"

Similarly, RELSUB files for clinical data are mappings from the visit IDs to subject IDs and should be used in a similar way as countryMap. However, unlike the above, RELSUB files should not be committed to version control as they are sensitive data (patient IDs). In that case, we could call adtl with the --def option as follows

adtl parsers/someparser.toml data.csv --def relsub.json

Assuming relsub.json has the following structure

{ "RELSUB":
  {
     "values": {
	 "S-001": 1,
	 "S-002": 2,
	 "S-003": 3,
     }
  }
}

this will create a RELSUB reference that within the adtl parser that can be used like any other reference.