[Bioperl-l] Bio::DB::GFF/Postgres test failures
Lincoln Stein
lincoln.stein at gmail.com
Sun Apr 10 21:10:24 UTC 2011
Hi Folks,
Is this what's blocking the netx bioperl release, or are there other
blockers?
I just released GBrowse 2.27, which requires bioperl 1.0069 or higher.
Lincoln
On Fri, Apr 8, 2011 at 8:53 PM, Chris Fields <cjfields at illinois.edu> wrote:
> That was introduced here by Florent:
>
>
> https://github.com/bioperl/bioperl-live/commit/6f65223ef5aabc3ceaa815d3cb71982f81ae6b30#t/LocalDB/SeqFeature.t
>
> So, essentially the MySQL adaptor is getting this wrong. Any way we can
> somehow enable strict mode?
>
> http://dev.mysql.com/doc/refman/5.0/en/server-sql-mode.html
>
> chris
>
> On Apr 8, 2011, at 4:32 PM, Scott Cain wrote:
>
> > Argh! MySQL is not a RDMS! Anyone who tells you otherwise is lying!
> >
> > The first test failure for the Pg SFS adaptor is failing because it is
> > trying to execute this query (which it inherited from the mysql
> > adaptor, where it works just fine):
> >
> > select id,object FROM bioperl_seqfeature_t_test_schema_feature where
> > id='doesnotexit';
> >
> > Of course, the id column is defined as an integer column. MySQL must
> > be silently casting this string to an integer value (? I guess
> > anyway--who knows). Anyway, PostgreSQL does the right thing and
> > throws an error with this query. I don't see how I can make the
> > Postgres adaptor pass this test as written, as it is nonsensical.
> >
> > Scott
> >
> >
> >
> > On Fri, Apr 8, 2011 at 2:56 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> >> Scott,
> >>
> >> I'll try documenting the Pg error for SF::Store in the next hour. Had
> my hands full with the GSoC onslaught of emails and local $job stuff. Would
> like to get it fixed for the CPAN release.
> >>
> >> chris
> >>
> >> On Apr 8, 2011, at 12:58 PM, Scott Cain wrote:
> >>
> >>> OK, I'll take it out and move on to the next problem.
> >>>
> >>> Thanks,
> >>> Scott
> >>>
> >>>
> >>> On Fri, Apr 8, 2011 at 1:51 PM, Lincoln Stein <lincoln.stein at gmail.com>
> wrote:
> >>>> Oh right. The Bio::DB::GFF adaptor has that broken behavior and it is
> too
> >>>> late to change it now. (Bio::DB::SeqFeature::Store had better not!)
> Best to
> >>>> remove the test altogether.
> >>>> Lincoln
> >>>>
> >>>> On Fri, Apr 8, 2011 at 1:18 PM, Scott Cain <scott at scottcain.net>
> wrote:
> >>>>>
> >>>>> Hi Lincoln,
> >>>>>
> >>>>> Yes, apparently, it does. It does this for both the memory and the
> >>>>> postgres adaptors. I looked at how the data was stored in the
> feature
> >>>>> object with Data::Dumper and that is how it is represented in the
> hash
> >>>>> too. Perhaps this test should be calling the "absolute" method
> first?
> >>>>>
> >>>>> Scott
> >>>>>
> >>>>>
> >>>>> On Fri, Apr 8, 2011 at 1:10 PM, Lincoln Stein <
> lincoln.stein at gmail.com>
> >>>>> wrote:
> >>>>>> Do start() and end() flip values for minus strand features? This
> isn't
> >>>>>> supposed to happen.
> >>>>>> Lincoln
> >>>>>>
> >>>>>> On Fri, Apr 8, 2011 at 11:41 AM, Scott Cain <scott at scottcain.net>
> wrote:
> >>>>>>>
> >>>>>>> Hi Lincoln,
> >>>>>>>
> >>>>>>> I've been looking into some test failures with the postgres adaptor
> >>>>>>> for Bio::DB::GFF and I wanted to check with you that I'm
> interpreting
> >>>>>>> this correctly. In t/LocalDB/BioDBGFF.t there are these lines:
> >>>>>>>
> >>>>>>> @features = sort {$a->start<=>$b->start} @features;
> >>>>>>>
> >>>>>>> is($features[0]->type,'Component:reference');
> >>>>>>> is($features[-1]->type,'exon:confirmed');
> >>>>>>>
> >>>>>>> So that the features in the data set are sorted by their start
> values
> >>>>>>> and the beginning and end of the list are checked. The test refers
> to
> >>>>>>> the test.gff data file, that contains among others these lines:
> >>>>>>>
> >>>>>>> Contig1 confirmed transcript 30001 31000 . - .
> >>>>>>> Transcript trans-2; Gene "xyz-2"; Note "Terribly interesting"
> >>>>>>> Contig1 confirmed exon 30001 30100 . - . Transcript
> >>>>>>> trans-2; Gene "abc-1"; Note "function unknown"
> >>>>>>> Contig1 confirmed exon 30701 30800 . - . Transcript
> >>>>>>> trans-2
> >>>>>>> Contig1 confirmed exon 30801 31000 . - . Transcript
> >>>>>>> trans-2
> >>>>>>>
> >>>>>>> Since this transcript and its exons are on the minus strand, the
> >>>>>>> values that the start and stop method return will be reversed, so
> that
> >>>>>>> start for the transcript will be 31000 and stop will be 30001. The
> >>>>>>> problem with this test is since the last exon and the transcript
> share
> >>>>>>> a start value (31000), you can't really be sure which one will be
> at
> >>>>>>> the bottom of the list after sorting, right? In the case of the
> >>>>>>> postgres adaptor, it fails this test on my machine because the
> >>>>>>> transcript is at the bottom of the list. The test for the
> beginning
> >>>>>>> of the list similarly could fail though it didn't in my case, as
> other
> >>>>>>> features that have 1 as a start are of type "Component:clone".
> >>>>>>>
> >>>>>>> So, my question is this: am I missing something, and the postgres
> >>>>>>> adaptor is not behaving as expected, or are these tests ambiguous?
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>> Scott
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>>
> ------------------------------------------------------------------------
> >>>>>>> Scott Cain, Ph. D. scott at
> scottcain
> >>>>>>> dot net
> >>>>>>> GMOD Coordinator (http://gmod.org/)
> 216-392-3087
> >>>>>>> Ontario Institute for Cancer Research
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Lincoln D. Stein
> >>>>>> Director, Informatics and Biocomputing Platform
> >>>>>> Ontario Institute for Cancer Research
> >>>>>> 101 College St., Suite 800
> >>>>>> Toronto, ON, Canada M5G0A3
> >>>>>> 416 673-8514
> >>>>>> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>>
> ------------------------------------------------------------------------
> >>>>> Scott Cain, Ph. D. scott at
> scottcain
> >>>>> dot net
> >>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
> >>>>> Ontario Institute for Cancer Research
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Lincoln D. Stein
> >>>> Director, Informatics and Biocomputing Platform
> >>>> Ontario Institute for Cancer Research
> >>>> 101 College St., Suite 800
> >>>> Toronto, ON, Canada M5G0A3
> >>>> 416 673-8514
> >>>> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>>
> ------------------------------------------------------------------------
> >>> Scott Cain, Ph. D. scott at scottcain
> dot net
> >>> GMOD Coordinator (http://gmod.org/) 216-392-3087
> >>> Ontario Institute for Cancer Research
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D. scott at scottcain
> dot net
> > GMOD Coordinator (http://gmod.org/) 216-392-3087
> > Ontario Institute for Cancer Research
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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