@@ -394,5 +394,6 @@ importFrom(stats,na.omit)

 importFrom(stats,setNames)

 importFrom(utils,URLencode)

 importFrom(utils,browseURL)

+importFrom(utils,file_test)

 importFrom(utils,head)

 importFrom(utils,tail)

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

 # ------------------------------------------------------------------------------

 #' @title sandboxInitializer

 #'

-#' @description sandboxInitializer

+#' @description Start with a sandbox template and update properties using whatever is found in the new_sandbox.

 #' @param newSandbox newSandbox

 #' @param ... ...

 #' @return sandbox

@@ -30,7 +30,7 @@ sandboxInitializer <- function(newSandbox=NULL, ...){

 # ------------------------------------------------------------------------------

 #' @title setDefaultSandbox

 #'

-#' @description setDefaultSandbox

+#' @description Set and return the sandbox properties to be used as a default, probably based on whether a Notebook is running.

 #' @param newSandbox newSandbox

 #' @param ... ...

 #' @return default sandbox

@@ -46,7 +46,7 @@ setDefaultSandbox <- function(newSandbox=NULL, ...){

 # ------------------------------------------------------------------------------

 #' @title getDefaultSandbox

 #'

-#' @description getDefaultSandbox

+#' @description Return whatever is the current default sandbox properties.

 #' @return default sandbox

 #' @examples \donttest{

 #' getDefaultSandbox()

@@ -59,7 +59,7 @@ getDefaultSandbox <- function(){

 # ------------------------------------------------------------------------------

 #' @title setDefaultSandboxPath

 #'

-#' @description setDefaultSandboxPath

+#' @description Set and return the default path, which isn't one of the properties tracked in the default_sandbox.

 #' @param newPath new path of default sandbox 

 #' @return default sandbox path

 #' @examples \donttest{

@@ -74,7 +74,7 @@ setDefaultSandboxPath <- function(newPath){

 # ------------------------------------------------------------------------------

 #' @title getDefaultSandboxPath

 #'

-#' @description getDefaultSandboxPath

+#' @description Return the default path, which isn't one of the properties tracked in the default_sandbox.

 #' @return default sandbox path

 #' @examples \donttest{

 #' getDefaultSandboxPath()

@@ -87,7 +87,7 @@ getDefaultSandboxPath <- function(){

 # ------------------------------------------------------------------------------

 #' @title getCurrentSandboxName

 #'

-#' @description getCurrentSandboxName

+#' @description Return the current sandbox name.

 #' @return current sandbox name

 #' @examples \donttest{

 #' getCurrentSandboxName()

@@ -100,7 +100,7 @@ getCurrentSandboxName <- function(){

 # ------------------------------------------------------------------------------

 #' @title getCurrentSandboxPath

 #'

-#' @description getCurrentSandboxPath

+#' @description Return the current sandbox path.

 #' @return current sandbox path

 #' @examples \donttest{

 #' getCurrentSandboxPath()

@@ -113,7 +113,7 @@ getCurrentSandboxPath <- function(){

 # ------------------------------------------------------------------------------

 #' @title getCurrentSandbox

 #'

-#' @description getCurrentSandbox

+#' @description Return both the current sandbox name and path.

 #' @return current sandbox

 #' @examples \donttest{

 #' getCurrentSandbox()

@@ -127,7 +127,7 @@ getCurrentSandbox <- function(){

 # ------------------------------------------------------------------------------

 #' @title setCurrentSandbox

 #'

-#' @description setCurrentSandbox

+#' @description Set and return the current sandbox name and path.

 #' @param sandboxName sandboxName 

 #' @param sandboxPath sandboxPath 

 #' @return current sandbox

@@ -144,7 +144,7 @@ setCurrentSandbox <- function(sandboxName, sandboxPath){

 # ------------------------------------------------------------------------------

 #' @title setSandboxReinitialize

 #'

-#' @description setSandboxReinitialize

+#' @description Set and return flag indicating that next command should reinitialize the sandbox according to the default_sandbox.

 #' @param doReinitialize default is TRUE 

 #' @return sandbox reinitialize

 #' @examples \donttest{

@@ -159,7 +159,7 @@ setSandboxReinitialize <- function(doReinitialize=TRUE){

 # ------------------------------------------------------------------------------

 #' @title getSandboxReinitialize

 #'

-#' @description getSandboxReinitialize

+#' @description Return flag indicating that next command should reinitialize the sandbox according to the default_sandbox.

