Menu
▾
▴
sed-ml-discuss
|
From: Richard A. <ra...@st...> - 2009-02-14 23:04:01
|
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>
</xs:annotation>
into the 'notes' definition and similarly into the 'annotation' definition.
I have a feeling that this will be frowned upon but I just wanted to
make sure before ruling it out :)
Thanks
Richard
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
|
|
From: Richard A. <ra...@st...> - 2009-02-16 16:44:02
|
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. |
|
From: Richard A. <ra...@st...> - 2009-02-16 21:25:24
|
Hi all, There is a skeletal validator for example sedml files available here : http://www.bioinformatics.ed.ac.uk:8080/SBSVisualWebApp/html/sedml/ based upon the current version 0 schema. It validates against the schema and highlights schema errors. It's pretty basic at present - no line numbers for XML well-formedness errors or 'semantic' errors - but the two example files in SVN pass OK. If you're preparing an example file, please give it a go, and let me know if it doesn't behave as expected. Richard 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. |
|
From: Richard A. <ra...@st...> - 2009-02-16 21:27:30
|
Hi all, There is a skeletal validator for example sedml files available here : http://www.bioinformatics.ed.ac.uk:8080/SBSVisualWebApp/html/sedml/ based upon the current version 0 schema. It validates against the schema and highlights schema errors. It's pretty basic at present - no line numbers for XML well-formedness errors or 'semantic' errors - but the two example files in SVN pass OK. If you're preparing an example file, please give it a go, and let me know if it doesn't behave as expected. Richard 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. |
|
From: Frank B. <fbergman@u.washington.edu> - 2009-02-17 00:09:10
|
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 |
|
From: Richard A. <ra...@st...> - 2009-02-17 11:21:22
|
Quoting Frank Bergmann <fbergman@u.washington.edu>: > 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. I think that could be the best all round solution for now, it keeps the main schema nice and clean - while 'notes' and 'annotation' may not be essential for the mathml elements it probably sets a bad precedent to start altering the schema to fit in with the whims of implementations. > Richard > 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 > > -- 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. |
|
From: Richard A. <ra...@st...> - 2009-02-17 11:21:25
|
Quoting Frank Bergmann <fbergman@u.washington.edu>: > 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. I think that could be the best all round solution for now, it keeps the main schema nice and clean - while 'notes' and 'annotation' may not be essential for the mathml elements it probably sets a bad precedent to start altering the schema to fit in with the whims of implementations. > Richard > 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 > > -- 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. |
|
From: Dagmar K. <da...@eb...> - 2009-02-17 13:18:38
|
Did you consider the option of renaming the annotation and notes element to something else in SED-ML if we run into namespace conflicts? 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 > |
|
From: Frank B. <fbergman@u.washington.edu> - 2009-02-17 16:42:51
|
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 |
|
From: Michael H. <mh...@ca...> - 2009-02-18 01:24:44
|
fbergman> if renaming is to be done, i think it should be
fbergman> on the math-ML level. I consider notes and
fbergman> annotation for Sed-ML vital, but not at the
fbergman> math- ml level. That would limit all changes to
fbergman> the sbml-mathml.xsd file. Maybe Mike could chip
fbergman> in, how this feature is used in SBML.
Hi,
Do I understand it correctly that the 'annotation' we are
talking about is the following in the sbml-mathml schema?:
<xs:complexType name="Annotation">
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attributeGroup ref="AnnotationAttributes"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
If so, then this is not something we have much control over
-- it's part of the definition of MathML 2.0 (it's not even
an SBML issue). The <annotation> and <annotation-xml>
constructs are involved in the definition of MathML's
<semantics> element.
At present, I don't think there is a lot of use of
<semantics> and its associated constructs in SBML software;
however, it *is* used by SBO, in the rate law MathML
expressions. It's pretty vital in that role. (Although,
now that I look at it, it doesn't seem that <annotation> and
<annotation-xml> per se are being used in the SBO terms I've
looked at, only <semantics>.)
I'm not sure what to suggest as far as the jaxb issue is
concerned. I haven't looked at the jaxb code, but it seems
strange that jaxb would not let a person specify some sort
of prefix at the software level, so that it can be told to
generate alternate names for chosen elements. One could
rename them to "mathml-annotation" or some such then.
MH
|
|
From: Frank B. <fbergman@u.washington.edu> - 2009-02-18 03:06:37
|
> > Do I understand it correctly that the 'annotation' we are > talking about is the following in the sbml-mathml schema?: > Yes I believe those were the lines. Though I'm not sure as to the precise error message. Richard could you post it? > > I'm not sure what to suggest as far as the jaxb issue is > concerned. I haven't looked at the jaxb code, but it seems > strange that jaxb would not let a person specify some sort > of prefix at the software level, so that it can be told to > generate alternate names for chosen elements. I agree there has to be a way this can be handled at the software level. If not it might be something to be taken up with the jaxb community :) ... For now however we have a working solution with keeping the processing instructions separate. Best Frank |
|
From: Richard A. <ra...@st...> - 2009-02-17 15:54:04
|
But the concept - of needing a human readable and machine readable exegesis of an element - is still needed. Possible 'note' could be replaced with 'comment'? Harder to think of a replacement for 'annotation'. Richard > Richard Adams wrote: >> >> Yes, that's another option, although using the same terms people >> are familiar with from sbml is probably desirable, and its up to >> the implementation to deal with it. > > True as well - although I thought actually that a disadvantage of > using "annotation" and "notes" was that it is too close to SBML - and > we definitely want other people to join as well, not only SBMLer ;-) > > The problem that I rather see is that it is hard to find appropriate > other terms... > > Oh, and can you try to answer to the list - I think only I got your > mail this time. I remember Nicolas had the same problem when using the > "reply" button, but can't remember how he solved it!? > Dagmar > >> >> >>> Did you consider the option of renaming the annotation and notes element >>> to something else in SED-ML if we run into namespace conflicts? >>> >>> 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 >>> >>> >> >> >> -- 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. |
|
From: Frank B. <fbergman@u.washington.edu> - 2009-02-15 02:33:56
|
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> > </xs:annotation> > into the 'notes' definition and similarly into the 'annotation' > definition. > > I have a feeling that this will be frowned upon but I just wanted to > make sure before ruling it out :) > > Thanks > Richard > > > -- > 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 |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X