[Bioperl-l] Bio::Root::RootI->throw($msg,$class) overloading?

Wed Jul 12 03:27:37 UTC 2006

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
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>> 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