 #' @return sandbox reinitialize

 #' @examples \donttest{

 #' getSandboxReinitialize()

@@ -172,7 +172,7 @@ getSandboxReinitialize <- function(){

 # ------------------------------------------------------------------------------

 #' @title getAbsSandboxPath

 #'

-#' @description getAbsSandboxPath

+#' @description Get absolute sandbox path.

 #' @param fileLocation fileLocation 

 #' @return file location

 #' @examples \donttest{

@@ -195,7 +195,7 @@ getAbsSandboxPath <- function(fileLocation){

 # ------------------------------------------------------------------------------

 #' @title resetDefaultSandbox

 #'

-#' @description resetDefaultSandbox

+#' @description Reset the entire state of the sandbox system.

 #' @examples \donttest{

 #' resetDefaultSandbox()

 #' }

@@ -3,7 +3,16 @@

 # ------------------------------------------------------------------------------

 #' @title sandboxSet

 #'

-#' @description sandboxSet

+#' @description Set a new default sandbox, creating it if necessary.

+#' A sandbox is the root for the file system used for all file operations. When running standalone

+#' on the same workstation as Cytoscape, the default sandbox is the directory that's current for

+#' the R kernel. When running in a Notebook or remote server, the default sandbox is the

+#' 'default_sandbox' created automatically under the under the filetransfer directory in the

+#' CytoscapeConfiguration directory. Naming a sandbox with this function creates a new

+#' sub-directory as a sibling to 'default_sandbox' and uses it for subsequent file operations.

+#' Setting a None sandbox uses the default sandbox instead.

+#' Sandboxes are highly recommended as an aid to creating workflows that can be shared with

+#' others.

 #' @param sandboxName Name of new default sandbox. None means to use the original default sandbox 

 #' @param copySamples True to copy the Cytoscape sampleData into the sandbox

 #' @param reinitialize True to delete sandbox contents (if any) if sandbox already exists

@@ -26,7 +35,14 @@ sandboxSet <- function(sandboxName, copySamples=TRUE, reinitialize=TRUE, base.ur

 # ------------------------------------------------------------------------------

 #' @title sandboxRemove

 #'

-#' @description sandboxRemove

+#' @description Delete sandbox contents and remove its directory.

+#' If the current sandbox is the entire file system on a Cytoscape workstation, trying to delete it

+#' is an error. Otherwise, deleting the current sandbox results in the default sandbox becoming the

+#' new current sandbox. When running standalone on the same workstation as Cytoscape, the default

+#' sandbox is the entire file system on the Cytoscape workstation. When running in a Notebook or

+#' remote server, the default sandbox is the 'default_sandbox' created automatically under the

+#' under the filetransfer directory in the CytoscapeConfiguration directory. If that sandbox is

+#' deleted, it will be re-created so that subsequent file operations can complete successfully.

 #' @param sandboxName Name of sandbox to delete. None means to delete the current sandbox. If that sandbox is the default sandbox, it is automatically re-created.

 #' @param base.url Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of RCy3.

 #' @return dict: {'sandboxPath': <directory on Cytoscape workstation>, 'existed': <True if sandbox existed>}

@@ -56,7 +72,15 @@ sandboxRemove <- function(sandboxName=NULL, base.url=.defaultBaseUrl){

 # ------------------------------------------------------------------------------

 #' @title sandboxGetFileInfo

 #'

-#' @description sandboxGetFileInfo

+#' @description Get metadata on file in sandbox (or entire sandbox).

+#' If the current sandbox is the entire file system on a Cytoscape workstation, trying to delete it

+#' is an error. Otherwise, deleting the current sandbox results in the default sandbox becoming the

+#' new current sandbox. When running standalone on the same workstation as Cytoscape, the default

+#' sandbox is the entire file system on the Cytoscape workstation. When running in a Notebook or

+#' remote server, the default sandbox is the 'default_sandbox' created automatically under the

+#' under the filetransfer directory in the CytoscapeConfiguration directory. If that sandbox is

+#' deleted, it will be re-created so that subsequent file operations can complete successfully.

+#' Note that this function can be used to query either a file or a directory.

 #' @param fileName Name of file whose metadata to return ... can be sandbox-relative path ... ``.`` returns metadata on sandbox itself

 #' @param sandboxName Name of sandbox containing file. None means "the current sandbox".

 #' @param base.url Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of RCy3.

