Re: [Miase-discuss] listOfModels query

[Dagmar K. <da...@eb...>]

Just to say that I agree with everything Frank wrote (hopefully I 
understood right what he meant ;-)).

Dagmar



Frank Bergmann wrote:
> Hello ... 
>
>   
>> Hi,
>>   Just a query about the listOfModels element - is it assumed to be
>> the case that, for a given sedml document, it will describe a single
>> 'reference' model version, which will be the first model in the list,
>> and subsequent entries in the list will refer to that base model,
>> applying changes (as is the case with the example 'oscillation to
>> chaos' model)? Or, is it possible that a given sedml document could
>> refer to >1 reference model?
>>     
>
> Definitely ... you can (and should be able to) refer to more than one model.
>
>
>   
>>   I'm asking from the point of view of how a self-contained .miase
>> archive file might look. (By self contained, I mean that the
>> application using it will be able to access all the information needed
>> to run a simulation without having to query repositories -  with the
>> help of a supporting library. ) In the first case above,  it would
>> only ever contain a single model file, in the second case, it could
>> contain multiple models.
>>     
>
> In my implementation, the self-contained .miase file, still has the option
> of referring to external sources. Thus There could be 0 or more models
> contained in the archive. 
>
>   
>> Also, do we want to allow archives which contain all model variants as
>> complete models, or are we going to stick with a 'reference' version
>> of the model, and generate new, altered versions of the model by
>> applying Xpath changes on the fly at runtime? I assume the latter, but
>> I can't find anything in the current examples, or in the CMSB2008.pdf
>> to distinguish between these possibilities.
>>
>>     
>
> I hoped to keep the .miase file as simple as possible. It really just
> provides the option of storing (locally) referenced files conveniently.
> Apart from that there should not be more logic needed to interpret a .miase
> file, as compared to the original experiment description. For that reason
> I'd opt of making the changes on the fly, they won't be expensive to do.
> While writing out you can opt to refer to the altered models if you so
> desire, however with that you loose the information, that the second model
> is actually the first model with a handful of changes ... 
>
>   
>>   From the point of view of supporting library methods, I was thinking
>> something along the lines of:
>>
>>   MiaseArchive archive = libSedml.readArchive(String
>> filepathToMiaseArchive);
>>
>>   // A MiaseArchive enables access to a sedml document, and model
>> file(s?)
>>   SedmlDocument document = archive.getSedMlDocument();
>>   // access Sedml DOM via
>>   document.getSedMlModel();
>>
>>   //access model file ( or is it possible to have > 1 model file
>> here??)
>>     
>
> YES it is ... :) ... 
>
>   
>>   // if the latter, need method to iterate over multiple model files.
>>    String referenceModelContents = archive.getModelAsString();
>>
>>    //now, get XPath change from SedML model and apply it
>>    ListOfChanges changes =
>> sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
>>    String alteredModelContents =
>> document.applyChanges(referenceModelContents,changes);
>>
>>     
>
> Instead of 
>
> 	document.applyChanges(referenceModelContents,changes);
>
> I'd prefer to just grab the changed model. That's what I did in my
> implementation, for a user there is hardly a difference on the two model
> types. Thy have the option of getting the model source from both, and in
> that case the changed model, applies the changes automatically. 
>
> Best
> Frank
>
>
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