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authorKyle Meyer <kyle@kyleam.com>2016-10-31 20:08:31 -0400
committerKyle Meyer <kyle@kyleam.com>2016-11-01 22:04:11 -0400
commit82afce155a22c5b93a165945cc17e095485d6b7e (patch)
tree18e0d09b24dd78317e5e32c09d3c00ce2b0a12f8
parent13620417f99495f74b17cd2d9ca3c37551dbb120 (diff)
downloadsnakemake-mode-82afce155a22c5b93a165945cc17e095485d6b7e.tar.gz
Change approach for detecting invalid targets
Initially (7374840), snakemake-check-target only used regular expressions to detect invalid targets based on the presence of a MissingRuleException or RuleException in Snakemake's output. The target was assumed to be valid if these exceptions weren't found. If there was a non-zero exit status for another reason, it bubbled up to the compile call where it was visible to the user. 33a7c90 (snakemake-check-target: Adjust for upstream output, 2016-09-01) restricted the invalid target check to calls with an exit status of zero. This makes the regular expression check useless because snakemake should always exit with a non-zero status if a MissingRuleException or RuleException is thrown. Due to this change, snakemake-check-target classified all non-zero exits as invalid and all zero exits as valid. While this often gives the right answer, it doesn't in cases where the non-zero exit is unrelated to an invalid target. 2bceb7f (snakemake-check-target: Recognize protected items, 2016-09-05) addressed one case. To deal with other cases (such as an ambiguous rule error or a syntax error in the Snakefile), use the following approach. * An exit status of zero indicates a valid target. * A non-zero exit status indicates an invalid target if snakemake-all-rules has an exit status of zero. Otherwise, snakemake-all-rules will signal an error and display the Snakemake output. The main downside of this approach is the need to call snakemake twice. The output of snakmake-all-rules is cached, so this is only the case on the first call to snakemake-check-target for a given version of a Snakefile.
-rw-r--r--snakemake-test.el23
-rw-r--r--snakemake.el23
2 files changed, 34 insertions, 12 deletions
diff --git a/snakemake-test.el b/snakemake-test.el
index 80b6bcd..19a0b99 100644
--- a/snakemake-test.el
+++ b/snakemake-test.el
@@ -820,6 +820,29 @@ two words"
(should-not
(snakemake-with-temp-dir
(snakemake-check-target "cc_wildcards")))
+ ;; Errors with the Snakefile, like ambiguous rules and syntax
+ ;; errors, should be reported as errors rather than treated as
+ ;; invalid targets.
+ (should-error
+ (snakemake-with-temp-dir
+ (write-region "\ndef incomplete_def:"
+ nil
+ "Snakefile"
+ 'append)
+ (snakemake-check-target "aa"))
+ :type 'snakemake-error)
+ (should-error
+ (snakemake-with-temp-dir
+ (write-region "\
+
+rule aa:
+ output: \"aa.ambig.out\"
+ shell: \"echo aa.ambig.content > {output}\""
+ nil
+ "Snakefile"
+ 'append)
+ (snakemake-check-target "aa"))
+ :type 'snakemake-error)
;; Write-protected targets should be recognized as valid targets
;; despite Snakemake throwing an error.
(should
diff --git a/snakemake.el b/snakemake.el
index 5baeae1..33f5f5d 100644
--- a/snakemake.el
+++ b/snakemake.el
@@ -266,10 +266,6 @@ The file list is determined by the output of
(buffer-string)
(snakemake--display-error)))))))
-(defconst snakemake-invalid-target-re
- (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
@@ -280,14 +276,17 @@ exit status is non-zero.")
(snakemake-with-cache directory (target)
(with-temp-buffer
(let ((ex-code (snakemake-insert-output "--quiet" "--dryrun" target)))
- (goto-char (point-min))
- (cond
- ((re-search-forward snakemake-valid-target-re nil t))
- ((and (zerop ex-code)
- ;; Lean towards misclassifying targets as valid rather
- ;; than silently dropping valid targets as invalid.
- (not (re-search-forward snakemake-invalid-target-re
- nil t)))))))))
+ (or (zerop ex-code)
+ (progn (goto-char (point-min))
+ (re-search-forward snakemake-valid-target-re nil t))
+ ;; A non-zero exit status could indicate that TARGET is
+ ;; invalid, but it could also be the result of an issue
+ ;; like a syntax error or an ambiguous rule. To check
+ ;; this, see whether `snakemake-all-rules' signals a
+ ;; `snakemake-error'. This avoids relying on parsing
+ ;; Snakemake exception output, which isn't stable across
+ ;; Snakemake versions.
+ (progn (snakemake-all-rules) nil))))))
(declare-function org-element-context "org-element")
(declare-function org-element-property "org-element")