@@ -64,7 +88,7 @@ sandboxRemove <- function(sandboxName=NULL, base.url=.defaultBaseUrl){

 #' @examples \donttest{

 #' sandboxGetFileInfo()

 #' }

-#' @importFrom file_test utils

+#' @importFrom utils file_test

 #' @export

 sandboxGetFileInfo <- function(fileName, sandboxName=NULL, base.url=.defaultBaseUrl){

     tryCatch(

@@ -92,7 +116,14 @@ sandboxGetFileInfo <- function(fileName, sandboxName=NULL, base.url=.defaultBase

 # ------------------------------------------------------------------------------

 #' @title sandboxSendTo

 #'

-#' @description sandboxSendTo

+#' @description Transfer a file to a sandbox.

+#' The source file is transferred to the named (or current) sandbox, overwriting an existing file if one

+#' already exists. The destFile can be an absolute path if the sandbox is the entire file system (i.e., for

+#' standalone R execution) or a path relative to the sandbox (i.e., for Notebook or remote execution or if a

+#' sandbox was explicitly created).

+#' Note that there is no function that transfers an entire directory. Note, though, that when using sandboxSet()

+#' to make a sandbox current, it is possible to copy the Cytoscape sample data directories into to the sandbox at the

+#' same time.

 #' @param sourceFile Name of file to read (as absolute path or sandbox-relative path)

 #' @param destFile Name of file in the R workflow's file system ... if None, use file name in source_file

 #' @param overwrite Name of sandbox containing file. None means "the current sandbox".

@@ -138,7 +169,11 @@ sandboxSendTo <- function(sourceFile, destFile=NULL, overwrite=TRUE, sandboxName

 # ------------------------------------------------------------------------------

 #' @title sandboxUrlTo

 #'

-#' @description sandboxUrlTo

+#' @description Transfer a cloud-based file to a sandbox.

+#' The source URL identifies a file to be transferred to the named (or current) sandbox, overwriting an existing

+#' file if one already exists. The destFile can be an absolute path if the sandbox is the entire file

+#' system (i.e., for standalone R execution), or it can be a path relative to the sandbox (i.e., for Notebook or

+#' remote execution or if a sandbox was explicitly created).                                                                                     

 #' @param sourceURL URL addressing cloud file to download

 #' @param destFile Name of file in the R workflow's file system ... if None, use file name in source_file

 #' @param overwrite Name of sandbox containing file. None means "the current sandbox".

@@ -165,7 +200,11 @@ sandboxUrlTo <- function(sourceURL, destFile, overwrite=TRUE, sandboxName=NULL,

 # ------------------------------------------------------------------------------

 #' @title sandboxGetFrom

 #'

-#' @description sandboxGetFrom

+#' @description Transfer a file from a sandbox.

+#' The source file is transferred from the named (or current) sandbox to the R workflow's file system,

+#' overwriting an existing file if one already exists. The sourceFile can be an absolute path if the sandbox is

+#' the entire file system (i.e., for standalone R execution) or a path relative to the sandbox

+#' (i.e., for Notebook or remote execution or if a sandbox was explicitly created).

 #' @param sourceFile Name of file to read (as absolute path or sandbox-relative path)

 #' @param destFile Name of file in the R workflow's file system ... if None, use file name in source_file

 #' @param overwrite Name of sandbox containing file. None means "the current sandbox".

@@ -213,7 +252,11 @@ sandboxGetFrom <- function(sourceFile, destFile=NULL, overwrite=TRUE, sandboxNam

 # ------------------------------------------------------------------------------

 #' @title sandboxRemoveFile

 #'

-#' @description sandboxRemoveFile

+#' @description Remove a file from a sandbox.

+#' The named file is removed from the named sandbox. If the sandbox is the entire file system (i.e., for standalone

+#' R execution), the file name can be an absolute path. Otherwise, it is a path relative to the named sandbox.

+#' Note that there is no function that deletes a directory, except for sandboxRemove(), which deletes a sandbox

+#' and all of its contents.

 #' @param fileName Name of file to delete (as absolute path or sandbox-relative path)

 #' @param sandboxName Name of sandbox containing file. None means "the current sandbox".

 #' @param base.url Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of RCy3.

