Compose BioCompute Object - Extension Domain (v1.4.2)

compose_extension_v1.4.2(fhir = NULL, scm = NULL)

compose_extension(fhir = NULL, scm = NULL)

Arguments

fhir: FHIR extension domain composed by compose_fhir.
scm: SCM extension domain composed by compose_scm.

Value

A list of class bco.domain

Examples

fhir_endpoint <- "https://fhirtest.uhn.ca/baseDstu3"
fhir_version <- "3"
fhir_resources <- data.frame(
  "id" = c("21376", "6288583", "25544", "92440", "4588936"),
  "resource" = c(
    "Sequence", "DiagnosticReport", "ProcedureRequest",
    "Observation", "FamilyMemberHistory"
  ),
  stringsAsFactors = FALSE
)

fhir <- compose_fhir(fhir_endpoint, fhir_version, fhir_resources)

scm_repository <- "https://github.com/example/repo"
scm_type <- "git"
scm_commit <- "c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21"
scm_path <- "workflow/hive-viral-mutation-detection.cwl"
scm_preview <- "https://github.com/example/repo/blob/master/mutation-detection.cwl"

scm <- compose_scm(scm_repository, scm_type, scm_commit, scm_path, scm_preview)

compose_extension(fhir, scm) %>% convert_json()
#> {
#>   "fhir_extension": {
#>     "fhir_endpoint": "https://fhirtest.uhn.ca/baseDstu3",
#>     "fhir_version": "3",
#>     "fhir_resources": [
#>       [
#>         {
#>           "fhir_id": "21376",
#>           "fhir_resource": "Sequence"
#>         }
#>       ],
#>       [
#>         {
#>           "fhir_id": "6288583",
#>           "fhir_resource": "DiagnosticReport"
#>         }
#>       ],
#>       [
#>         {
#>           "fhir_id": "25544",
#>           "fhir_resource": "ProcedureRequest"
#>         }
#>       ],
#>       [
#>         {
#>           "fhir_id": "92440",
#>           "fhir_resource": "Observation"
#>         }
#>       ],
#>       [
#>         {
#>           "fhir_id": "4588936",
#>           "fhir_resource": "FamilyMemberHistory"
#>         }
#>       ]
#>     ]
#>   },
#>   "scm_extension": {
#>     "scm_repository": "https://github.com/example/repo",
#>     "scm_type": "git",
#>     "scm_commit": "c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21",
#>     "scm_path": "workflow/hive-viral-mutation-detection.cwl",
#>     "scm_preview": "https://github.com/example/repo/blob/master/mutation-detection.cwl"
#>   }
#> }