[Bioperl-l] Bio::Root::RootI->throw($msg,$class) overloading?
Chris Fields
cjfields at uiuc.edu
Wed Jul 12 19:23:33 UTC 2006
Thanks Steve!
Chris
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Steve_Chervitz
> Sent: Wednesday, July 12, 2006 1:53 PM
> To: Chris Fields
> Cc: Rutger Vos; Bioperl List
> Subject: Re: [Bioperl-l] Bio::Root::RootI->throw($msg,$class) overloading?
>
> For modules that derive from Bio::Root::Root, there's no need to
> import Bio::Root::Exception since the Root object does it.
>
> I also favor adding the -class parameter to throw_not_implemented in
> RootI. I just committed this change in in bioperl-live. I also added
> a test for it in t/RootI.t
>
> I haven't run the complete suite of tests after making this change,
> but I don't suspect there'll be any trouble (famous last words).
> Really, if any test leads to the calling of throw_not_implemented
> (besides the test I just added), that in itself is trouble.
>
> Steve
>
> On Jul 11, 2006, at 8:27 PM, Chris Fields wrote:
>
> > Makes sense to keep most of the magic in Root instead of RootI.pm.
> > The POD for RootI does state that the class exception thrown is
> > Bio::Root::NotImplemented, so we should probably either change the
> > POD to reflect what really happens or change throw_not_implemented
> > like you suggest (my vote is the latter). I don't think many (if
> > any) implementing classes fall into your 'trouble' category, though I
> > can't be sure how many actually import Bio::Root::Exception.
> >
> > Chris
> >
> > On Jul 11, 2006, at 8:07 PM, Steve_Chervitz wrote:
> >
> >> On Jul 11, 2006, at 1:42 PM, Chris Fields wrote:
> >>
> >>> Bio::Root::Root doesn't overload throw_not_implemented from
> >>> Bio::Root::RootI; from the comments looks like Steve C and Ewan B
> >>> couldn't
> >>> work out some of the Error.pm issues.
> >>
> >> The issue (I believe) was that
> >> Bio::Root::RootI::throw_not_implemented was doing some checking for
> >> the presence of Error.pm and calling Error::throw. I changed it so
> >> that this fanciness only happens in Root.pm.
> >>
> >>> Judging by the POD for Bio::Root::RootI, throw_not_implemented
> >>> doesn't
> >>> accept arguments; it throws a Bio::Root::NotImplemented exception
> >>> automatically.
> >>
> >> Looking at the code now, throw_not_implemented() does not throw a
> >> Bio::Root::NotImplemented exception. It just throws a simple,
> >> unclassed message. We could allow it to throw an exception of class
> >> Bio::Root:NotImplemented by changing this code:
> >>
> >> if( $self->can('throw') ) {
> >> $self->throw($message);
> >> }...
> >>
> >> to this
> >>
> >> if( $self->can('throw') ) {
> >> $self->throw(-text=>$message, -
> >> class=>'Bio::Root::NotImplemented');
> >> }...
> >>
> >> This does not create any dependency on Error.pm, but permits it to
> >> be used if available. If Error.pm is not loaded, the only change is
> >> that the class string is included in the error message, which is
> >> kind of handy.
> >>
> >> Trouble would occur if the implementing class:
> >>
> >> * does not derive from Bio::Root::Root,
> >> * does not import Bio::Root::Exception,
> >> * fails to implement a method which gets called, and
> >> * Error.pm is available.
> >>
> >> I don't know if such implementations exist in bioperl now, but I
> >> suspect they would be rare (and discouraged).
> >>
> >> Steve
> >>
> >>
> >>> Chris
> >>>
> >>>> -----Original Message-----
> >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>> bounces at lists.open-bio.org] On Behalf Of Rutger Vos
> >>>> Sent: Tuesday, July 11, 2006 1:58 PM
> >>>> To: Chris Fields
> >>>> Cc: 'Bioperl List'
> >>>> Subject: Re: [Bioperl-l] Bio::Root::RootI->throw($msg,$class)
> >>>> overloading?
> >>>>
> >>>> I must have overlooked this. I think it does what I want. So
> >>>> could I do
> >>>> something like:
> >>>>
> >>>> $obj->thow_not_implemented( -class =>
> >>>> 'Bio::Root::NotImplemented' );
> >>>>
> >>>> ...in interfaces?
> >>>>
> >>>> Chris Fields wrote:
> >>>>> I suppose you could; Bio::Root::Root does that using Error.pm
> >>>>> (if it
> >>>>> is installed). It almost sounds like what Bio::Root::Root does is
> >>>>> what you want, but you want a little more information when
> >>>>> exceptions
> >>>>> are thrown maybe?
