[DAS2] Re: Apollo and DAS/2 priorities

[Allen Day]

Okay folks, an implementation of the document cited below is available 
here:

http://das.biopackages.net/codesprint
http://das.biopackages.net/codesprint/sequence
http://das.biopackages.net/codesprint/sequence/yeast/S228C/segment
etc.

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?

http://das.biopackages.net/codesprint/sequence/yeast
http://das.biopackages.net/codesprint/sequence/yeast/S228C

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:

http://das.biopackages.net/das

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).

-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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