R/getTemplateDF.R

In RGLab/R2i: Tools for preparing an ImmPort Data Submission

###########################################
###      Interactive Use Functions      ###
###########################################
# ---- HELPER FN --------------------------
# Used in checkTemplate() and below
getSingleTemplate <- function(ImmPortTemplateName) {
  ipt <- R2i::ImmPortTemplates
  if (!(ImmPortTemplateName %in% unique(ipt$templateName))) {
    stop("Given template name is not in ImmPortTemplates$templateName. Please re-run.")
  }

  ipt[ipt$templateName == ImmPortTemplateName, ]
}

# Used in checkTemplate() and below
# Assume that that ImmPortTemplates$columnType is more accurate
# than ImmPortTemplates$jsonDataType
updateTypes <- function(jsonDataType) {
  jsonDataType <- gsub("string|date|enum|array", "character", jsonDataType)
  jsonDataType <- gsub("number|positive", "double", jsonDataType)

  jsonDataType
}

# ---- MAIN FN --------------------------------------------------------
#' @title generate a template data frame for a given ImmPort Template Name
#'
#' @description Based on ImmPort's specifications, the function creates an
#'     empty dataframe with the correct column headers for the user to update
#'     as part of the ImmPort submission development.
#'
#' @param ImmPortTemplateName name of the ImmPort Template to create
#' @param rowNum sets the number of rows for the ImmPort Template. Defaults to one row.
#' @export
# Use method dynamically to generate DF for interactive work in preparing data.
# Template DFs are not kept as rda objects because the ImmPort tables and lookups
# can change with each data release.  Therefore using a function ensures that latest
# changes are all coming from same json files (templates and lookups) in the zip file
# at `http://www.immport.org/downloads/data/upload/templates/ImmPortTemplates.zip`.
getTemplateDF <- function(ImmPortTemplateName, rowNum = 1) {
  templateInfo <- getSingleTemplate(ImmPortTemplateName)

  templateInfo$jsonDataType <- updateTypes(templateInfo$jsonDataType)

  # create a temp data frame with template columns
  tmpDF <- data.frame(matrix("", ncol = nrow(templateInfo), nrow = rowNum),
    stringsAsFactors = FALSE
  )
  colnames(tmpDF) <- templateInfo$templateColumn

  # update column type
  for (x in seq(1:length(templateInfo$jsonDataType))) {
    changeType <- get(paste0("as.", templateInfo$jsonDataType[x]))
    tmpDF[, x] <- changeType(tmpDF[, x])
  }

  # add name attribute for use in other fn
  attr(tmpDF, "templateName") <- ImmPortTemplateName

  tmpDF
}