@@ -229,7 +272,7 @@ sandboxRemoveFile <- function(fileName, sandboxName=NULL, base.url=.defaultBaseU

 # ------------------------------------------------------------------------------

 #' @title sandboxOp

 #'

-#' @description sandboxOp

+#' @description internal function for sandbox operation

 #' @param command command

 #' @param sandboxName Name of file to read (as absolute path or sandbox-relative path)

 #' @param fileName Name of file to read (as absolute path or sandbox-relative path)

@@ -13,7 +13,7 @@ getAbsSandboxPath(fileLocation)

 file location

 }

 \description{

-getAbsSandboxPath

+Get absolute sandbox path.

 }

 \examples{

 \donttest{

@@ -10,7 +10,7 @@ getCurrentSandbox()

 current sandbox

 }

 \description{

-getCurrentSandbox

+Return both the current sandbox name and path.

 }

 \examples{

 \donttest{

@@ -10,7 +10,7 @@ getCurrentSandboxName()

 current sandbox name

 }

 \description{

-getCurrentSandboxName

+Return the current sandbox name.

 }

 \examples{

 \donttest{

@@ -10,7 +10,7 @@ getCurrentSandboxPath()

 current sandbox path

 }

 \description{

-getCurrentSandboxPath

+Return the current sandbox path.

 }

 \examples{

 \donttest{

@@ -10,7 +10,7 @@ getDefaultSandbox()

 default sandbox

 }

 \description{

-getDefaultSandbox

+Return whatever is the current default sandbox properties.

 }

 \examples{

 \donttest{

@@ -10,7 +10,7 @@ getDefaultSandboxPath()

 default sandbox path

 }

 \description{

-getDefaultSandboxPath

+Return the default path, which isn't one of the properties tracked in the default_sandbox.

 }

 \examples{

 \donttest{

@@ -10,7 +10,7 @@ getSandboxReinitialize()

 sandbox reinitialize

 }

 \description{

-getSandboxReinitialize

+Return flag indicating that next command should reinitialize the sandbox according to the default_sandbox.

 }

 \examples{

 \donttest{

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

 resetDefaultSandbox()

 }

 \description{

-resetDefaultSandbox

+Reset the entire state of the sandbox system.

 }

 \examples{

 \donttest{

@@ -17,7 +17,15 @@ sandboxGetFileInfo(fileName, sandboxName = NULL, base.url = .defaultBaseUrl)

 dict: {'filePath': <full path on Cytoscape workstation>, 'modifiedTime': <last changed time, '' if file doesn't exist>, 'isFile': <True if file, False if directory>}

 }

 \description{

-sandboxGetFileInfo

+Get metadata on file in sandbox (or entire sandbox).

+If the current sandbox is the entire file system on a Cytoscape workstation, trying to delete it

+is an error. Otherwise, deleting the current sandbox results in the default sandbox becoming the

+new current sandbox. When running standalone on the same workstation as Cytoscape, the default

+sandbox is the entire file system on the Cytoscape workstation. When running in a Notebook or

+remote server, the default sandbox is the 'default_sandbox' created automatically under the

+under the filetransfer directory in the CytoscapeConfiguration directory. If that sandbox is

+deleted, it will be re-created so that subsequent file operations can complete successfully.

+Note that this function can be used to query either a file or a directory.

 }

 \examples{

 \donttest{

@@ -27,7 +27,11 @@ sandboxGetFrom(

 sandboxGetFrom

 }

 \description{

-sandboxGetFrom

+Transfer a file from a sandbox.

+The source file is transferred from the named (or current) sandbox to the R workflow's file system,

+overwriting an existing file if one already exists. The sourceFile can be an absolute path if the sandbox is

+the entire file system (i.e., for standalone R execution) or a path relative to the sandbox

+(i.e., for Notebook or remote execution or if a sandbox was explicitly created).

 }

 \examples{

 \donttest{

@@ -15,7 +15,7 @@ sandboxInitializer(newSandbox = NULL, ...)

 sandbox

 }

 \description{

-sandboxInitializer

+Start with a sandbox template and update properties using whatever is found in the new_sandbox.

 }

 \examples{

 \donttest{

@@ -19,7 +19,7 @@ sandboxOp(command, sandboxName, fileName = NULL, base.url = .defaultBaseUrl)

 sandbox result

 }

 \description{

-sandboxOp

+internal function for sandbox operation

 }

 \examples{

 \donttest{

@@ -15,7 +15,14 @@ sandboxRemove(sandboxName = NULL, base.url = .defaultBaseUrl)

 dict: {'sandboxPath': <directory on Cytoscape workstation>, 'existed': <True if sandbox existed>}

 }

 \description{

-sandboxRemove

+Delete sandbox contents and remove its directory.

