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#' Read a DataFrame from disk
#'
#' Read a \linkS4class{DataFrame} from its on-disk representation.
#' This is usually not directly called by users, but is instead called by dispatch in \code{\link{readObject}}.
#'
#' @param path String containing a path to the directory, itself created with \code{\link{saveObject}} method for \linkS4class{DataFrame}s.
#' @param metadata Named list containing metadata for the object, see \code{\link{readObjectFile}} for details.
#' @param ... Further arguments, passed to \code{\link{altLoadObject}} for complex nested columns.
#'
#' @return The \linkS4class{DataFrame} represented by \code{path}.
#'
#' @seealso
#' \code{"\link{saveObject,DataFrame-method}"}, for the staging method.
#'
#' @author Aaron Lun
#'
#' @examples
#' library(S4Vectors)
#' df <- DataFrame(A=1:10, B=LETTERS[1:10])
#'
#' tmp <- tempfile()
#' saveObject(df, tmp)
#' readObject(tmp)
#'
#' @export
#' @aliases loadDataFrame
#' @importFrom S4Vectors DataFrame make_zero_col_DFrame
readDataFrame <- function(path, metadata, ...) {
fpath <- file.path(path, "basic_columns.h5")
fhandle <- H5Fopen(fpath, flags="H5F_ACC_RDONLY")
on.exit(H5Fclose(fhandle), add=TRUE, after=FALSE)
host <- "data_frame"
ghandle <- H5Gopen(fhandle, host)
on.exit(H5Gclose(ghandle), add=TRUE, after=FALSE)
nrows <- h5_read_attribute(ghandle, "row-count")
colnames <- h5_read_vector(ghandle, "column_names")
rownames <- NULL
if (h5_object_exists(ghandle, "row_names")) {
rownames <- h5_read_vector(ghandle, "row_names")
}
gdhandle <- H5Gopen(ghandle, "data")
on.exit(H5Gclose(gdhandle), add=TRUE, after=FALSE)
all.children <- h5ls(gdhandle, recursive=FALSE, datasetinfo=FALSE)$name
columns <- vector("list", length(colnames))
for (col in seq_along(colnames)) {
expected <- as.character(col - 1L)
if (expected %in% all.children) {
type <- local({
precolhandle <- H5Oopen(gdhandle, expected)
on.exit(H5Oclose(precolhandle), add=TRUE, after=FALSE)
h5_read_attribute(precolhandle, "type")
})
if (type == "factor") {
columns[[col]] <- local({
colhandle <- H5Gopen(gdhandle, expected)
on.exit(H5Gclose(colhandle), add=TRUE, after=FALSE)
codes <- .simple_read_codes(colhandle)
levels <- h5_read_vector(colhandle, "levels")
ordered <- h5_read_attribute(colhandle, "ordered", check=TRUE, default=NULL)
factor(levels[codes], levels=levels, ordered=isTRUE(ordered > 0L))
})
} else {
columns[[col]] <- local({
colhandle <- H5Dopen(gdhandle, expected)
on.exit(H5Dclose(colhandle), add=TRUE, after=FALSE)
contents <- H5Dread(colhandle, drop=TRUE)
missing.placeholder <- h5_read_attribute(colhandle, missingPlaceholderName, check=TRUE, default=NULL)
contents <- h5_cast(contents, expected.type=type, missing.placeholder=missing.placeholder)
if (type == "string") {
if (H5Aexists(colhandle, "format")) {
format <- h5_read_attribute(colhandle, "format")
if (format == "date") {
contents <- as.Date(contents)
} else if (format == "date-time") {
contents <- as.Rfc3339(contents)
}
}
}
contents
})
}
} else {
columns[[col]] <- S4Vectors::I(altReadObject(file.path(path, "other_columns", expected), ...))
}
}
names(columns) <- colnames
if (length(columns) || !is.null(rownames)) {
output <- DataFrame(columns, check.names=FALSE, row.names=rownames)
} else {
output <- make_zero_col_DFrame(nrow=nrows)
}
readMetadata(
output,
metadata.path=file.path(path, "other_annotations"),
mcols.path=file.path(path, "column_annotations"),
...
