planemo reports test failure when test succeeds
Hi there When testing the latest trimmomatic tool (from https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmoma..., planemo test reports an error on the last test, but according to the test report the test has succeeded (see attached HTML and JSON). For the test setup you need to set some environment variables: TRIMMOMATIC_DIR - the location of the trimmomatic jar TRIMMOMATIC_JAR - the name of the jar file TRIMMOMATIC_ADAPTERS_DIR - location of adapters This is with planemo 0.22.2 and a fresh $HOME/.planemo. Any ideas? Peter
Hello again Peter I also see this when using planemo to run the tool tests both on trimmomatic and also on another of our tools i.e. one or more of the tests will be reported as 'failed' on the command line when the HTML report indicates that all tests executed successfully. Now I think about it, planemo itself must exit with status 0 in these cases as my tests on Travis-CI also report success, for example see: https://travis-ci.org/fls-bioinformatics-core/galaxy-tools/jobs/104643315 Scroll to the bottom of the log and the last test is reported as 'failed', however the Travis test overall passes. I hadn't really thought about it before since the planemo exit status seems to be correct (i.e. in cases where there are genuine tool test failures, it will return a non-zero status at the end which causes Travis to correctly report a failure). (Btw this referenced above used planemo 0.22.2 but I've seen it in older versions too.) I don't think I've ever seen planemo report a 'passed' test as 'failed', but generally I check the HTML to verify whether the failures are real or not. Best wishes Peter On 22/01/16 11:40, Peter van Heusden wrote:
Hi there
When testing the latest trimmomatic tool (from https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmoma..., planemo test reports an error on the last test, but according to the test report the test has succeeded (see attached HTML and JSON). For the test setup you need to set some environment variables:
TRIMMOMATIC_DIR - the location of the trimmomatic jar TRIMMOMATIC_JAR - the name of the jar file TRIMMOMATIC_ADAPTERS_DIR - location of adapters
This is with planemo 0.22.2 and a fresh $HOME/.planemo.
Any ideas?
Peter
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-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Zipho looked at this over here and had some ideas about how some warning output might trigger this spurious failure - I haven't had time to follow up on that theory. On 4 February 2016 at 14:26, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hello again Peter
I also see this when using planemo to run the tool tests both on trimmomatic and also on another of our tools i.e. one or more of the tests will be reported as 'failed' on the command line when the HTML report indicates that all tests executed successfully.
Now I think about it, planemo itself must exit with status 0 in these cases as my tests on Travis-CI also report success, for example see:
https://travis-ci.org/fls-bioinformatics-core/galaxy-tools/jobs/104643315
Scroll to the bottom of the log and the last test is reported as 'failed', however the Travis test overall passes. I hadn't really thought about it before since the planemo exit status seems to be correct (i.e. in cases where there are genuine tool test failures, it will return a non-zero status at the end which causes Travis to correctly report a failure).
(Btw this referenced above used planemo 0.22.2 but I've seen it in older versions too.)
I don't think I've ever seen planemo report a 'passed' test as 'failed', but generally I check the HTML to verify whether the failures are real or not.
Best wishes
Peter
On 22/01/16 11:40, Peter van Heusden wrote:
Hi there
When testing the latest trimmomatic tool (from
https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmoma... , planemo test reports an error on the last test, but according to the test report the test has succeeded (see attached HTML and JSON). For the test setup you need to set some environment variables:
TRIMMOMATIC_DIR - the location of the trimmomatic jar TRIMMOMATIC_JAR - the name of the jar file TRIMMOMATIC_ADAPTERS_DIR - location of adapters
This is with planemo 0.22.2 and a fresh $HOME/.planemo.
Any ideas?
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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