R/populate.R

In lifecycle-project/ds-upload: Upload Functions for DataSHIELD Backends

#' Populate your Opal instance with the new version of the data dictionary
#' Involves only the core variables
#'
#' @param dict_version dictionary version
#' @param cohort_id cohort identifier (possible values are: [du.enum.cohorts])
#' @param data_version version of the data (specific to the cohort)
#' @param database_name the database name specified in your Opal instance (defaults to 'opal_data')
#' @param dict_kind dictionnary kind, can be 'core' or 'outcome'
#' @param override_project overrides the generated project name
#'
#' @return project id to use in central quality control
#'
#' @noRd
du.populate <- function(dict_version, cohort_id, data_version, database_name, dict_kind, override_project) {
  message("######################################################")
  message("  Start importing data dictionaries                   ")
  message("######################################################")

  project <- paste0("lc_", cohort_id, "_", dict_kind, "_", dict_version)
  if(!is.null(override_project)) project = override_project
  
  dictionaries <- du.dict.retrieve.tables(ds_upload.globals$api_dict_released_url, dict_kind, dict_version, data_version)

  if (ds_upload.globals$login_data$driver == du.enum.backends()$ARMADILLO) {
    project <- str_replace_all(cohort_id, "-", "")
    if(!is.null(override_project)) project = override_project
    du.armadillo.create.project(project)
  }

  if (ds_upload.globals$login_data$driver == du.enum.backends()$OPAL) {
    du.opal.project.create(project, database_name)
    du.opal.dict.import(project, dictionaries, dict_kind)
  }

  return(project)

  message("######################################################")
  message("  Importing data dictionaries has finished            ")
  message("######################################################")
}