R/serialize.R

In pamgene/bnutil: BN utility package

library(rtson)

#' @import rtson
#' @export
matrix.asTSON <- function(m){
  return(list(
    kind=tson.character("matrix"),
    ncol=tson.scalar(dim(m)[2]),
    data=as.vector(t(m))
  ))
}

#' @export
matrix.fromTSON <- function(tson){
  ncol = tson$ncol
  data = tson$data
  return(matrix(data=data,ncol=ncol))
}


#' @export
data.frame.asTSON <- function(df){
  data = lapply(df, function(c){
    if (is.factor(c)){
      return (list(kind=tson.character("factor"), values=as.integer(c), labels=levels(c)))
    } else if (is.logical(c)){
      return (list(kind=tson.character("bool"), values=tson.int8.vec(as.integer(c))))
    } else {
      return (as.vector(c))
    }
  })

  return (list(kind=tson.character("data.frame") ,  data=data ))
}

#' @export
data.frame.fromTSON <- function(tson){
  list = tson$data
  dfc = list()
  for (c in list){
    if (is.list(c)){
      kind = c$kind
      if (!is.null(kind)){
        if (kind == "bool"){
          values = c$values
          if (is.null(values)) stop("data.frame.fromTSON failed values missing")
          dfc[[length(dfc) + 1]] = as.logical(c$values)
        } else if (kind == 'factor'){
          dfc[[length(dfc) + 1]] = factor(c$values, labels=c$labels)
        } else {
          stop(paste0("data.frame.fromTSON failed kind is unknown : ", kind))
        }
      } else {
        stop("data.frame.fromTSON failed kind is null")
      }
    } else {
      dfc[[length(dfc) + 1]] = c
    }
  }
  d <- data.frame(dfc)

  colnames(d) <- make.names(names(list))

  if (!is.null(tson$attr)){
    attributes(d) <- c(attributes(d), tson$attr)
  }

  return (d)
}

#' @export
annotated.data.frame.asTSON <- function(annotatedDataframe){
  return (list(kind=tson.character("AnnotatedDataFrame"), varMetadata=data.frame.asTSON(Biobase::varMetadata(annotatedDataframe)), data=data.frame.asTSON(Biobase::pData(annotatedDataframe))))
}

#' @export
annotated.data.frame.fromTSON <- function(tson){
  data = data.frame.fromTSON(tson$data)
  varMetadata=data.frame.fromTSON(tson$varMetadata)
  ann = (Biobase::AnnotatedDataFrame(data=data, varMetadata=varMetadata))
  return (ann)
}

#' @export
object.asTSON <- function(result){
  list = NULL
  if (inherits(result, "data.frame")){
    list <- data.frame.asTSON(result)
  } else if (inherits(result, "AnnotatedDataFrame")){
    list <- annotated.data.frame.asTSON(result)
  } else if (inherits(result, "AnnotatedData")) {
    list <- result$toJson()
  } else if (inherits(result, "Cube")) {
    list <- result$toJson()
  } else {
    stop("object.asTSON failed : unknown class ")
  }
  return(list)
}