-source("./R/Subcollection.R")
-source("./R/ArvadosFile.R")
-source("./R/RESTService.R")
-source("./R/util.R")
-
-#' Collection
-#'
-#' Collection class provides interface for working with Arvados collections.
-#'
-#' @section Usage:
-#' \preformatted{collection = Collection$new(arv, uuid)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{arv}{Arvados object.}
-#' \item{uuid}{UUID of a collection.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-#' \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
-#' \item{remove(fileNames)}{Remove one or more files from the collection.}
-#' \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
-#' \item{getFileListing()}{Returns collections file content as character vector.}
-#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
-#' }
-#'
-#' @name Collection
-#' @examples
-#' \dontrun{
-#' arv <- Arvados$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/")
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+#' R6 Class Representing Arvados Collection
#'
-#' collection$remove("location/to/my/file.cpp")
+#' @description
+#' Collection class provides interface for working with Arvados collections,
+#' for exaplme actions like creating, updating, moving or removing are possible.
#'
-#' collection$move("folder/file.cpp", "file.cpp")
+#' @seealso
+#' https://git.arvados.org/arvados.git/tree/HEAD:/sdk/R
#'
-#' arvadosFile <- collection$get("location/to/my/file.cpp")
-#' arvadosSubcollection <- collection$get("location/to/my/directory/")
-#' }
-NULL
-
#' @export
+
Collection <- R6::R6Class(
"Collection",
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)
+ #' @field uuid Autentic for Collection UUID.
+ uuid = NULL,
+
+ #' @description
+ #' Initialize new enviroment.
+ #' @param api Arvados enviroment.
+ #' @param uuid The UUID Autentic for Collection UUID.
+ #' @return A new `Collection` object.
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$new(arv, CollectionUUID)
+ #' }
+ initialize = function(api, uuid)
{
- self$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
},
+ #' @description
+ #' Adds ArvadosFile or Subcollection specified by content to the collection. Used only with ArvadosFile or Subcollection.
+ #' @param content Content to be added.
+ #' @param relativePath Path to add content.
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$getName() == "")
stop("Content has invalid name.")
}
},
- create = function(fileNames, relativePath = "")
+ #' @description
+ #' Read file content.
+ #' @param file Name of the file.
+ #' @param col Collection from which the file is read.
+ #' @param sep Separator used in reading tsv, csv file format.
+ #' @param istable Used in reading txt file to check if the file is table or not.
+ #' @param fileclass Used in reading fasta file to set file class.
+ #' @param Ncol Used in reading binary file to set numbers of columns in data.frame.
+ #' @param Nrow Used in reading binary file to set numbers of rows in data.frame size.
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
+ #' readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
+ #' readFile <- collection$readArvFile(arvadosFile) # xlsx, csv, tsv, rds, rdata
+ #' readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
+ #' readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
+ #' readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ #' }
+ readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
{
- if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
-
- if(relativePath == "" ||
- relativePath == "." ||
- relativePath == "./")
- {
- subcollection <- private$tree$getTree()
+ arvFile <- self$get(file)
+ FileName <- arvFile$getName()
+ FileName <- tolower(FileName)
+ FileFormat <- gsub(".*\\.", "", FileName)
+
+ # set enviroment
+ ARVADOS_API_TOKEN <- Sys.getenv("ARVADOS_API_TOKEN")
+ ARVADOS_API_HOST <- Sys.getenv("ARVADOS_API_HOST")
+ my_collection <- self$uuid
+ key <- gsub("/", "_", ARVADOS_API_TOKEN)
+
+ Sys.setenv(
+ "AWS_ACCESS_KEY_ID" = key,
+ "AWS_SECRET_ACCESS_KEY" = key,
+ "AWS_DEFAULT_REGION" = "collections",
+ "AWS_S3_ENDPOINT" = gsub("api[.]", "", ARVADOS_API_HOST))
+
+ if (FileFormat == "txt") {
+ if (is.null(istable)){
+ stop(paste('You need to paste whether it is a text or table file'))
