[MOBY-dev] a question and a comment about the new Objectinheritance

Thu May 26 11:35:17 UTC 2005

Hi Yan,

  You make many good points (despite your anti-Java vibe!).  The reason 
that we suggest keeping the primitives in their somewhat strange 
location within the object ontology is to provide the opportunity for 
low level services to be discovered in the same manner as all the other 
services.  For example, say we want to post a service that does 
arithmetic operations or String concatenations or something.  If we use 
the suggested approach, such services can be discovered using exactly 
the same mechanism that all other services can be discovered.  If on 
the other hand we completely separate these primitives from the 
ontology,  we will have to invent new discovery protocols for handling 
this use case.

  You are right, this is a strange beast of an ontology.  Its principal 
purpose is to describe the nature of being a data-type.  As such, 
including descriptions of what it means to be a primitive piece of a 
data-type does not seem wrong.  I think that when we start using a more 
typical ontology in addition to this one, whose purpose is to describe 
the nature of the information represented by these data-types, the 
distinction will be more clear and the real utility of the Object 
ontology will be made less ambiguous.

-Ben

On May 26, 2005, at 4:19 AM, Yan Wong wrote:

> mark wilkinson wrote:
>
>> Good idea!
>> The reason they weren't implemented initially was simple lack of need.
>>
>> M
>>
>> -----Original Message-----
>> From: Benjamin Good <bmg at sfu.ca>
>> Date: Wed, 25 May 2005 21:03:12 To:Core developer announcements 
>> <moby-dev at portal.open-bio.org>,       markw at illuminae.com
>> Cc:mobydev <moby-dev at biomoby.org>
>> Subject: Re: [MOBY-dev] a question and a comment about the new Object
>> 	inheritance
>>
>> It might actually make sense to implement a few more primitives to 
>> facilitate WSDL interoperability.  Below see a set of standard 
>> primitives from the Axis user-guide.  (Primitives being the things in 
>> the xml message that easily bind to existing Java classes).  I wasn't 
>> around when you picked the ones you did, so maybe there are reasons 
>> not to include all of these?
>>
>> Standard mappings from WSDL to Java
>> xsd:base64Binary -> byte[]
>> xsd:boolean -> boolean
>> xsd:byte -> byte
>> xsd:dateTime -> java.util.Calendar
>> xsd:decimal -> java.math.BigDecimal
>> xsd:double -> double
>> xsd:float -> float
>> xsd:hexBinary -> byte[]
>> xsd:int -> int
>> xsd:integer -> java.math.BigInteger
>> xsd:long -> long
>> xsd:QName -> javax.xml.namespace.QName
>> xsd:short -> short
>> xsd:string -> java.lang.String
>>
>> -ben
>>
>>
>>
>> On May 25, 2005, at 12:32 PM, Mark Wilkinson wrote:
>>
>>
>>> Hi all,
>>>
>>> So, I just went through and updated all of my services to follow the 
>>> new
>>> Object inheritance system. It took 5 minutes :-)  Turns out that 
>>> most of
>>> my services only output "Object" anyway, so they don't need any work,
>>> and the ones that output other things like DNASequence and GO_Term 
>>> were
>>> already following the proposed API anyway, so... only TWO of my 
>>> services
>>> actually were affected by the proposed change!  I hope that others 
>>> have
>>> the same experience.
>>>
>>> I did, however, notice a potential hiccup that we didn't foresee at 
>>> the
>>> meeting.  At the moment, binary data in MOBY is passed as a child of
>>> base-64-encoded, which is a child of String.  Under the new system, 
>>> we
>>> can't have children of String, so do we then need a new primitive 
>>> class
>>> for binary data?  I think it still needs to be b64 encoded, but it 
>>> seems
>>> to me that it does need its own primitive now.
>>>
>>> opinions anyone?
>>>
>>> M
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at biomoby.org
>>> http://www.biomoby.org/mailman/listinfo/moby-dev
>>>
>>>
>>>
>> http://bioinfo.icapture.ubc.ca/bgood
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>>
>> --
>> Mark Wilkinson
>> ...on the road!
>> _______________________________________________
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>>
>>
> Some remarks about Primitives and ontology:
>
> First: Do you think that <Integer>FF</Integer> is an integer???
>
> If you say no, then you are wrong because FF is a valid hexadecimal 
> REPRESENTATION of an integer number: 255
>
> Reason: The client give the meaning for a message. Forany ordinary 
> human who achieved child school FF is not an integer but for a 
> computer IT CAN BE!  Of course it is a bit extreme as an example. We 
> all agree, by convention, that integers are written with Arab figures.
>
> In France (I don't know how it is in the rest of Europe) floating 
> numbers are described as 3,1415 instead of 3.1415 (comma instead of 
> point)  In this case also, we agree by convention, that floating 
> numbers use the american representation (integer part point fractional 
> part etc..)
>
> Did you know that a Unicode string was inherited from a string ??? to 
> display exotic but useful characters that does not exist in English (I 
> don't speak of the strange french characters but also for spanish 
> german etc..)!) and why not Bytes ??? after all a string is an array 
> of bytes so bytes should be the actual primitive (String is an object 
> has Byte)  etc.. etc.. In java by default, all strings are unicode 
> strings (AFAIK) but not all language adopted this convention.
>
> Primitives are computer related problems. I don't think it is wise to 
> implement primitives inside the ontology because it is not in its 
> place!
>
> Primitives were intended to solve problems of performance in language 
> like Java (just see the superb mess between an Integer and an int both 
> speaks about the same mathematical object everybody knows BUT for 
> performance issues, it has been implemented this way poisoning life of 
> millions software enginner and writers - you don't find that kind of 
> issue in other languages -)
>
> As I understand from Moby and the ontology of Moby, we should not mix 
> computer related problems with "Business logic"  related problems.
>
> did you know that in ADA (for strict type checking and overflow 
> control) you can actually subclass an integer in order to define the 
> precision you want in your numbers and it doesn't violate (in any 
> case) the object programming paragdim.
>
> For example:
>
> subtype Natural is Integer range 0.. Integer'Last;
> subtype Positive is Integer range 1.. Integer'Last;
> (I hope no one will have a heart attack on seeing these two lines :p)
>
> So if you want to know if an Integer is an integer CAST it (that what 
> I do in Python (for the object mapping with bioMoby XML) ) for example 
> with java use Integer.parse(etc) for Python use int(string) etc.. 
> etc..
>
> These instructions tells the program that the content of the XML is an 
> integer (according to your language convention)
>
> I think I have been clear and hope I didn't bash anyone too hard :p
>
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>
>
http://bioinfo.icapture.ubc.ca/bgood