[DAS2] Re: Apollo and DAS/2 priorities

[Helt,Gregg]

That would be great if you could update the biopackages server before
the code sprint starts!  Then client implementers will have a server to
test with.

	thanks,
	gregg

> -----Original Message-----
> From: das2-bounces at portal.open-bio.org
[mailto:das2-bounces at portal.open-
> bio.org] On Behalf Of Allen Day
> Sent: Wednesday, February 01, 2006 2:42 PM
> To: Andrew Dalke
> Cc: DAS/2
> Subject: Re: [DAS2] Re: Apollo and DAS/2 priorities
> 
> I just looked over your changes, and will begin making the changes to
the
> server repository today.
> 
> I'd like to update the server at das.biopackages.net with my changes
on
> Friday, unless there are objections.
> 
> I'll be taking notes along the way and will post to the list if
anything
> in your document is unclear to me.
> 
> At first glance, I agree -- the changes are minor.
> 
> -Allen
> 
> 
> On Mon, 30 Jan 2006, Andrew Dalke wrote:
> 
> > Allen:
> > > 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.
> >
> > I have just (within the last few minutes) completed the first draft
> > of the update of the spec.
> >
> > It's not in HTML - that calls for too much work for this stage.
> > It's text, in CVS under das/das2/new_spec.txt
> >
> > There are many parts which need clarification.  These are marked
> > with a "XXX" along with my comments.
> >
> > The RNC files are in
> >
> >    das/das2/scratch/*.rnc
> > along with some test XML files.  These XML files are not meant
> > to be realistic.  They are meant more to check edge cases.
> >
> > I do no think there are major changes to the spec.  Most of the
> > changes have actually trimmed things down, like getting rid of
> > the "properties" subtree and merging the different "sources"
requests
> > into a single document.
> >
> >
> > Here are the major interfaces
> >
> > $PREFIX/sequence - a "sources" request
> >    This is the top-level entry point to a DAS 2 server.  It returns
a
> >    list of the available genomic sequence and their versions.
> >    [sequence-namespace]
> >
> > $PREFIX/sequence/$SOURCE - a "source" request
> >    Returns the available versions of the given genomic sequence.
> >
> > $PREFIX/sequence/$SOURCE/$VERSION - a "versioned source" request
> >    Returns information about a given version of a genomic sequence.
> >    Clients may assume that the sequence and assembly are constant
for a
> >    given version of a source. Note that annotation data on a server
> >    with curational write-back support may change without changing
the
> >    version.
> >
> >
> > For a given version here are the sub-parts.  Note that I've gone
ahead
> > and split the query urls (segment, features and types each have
query
> > interfaces) from the base directory used as containers for the
segments,
> > features and types.
> >
> >   $VERSION/segments - the segments query URL; summarizes the
top-level
> >      segments in the data source
> >
> >   $VERSION/segment/$SEGMENT_ID - a segment query; used to get
detailed
> >      information about the identified segment
> >
> >   $VERSION/features - the feature filter query URL.  Features are
> >     locatable annotations or experimental results.  The feature
filter
> >     URL supports query parameters to select a subset of the features
> >     based on position, feature type and other properties.
> >
> >   $VERSION/feature/$FEATURE_ID - a feature query; used to get
detailed
> >      information about the identified feature
> >
> >   $VERSION/types - the types query URL which returns a list of all
> >     feature types.  Feature types include ontology and depiction
> >     details for all features of the given type.
> >
> >   $VERSION/type/$TYPE_ID - details about the specified feature type
> >
> > Oh, and there are internal conflicts which will be straightened
> > out in the next draft.  These shouldn't be big.
> >
> > 					Andrew
> > 					dalke at dalkescientific.com
> >
> > _______________________________________________
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> >
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