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### =========================================================================
### Import/export support
### -------------------------------------------------------------------------
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Classes files and connections
###
### BiocFile is a base class for high-level file abstractions, where
### subclasses are associated with a particular file format/type. It
### wraps a low-level representation of a file, currently either a
### path/URL or connection.
#' @importFrom BiocGenerics path
#' @importFrom S4Vectors SimpleList isSingleString
#' @importFrom methods findMethods getClass getClassDef is new packageSlot show
#' @importFrom tools file_ext file_path_as_absolute file_path_sans_ext
#' @export
setClass("BiocFile", representation(resource = "character_OR_connection"),
contains = "VIRTUAL")
#' @export
setClass("BiocFileList",
prototype = prototype(elementType = "BiocFile"),
contains = "SimpleList")
#' @export
BiocFileList <- function(files) {
new("BiocFileList", listData = files)
}
###' @export
###setMethod("showAsCell", "BiocFileList", function(object) {
### showAsCell(vapply(object, path, character(1L)))
###})
#' @export
resource <- function(x) x@resource
#' @export
`resource<-` <- function(x, value) {
x@resource <- value
x
}
#' @export
setGeneric("fileFormat", function(x) NULL)
#' @export
setMethod("fileFormat", "character", function(x) fileFormat(FileForFormat(x)))
#' @export
setMethod("fileFormat", "BiocFile", function(x)
tolower(sub("File$", "", class(x))))
#' @export
setMethod("path", "BiocFile", function(object, ...) {
r <- resource(object)
if (!is.character(r))
stop("Connection resource requested as a path")
r
})
#' @export
setMethod("show", "BiocFile", function(object) {
r <- resource(object)
if (!isSingleString(r))
r <- summary(r)$description
cat(class(object), "object\nresource:", r, "\n")
})
#' @export
FileForFormat <- function(path, format = file_ext(path)) {
if (!(isSingleString(path) || is(path, "connection")))
stop("'path' must be a single string or a connection object")
if (!isSingleString(format))
stop("'format' must be a single string")
if (format == "")
stop("Cannot detect format (no extension found in file name)")
fileClassName <- paste0(format, "File")
signatureClasses <- function(fun, pos) {
matrix(unlist(findMethods(fun)@signatures), 3)[pos,]
}
fileClassNames <- unique(c(signatureClasses(export, 2),
signatureClasses(import, 1)))
fileClassNames <- fileClassNames[grepl("File$", fileClassNames)]
fileSubClassNames <- unlist(lapply(fileClassNames, function(x) {
names(getClassDef(x)@subclasses)
}), use.names = FALSE)
fileClassNames <- c(fileClassNames, fileSubClassNames)
fileClassIndex <- match(tolower(fileClassName),
tolower(fileClassNames))
if (is.na(fileClassIndex))
stop("Format '", format, "' unsupported")
fileClassName <- fileClassNames[fileClassIndex]
fileClass <- getClass(fileClassName)
pkg <- packageSlot(fileClass)
if (is.null(pkg) || identical(pkg, ".GlobalEnv"))
ns <- topenv()
else ns <- getNamespace(pkg[1])
constructorName <- fileClassName
if(!exists(constructorName, ns)) {
parentClassNames <- names(getClass(constructorName)@contains)
constructorName <- names(which(vapply(parentClassNames,
exists, logical(1), ns)))[1]
if (is.na(constructorName))
stop("No constructor found for ", fileClassName)
}
get(constructorName, ns)(path)
}
#' @export
setMethod("as.character", "BiocFile", function(x) path(x))
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Utilities
###
isURL <- function(uri) {
if (!isSingleString(uri))
return(FALSE)
windowsDriveLetter <- .Platform$OS.type == "windows" &&
grepl("^[A-Za-z]:[/\\]", uri)
grepl("^[A-Za-z]+:", uri) && !windowsDriveLetter
}
.parseURI <- function(uri) {
if (!isURL(uri)) {
parsed <- list(scheme = "", path = uri)
} else {
parsed <- list(scheme = "", path = uri)
protocols <- c("file", "http", "https", "ftp", "smtp")
if (length(protocol <- protocols[startsWith(uri, paste0(protocols, ':'))])) {
parsed$scheme <- protocol
rem <- paste0(protocol, "://")
if (protocol %in% protocols[-1]) {
domain <- strsplit(gsub("http://|https://|ftp://|smtp://|www\\.", "", uri), "/")[[c(1, 1)]]
parsed$path <- sub(paste0(rem, domain), "", uri)
}
else
parsed$path <- sub(rem, "", uri)
}
else
parsed$scheme <- "file"
#if (parsed$scheme == "file" && .Platform$OS.type == "windows")
#parsed$path <- substring(parsed$path, 2) # trim '/' from '/C:/foo/bar.txt'
}
parsed
}
resourceDescription <- function(x) {
r <- resource(x)
if (is(r, "connection"))
r <- summary(r)$description
r
}
.ConnectionManager <- setRefClass("ConnectionManager",
fields = c(connections = "list"))
manager <- function() .ConnectionManager()
connectionForResource <- function(manager, x, open = "") {
resource <- decompress(manager, x)
if (is.character(resource)) {
if (!nzchar(resource))
stop("path cannot be an empty string")
uri <- .parseURI(resource)
if (uri$scheme != "")
con <- url(resource)
else con <- file(resource)
} else con <- resource
if (!isOpen(con) && nzchar(open)) {
open(con, open)
con <- manage(manager, con)
}
con
}
connection <- function(manager, x, open = "") {
connectionForResource(manager, resource(x), open = open)
}
## Connection management (similar to memory management)
manage <- function(manager, con) {
manager$connections <- unique(c(manager$connections, list(con)))
attr(con, "manager") <- manager
con
}
managed <- function(manager, con) {
con %in% manager$connections
}
unmanage <- function(manager, con) {
manager$connections <- setdiff(manager$connections, con)
attr(con, "manager") <- NULL
con
}
release <- function(manager, con) {
if (managed(manager, con)) {
unmanage(manager, con)
close(con)
}
con
}
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