R/FGDatasetUploadParameters.R

In FASTGenomics/r_client: Manage FASTGenomics Instances

check_FGDatasetUploadParameters <- function(object) {
  errors <- character()
  # technology check needs the connection, chec therefore done later.
  # same for current_normalization_status

  if (object@cell_metadata != "" && !file.exists(object@cell_metadata)) {
    msg <- stringr::str_interp("The given cell metadata file '${object@cell_metadata}' does not exist!")
    errors <- c(errors, msg)
  }

  if (object@gene_metadata != "" && !file.exists(object@gene_metadata)) {
    msg <- stringr::str_interp("The given gene metadata file '${object@gene_metadata}' does not exist!")
    errors <- c(errors, msg)
  }

  if (length(errors) == 0) TRUE else errors
}

setClass("FGDatasetUploadParameters",
         slots = c(
           license  = "character",
           web_link  = "character",
           citation = "character",
           technology = "character",
           current_normalization_status = "character",
           cell_metadata = "character",
           gene_metadata = "character"
         ),
         validity = check_FGDatasetUploadParameters
)


#' Get the optional parameters to create a dataset
#'
#'  If you provide cell or gene metadata via a dataframe, please note that the dataframe is stored on disk in the tempdir of the current R session. As this might get cleaned on exit of R, be cautious when using this from a stored R session.
#'
#' @param license The license to be used. If the data are owned by yourself, you can use https://creativecommons.org/choose/ to choose a license. If not, you have to find the license used by the dataset, e.g. talk to your supervisor.
#' @param web_link The website of your dataset.
#' @param citation How to cite this dataset
#' @param technology The technology used to obtain this dataset. call \code{\link{get_valid_technologies}} to get a list of already known technologies or freely choose a name.
#' @param current_normalization_status The current_normalization_status used to obtain this dataset. call \code{\link{get_valid_current_normalization_status}} to get a list of already known normalization techniques or freely choose a name.
#' @param cell_metadata The path to your cell metadata file OR a dataframe, for valid formats see \href{https://github.com/FASTGenomics/fastgenomics-docs/blob/master/doc/api/dataset_api.md}{here}.
#' @param gene_metadata The path to your gene metadata OR a dataframe, for valid formats see \href{https://github.com/FASTGenomics/fastgenomics-docs/blob/master/doc/api/dataset_api.md}{here}.
#'
#' @return class FGDatasetUploadParameters
#' @export
#'
#' @examples
#' optional <- fastgenomicsRclient::FGDatasetUploadParameters(
#'                                         license ="MIT",
#'                                         technology = "Smart-Seq",
#'                                         web_link="https://example.com",
#'                                         notes="This is a TEST",
#'                                         citation="FG et al",
#'                                         batch_column="sample",
#'                                         current_normalization_status="Counts",
#'                                         cell_metadata="./cell_metadata.tsv",
#'                                         gene_metadata="./gene_metadata.tsv"  )
FGDatasetUploadParameters <- function( license  = "",
                                       web_link  = "",
                                       citation = "",
                                       technology = "",
                                       current_normalization_status = "",
                                       cell_metadata = "",
                                       gene_metadata = "") {

  cell_metadata_path <- ""
  if (is.character(cell_metadata)) {
    cell_metadata_path <- cell_metadata
  }
  else if (is.data.frame(cell_metadata))
  {
    cell_metadata_path <- get_df_as_file(df, "cell_metadata.csv")
  }
  else
  {
    stop("the given cell_metadata is neither a file path nor a dataframe!")
  }

  gene_metadata_path <- ""
  if (is.character(gene_metadata)) {
    gene_metadata_path <- gene_metadata
  }
  else if (is.data.frame(gene_metadata))
  {
    gene_metadata_path <- get_df_as_file(df, "gene_metadata.csv")
  }
  else
  {
    stop("the given gene_metadata is neither a file path nor a dataframe!")
  }

  new("FGDatasetUploadParameters",
      license = license,
      web_link = web_link,
      citation = citation,
      technology = technology,
      current_normalization_status = current_normalization_status,
      cell_metadata = cell_metadata_path,
      gene_metadata = gene_metadata_path)
}

get_data_from_FGDatasetUploadParameters <- function(object, connection){
  data <- list()
  if (!object@license == "")
  {
    data["license"] <- object@license
  }

  if (!object@web_link == "")
  {
    data["web_link"] <- object@web_link
  }

  if (!object@citation == "")
  {
    data["citation"] <- object@citation
  }

  if (!object@technology == "")
  {
    technologies <- get_valid_technologies(connection)

    if (!object@technology %in% technologies)
    {
      str = paste(as.character(technologies), collapse=", ")
      stop(stringr::str_interp("The Technology '${object@technology} is unknown. Choose one of: ${str}' "))
    }

    data["technology"] <- object@technology
  }

  if (!object@current_normalization_status == "")
  {
    data["current_normalization_status"] <- object@current_normalization_status
  }

  if (!object@cell_metadata == "")
  {
    data[["cell_metadata"]] = httr::upload_file(object@cell_metadata)
  }

  if (!object@gene_metadata == "")
  {
    data[["gene_metadata"]] = httr::upload_file(object@gene_metadata)
  }

  return(data)
}