feat: initial commit

.Rbuildignore

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+^Makefile
+^readme.md

.gitignore

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+*.Rcheck
+*.tar.gz
+man
+NAMESPACE

DESCRIPTION

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+Package: normalizepath
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.1
+Authors@R: 
+    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+Imports: jsonlite (>= 1.8.0)
+RoxygenNote: 7.3.2

Makefile

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+default: build
+
+.PHONY: document test clean check build clean 
+
+PKG_NAME := normalizepath
+PKG_VERS := 0.0.1
+PKG_TAR := $(PKG_NAME)_$(PKG_VERS).tar.gz
+
+R := R
+
+document:
+	$(R) -e "devtools::document()"
+
+test:
+	true # Placeholder.
+
+clean:
+	rm -rf $(PKG_TAR) $(PKG_NAME).Rcheck
+
+check: build
+	R CMD check $(PKG_TAR)
+
+build: clean document test
+	$(R) CMD build .
+
+clean:
+	rm -rf $(PKG_NAME).Rcheck $(PKG_TAR)

R/normalize_path.R

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+#' Check if the script is running in a container.
+#'
+#' @returns A truthy value indicating the state.
+is_running_in_docker <- function() {
+  dockerenv_exists <- file.exists("/.dockerenv")
+  cgroup_exists <- file.exists("/proc/1/cgroup")
+  in_container_runtime <- FALSE
+  if (cgroup_exists) {
+    in_container_runtime <- any(
+      grepl("docker", readLines("/proc/1/cgroup", warn = FALSE))
+    )
+  }
+  return(dockerenv_exists || in_container_runtime)
+}
+
+#' Gets the absolute path of a file.
+#'
+#' @param path a normalized, absolute path.
+#' @return The absolute host path, if it exists.
+#' @export
+absolute_path_mapper <- function(path) {
+  return(normalizePath(path, mustWork = FALSE))
+}
+
+#' Normalizes a path
+#'
+#' @param path The path to normalize.
+#' @param path_mappers The mappers to be utilized to normalize the path.
+#' @returns The normalized path.
+#' @export
+normalize_path <- function(path, path_mappers = c()) {
+  path_mappers <- c(
+    absolute_path_mapper, # Adds absolute_path_mapper at the beginning.
+    path_mappers
+  )
+  for (mapper in path_mappers) {
+    path <- mapper(path)
+  }
+  return(path)
+}
+
+#' Maps a path to host volumes.
+#'
+#' @param path a normalized, absolute path.
+#' @return The absolute host path, if it exists.
+#' @export
+docker_mount_mapper <- function(path) {
+  if (!is_running_in_docker()) {
+    return(path)
+  }
+
+  # Since we are running in docker, we can use our hostname as an heuristic
+  # to obtain our id.
+  # TODO: Check if this assumption is right for other container engines and
+  #       generalize this implementation.
+  hostname <- Sys.info()["nodename"]
+  output <- system2("docker",
+    args = paste("inspect -f '{{ json .Mounts }}'", hostname),
+    stdout = TRUE,
+  )
+  parsed_output <- jsonlite::fromJSON(output)
+
+  # Iterate over mounts, return first match.
+  for (i in seq_len(nrow(parsed_output))) {
+    destination <- parsed_output[i, ]$Destination
+    if (startsWith(path, destination)) {
+      source <- parsed_output[i, ]$Source
+      path <- sub(destination, source, path)
+      return(path)
+    }
+  }
+  return(path)
+}

readme.md

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+# normalizepath
+
+Normalizes path using one (or more) heuristics.
+
+---
+
+Get the latest [release](https://github.com/Reproducible-Bioinformatics/normalizepath/releases/latest).
+
+Usage example:
+
+```R
+normalized <- normalize_path(
+    path = "../the/path/to_normalize",
+    path_mappers = c(docker_mount_mapper)
+)
+```