R/drug_pathway_node_parsers.R

In Dainanahan/dbparser: Drugs Databases Parser

PathwayParser <- R6::R6Class(
  "PathwayParser",
  inherit = AbstractParser,
  private = list(
    parse_record = function() {
      drugs <-  xmlChildren(pkg_env$root)
      pb    <- progress_bar$new(total = xmlSize(drugs))
      map_df(drugs, ~ private$get_pathways_df(.x, pb)) %>%
        unique()
    },
    get_pathways_df = function(rec, pb) {
      pb$tick()
      map_df(
        xmlChildren(rec[["pathways"]]),
        ~ private$get_pathway_rec(.x, xmlValue(rec["drugbank-id"][[1]])))
    },
    get_pathway_rec = function(r, drug_key) {
      tibble(
        smpdb_id    = xmlValue(r[["smpdb-id"]]),
        name        = xmlValue(r[["name"]]),
        category    = xmlValue(r[["category"]]),
        drugbank_id = drug_key
      )
    }
  )
)

PathwaySubNodesParser <- R6::R6Class(
  "PathwaySubNodesParser",
  inherit = AbstractParser,
  private = list(
    parse_record = function() {
      drugs      <-  xmlChildren(pkg_env$root)
      pb         <- progress_bar$new(total = xmlSize(drugs))
      parsed_tbl <-
        map_df(drugs, ~ private$get_pathways_sub(., pb)) %>%
        unique()
      if (NROW(parsed_tbl) > 0) {
        switch(
          private$main_node,
          "enzymes" = names(parsed_tbl) <-
            c("enzyme", "smpdb_id")
        )
      }

      parsed_tbl
    },
    get_pathways_sub = function(rec, pb) {
      pb$tick()
      map_df(
        xmlChildren(rec[[private$object_node]]),
        ~ drug_sub_df(., private$main_node, id = private$id)
      )
    }
  )
)

#' Drug Pathway Enzymes parser
#'
#' Enzymes involved in this pathway.
#'
#' @return  a tibble with pathway properties
#' @keywords internal
drug_pathway_enzyme <- function() {
  PathwaySubNodesParser$new(
      tibble_name = "drug_pathway_enzymes",
      object_node = "pathways",
      main_node   = "enzymes",
      id          = "smpdb-id"
    )$parse()
}

#' Drug Pathway Drugs parser
#'
#' Drugs involved in this pathway.
#'
#' @return  a tibble with pathway drugs properties
#' @keywords internal
drug_pathway_drugs <- function() {
  enzyme <- PathwaySubNodesParser$new(
      tibble_name = "drug_pathway_drugs",
      object_node = "pathways",
      main_node = "drugs",
      id = "smpdb-id"
    )$parse()

  if (NROW(enzyme) > 0) {
    enzyme <- enzyme %>%
      rename("smpdb_id" = "parent_key")
  }

  enzyme
}

#' Drug Pathway parser
#'
#' Metabolic, disease, and biological pathways that the drug is involved in, as
#' identified by the Small Molecule Protein Database (SMPDB).
#'
#' @return  a tibble with the following variables:
#' \describe{
#'  \item{smpdb-id}{Small Molecule Pathway Database identifier for this
#'  pathway.}
#'  \item{name}{Pathway name}
#'  \item{category}{Pathway category}
#'  \item{\emph{drugbank_id}}{drugbank id}
#' }
#' @keywords internal
drug_pathway <- function() {
    PathwayParser$new("drug_pathway")$parse()
}