-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
-#' Arvados Collection Object
+#' R6 Class Representing Arvados Collection
#'
-#' Update description
+#' @description
+#' Collection class provides interface for working with Arvados collections,
+#' for exaplme actions like creating, updating, moving or removing are possible.
#'
-#' @examples arv = Collection$new(api, uuid)
-#' @export Collection
+#' @seealso
+#' \code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}
+#'
+#' @export
+
Collection <- R6::R6Class(
"Collection",
public = list(
- api = NULL,
+ #' @field uuid Autentic for Collection UUID.
uuid = NULL,
+ #' @description
+ #' Initialize new enviroment.
+ #' @param api Arvados enviroment.
+ #' @param uuid The UUID Autentic for Collection UUID.
+ #' @return A new `Collection` object.
+ #' @examples
+ #' collection <- Collection$new(arv, CollectionUUID)
initialize = function(api, uuid)
{
- self$api <- api
private$REST <- api$getRESTService()
-
self$uuid <- uuid
-
- private$fileContent <- private$REST$getCollectionContent(uuid)
- private$tree <- CollectionTree$new(private$fileContent, self)
},
+ #' @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$tree))
+ private$generateCollectionTreeStructure()
+
if(relativePath == "" ||
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
+ #' 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$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
{
- if(relativePath == "" ||
- relativePath == "." ||
- relativePath == "./")
- {
- subcollection <- private$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
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' writeFile <- collection$writeFile("myoutput.csv", file, istable = NULL) # csv
+ #' writeFile <- collection$writeFile("myoutput.fasta", file, istable = NULL) # fasta
+ #' writeFile <- collection$writeFile("myoutputtable.txt", file, istable = "yes") # txt table
+ #' writeFile <- collection$writeFile("myoutputtext.txt", file, istable = "no") # txt text
+ #' writeFile <- collection$writeFile("myoutputbinary.dat", file) # binary
+ #' writeFile <- collection$writeFile("myoutputxlsx.xlsx", file) # xlsx
+ writeFile = function(name, file, istable = NULL, seqName = NULL)
+ {
+ # prepare file and connection
+ arvFile <- collection$create(name)[[1]]
+ arvFile <- collection$get(name)
+ arvConnection <- arvFile$connection("w")
+ # get file format
+ 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 (istable == "yes") {
+ aws.s3::s3write_using(file, FUN = write.table, object = name, bucket = my_collection)
+ } else if (istable == "no") {
+ aws.s3::s3write_using(file, FUN = writeChar, object = name, bucket = my_collection)
+ } else {
+ stop(paste("Specify parametr istable"))
+ }
+ } else if (FileFormat == "csv") {
+ aws.s3::s3write_using(file, FUN = write.csv, object = name, bucket = my_collection)
+ } else if (FileFormat == "fasta") {
+ aws.s3::s3write_using(file, FUN = seqinr::write.fasta, name = seqName, object = name, bucket = my_collection)
+ } else if (FileFormat == "xlsx") {
+ aws.s3::s3write_using(file, FUN = openxlsx::write.xlsx, object = name, bucket = my_collection)
+ } else if (FileFormat == "dat" || FileFormat == "bin") {
+ aws.s3::s3write_using(file, FUN = writeBin, object = name, bucket = my_collection)
+ } else {
+ stop(parse(('File format not supported, use arvadosFile$connection() and customise it')))
+ }
+ },
+
+ #' @description
+ #' Creates one or more ArvadosFiles and adds them to the collection at specified path.
+ #' @param files Content to be created.
+ #' @examples
+ #' collection <- arv$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(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)
+ 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
+ #' collection$remove(fileName.format)
remove = function(paths)
{
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
if(is.character(paths))
{
sapply(paths, function(filePath)
"Content removed"
}
- else
+ else
{
stop(paste0("Expected character vector, got ",
paste0("(", paste0(class(paths), collapse = ", "), ")"),
}
},
- move = function(content, newLocation)
+ #' @description
+ #' Moves ArvadosFile or Subcollection to another location in the collection.
+ #' @param content Content to be moved.
+ #' @param destination Path to move content.
+ #' @examples
+ #' collection$move("fileName.format", path)
+ move = function(content, destination)
{
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure()
+
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)
+ elementToMove$move(destination)
+ },
+
+ #' @description
+ #' Copies ArvadosFile or Subcollection to another location in the collection.
+ #' @param content Content to be moved.
+ #' @param destination Path to move content.
+ #' @examples
+ #' copied <- collection$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
+ #' 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
+ #' list <- collection$getFileListing()
getFileListing = function()
{
+ if(is.null(private$tree))
+ 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
+ #' arvadosFile <- collection$get(fileName)
get = function(relativePath)
{
+ if(is.null(private$tree))
+ private$generateCollectionTreeStructure(relativePath)
+
private$tree$getElement(relativePath)
},
getRESTService = function() private$REST,
setRESTService = function(newRESTService) private$REST <- newRESTService
),
-
private = list(
REST = NULL,
+ #' @tree beautiful tree of sth
tree = NULL,
- fileContent = NULL
+ fileContent = NULL,
+
+ generateCollectionTreeStructure = function(relativePath = NULL)
+ {
+ if(is.null(self$uuid))
+ stop("Collection uuid is not defined.")
+
+ if(is.null(private$REST))
+ stop("REST service is not defined.")
+
+ private$fileContent <- private$REST$getCollectionContent(self$uuid, relativePath)
+ private$tree <- CollectionTree$new(private$fileContent, self)
+ }
),
cloneable = FALSE
)
-#' @export print.Collection
-print.Collection = function(collection)
+#' 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: ", "\"", collection$uuid, "\""), sep = "\n")
+ cat(paste0("uuid: ", "\"", x$uuid, "\""), sep = "\n")
}
+
+
+
+
+
+
+
projects / arvados.git / blobdiff