R/dataset_functions.R

In BioData/LabguruR: Labguru API wrapper for R

#' Labguru Upload Dataset
#'
#' Upload a dataset to labguru
#'
#' @param dataset data frame you wish to upload to Labguru
#' @param name character(1)
#' @param server character(1) indicating the server URL
#' @param token character(1) access token for API authentication
#'
#' @return dataset_id
#' @export
#'
#' @import httr
#' @importFrom jsonlite fromJSON
#' 
#' @examples
#' \dontrun{
#' labguru_upload_dataset(dataset    = mtcars,
#'                        name       = "mtcars")
#' }
labguru_upload_dataset <- function(dataset, 
                                   name, 
                                   # description = NULL, 
                                   server = Sys.getenv("LABGURU_SERVER"), 
                                   token  = Sys.getenv("LABGURU_TOKEN")) {
  
  # Test arguments
  check_arg_dataframe(dataset)
  check_arg_single_character(name, null = FALSE)
  # check_arg_single_character(description, null = TRUE)
  check_arg_server(server)
  check_arg_token(token)

  # base_url <- server
  # path     <- "/api/v1/datasets"
  # query    <- paste0("token=", token, 
  #                    "&name=", name)#, 
  #                    # if (!is.null(description)) {paste0("&description=", description)})
  # 
  # url <- httr::modify_url(url   = base_url, 
  #                         path  = path, 
  #                         query = query)
  # # Post
  # resp <- httr::POST(url    = url, 
  #                    body   = as.data.frame(dataset), 
  #                    encode = "json")
  # 
  
  # URL
  url <- httr::modify_url(url   = server, 
                          path  = "/api/v1/datasets", 
                          query = paste0("token=", token, 
                                         "&name=", name))
  
  parsed <- labguru_post_item(url    = url,
                              body   = as.data.frame(dataset),
                              encode = "json")
  # # Post
  # resp <- httr::POST(url    = url, 
  #                    body   = as.data.frame(dataset), 
  #                    encode = "json")
  # 
  # # Expect resp to be JSON 
  # if (httr::http_type(resp) != "application/json") {
  #   stop("API did not return JSON", call. = FALSE)
  # }
  # 
  # # Parse without simplifaction for consistency
  # parsed <- jsonlite::fromJSON(httr::content(resp, as = "text"), simplifyVector = FALSE)
  # 
  # # check for request error
  # if (httr::http_error(resp)) {
  #   stop(sprintf("API request failed [%s]\n%s", parsed$status, parsed$error), call. = FALSE)
  # }
  
  # invisible(TRUE)
  # Return ID
  list(id = parsed$dataset_id)
}




#' Labguru list datasets
#' 
#' This function returns information of the available datasets in a data frame.
#'
#' @param page numeric(1) representing the page number of data to request. Limited data can be return in 1 request, incrementally try higher page numbers for more datasets
#' @param get_cols character(1) either 'limited' or 'all' to return a subset or all of the information regarding the datasets
#' @param server character(1) indicating the server URL
#' @param token character(1) access token for API authentication
#'
#' @return dataframe with information of datasets, NULL if no datasets were available for the request
#' @export
#' 
#' @import httr
#' @importFrom jsonlite fromJSON
#' 
#' @examples
#' \dontrun{
#' labguru_list_datasets()
#' }
labguru_list_datasets <- function(page     = 1,
                                  get_cols = "limited",
                                  server   = Sys.getenv("LABGURU_SERVER"), 
                                  token    = Sys.getenv("LABGURU_TOKEN")) {
  
  check_arg_single_integer(page, null = FALSE)
  check_arg_server(server)
  check_arg_token(token)
  check_arg_char_opts(get_cols, c("limited", "all"), null = FALSE)
  
  # URL
  url <- httr::modify_url(url   = server, 
                          path  = "/api/v1/datasets",
                          query = paste0("token=", token, 
                                         "&page=", page))
  
  resp <- httr::GET(url)
  
  # Expect resp to be JSON 
  if (httr::http_type(resp) != "application/json") {
    stop("API did not return JSON", call. = FALSE)
  }
  
  # Parse with simplifaction to dataframe
  parsed <- jsonlite::fromJSON(httr::content(resp, as = "text"), 
                               simplifyVector    = FALSE, 
                               simplifyDataFrame = TRUE, 
                               flatten           = TRUE)
  
  # check for request error
  if (httr::http_error(resp)) {
    stop(sprintf("API request failed [%s]\n%s", parsed$status, parsed$error), call. = FALSE)
  }
  
  if (length(parsed) == 0) {
    message("No data was available for this request")
    return(NULL)
  }
  
  # Subset primary elements that can't be NULL
  if (get_cols == "limited") {
    parsed[c("id", "name", "description", "api_url")]
  } else {
    parsed
  }
}






#' Labguru download dataset
#' 
#' Takes a dataset id and donwloads the dataset.
#'
#' @param dataset_id numeric(1) id indicating a dataset on labguru server
#' @param server character(1) indicating the server URL
#' @param token character(1) access token for API authentication
#'
#' @return data frame of labguru dataset
#' @export
#'
#' @import httr
#' @importFrom jsonlite fromJSON
#' 
#' @examples
#' \dontrun{
#' labguru_downlaod_datasets(dataset_id = 1)
#' }
labguru_download_dataset <- function(dataset_id,
                                     server = Sys.getenv("LABGURU_SERVER"), 
                                     token  = Sys.getenv("LABGURU_TOKEN")) {

  check_arg_single_integer(dataset_id, null = FALSE)
  check_arg_server(server)
  check_arg_token(token)
  
  parsed <- labguru_get_by_id(type   = "datasets",
                              id     = dataset_id,
                              server = server,
                              token  = token)
  
  parsed$vectors
    
  # # URL
  # base_url <- server
  # path     <- paste0("/api/v1/datasets/", dataset_id)
  # query    <- paste0("token=", token)
  # 
  # url <- httr::modify_url(url   = base_url, 
  #                         path  = path,
  #                         query = query)
  # 
  # resp <- httr::GET(url)
  # 
  # # Expect resp to be JSON 
  # if (httr::http_type(resp) != "application/json") {
  #   stop("API did not return JSON", call. = FALSE)
  # }
  # 
  # # Parse without simplifaction for consistency
  # parsed <- jsonlite::fromJSON(httr::content(resp, as = "text"), 
  #                              simplifyVector    = FALSE, 
  #                              simplifyDataFrame = TRUE, 
  #                              flatten           = TRUE)
  # 
  # # check for request error
  # if (httr::http_error(resp)) {
  #   stop(sprintf("API request failed [%s]\n%s", parsed$status, parsed$error), call. = FALSE)
  # }
  # 
  # parsed$vectors
}