[DAS2] Re: Apollo and DAS/2 priorities
allenday at ucla.edu
Mon Feb 6 07:13:59 UTC 2006
Okay folks, an implementation of the document cited below is available
After looking closely over this first draft of new_spec.txt, it's apparent
that there are still some holes, e.g. what should the response to the
following requests look like?
For now I have left responses the same as in the old HTML version of the
spec. Of course if you find bugs, let me know.
The server at:
is currently unavailable. This is due to limitations in Apache/mod_perl
that won't allow different versions of the same class to coexist in a
family of processes. I'd like to discuss how we should handle this in the
conference call tomrorow (today, if you're not in GMT+8).
On Mon, 30 Jan 2006, Andrew Dalke wrote:
> > 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
> 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.
> $PREFIX/sequence/$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
> 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.
> dalke at dalkescientific.com
> DAS2 mailing list
> DAS2 at portal.open-bio.org
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