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Re: MODIS HDF-EOS Data in the NetCDF-Java CDM and THREDDS



Hi Dave:

the projection info and time coordinates are added automatically (not the 2D lat/lon), but its done in the NetcdfDataset layer. See ucar.nc2.dataset.conv.HdfEosModisConvention if you want the details

that info is not in opendap, because we treat opendap as remote access to the NetcdfFile layer. There might be a way to configure TDS to add the coordinates first im not sure yet. For various reasons, we prefer to let the client do it; basically you get more control that way.

John

On 8/14/2013 10:11 AM, Blodgett, David wrote:
Hmmm, we probably could, or maybe we do, I'm not sure how it's
implemented. Tom Kunicki implemented it, and he's not with CIDA anymore.
I'll look into it. We may just add the lat/lon as a union and not worry
about it, but the guys at EROS were curious if it could be added like
they do with Hyrax, automatically.

- Dave


On Wed, Aug 14, 2013 at 10:07 AM, John Caron <address@hidden <mailto:address@hidden>> wrote:

    Sort of.

    1. Can your Geo Data Portal software open the opendap dataset
    through netcdf-java?

    2. Is this your server, so you can configure it ?

    On 8/14/2013 9:35 AM, Blodgett, David wrote:

        Our Geo Data Portal software that takes OPeNDAP-sourced
        NetCDF-CF (ish)
        data and intersects it with some shapefile encoded as GML-Simple
        Features.

        I think what we're after is the functionality that Hyrax implemented
        where they add the lat/lon coordinates to bring the OPeNDAP
        representation into CF-compliant land.

        That make sense?

        - Dave


On Wed, Aug 14, 2013 at 9:32 AM, John Caron <address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>> wrote:

             what is the use case?

             On 8/13/2013 8:47 PM, Blodgett, David wrote:

                 Right, ok, that's what I understood. So we would need
        to join
                 the x/y
                 coordinates of 2D lat/lon arrays to the data so an OPeNDAP
                 client could
                 work with it?


On Tue, Aug 13, 2013 at 5:06 PM, John Caron <address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__>> wrote:

                      geolocation is working ok in 4.3.18.

                      however, TDS opendap doesnt add the coordinate
        system info
                      automatically, typically its added in the client
        if its a
                      netcdf-java client.

                      ie, open it through NetcdfDataset.open("dods url").

                      On 8/13/2013 4:55 PM, Blodgett, David wrote:

                          Not sure if you need a time series, but here are a
                 couple time
                          steps for
                          the same tile.

        
http://e4ftl01.cr.usgs.gov/______MOLT/MOD13Q1.005/2000.02.18/______MOD13Q1.A2000049.h11v04.__005.____2006269082255.hdf
        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.02.18/____MOD13Q1.A2000049.h11v04.005.____2006269082255.hdf>

        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.02.18/____MOD13Q1.A2000049.h11v04.005.____2006269082255.hdf
        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.02.18/__MOD13Q1.A2000049.h11v04.005.__2006269082255.hdf>>


<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.02.18/____MOD13Q1.A2000049.h11v04.005.____2006269082255.hdf <http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.02.18/__MOD13Q1.A2000049.h11v04.005.__2006269082255.hdf>

        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.02.18/__MOD13Q1.A2000049.h11v04.005.__2006269082255.hdf
        
<http://e4ftl01.cr.usgs.gov/MOLT/MOD13Q1.005/2000.02.18/MOD13Q1.A2000049.h11v04.005.2006269082255.hdf>>>
        
http://e4ftl01.cr.usgs.gov/______MOLT/MOD13Q1.005/2000.02.18/______MOD13Q1.A2000049.h11v04.__005.____2006269082255.hdf.xml
        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.02.18/____MOD13Q1.A2000049.h11v04.005.____2006269082255.hdf.xml>

        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.02.18/____MOD13Q1.A2000049.h11v04.005.____2006269082255.hdf.xml
        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.02.18/__MOD13Q1.A2000049.h11v04.005.__2006269082255.hdf.xml>>


