-source("./R/Subcollection.R")
-source("./R/ArvadosFile.R")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
-#' Arvados Collection Object
+#' Collection
#'
-#' Update description
+#' Collection class provides interface for working with Arvados collections.
#'
-#' @examples arv = Collection$new(api, uuid)
-#' @export Collection
+#' @section Usage:
+#' \preformatted{collection = Collection$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(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$get("location/to/my/directory/")
+#' }
+NULL
+
+#' @export
Collection <- R6::R6Class(
"Collection",
public = list(
- #Todo(Fudo): Encapsulate this?
- uuid = NULL,
- etag = NULL,
- owner_uuid = NULL,
- created_at = NULL,
- modified_by_client_uuid = NULL,
- modified_by_user_uuid = NULL,
- modified_at = NULL,
- portable_data_hash = NULL,
- replication_desired = NULL,
- replication_confirmed_at = NULL,
- replication_confirmed = NULL,
- updated_at = NULL,
- manifest_text = NULL,
- name = NULL,
- description = NULL,
- properties = NULL,
- delete_at = NULL,
- file_names = NULL,
- trash_at = NULL,
- is_trashed = NULL,
-
- initialize = function(api, uuid)
- {
- private$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
-
- #Todo(Fudo): Replace this when you get access to webDAV server.
- private$fileItems <- private$getCollectionContent()
-
- private$fileTree <- private$generateTree(private$fileItems)
- },
+ uuid = NULL,
- printFileContent = function(pretty = TRUE)
+ initialize = function(api, uuid)
{
- if(pretty)
- private$fileTree$printContent(0)
- else
- print(private$fileItems)
-
+ private$REST <- api$getRESTService()
+ self$uuid <- uuid
},
- get = function(relativePath)
+ add = function(content, relativePath = "")
{
- treeNode <- private$traverseInOrder(private$fileTree, function(node)
- {
- if(node$relativePath == relativePath)
- return(node)
- else
- return(NULL)
- })
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- if(!is.null(treeNode))
+ if(relativePath == "" ||
+ relativePath == "." ||
+ relativePath == "./")
{
- return(private$createSubcollectionTree(treeNode))
+ subcollection <- private$tree$getTree()
}
else
{
- return(NULL)
+ relativePath <- trimFromEnd(relativePath, "/")
+ subcollection <- self$get(relativePath)
}
- }
- ),
- active = list(
- items = function(value)
- {
- if(missing(value))
- return(private$fileItems)
- else
- print("Value is read-only.")
+ if(is.null(subcollection))
+ stop(paste("Subcollection", relativePath, "doesn't exist."))
- return(NULL)
- }
- ),
-
- private = list(
-
- api = NULL,
- fileItems = NULL,
- fileTree = NULL,
-
- createSubcollectionTree = function(treeNode)
- {
- if(treeNode$hasChildren())
+ if("ArvadosFile" %in% class(content) ||
+ "Subcollection" %in% class(content))
{
- children = NULL
+ if(!is.null(content$getCollection()))
+ stop("Content already belongs to a collection.")
- for(child in treeNode$children)
- {
- child <- private$createSubcollectionTree(child)
- children <- c(children, child)
- }
+ if(content$getName() == "")
+ stop("Content has invalid name.")
- return(Subcollection$new(treeNode$name, treeNode$relativePath, children))
+ subcollection$add(content)
+ content
}
else
{
- if(treeNode$type == "file")
- return(ArvadosFile$new(treeNode$name, treeNode$relativePath, private$api, self))
- else if(treeNode$type == "folder" || treeNode$type == "root")
- return(Subcollection$new(treeNode$name, treeNode$relativePath, NULL))
+ stop(paste0("Expected AravodsFile or Subcollection object, got ",
+ paste0("(", paste0(class(content), collapse = ", "), ")"),
+ "."))
}
},
- createSubcollectionFromNode = function(treeNode, children)
- {
- subcollection = NULL
- if(treeNode$type == "file")
- subcollection = ArvadosFile$new(treeNode$name, treeNode$relativePath)
- else if(treeNode$type == "folder" || treeNode$type == "root")
- subcollection = Subcollection$new(treeNode$name, treeNode$relativePath, children)
-
- subcollection
- },
-
- getCollectionContent = function()
- {
- #TODO(Fudo): Use proper URL here.
- uri <- URLencode(paste0(private$api$getWebDavHostName(), "c=", self$uuid))
-
- # fetch directory listing via curl and parse XML response
- h <- curl::new_handle()
- curl::handle_setopt(h, customrequest = "PROPFIND")
-
- #TODO(Fudo): Use proper token here.
- curl::handle_setheaders(h, "Authorization" = paste("OAuth2", private$api$getToken()))
- response <- curl::curl_fetch_memory(uri, h)
-
- HttpParser$new()$parseWebDAVResponse(response, uri)
- },
-
- #Todo(Fudo): Move tree creation to another file.
