[DAS2] Re: Apollo and DAS/2 priorities

[Ed Erwin]

Gregg asked me to say "No".  Please do not break the current server that 
IGB is using.

Please make your changes on a server at a different URL.

Thanks
Ed

Allen Day wrote:
> That's what I was thinking too, but I was worried about the existing 
> Genoviz clients "in the wild" having the server suddenly break.
> 
> So you're saying it's okay with you if those clients have a service
> interruption?
> 
> -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
>>>>
>>>
>>>_______________________________________________
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>>
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