[DAS2] Re: Apollo and DAS/2 priorities

[Allen Day]

There are still many references to "region" in Andrew's .txt document.  
Is it safe to assume that anywhere "region" is mentioned, it should really
be "segment" now?  I believe the answer is yes.

I'm asking to see if I need to change the feature filter implementation.

-Allen


On Wed, 1 Feb 2006, Helt,Gregg wrote:

> 
> 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
> > >
> > > _______________________________________________
> > > DAS2 mailing list
> > > DAS2 at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/das2
> > >
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/das2
>