+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
source("./R/Subcollection.R")
source("./R/ArvadosFile.R")
-source("./R/FileTree.R")
-source("./R/HttpRequest.R")
-source("./R/HttpParser.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$new(arv, uuid)}
+#'
+#' @section Arguments:
+#' \describe{
+#' \item{arv}{Arvados object.}
+#' \item{uuid}{UUID of a collection.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
+#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#' \item{remove(fileNames)}{Remove one or more files from the collection.}
+#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#' \item{getFileListing()}{Returns collections file content as character vector.}
+#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
+#' }
#'
-#' Update description
+#' @name Collection
+#' @examples
+#' \dontrun{
+#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+#' collection <- Collection$new(arv, "uuid")
#'
-#' @examples arv = Collection$new(api, uuid)
-#' @export Collection
+#' 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")
+#'
+#' collection$move("folder/file.cpp", "file.cpp")
+#'
+#' arvadosFile <- collection$get("location/to/my/file.cpp")
+#' arvadosSubcollection <- collection$get("location/to/my/directory/")
+#' }
+NULL
+
+#' @export
Collection <- R6::R6Class(
"Collection",
public = list(
- #Todo(Fudo): Encapsulate this?
- uuid = NULL,
- etag = NULL,
- owner_uuid = NULL,
- created_at = NULL,
- modified_by_client_uuid = NULL,
- modified_by_user_uuid = NULL,
- modified_at = NULL,
- portable_data_hash = NULL,
- replication_desired = NULL,
- replication_confirmed_at = NULL,
- replication_confirmed = NULL,
- updated_at = NULL,
- manifest_text = NULL,
- name = NULL,
- description = NULL,
- properties = NULL,
- delete_at = NULL,
- file_names = NULL,
- trash_at = NULL,
- is_trashed = NULL,
-
- initialize = function(api, uuid)
- {
- private$api <- api
- result <- private$api$getCollection(uuid)
-
- self$uuid <- result$uuid
- self$etag <- result$etag
- self$owner_uuid <- result$owner_uuid
- self$created_at <- result$created_at
- self$modified_by_client_uuid <- result$modified_by_client_uuid
- self$modified_by_user_uuid <- result$modified_by_user_uuid
- self$modified_at <- result$modified_at
- self$portable_data_hash <- result$portable_data_hash
- self$replication_desired <- result$replication_desired
- self$replication_confirmed_at <- result$replication_confirmed_at
- self$replication_confirmed <- result$replication_confirmed
- self$updated_at <- result$updated_at
- self$manifest_text <- result$manifest_text
- self$name <- result$name
- self$description <- result$description
- self$properties <- result$properties
- self$delete_at <- result$delete_at
- self$file_names <- result$file_names
- self$trash_at <- result$trash_at
- self$is_trashed <- result$is_trashed
-
- private$http <- HttpRequest$new()
- private$httpParser <- HttpParser$new()
-
- private$fileItems <- private$getCollectionContent()
- private$fileTree <- FileTree$new(private$fileItems)
-
- },
+ uuid = NULL,
- printFileContent = function()
+ initialize = function(api, uuid)
{
- private$fileTree$printContent(private$fileTree$getRoot(), 0)
+ private$REST <- api$getRESTService()
+ self$uuid <- uuid
},
- getFileContent = function()
+ add = function(content, relativePath = "")
{
- sapply(private$fileItems, function(file)
- {
- file$name
- })
- },
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- get = function(relativePath)
- {
- treeNode <- private$fileTree$traverseInOrder(private$fileTree$getRoot(), function(node)
+ if(relativePath == "" ||
+ relativePath == "." ||
+ relativePath == "./")
{
- if(node$relativePath == relativePath)
- return(node)
- else
- return(NULL)
- })
+ subcollection <- private$tree$getTree()
+ }
+ else
+ {
+ relativePath <- trimFromEnd(relativePath, "/")
+ subcollection <- self$get(relativePath)
+ }
- if(!is.null(treeNode))
+ if(is.null(subcollection))
+ stop(paste("Subcollection", relativePath, "doesn't exist."))
+
+ if("ArvadosFile" %in% class(content) ||
+ "Subcollection" %in% class(content))
{
- return(private$createSubcollectionTree(treeNode))
+ if(content$getName() == "")
+ stop("Content has invalid name.")
+
+ subcollection$add(content)
+ content
}
else
{
- return(NULL)
+ stop(paste0("Expected AravodsFile or Subcollection object, got ",
+ paste0("(", paste0(class(content), collapse = ", "), ")"),
+ "."))
}
},
- createNewFile = function(relativePath, content, contentType)
+ create = function(fileNames, relativePath = "")
{
- fileURL <- paste0(private$api$getWebDavHostName(), "c=", self$uuid, "/", relativePath);
- headers <- list(Authorization = paste("OAuth2", private$api$getToken()),
- "Content-Type" = contentType)
- body <- content
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ if(relativePath == "" ||
+ relativePath == "." ||
+ relativePath == "./")
+ {
+ subcollection <- private$tree$getTree()
+ }
+ else
+ {
+ relativePath <- trimFromEnd(relativePath, "/")
+ subcollection <- self$get(relativePath)
+ }
+
+ if(is.null(subcollection))
+ stop(paste("Subcollection", relativePath, "doesn't exist."))
