Control: tag -1 upstream Control: forwarded -1 https://github.com/bioperl/Bio-DB-NCBIHelper/issues/6
Hi Aaron,
I have been looking in the issue below in the package
libbio-db-ncbihelper-perl. If I understood correctly, the main
point of the package is to rely on resources made available on
the Internet.
On Sun, 21 Feb 2021 14:05:39 +0100 gregor herrmann <gre...@debian.org> wrote:
> not ok 44
>
> # Failed test at t/Taxonomy.t line 102.
> # got: 'Actinomycetia'
> # expected: 'Actinobacteria'
For reference, I see along those lines:
101 ok $n = $db->get_Taxonomy_Node('1760');
102 is $n->scientific_name, 'Actinobacteria';
I would think the test 44 in t/Taxonomy.t is fooled following an
update in the resource the package fetches on the Internet
(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi if I
trust the package description). Hence I would be tempted to
think the kind of bacteria is not necessarily that important,
but that a character string could be fetched. But I'm not at
all a specialist of the field so prefer referring to your expert
view. (and I am also concerned that the previous tests rely on
a perhaps magic index to refer to human genome, but maybe it is
a "well known index".)
In any case, I though upstream would be interested, so I took
the liberty to open an issue in their VCS[0].
[0] https://github.com/bioperl/Bio-DB-NCBIHelper/issues/6
Gregor, Many Thanks for having spotted this in the first place!
As the purpose of the package is to fetch resources on the web,
I did something better described by the following commit[1].
[1]
https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/-/commit/bde35697e319417ae17367d51aaa868c43e1715d
It looked to me like the most sensible thing to do, since the
entire set of tests part of smoke are otherwise skipped.
I am not sure if there were more simple ways to approach that.
I am concerned that all test are skipped and considered valid.
Here is what I see if I smoke-env NO_NETWORK_TESTING=1:
autopkgtest [18:43:55]: test autodep8-perl-build-deps:
/usr/share/pkg-perl-autopkgtest/runner build-deps
autopkgtest [18:43:55]: test autodep8-perl-build-deps:
[-----------------------
t/EntrezGene.t ..... skipped: NO_NETWORK_TESTING
t/GenBank.t ........ skipped: NO_NETWORK_TESTING
t/GenPept.t ........ skipped: NO_NETWORK_TESTING
t/Query-Genbank.t .. skipped: NO_NETWORK_TESTING
t/RefSeq.t ......... skipped: NO_NETWORK_TESTING
t/Taxonomy.t ....... skipped: NO_NETWORK_TESTING
Files=6, Tests=0, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.07 cusr
0.00 csys = 0.09 CPU)
Result: NOTESTS
autopkgtest [18:43:55]: test autodep8-perl-build-deps:
-----------------------]
autopkgtest [18:43:55]: test autodep8-perl-build-deps: - - - - - - - -
- - results - - - - - - - - - -
autodep8-perl-build-deps PASS
I'm sorry, I'm not sure that was that much of a Low Hanging
Fruit, but that might do for this month's session hopefully. :)
Thanks for your thoughts,
--
Étienne Mollier <etienne.moll...@mailoo.org>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/8, please excuse my verbosity.
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