@@ -25,18 +25,14 @@ Imports:

     graph,

     graphics,

     utils,

-    base64enc,

+    jsonlite,

     dplyr,

     grDevices,

     methods,

     ggcyto (>= 1.11.4),

     yaml,

-    lattice,

     stats,

-    corpcor,

-    RUnit,

-    tibble,

-    xml2

+    tibble

 biocViews: ImmunoOncology, FlowCytometry, DataImport, DataRepresentation

 LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace

 Suggests:

@@ -70,6 +66,5 @@ Collate:

     'transforms.R'

     'utils.R'

     'writeGatingML.R'

-    'zzz.R'

 SystemRequirements: xml2, GNU make, C++11    

 Encoding: UTF-8

@@ -6,8 +6,6 @@ S3method(extend,ellipsoidGate)

 S3method(extend,polygonGate)

 S3method(extend,rectangleGate)

 S3method(print,cytobank_experiment)

-export(CytoML.par.get)

-export(CytoML.par.set)

 export(GatingSet2cytobank)

 export(GatingSet2flowJo)

 export(ce_get_channels)

@@ -84,11 +82,10 @@ importFrom(XML,xmlTreeParse)

 importFrom(XML,xmlValue)

 importFrom(XML,xpathApply)

 importFrom(XML,xpathSApply)

-importFrom(base64enc,base64decode)

-importFrom(base64enc,base64encode)

 importFrom(cytolib,cytolib_LdFlags)

 importFrom(dplyr,"%>%")

 importFrom(dplyr,arrange)

+importFrom(dplyr,bind_rows)

 importFrom(dplyr,count)

 importFrom(dplyr,enquo)

 importFrom(dplyr,filter)

@@ -189,6 +186,8 @@ importFrom(graph,removeNode)

 importFrom(graphics,abline)

 importFrom(graphics,polygon)

 importFrom(graphics,text)

+importFrom(jsonlite,base64_dec)

+importFrom(jsonlite,base64_enc)

 importFrom(jsonlite,fromJSON)

 importFrom(jsonlite,toJSON)

 importFrom(methods,as)

@@ -202,9 +201,5 @@ importFrom(tibble,tibble)

 importFrom(utils,localeToCharset)

 importFrom(utils,menu)

 importFrom(utils,packageVersion)

-importFrom(xml2,read_xml)

-importFrom(xml2,write_xml)

-importFrom(xml2,xml_add_sibling)

-importFrom(xml2,xml_comment)

 importFrom(yaml,read_yaml)

 useDynLib(CytoML,.registration = TRUE)

@@ -174,9 +174,9 @@ export_gates_cytobank <- function(gs, flowEnv, trans.Gm2objs, trans, compId, sho

 }

-#' @importFrom base64enc base64encode base64decode

+#' @importFrom jsonlite base64_enc base64_dec

 base64encode_cytobank <- function(x){

-  x <- base64encode(charToRaw(x))

+  x <- base64_enc(charToRaw(x))

   x <- gsub("=", ".", x)

   x <- gsub("\\+", "_", x)

   x <- gsub("/", "-", x)

@@ -186,7 +186,7 @@ base64decode_cytobank <- function(x){

   x <- gsub("\\.", "=", x)

   x <- gsub("_", "\\+", x)

   x <- gsub("-", "/", x)

-  base64decode(x)

+  base64_dec(x)

 }

@@ -47,7 +47,6 @@ GatingSet2flowJo <- function(...){

 #' @importFrom flowWorkspace gs_clone gs_update_channels pData<- cs_unlock cs_lock gs_copy_tree_only cs_load_meta 

 #' @export

 #' @rdname gatingset_to_flowjo

-#' @importFrom xml2 read_xml write_xml

 gatingset_to_flowjo <- function(gs, outFile, showHidden = FALSE, docker_img = NULL, ...){

   res <- check_binary_status()

   if(res!="binary_ok"){

@@ -93,24 +92,13 @@ gatingset_to_flowjo <- function(gs, outFile, showHidden = FALSE, docker_img = NU

   if(length(res) > 0)

     stop(res)

-  else

-  {

-    tree <- read_xml(tmpfile)

-    add_version_info(tree) 

-    invisible(write_xml(tree, file = outFile))

-    

+  else {

+     file.rename(tmpfile, outFile)

   }

 }

-#' @importFrom xml2 xml_comment xml_add_sibling

-add_version_info <- function(tree)

-{

-  info <- Sys.info()

-  xml_add_sibling(tree, xml_comment(paste0("CytoML-version: ", packageVersion("CytoML"))), .where = "before")

-  xml_add_sibling(tree, xml_comment(paste0("hostname: ", info[["nodename"]])), .where = "before")

-  xml_add_sibling(tree,  xml_comment(paste0("user: ", info[["user"]])), .where = "before")

-}

+

 check_docker_status <- function(docker_img = NULL){

   if(Sys.info()["sysname"] == "Windows")

     errcode <- system2("WHERE", "docker", stdout = FALSE)

@@ -293,6 +293,7 @@ setMethod("pData","cytobank_experiment",function(object){

   get_pd(object)

 })

+#' @importFrom dplyr bind_rows

 get_pd <- function(ce){

   res <- bind_rows(lapply(ce$experiment$fcsFiles, function(sample){

                                 data.frame(as.list(

deleted file mode 100644

@@ -1,106 +0,0 @@

-## Store state info in this internal global environment

-CytoML.state <- new.env(hash = FALSE)

-CytoML.state[["par"]] <- list()

