@@ -21,6 +21,7 @@ export(recipeSearch)

 export(recipeUpdate)

 export(toList)

 exportMethods("[")

+exportMethods("[<-")

 exportMethods(c)

 exportMethods(show)

 import(BiocFileCache)

@@ -127,6 +127,7 @@ setGeneric("dataTags", function(object)standardGeneric("dataTags"))

 #' @rdname dataHub-class

 setMethod("dataTags", "dataHub", function(object) {

     if("tag" %in% colnames(mcols(object))){

+        ## mcols(object)[, c("rname", "tag")]

         mcols(object)$tag

     }else{

         NULL

@@ -134,7 +135,8 @@ setMethod("dataTags", "dataHub", function(object) {

 })

 #' @rdname dataHub-class

-#' @param value The tag values to assign to datasets in `dataHub` object.

+#' @param value Character string specifying the tag values to assign

+#'     to datasets in `dataHub` object.

 #' @param append Whether to append new tag or replace all tags.

 #' @export

 setGeneric("dataTags<-", function(object, append=TRUE, value)

@@ -158,12 +160,20 @@ setReplaceMethod("dataTags", "dataHub", function(object, append=FALSE, value){

 #' @param x A `dataHub` object.

 #' @param i The integer index of the `dataHub` object, or a logical

 #'     vector same length as the `dataHub` object.

+#' @param j inherited from `[` generic.

+#' @param drop Inherited from `[` generic.

 #' @export

-setMethod("[", c("dataHub"), function(x, i) {

+setMethod("[", c("dataHub"), function(x, i, j, drop) {

     rids <- x@rid[i]

     return(x[rids])

 })

-setGeneric("[")

+

+#' @rdname dataHub-class

+#' @param value A `dataHub` object  

+#' @export

+setReplaceMethod("[", "dataHub", function(x, i, j, value){

+    return(x)

+})

 #' combine dataHub

 #' @rdname dataHub-class

@@ -25,7 +25,7 @@

 meta_data <- function(dir = "", cleanup = FALSE, checkData = TRUE) {

     ymls <- normalizePath(list.files(dir, pattern = ".yml", full.names = TRUE, recursive = TRUE))

     dnames <- sub(".yml$", "", basename(ymls))  ## file name.

-    keys <- c("output", "notes", "date", "tag")

+    keys <- c("output", "notes", "date")

     if (!length(dnames)) {

         meta <- setNames(data.frame(matrix(ncol = 6, nrow = 0)), c("yml", "params", keys))

@@ -7,7 +7,7 @@

             "Use inputs(", ifelse(return, value, ""),

             ") to check required input parameters before evaluation.",

             "\nCheck here: https://rcwl.org/dataRecipes/", value, ".html",

-            "\nfor recipe instructions (e.g., eligible input values, data source, etc.)\n"

+            "\nfor user instructions (e.g., eligible input values, data source, etc.)\n"

             )

 }

 .load_rcp <- function(rscript, env = .GlobalEnv, return = FALSE){

@@ -13,6 +13,7 @@

 \alias{dataTags<-}

 \alias{dataTags<-,dataHub-method}

 \alias{[,dataHub,ANY,ANY,ANY-method}

+\alias{[<-,dataHub,ANY,ANY,ANY-method}

 \alias{c,dataHub-method}

 \alias{toList}

 \title{dataHub Class}

@@ -37,11 +38,13 @@ dataTags(object)

 \S4method{dataTags}{dataHub}(object)

-dataTags(object, append = TRUE) <- value

+dataTags(object, append = TRUE, newtag) <- value

-\S4method{dataTags}{dataHub}(object, append = FALSE) <- value

+\S4method{dataTags}{dataHub}(object, append = FALSE, newtag) <- value

-\S4method{[}{dataHub,ANY,ANY,ANY}(x, i)

+\S4method{[}{dataHub,ANY,ANY,ANY}(x, i, j, drop)

+

+\S4method{[}{dataHub,ANY,ANY,ANY}(x, i, j) <- value

 \S4method{c}{dataHub}(x, ...)

@@ -54,13 +57,20 @@ toList(x, format = c("list", "json", "yaml"), type = NULL)

 \item{append}{Whether to append new tag or replace all tags.}

-\item{value}{The tag values to assign to datasets in \code{dataHub} object.}

+\item{newtag}{Character string specifying the tag values to assign

+to datasets in \code{dataHub} object.}

 \item{x}{A \code{dataHub} object.}

 \item{i}{The integer index of the \code{dataHub} object, or a logical

 vector same length as the \code{dataHub} object.}

+\item{j}{inherited from \code{[} generic.}

+

+\item{drop}{Inherited from \code{[} generic.}

+

+\item{value}{A \code{dataHub} object}

+

 \item{...}{More \code{dataHub} objects to combine.}

 \item{format}{can be "list", "json" or "yaml". Supports partial