Re: [Nexml-discuss] [OpenTree-software] id attribute syntax

[Jonathan A R. <re...@mu...>]

Hmm... I am having trouble now finding an opentree nexml file with a
numeric id attribute, so perhaps this is all moot. I think I may have been
confused by the way tree ids are processed elsewhere in the system (i.e.
the bug may be elsewhere). If I find one then I'll report it on the peyotl
repo.

I ran the validator (Jeet's version) on pg_109.nexml and got a couple of
diagnostics which I'll report separately. (It took a very long time to
start up - probably because W3C hates to serve up schema files? which it
rightly thinks people ought to cache/"install".)

Jonathan

On Tue, Sep 30, 2014 at 3:15 PM, Mark Holder <mth...@gm...> wrote:

> There was a thread [1] that I think is related to this.
>
> In an attempt to make sure that open tree tools were getting most of
> the info in the right spots in NeXML, I loosened the schema in a few
> spots (in an attempt to get the treebase nexml to validate see [2]).
> My roundtrip tests (in peyotl) use a fork of the schema[3]. Clearly
> that is not optimal, and it would be good to be using official schema.
>
> cheers,
> Mark
>
>
> [1]
> http://sourceforge.net/p/nexml/mailman/nexml-discuss/thread/CAB2isBT1paiV9r%2BsVhdDMxNrxfP_fNZ%2B%2BnOvfQ%2BH4i12zhobjg%40mail.gmail.com/#msg31798831
>
> [2]
> http://sourceforge.net/p/nexml/mailman/nexml-discuss/thread/CAB2isBR5DB0d8-rn8cvJVNB-a0aK9xg6u9BVjYA7tJnbZhEXLQ%40mail.gmail.com/#msg31808808
>
> [3] https://github.com/mtholder/nexml
>
> On Tue, Sep 30, 2014 at 6:49 PM, Jim Balhoff <ba...@ne...> wrote:
> > Yes, that's right, IDs can't start with digits. Many of the Phenoscape
> files do still contain such IDs, because I haven't done a mass migration
> since I updated this in Phenex.
> >
> > - Jim
> >
> >
> > On Sep 30, 2014, at 12:20 PM, Hilmar Lapp <hl...@ne...> wrote:
> >
> >> FYI. I believe we did encounter the no-leading-digit issue with IDs in
> Phenex and had to fix it (Jim?).
> >>
> >>    -hilmar
> >>
> >> ---------- Forwarded message ----------
> >> From: Jonathan A Rees <re...@mu...>
> >> Date: Tue, Sep 30, 2014 at 11:15 AM
> >> Subject: [OpenTree-software] id attribute syntax
> >> To: "ope...@go..." <
> ope...@go...>
> >>
> >>
> >> Have our nexml files passed the nexml validator? If so I think there's
> a bug in the nexml validator.
> >>
> >> If I follow the convoluted documentation chain correctly, a nexml 'id'
> attribute has syntax and semantics inherited from XML schema's xs:id, and
> xs:id has syntax coming from XML's xml:id:
> >>
> >> https://github.com/nexml/nexml/blob/master/xsd/external/xml.xsd
> >> http://www.w3.org/TR/2004/REC-xmlschema-2-20041028/datatypes.html#ID
> >> http://www.w3.org/TR/2000/WD-xml-2e-20000814#NT-TokenizedType
> >>
> >> Members of the value space have to match the 'Name' production:
> >>
> >> http://www.w3.org/TR/2000/WD-xml-2e-20000814#NT-Name
> >> Name     ::=          (Letter | '_' | ':') ( NameChar)*
> >>
> >> A lot of our ids begin with digits, which are disallowed. If this isn't
> being caught by the nexml validator, then there is a bug in the nexml
> validator.
> >>
> >> If I'm right then
> >> - a validator bug should be reported
> >> - when converting from nexson to nexml, an underscore should be
> prepended if the first character is a digit (applies to all attributes with
> id values, such as @source)
> >>
> >> If someone (Mark?) can confirm this I'll file the two issues.
> >>
> >> --
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> >>
> >>
> >> --
> >> Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
> >>
> >
> >
> >
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>
> --
> Mark Holder
>
> mth...@gm...
> mth...@ku...
> http://phylo.bio.ku.edu/mark-holder
>
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