<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.02.18/____MOD13Q1.A2000049.h11v04.005.____2006269082255.hdf.xml <http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.02.18/__MOD13Q1.A2000049.h11v04.005.__2006269082255.hdf.xml>

        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.02.18/__MOD13Q1.A2000049.h11v04.005.__2006269082255.hdf.xml
        
<http://e4ftl01.cr.usgs.gov/MOLT/MOD13Q1.005/2000.02.18/MOD13Q1.A2000049.h11v04.005.2006269082255.hdf.xml>>>

        
http://e4ftl01.cr.usgs.gov/______MOLT/MOD13Q1.005/2000.03.05/______MOD13Q1.A2000065.h11v04.__005.____2008238031620.hdf
        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.03.05/____MOD13Q1.A2000065.h11v04.005.____2008238031620.hdf>

        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.03.05/____MOD13Q1.A2000065.h11v04.005.____2008238031620.hdf
        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.03.05/__MOD13Q1.A2000065.h11v04.005.__2008238031620.hdf>>


<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.03.05/____MOD13Q1.A2000065.h11v04.005.____2008238031620.hdf <http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.03.05/__MOD13Q1.A2000065.h11v04.005.__2008238031620.hdf>

        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.03.05/__MOD13Q1.A2000065.h11v04.005.__2008238031620.hdf
        
<http://e4ftl01.cr.usgs.gov/MOLT/MOD13Q1.005/2000.03.05/MOD13Q1.A2000065.h11v04.005.2008238031620.hdf>>>
        
http://e4ftl01.cr.usgs.gov/______MOLT/MOD13Q1.005/2000.03.05/______MOD13Q1.A2000065.h11v04.__005.____2008238031620.hdf.xml
        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.03.05/____MOD13Q1.A2000065.h11v04.005.____2008238031620.hdf.xml>

        
<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.03.05/____MOD13Q1.A2000065.h11v04.005.____2008238031620.hdf.xml
        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.03.05/__MOD13Q1.A2000065.h11v04.005.__2008238031620.hdf.xml>>


<http://e4ftl01.cr.usgs.gov/____MOLT/MOD13Q1.005/2000.03.05/____MOD13Q1.A2000065.h11v04.005.____2008238031620.hdf.xml <http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.03.05/__MOD13Q1.A2000065.h11v04.005.__2008238031620.hdf.xml>

        
<http://e4ftl01.cr.usgs.gov/__MOLT/MOD13Q1.005/2000.03.05/__MOD13Q1.A2000065.h11v04.005.__2008238031620.hdf.xml
        
<http://e4ftl01.cr.usgs.gov/MOLT/MOD13Q1.005/2000.03.05/MOD13Q1.A2000065.h11v04.005.2008238031620.hdf.xml>>>




On Tue, Aug 13, 2013 at 4:22 PM, John Caron <address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__>__>> wrote:

                               send me some files


On 8/13/2013 4:18 PM, Blodgett, David wrote:

                                   John, the LPDAAC got a bunch of HDF
        EOS data
                 up behind
                          THREDDS.
                                   For some
                                   reason I thought that it would add
        coordinate
                 variables
                          to the
                                   data when
                                   accessed via OPeNDAP. Looks like we
        are good
                 to go with
                          WCS and
                                   WMS, but
                                   we still need coordinate variables
        for direct
                 OPeNDAP
                          access.
                                   Any ideas
                                   of a quick way to add them?

                                   Thanks!

                                   Dave



                                   On Tue, Mar 26, 2013 at 1:43 PM, John
        Caron
                                   <address@hidden
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                          <mailto:address@hidden
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                 <mailto:address@hidden
        <mailto:address@hidden>__>__>__>__>> wrote:

                                        hope so.