-

-#' workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

-#' and matched with this list to dispatch to the one of the three workspace parsers 

-CytoML.par.init <- function(){

-  

-  fj_ver <- list(win = c("1.61", "1.6")

-                , macII = c("2.0")

-                , macIII = c("3.0")

-                , vX = c("1.8", "20.0")

-                )

-                          

-   mac_II_path <- list(group = "/Workspace/Groups/GroupNode"# abs path

-                    , sampleRef = ".//SampleRefs/SampleRef"#relative GroupNode

-                    , sample = "/Workspace/SampleList/Sample"#abs path

-                    , sampleNode = "./SampleNode"#relative to sample

-                    , popNode = "./Population"#relative to sampleNode

-                    , attrName = "name"

-                    , compMatName = "name"

-                    , compMatChName = "name"

-                    , compMatVal = "value"

-                    )

-  mac_II_path[["sampleID"]] <- mac_II_path[["sample"]]

-                    

-  #mac version 3.0 (flowJo version 9.7.2-9.7.4)

-  mac_III_path <- mac_II_path

-  mac_III_path[["sample"]] <- sub("SampleList", "Samples", mac_III_path[["sample"]]) 

-  mac_III_path[["attrName"]] <- "nodeName"

-  mac_III_path[["compMatName"]] <- "matrixName"

-  mac_III_path[["compMatChName"]] <- "fluorName"

-  mac_III_path[["compMatVal"]] <- "spillValue"

-  mac_III_path[["sampleID"]] <- mac_III_path[["sample"]]

-  ####windows version

-  #inherit most paths from mac                                      

-  win_path <- mac_II_path

-  win_path[["popNode"]] <- "./*/Population"

-  win_path[["gateDim"]] <- "*[local-name()='dimension']"#relative to gateNode

-  win_path[["gateParam"]] <- "*[local-name()='parameter']"#relative to dimNode

-  win_path[["sampleID"]] <- file.path(win_path[["sample"]],"DataSet")

-

-  ####version X

-  #inherit most paths from win

-  vX_path <- win_path

-  vX_path[["gateParam"]] <- "*[local-name()='fcs-dimension']";                                        

-  

-  CytoML.state[["par"]] <- list(flowJo_versions = fj_ver 

-                                      , nodePath = list(win = win_path

-                                                        , macII = mac_II_path

-                                                        , macIII = mac_III_path

-                                                        , vX = vX_path

-                                                        )

-                                                                 )

-  

-}

-

-## call the init function

-CytoML.par.init()                                                           

-

-#' CytoML.par.set sets a set of parameters in the CytoML package namespace.

-#' 

-#' @param value A named list of values to set for category name or a list of such lists if name is missing.

-#' @rdname CytoML.par.get

-#' @export

-CytoML.par.set <- function (name, value) 

-{

-    old <- CytoML.state[["par"]]

-    if(name%in%names(old)){

-      CytoML.state[["par"]][[name]] <- lattice:::updateList(old[[name]], value)  

-    }else

-      stop(name, " is not a valid CytoML parameters!")

-    

-  invisible()

-}

-

-#' Query and set session-wide parameter defaults.

-#' 

-#' CytoML.par.get gets a set of parameters in the CytoML package namespace.

-#' 

-#' It is currently used to add/remove the support for a specific flowJo versions (parsed from xml node '/Workspace/version' in flowJo workspace)

-#' 

-#' @param name The name of a parameter category to get or set.

-#'

-#' 

-#' @examples

-#'  #get the flowJo versions currently supported 

-#'  old <- CytoML.par.get("flowJo_versions")

-#' 

-#'  #add the new version

-#'  old[["win"]] <- c(old[["win"]], "1.7")    

-#'  CytoML.par.set("flowJo_versions", old)

-#'  

-#'  CytoML.par.get("flowJo_versions")

-#' 

-#' @export 

-#' @rdname CytoML.par.get

-CytoML.par.get <- function (name = NULL) 

-{

-  lPars <- CytoML.state[["par"]]

-  if (is.null(name)) 

-    lPars

-  else if (name %in% names(lPars)) 

-    lPars[[name]]

-  else NULL

-}

deleted file mode 100644

@@ -1,33 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/zzz.R

-\name{CytoML.par.set}

-\alias{CytoML.par.set}

-\alias{CytoML.par.get}

-\title{CytoML.par.set sets a set of parameters in the CytoML package namespace.}

-\usage{

-CytoML.par.set(name, value)

-

-CytoML.par.get(name = NULL)

-}

-\arguments{

-\item{name}{The name of a parameter category to get or set.}

-

-\item{value}{A named list of values to set for category name or a list of such lists if name is missing.}

-}

-\description{

-CytoML.par.get gets a set of parameters in the CytoML package namespace.

-}

-\details{

-It is currently used to add/remove the support for a specific flowJo versions (parsed from xml node '/Workspace/version' in flowJo workspace)

-}

-\examples{

- #get the flowJo versions currently supported 

- old <- CytoML.par.get("flowJo_versions")

-

- #add the new version

- old[["win"]] <- c(old[["win"]], "1.7")    

- CytoML.par.set("flowJo_versions", old)

- 

- CytoML.par.get("flowJo_versions")

-

-}

deleted file mode 100644

@@ -1,13 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/zzz.R

-\name{CytoML.par.init}

-\alias{CytoML.par.init}

-\title{workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

-and matched with this list to dispatch to the one of the three workspace parsers}

-\usage{

-CytoML.par.init()

-}

-\description{

-workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

-and matched with this list to dispatch to the one of the three workspace parsers

-}