From bd516e958af22e57c18cacf0cb22552c2a237bd8 Mon Sep 17 00:00:00 2001
From: Josh Cook <39419448+jhrcook@users.noreply.github.com>
Date: Tue, 23 Nov 2021 10:28:49 -0500
Subject: [PATCH] fix: R encoding of pathlib.Path objects (#1201)
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* feat: support converting Path objects for R

* test: test for converting Path objects to R

* Update script.py

* test: Snakemake test for R encoding pathlib.Path objects (missing files)

* fix: touch file to make expected-results dir appear in git

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
---
 .../Snakefile                                  | 18 ++++++++++++++++++
 .../expected-results/.github_touch             |  0
 .../r-script.R                                 |  9 +++++++++
 .../text-file.txt                              |  0
 tests/tests.py                                 |  4 ++++
 5 files changed, 31 insertions(+)
 create mode 100644 tests/test_converting_path_for_r_script/Snakefile
 create mode 100644 tests/test_converting_path_for_r_script/expected-results/.github_touch
 create mode 100644 tests/test_converting_path_for_r_script/r-script.R
 create mode 100644 tests/test_converting_path_for_r_script/text-file.txt

diff --git a/tests/test_converting_path_for_r_script/Snakefile b/tests/test_converting_path_for_r_script/Snakefile
new file mode 100644
index 000000000..c19e776e7
--- /dev/null
+++ b/tests/test_converting_path_for_r_script/Snakefile
@@ -0,0 +1,18 @@
+
+from pathlib import Path
+
+
+rule all:
+  input:
+    out_file="out-file.txt"
+
+
+rule step1:
+  input:
+    text_file=Path("text-file.txt")
+  params:
+    param_dir=Path("dir")
+  output:
+    out_file=Path("out-file.txt")
+  script:
+    "r-script.R"
diff --git a/tests/test_converting_path_for_r_script/expected-results/.github_touch b/tests/test_converting_path_for_r_script/expected-results/.github_touch
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/test_converting_path_for_r_script/r-script.R b/tests/test_converting_path_for_r_script/r-script.R
new file mode 100644
index 000000000..23ae87960
--- /dev/null
+++ b/tests/test_converting_path_for_r_script/r-script.R
@@ -0,0 +1,9 @@
+
+infile <- snakemake@input[["text_file"]]
+
+# Check the read value is as expected in R.
+param_dir <- snakemake@params[["param_dir"]]
+stopifnot(param_dir == "dir")
+
+outfile <- snakemake@output[["out_file"]]
+file.create(outfile)
diff --git a/tests/test_converting_path_for_r_script/text-file.txt b/tests/test_converting_path_for_r_script/text-file.txt
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/tests.py b/tests/tests.py
index 0fbea1540..a86f06ce6 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -1340,5 +1340,9 @@ def test_github_issue1158():
     )
 
 
+def test_converting_path_for_r_script():
+    run(dpath("test_converting_path_for_r_script"), cores=1)
+
+
 def test_ancient_dag():
     run(dpath("test_ancient_dag"))