- generateTree = function(collectionContent)
+ create = function(files)
{
- treeBranches <- sapply(collectionContent, function(filePath)
- {
- splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
-
- pathEndsWithSlash <- substr(filePath, nchar(filePath), nchar(filePath)) == "/"
-
- branch = private$createBranch(splitPath, pathEndsWithSlash)
- })
-
- root <- TreeNode$new("./", "root")
- root$relativePath = ""
-
- sapply(treeBranches, function(branch)
- {
- private$addNode(root, branch)
- })
-
- root
- },
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- createBranch = function(splitPath, pathEndsWithSlash)
- {
- branch <- NULL
- lastElementIndex <- length(splitPath)
-
- lastElementInPathType = "file"
- if(pathEndsWithSlash)
- lastElementInPathType = "folder"
-
- for(elementIndex in lastElementIndex:1)
+ if(is.character(files))
{
- if(elementIndex == lastElementIndex)
- {
- branch = TreeNode$new(splitPath[[elementIndex]], lastElementInPathType)
- }
- else
+ sapply(files, function(file)
{
- newFolder = TreeNode$new(splitPath[[elementIndex]], "folder")
- newFolder$addChild(branch)
- branch = newFolder
- }
-
- branch$relativePath <- paste(unlist(splitPath[1:elementIndex]), collapse = "/")
- }
+ childWithSameName <- self$get(file)
+ if(!is.null(childWithSameName))
+ stop("Destination already contains file with same name.")
- branch
- },
+ newTreeBranch <- private$tree$createBranch(file)
+ private$tree$addBranch(private$tree$getTree(), newTreeBranch)
- addNode = function(container, node)
- {
- child = container$getChild(node$name)
+ private$REST$create(file, self$uuid)
+ newTreeBranch$setCollection(self)
+ })
- if(is.null(child))
- {
- container$addChild(node)
+ "Created"
}
else
{
- private$addNode(child, node$getFirstChild())
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(files), collapse = ", "), ")"),
+ "."))
}
},
- traverseInOrder = function(node, predicate)
+ remove = function(paths)
{
- if(node$hasChildren())
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ if(is.character(paths))
{
- result <- predicate(node)
+ sapply(paths, function(filePath)
+ {
+ filePath <- trimFromEnd(filePath, "/")
+ file <- self$get(filePath)
- if(!is.null(result))
- return(result)
+ if(is.null(file))
+ stop(paste("File", filePath, "doesn't exist."))
- for(child in node$children)
- {
- result <- private$traverseInOrder(child, predicate)
+ parent <- file$getParent()
+
+ if(is.null(parent))
+ stop("You can't delete root folder.")
- if(!is.null(result))
- return(result)
- }
+ parent$remove(file$getName())
+ })
- return(NULL)
+ "Content removed"
}
else
{
- return(predicate(node))
+ stop(paste0("Expected character vector, got ",
+ paste0("(", paste0(class(paths), collapse = ", "), ")"),
+ "."))
}
- }
-
- ),
+ },
- cloneable = FALSE
-)
+ move = function(content, destination)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
-TreeNode <- R6::R6Class(
+ content <- trimFromEnd(content, "/")
- "TreeNode",
+ elementToMove <- self$get(content)
- public = list(
+ if(is.null(elementToMove))
+ stop("Content you want to move doesn't exist in the collection.")
- name = NULL,
- relativePath = NULL,
- children = NULL,
- parent = NULL,
- type = NULL,
+ elementToMove$move(destination)
+ },
- initialize = function(name, type)
+ copy = function(content, destination)
{
- if(type == "folder")
- name <- paste0(name, "/")
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
- self$name <- name
- self$type <- type
- self$children <- list()
- },
+ content <- trimFromEnd(content, "/")
- addChild = function(node)
- {
- self$children <- c(self$children, node)
- node$setParent(self)
- self
- },
+ elementToCopy <- self$get(content)
- setParent = function(parent)
- {
- self$parent = parent
+ if(is.null(elementToCopy))
+ stop("Content you want to copy doesn't exist in the collection.")
+
+ elementToCopy$copy(destination)
},
- getChild = function(childName)
+ refresh = function()
{
- for(child in self$children)
+ if(!is.null(private$tree))
{
- if(childName == child$name)
- return(child)
+ private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+ private$tree <- NULL
}
-
- return(NULL)
},
- hasChildren = function()
+ getFileListing = function()
{
- if(length(self$children) != 0)
- return(TRUE)
- else
- return(FALSE)
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ content <- private$REST$getCollectionContent(self$uuid)
+ content[order(tolower(content))]
},
- getFirstChild = function()
+ get = function(relativePath)
{
- if(!self$hasChildren())
- return(NULL)
- else
- return(self$children[[1]])
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ private$tree$getElement(relativePath)
},
- printContent = function(depth)
+ getRESTService = function() private$REST,
+ setRESTService = function(newRESTService) private$REST <- newRESTService
+ ),
+
+ private = list(
+
+ REST = NULL,
+ tree = NULL,
+ fileContent = NULL,
+
+ generateCollectionTreeStructure = function()
{
- indentation <- paste(rep("....", depth), collapse = "")
- print(paste0(indentation, self$name))
-
- for(child in self$children)
- child$printContent(depth + 1)
+ 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