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Re: [Miase-discuss] listOfModels query
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From: Frank B. <fbergman@u.washington.edu> - 2009-03-22 23:54:38
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> > Frank, so you mean something like: > > String sedMLDoc.getModel(String modelId); > Almost, while constructing models, you'd still want to deal with properties of changed model. Something like: changedModel = new Model(sourceModelReference); changedModel.AddChange(new ChangeAttribute(sbmlId, newValue)); but then you'd have: changedModel.ToSBML() / changedModel.ToCellML() / changedModel.ToModelString() which return you the actual model string. > which would hide all the need for getting XPath terms, and return > a String of the model? That would be more direct, for sure. If I'm consuming a Miase description, I'd definitely not be interested in the nitty-gritty of applying the Xpath queries, that's what the library should do. Cheers Frank > > Richard > > > 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 > >> > >> > >> -------------------------------------------------------------------- > ---------- > >> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) > are > >> powering Web 2.0 with engaging, cross-platform capabilities. Quickly > and > >> easily build your RIAs with Flex Builder, the Eclipse(TM)based > development > >> software that enables intelligent coding and step-through debugging. > >> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > >> _______________________________________________ > >> Miase-discuss mailing list > >> Mia...@li... > >> https://lists.sourceforge.net/lists/listinfo/miase-discuss > >> > > > > > > --------------------------------------------------------------------- > --------- > > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) > are > > powering Web 2.0 with engaging, cross-platform capabilities. Quickly > and > > easily build your RIAs with Flex Builder, the Eclipse(TM)based > development > > software that enables intelligent coding and step-through debugging. > > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > > _______________________________________________ > > Miase-discuss mailing list > > Mia...@li... > > https://lists.sourceforge.net/lists/listinfo/miase-discuss > > > > > > > > -- > Dr Richard Adams > Senior Software Developer, > Computational Systems Biology Group, > University of Edinburgh > Tel: 0131 650 8285 > email : ric...@ed... > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > ----------------------------------------------------------------------- > ------- > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly > and > easily build your RIAs with Flex Builder, the Eclipse(TM)based > development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
