+ #' @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$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ #' }
+ readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
+ {
+ arvFile <- self$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 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$connection() and customise it')))
+ }
+ },
+
+ #' @description
+ #' Write file content
+ #' @param name Name of the file.
+ #' @param file File to be saved.
+ #' @param istable Used in writing txt file to check if the file is table or not.
+ #' @examples
+ #' \dontrun{
+ #' collection <- Collection$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$connection() and customise it')))
+ }
+ },
+
+ #' @description
+ #' Creates one or more ArvadosFiles and adds them to the collection at specified path.
+ #' @param files Content to be created.
+ #' @examples
+ #' \dontrun{
+ #' collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+ #' }