Framework configuration (_mighty.yml)

Overview

The _mighty.yml file provides framework configuration that spans across all ADaM domains. This file should be placed in the study directory alongside individual ADaM domain specification files.

External data

The external_data section specifies primary keys for all external datasets that will be available at runtime. This includes:

  • SDTM domains (e.g., DM, EX, LB)
  • Metadata datasets (e.g., MDPARAM, MDVISIT)
  • Pre-existing ADaM datasets (e.g., any ADaM dataset not being generated by mighty)

IMPORTANT: ADaM domains being generated by mighty should have their keys defined in their individual domain specification files (see vignette("adam_specification")), NOT in _mighty.yml.

IMPORTANT: Domain names must be specified in uppercase following CDISC standards (e.g., DM, EX, LB), regardless of the file name casing. The system automatically handles case conversion when reading data files.

Example:

external_data:
  - id: DM
    keys: [USUBJID, STUDYID]
  - id: EX
    keys: [USUBJID]
  - id: MDPARAM
    keys: [STUDYID, TOPICCD]

Component repositories

The repos field tells mighty where to look for code components. Repositories are searched in the order listed, and the first match wins.

A component with the same name in a later repository is ignored. This also applies to mighty’s internal templates (for example mighty_init_domain). To use your own version of an internal template, put its repository before the one with the internal templates. Otherwise, list the internal templates first.

Each entry can be:

  • github::owner/repo — a GitHub repository
  • github::owner/repo/subdir — a subdirectory inside a GitHub repository
  • github::owner/repo/subdir@ref — a specific branch, tag, or commit
  • A local filesystem path (absolute or relative to the working directory), optionally prefixed with local::

mighty resolves each GitHub ref to a commit once per R session, and downloads each commit once per session. Later calls to generate_adam_code() reuse the cached copy. Restart R to pick up new commits on a branch.

Example:

repos:
  - github::NovoNordisk-OpenSource/mighty.standards/components
  - github::my-org/[email protected]
  - "./local-components"

IMPORTANT: repos must include a source for mighty’s internal templates (typically github::NovoNordisk-OpenSource/mighty.standards/components). Without it, mighty cannot resolve the special components used during code generation.

Component IDs

The id of a component in an ADaM specification is looked up in repos. It is not a file path. Inside each repository, id: relative_day matches:

  • relative_day.R or relative_day.mustache
  • the same file names inside a relative_day/ subdirectory

If one repository has more than one match (for example both relative_day.R and relative_day.mustache), mighty stops with an error. Use the file name with its extension to select one.