+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/Subcollection.R")
source("./R/ArvadosFile.R")
source("./R/RESTService.R")
source("./R/util.R")
-#' Arvados Collection Object
+#' Collection
+#'
+#' Collection class provides interface for working with Arvados collections.
+#'
+#' @section Usage:
+#' \preformatted{collection = Collection$new(arv, uuid)}
+#'
+#' @section Arguments:
+#' \describe{
+#' \item{arv}{Arvados object.}
+#' \item{uuid}{UUID of a collection.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
+#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#' \item{remove(fileNames)}{Remove one or more files from the collection.}
+#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{getFileListing()}{Returns collections file content as character vector.}
+#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+#' }
+#'
+#' @name Collection
+#' @examples
+#' \dontrun{
+#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+#' collection <- Collection$new(arv, "uuid")
+#'
+#' newFile <- ArvadosFile$new("myFile")
+#' collection$add(newFile, "myFolder")
+#'
+#' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+#'
+#' collection$remove("location/to/my/file.cpp")
#'
-#' Update description
+#' collection$move("folder/file.cpp", "file.cpp")
#'
-#' @examples arv = Collection$new(api, uuid)
-#' @export Collection
+#' arvadosFile <- collection$get("location/to/my/file.cpp")
+#' arvadosSubcollection <- collection$get("location/to/my/directory/")
+#' }
+NULL
+
+#' @export
Collection <- R6::R6Class(
"Collection",
public = list(
- api = NULL,
- uuid = NULL,
+ uuid = NULL,
+ # api = NULL,
- initialize = function(api, uuid)
+ initialize = function(api, uuid)
{
- self$api <- api
+ # self$api <- api
private$REST <- api$getRESTService()
self$uuid <- uuid
add = function(content, relativePath = "")
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
if(relativePath == "" ||
relativePath == "." ||
relativePath == "./")
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
- subcollection$add(content)
+ if(content$getName() == "")
+ stop("Content has invalid name.")
+ subcollection$add(content)
content
}
else
create = function(fileNames, relativePath = "")
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
if(relativePath == "" ||
relativePath == "." ||
relativePath == "./")
}
else
{
- relativePath <- trimFromEnd(relativePath, "/")
+ relativePath <- trimFromEnd(relativePath, "/")
subcollection <- self$get(relativePath)
}
else
return(arvadosFiles)
}
- else
+ else
{
stop(paste0("Expected character vector, got ",
paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
remove = function(paths)
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
if(is.character(paths))
{
sapply(paths, function(filePath)
stop(paste("File", filePath, "doesn't exist."))
parent <- file$getParent()
+
+ if(is.null(parent))
+ stop("You can't delete root folder.")
+
parent$remove(file$getName())
})
+
+ "Content removed"
}
- else
+ else
{
stop(paste0("Expected character vector, got ",
paste0("(", paste0(class(paths), collapse = ", "), ")"),
move = function(content, newLocation)
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
content <- trimFromEnd(content, "/")
elementToMove <- self$get(content)
if(is.null(elementToMove))
- stop("Element you want to move doesn't exist in the collection.")
+ stop("Content you want to move doesn't exist in the collection.")
elementToMove$move(newLocation)
},
- getFileListing = function() private$REST$getCollectionContent(self$uuid),
+ getFileListing = function()
+ {
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
+ content <- private$REST$getCollectionContent(self$uuid)
+ content[order(tolower(content))]
+ },
get = function(relativePath)
{
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
private$tree$getElement(relativePath)
},
+ toJSON = function()
+ {
+ fields <- sapply(private$classFields, function(field)
+ {
+ self[[field]]
+ }, USE.NAMES = TRUE)
+
+ jsonlite::toJSON(list("collection" =
+ Filter(Negate(is.null), fields)), auto_unbox = TRUE)
+ },
+
+ isEmpty = function() {
+ fields <- sapply(private$classFields,
+ function(field) self[[field]])
+
+ if(any(sapply(fields, function(field) !is.null(field) && field != "")))
+ FALSE
+ else
+ TRUE
+ },
+
getRESTService = function() private$REST,
setRESTService = function(newRESTService) private$REST <- newRESTService
),
REST = NULL,
tree = NULL,
fileContent = NULL,
+ classFields = NULL,
- generateTree = function(content)
+ genereateCollectionTreeStructure = function()
{
- treeBranches <- sapply(collectionContent, function(filePath)
- {
- splitPath <- unlist(strsplit(filePath$name, "/", fixed = TRUE))
+ if(is.null(self$uuid))
+ stop("Collection uuid is not defined.")
+
+ if(is.null(private$REST))
+ stop("REST service is not defined.")
- branch = private$createBranch(splitPath, filePath$fileSize)
- })
+ private$fileContent <- private$REST$getCollectionContent(self$uuid)
+ private$tree <- CollectionTree$new(private$fileContent, self)
}
),
cloneable = FALSE
)
+
+#' print.Collection
+#'
+#' Custom print function for Collection class
+#'
+#' @param x Instance of Collection class
+#' @param ... Optional arguments.
+#' @export
+print.Collection = function(x, ...)
+{
+ cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
+ cat(paste0("uuid: ", "\"", x$uuid, "\""), sep = "\n")
+}
projects / arvados.git / blobdiff