                                        note that the
                          dateFormatMark="MOD13Q1.A#__________yyyyDDD" is
                                   just counting

                                        chars, then applying the java
                 SimpleDateFormat, so
                          the date
                                   in the
                                        filename just has to start at
        character 9, it
                          doesnt have
                                   to match
                                        MOD13Q1.A


On 3/26/2013 1:38 PM, Blodgett, David wrote:

                                            Ahhh, so the "/" in the
        variable name
                 will work to
                                   represent
                                            groups. I
                                            didn't want to believe that
        would
                 work, glad
                          it will.

                                            Thanks!

                                            - Dave


On Tue, Mar 26, 2013 at 2:36 PM, John Caron <address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__> <mailto:address@hidden <mailto:address@hidden> <mailto:address@hidden <mailto:address@hidden>__>__>__>__>

          <mailto:address@hidden <mailto:address@hidden>
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                          <mailto:address@hidden
        <mailto:address@hidden>
                 <mailto:address@hidden
        <mailto:address@hidden>__>__>__>__>__>> wrote:

                                                 update stardate
        2349873.432874

                                                 ok, enhance actually
        already
                 works, but i
                          ran into
                                   another
                                            problem
                                                 with joinExisting.

                                                 So I retreated to
        joinNew using
                 the kludge of
                                   extracting
                                            the date
                                                 from the filename.

                                                 this only works if the
        filenames
                 are uniform:

                                                 <?xml version='1.0'
                 encoding='UTF-8'?>
                                                 <netcdf




xmlns='http://www.unidata.__uc________ar.edu/namespaces/__netcdf/________ncml-2.2 <http://uc______ar.edu/namespaces/netcdf/________ncml-2.2>

        <http://uc____ar.edu/__namespaces/netcdf/______ncml-__2.2
        <http://uc____ar.edu/namespaces/netcdf/______ncml-2.2>>

          <http://uc__ar.edu/namespaces/____netcdf/____ncml-2.2
        <http://uc__ar.edu/namespaces/__netcdf/____ncml-2.2>
                 <http://uc__ar.edu/namespaces/__netcdf/____ncml-2.2
        <http://uc__ar.edu/namespaces/netcdf/____ncml-2.2>>>

                   <http://ucar.edu/namespaces/______netcdf/__ncml-2.2
        <http://ucar.edu/namespaces/____netcdf/__ncml-2.2>
                 <http://ucar.edu/namespaces/____netcdf/__ncml-2.2
        <http://ucar.edu/namespaces/__netcdf/__ncml-2.2>>

          <http://ucar.edu/namespaces/____netcdf/__ncml-2.2
        <http://ucar.edu/namespaces/__netcdf/__ncml-2.2>
                 <http://ucar.edu/namespaces/__netcdf/__ncml-2.2
        <http://ucar.edu/namespaces/netcdf/__ncml-2.2>>>>



        <http://www.unidata.ucar.edu/________namespaces/netcdf/ncml-2.__2 
<http://www.unidata.ucar.edu/______namespaces/netcdf/ncml-2.2>

        <http://www.unidata.ucar.edu/______namespaces/netcdf/ncml-2.2
        <http://www.unidata.ucar.edu/____namespaces/netcdf/ncml-2.2>>


<http://www.unidata.ucar.edu/______namespaces/netcdf/ncml-2.2 <http://www.unidata.ucar.edu/____namespaces/netcdf/ncml-2.2>

        <http://www.unidata.ucar.edu/____namespaces/netcdf/ncml-2.2
        <http://www.unidata.ucar.edu/__namespaces/netcdf/ncml-2.2>>>



        <http://www.unidata.ucar.edu/______namespaces/netcdf/ncml-2.2
        <http://www.unidata.ucar.edu/____namespaces/netcdf/ncml-2.2>

        <http://www.unidata.ucar.edu/____namespaces/netcdf/ncml-2.2
        <http://www.unidata.ucar.edu/__namespaces/netcdf/ncml-2.2>>


