[MOBY-dev] Registering a MOBY service

Javier de la Torre jatorre at gmail.com
Thu Sep 28 17:56:57 UTC 2006


Hi Martin,

Well if I can help a bit...

Martin is right and I think what you exposed is clear. Ampersand are
not allowed within xml documents and must be scaped. So when a client
comunicates with the moby registry if somehwere inside the message
there is an ampersand it will have to be scaped.

And pyBiomoby does it correctly by the way (I was wrong in my last
email). My service got registered correctly, and I suppose is
correctly inside the biomoby registry database.

But then when I connect to the registry, let say with dashboard and
try to retrieve the list of services, the registry takes the data from
its database (there is a database behind right?) and produces and XML
with the services registered. This XML is wrong, it does not scape the
ampersand and therefore is a wrong xml document/message. When
dashboard tries to open, the parser complains because it finds a
non-valid xml document and refuse to open it.

The conslussion. Because there is an ampersand in a service end point
in the registry right now registered, every message that includes this
service with the end point produces an invalid XML document.

Why is this urgent? Every user that dowloads, for example, dashboard,
and try to browse the registry will not be able to do it because
dashboard see that the messages coming from the registry are
malformed.
So, although is not dashboard issue, dashboard has become unusuable
because the registry is producing malformed xml.

Hope this helps.

Javier.


On 9/28/06, Martin Senger <martin.senger at gmail.com> wrote:
> > If I try to register a service in dashboard where I escape the &
>
>
> You are not supposed to escape anything. Whatever you put in the text field
> with the sevice URL, will be delivered, properly escaped, to the registry.
> So if you want to have an ampersand in the URL, you put there just
> ampersand. If you - from whatever reasons - want to have a strange UYL that
> contains something like:
>
>    http://what.com/strange?yes&amp;dear
>
> you put it there and it is again delivers properly to the registry (btw, as:
>
>    http://what.com/strange?yes&amp;amp;dear
>
> which is correct).
>
>
> > Anyways, if I register a service with &, a find service (using a perl
> > client)
> > returns &
>
>
> But it should not. It should return a valid XML string - and a string with a
> un-escaped ampersand is not a valid XML string. The rgistry should return
> &amp; instead.
>
>
> What am I missing?
>
>
> Perhaps someone else can enter this discussion and try to explain it better
> than I do. (Unless, of course, I am missing something). Or skype me... (user
> name 'thesengers').
>
> But the problem is important to be solved soon. I would say, it is utgent.
>
> Cheers,
> Martin
>
>
> --
> Martin Senger
>    email: martin.senger at gmail.com
>    skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>



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