R/import.R

In heckendorfc/BTDR: 'BUPID' Top-Down Result Conversion, Analysis, and Visualization

.geturldata <- function(url){
	curlopts <- list(useragent="BTDR",verbose=F,followLocation=T)
	url <- sub("results.html","cgi-bin/get_results.cgi",url)
	#stop("Reading from URL not yet supported")

	rawdata <- RCurl::getURL(url,followLocation=T,.opts=curlopts)

	if(rawdata=="")
		stop("This URL contains no information. Either the URL is invalid or the data is still processing.")

	yaml.load(rawdata)
}

#' Read BUPID results.
#' 
#' Read BUPID results and create and object from them.
#' 
#' The data can be passed either as the name of a file on the local machine or
#' a URL on the BUPID server containing the results.
#' 
#' @param file
#' a file on the local machine to use as input
#' @param url
#' a url where the data can be retreived
#'
#' @return Returns the results as a bupid object.
#'
#' @examples
#' \dontrun{
#' server <- "http://bupid.bumc.bu.edu/cgi-bin/get_results.cgi"
#' infile <- "key=WBNqTswT5DPg3aDO&ID=320&date=20150309"
#' data <- read.bupid(url=paste(server,infile,sep="?"))
#' }
#' 
#' @export read.bupid
read.bupid <- function(file=NULL,url=NULL){
	if(is.null(file) && is.null(url))
		stop("Either file or url must be provided.")

	#if(is.null(file))
		#res <- .geturldata(url)
	#else
		#res <- yaml.load_file(file)

	#cres <- bupidpopulate(res)
	out <- .Call("bupidpopulate",file);
	cres <- new(Class="bupid",scan=out$scan,decon=out$decon,param=out$param,mod=out$mod,prot=out$prot,search=out$search,tag=out$tag,fit=out$fit,xlink=out$xlink,xlpep=out$xlpep)

	cres
}