This check is three-fold: 1) verify the current working directory is as expected, 2) verify the user can access the file, and 3) verify the file contents are as expected (via md5sum).
Usage
file_check(
paths,
md5sums = NULL,
absolute_paths = c("warn", "stop", "silent"),
stop = FALSE
)Arguments
- paths
a character path to the target file
- md5sums
a character string for the expected md5sum of the target file. If
NULLthen only afile.existscheck will be done.- absolute_paths
a character string to set the behavior of warning (default), stopping, or silent if/when absolute file paths are used.
- stop
if
TRUEthen an error is thrown if any of the checks fail, else returns a logical. IfFALSE(default) a logical is returned.
Details
The test for the file access is done to verify the file can be read by the current user.
The return of the function is TRUE if all the files in paths
are accessible, are case matched (optional), and all of requested md5sum
checks pass. Windows and macOS are generally case-insensitive systems, but
many Linux systems are case-sensitive. As such
file.exists and file.access may
return different values depending the OS that is active. file_check
looks for a case match as part of its checks to hopefully prevent issues
across operating systems.
By default, if the return is TRUE then only TRUE will
be printed to the console. If the return is FALSE then the
attr(, "checks") is printed by default as well.
Good practice would be to use relative paths, a warning will be given if any
of the paths are determined to be absolute paths. That said, there
are cases when an absolute path is needed, e.g., a common data file on a
server with multiple users accessing the file(s). Set absolute_paths =
c("silent") to silence the warnings.
Examples
# create example files
relative_example_file1 <-
basename(
tempfile(
pattern = "QWRAPS2_EXAMPLE_1"
, fileext = ".txt"
, tmpdir = getwd()
)
)
relative_example_file2 <-
basename(
tempfile(
pattern = "QWRAPS2_EXAMPLE_2"
, fileext = ".txt"
, tmpdir = getwd()
)
)
absolute_example_file <- tempfile()
cat("example file.", file = relative_example_file1)
cat("Another example file.", file = relative_example_file2)
cat("Another example file.", file = absolute_example_file)
# Check that you have access to the files in the working directory.
test1 <- file_check(c(relative_example_file1, relative_example_file2))
test1
#> [1] TRUE
# By default, when the checks return TRUE the details of the checks are not
# printed. You can view the details of the checks as follows:
attr(test1, "checks")
#> path
#> QWRAPS2_EXAMPLE_118564c78f13d.txt QWRAPS2_EXAMPLE_118564c78f13d.txt
#> QWRAPS2_EXAMPLE_2185633422cb2.txt QWRAPS2_EXAMPLE_2185633422cb2.txt
#> absolute_path accessible case_match
#> QWRAPS2_EXAMPLE_118564c78f13d.txt FALSE TRUE TRUE
#> QWRAPS2_EXAMPLE_2185633422cb2.txt FALSE TRUE TRUE
#> current_md5sum
#> QWRAPS2_EXAMPLE_118564c78f13d.txt 7a3409e17f9de067740e64448a86e708
#> QWRAPS2_EXAMPLE_2185633422cb2.txt 798e52b92e0ae0e60f3f3db1273235d0
#> expected_md5sum md5check
#> QWRAPS2_EXAMPLE_118564c78f13d.txt <NA> NA
#> QWRAPS2_EXAMPLE_2185633422cb2.txt <NA> NA
# access to absolute_example_file will generate a warning about
# absolute_paths by default
test2 <- file_check(absolute_example_file)
#> Warning: Absolute path used. It would be preferable if you used a relative path.
test2 <- file_check(absolute_example_file, absolute_paths = "silent")
test2
#> [1] TRUE
# Case Match
test_case_match <-
file_check(
c(relative_example_file1, tolower(relative_example_file1))
)
test_case_match
#> [1] FALSE
#> attr(,"checks")
#> path
#> QWRAPS2_EXAMPLE_118564c78f13d.txt QWRAPS2_EXAMPLE_118564c78f13d.txt
#> qwraps2_example_118564c78f13d.txt qwraps2_example_118564c78f13d.txt
#> absolute_path accessible case_match
#> QWRAPS2_EXAMPLE_118564c78f13d.txt FALSE TRUE TRUE
#> qwraps2_example_118564c78f13d.txt FALSE FALSE FALSE
#> current_md5sum
#> QWRAPS2_EXAMPLE_118564c78f13d.txt 7a3409e17f9de067740e64448a86e708
#> qwraps2_example_118564c78f13d.txt <NA>
#> expected_md5sum md5check
#> QWRAPS2_EXAMPLE_118564c78f13d.txt <NA> NA
#> qwraps2_example_118564c78f13d.txt <NA> NA
# If one or more files is not accessable then return is FALSE and the meta data
# is printed by default.
test_non_existent_file <-
file_check(
c("UNLIKELYFILENAME", relative_example_file1, relative_example_file2)
)
test_non_existent_file
#> [1] FALSE
#> attr(,"checks")
#> path
#> UNLIKELYFILENAME UNLIKELYFILENAME
#> QWRAPS2_EXAMPLE_118564c78f13d.txt QWRAPS2_EXAMPLE_118564c78f13d.txt
#> QWRAPS2_EXAMPLE_2185633422cb2.txt QWRAPS2_EXAMPLE_2185633422cb2.txt
#> absolute_path accessible case_match
#> UNLIKELYFILENAME FALSE FALSE FALSE
#> QWRAPS2_EXAMPLE_118564c78f13d.txt FALSE TRUE TRUE
#> QWRAPS2_EXAMPLE_2185633422cb2.txt FALSE TRUE TRUE
#> current_md5sum
#> UNLIKELYFILENAME <NA>
#> QWRAPS2_EXAMPLE_118564c78f13d.txt 7a3409e17f9de067740e64448a86e708
#> QWRAPS2_EXAMPLE_2185633422cb2.txt 798e52b92e0ae0e60f3f3db1273235d0
#> expected_md5sum md5check
#> UNLIKELYFILENAME <NA> NA
#> QWRAPS2_EXAMPLE_118564c78f13d.txt <NA> NA
#> QWRAPS2_EXAMPLE_2185633422cb2.txt <NA> NA
# Or have an error thrown:
if (FALSE) {
file_check(
c("UNLIKELYFILENAME", relative_example_file1, relative_example_file2)
, stop = TRUE
)
}
# Verify the md5sums as well as file access:
md5_check1 <- file_check(relative_example_file1, "7a3409e17f9de067740e64448a86e708")
md5_check1
#> [1] TRUE
# If you only need to verify a subset of md5sums then use an NA in the md5sums
# argument:
md5_check2 <-
file_check(c(relative_example_file1, relative_example_file2),
c("7a3409e17f9de067740e64448a86e708", NA))
md5_check2
#> [1] TRUE
# Verify all the md5sums
md5_check3 <-
file_check(c(relative_example_file1, relative_example_file2),
c("7a3409e17f9de067740e64448a86e708", "798e52b92e0ae0e60f3f3db1273235d0"))
md5_check3
#> [1] TRUE
# clean up working directory
unlink(relative_example_file1)
unlink(relative_example_file2)
unlink(absolute_example_file)