[DAS2] Re: Apollo and DAS/2 priorities

Allen Day allenday at ucla.edu
Wed Feb 1 22:42:26 UTC 2006

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.


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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