Re: [thredds] NcML Aggregation

• To: THREDDS community <thredds@xxxxxxxxxxxxxxxx>
• Subject: Re: [thredds] NcML Aggregation
• From: Roy Mendelssohn - NOAA Federal <roy.mendelssohn@xxxxxxxx>
• Date: Tue, 19 Mar 2013 13:09:09 -0700

I should add that this arises only because the dateFormatMark  when used in 
aggregation creates a string for time, rather than a number, and therefore 
breaks tools looking for CF compliance.  This issue has been brought up several 
times before.

Even more curious, under  TDS 4.3.15, if i have a GRIB featureCollection and 
use dateFormatMark  on the file name to aggregate times, the times are numbers 
in the usual "units-since-some-basetime"

So, can we either get GRIDS under featureCollections with the dateFormatMark  
behaving in a similar manner, or at least have the option in the normal scan 
aggregation to tell dateFormatMark to return the time as a number?  Without 
naming names, I know there are others who would benefit from this.

Thanks,

-Roy
On Mar 19, 2013, at 12:36 PM, Bob Simons - NOAA Federal <bob.simons@xxxxxxxx> 
wrote:

> Is there a way to promote a global numeric attribute to be a new coordinate 
> variable?
> I read the bottom of
> http://www.unidata.ucar.edu/software/netcdf/ncml/v2.2/Cookbook.html
> but I am confused (time vs times? and why dateFormatMark which also seems to 
> be creating an ISO 8601 time axis?).
> Can someone provide a more complete, less confusing, working example?
> 
> My best guess at the ncml is:
> 
> <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";>
>  <variable name="time" type="int" shape="time" >
>    <attribute name="units" value="days since 2012-12-31"/>
>    <attribute name="_CoordinateAxisType" value="Time" />
>  </variable>
>  <aggregation dimName="time" type="joinNew" recheckEvery="15 min" >
>    <variableAgg name="chla"/>
>    <promoteGlobalAttribute name="time" orgName="startDay" />
>    <scan location="/testFiles/" suffix=".hdf" subdirs="false" />
>  </aggregation>
> ...
> 
> I have tried lots of variations, to no avail.
> I have tried lots of variations with joinExisting, with and without the 
> <variable>, to no avail.
> They almost all generate an unhelpful error message like:
> 
> Exception in thread "main" java.lang.NullPointerException
>        at 
> ucar.nc2.ncml.AggregationOuterDimension.promoteGlobalAttributes(AggregationOuterDimension.java:176)
>        at 
> ucar.nc2.ncml.AggregationNew.buildNetcdfDataset(AggregationNew.java:73)
>        at ucar.nc2.ncml.Aggregation.finish(Aggregation.java:404)
>        at ucar.nc2.ncml.NcMLReader.readNetcdf(NcMLReader.java:492)
>        at ucar.nc2.ncml.NcMLReader.readNcML(NcMLReader.java:437)
>        at ucar.nc2.ncml.NcMLReader.access$100(NcMLReader.java:60)
>        at 
> ucar.nc2.ncml.NcMLReader$NcmlElementReader.open(NcMLReader.java:1406)
>        at 
> ucar.nc2.ncml.NcMLReader$NcmlElementReader.open(NcMLReader.java:1394)
>        at ucar.nc2.dataset.NetcdfDataset.acquireFile(NetcdfDataset.java:625)
>        at ucar.nc2.ncml.Aggregation$Dataset.acquireFile(Aggregation.java:634)
>        at 
> ucar.nc2.ncml.AggregationUnion.buildNetcdfDataset(AggregationUnion.java:65)
>        at ucar.nc2.ncml.Aggregation.finish(Aggregation.java:404)
>        at ucar.nc2.ncml.NcMLReader.readNetcdf(NcMLReader.java:492)
>        at ucar.nc2.ncml.NcMLReader.readNcML(NcMLReader.java:437)
>        at ucar.nc2.ncml.NcMLReader.readNcML(NcMLReader.java:252)
>        at ucar.nc2.ncml.NcMLReader.readNcML(NcMLReader.java:202)
>        at ucar.nc2.dataset.NetcdfDataset.acquireNcml(NetcdfDataset.java:847)
>        at 
> ucar.nc2.dataset.NetcdfDataset.openOrAcquireFile(NetcdfDataset.java:686)
>        at ucar.nc2.dataset.NetcdfDataset.openFile(NetcdfDataset.java:563)
>        at ucar.nc2.NCdumpW.print(NCdumpW.java:212)
> 
> 
> Any suggestions?
> 
> Thank you.
> 
> Sincerely,
> 
> Bob Simons
> IT Specialist
> Environmental Research Division
> NOAA Southwest Fisheries Science Center
> 1352 Lighthouse Ave
> Pacific Grove, CA 93950-2079
> Phone: (831)658-3205
> Fax:   (831)648-8440
> Email: bob.simons@xxxxxxxx
> 
> The contents of this message are mine personally and
> do not necessarily reflect any position of the
> Government or the National Oceanic and Atmospheric
> Administration.
> <>< <>< <>< <>< <>< <>< <>< <>< <><
> 
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**********************
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn@xxxxxxxx (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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• References:
  • [thredds] NcML Aggregation
    • From: Bob Simons - NOAA Federal