<http://www.unidata.ucar.edu/____namespaces/netcdf/ncml-2.2 <http://www.unidata.ucar.edu/__namespaces/netcdf/ncml-2.2>

        <http://www.unidata.ucar.edu/__namespaces/netcdf/ncml-2.2
        <http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2>>>>>__'__>

                                                    <aggregation
        dimName='time'
                          type='joinNew'>
                                                      <variableAgg





        
name='MODIS_Grid_16DAY_250m___________500m_VI/Data_Fields/__250m___16_______days_NDVI'

                                            />
                                                      <scan
                 location='G:/work/blodgett/'
                          suffix='.hdf'
                                                 subdirs='false'

        dateFormatMark="MOD13Q1.A#__________yyyyDDD"/>

                                                    </aggregation>
                                                 </netcdf>

                                                 you also have to list the
                 variables you want
                                   aggregated
                                            explicitly;
                                                 i only did one, you can
        add the
                 others:

                                                      <variableAgg





        
name='MODIS_Grid_16DAY_250m___________500m_VI/Data_Fields/__250m___16_______days_NDVI'

                                            />

                                                 this form should work
        with the
                 4.3.16
                          release.

                                                 let me know if this is
        adequate
                 for you
                          for now,
                                   and any
                                            problems.

                                                 john

                                                 ps: use this as reference:

        
http://www.unidata.ucar.edu/__________software/netcdf/ncml/v2.__2/________AnnotatedSchema4.__html#________aggregation
        
<http://www.unidata.ucar.edu/________software/netcdf/ncml/v2.2/________AnnotatedSchema4.html#________aggregation>

        
<http://www.unidata.ucar.edu/________software/netcdf/ncml/v2.__2/______AnnotatedSchema4.html#________aggregation
        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation>>


<http://www.unidata.ucar.edu/________software/netcdf/ncml/v2.__2/______AnnotatedSchema4.html#________aggregation <http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation>

        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation
        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation>>>



        
<http://www.unidata.ucar.edu/________software/netcdf/ncml/v2.__2/______AnnotatedSchema4.html#________aggregation
        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation>

        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation
        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation>>


<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation <http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation>

        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation
        
<http://www.unidata.ucar.edu/__software/netcdf/ncml/v2.2/__AnnotatedSchema4.html#__aggregation>>>>





        
<http://www.unidata.ucar.edu/________software/netcdf/ncml/v2.__2/______AnnotatedSchema4.html#________aggregation
        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation>

        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation
        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation>>


<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation <http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation>

        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation
        
<http://www.unidata.ucar.edu/__software/netcdf/ncml/v2.2/__AnnotatedSchema4.html#__aggregation>>>



        
<http://www.unidata.ucar.edu/______software/netcdf/ncml/v2.2/______AnnotatedSchema4.html#______aggregation
        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation>

        
<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation
        
<http://www.unidata.ucar.edu/__software/netcdf/ncml/v2.2/__AnnotatedSchema4.html#__aggregation>>


<http://www.unidata.ucar.edu/____software/netcdf/ncml/v2.2/____AnnotatedSchema4.html#____aggregation <http://www.unidata.ucar.edu/__software/netcdf/ncml/v2.2/__AnnotatedSchema4.html#__aggregation>

        
<http://www.unidata.ucar.edu/__software/netcdf/ncml/v2.2/__AnnotatedSchema4.html#__aggregation
        
<http://www.unidata.ucar.edu/software/netcdf/ncml/v2.2/AnnotatedSchema4.html#aggregation>>>>>



