#' for exaplme actions like creating, updating, moving or removing are possible.
#'
#' @seealso
-#' \code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}
+#' https://git.arvados.org/arvados.git/tree/HEAD:/sdk/R
#'
#' @export
#' @param uuid The UUID Autentic for Collection UUID.
#' @return A new `Collection` object.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, CollectionUUID)
+ #' }
initialize = function(api, uuid)
{
private$REST <- api$getRESTService()
#' @param Ncol Used in reading binary file to set numbers of columns in data.frame.
#' @param Nrow Used in reading binary file to set numbers of rows in data.frame size.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
#' readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
#' readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
#' readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
#' readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ #' }
readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
{
arvFile <- self$get(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("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$writeFile("myoutputxlsx.xlsx", file) # xlsx
- writeFile = function(name, file, istable = NULL, seqName = NULL)
+ #' writeFile <- collection$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)
{
- # 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")
"AWS_DEFAULT_REGION" = "collections",
"AWS_S3_ENDPOINT" = gsub("api[.]", "", ARVADOS_API_HOST))
- if (FileFormat == "txt") {
+ # save file
+ if (fileFormat == "txt") {
if (istable == "yes") {
- aws.s3::s3write_using(file, FUN = write.table, object = name, bucket = my_collection)
+ 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 = my_collection)
+ 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 = 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 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$connection() and customise it')))
}
#' Creates one or more ArvadosFiles and adds them to the collection at specified path.
#' @param files Content to be created.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+ #' }
create = function(files)
{
if(is.null(private$tree))
#' Remove one or more files from the collection.
#' @param paths Content to be removed.
#' @examples
+ #' \dontrun{
#' collection$remove(fileName.format)
+ #' }
remove = function(paths)
{
if(is.null(private$tree))
#' @param content Content to be moved.
#' @param destination Path to move content.
#' @examples
+ #' \dontrun{
#' collection$move("fileName.format", path)
+ #' }
move = function(content, destination)
{
if(is.null(private$tree))
#' @param content Content to be moved.
#' @param destination Path to move content.
#' @examples
+ #' \dontrun{
#' copied <- collection$copy("oldName.format", "newName.format")
+ #' }
copy = function(content, destination)
{
if(is.null(private$tree))
#' @description
#' Refreshes the environment.
#' @examples
+ #' \dontrun{
#' collection$refresh()
+ #' }
refresh = function()
{
if(!is.null(private$tree))
#' @description
#' Returns collections file content as character vector.
#' @examples
+ #' \dontrun{
#' list <- collection$getFileListing()
+ #' }
getFileListing = function()
{
if(is.null(private$tree))
#' If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
#' @param relativePath Path from content is taken.
#' @examples
+ #' \dontrun{
#' arvadosFile <- collection$get(fileName)
+ #' }
get = function(relativePath)
{
if(is.null(private$tree))
- private$generateCollectionTreeStructure(relativePath)
+ private$generateCollectionTreeStructure()
private$tree$getElement(relativePath)
},
cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
cat(paste0("uuid: ", "\"", x$uuid, "\""), sep = "\n")
}
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projects / arvados.git / blobdiff