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validate-schema.R
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validate-schema.R
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#' BioCompute Objects schema validator (v1.4.2)
#'
#' @param file Path to the BCO JSON file
#'
#' @return None
#'
#' @importFrom jsonvalidate json_validate json_validator
#'
#' @rdname validate_schema
#' @export validate_schema_v1.4.2
#'
#' @note JSON schema validators for BCO domains and complete BCO based on
#' jsonvalidate. Refer to the
#' \href{https://github.com/biocompute-objects/BCO_Specification/tree/1.4.2/ieee-2791-schema}{BioCompute Objects Schema}
#' for specific JSON schemas.
#'
#' @examples
#' bco <- tempfile(fileext = ".json")
#' generate_example("HCV1a") %>%
#' convert_json() %>%
#' export_json(bco)
#' bco %>% validate_schema()
validate_schema_v1.4.2 <- function(file) {
rule_text("0: Validating BioCompute Object")
txt <- paste(readLines(file), collapse = "")
schema <- system.file("schemas/1.4.2/2791object.json", package = "biocompute")
v <- jsonvalidate::json_validator(schema)
print(v(txt, verbose = TRUE, greedy = TRUE))
cat("\n")
validate_domain <- function(domain, schema) {
lst <- jsonlite::read_json(file)
txt <- jsonlite::toJSON(lst[[domain]], auto_unbox = TRUE)
schema <- system.file(schema, package = "biocompute")
v <- jsonvalidate::json_validator(schema)
print(v(txt, verbose = TRUE, greedy = TRUE))
cat("\n")
}
validate_domain_extension <- function(domain, schema) {
lst <- jsonlite::read_json(file)
txt <- jsonlite::toJSON(lst[["extension_domain"]][[domain]], auto_unbox = TRUE)
schema <- system.file(schema, package = "biocompute")
v <- jsonvalidate::json_validator(schema)
print(v(txt, verbose = TRUE, greedy = TRUE))
cat("\n")
}
rule_text("1: Validating Provenance Domain")
validate_domain("provenance_domain", "schemas/1.4.2/provenance_domain.json")
rule_text("2: Validating Usability Domain")
validate_domain("usability_domain", "schemas/1.4.2/usability_domain.json")
rule_text("3: Validating Description Domain")
validate_domain("description_domain", "schemas/1.4.2/description_domain.json")
rule_text("4: Validating Execution Domain")
validate_domain("execution_domain", "schemas/1.4.2/execution_domain.json")
rule_text("5: Validating Parametric Domain")
validate_domain("parametric_domain", "schemas/1.4.2/parametric_domain.json")
rule_text("6: Validating I/O Domain")
validate_domain("io_domain", "schemas/1.4.2/io_domain.json")
rule_text("7: Validating Error Domain")
validate_domain("error_domain", "schemas/1.4.2/error_domain.json")
invisible(NULL)
}
#' @rdname validate_schema
#' @export validate_schema
validate_schema <- validate_schema_v1.4.2