[MOBY-dev] java api

[ywong at infobiogen.fr]

Hi,
  No, unlike Python, I can't generate on the fly classes so the MobyObject
class is generic, it describes an Moby XML object as a class with
attributes:

  -prefix (default is moby, for XML serialization)
  -tag (for the XML serialization and specify what kind of Moby object it is)
  -namespace (Moby namespace eg AGI_LocusCode)
  -id (object identifier)
  -articleName (name of this object)
  -other moby objects (described in the ontology)
  -a raw content (the serializer only require this object to have a
toString method)

To determine what kind of object it is, I just look at the tag property
with a getTag method.

It is possible to build a specific object from this one using inheritance.

This structure should be enough exhaustive to describe all possible Moby
objects:

    <Object1 namespace="aNamespace" id="anId">
        <Object2 articleName="something">
            <Object3 articleName="A">
                   <Xref .../>
                   <Xref ...>Description</Xref>
                   RAW CONTENT for Object with article Name A
            </Object3>
        </Object2>
        <Object4 namespace="aNamespace" id="anId"/>
        RAW Content for Object 1
    </Object1>

Just have a look at the MobyObject class and the example MobyWebservice
(the method getRandomDNASequence return a DNA sequence object).

Yan

> What about accessing the rest of the contents of the data in a MobyData
> block (ie the primitive values)?
>
> -Ben
>
> Octave Noubibou wrote:
>
>> Hi all,
>>
>> as Yan has mentioned, i have joined  the PlaNet  project  at MIPS
>> since  3  months  now. one of my first tasks was to provide a generic
>> API to  simplify access to the pameters (queryID, namespace, id)
>> one needs from the moby input xml to run the services and also methods
>> to generate moby conform xml result.
>>
>> I have used DOM4J and XPATH to implement concrete classes for this
>> purpose.
>> At the moment all you need to get your parameters is to use the method
>> "allParsedData(inputxml)" no matter how complex the inputxml is.
>> This method return a vector of the form e.g.:
>>
>> (((queryID1,ns,id))) for a simple type
>>
>> or (((queryID1,ns1,id1),(queryID1,ns2,id2),(queryID1,ns3,id3))) for a
>> collection
>>
>> or
>> (((queryID1,ns,id),(queryID1,ns,id),(queryID1,ns,id)),((queryID2,ns1,id1)))
>> for an input with 2 invocations, the first been a collection and the
>> second a simple type.
>>
>> currently i do not handle secondary articles, but this should not be
>> difficult.
>>
>> we habe tried in our java services and everything seems to be ok.
>>
>> i am commenting the code now. once it is finished, i will like to
>> share it with you for comment or rectification and of course use.
>> Is there any possibility to upload this in central repository?
>>
>> best regards
>>
>> octave
>>
>>>
>>>
>>> Hi,
>>>  I know that someone at mips (Octave Noubibou) is also working on that
>>> field, on my side, I have an API in Java (based on the Python API) that
>>> helps me to build moby webservices (with axis or j2ee)
>>>
>>>
>>>>> Hi Mark,
>>>>>
>>>>> I'll see how things are looking and get the documentation together.
>>>>> The
>>>>> basic goal was to create some basic classes to simplify access to the
>>>>> MOBY payload of a webservice call so that we could concentrate on
>>>>> getting the services up rather than parsing the MOBY XML and
>>>>> rewriting
>>>>> the XML prior to returning the result. We've been using Axis to
>>>>> handle
>>>>> the webservice part of the equation, we've created some core classes
>>>>> and have a simple test service prototype that we are gearing up to do
>>>>> something meaningful with. If you have people doing similar things it
>>>>> would be great to get an overview of what you are working on too so
>>>>> we
>>>>> can divide and conquer where possible.
>>>>>
>>>>> Simon.
>>>>>
>>>>>
>>>>> On Feb 14, 2005, at 10:04 PM, mwilkinson wrote:
>>>>>
>>
>> _______________________________________________
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>>
>>
>
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