[DAS2] Re: Apollo and DAS/2 priorities

Helt,Gregg Gregg_Helt at affymetrix.com
Wed Feb 1 23:51:23 UTC 2006


Yes, what Ed said, that's what I meant.  Updated server, but at a
different address.  Otherwise the current release of IGB will break when
trying to use the biopackages server.

Once our IGB code has caught up to the updated server, we can roll out a
new release to point to the new server instead of the old one.  But not
yet.

	Thanks,
	Gregg

> -----Original Message-----
> From: das2-bounces at portal.open-bio.org
[mailto:das2-bounces at portal.open-
> bio.org] On Behalf Of Ed Erwin
> Sent: Wednesday, February 01, 2006 3:45 PM
> To: Allen Day
> Cc: DAS/2
> Subject: Re: [DAS2] Re: Apollo and DAS/2 priorities
> 
> 
> 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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