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It worked. :)
I was also trying to put some notes and i am not being able to. I used the
following command just after the setting the metaid:
model.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'>here is my
note</p></body>")
Do I need to do add anything more?
Thank you,
Rodrigo
On 20 March 2012 14:51, Frank T. Bergmann <fbergman@caltech.edu> wrote:
> You were almost there, it was just that the type of cvterm was not
> correctly set, please use:
>
> sbmlDoc = SBMLDocument(2, 3)
> model = sbmlDoc.createModel()
> model.setId("GTModel")
> model.setMetaId("metaId_GTModel")
>
>
> h = ModelHistory()
> c = ModelCreator()
> c.setFamilyName("Silva")
> c.setGivenName("Jose")
> h.addCreator(c)
>
> d = Date(2012,03,19,12,50,0,0,0,0)
> sga=h.setCreatedDate(d)
> sga=h.setModifiedDate(d)
> tt=model.unsetModelHistory()
> ee=model.setModelHistory(h)
>
> new_cvt = CVTerm()
> new_cvt.setQualifierType(BIOLOGICAL_QUALIFIER)
> new_cvt.setBiologicalQualifierType(BQB_IS)
> new_cvt.addResource("urn:miriam:taxonomy:634956")
> model.addCVTerm(new_cvt)
>
>
> best
> Frank
>
> On Mar 20, 2012, at 3:39 PM, Rodrigo Liberal wrote:
>
> > Hi Frank,
> >
> > I made the following changes, setting in the beginning the id and MetaId
> of
> > the model. However, the cvterm is still not being added.
> >
> > sbmlDoc = SBMLDocument(2, 3)
> > model = sbmlDoc.createModel()
> >
> > model.setId("GTModel")
> > model.setMetaId("metaId_GTModel")
> >
> >
> >
> > Thanks,
> > Rodrigo
> >
> > On 20 March 2012 14:24, Frank T. Bergmann <fbergman@caltech.edu> wrote:
> >
> >> Hello Rodrigo,
> >>
> >> you want to make sure that you always first set the metaId of all
> elements
> >> before using MIRIAM annotations such as ModelHistory or CVTerms.
> >>
> >> When you debug your code with model histories, you can always try and
> ask
> >> the object, whether it is complete, by calling
> >> modelHistory.hasRequiredAttributes() this is the reason that the model
> >> rejects the object. It is valid when you have at least one creator, and
> a
> >> modification and created date.
> >>
> >> So i think in your case, the model history is rejected, either because
> it
> >> does not have the modification date, or because the meta id on the
> model is
> >> missing.
> >>
> >> best
> >> Frank
> >>
> >>
> >>
> >> On Mar 20, 2012, at 3:03 PM, Rodrigo Liberal wrote:
> >>
> >>> Hi all,
> >>>
> >>> I have been having some problems working with modelHistory and
> cvterms. I
> >>> have used the following code:
> >>>
> >>>
> >>> 1 sbmlDoc = SBMLDocument(2, 3)
> >>>
> >>> 2 model = sbmlDoc.createModel()
> >>>
> >>>
> >>> 3 h = ModelHistory()
> >>>
> >>> 4 c = ModelCreator()
> >>>
> >>> 5 c.setFamilyName("Silva")
> >>>
> >>> 6 c.setGivenName("Jose")
> >>>
> >>> 7 h.addCreator(c)
> >>>
> >>>
> >>> 8 d = Date(2012,03,19,12,50,0,0,0,0)
> >>>
> >>> 9 sga=h.setCreatedDate(d)
> >>>
> >>>
> >>> 10 sga=h.setModifiedDate(d)
> >>>
> >>> 11 tt=model.unsetModelHistory()
> >>>
> >>> 12 ee=model.setModelHistory(h)
> >>>
> >>>
> >>> 13 new_cvt = CVTerm()
> >>>
> >>> 14 new_cvt.setQualifierType(0)
> >>>
> >>> 15 new_cvt.setBiologicalQualifierType(BQB_IS)
> >>>
> >>> 16 new_cvt.addResource("urn:miriam:taxonomy:634956")
> >>>
> >>> 17 model.addCVTerm(new_cvt)
> >>>
> >>>
> >>>
> >>> The 2 main problems are:
> >>>
> >>> - the line 17 command is always returning "-2". Which I believe it
> means
> >>> something is wrong.
> >>>
> >>> - when I comment line 10, the line 12 command returns "-5" which I
> >> believe
> >>> it means something is wrong. This second problem only appears when I
> >>> comment the line 10.
> >>>
> >>> Thanks ,
> >>>
> >>> Rodrigo
> >>> ____________________________________________________________
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> >>>
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> >>> http://sbml.org/Forums/
> >>>
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> >>> contact sbml-team@caltech.edu
> >>
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> >>
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> >>
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> >> contact sbml-team@caltech.edu
> >>
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> >
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> >
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> > contact sbml-team@caltech.edu
>
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>
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>
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> contact sbml-team@caltech.edu
>
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20 Mar '12 08:36
