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

John Graybeal jbgraybeal at mindspring.com
Mon Mar 17 15:00:30 EDT 2014 

Great analogy, it makes my points exactly: (a) after taking the two bananas, you're putting/leaving a sticker on the bananas that says they weigh more than they do; (b) weighing has a cost. For those dealing with large volumes of data, weighing has a really large cost; and (c) for those who can read the sticker but don't have a scale, weighing is not possible.  

(In Europe the bananas are weighed and priced at the fruit section, by the buyer. They wouldn't be pleased if you weighed them and printed the sticker, then removed the 2 bananas.)

John

On Mar 17, 2014, at 11:49, "Signell, Richard" <rsignell at usgs.gov> wrote:

> Gang,
> 
> Since this is a cluster discussion, how about a bananas analogy.  ;-)
> 
> When you buy a bunch of bananas, the checker weighs them and you pay the correct amount.
> If you take two bananas off the bunch, the checker weights them and you pay the correct amount.
> 
> ACDD wants to put a  weight label on the bunch of bananas, hopefully by weighing them (but no guarantees!), and you *should* be good if you buy the whole amount (but no guarantees).    And if someone takes a few bananas, the labeled weight will be wrong.   So the system is broken!   Make sure all people correctly weigh the bananas they take and put on the right labels!!!!
> 
> But why not just weigh the bananas at checkout?  It works. It's not broken.
> 
> I'm not arguing that software not be upgraded to track metadata changes.  It's just in this case the information we are providing is already contained in the file.  I can see that it's useful in situations where you know the bounds are right because your software wrote them.  But I believe that in general, in the distributed geoscience infrastructure we are building where we encourage people to subsetting all the time with a plethora of tools, the metadata bounds are wrong so often that it runs the risk of making people say "see, this metadata stuff *is* a waste of time, just like I thought it was."
> 
> -Rich
> 
> 
> 
> 
> On Mon, Mar 17, 2014 at 2:09 PM, Ted Habermann <thabermann at hdfgroup.org> wrote:
> Steve et al.,
> 
> The NCML that is generated by ncISO includes global attributes from the file outside of any group and the CF bounds calculated from the data in the CFMetadata group. Comparing these is straightforward... Would be interesting (and probably helpful) to embed this comparison in the transform that makes the rubric. I think we discussed this idea ahile ago at NGDC, but it was not implemented...
> 
> See http://www.ngdc.noaa.gov/thredds/ncml/relief/ETOPO1/thredds/ETOPO1_Ice_g_gmt4.nc?catalog=http%3A%2F%2Fwww.ngdc.noaa.gov%2Fthredds%2FbathyCatalog.html&dataset=etopo1Ice
> for an example...
> 
> Ted
> 
> BTW, it looks like my clean catalog link has gone stale as well as the one on https://www.nosc.noaa.gov/EDMC/swg.php... Is the clean catalog still available...?
> 
> On Mar 17, 2014, at 11:51 AM, John Graybeal <jbgraybeal at mindspring.com> wrote:
> 
>> Steve,
>> 
>> Let me see if you take issue with my simplified version of what you said:
>> 
>> "NetCDF attributes should never be used to describe value-based or processing-specific features of any data set, because data processors (tools and people) can't help but corrupt derivative data sets with that information. "
>> 
>> Don't get me wrong; I think this presents a consistent philosophy in response to today's practical realities. As of today, with 5 out of 6 tools failing the 'metadata consistency' test, it likely minimizes the ratio of bad metadata in the wild. 
>> 
>> What it does *not* do is establish a mature, flexible, interoperable, metadata-aware community of practice going forward. It also does not fix the problem caused by these tools, it just eliminates the most-likely-to-fail attributes (from any standard, forevermore). And it directly undercuts the greatest value of a self-describing data format, the easy-to-access description.
>> 
>> The fact that much software pre-dates the standards is a red herring. Software that takes any self-describing file, modifies the contents, yet passes through the original description _without validation_ to the output file, will almost always produce a broken output file. This isn't a feature, nor inevitable; it's a bug. Our underlying challenge is to fix that problem.
>> 
>> And in the meantime, we still have to maintain ALL the metadata affected by that problem, not just the CF coordinate bounds. So we should fix all that software soon. (As I can think of 3 trivial fixes off the top of my head, I'm not sure why previous beat-arounds didn't induce change. It's time. And it's a lot easier than modifying all the software to include statements in the files about how unreliable the metadata is.)
>> 
>> John
>> 
>> On Mar 17, 2014, at 09:23, Steve Hankin <steven.c.hankin at noaa.gov> wrote:
>> 
>>> 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> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Esip-documentation mailing list
>>>>> Esip-documentation at lists.esipfed.org
>>>>> http://www.lists.esipfed.org/mailman/listinfo/esip-documentation
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Dr. Richard P. Signell   (508) 457-2229
>>>>> USGS, 384 Woods Hole Rd.
>>>>> Woods Hole, MA 02543-1598
>>>>> 
>>>>> _______________________________________________
>>>>> Esip-documentation mailing list
>>>>> Esip-documentation at lists.esipfed.org
>>>>> http://www.lists.esipfed.org/mailman/listinfo/esip-documentation
>>>> 
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>>>> 
>>> 
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>>> http://www.lists.esipfed.org/mailman/listinfo/esip-documentation
>> 
>> John Graybeal
>> jbgraybeal at mindspring.com
>> 
>> 
>> 
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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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John Graybeal
jbgraybeal at mindspring.com



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