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#179 URIs in Segment, Type, and others

closed-fixed
DAS2 (40)
9
2006-08-19
2006-08-15
Brian O'Connor
No

The URI should be resolvable against the base URI. In
the biopackages DAS/2 some of the URIs are actually
created by slicing and dicing strings. This should
really not be done.

Discussion

  • Brian O'Connor
    Brian O'Connor
    2006-08-15

    • priority: 5 --> 8
    • assigned_to: allenday --> boconnor
     
  • Allen Day
    Allen Day
    2006-08-15

    • priority: 8 --> 9
     
  • Brian O'Connor
    Brian O'Connor
    2006-08-15

    Logged In: YES
    user_id=587499

    Some notes:

    This is really talking about the filters in the DAS/2
    server. Currently, the filters use ids. But these really
    should be fully resolvable URIs i.e.

    type=http://foo.com/genome...

    rather than

    type=MA:0000345

    Apparently the following filters should be converted:
    type
    sequence/region (all location based)
    segment
    overlaps
    inside
    exact

    A first pass on this would extract the correct value from a
    das.biopackages.net URL and then use that normally. In the
    future, it won't be possible to make assumptions about where
    the URIs point and what they resolve to.

     
  • Brian O'Connor
    Brian O'Connor
    2006-08-16

    Logged In: YES
    user_id=587499

    Some notes:

    After talking with Gregg and Allen about this one there are
    two "solutions". The first (not so flexible) solution is to
    mangle the URI and clip off the known ending and use that to
    produce a response by the server. The problem with this is
    it assumes the URI formats are all the same and that the
    local DAS/2 server is using the same build of the genome(s).
    The better solution is to use a mapping file based on
    Lincoln's official URIs in the wiki. That way everyone
    would use the same URI passed to, say, an overlaps query and
    the DAS/2 server would know how to map that URI to an
    internal ID used to locate and produce a response.

     
  • Brian O'Connor
    Brian O'Connor
    2006-08-19

    Logged In: YES
    user_id=587499

    OK... this is "fixed".

    The following need to use URIs:
    * xid
    * type
    * segment
    * coordinates

    These work but xid isn't supported in our server (but in the
    spec and needs to be implemented).

     
  • Brian O'Connor
    Brian O'Connor
    2006-08-19

    • status: open --> closed
     
  • Brian O'Connor
    Brian O'Connor
    2006-08-19

    • status: closed --> closed-fixed