@@ -1,6 +1,6 @@

 Package: MultiAssayExperimentData

 Title: Exposes and makes available data from web resources such as cBioPortal

-Version: 0.99.33

+Version: 0.99.34

 Authors@R: c(person("Levi", "Waldron", email = "[email protected]",

     role = "aut"),

     person("Marcel", "Ramos", email = "[email protected]",

@@ -27,6 +27,6 @@ BugReports: https://github.com/waldronlab/MultiAssayExperimentData/issues

 RoxygenNote: 6.0.1

 Collate: 

     'MultiAssayExperimentData-pkg.R'

+    'cache.R'

     'utils.R'

     'importcBioPortal.R'

-    'removeCache.R'

@@ -1,7 +1,9 @@

 # Generated by roxygen2: do not edit by hand

+export(cBio_cache)

 export(importcBioPortal)

 export(removeCache)

+export(setCache)

 import(RTCGAToolbox)

 importFrom(BiocFileCache,BiocFileCache)

 importFrom(BiocFileCache,bfcadd)

new file mode 100644

@@ -0,0 +1,78 @@

+#' @name cBio_cache

+#'

+#' @title Manage cache / download directories for study data

+#'

+#' @description Managing data downloads is important to save disk space and

+#' re-downloading data files. This can be done effortlessly via the integrated

+#' BiocFileCache system.

+#'

+#' @section setCache:

+#' Specify the directory location of the data cache. By default, it will

+#' got to the user's home directory and project directory as specified by

+#' \link{user_cache_dir}

+#'

+#' @section removeCache:

+#' Some files may become corrupt when downloading, this function allows

+#' the user to delete the tarball associated with a `cancer_study_id``

+#'

+#' @param cancer_study_id A single string from `studiesTable` associated

+#' with a study tarball

+#' @param directory The file location where the cache is located. Once set

+#' future downloads will go to this folder.

+#'

+#' @md

+#'

+#' @export

+removeCache <- function(cancer_study_id) {

+    bfc <- .get_cache(TRUE)

+    rid <- bfcquery(bfc, cancer_study_id, "rname")$rid

+    if (length(rid)) {

+        bfcremove(bfc, rid)

+        message("Cache record: ", cancer_study_id, ".tar.gz removed")

+    } else

+        message("No record found: ", cancer_study_id, ".tar.gz")

+}

+

+#' @rdname cBio_cache

+#' @export

+setCache <-

+function(directory = rappdirs::user_cache_dir("MultiAssayExperimentData"),

+    verbose = TRUE,

+    ask = interactive())

+{

+    create_path <- function(directory) {

+        dir.create(directory, recursive = TRUE, showWarnings = FALSE)

+    }

+

+    stopifnot(is.character(directory),

+        isSingleString(directory), !is.na(directory))

+

+    if (!ask)

+        create_path(directory)

+    else {

+        qtxt <- sprintf(

+            "Create MultiAssayExperimentData cache at \n    %s? [y/n]: ",

+            directory

+        )

+        answer <- .getAnswer(qtxt, allowed = c("y", "Y", "n", "N"))

+        if ("n" == answer)

+            stop("'cBio_cache' directory will not be created")

+    }

+    create_path(directory)

+    options("cBio_cache" = directory)

+

+    if (verbose)

+        message("MultiAssayExperimentData cache directory set to: ",

+                directory)

+    invisible(directory)

+}

+

+#' @rdname cBio_cache

+#' @export

+cBio_cache <- function() {

+    cache_dir <- getOption("cBio_cache", setCache(verbose = FALSE))

+    if (!dir.exists(cache_dir))

+        setCache(cache_dir)

+

+    return(cache_dir)

+}

deleted file mode 100644

@@ -1,20 +0,0 @@

-#' Delete downloaded study tarballs from cache

-#'

-#' Some files may become corrupt when downloading, this function allows

-#' the user to delete the tarball associated with a `cancer_study_id``

-#'

-#' @param cancer_study_id A single string from `studiesTable` associated

-#' with a study tarball

-#'

-#' @md

-#'

-#' @export

-removeCache <- function(cancer_study_id) {

-    bfc <- .get_cache(TRUE)

-    rid <- bfcquery(bfc, cancer_study_id, "rname")$rid

-    if (length(rid)) {

-        bfcremove(bfc, rid)

-        message("Cache record: ", cancer_study_id, ".tar.gz removed")

-    } else

-        message("No record found: ", cancer_study_id, ".tar.gz")

-}

@@ -120,3 +120,18 @@

     samp <- RTCGAToolbox:::.findCol(coldat, "SAMPLE_ID")

     length(pt) && length(samp)

 }

+

+.getAnswer <- function(msg, allowed)

+{

+    if (interactive()) {

+        repeat {

+            cat(msg)

+            answer <- readLines(n = 1)

+            if (answer %in% allowed)

+                break

+        }

+        tolower(answer)

+    } else {

+        "n"

+    }

+}

new file mode 100644

@@ -0,0 +1,41 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/cache.R

+\name{cBio_cache}

+\alias{cBio_cache}

+\alias{removeCache}

+\alias{setCache}

+\alias{cBio_cache}

+\title{Manage cache / download directories for study data}

+\usage{

+removeCache(cancer_study_id)

+

+setCache(directory = rappdirs::user_cache_dir("MultiAssayExperimentData"),

+  verbose = TRUE, ask = interactive())

+

+cBio_cache()

+}

+\arguments{

+\item{cancer_study_id}{A single string from \code{studiesTable} associated

+with a study tarball}

+

+\item{directory}{The file location where the cache is located. Once set

+future downloads will go to this folder.}

+}

+\description{

+Managing data downloads is important to save disk space and

+re-downloading data files. This can be done effortlessly via the integrated

+BiocFileCache system.

+}

+\section{setCache}{

+

+Specify the directory location of the data cache. By default, it will

+got to the user's home directory and project directory as specified by

+\link{user_cache_dir}

+}

+

+\section{removeCache}{

+

+Some files may become corrupt when downloading, this function allows

+the user to delete the tarball associated with a `cancer_study_id``

+}

+

deleted file mode 100644

@@ -1,16 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/removeCache.R

-\name{removeCache}

-\alias{removeCache}

-\title{Delete downloaded study tarballs from cache}

-\usage{

-removeCache(cancer_study_id)

-}

-\arguments{

-\item{cancer_study_id}{A single string from \code{studiesTable} associated

-with a study tarball}

-}

-\description{

-Some files may become corrupt when downloading, this function allows

-the user to delete the tarball associated with a `cancer_study_id``

-}