[MOBY-dev] java api

Thu Feb 17 15:34:50 UTC 2005

No, the API I wrote is 100% java :p, the Python API was the model on which
I based the development.

> It's great to see all of this code coming out, who new there were so
> many Java MOBY developers! :-)
>
> We should really think about how to consolidate the best parts of the
> everyone's code into a cohesive object hierarchy.  This can be a bit
> tricky, since it's easy to feel insulted because some great code you
> wrote doesn't make it into the amalgam.  In practice, current coders
> will probably continue to use the classes they have already developed,
> since they've build other code around it, so the amalgam is more for the
> benefit of new Java coders.  I'm volunteering myself to take some of Ben
> and Eddie's PIB and RDF type-checking code and fold it into the existing
> MobyDataSimpleInstance.
>
> Yan, I haven't looked thoroughly, does your Java code use Jython to
> access your underlying Python implementation of the API?
>
> Simon, what data instance classes are you planning on using for the Axis
> streamlining?
>
>>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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>>>
>>>
>>
>>
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