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Re: [Miase-discuss] Schema annotations
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From: Frank B. <fbergman@u.washington.edu> - 2009-02-17 16:42:51
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On Feb 17, 2009, at 5:18 AM, Dagmar Köhn wrote: > Did you consider the option of renaming the annotation and notes > element > to something else in SED-ML if we run into namespace conflicts? if renaming is to be done, i think it should be on the math-ML level. I consider notes and annotation for Sed-ML vital, but not at the math- ml level. That would limit all changes to the sbml-mathml.xsd file. Maybe Mike could chip in, how this feature is used in SBML. Frank > > > Dagmar > > > Frank Bergmann wrote: >> Personally I don't mind, as I would not consume the schema as such. >> Though >> your concerns are valid at which point would we stop adding non- >> critical >> elements. For the problem at hand it might make more sense to take >> 'notes' >> and 'annotation' out from the sbml-math schema. I would prefer to >> have the >> sed-ml file annotated, rather than the math-ml ... >> >> If that won't work, perhaps you could keep the JAXB annotations >> separate >> from the miase schema in jlibsedml, perhaps having your ant script >> merge the >> two. >> >> What do you think? >> >> Best >> Frank >> >> >>> -----Original Message----- >>> From: Richard Adams [mailto:ra...@st...] >>> Sent: Monday, February 16, 2009 8:08 AM >>> To: mia...@li... >>> Subject: [Miase-discuss] Schema annotations >>> >>> >>> Sorry, probably didn't explain very well - the .xsd schema >>> definition >>> allows application specific annotations. The changes to the schema >>> I'm >>> proposing would >>> not be included in .miase files, but in the schema itself, inside >>> the >>> notes and annotation element definitions. >>> >>> The problem arises, as JAXB comes across 'notes' and 'annotation' >>> defined in both sbml-mathml and sedml schemas. When generating >>> classes >>> from the schema, it gets confused as it attempts to create classes >>> of >>> the same name twice. To prevent this happening, you can add a >>> processing instruction in the notes element declaration in the sedml >>> schema, saying 'don't create another notes class for this notes >>> element, create a class called 'SedmlNotes instead'. >>> >>> Just looking through the JAXB docs, there doesn't seem to be an >>> obvious solution readily available, e.g., to make the classes in two >>> different packages, >>> which would prevent the need for these annotations. >>> >>> Basically, there are a quite a lot of processing instructions which >>> could be included, for example, specifying java collection classes, >>> method names, class names, javadoc. Some of these, but not all, >>> can be >>> put in an external file, called a binding file, so I'm just thinking >>> that these schema annotations could pollute the schema definition >>> somewhat. >>> >>> Cheers >>> Richard >>> >>> >>> >>> >>>> I'm sorry, i don't quite see the issue ... the schema right now >>>> says >>>> that you are free to put under the annotation element pretty much >>>> anything, and as far as MIASE goes, it will be ignored. The same >>>> goes >>>> for the notes section. >>>> >>>> i've never used jaxb so I'm not sure what the issues are. Could you >>>> explain further? >>>> >>> best >>> Frank >>> >>> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: >>> >>> >>>> Hi all, >>>> Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> >>>> elements >>>> into a schema for tool-specific customization of schema processing. >>>> Is this tolerable in the sed-ml schema, or would it clutter up the >>>> schema too much? >>>> >>>> Just wondered as Dagmar's last change ( to add the notes/annotation >>>> elements) causes a namespace conflict to the JAXB schema parser >>>> with >>>> the elements of the same name defined in sbml-mathml. One way round >>>> this is to add this jaxb specific annotations in the .xsd file to >>>> produce classes with different names. An alternative is to specify >>>> instructions in a separate 'binding' file, this would be ideal but >>>> I've not got it to work yet. >>>> >>>> Basically it would add: >>>> >>>> <xs:annotation> >>>> <xs:appinfo> >>>> <jxb:class name="SedMLNotes"> >>>> </jxb:class> >>>> </xs:appinfo> >>>> >>> -- >>> Dr Richard Adams >>> Senior Software Developer, >>> Computational Systems Biology Group, >>> University of Edinburgh >>> Tel: 0131 650 8281/8285 >>> email : ric...@ed... >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> >>> >>> ----------------------------------------------------------------------- >>> ------- >>> Open Source Business Conference (OSBC), March 24-25, 2009, San >>> Francisco, CA >>> -OSBC tackles the biggest issue in open source: Open Sourcing the >>> Enterprise >>> -Strategies to boost innovation and cut costs with open source >>> participation >>> -Receive a $600 discount off the registration fee with the source >>> code: >>> SFAD >>> http://p.sf.net/sfu/XcvMzF8H >>> _______________________________________________ >>> Miase-discuss mailing list >>> Mia...@li... >>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> Open Source Business Conference (OSBC), March 24-25, 2009, San >> Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source >> code: SFAD >> http://p.sf.net/sfu/XcvMzF8H >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss >> > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
