R/getAllBeIdSources.R

In patzaw/BED: Biological Entity Dictionary (BED)

#' List all the source databases of BE identifiers whatever the BE type
#'
#' @param recache boolean indicating if the CQL query should be run even if
#' the table is already in cache
#'
#' @return A data.frame indicating the BE related to the ID source (database).
#'
#' @seealso [listBeIdSources], [listPlatforms]
#'
#' @export
#'
getAllBeIdSources <- function(recache=FALSE){
    fn <- sub(
        sprintf("^%s[:][::]", utils::packageName()), "",
        sub("[(].*$", "", deparse(sys.call(), nlines=1, width.cutoff=500L))
    )
    cql <- neo2R::prepCql(
        'MATCH (n:BEID) RETURN DISTINCT n.database as database, labels(n) as BE'
    )
    tn <- fn
    toRet <- cacheBedCall(
        f=neo2R::cypher,
        query=cql,
        tn=tn,
        recache=recache
    )
    toRet$BE <- sub(
        "ID$", "",
        sub(
            "BEID [|][|] ", "",
            sub(" [|][|] BEID", "", toRet$BE)
        )
    )
    return(toRet)
}