+If the current sandbox is the entire file system on a Cytoscape workstation, trying to delete it

+is an error. Otherwise, deleting the current sandbox results in the default sandbox becoming the

+new current sandbox. When running standalone on the same workstation as Cytoscape, the default

+sandbox is the entire file system on the Cytoscape workstation. When running in a Notebook or

+remote server, the default sandbox is the 'default_sandbox' created automatically under the

+under the filetransfer directory in the CytoscapeConfiguration directory. If that sandbox is

+deleted, it will be re-created so that subsequent file operations can complete successfully.

 }

 \examples{

 \donttest{

@@ -17,7 +17,11 @@ sandboxRemoveFile(fileName, sandboxName = NULL, base.url = .defaultBaseUrl)

 dict: {'filePath': <file's absolute path in Cytoscape workstation>, 'existed': True if file existed before being deleted}

 }

 \description{

-sandboxRemoveFile

+Remove a file from a sandbox.

+The named file is removed from the named sandbox. If the sandbox is the entire file system (i.e., for standalone

+R execution), the file name can be an absolute path. Otherwise, it is a path relative to the named sandbox.

+Note that there is no function that deletes a directory, except for sandboxRemove(), which deletes a sandbox

+and all of its contents.

 }

 \examples{

 \donttest{

@@ -27,7 +27,14 @@ sandboxSendTo(

 sandboxSendTo

 }

 \description{

-sandboxSendTo

+Transfer a file to a sandbox.

+The source file is transferred to the named (or current) sandbox, overwriting an existing file if one

+already exists. The destFile can be an absolute path if the sandbox is the entire file system (i.e., for

+standalone R execution) or a path relative to the sandbox (i.e., for Notebook or remote execution or if a

+sandbox was explicitly created).

+Note that there is no function that transfers an entire directory. Note, though, that when using sandboxSet()

+to make a sandbox current, it is possible to copy the Cytoscape sample data directories into to the sandbox at the

+same time.

 }

 \examples{

 \donttest{

@@ -24,7 +24,16 @@ sandboxSet(

 sandbox path in Cytoscape workstation's file system

 }

 \description{

-sandboxSet

+Set a new default sandbox, creating it if necessary.

+A sandbox is the root for the file system used for all file operations. When running standalone

+on the same workstation as Cytoscape, the default sandbox is the directory that's current for

+the R kernel. When running in a Notebook or remote server, the default sandbox is the

+'default_sandbox' created automatically under the under the filetransfer directory in the

+CytoscapeConfiguration directory. Naming a sandbox with this function creates a new

+sub-directory as a sibling to 'default_sandbox' and uses it for subsequent file operations.

+Setting a None sandbox uses the default sandbox instead.

+Sandboxes are highly recommended as an aid to creating workflows that can be shared with

+others.

 }

 \examples{

 \donttest{

@@ -27,7 +27,11 @@ sandboxUrlTo(

 dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}

 }

 \description{

-sandboxUrlTo

+Transfer a cloud-based file to a sandbox.

+The source URL identifies a file to be transferred to the named (or current) sandbox, overwriting an existing

+file if one already exists. The destFile can be an absolute path if the sandbox is the entire file

+system (i.e., for standalone R execution), or it can be a path relative to the sandbox (i.e., for Notebook or

+remote execution or if a sandbox was explicitly created).

 }

 \examples{

 \donttest{

@@ -15,7 +15,7 @@ setCurrentSandbox(sandboxName, sandboxPath)

 current sandbox

 }

 \description{

-setCurrentSandbox

+Set and return the current sandbox name and path.

 }

 \examples{

 \donttest{

@@ -15,7 +15,7 @@ setDefaultSandbox(newSandbox = NULL, ...)

 default sandbox

 }

 \description{

-setDefaultSandbox

+Set and return the sandbox properties to be used as a default, probably based on whether a Notebook is running.

 }

 \examples{

 \donttest{

@@ -13,7 +13,7 @@ setDefaultSandboxPath(newPath)

 default sandbox path

 }

 \description{

-setDefaultSandboxPath

+Set and return the default path, which isn't one of the properties tracked in the default_sandbox.

 }

 \examples{

 \donttest{

@@ -13,7 +13,7 @@ setSandboxReinitialize(doReinitialize = TRUE)

 sandbox reinitialize

 }

 \description{

-setSandboxReinitialize

+Set and return flag indicating that next command should reinitialize the sandbox according to the default_sandbox.

 }

 \examples{

 \donttest{