+ } else if (istable == 'no') {
+ fileContent <- arvFile$read("text") # used to read
+ fileContent <- gsub("[\r\n]", " ", fileContent)
+ } else if (istable == 'yes') {
+ arvConnection <- arvFile$connection("r") # used to make possible use different function later
+ fileContent <- read.table(arvConnection)
+ }
}
- else
- {
- relativePath <- trimFromEnd(relativePath, "/")
- subcollection <- self$get(relativePath)
+ else if (FileFormat == "xlsx") {
+ fileContent <- aws.s3::s3read_using(FUN = openxlsx::read.xlsx, object = file, bucket = my_collection)
+ }
+ else if (FileFormat == "csv" || FileFormat == "tsv") {
+ arvConnection <- arvFile$connection("r")
+ if (FileFormat == "tsv"){
+ mytable <- read.table(arvConnection, sep = '\t')
+ } else if (FileFormat == "csv" & sep == '\t') {
+ mytable <- read.table(arvConnection, sep = '\t')
+ } else if (FileFormat == "csv") {
+ mytable <- read.table(arvConnection, sep = ',')
+ } else {
+ stop(paste('File format not supported, use arvadosFile$connection() and customise it'))
+ }
+ }
+ else if (FileFormat == "fasta") {
+ fastafile <- aws.s3::s3read_using(FUN = seqinr::read.fasta, as.string = TRUE, object = file, bucket = my_collection)
+ }
+ else if (FileFormat == "dat" || FileFormat == "bin") {
+ fileContent <- gzcon(arvFile$connection("rb"))
+
+ # function to precess data to binary format
+ read_bin.file <- function(fileContent) {
+ # read binfile
+ column.names <- readBin(fileContent, character(), n = Ncol)
+ bindata <- readBin(fileContent, numeric(), Nrow*Ncol+Ncol)
+ # check
+ res <- which(bindata < 0.0000001)
+ if (is.list(res)) {
+ bindata <- bindata[-res]
+ } else {
+ bindata <- bindata
+ }
+ # make a dataframe
+ data <- data.frame(matrix(data = NA, nrow = Nrow, ncol = Ncol))
+ for (i in 1:Ncol) {
+ data[,i] <- bindata[(1+Nrow*(i-1)):(Nrow*i)]
+ }
+ colnames(data) = column.names
+
+ len <- which(is.na(data[,Ncol])) # error if sth went wrong
+ if (length(len) == 0) {
+ data
+ } else {
+ stop(paste("there is a factor or text in the table, customize the function by typing more arguments"))
+ }
+ }
+ if (is.null(Nrow) | is.null(Ncol)){
+ stop(paste('You need to specify numbers of columns and rows'))
+ }
+ if (is.null(istable)) {
+ fileContent <- read_bin.file(fileContent) # call a function
+ } else if (istable == "factor") { # if there is a table with col name
+ fileContent <- read_bin.file(fileContent)
+ }
}
+ else if (FileFormat == "rds" || FileFormat == "rdata") {
+ arvConnection <- arvFile$connection("rb")
+ mytable <- readRDS(gzcon(arvConnection))
+ }
+ else {
+ stop(parse(('File format not supported, use arvadosFile$connection() and customise it')))
+ }
+ },
- if(is.null(subcollection))
- stop(paste("Subcollection", relativePath, "doesn't exist."))
+ #' @description
+ #' Write file content
+ #' @param name Name of the file.
+ #' @param file File to be saved.
+ #' @param istable Used in writing txt file to check if the file is table or not.
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID) # csv
+ #' writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID) # tsv
+ #' writeFile <- collection$writeFile(name = "myoutput.fasta", file = file, fileFormat = "fasta", istable = NULL, collectionUUID = collectionUUID) # fasta
+ #' writeFile <- collection$writeFile(name = "myoutputtable.txt", file = file, fileFormat = "txt", istable = "yes", collectionUUID = collectionUUID) # txt table
+ #' writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID) # txt text
+ #' writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID) # binary
+ #' writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID) # xlsx
+ #' }
+ writeFile = function(name, file, collectionUUID, fileFormat, istable = NULL, seqName = NULL)
+ {
+ # set enviroment
+ ARVADOS_API_TOKEN <- Sys.getenv("ARVADOS_API_TOKEN")
+ ARVADOS_API_HOST <- Sys.getenv("ARVADOS_API_HOST")
+ my_collection <- self$uuid
+ key <- gsub("/", "_", ARVADOS_API_TOKEN)
+
+ Sys.setenv(
+ "AWS_ACCESS_KEY_ID" = key,
+ "AWS_SECRET_ACCESS_KEY" = key,
+ "AWS_DEFAULT_REGION" = "collections",
+ "AWS_S3_ENDPOINT" = gsub("api[.]", "", ARVADOS_API_HOST))
+
+ # save file
+ if (fileFormat == "txt") {
+ if (istable == "yes") {
+ aws.s3::s3write_using(file, FUN = write.table, object = name, bucket = collectionUUID)
+ } else if (istable == "no") {
