R/18_METACYC.R

In tidymass/massdatabase: Play with databases about mass spectrometry

#' #' @title Download the metacyc compound database
#' #' @description Download the metacyc compound database
#' #' @author Xiaotao Shen
#' #' \email{shenxt1990@@outlook.com}
#' #' @param url Default is "http://websvc.biocyc.org/xmlquery?[x:x<-meta^^reactions]".
#' #' @param path Default is ..
#' #' @return Downloaded files.
#' #' @importFrom magrittr %>%
#' #' @export
#' download_metacyc_reaction <-
#'   function(url = 'http://websvc.biocyc.org/xmlquery?[x:x<-meta^^reactions]',
#'            path = ".") {
#'     message('Download MetaCyc reaction list. It takes a while')
#'     h = basicTextGatherer()
#'
#'     curl.result = tryCatch({
#'       curlPerform(url = url, writefunction = h$update)
#'     }, warning = function(w) {
#'       message(
#'         'WARNING: MetaCyc server is unstable now. We are trying to get alternative server, but we recommend try this function again later'
#'       )
#'     }, error = function(e) {
#'       message(
#'         'WARNING: MetaCyc server is unstable now. We are trying to get alternative server, but we recommend try this function again later'
#'       )
#'       alter_url = 'http://compbio.korea.ac.kr/rbiorxn/metacyc_all.html'
#'       curlPerform(url = alter_url, writefunction = h$update)
#'     })
#'
#'     xml = h$value()
#'     if (xml == '') {
#'       message(
#'         'get.metacyc.all() function is not properly performed. Please email the author if it keeps happening'
#'       )
#'       return(NA)
#'     }
#'
#'     xml = unlist(strsplit(xml, '\n'))
#'
#'     index = grep('^  <Reaction ID', xml)
#'     reg_ex = "(.*META:)(.*)(' orgid.+)"
#'     reactionIds = sub(reg_ex, '\\2', xml[index])
#'
#'     message(sprintf(
#'       '%s reaction entries are being downloaded',
#'       length(reactionIds)
#'     ))
#'     metacycDf = .parse.metacyc.biopax(reactionIds)
#'     return(metacycDf)
#'   }