R/rxdbHandling.R

In vjcitn/pogos: PharmacOGenomics Ontology Support

#' enumerate top level endpoint terms for bhklab PharmacoDB API
#' @return a character vector of available endpoints
#' @examples 
#' topEndpoints_v1()
#' @export
topEndpoints_v1 = function() {
    c("cell_lines", "tissues", "compounds", "datasets", "experiments", "intersections", 
        "stats")
}

#' convert binary output of GET()$content to list 
#' @import httr
#' @import rjson
#' @param x string suitable for input to GET as GET(x)
#' @return output of fromJSON, typically a list
#' @examples
#' cl = basicDecoder('https://pharmacodb.pmgenomics.ca/api/v1/cell_lines')
#' unlist(cl)
#' @export
basicDecoder = function(x) fromJSON(readBin(GET(x)$content, what = "character"))

#' very simple query formulation, build queries using endpoints of bhklab PharmacoDB API
#' @importFrom S4Vectors DataFrame
#' @param url of a PharmacoDB server API target
#' @param \dots typically a string representing an API endpoint, will be processed by unlist() and then to paste0 preceded by \code{url}
#' @param decoder a function of one argument that will be applied to API response (typically JSON)
#' @return typically a list, dependent on decoder parameter
#' @examples
#' qout = rxdbQuery_v1('cell_lines') # yields 30; append '?all=true' to retrieve all
#' unlist(lapply(qout, function(x) x[[2]]))
#' @export
rxdbQuery_v1 = function(..., url = "https://pharmacodb.pmgenomics.ca/api/v1/", decoder = basicDecoder) {
    parms = list(...)
    decoder(paste0(url, unlist(parms)))
}

compoundTable = function(postfix = "?all=true") {
    comps = rxdbQuery_v1(paste0("compounds", postfix))
    ids = vapply(comps, "[[", "id", character(1))
    nms = vapply(comps, "[[", "name", character(1))
    DataFrame(compound_id = ids, compound = nms)
}

buildMap = function(endpoint = "cell_lines", postfix = "?all=true") {
    recs = rxdbQuery_v1(paste0(endpoint, postfix))
    ids = vapply(recs, "[[", "id", character(1))
    nms = vapply(recs, "[[", "name", character(1))
    DataFrame(id = ids, name = nms)
}