[DAS2] Re: Apollo and DAS/2 priorities

[Allen Day]

Is the spec going to be in a stable state for the code sprint?  I'd like
to use this time to sync the server implementation with a stable version
of the spec.  It looks like there have been many substantial changes.

-Allen



On Sat, 28 Jan 2006, Andrew Dalke wrote:

> Nomi:
> >  the part i've
> > completed--loading features from das2xml and displaying them in
> > apollo--is definitely good in terms of bang for the buck, because you 
> > can
> > look at an IGB display and an apollo display of the same data and it's
> > clear that they match.
> 
> The das2xml for features has changed some, but not much.  Most
> changes are elsewhere.
> 
> > it's obviously important to get the GET requests working before we 
> > submit
> > the progress report; gregg and i hoping the updates to the GET spec 
> > will
> > be done very soon so that he can bring the server up to spec before the
> > code sprint, since we clearly need a current working server available
> > during the code sprint to use for testing.
> 
> I haven't changed the GET query parameters.  There might be some
> changes to the feature filters as it handles the "att" queries.
> Otherwise that's it.
> 
> I would like to make a semi-structural change.  I want to
> split the search interface from the list of features.  Right
> now we have
> 
>    /feature?filter=something
> 
> for searching and
> 
>    /feature/ABC123
> 
> for the actual feature.  The spec doesn't actually require that.
> It only says that features have URL and that there's some way
> to get to a URL for queries.
> 
> The SOURCE document contains a "SET" element which looks like
> 
>        <SET type="features" id="human/Fall_2005/features">
>            <FORMAT name="das2xml" mimetype="text/x-das-type+xml" />
>        </SET>
> 
> It says the DAS features are accessible through the URL
> "http://../Fall_2005/features".  It doesn't mean those features
> are located under that URL. This means we can have
> 
>    http://.../human/Fall_2005/features? -- the query interface
>    http://.../human/Fall_2005/feature/0001 -- a feature
> 
> I like this better because I've been confused on the
> differences between
> 
>    http://.../human/Fall_2005/features
> and
>    http://.../human/Fall_2005/features/
> 
> and between
> 
>    http://.../human/Fall_2005/features?exacttype=exon
> and
>    http://.../human/Fall_2005/features/?exacttype=exon
> 
> By separating the two there is no confusion.
> 
> Ditto for the "type" information.
> 
> > - gregg thinks the specs for source and type GETs are more stable than
> > the feature GETs, so i could start trying to get source & type.
> 
> They are more stable.  The sources and types only return a list
> of the available sources and types.  There is no other
> query interface (as yet?).
> 
> > - andrew, if you could give me an updated das2xml example of features, 
> > i
> > can make sure that my das2xml reader is up to spec (right now i'm using
> > das2xml from gregg's server, which is at least three months out of 
> > date).
> 
> Done.  See just sent email.
> 
> >   - read sequence from a das2xml file
> 
> The term "das2xml" is used in the spec as the "name" for
> various format types.  Against a "features" URL it returns a
> features document, against a "types" URL it returns types.
> 
> I think that's also the context in which you are using it,
> but I wasn't sure so decided to mention it.
> 
> 
> > i may start working on reading sequence from a das2xml file first, 
> > since
> > that's a necessary step in order to read it from a server anyway.
> 
> I don't have any sample sequence files.  Those are going to
> be in FASTA format.  There is a new query interface for this.  It
> will look something like
> 
>    .../residues/Chr4?range=300:500:-1
> 
> (for the RC of the given range).  This is different than the old
> spec which had something like
> 
>    .../residues/Chr4/300:500:-1
> 
> We discussed this in December and everyone (as I recall) was
> fine with the change.  That hasn't made it into the updated
> draft of the spec.  *sigh*
> 
> 					Andrew
> 					dalke at dalkescientific.com
> 
> _______________________________________________
> DAS2 mailing list
> DAS2 at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/das2
>