[Esip-documentation] Let's get rid of spatial and temporal bounds in ACDD

Steve Hankin steven.c.hankin at noaa.gov
Mon Mar 17 12:23:19 EDT 2014 

Greetings Ted!

As rants go, the message you sent on Friday was pretty restrained. I 
particularly like your suggestion that the UAF Catalog Cleaner could 
detect and report corrupted ACDD geo-positioning attributes. We will see 
what we can do with that idea.  (aside:  Is there a way to ask ncISO 
when it has found this form of corruption in a dataset?)

It would be nice if we could all wrestle this topic to a workable 
compromise.  I agree that the problem should be "fixed at the source".   
But characterizing the source of the problem as "sloppy data management" 
seems off the mark.   This data management problem didn't exist until we 
created the potential for easy corruption by _defining easily-corrupted, 
redundant information in the CF datasets_.

The duplication of information between the global attributes and the CF 
coordinates is an 'attractive nuisance'.   No matter how much we exhort 
data managers to clean up their act, the problem is going to continue 
showing up over and over and over.   Some of the data management tools 
that stumble into this problem are not even CF-aware;  generic netCDF 
utilities like nco create this form of corruption.   Offhand I can think 
of 6 independent pieces of software that perform aggregations on CF 
datasets.  Five of these predate the use of the ACDD geo-bounds 
attributes within CF files; all of these exhibit this corruption.  Ed's 
example is yet another.

Our underlying challenge is to expose the CF coordinate bounds for easy 
use wherever that information is needed for purposes of data 
discovery.   The ncISO tool contributed by your group has addressed this 
very successfully for formal ISO metadata.  (A big thanks to you, Dave 
N. et. al..)  There is similar excellent potential to address the more 
informal cases through software.  You mentioned the limitations of 
"ncdump  -h" as an illustration.  How about code contributed to Unidata 
to create "ncdump -bounds"?    This would be a smaller effort with a 
more robust outcome than to ask all current and future developers of CF 
aggregation techniques to make accommodation for the redundant, easily 
corrupted attributes in their datasets.

