-source("./R/Subcollection.R")
-source("./R/ArvadosFile.R")
-source("./R/RESTService.R")
-source("./R/util.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
#' Collection
-#'
+#'
#' Collection class provides interface for working with Arvados collections.
-#'
+#'
#' @section Usage:
#' \preformatted{collection = Collection$new(arv, uuid)}
#'
#' \item{arv}{Arvados object.}
#' \item{uuid}{UUID of a collection.}
#' }
-#'
+#'
#' @section Methods:
#' \describe{
#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#' \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
#' \item{remove(fileNames)}{Remove one or more files from the collection.}
-#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
#' \item{getFileListing()}{Returns collections file content as character vector.}
#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
#' }
#' arv <- Arvados$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$remove("location/to/my/file.cpp")
public = list(
- uuid = NULL,
- etag = NULL,
- owner_uuid = NULL,
- created_at = NULL,
- modified_by_client_uuid = NULL,
- modified_by_user_uuid = NULL,
- modified_at = NULL,
- portable_data_hash = NULL,
- replication_desired = NULL,
- replication_confirmed_at = NULL,
- replication_confirmed = NULL,
- updated_at = NULL,
- manifest_text = NULL,
- name = NULL,
- description = NULL,
- properties = NULL,
- delete_at = NULL,
- file_names = NULL,
- trash_at = NULL,
- is_trashed = NULL,
- storage_classes_desired = NULL,
- storage_classes_confirmed = NULL,
- storage_classes_confirmed_at = NULL,
-
- initialize = function(uuid = NULL, etag = NULL, owner_uuid = NULL,
- created_at = NULL, modified_by_client_uuid = NULL,
- modified_by_user_uuid = NULL, modified_at = NULL,
- portable_data_hash = NULL, replication_desired = NULL,
- replication_confirmed_at = NULL,
- replication_confirmed = NULL, updated_at = NULL,
- manifest_text = NULL, name = NULL, description = NULL,
- properties = NULL, delete_at = NULL, file_names = NULL,
- trash_at = NULL, is_trashed = NULL,
- storage_classes_desired = NULL,
- storage_classes_confirmed = NULL,
- storage_classes_confirmed_at = NULL)
+ uuid = NULL,
+
+ initialize = function(api, uuid)
{
- self$uuid <- uuid
- self$etag <- etag
- self$owner_uuid <- owner_uuid
- self$created_at <- created_at
- self$modified_by_client_uuid <- modified_by_client_uuid
- self$modified_by_user_uuid <- modified_by_user_uuid
- self$modified_at <- modified_at
- self$portable_data_hash <- portable_data_hash
- self$replication_desired <- replication_desired
- self$replication_confirmed_at <- replication_confirmed_at
- self$replication_confirmed <- replication_confirmed
- self$updated_at <- updated_at
- self$manifest_text <- manifest_text
- self$name <- name
- self$description <- description
- self$properties <- properties
- self$delete_at <- delete_at
- self$file_names <- file_names
- self$trash_at <- trash_at
- self$is_trashed <- is_trashed
- self$storage_classes_desired <- storage_classes_desired
- self$storage_classes_confirmed <- storage_classes_confirmed
- self$storage_classes_confirmed_at <- storage_classes_confirmed_at
-
- private$classFields <- c("uuid", "etag", "owner_uuid",
- "created_at", "modified_by_client_uuid",
- "modified_by_user_uuid", "modified_at",
- "portable_data_hash", "replication_desired",
- "replication_confirmed_at",
- "replication_confirmed", "updated_at",
- "manifest_text", "name", "description",
- "properties", "delete_at", "file_names",
- "trash_at", "is_trashed")
+ private$REST <- api$getRESTService()
+ self$uuid <- uuid
},
add = function(content, relativePath = "")
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
if(relativePath == "" ||
relativePath == "." ||
if("ArvadosFile" %in% class(content) ||
"Subcollection" %in% class(content))
{
+ if(!is.null(content$getCollection()))
+ stop("Content already belongs to a collection.")
+
if(content$getName() == "")
stop("Content has invalid name.")
}
},
- create = function(fileNames, relativePath = "")
+ create = function(files)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
-
- if(relativePath == "" ||
- relativePath == "." ||
- relativePath == "./")
- {
- subcollection <- private$tree$getTree()
- }
- else
- {
- relativePath <- trimFromEnd(relativePath, "/")
- subcollection <- self$get(relativePath)
- }
-
- if(is.null(subcollection))
- stop(paste("Subcollection", relativePath, "doesn't exist."))
+ private$generateCollectionTreeStructure()
- if(is.character(fileNames))
+ if(is.character(files))
{
- arvadosFiles <- NULL
- sapply(fileNames, function(fileName)
+ sapply(files, function(file)
{
- childWithSameName <- subcollection$get(fileName)
+ childWithSameName <- self$get(file)
if(!is.null(childWithSameName))
stop("Destination already contains file with same name.")
- newFile <- ArvadosFile$new(fileName)
- subcollection$add(newFile)
+ newTreeBranch <- private$tree$createBranch(file)
+ private$tree$addBranch(private$tree$getTree(), newTreeBranch)
- arvadosFiles <<- c(arvadosFiles, newFile)
+ private$REST$create(file, self$uuid)
+ newTreeBranch$setCollection(self)
})
- if(length(arvadosFiles) == 1)
- return(arvadosFiles[[1]])
- else
- return(arvadosFiles)
+ "Created"
}
- else
+ else
{
stop(paste0("Expected character vector, got ",
- paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
+ paste0("(", paste0(class(files), collapse = ", "), ")"),
"."))
}
},
remove = function(paths)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
if(is.character(paths))
{
"Content removed"
}
- else
+ else
{
stop(paste0("Expected character vector, got ",
paste0("(", paste0(class(paths), collapse = ", "), ")"),
}
},
- move = function(content, newLocation)
+ move = function(content, destination)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
content <- trimFromEnd(content, "/")
if(is.null(elementToMove))
stop("Content you want to move doesn't exist in the collection.")
- elementToMove$move(newLocation)
+ 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$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
content <- private$REST$getCollectionContent(self$uuid)
content[order(tolower(content))]
get = function(relativePath)
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
private$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$REST <- newRESTService
),
REST = NULL,
tree = NULL,
fileContent = NULL,
- classFields = NULL,
- genereateCollectionTreeStructure = function()
+ generateCollectionTreeStructure = function()
{
if(is.null(self$uuid))
stop("Collection uuid is not defined.")
#'
#' @param x Instance of Collection class
#' @param ... Optional arguments.
-#' @export
+#' @export
print.Collection = function(x, ...)
{
cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
projects / arvados.git / blobdiff