R/geoChina.R

In AnnoProbe: Annotate the Gene Symbols for Probes in Expression Array

##' Download expression dataset by GSE id
##'
##' \code{geoChina} will download the expression matrix and phenotype data as ExpressionSet format
##'      from cloud in mainland China,
##'      it's a alternative method for getGEO function from GEOquery package.
##'      geoChina('gse1009') is the same as eSet=getGEO('gse1009', getGPL = F)
##'
##' @param gse input GSE id, such as GSE1009, GSE2546, gse1009.
##' @param mirror "tencent" only for now.
##' @param destdir The destination directory for data downloads.
##' @return a list of ExpressionSet, which contains the  expression matrix and phenotype data
##' @importFrom utils download.file
##' @importClassesFrom Biobase ExpressionSet
##' @examples
##' \dontrun{
##' geoChina('GSE1009',destdir=tempdir())
##' }
##' @export geoChina

geoChina <- function(gse='GSE2546',mirror='tencent',destdir=getwd()){
  # eSet=getGEO('GSE2546', destdir=".", AnnotGPL = F, getGPL = F)
  # http://49.235.27.111/GEOmirror/GSE2nnn/GSE2546_eSet.Rdata
  # gse='GSE2546';mirror='tencent'
  gse=toupper(gse)
  if(!gse %in% series.accession){
    stop('Your GSE may not be expression by array, or even not a GSE')
  }
  if (is.null('http://49.235.27.111')) {
    message("Data source broken.")
  }
  down=ifelse(as.numeric(gsub('GSE','',gse))<1000,
              paste0('/GEOmirror/GSEnnn/',gse,
                     '_eSet.Rdata'),
              paste0('/GEOmirror/',
                     gsub('[0-9][0-9][0-9]$','nnn',gse),'/',gse,
                     '_eSet.Rdata'))

  if(mirror=='tencent'){
    up='http://49.235.27.111'
  }
  OS <- .Platform$OS.type

  if (OS == "unix"){
    tpf=paste0(destdir,"/", gse, '_eSet.Rdata') # MAC file path
  } else if (OS == "windows"){
    tpf=paste0(destdir,"\\", gse, '_eSet.Rdata') # windows file path
  } else {
    stop("ERROR: OS could not be identified")
  }

  download.file(paste0(up,down),tpf,mode = "wb")
  suppressWarnings(load(tpf))
  # getGEO('GSE2546', destdir=".", AnnotGPL = F, getGPL = F)
  message(paste0("file downloaded in ",destdir,'\nyou can also use getGEO from GEOquery, by \ngetGEO(',
               shQuote(gse),
               ', destdir=".", AnnotGPL = F, getGPL = F)'
               ))
  return(gset)
}

## https://community.rstudio.com/t/internet-resources-should-fail-gracefully/49199/11
gracefully_fail <- function(remote_file) {
  try_GET <- function(x, ...) {
    tryCatch(
      httr::GET(url = x, httr::timeout(1), ...),
      error = function(e) conditionMessage(e),
      warning = function(w) conditionMessage(w)
    )
  }
  is_response <- function(x) {
    class(x) == "response"
  }
  
  # First check internet connection
  if (!curl::has_internet()) {
    message("No internet connection.")
    return(invisible(NULL))
  }
  # Then try for timeout problems
  resp <- try_GET(remote_file)
  if (!is_response(resp)) {
    message(resp)
    return(invisible(NULL))
  }
  # Then stop if status > 400
  if (httr::http_error(resp)) { 
    httr::message_for_status(resp)
    return(invisible(NULL))
  }
  
  # If you are using rvest as I do you can easily read_html in the response
  xml2::read_html(resp)
}