> >>>>>
> >>>>> from perldoc Bio::Root::Root:
> >>>>>
> >>>>> ...
> >>>>> # Alternatively, using the new typed exception syntax in
> >>>>> the throw() call:
> >>>>>
> >>>>> $obj->throw( -class => 'Bio::Root::BadParameter',
> >>>>> -text => "Can not open file $file",
> >>>>> -value => $file);
> >>>>> ...
> >>>>>
> >>>>> Typed Exception Syntax
> >>>>>
> >>>>> The typed exception syntax of throw() has the advantage of
> >>>>> plainly
> >>>>> indicating the nature of the trouble, since the name of
> >>>>> the
> >>>>> class is
> >>>>> included in the title of the exception output.
> >>>>>
> >>>>> To take advantage of this capability, you must specify
> >>>>> arguments as
> >>>>> named parameters in the throw() call. Here are the
> >>>>> parameters:
> >>>>>
> >>>>> -class
> >>>>> name of the class of the exception. This should be
> >>>>> one
> >>>>> of the
> >>>>> classes defined in Bio::Root::Exception, or a custom
> >>>>> error of yours
> >>>>> that extends one of the exceptions defined in
> >>>>> Bio::Root::Exception.
> >>>>>
> >>>>> -text
> >>>>> a sensible message for the exception
> >>>>>
> >>>>> -value
> >>>>> the value causing the exception or $!, if appropriate.
> >>>>>
> >>>>> Note that Bio::Root::Exception does not need to be
> >>>>> imported
> >>>>> into your
> >>>>> module (or script) namespace in order to throw
> >>>>> exceptions via
> >>>>> Bio::Root::Root::throw(), since Bio::Root::Root imports
> >>>>> it.
> >>>>>
> >>>>>
> >>>>> Chris
> >>>>>
> >>>>> On Jul 11, 2006, at 3:58 AM, Rutger Vos wrote:
> >>>>>
> >>>>>
> >>>>>> Dear all,
> >>>>>>
> >>>>>> would it be possible to overload Bio::Root::RootI's 'throw'
> >>>>>> method to
> >>>>>> accept an additional, optional (positional) argument to define
> >>>>>> the
> >>>>>> exception class, e.g. using Exception::Class:
> >>>>>>
> >>>>>> # ...somewhere ...
> >>>>>>
> >>>>>> sub makefh {
> >>>>>> my ( $self, $filename ) = @_;
> >>>>>> open my $fh, '<' $filename or $self->throw("Can't open
> >>>>>> file: $!",
> >>>>>> 'Bio::Exceptions::FileIO'); # NOTE second argument
> >>>>>> return $fh;
> >>>>>> }
> >>>>>>
> >>>>>> #.... somewhere else
> >>>>>> my $fh;
> >>>>>> eval {
> >>>>>> $fh = $obj->makefh( 'data.txt');
> >>>>>> }
> >>>>>> if ( $@ and $@->isa('Bio::Exceptions::FileIO') ) {
> >>>>>> # something's wrong with the file?
> >>>>>> }
> >>>>>>
> >>>>>> --
> >>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>>> Rutger Vos, PhD. candidate
> >>>>>> Department of Biological Sciences
> >>>>>> Simon Fraser University
> >>>>>> 8888 University Drive
> >>>>>> Burnaby, BC, V5A1S6
> >>>>>> Phone: 604-291-5625
> >>>>>> Fax: 604-291-3496
> >>>>>> Personal site: http://www.sfu.ca/~rvosa
> >>>>>> FAB* lab: http://www.sfu.ca/~fabstar
> >>>>>> Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
> >>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioperl-l mailing list
> >>>>>> Bioperl-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>
> >>>>>
> >>>>> Christopher Fields
> >>>>> Postdoctoral Researcher
> >>>>> Lab of Dr. Robert Switzer
> >>>>> Dept of Biochemistry
> >>>>> University of Illinois Urbana-Champaign
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioperl-l mailing list
> >>>>> Bioperl-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>> Rutger Vos, PhD. candidate
> >>>> Department of Biological Sciences
> >>>> Simon Fraser University
> >>>> 8888 University Drive
> >>>> Burnaby, BC, V5A1S6
> >>>> Phone: 604-291-5625
> >>>> Fax: 604-291-3496
> >>>> Personal site: http://www.sfu.ca/~rvosa
> >>>> FAB* lab: http://www.sfu.ca/~fabstar
> >>>> Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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