submit manifests in a google drive folder to validation by manifest

validate.R

library(googlesheets4)
library(nfportalutils)

submit_gs_to_api <- function(sheet_id,
                            schema_url) {
   # Retrieve the Google Sheets document
   sheet <- googlesheets4::gs4_get(sheet_id)
   
   # Extract the workbook name and remove '.manifest' and split it on the underscore ("_")
   workbook_name <- sheet$name
   workbook_name <- sub("\\.manifest", "", workbook_name)
   component <- strsplit(workbook_name, "_")[[1]][2]
   
  # Read the data from the Google Sheets document
  data <- googlesheets4::read_sheet(sheet_id, col_types = "c")
  
  # Convert the data to a CSV file
  temp_file <- tempfile(fileext = ".csv")
  readr::write_csv(data, temp_file)
  
  # POST manifest to schematic API with nfportalutils helper function
  content <- nfportalutils::manifest_validate(
    data_type = component,
    file_name = temp_file,
    schema_url = schema_url
  )
  
  # sleep to prevent hitting google API rate limits.
  Sys.sleep(5)
  
  return(content)
}


#' Terse error messages please
#'
#' @param error An error object from schematic.
#' @keywords internal
tersely <- function(error) {
  row <- error[[1]]
  column <- error[[2]]
  message <- error[[3]]
  value <- error[[4]]
  
  wording <- if(grepl("is not one of", message)) paste(shQuote(value), "is not a valid value for", column) else message
  wording
}

manifest_passed <- function(result) {
  
  errors <- length(result$errors)
  if(errors) {
    messages <- unique(sapply(result$errors, tersely))
    notes <- paste(messages, collapse = ", ")
    return(list(result = FALSE, notes = notes))
  } else {
    return(list(result = TRUE, notes = "No errors"))
  }
}



bar <- googledrive::drive_ls(
  "https://drive.google.com/drive/u/1/folders/1yblPMk-kgMj5KJi7P0AFOobZ9vkl6Nkk",
  type = 'spreadsheet',
  recursive = T)

validation_responses <- lapply(bar$id, submit_gs_to_api, schema_url = "https://raw.githubusercontent.com/nf-osi/nf-research-tools-schema/update_schema/nf-research-tools.jsonld")

sapply(validation_responses, manifest_passed)

Some light documentation here https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3045621809/Validating+multiple+google+sheets+manifests+against+different+components

Updated to use nf-osi/nfportalutils functions