is.safeFileName: Verify that a fileName is safe for use in shell commands.
In jefferys/fusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description Usage Arguments Value Valid names

Validates filenames for use in system commands. Allows for either blacklist and whitelist filtering, and independently controls several characters in common use in filenames that could be dangerous in some contexts. Optionally may also require a filename to exist or not to exist.

1 2	is.safeFileName(names, exists = NULL, weak = FALSE, okSpace = TRUE, okTilde = TRUE, okBackslash = FALSE, okComma = FALSE, okColon = FALSE)

`names`	A vector of filenames to check.
`exists`	NULL Can set `TRUE` to ensure file exists, or `FALSE` to ensure file does NOT exist. (Note, don't rely on this as only error check for reading/writting file as that introduces a race condition).
`weak`	default this is `FALSE` and validation is done using white-listed characters. Set `TRUE` to do validation using blacklisted characters. See Valid names below for additional info
`okSpace`	Set `TRUE` to ban a space. Allows " " by default.
`okTilde`	Set `TRUE` to ban a tilde. Allows "~" by default (anywhere!).
`okBackslash`	Set `TRUE` to allow a backslash. No `\` are allowed by default.
`okComma`	Set `TRUE` to allow a comma. No `,` are allowed by default.
`okColon`	Set `TRUE` to allow a colon. No `:` are allowed by default.

Returns a vector of booleans the same length as the input names, TRUE if the file is safe, FALSE if it fails any test.

Filtering at a single character level will catch most bad names:

Always bad	` $ ( ) \| ; & > <
Always ok	`A:Z a:z 0:9 _ . - /`
Can set bad	`" "` (space)
Can set bad	`~` (tilde will be allowed anywhere)
Can set ok	`\ , :`
May not start with	`+ -`

In addition, no filename may contain either " -" or " +" ( the - or + character preceded by a space.) This prevents injecting new options.

By default, whitelist validation is used. Files may only use charcters explicitly allowed. Can switch to blacklist validation by setting weak= TRUE, which allows any character not explicitly banned.

jefferys/fusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.