-source("./R/Arvados.R")
-source("./R/HttpParser.R")
+# 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")
-#' Collection Object
-#'
-#' @details
-#' Todo: Update description
#' Collection
-#'
-#' @param uuid Object ID
-#' @param etag Object version
-#' @param owner_uuid No description
-#' @param created_at No description
-#' @param modified_by_client_uuid No description
-#' @param modified_by_user_uuid No description
-#' @param modified_at No description
-#' @param portable_data_hash No description
-#' @param replication_desired No description
-#' @param replication_confirmed_at No description
-#' @param replication_confirmed No description
-#' @param updated_at No description
-#' @param manifest_text No description
-#' @param name No description
-#' @param description No description
-#' @param properties No description
-#' @param delete_at No description
-#' @param file_names No description
-#' @param trash_at No description
-#' @param is_trashed No description
-#'
+#'
+#' Collection class provides interface for working with Arvados collections.
+#'
+#' @section Usage:
+#' \preformatted{collection = Collection$new(arv, uuid)}
+#'
+#' @section Arguments:
+#' \describe{
+#' \item{arv}{Arvados object.}
+#' \item{uuid}{UUID of a collection.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
+#' \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#' \item{remove(fileNames)}{Remove one or more files from the collection.}
+#' \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
+#' \item{getFileListing()}{Returns collections file content as character vector.}
+#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+#' }
+#'
+#' @name Collection
+#' @examples
+#' \dontrun{
+#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+#' collection <- Collection$new(arv, "uuid")
+#'
+#' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+#'
+#' collection$remove("location/to/my/file.cpp")
+#'
+#' collection$move("folder/file.cpp", "file.cpp")
+#'
+#' arvadosFile <- collection$get("location/to/my/file.cpp")
+#' arvadosSubcollection <- collection$get("location/to/my/directory/")
+#' }
+NULL
+
#' @export
-Collection <- setRefClass(
+Collection <- R6::R6Class(
"Collection",
- fields = list(uuid = "ANY",
- items = "ANY",
- etag = "ANY",
- owner_uuid = "ANY",
- created_at = "ANY",
- modified_by_client_uuid = "ANY",
- modified_by_user_uuid = "ANY",
- modified_at = "ANY",
- portable_data_hash = "ANY",
- replication_desired = "ANY",
- replication_confirmed_at = "ANY",
- replication_confirmed = "ANY",
- updated_at = "ANY",
- manifest_text = "ANY",
- name = "ANY",
- description = "ANY",
- properties = "ANY",
- delete_at = "ANY",
- file_names = "ANY",
- trash_at = "ANY",
- is_trashed = "ANY",
-
- getCollectionContent = "function"
- ),
+ public = list(
+
+ uuid = NULL,
+
+ initialize = function(api, uuid)
+ {
+ private$REST <- api$getRESTService()
+ self$uuid <- uuid
+ },
+
+ add = function(content, relativePath = "")
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ if(relativePath == "" ||
+ relativePath == "." ||
+ relativePath == "./")
+ {
+ subcollection <- private$tree$getTree()
+ }
+ else
+ {
+ relativePath <- trimFromEnd(relativePath, "/")
+ subcollection <- self$get(relativePath)
+ }
+
+ if(is.null(subcollection))
+ stop(paste("Subcollection", relativePath, "doesn't exist."))
+
+ if("ArvadosFile" %in% class(content) ||
+ "Subcollection" %in% class(content))
+ {
+ if(!is.null(content$getCollection()))
+ stop("Content already belongs to a collection.")
+
+ if(content$getName() == "")
+ stop("Content has invalid name.")
- methods = list(
+ subcollection$add(content)
+ content
+ }
+ else
+ {
+ stop(paste0("Expected AravodsFile or Subcollection object, got ",
+ paste0("(", paste0(class(content), collapse = ", "), ")"),
+ "."))
