From 82afce155a22c5b93a165945cc17e095485d6b7e Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Mon, 31 Oct 2016 20:08:31 -0400 Subject: 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. --- snakemake-test.el | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'snakemake-test.el') 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 -- cgit v1.2.3