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Mighty Config

Source: R/a_mighty_config.R
mighty_config.Rd

mighty_config() provides a robust way of working with the _mighty.yml configuration file in the {mighty} framework.

A new object is initialized by supplying either the path to a _mighty.yml file or an in-memory list of the same content. Both are automatically validated against the mighty.json schema.

mighty_config() inherits from S7schema::S7schema(). You can validate an object at any time by calling validate() and use write_config() to save it back as a yaml file.

Usage

mighty_config(file, .data)

Arguments

file

character(1) path to a _mighty.yml file. Mutually exclusive with .data.

.data

list holding a _mighty.yml configuration already in memory. Mutually exclusive with file.

Value

A mighty_config S7 object extending S7schema::S7schema.

external_data

A list of external data source specifications, each with an id and keys field.

repos

Optional character vector of component repository locations, or NULL if not specified.

Details

The _mighty.yml file is validated against the mighty.json schema on load. The file must contain an external_data array declaring the primary keys of any datasets external to the ADaM study (e.g. SDTM or reference datasets) that ADaM domain specifications may depend on.

The optional repos field specifies where mighty.component should look for shared components. Each entry is either a local path (e.g. ".") or a GitHub reference in owner/repo/subdir@ref format (e.g. "NovoNordisk-OpenSource/mighty.standards/components@main").

Write Config

Use write_config() to serialize a mighty_config() object back to a _mighty.yml file. Supply path to write to a specific file; defaults to the file the object was loaded from.

See also

mighty_study, study_config, mighty_domain, write_config()

Examples

x <- mighty_config(
  file = system.file("examples", "_mighty.yml", package = "mighty.metadata")
)

# Custom print method gives a small overview
print(x)
#> <mighty.metadata::mighty_config>
#> External data: 3 sources (`DM`, `VS`, and `AE`)
#> Repos: 2 (`NovoNordisk-OpenSource/mighty.standards/components@main` and `.`)

# Underlying object is a `list`
str(x)
#> <mighty.metadata::mighty_config> List of 2
#>  $ external_data:List of 3
#>   ..$ :List of 2
#>   .. ..$ id  : chr "DM"
#>   .. ..$ keys: chr [1:2] "STUDYID" "USUBJID"
#>   ..$ :List of 2
#>   .. ..$ id  : chr "VS"
#>   .. ..$ keys: chr [1:2] "STUDYID" "USUBJID"
#>   ..$ :List of 2
#>   .. ..$ id  : chr "AE"
#>   .. ..$ keys: chr [1:2] "STUDYID" "USUBJID"
#>  $ repos        : chr [1:2] "NovoNordisk-OpenSource/mighty.standards/components@main" "."
#>  @ schema   : chr "/home/runner/work/_temp/Library/mighty.metadata/schema/mighty.json"
#>  @ validator: <S7schema::validator>
#>  .. @ context:Classes 'V8', 'environment' <environment: 0x55eb84cc1440> 
#>  @ file     : chr "/home/runner/work/_temp/Library/mighty.metadata/examples/_mighty.yml"

# Write back to a file
tmp <- tempfile(fileext = ".yml")
write_config(x, path = tmp)

# Or build one in memory
mighty_config(
  .data = list(
    external_data = list(list(id = "DM", keys = "USUBJID")),
    repos = "."
  )
)
#> <mighty.metadata::mighty_config>
#> External data: 1 source (`DM`)
#> Repos: 1 (`.`)