From 2bceb7f266f71cd85f9b328de02797eb457da17c Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Mon, 5 Sep 2016 23:49:22 -0400
Subject: snakemake-check-target: Recognize protected items

With 33a7c90 (snakemake-check-target: Adjust for upstream output,
2016-09-01), write-protected targets were no longer considered valid
targets.
---
 snakemake-test.el | 10 +++++++++-
 snakemake.el      | 17 +++++++++++++----
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/snakemake-test.el b/snakemake-test.el
index 25713af..213d13c 100644
--- a/snakemake-test.el
+++ b/snakemake-test.el
@@ -812,7 +812,15 @@ two words"
      (snakemake-check-target "aa.out")))
   (should-not
    (snakemake-with-temp-dir
-     (snakemake-check-target "aa.out.not-target"))))
+     (snakemake-check-target "aa.out.not-target")))
+  ;; Write-protected targets should be recognized as valid targets
+  ;; despite Snakemake throwing an error.
+  (should
+   (snakemake-with-temp-dir
+     (with-temp-file "bb.out" (insert ""))
+     (set-file-modes "bb.out" (file-modes-symbolic-to-number "u=r"))
+     (with-temp-file "aa.out" (insert ""))
+     (snakemake-check-target "bb.out"))))
 
 (ert-deftest snakemake-test-org-link-file-targets ()
   (should (equal '("/path/to/fname")
diff --git a/snakemake.el b/snakemake.el
index 9a93f9e..9ec7b42 100644
--- a/snakemake.el
+++ b/snakemake.el
@@ -258,15 +258,24 @@ The file list is determined by the output of
   (regexp-opt (list "MissingRuleException"
                     "RuleException")))
 
+(defconst snakemake-valid-target-re "ProtectedOutputException"
+  "Regular expression indicating valid target.
+If this matches, the target will be considered valid even if the
+exit status is non-zero.")
+
 (defun snakemake-check-target (target &optional directory)
   "Return non-nil if TARGET is a valid target for DIRECTORY's Snakefile."
   (snakemake-with-cache directory (target)
     (with-temp-buffer
-      (when (= 0 (snakemake-insert-output "--quiet" "--dryrun" target))
+      (let ((ex-code (snakemake-insert-output "--quiet" "--dryrun" target)))
         (goto-char (point-min))
-        ;; Lean towards misclassifying targets as valid rather than
-        ;; silently dropping valid targets as invalid.
-        (not (re-search-forward snakemake-invalid-target-re nil t))))))
+        (cond
+         ((re-search-forward snakemake-valid-target-re nil t))
+         ((and (= ex-code 0)
+               ;; Lean towards misclassifying targets as valid rather
+               ;; than silently dropping valid targets as invalid.
+               (not (re-search-forward snakemake-invalid-target-re
+                                       nil t)))))))))
 
 (declare-function org-element-context "org-element")
 (declare-function org-element-property "org-element")
-- 
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