)
}
#######################################
########### OLD STUFF HERE ############
#######################################
#' @export
loadDataFrame <- function(info, project, include.nested=TRUE, parallel=TRUE) {
has.rownames <- isTRUE(info$data_frame$row_names)
col.info <- info$data_frame$columns
has.columns <- length(col.info) > 0
nrows <- as.integer(info$data_frame$dimensions[[1]])
if (!has.rownames && !has.columns) {
return(make_zero_col_DFrame(nrow=nrows))
}
# Reading the file into a data frame.
path <- acquireFile(project, info$path)
if ("hdf5_data_frame" %in% names(info)) {
prefix <- function(x) paste0(info$hdf5_data_frame$group, "/", x)
if (!has.columns) {
df <- make_zero_col_DFrame(nrow=nrows)
} else {
raw <- h5read(path, prefix("data"))
df <- vector("list", length(col.info))
for (i in seq_along(col.info)) {
curinfo <- col.info[[i]]
d <- as.character(i - 1L) # -1 to get back to 0-based indices.
current <- raw[[d]]
if (!is.null(current)) {
attrs <- h5readAttributes(path, prefix(paste0("data/", d)))
current <- h5_cast(current, expected.type=NULL, missing.placeholder=attrs[[missingPlaceholderName]], respect.nan.payload=TRUE)
df[[i]] <- as.vector(current) # remove 1d arrays.
} else {
df[[i]] <- logical(nrows) # placeholders
}
}
names(df) <- as.vector(h5read(path, prefix("column_names")))
df <- DataFrame(df, check.names=FALSE)
}
if (has.rownames) {
rownames(df) <- as.vector(h5read(path, prefix("row_names")))
}
} else {
df <- read.csv3(path, compression=info$csv_data_frame$compression, nrows=nrows)
df <- DataFrame(df)
if (has.rownames) {
rownames(df) <- df[,1]
df <- df[,-1,drop=FALSE]
} else {
rownames(df) <- NULL
}
}
df <- .coerce_df_column_type(df, col.info, project, include.nested=include.nested)
.restoreMetadata(df, mcol.data=info$data_frame$column_data, meta.data=info$data_frame$other_data, project=project)
}
.coerce_df_column_type <- function(df, col.info, project, include.nested) {
stopifnot(length(df) == length(col.info))
true.names <- character(length(col.info))
for (i in seq_along(col.info)) {
current.info <- col.info[[i]]
true.names[i] <- current.info$name
col.type <- current.info$type
col <- df[[i]]
if (col.type=="factor" || col.type=="ordered") {
if (!is.factor(col)) { # we may have already transformed the column to a factor, in which case we can skip this.
level.info <- acquireMetadata(project, current.info$levels$resource$path)
levels <- altLoadObject(level.info, project=project)
if (is(levels, "DataFrame")) { # account for old objects that store levels as a DF.
levels <- levels[,1]
}
if (is.numeric(col)) {
col <- levels[col + 1L]
}
ordered <- col.type == "ordered" || isTRUE(current.info$ordered)
col <- factor(col, levels=levels, ordered=ordered)
}
} else if (col.type=="date") {
col <- as.Date(col)
} else if (col.type=="date-time") {
col <- .cast_datetime(col)
} else if (.is_atomic(col.type)) {
if (col.type == "integer") {
if (is.double(col) && any(col == -2^31, na.rm=TRUE)) {
# Don't cast to an integer if there's the special -2^31 value.
} else {
col <- .cast_atomic(col, col.type)
}
} else if (col.type == "string") {
f <- current.info$format
if (identical(f, "date")) {
col <- as.Date(col)
} else if (identical(f, "date-time")) {
col <- .cast_datetime(col)
}
} else {
col <- .cast_atomic(col, col.type)
}
} else if (col.type == "other") {
current <- acquireMetadata(project, current.info$resource$path)
if (include.nested || !("data_frame" %in% names(current))) {
col <- altLoadObject(current, project=project)
} else {
true.names[i] <- NA_character_
}
} else {
stop("unsupported column type '", col.type, "'")
}
df[[i]] <- col
}
# Removing nested DFs.
if (!all(keep <- !is.na(true.names))) {
df <- df[,keep,drop=FALSE]
true.names <- true.names[keep]
}
colnames(df) <- true.names
df
}
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