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Write RDS files atomically (write to *.rds.tmp, then rename to *.rds) #316

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Write RDS files atomically (write to *.rds.tmp, then rename to *.rds) #316

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7e153c5
Write RDS files atomically (write to *.rds.tmp, then rename to *.rds)
HenrikBengtsson Aug 17, 2025
c18e6f9
ROBUSTNESS: Now sweepRegistry(), syncRegistry(), updateRegistry() sea…
HenrikBengtsson Aug 17, 2025
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27 changes: 23 additions & 4 deletions R/files.R
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Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,28 @@ file_mtime = function(x) {
fs::file_info(x)$modification_time
}

writeRDS = function(object, file, compress = "gzip") {
file_remove(file)
saveRDS(object, file = file, version = 2L, compress = compress)
waitForFile(file, 300)
writeRDS = function(object, file, compress = "gzip", wait = 300) {
# (a) Write to *.rds.tmp
tmp_file <- sprintf("%s.tmp", file)
saveRDS(object, file = tmp_file, version = 2L, compress = compress)

# (b) Wait for it to be found
if (wait > 0) waitForFile(tmp_file, timeout = wait)

# (c) Assert file exists
if (!file_test("-f", tmp_file)) {
stop(sprintf("Failed to save to temporary RDS file: %s", sQuote(tmp_file)))
}

# (d) Remove old file, if it exists
if (file_test("-f", file)) file_remove(file)

# (e) Rename *.rds.tmp to *.rds
file.rename(tmp_file, file)
if (!file_test("-f", file)) {
stop(sprintf("Failed to rename temporarily saved RDS file: %s -> %s",
sQuote(tmp_file), sQuote(file)))
}

invisible(TRUE)
}
4 changes: 2 additions & 2 deletions R/sweepRegistry.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ sweepRegistry = function(reg = getDefaultRegistry()) {

submitted = reg$status[.findSubmitted(reg = reg), c("job.id", "job.hash")]
obsolete = chsetdiff(
list.files(dir(reg, "results"), full.names = TRUE),
list.files(dir(reg, "results"), pattern = "\\.rds$", full.names = TRUE),
getResultFiles(reg, submitted)
)
if (length(obsolete)) {
Expand All @@ -31,7 +31,7 @@ sweepRegistry = function(reg = getDefaultRegistry()) {
fs::file_delete(obsolete)
}

obsolete = list.files(dir(reg, "jobs"), pattern = "\\.rds", full.names = TRUE)
obsolete = list.files(dir(reg, "jobs"), pattern = "\\.rds$", full.names = TRUE)
if (length(obsolete)) {
info("Removing %i obsolete job collection files ...", length(obsolete))
fs::file_delete(obsolete)
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2 changes: 1 addition & 1 deletion R/syncRegistry.R
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Expand Up @@ -21,7 +21,7 @@ syncRegistry = function(reg = getDefaultRegistry()) {

sync = function(reg) {
"!DEBUG [syncRegistry]: Triggered syncRegistry"
fns = list.files(dir(reg, "updates"), full.names = TRUE)
fns = list.files(dir(reg, "updates"), pattern = "\\.rds$", full.names = TRUE)
if (length(fns) == 0L)
return(character())

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6 changes: 3 additions & 3 deletions R/updateRegisty.R
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Expand Up @@ -78,7 +78,7 @@ updateRegistry = function(reg = getDefaultRegistry()) { # nocov start
uri = getProblemURI(reg, id)
p = readRDS(uri)
p$cache = FALSE
saveRDS(p, file = uri, version = 2L)
writeRDS(p, file = uri, compress = TRUE, wait = 0)
}
}
}
Expand All @@ -89,7 +89,7 @@ updateRegistry = function(reg = getDefaultRegistry()) { # nocov start
setnames(reg$status, "memory", "mem.used")
}

fns = list.files(dir(reg, "updates"), full.names = TRUE)
fns = list.files(dir(reg, "updates"), pattern = "\\.rds$", full.names = TRUE)
if (length(fns) > 0L) {
info("Renaming memory column in update files")
updates = lapply(fns, function(fn) {
Expand All @@ -99,7 +99,7 @@ updateRegistry = function(reg = getDefaultRegistry()) { # nocov start
} else {
if (hasName(x, "memory")) {
setnames(x, "memory", "mem.used")
saveRDS(x, file = fn, version = 2L)
writeRDS(x, file = fn, compress = TRUE, wait = 0)
}
}
})
Expand Down