+ aws.s3::s3write_using(file, FUN = writeChar, object = name, bucket = collectionUUID)
+ } else {
+ stop(paste("Specify parametr istable"))
+ }
+ } else if (fileFormat == "csv") {
+ aws.s3::s3write_using(file, FUN = write.csv, object = name, bucket = collectionUUID)
+ } else if (fileFormat == "tsv") {
+ aws.s3::s3write_using(file, FUN = write.table, row.names = FALSE, sep = "\t", object = name, bucket = collectionUUID)
+ } else if (fileFormat == "fasta") {
+ aws.s3::s3write_using(file, FUN = seqinr::write.fasta, name = seqName, object = name, bucket = collectionUUID)
+ } else if (fileFormat == "xlsx") {
+ aws.s3::s3write_using(file, FUN = openxlsx::write.xlsx, object = name, bucket = collectionUUID)
+ } else if (fileFormat == "dat" || fileFormat == "bin") {
+ aws.s3::s3write_using(file, FUN = writeBin, object = name, bucket = collectionUUID)
+ } else {
+ stop(parse(('File format not supported, use arvadosFile$connection() and customise it')))
+ }
+ },
- if(is.character(fileNames))
+ #' @description
+ #' Creates one or more ArvadosFiles and adds them to the collection at specified path.
+ #' @param files Content to be created.
+ #' @examples
+ #' \dontrun{
+ #' collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+ #' }
+ create = function(files)
+ {
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
+ 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)
+ newTreeBranch
})
-
- if(length(arvadosFiles) == 1)
- return(arvadosFiles[[1]])
- else
- return(arvadosFiles)
}
- else
+ else
{
stop(paste0("Expected character vector, got ",
- paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
+ paste0("(", paste0(class(files), collapse = ", "), ")"),
"."))
}
},
+ #' @description
+ #' Remove one or more files from the collection.
+ #' @param paths Content to be removed.
+ #' @examples
+ #' \dontrun{
+ #' collection$remove(fileName.format)
+ #' }
remove = function(paths)
{
if(is.null(private$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)
+ #' @description
+ #' Moves ArvadosFile or Subcollection to another location in the collection.
+ #' @param content Content to be moved.
+ #' @param destination Path to move content.
+ #' @examples
+ #' \dontrun{
+ #' collection$move("fileName.format", path)
+ #' }
+ move = function(content, destination)
{
if(is.null(private$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)
+ },
+
+ #' @description
+ #' Copies ArvadosFile or Subcollection to another location in the collection.
+ #' @param content Content to be moved.
+ #' @param destination Path to move content.
+ #' @examples
+ #' \dontrun{
+ #' copied <- collection$copy("oldName.format", "newName.format")
+ #' }
+ copy = function(content, destination)
+ {
+ if(is.null(private$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$copy(destination)
},
+ #' @description
+ #' Refreshes the environment.
+ #' @examples
+ #' \dontrun{
+ #' collection$refresh()
+ #' }
+ refresh = function()
+ {
+ if(!is.null(private$tree))
+ {
+ private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+ private$tree <- NULL
+ }
+ },
+
+ #' @description
+ #' Returns collections file content as character vector.
+ #' @examples
+ #' \dontrun{
+ #' list <- collection$getFileListing()
+ #' }
getFileListing = function()
{
if(is.null(private$tree))
- private$genereateCollectionTreeStructure()
+ private$generateCollectionTreeStructure()
content <- private$REST$getCollectionContent(self$uuid)
content[order(tolower(content))]
},
+ #' @description
+ #' If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+ #' @param relativePath Path from content is taken.
+ #' @examples
+ #' \dontrun{
+ #' arvadosFile <- collection$get(fileName)
+ #' }
get = function(relativePath)
{
if(is.null(private$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
),
-
private = list(
REST = NULL,
+ #' @tree beautiful tree of sth
tree = NULL,
fileContent = NULL,
- classFields = NULL,
- genereateCollectionTreeStructure = function()
+ generateCollectionTreeStructure = function(relativePath = NULL)
{
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$fileContent <- private$REST$getCollectionContent(self$uuid, relativePath)
private$tree <- CollectionTree$new(private$fileContent, self)
}
),
#'
#' @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