R/getMarts.R

In biomartr: Genomic Data Retrieval

#' @title Retrieve information about available Ensembl Biomart databases
#' @description This funcion queries the Ensembl Biomart API and returns a table
#' storing information about all available Ensembl Biomart databases.
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' # get a table of all available databases from Ensembl Biomart
#' getMarts()
#'  }
#' @seealso \code{\link{getDatasets}}, \code{\link{getAttributes}},
#' \code{\link{getFilters}}, \code{\link{organismBM}},
#' \code{\link{organismFilters}}, \code{\link{organismAttributes}}
#' @export
getMarts <- function(){

    submarts <- ensembl_divisions_short(FALSE, bacteria = FALSE)
    submarts.df <- vector("list", length(submarts))

    # Only fail if primary mart is down, else notify which are down
    for (i in seq_along(submarts)) {
      tryCatch({
        submarts.df[i] <- list(getSubMarts(submarts[i]))

        }, error = function(e) {
        message(
            "It seems like the BioMart server could not be reached for mart: ", submarts[i],
            ". This is either due to a server maintainence downtime or may be due to an instable internet connection on your side."
        )
        if (i == 1) stop()
        })

    }

    return(dplyr::bind_rows(submarts.df))
}