In 1.53, the method element's id attribute and CDATA were both optional.
This meant the following was legal (but clearly wrong!):
<METHOD />
Now in 1.6, the id attribute is required but tag content is optional:
<METHOD id="foo" />
<METHOD id="foo">bar</METHOD>
Likewise the TYPE element follows the same principle. IMO this is the
"correct" thing to do.
ProServer -currently- (i.e. 1.53) will copy the ID into the tag contents
if not provided explicitly, so the tag contents is always present:
<METHOD id="foo">foo</METHOD>
Most implementations don't bother to provide a separate "pretty" name
for the method, so look like this.
This is generally what clients would do anyway if they display the
method - i.e. if the server doesn't provide a human readable method (tag
content), the ID is used for display instead. But I have no qualms in
changing ProServer to obey the spirit of the spec more closely, if that
is seen as preferable.
Andy
Jonathan Warren wrote:
looking through the das sources and the 1.6 spec it looks like
duplication in the features method and type attributes and element
contents happens a lot. Have we got some usage where the attribute and
element are not just duplicated? would be good if anyone has any
examples of these being used properly...
<FEATURE id="rs1042011" label="rs1042011">
<TYPE id="nsSNP">nsSNP</TYPE>
<METHOD id="dbSNP">dbSNP</METHOD>
or in some cases completely ignored such as type:
<TYPE id=""></TYPE><START>3756</START><END>3756</END><METHOD
id="ssahaSNP">ssahaSNP</METHOD>
On 30 Mar 2009, at 14:47, Andy Jenkinson wrote:
Hi all,
As many of you will know, we plan to update the ageing 1.53 version of
the DAS specification currently available on the BioDAS website with
one that hopefully better reflects current usage of DAS. Most changes
are taken from the extensions defined in the extended 1.53E spec, but
with some differences and further additions.
We aim to formally release 1.6 at the end of June, but I have made
available the first draft:
http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html
The hope is that this will give software authors time to prepare, in
order to minimise the impact of the transition. Updated versions of
core client/server libraries (ProServer, Bio-Das-Lite, Dazzle,
Dasobert) will be made available in due course.
I am happy to gather feedback and engage in discussion about the
changes (I won't list them individually here). Especially helpful
would be amendments for sections of the document that would improve
clarity, examples etc. Note that this is still a draft however - in
particular, the structure and alignment commands may be "tidied up"
and the stylesheet glyphs section further fleshed out.
Cheers,
Andy
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