-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 Class
-#'
-#' @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.
#'
-#' @export Collection
+#' @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$remove("location/to/my/file.cpp")
+#'
+#' collection$move("folder/file.cpp", "file.cpp")
+#'
+#' arvadosFile <- collection$get("location/to/my/file.cpp")
+#' arvadosSubcollection <- collection$get("location/to/my/directory/")
+#' }
+NULL
-#' @exportClass Collection
-Collection <- setRefClass(
+#' @export
+Collection <- R6::R6Class(
"Collection",
- fields = list(uuid = "ANY",
- items = "ANY",
- fileContent = "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",
- get = "function"
- ),
+ public = list(
- methods = list(
+ uuid = NULL,
+ # api = NULL,
- initialize = function(api, uuid)
+ initialize = function(api, uuid)
{
- 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$is_trashed
-
- # Public methods
-
- getCollectionContent <<- function()
- {
- #TODO(Fudo): Use proper URL here.
- uri <- URLencode(api$getWebDavHostName())
+ # self$api <- api
+ private$REST <- api$getRESTService()
+
+ self$uuid <- uuid
- # fetch directory listing via curl and parse XML response
- h <- curl::new_handle()
- curl::handle_setopt(h, customrequest = "PROPFIND")
+ private$fileContent <- private$REST$getCollectionContent(uuid)
+ private$tree <- CollectionTree$new(private$fileContent, self)
+ },
- #TODO(Fudo): Use proper token here.
- curl::handle_setheaders(h, "Authorization" = paste("OAuth2", api$getWebDavToken()))
- response <- curl::curl_fetch_memory(uri, h)
+ add = function(content, relativePath = "")
+ {
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
- HttpParser()$parseWebDAVResponse(response, uri)
+ if(relativePath == "" ||
+ relativePath == "." ||
+ relativePath == "./")
+ {
+ subcollection <- private$tree$getTree()
+ }
+ else
+ {
+ relativePath <- trimFromEnd(relativePath, "/")
+ subcollection <- self$get(relativePath)
}
- get <<- function(pathToTheFile)
+ if(is.null(subcollection))
+ stop(paste("Subcollection", relativePath, "doesn't exist."))
+
+ if("ArvadosFile" %in% class(content) ||
+ "Subcollection" %in% class(content))
{
- fileWithPath <- unlist(stringr::str_split(pathToTheFile, "/"))
- fileWithPath <- fileWithPath[fileWithPath != ""]
+ if(content$getName() == "")
+ stop("Content has invalid name.")
- findFileIfExists <- function(name, node)
- {
- matchPosition <- match(name, sapply(node$content, function(nodeInSubcollection) {nodeInSubcollection$name}), -1)
- if(matchPosition != -1)
- {
- return(node$content[[matchPosition]])
- }
- else
- {
- return(NULL)
- }
- }
-
- nodeToCheck = .self$fileContent
- for(fileNameIndex in 1:length(fileWithPath))
- {
- nodeToCheck <- findFileIfExists(fileWithPath[fileNameIndex], nodeToCheck)
- if(is.null(nodeToCheck))
- stop("File or folder you asked for is not part of the collection.")
- }
+ subcollection$add(content)
+ content
+ }
+ else
+ {
+ stop(paste0("Expected AravodsFile or Subcollection object, got ",
+ paste0("(", paste0(class(content), collapse = ", "), ")"),
+ "."))
+ }
+ },
- nodeToCheck
+ create = function(fileNames, relativePath = "")
+ {
+ if(is.null(private$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 methods
- .createCollectionContentTree <- function(fileStructure)
+ if(is.character(fileNames))
{
- #TODO(Fudo): Refactor this.
- #TODO(Fudo): Find a way to link children to parents. (R has no pointers or references).
- treeBranches <- sapply(fileStructure, function(filePath)
+ arvadosFiles <- NULL
+ sapply(fileNames, function(fileName)
{
- fileWithPath <- unlist(stringr::str_split(filePath, "/"))
- file <- fileWithPath[length(fileWithPath), drop = T]
-
- if(file != "")
- {
- file <- ArvadosFile(file, api)
- file$relativePath <- filePath
- }
- else
- {
- file <- NULL
- }
-
- folders <- fileWithPath[-length(fileWithPath)]
-
- subcollections <- sapply(folders, function(folder)
- {
- folder <- Subcollection(folder)
- unname(folder)
- })
-
- if(!is.null(file))
- subcollections <- c(subcollections, file)
-
- if(length(subcollections) > 1)
- {
- for(subcollectionIndex in 1:(length(subcollections) - 1))
- {
- subcollections[[subcollectionIndex]]$relativePath <- paste(folders[1:(subcollectionIndex)], collapse = "/")
- subcollections[[subcollectionIndex]]$add(subcollections[[subcollectionIndex + 1]])
- }
- }
- subcollections[[1]]
+ childWithSameName <- subcollection$get(fileName)
+ if(!is.null(childWithSameName))
+ stop("Destination already contains file with same name.")
+
+ newFile <- ArvadosFile$new(fileName)
+ subcollection$add(newFile)
+
+ arvadosFiles <<- c(arvadosFiles, newFile)
})
- root <- Subcollection(".")
+ if(length(arvadosFiles) == 1)
+ return(arvadosFiles[[1]])
+ else
+ return(arvadosFiles)
+ }
+ else
+ {
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
+ "."))
+ }
+ },
- addIfExists <- function(firstNode, secondNode)
- {
- firstNodeContent <- sapply(firstNode$content, function(node) {node$name})
- if(length(firstNodeContent) == 0)
- {
- firstNode$add(secondNode)
- return()
- }
-
- matchPosition <- match(secondNode$name, firstNodeContent, -1)
- if(matchPosition != -1)
- {
- addIfExists(firstNode$content[[matchPosition]], secondNode$content[[1]])
- }
- else
- {
- firstNode$add(secondNode)
- }
- }
-
- sapply(treeBranches, function(branch)
+ remove = function(paths)
+ {
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
+ if(is.character(paths))
+ {
+ sapply(paths, function(filePath)
{
- addIfExists(root, branch)
+ filePath <- trimFromEnd(filePath, "/")
+ file <- self$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$getName())
})
- root
+ "Content removed"
+ }
+ else
+ {
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(paths), collapse = ", "), ")"),
+ "."))
}
+ },
+
+ move = function(content, newLocation)
+ {
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
+ content <- trimFromEnd(content, "/")
+
+ elementToMove <- self$get(content)
+
+ if(is.null(elementToMove))
+ stop("Content you want to move doesn't exist in the collection.")
+
+ elementToMove$move(newLocation)
+ },
+
+ getFileListing = function()
+ {
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
+
+ content <- private$REST$getCollectionContent(self$uuid)
+ content[order(tolower(content))]
+ },
+
+ get = function(relativePath)
+ {
+ if(is.null(private$tree))
+ private$genereateCollectionTreeStructure()
- #Todo(Fudo): This is dummy data. Real content will come from WebDAV server.
- # testFileStructure <- c("math.h", "main.cpp", "emptyFolder/",
- # "java/render.java", "java/test/observer.java",
- # "java/test/observable.java",
- # "csharp/this.cs", "csharp/is.cs",
- # "csharp/dummy.cs", "csharp/file.cs")
- items <<- getCollectionContent()
- fileContent <<- .createCollectionContentTree(items)
+ 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
+ ),
+
+ private = list(
+
+ REST = NULL,
+ tree = NULL,
+ fileContent = NULL,
+ classFields = NULL,
+
+ genereateCollectionTreeStructure = 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