- serverResponse <- private$http$PUT(fileURL, headers, body)
+ if(is.character(fileNames))
+ {
+ arvadosFiles <- NULL
+ sapply(fileNames, function(fileName)
+ {
+ childWithSameName <- subcollection$get(fileName)
+ if(!is.null(childWithSameName))
+ stop("Destination already contains file with same name.")
- if(serverResponse$status_code != 201)
- stop(paste("Server code:", serverResponse$status_code))
+ newFile <- ArvadosFile$new(fileName)
+ subcollection$add(newFile)
- fileSize = private$getNewFileSize(relativePath)
- private$fileTree$addNode(relativePath, fileSize)
+ arvadosFiles <<- c(arvadosFiles, newFile)
+ })
- paste0("File created (size = ", fileSize , ")")
+ if(length(arvadosFiles) == 1)
+ return(arvadosFiles[[1]])
+ else
+ return(arvadosFiles)
+ }
+ else
+ {
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
+ "."))
+ }
},
- removeFile = function(relativePath)
+ remove = function(paths)
{
- node <- private$fileTree$getNode(relativePath)
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- if(is.null(node))
- stop("File doesn't exists.")
+ if(is.character(paths))
+ {
+ sapply(paths, function(filePath)
+ {
+ filePath <- trimFromEnd(filePath, "/")
+ file <- self$get(filePath)
- fileURL <- paste0(private$api$getWebDavHostName(), "c=", self$uuid, "/", relativePath);
- headers <- list(Authorization = paste("OAuth2", private$api$getToken()))
+ if(is.null(file))
+ stop(paste("File", filePath, "doesn't exist."))
- serverResponse <- private$http$DELETE(fileURL, headers)
+ parent <- file$getParent()
- if(serverResponse$status_code != 204)
- stop(paste("Server code:", serverResponse$status_code))
+ if(is.null(parent))
+ stop("You can't delete root folder.")
- "File deleted"
- },
+ parent$remove(file$getName())
+ })
- update = function(subcollection, event)
- {
- #Todo(Fudo): Add some king of check here later on.
- if(event == "File size changed")
+ "Content removed"
+ }
+ else
{
- private$handleFileSizeChange(subcollection$getRelativePath(),
- subcollection$getSizeInBytes())
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(paths), collapse = ", "), ")"),
+ "."))
}
- }
- ),
+ },
- active = list(
- items = function(value)
+ move = function(content, destination)
{
- if(missing(value))
- return(private$fileItems)
- else
- print("Value is read-only.")
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- return(NULL)
- }
- ),
-
- private = list(
+ content <- trimFromEnd(content, "/")
+
+ elementToMove <- self$get(content)
- fileItems = NULL,
- api = NULL,
- fileTree = NULL,
- http = NULL,
- httpParser = NULL,
+ if(is.null(elementToMove))
+ stop("Content you want to move doesn't exist in the collection.")
- handleFileSizeChange = function(filePath, newSize)
+ elementToMove$move(destination)
+ },
+
+ copy = function(content, destination)
{
- node <- private$fileTree$getNode(filePath)
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ content <- trimFromEnd(content, "/")
+
+ elementToCopy <- self$get(content)
- if(is.null(node))
- stop("File doesn't exits")
+ if(is.null(elementToCopy))
+ stop("Content you want to copy doesn't exist in the collection.")
- node$size <- newSize
+ elementToCopy$copy(destination)
},
- createSubcollectionTree = function(treeNode)
+ refresh = function()
{
- if(treeNode$hasChildren())
- {
- children = NULL
+ private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+ private$tree <- NULL
+ },
- for(child in treeNode$children)
- {
- child <- private$createSubcollectionTree(child)
- children <- c(children, child)
- }
+ getFileListing = function()
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- return(Subcollection$new(treeNode$name, treeNode$relativePath, children))
- }
- else
- {
- if(treeNode$type == "file")
- return(ArvadosFile$new(treeNode$name, treeNode$relativePath, treeNode$size, private$api, self))
- else
- return(Subcollection$new(treeNode$name, treeNode$relativePath, NULL))
- }
+ content <- private$REST$getCollectionContent(self$uuid)
+ content[order(tolower(content))]
},
- getCollectionContent = function()
+ get = function(relativePath)
{
- collectionURL <- URLencode(paste0(private$api$getWebDavHostName(), "c=", self$uuid))
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- headers = list("Authorization" = paste("OAuth2", private$api$getToken()))
+ private$tree$getElement(relativePath)
+ },
- response <- private$http$PROPFIND(collectionURL, headers)
+ getRESTService = function() private$REST,
+ setRESTService = function(newRESTService) private$REST <- newRESTService
+ ),
- parsedResponse <- private$httpParser$parseWebDAVResponse(response, collectionURL)
- parsedResponse[-1]
- },
+ private = list(
- getNewFileSize = function(relativePath)
- {
- collectionURL <- URLencode(paste0(private$api$getWebDavHostName(), "c=", self$uuid))
- fileURL = paste0(collectionURL, "/", relativePath);
- headers = list("Authorization" = paste("OAuth2", private$api$getToken()))
+ REST = NULL,
+ tree = NULL,
+ fileContent = NULL,
- propfindResponse <- private$http$PROPFIND(fileURL, headers)
+ generateCollectionTreeStructure = function()
+ {
+ if(is.null(self$uuid))
+ stop("Collection uuid is not defined.")
- fileInfo <- private$httpParser$parseWebDAVResponse(propfindResponse, collectionURL)
+ if(is.null(private$REST))
+ stop("REST service is not defined.")
- fileInfo[[1]]$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