     - Steve

===========================================

On 3/14/2014 1:14 PM, Ted Habermann wrote:
> All,
>
> I agree with Ed and John, *this is a software tool problem that should 
> be fixed at the source.* The description of the history attribute has 
> always implied that it should be updated when a file is processed 
> (even though, IMHO, it is almost entirely unsuited for doing that). 
> The same is true for many others (listed by John G. earlier in this 
> thread). *The current practice is sloppy data management* that, from 
> the sound of this thread, is pervasive in the community. Of course, 
> ncISO provides a very easy way to identify occurrences of this problem 
> throughout a THREDDS catalog. The "Catalog Cleaner" is another venue 
> for quantifying the damage. CF is a community standard. Maybe it is 
> time for the community to recommend providing correct metadata with 
> the files and to avoid developers and datasets that don't.
>
> A related problem is that the bounds calculated from the data are only 
> available if you read the data. Many users may not be equipped to 
> easily read the data during a data discovery process. They may not 
> want to go beyond ncdump -x -h (or something like that) before they 
> fire up the whole netCDF machine...
>
> BTW, this problem is trivial relative to that associated with virtual 
> datasets created through aggregation. In those cases, there is no 
> clear mechanism for providing meaningful metadata, although the rich 
> inventory we created several years ago comes close... That situation 
> is much more prone to mistakes as all semblance of the historic record 
> is wiped out.
>
> Its Friday, and spring... As Dave said last week, a good time for a rant!
> Ted
>
>
> On Mar 14, 2014, at 1:44 PM, Steve Hankin <steven.c.hankin at noaa.gov 
> <mailto:steven.c.hankin at noaa.gov>> wrote:
>
>> Hi All,
>>
>> I'm joining into this discussion from the wings.  The topic here -- 
>> the common tendency for the ACDD geo-spacio-temporal bounds 
>> attributes to get corrupted -- has been beaten around a number of 
>> times among different groups.  At this point it isn't clear that 
>> there is a "clean" resolution to the problem;  there are already so 
>> many files out there that contain these attributes that there may be 
>> no easy way to unwind the problem.  Might the best path forward be to 
>> see about adding some words of caution into the the documents that 
>> suggest the use of these attributes?  Something along these lines:
>>
>>     /*Caution:*//   The encoding of geo-spatial bounds values as
>>     global attributes is a practice that should be used with caution
>>     or avoided. //
>>     //
>>     //The encoding of geo-spatial bounds values as global attributes
>>     introduces a high likelihood of corruption, because the attibute
>>     values duplicate information already contained in the
>>     self-describing coordinates of the dataset.   A number of data
>>     management operations that are common with netCDF files will
>>     invalidate the values stored as global attributes.  Such
>>     operations include extending the coordinate range of a netCDF
>>     file along its record axis;  aggregating a collection of netCDF
>>     files into a larger datasets (for example aggregating model
>>     outputs along their time axes); or appending files using
>>     file-based utilities (e.g. nco).//
>>     //
>>     //It is recommended that 1) the use of these global attributes be
>>     restricted to files whose contents are known to be completely
>>     stable -- i.e. files very unlikely to be aggregated into larger
>>     collections;  and 2) as a matter of best practice, software
>>     reading CF files should ignore these global attributes; instead
>>     it should compute the geo-spatial bounds by scanning the
>>     coordinate ranges found within the CF dataset, itself. /
>>
>> Comments?
>>
>>     - Steve
>>
>> ------------------------------------------------------------------------
>>
>> From: Armstrong, Edward M (398M) <Edward.M.Armstrong at jpl.nasa.gov>
>> Date: Wed, Mar 12, 2014 at 6:03 PM
>> Subject: Re: [Esip-documentation] Let's get rid of spatial and
>> temporal bounds in ACDD
>> To: Nan Galbraith <ngalbraith at whoi.edu>
>> Cc: Cluster Documentation <esip-documentation at lists.esipfed.org>
>>
>>
>> I think that is an excellent idea.
>>
>> The output of the PO.DAAC HiTIDE subsetter that I mentioned in a
>> previous email does exactly that and includes some useful information
>> about the granule and the wrapped subsetting request via OPeNDAP.
>> Below is a snapshot of some of the global attributes from  a subsetted
>> AVHRR SST granule (look at the naiad_ attributes):
>>
>>   :southernmost_latitude = -89.72987f; // float
>>   :northernmost_latitude = 89.80405f; // float
>>   :westernmost_longitude = -179.9997f; // float
>>   :easternmost_longitude = 179.99994f; // float
>>   :file_quality_index = 1S; // short
>>   :comment = "none";
>>   :naiad_download_date = "2014-03-10 21:25:47";
>>   :naiad_granule_url =
>> "http://podaac-opendap.jpl.nasa.gov/opendap/allData/ghrsst/data/L2P/AVHRR19_G/NAVO/2013/358/20131224-AVHRR19_G-NAVO-L2P-SST_s0827_e1009-v01.nc.bz2";
>>   :naiad_constraint_expression =
>> "lat[8000:1:9200][104:1:408],lon[8000:1:9200][104:1:408],time[0:1:0],sst_dtime[0:1:0][8000:1:9200][104:1:408],rejection_flag[0:1:0][8000:1:9200][104:1:408],SSES_bias_error[0:1:0][8000:1:9200][104:1:408],aod_dtime_from_sst[0:1:0][8000:1:9200][104:1:408],DT_analysis[0:1:0][8000:1:9200][104:1:408],brightness_temperature_11um[0:1:0][8000:1:9200][104:1:408],aerosol_optical_depth[0:1:0][8000:1:9200][104:1:408],sources_of_aod[0:1:0][8000:1:9200][104:1:408],confidence_flag[0:1:0][8000:1:9200][104:1:408],brightness_temperature_4um[0:1:0][8000:1:9200][104:1:408],SSES_standard_deviation_error[0:1:0][8000:1:9200][104:1:408],sea_surface_temperature[0:1:0][8000:1:9200][104:1:408],brightness_temperature_12um[0:1:0][8000:1:9200][104:1:408],proximity_confidence[0:1:0][8000:1:9200][104:1:408],satellite_zenith_angle[0:1:0][8000:1:9200][104:1:408]";
>> }
>>
>> I did misspeak earlier when I indicated that the spatial bounds were
>> also updated, in this case southernmost_latitude etc. They are the
>> original (global) bounds.  I have requested to the developer that
>> these bounds be updated for every subset request. Hopefully it will
>> get in the next version.
>>
>>
>>
>> On Mar 8, 2014, at 3:13 AM, Nan Galbraith <ngalbraith at whoi.edu> wrote:
>>
>> > Hows about adding an attribute that contains the URL of the data
>> > file to which the bounds apply? If your aggregator/sub-setter
>> > has misled you by failing to update the bounds attribute, he's also
>> > provided you with the link to the data you actually wanted.
>> >
>> > For programs that collect lots of data and don't molest it, this would
>> > let them continue to use the bounds atts; for programs that slice
>> > and dice, they'd be motivated to either update the fields dynamically
>> > or remove them.
>> >
>> > Cheers - Nan
>> >
>> > Is it really Friday? I'm at sea (yes, people still do that, sometimes)
>> > and I've lost all sense of time and place (no geospatial and temporal
>> > bounds information).
>> >
>> >
>> >
>> >
>> > On 3/7/14 6:47 PM, David Neufeld - NOAA Affiliate wrote:
>> >>
>> >> Ok, since it's Friday and we are in rant mode, I'm going to have a 
>> little fun with this one...
>> >>
>> >> Recommended Attribute Disclaimer:
>> >>
>> >> Suggested text: "When using geospatial and temporal bounds 
>> information in your global attributes, please know that it introduces 
>> a likely source of error and that you are far better off reading 
>> these values from the data stored in the file.  If you do choose to 
>> use the attributes please also include a global checksum attribute 
>> that humans can look at to decide whether the file has changed since 
>> you originally recorded these values."
>> >>
>> >> On Fri, Mar 7, 2014 at 2:02 PM, Nan Galbraith <ngalbraith at whoi.edu 
>> <mailto:ngalbraith at whoi.edu>> wrote:
>> >>
>> >>
>> >>
>> >>    Maybe we should add some text about which attributes should be
>> >>    considered fragile and under what conditions they need to be
>> >>    recalculated or removed, but I'm not in favor of removing the
>> >>    terms from ACDD.
>> >>
>> >>
>> >
>> >
>> > --
>> > *******************************************************
>> > * Nan Galbraith                        (508) 289-2444 *
>> > * Upper Ocean Processes Group            Mail Stop 29 *
>> > * Woods Hole Oceanographic Institution                *
>> > * Woods Hole, MA 02543                                *
>> > *******************************************************
>> >
>> >
>> > _______________________________________________
>> > Esip-documentation mailing list
>> > Esip-documentation at lists.esipfed.org
>> > http://www.lists.esipfed.org/mailman/listinfo/esip-documentation
>>
>> -ed
>>
>> Ed Armstrong
>> JPL Physical Oceanography DAAC
>> 818 519-7607
>>
>>
>>
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>>
>>
>> -- 
>> Dr. Richard P. Signell   (508) 457-2229
>> USGS, 384 Woods Hole Rd.
>> Woods Hole, MA 02543-1598
>>
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