R/query_gwasapi.R

In rqtl/GWASapi: NHGRI-EBI GWAS Catalog of Summary Statistics

# query GWAS Catalog API
# convert to list if necessary
#' @importFrom httr GET content stop_for_status
query_gwasapi <-
    function(query=NULL, query_param=NULL, url=gwasapi_url(),
             output=c("parsed", "text", "raw"), encoding="UTF-8")
{
    output <- match.arg(output)

    delay_if_necessary()
    if(!is.null(query)) url <- paste0(url, "/", query)

    if(is.null(query_param)) {
        result <- httr::GET(url)
    } else {
        result <- httr::GET(url, query=query_param)
    }
    httr::stop_for_status(result)
    result <- httr::content(result, encoding=encoding, as=output)

    check_gwasapi_error(result)
}

# check whether the result is an error
check_gwasapi_error <-
    function(result)
{
    if(length(result) == 1 && !is.null(names(result)) && names(result)=="errors" &&
       length(result$errors)==1 && length(result$errors[[1]])==4 &&
       !is.null(names(result$errors[[1]])) &&
       all(names(result$errors[[1]]) == c("detail", "source", "status", "title"))) {
        # looks like an error

        if(length(result$errors[[1]]$status) == 1 && result$errors[[1]]$status==204 &&
           length(result$errors[[1]]$title) == 1 && result$errors[[1]]$title=="No Results") {
            return(NULL)
        }
        else {
            stop("Error ", result$errors[[1]]$status, " ",
                 result$errors[[1]]$title)
        }
    }

    result
}