R/getFilters.R

In biomartr: Genomic Data Retrieval

#' @title Retrieve All Available Filters for a Specific Dataset
#' @description This funcion queries the BioMart API and returns a table
#' storing all available filters for a specific dataset.
#' @param mart a character string specifying the database (mart) for which 
#' datasets shall be listed.
#' @param dataset a character string specifying the dataset for which filters 
#' shall be listed.
#' @param mute_citation logical value indicating whether citation message should be muted.
#' @author Hajk-Georg Drost
#' @examples
#' \dontrun{
#' # search for available datasets
#' # getMarts()
#' # choose database (mart): "ENSEMBL_MART_ENSEMBL"
#' # head(getDatasets(mart = "ENSEMBL_MART_ENSEMBL"), 10)
#' # choose dataset: "hsapiens_gene_ensembl"
#' head(getFilters(mart = "ENSEMBL_MART_ENSEMBL", 
#'                 dataset = "hsapiens_gene_ensembl") , 5)
#' }
#' @seealso \code{\link{getMarts}}, \code{\link{getDatasets}}, 
#' \code{\link{getAttributes}}, \code{\link{organismBM}}, 
#' \code{\link{organismFilters}}, \code{\link{organismAttributes}}
#' @export

getFilters <- function(mart, dataset, mute_citation = FALSE){
    
    if ((!is.character(mart)) || (!is.character(dataset)))
        stop("Please use a character string as mart or dataset.", call. = FALSE)
    
    message("Starting retrieval of filters information from mart ", mart, " and dataset ", dataset, " ...")
    
    
    if (stringr::str_detect(mart, "ENSEMBL"))
        # connect to BioMart API
        url <-
            paste0(
                "http://ensembl.org/biomart/martservice?type=filters&dataset=",
                dataset,
                "&requestid=biomart&mart=",
                mart
            )
    if (stringr::str_detect(mart, "plants"))
        # connect to BioMart API
        url <-
            paste0(
          "http://plants.ensembl.org/biomart/martservice?type=filters&dataset=",
                dataset,
                "&requestid=biomart&mart=",
                mart
            )
    if (stringr::str_detect(mart, "fung"))
        # connect to BioMart API
        url <-
            paste0(
           "http://fungi.ensembl.org/biomart/martservice?type=filters&dataset=",
                dataset,
                "&requestid=biomart&mart=",
                mart
            )
    
    if (stringr::str_detect(mart, "protist"))
        # connect to BioMart API
        url <-
            paste0(
         "http://protist.ensembl.org/biomart/martservice?type=filters&dataset=",
                dataset,
                "&requestid=biomart&mart=",
                mart
            )
    if (stringr::str_detect(mart, "metazoa"))
        # connect to BioMart API
        url <-
            paste0(
         "http://metazoa.ensembl.org/biomart/martservice?type=filters&dataset=",
                dataset,
                "&requestid=biomart&mart=",
                mart
            )
    
    
    testContent <- httr::content(httr::GET(url), as = "text")
    
    if ((testContent == "Attribute 'mains' does not exist\n") ||
        is.na(testContent)) {
        warning("No attributes were available for mart = ",
                mart,
                " and dataset = ",
                dataset,
                ".",
                call. = FALSE)
        filterBioMart <- data.frame(name = "NA", description = "NA")
        return(filterBioMart)
    }
    
    filterPage <- httr::handle(url)
    xmlContentFilters <- httr::GET(handle = filterPage)
    
    httr::stop_for_status(xmlContentFilters)
    
    
    tryCatch({
        # extract attribute name and attribute description
        suppressWarnings(rawDF <-
                             do.call("rbind", apply(as.data.frame(strsplit(
                                 httr::content(xmlContentFilters, as = "text", 
                                               encoding = "UTF-8"),
                                 "\n"
                             )), 1, function(x)
                                 unlist(strsplit(x, "\t")))))
        
        colnames(rawDF) <- paste0("V", seq_len(ncol(rawDF)))
        
        filterBioMart <-
            as.data.frame(rawDF[, c("V1", "V2")],
                          stringsAsFactors = FALSE,
                          colClasses = rep("character", 2))
        colnames(filterBioMart) <- c("name", "description")
        
        please_cite_biomartr(mute_citation = mute_citation)
        
        return(filterBioMart)
        
    }, error = function(e)
        stop(
            "Your input mart '",
            mart,
            "' or dataset '",
            dataset,
            "' could not be found. Please use getMarts() to choose from 
            available marts."
        ))
}