1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
|
#' Save atomic vectors to disk
#'
#' Save vectors containing atomic elements (or values that can be cast as such, e.g., dates and times) to an on-disk representation.
#'
#' @param x Any of the atomic vector types, or \link{Date} objects, or time objects, e.g., \link{POSIXct}.
#' @inheritParams saveObject
#' @param ... Further arguments that are ignored.
#'
#' @return
#' \code{x} is saved inside \code{path}.
#' \code{NULL} is invisibly returned.
#'
#' @author Aaron Lun
#'
#' @seealso
#' \code{\link{readAtomicVector}}, to read the files back into the session.
#'
#' @examples
#' tmp <- tempfile()
#' dir.create(tmp)
#' saveObject(LETTERS, file.path(tmp, "foo"))
#' saveObject(setNames(runif(26), letters), file.path(tmp, "bar"))
#' list.files(tmp, recursive=TRUE)
#'
#' @name saveAtomicVector
#' @aliases
#' stageObject,integer-method
#' stageObject,numeric-method
#' stageObject,logical-method
#' stageObject,character-method
#' stageObject,double-method
#' stageObject,POSIXct-method
#' stageObject,POSIXlt-method
#' stageObject,Date-method
NULL
.save_atomic_vector <- function(x, path, ...) {
dir.create(path)
ofile <- file.path(path, "contents.h5")
if (.is_datetime(x)) {
type <- "string"
format <- "date-time"
contents <- .sanitize_datetime(x)
} else if (is(x, "Date")) {
type <- "string"
format <- "date"
contents <- .sanitize_date(x)
} else {
stopifnot(is.atomic(x))
remapped <- .remap_atomic_type(x)
type <- remapped$type
contents <- remapped$values
format <- NULL
}
fhandle <- H5Fcreate(ofile, "H5F_ACC_TRUNC")
on.exit(H5Fclose(fhandle), add=TRUE, after=FALSE)
ghandle <- H5Gcreate(fhandle, "atomic_vector")
on.exit(H5Gclose(ghandle), add=TRUE, after=FALSE)
h5_write_attribute(ghandle, "type", type, scalar=TRUE)
if (!is.null(format)) {
h5_write_attribute(ghandle, "format", format, scalar=TRUE)
}
transformed <- transformVectorForHdf5(contents)
current <- transformed$transformed
missing.placeholder <- transformed$placeholder
dhandle <- h5_write_vector(ghandle, "values", current, emit=TRUE)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
if (!is.null(missing.placeholder)) {
h5_write_attribute(dhandle, missingPlaceholderName, missing.placeholder, scalar=TRUE)
}
if (!is.null(names(x))) {
h5_write_vector(ghandle, "names", names(x))
}
saveObjectFile(path, "atomic_vector", list(atomic_vector=list(version="1.0")))
invisible(NULL)
}
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "integer", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "character", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "logical", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "double", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "numeric", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "Date", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "POSIXlt", .save_atomic_vector)
#' @export
#' @rdname saveAtomicVector
setMethod("saveObject", "POSIXct", .save_atomic_vector)
#######################################
########### OLD STUFF HERE ############
#######################################
#' @importFrom S4Vectors DataFrame
.stage_atomic_vector <- function(x, dir, path, child=FALSE, ...) {
dir.create(file.path(dir, path), showWarnings=FALSE)
if (.is_datetime(x)) {
type <- "string"
format <- "date-time"
contents <- .sanitize_datetime(x)
} else if (is(x, "Date")) {
type <- "string"
format <- "date"
contents <- .sanitize_date(x)
} else {
stopifnot(is.atomic(x))
remapped <- .remap_atomic_type(x)
type <- remapped$type
contents <- remapped$values
format <- NULL
}
new_path <- paste0(path, "/simple.txt.gz")
mock <- DataFrame(values=contents)
if (!is.null(names(x))) {
mock <- cbind(names=names(x), mock)
}
quickWriteCsv(mock, file.path(dir, new_path), row.names=FALSE, compression="gzip")
list(
`$schema` = "atomic_vector/v1.json",
path = new_path,
is_child = child,
atomic_vector = list(
type = type,
length = length(contents),
names = !is.null(names(x)),
format = format,
compression="gzip"
)
)
}
#' @export
setMethod("stageObject", "integer", .stage_atomic_vector)
#' @export
setMethod("stageObject", "character", .stage_atomic_vector)
#' @export
setMethod("stageObject", "logical", .stage_atomic_vector)
#' @export
setMethod("stageObject", "double", .stage_atomic_vector)
#' @export
setMethod("stageObject", "numeric", .stage_atomic_vector)
#' @export
setMethod("stageObject", "Date", .stage_atomic_vector)
#' @export
setMethod("stageObject", "POSIXlt", .stage_atomic_vector)
#' @export
setMethod("stageObject", "POSIXct", .stage_atomic_vector)
|
