Check Integrity of Data Files — check

Validates a data file by checking its extension and attempting to load its contents. A file is considered valid if it exists, is non-empty, has a supported extension, and loads successfully with a non-null object. Supports RData, qs2, rds, and feather file types.

Usage

check_data(file = NULL, warning = TRUE, all_okay = TRUE, n_threads = 1L)

check_rdata(file, warning = TRUE)

check_qs(file, warning = TRUE, n_threads = 1L)

check_rds(file, warning = TRUE)

check_feather(file, warning = TRUE)

Arguments

file: Character vector. Path to a data file (e.g., .rdata, .qs2, .rds, .feather).
warning: Logical. If TRUE (default), warnings are issued for invalid files (e.g., non-existent, wrong extension, or loading failure).
all_okay: Logical. If TRUE (default), returns a single logical output indicating the integrity of all files; if FALSE, returns logical vectors for each file.
n_threads: Integer. Number of threads for reading qs2 files. Must be a positive integer. See qs2::qs_read for more details.

Value

Logical: TRUE if all checks pass; FALSE otherwise.

Details

The check_data() function determines the file type based on its extension (case-insensitive). If the extension is unrecognised, it returns FALSE. Supported file types:

RData: Checked with check_rdata(), read using load_as
qs2: Checked with check_qs(), read using qs2::qs_read
rds: Checked with check_rds(), read using readRDS
feather: Checked with check_feather(), read using arrow::read_feather

Author

Ahmed El-Gabbas

Examples

require(ecokit)
ecokit::load_packages(fs, arrow)

# Setup temporary directory
temp_dir <- fs::path_temp("load_multiple")
fs::dir_create(temp_dir)

# |||||||||||||||||||||||||||||||||||||||
# Validate RData files
# |||||||||||||||||||||||||||||||||||||||

# valid RData file
data <- data.frame(x = 1:5)
rdata_file <- fs::path(temp_dir, "valid.Rdata")
save(data, file = rdata_file)
check_rdata(rdata_file)
#> [1] TRUE

# Invalid RData file (corrupted)
bad_rdata <- fs::path(temp_dir, "invalid.Rdata")
writeLines("not an RData file", bad_rdata)
check_rdata(bad_rdata)
#> Warning: Failed to load RData file: /tmp/RtmpKgRiti/load_multiple/invalid.Rdata
#> [1] FALSE
check_rdata(bad_rdata, warning = FALSE)
#> [1] FALSE

# |||||||||||||||||||||||||||||||||||||||
# Validate qs2 files
# |||||||||||||||||||||||||||||||||||||||

# Valid qs2 file
qs_file <- fs::path(temp_dir, "valid.qs2")
qs2::qs_save(data, qs_file, nthreads = 1)
check_qs(qs_file, n_threads = 1L)
#> [1] TRUE

# Invalid qs2 file (corrupted)
bad_qs <- fs::path(temp_dir, "invalid.qs2")
writeLines("not a qs2 file", bad_qs)
check_qs(bad_qs, n_threads = 1L)
#> Warning: Failed to load qs2 file: /tmp/RtmpKgRiti/load_multiple/invalid.qs2
#> [1] FALSE
check_qs(bad_qs, n_threads = 1L, warning = FALSE)
#> [1] FALSE

# |||||||||||||||||||||||||||||||||||||||
# Validate rds files
# |||||||||||||||||||||||||||||||||||||||

# Valid rds file
rds_file <- fs::path(temp_dir, "valid.rds")
saveRDS(data, rds_file)
check_rds(rds_file)
#> [1] TRUE

# Invalid rds file (corrupted)
bad_rds <- fs::path(temp_dir, "invalid.rds")
writeLines("not an rds file", bad_rds)
check_rds(bad_rds)
#> Warning: Failed to load rds file: /tmp/RtmpKgRiti/load_multiple/invalid.rds
#> [1] FALSE
check_rds(bad_rds, warning = FALSE)
#> [1] FALSE

# |||||||||||||||||||||||||||||||||||||||
# Validate feather files
# |||||||||||||||||||||||||||||||||||||||

# Valid feather file
feather_file <- fs::path(temp_dir, "valid.feather")
arrow::write_feather(data, feather_file)
check_feather(feather_file)
#> [1] TRUE

# Invalid feather file (corrupted)
bad_feather <- fs::path(temp_dir, "invalid.feather")
writeLines("not a feather file", bad_feather)
check_feather(bad_feather)
#> Warning: Failed to load feather file: /tmp/RtmpKgRiti/load_multiple/invalid.feather
#> [1] FALSE
check_feather(bad_feather, warning = FALSE)
#> [1] FALSE

# |||||||||||||||||||||||||||||||||||||||
# Non-existent file
# |||||||||||||||||||||||||||||||||||||||
check_data("nonexistent.rds")
#> Warning: File does not exist: `/home/runner/work/ecokit/ecokit/docs/reference/nonexistent.rds`
#> [1] FALSE

# |||||||||||||||||||||||||||||||||||||||
# check_data
# |||||||||||||||||||||||||||||||||||||||
all_files <- c(
  rdata_file, bad_rdata, qs_file, bad_qs, rds_file, bad_rds,
  feather_file, bad_feather)
check_data(all_files)
#> Warning: Failed to load RData file: /tmp/RtmpKgRiti/load_multiple/invalid.Rdata
#> Warning: Failed to load qs2 file: /tmp/RtmpKgRiti/load_multiple/invalid.qs2
#> Warning: Failed to load rds file: /tmp/RtmpKgRiti/load_multiple/invalid.rds
#> Warning: Failed to load feather file: /tmp/RtmpKgRiti/load_multiple/invalid.feather
#> [1] FALSE
check_data(all_files, all_okay = FALSE)
#> Warning: Failed to load RData file: /tmp/RtmpKgRiti/load_multiple/invalid.Rdata
#> Warning: Failed to load qs2 file: /tmp/RtmpKgRiti/load_multiple/invalid.qs2
#> Warning: Failed to load rds file: /tmp/RtmpKgRiti/load_multiple/invalid.rds
#> Warning: Failed to load feather file: /tmp/RtmpKgRiti/load_multiple/invalid.feather
#> [1]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE
check_data(all_files, all_okay = FALSE, warning = FALSE)
#> [1]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE

# clean up
fs::file_delete(all_files)
fs::dir_delete(temp_dir)