                                                 On 3/26/2013 1:29 PM,
        Blodgett,
                 David wrote:
                                                  > ... enhance ...
        enhance ...
                 go back
                          ... enhance ...
                                                  >
                                                  > Love it!
                                                  >
                                                  > Thanks John, so no
        easy path
                 forward on
                                   aggregations
                                            yet, but the
                                                 master
                                                  > plan includes it?
                                                  >
                                                  > I'm happy with that.
                                                  >
                                                  >
                                                  > On Tue, Mar 26, 2013
        at 1:59
                 PM, John
                          Caron
                                                 <address@hidden
        <mailto:address@hidden>
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                                                 wrote:
                                                  >
                                                  >     Hi David:
                                                  >
                                                  >     I had a look at this
                 again. I changed
                                            HdfEosModisConvention
                                                 to use a
                                                  >     1D instead of a
        scalar time
                          coordinate.
                                                  >
                                                  >     However,
        joinExisting
                 isnt working
                          because the
                                            dataset needs
                                                 to be
                                                  >     "enhanced" (with
                          HdfEosModisConvention) first,
                                            before the time
                                                  >     coordinate is
        available.
                 Currently
                          joinExisting
                                            aggregation
                                                 doesnt
                                                  >     do that.
                                                  >
                                                  >     I can probably
        hack that in.
                          Really I want
                                   to get
                                            the GRID
                                                 feature
                                                  >     collection
        working, but thats
                          going to be a
                                   few months.
                                                 Aggregation
                                                  >     is old and crufty.
                                                  >
                                                  >     Anyway, Ill let
        you know
                 if i can get
                                   "enhanced"
                                            working.
                                                  >
                                                  >
                                                  >     John
                                                  >
                                                  >
                                                  >
                                                  >     On 3/20/2013
        7:50 AM,
                 Blodgett,
                          David wrote:
                                                  >
                                                  >         Morning John,
                                                  >
                                                  >         I pulled
        down the latest
                          thredds war
                                   and have been
                                                 testing a few
                                                  >         things
                                                  >         out. Did you
        get temporal
                          aggregation
                                   working on the
                                                 structured
                                                  >         data at
                                                  >         all? Any
        hints on how to
                          structure the
                                   ncml for
                                            that?
                                                  >
                                                  >         Looks like the
                 spatial stuff is
                                   working. Fantastic.
                                                  >
                                                  >         Thanks!
                                                  >
                                                  >         - Dave
                                                  >
                                                  >
                                                  >
                                                  >         On Mon, Mar
        4, 2013
                 at 9:07 AM,
                                   Blodgett, David
                                                  >
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                          wrote:
                                                  >
                                                  >              OK,
        we'll keep
                 an eye out
                          for the
                                   release,
                                            thanks so
                                                 much John!
                                                  >
                                                  >              No
        worries on the
                          aggregation, the
                                   tiles
                                            are big enough
                                                  >         that I think
                                                  >              we can
        deal without
                          aggregation.
                                                  >
                                                  >
                                                  >              On Mon,
        Mar 4,
                 2013 at
                          8:43 AM,
                                   John Caron
                                                  >
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        <mailto:address@hidden>__>__>__>__>__>>__>> wrote:
                                                  >
                                                  >                  On
        3/1/2013
                 12:03 PM,
                                   Blodgett, David
                                            wrote:
                                                  >
                                                  >
          John,
                                                  >
                                                  >
          Really
                 happy you
                          added
                                   this stuff
                                            in, what's
                                                 your
                                                  >             plan for
                                                  >
                   releasing it?
                                                  >
                                                  >
                                                  >
          going to try to
                          release 4.3.16
                                   in next
                                            week or two.
                                                  >
                                                  >
                                                  >
                                                  >                      You
                 think there's any
                                   chance that tiled
                                                 aggregation
                                                  >             will work?
                                                  >
                                                  >
                                                  >                  im
        reluctant
                 to recommend
                                   using whats there
                                                 currently.
                                                  >         But doing
                                                  >                  it
        right is a
                          challenge and
                                   wont be
                                            done soon.
                                                  >
                                                  >
                                                  >
                                                  >
                                                  >
          - Dave
                                                  >
                                                  >
                                                  >
          On Tue,
                 Feb 26,
                          2013 at
                                   8:30 AM,
        address@hidden <mailto:address@hidden> <mailto:address@hidden
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