+ }
+ },
- initialize = function(api, uuid)
+ create = function(files)
{
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- result <- api$collection_get(uuid)
-
- # Private members
- uuid <<- result$uuid
- etag <<- result$etag
- owner_uuid <<- result$owner_uuid
- created_at <<- result$created_at
- modified_by_client_uuid <<- result$modified_by_client_uuid
- modified_by_user_uuid <<- result$modified_by_user_uuid
- modified_at <<- result$modified_at
- portable_data_hash <<- result$portable_data_hash
- replication_desired <<- result$replication_desired
- replication_confirmed_at <<- result$replication_confirmed_at
- replication_confirmed <<- result$replication_confirmed
- updated_at <<- result$updated_at
- manifest_text <<- result$manifest_text
- name <<- result$name
- description <<- result$description
- properties <<- result$properties
- delete_at <<- result$delete_at
- file_names <<- result$file_names
- trash_at <<- result$trash_at
- is_trashed <<- result$is_trashed
-
-
- #Public methods
-
- # Private methods
- getCollectionContent <<- function()
+ if(is.character(files))
{
- #TODO(Fudo): Use proper URL here.
- uri <- URLencode(api$getWebDavHostName())
+ sapply(files, function(file)
+ {
+ childWithSameName <- self$get(file)
+ if(!is.null(childWithSameName))
+ stop("Destination already contains file with same name.")
- # fetch directory listing via curl and parse XML response
- h <- curl::new_handle()
- curl::handle_setopt(h, customrequest = "PROPFIND")
+ newTreeBranch <- private$tree$createBranch(file)
+ private$tree$addBranch(private$tree$getTree(), newTreeBranch)
- #TODO(Fudo): Use proper token here.
- curl::handle_setheaders(h, "Authorization" = paste("OAuth2", api$getWebDavToken()))
- response <- curl::curl_fetch_memory(uri, h)
+ private$REST$create(file, self$uuid)
+ newTreeBranch$setCollection(self)
+ })
+
+ "Created"
+ }
+ else
+ {
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(files), collapse = ", "), ")"),
+ "."))
+ }
+ },
+
+ remove = function(paths)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- HttpParser()$parseWebDAVResponse(response, uri)
+ if(is.character(paths))
+ {
+ sapply(paths, function(filePath)
+ {
+ filePath <- trimFromEnd(filePath, "/")
+ file <- self$get(filePath)
+
+ if(is.null(file))
+ stop(paste("File", filePath, "doesn't exist."))
+
+ parent <- file$getParent()
+
+ if(is.null(parent))
+ stop("You can't delete root folder.")
+
+ parent$remove(file$getName())
+ })
+
+ "Content removed"
+ }
+ else
+ {
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(paths), collapse = ", "), ")"),
+ "."))
}
+ },
- items <<- getCollectionContent()
+ move = function(content, destination)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ content <- trimFromEnd(content, "/")
+
+ elementToMove <- self$get(content)
+
+ if(is.null(elementToMove))
+ stop("Content you want to move doesn't exist in the collection.")
+
+ elementToMove$move(destination)
+ },
+
+ copy = function(content, destination)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ content <- trimFromEnd(content, "/")
+
+ elementToCopy <- self$get(content)
+
+ if(is.null(elementToCopy))
+ stop("Content you want to copy doesn't exist in the collection.")
+
+ elementToCopy$copy(destination)
+ },
+
+ refresh = function()
+ {
+ if(!is.null(private$tree))
+ {
+ private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+ private$tree <- NULL
+ }
+ },
+
+ getFileListing = function()
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ content <- private$REST$getCollectionContent(self$uuid)
+ content[order(tolower(content))]
+ },
+
+ get = function(relativePath)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ private$tree$getElement(relativePath)
+ },
+
+ getRESTService = function() private$REST,
+ setRESTService = function(newRESTService) private$REST <- newRESTService
+ ),
+
+ private = list(
+
+ REST = NULL,
+ tree = NULL,
+ fileContent = NULL,
+
+ generateCollectionTreeStructure = function()
+ {
+ if(is.null(self$uuid))
+ stop("Collection uuid is not defined.")
+
+ if(is.null(private$REST))
+ stop("REST service is not defined.")
+
+ 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