[Debian-med-packaging] Bug#950311: FastQC users attention: Please comment on the remaining failures! (Was: Bug#950311: fastqc: autopkgtest regression: debhelper bump moved files to different location)

[tony mancill]

On Mon, Apr 06, 2020 at 09:46:44PM +0200, Andreas Tille wrote:
> Hi Tony,
> 
> On Mon, Apr 06, 2020 at 12:19:17PM -0700, tony mancill wrote:
> > 
> > I spent a while looking into this bug (and thereby took a crash course
> > in the Sequence Alignment Map file format)
> 
> May be I need such a crash course as well. ;-)
> 
> > So I think the tool is doing the right thing outputting FAIL for these
> > files.  I propose that we update the test to ensure that a summary file is
> > produced and contains the requisite number of lines for each of the data
> > quality tests, and that each line contains one of "PASS|WARN|FAIL" to
> > indicate that FastQC was able to run the tests.
> > ...
> 
> This sounds all pretty convincing.  Feel free to do a team upload
> implementing your suggestion.

I went ahead and implemented this as a comparison of the summary output
with the "known good" output and pushed as a merge-request to Salsa [1].
I haven't done much with autopkgtests yet and hoped that someone could
take a look at the change I made to exit non-zero if the comparisons
fail.  This seems like what we want to happen, but I wasn't sure.

I tested by running autopkgtest with a good build and a "bad" build (by
altering one of the expected summary output files) and I think it works
as expected.

If it looks okay, I can take care of the team upload.

Cheers,
tony

[1] https://salsa.debian.org/med-team/fastqc/-/merge_requests/1
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