[Go-essp-tech] DRS corrections and extensions
Karl Taylor
taylor13 at llnl.gov
Wed Jun 13 18:07:45 MDT 2012
Hi Stephen, Martin, and all,
Thanks very much for thinking carefully about this. I've responded to
your input below:
Stephen:
Extending the use of the "-suffix" part of temporal subset to include
averaging looks reasonable. The geographic subset section is rather
complex and I worry that it will be difficult to implement unambiguous
parsers for it. This may not matter provided we can always interpret it
as an opaque string in filenames of the form:
"c1_c2_...cn_[temporal-subset]_[geospatial-info].nc". My specific
concerns about parsing are below.
Also, more generally, I wonder whether we are repeating too much
information from the CF metadata in the filename. I think the temporal
subset is already pushing to the limit what can be effectively
represent in a filename and this could push it too far. Filenames
within a dataset should be unique but maybe we could let data providers
decide how they are labelled?
Karl: Yes, this is an option. Including a uniform way of embedding the
time in the filename was essential since we wanted to be able to split
time-series across files. The motivation for treating simple spatial
subsetting and averaging in a standard way is that we hope to return to
users requested regional datasets, extracting the data on the server
side. Shouldn't a user expect the files to be named similarly, even if
they were created from different ESG nodes?
Stephen:
If we continue to add detailed syntax to the filename it would greatly
help to have a formal grammar in BNF notation
(http://en.wikipedia.org/wiki/Backus%E2%80%93Naur_Form).
Karl: I hope someone familiar with BNF might do this if it's deemed
important.
Stephen:
*Section 2.4 Geographic subsets*
As described the format is "g[-XXXX][-YYYY]" where both XXXX and YYYY
are optional and YYYY = "[yyy][-zzz]". XXXX can be omitted when YYYY is
present as in the example "g-ocn-areaavg".
I foresee problems in writing parsers that disambiguate the case
"g-XXXX" from "g-YYYY" particularly in the case where XXXX is a named
region. If we wanted to extend the valid vocabulary of YYYY we would
have to check for clashes with all named regions used in XXXX. This
would seam like a hostage to fortune, particularly if users start
defining their own regions.
Karl: Perhaps to simplify things we should require XXXX (and prohibit
hyphens within XXXX).
Stephen:
Similarly how do we disambiguate these cases:
g-XXXX-yyy
g-yyy-zzz
With a sufficiently complex parser we can differentiate these because
yyy and zzz are from controlled vocabularies but writing a generic
parser that forsees extensions to these vocabularies will be tricky and
error-prone.
Karl: requiring XXXX would eliminate this problem.
Martin:
> (1) Like Stephen, I’m concerned about the complexity of the “XXXX”
> section. My first suggestion would be to drop the first hyphen and
> “lat” and “lon”, changing “g-lat20S20Nlon170p5W130p5W” to
> “g20S20N170p5W130p5W”. I’d also be tempted to drop the “p5” terms: for
> some grids (e.g. Gaussian) the exact limits will have many decimal
> places and so there will need to be some specification of the level of
> truncation expected, and I think the most convenient would be to round
> to the nearest integer.
>
Karl: I like the suggestion to round to the nearest integer. I'd like
to hear others weigh in on whether to eliminate "lat" and "lon". I
guess this would be o.k.
> (2) To make parsing of the overall file name easier, you could use
> c1_c2_..... [_<time range>][.<spatial info>].nc – using a “.” Instead
> of “_” makes life easier for file parsers. Technically this is not
> necessary, as the “g” already makes it unambiguous, but parsers have
> to deal with the special case of gridspec files and adding more
> variants make life more complicated. Using “.” will make it easier to
> separate the parsing of the existing components from the new ones.
>
Karl: I don't find this argument compelling. I think it's pretty easy
to write a parser that can deal with the two optional suffixes (i.e.,
temporal subset and geographical info.) The first consists of only
numerals (and a hyphen), whereas the second begins with "g-". I think
some software doesn't like "." in filenames except to separate the final
"file-type" suffix (e.g, ".nc").
>
> (3) As Stephen points out, in the present form, in a string
> “g-aaa-bbb” the term “aaa” could be either a region from an gazetteer
> or a designation of a type of surface (“ocn” or “lnd”). Having to look
> through multiple vocabularies is a problem for file name
> interpretation, even if one of them only has two elements. To get over
> this, I’d suggest something like: “.....[_<time
> range>][.gXXXX_pYYY-ZZZ].nc”, where the “gXXXX” and “pYYY-ZZZ” terms
> are both optional and the underscore is only present if both are
> present. This approach will only work if you accept the use of “.”
> suggested in (2) to make a clear break between the first part of the
> name and the new. This would give us a first section of the file name
> in which components are identified by position and a 2^nd section in
> which components are identified by the first letter of the component.
>
Karl: I prefer simply requiring XXXX if you want to include YYYY.
I've made the changes inspired by your input in the attached file.
Further comments/suggestions are welcome.
Best regards,
Karl
>
> Regards,
>
> Martin
>
> *From:*Karl Taylor [mailto:taylor13 at llnl.gov]
> *Sent:* 06 June 2012 21:58
> *To:* Kettleborough, Jamie; V. Balaji; Steve Hankin; Juckes, Martin
> (STFC,RAL,RALSP); Lawrence, Bryan (STFC,RAL,RALSP); Pascoe, Stephen
> (STFC,RAL,RALSP); go-essp-tech at ucar.edu
> *Subject:* Re: [Go-essp-tech] DRS corrections and extensions
>
> Dear all,
>
> In February I asked for comments on my proposal to extend the DRS to
> include information about spatio-temporal subsets or means. I heard
> from Jamie, but no one else. I respond to Jamie below, but I also
> would like your input specifically about:
>
> 1. Is this method of describing spatio-temporal subsets acceptable?
> 2. Is it worth taking this step if we don't say anything about other
> "processed" output? For example how to describe "regridded" data or
> multi-model means.
>
> I've attached the proposed version of the DRS, which differs from the
> one I sent in January only in a couple mods made in response to Jamie.
>
> Best regards,
> Karl
>
> On 2/13/12 6:47 AM, Kettleborough, Jamie wrote:
>
> Hello Karl,
>
> this will be terse as I have time to review, but not to necessarily
> get the words right - hope I don't say anything too bad because of this.
>
> 1. section 2.3, Not sure 'output' should be mentioned under
> 'product'. I don't think 'output' ever makes it to publication level,
> so does not need to appear in a publication level id. I know cmor
> produces it, but I think that's kind of historical isn't it, rather
> than necessary? Maybe its too late for details like this?
>
> It's true that in the end the CMIP5 output should not remain as
> "output", but be assigned to "output1" or "output2". Nevertheless, I
> don't think there is any harm in keeping it in the DRS.
>
> 2. section 2.3 version number: to be consistent with what we really
> have in CMIP5 I think you need to note that v1, v2 are also present,
> though any *new* versions should use vYYYYMMDD.
>
> I have modified the text to indicate that software cannot rely on the
> version number reflecting a date.
>
> 3. section 2.3 version: I wonder if you need to say more (maybe not
> here, but if not where?) about what triggers a new version. I think its
>
> a. anything that changes the content of a file already published and
>
> b. the addition or deletion of files from any publication data set.
>
> Pure 'data management' meta data changes (addition of checksums,
> move to new URL's) need not trigger a new version.
>
> Do you also need to say there is no guarantee that old versions will
> be kept (unless they have a DOI).
>
> I've added some of this information now to the document.
>
> 4. section 2.4 Temporal Subsets or means: I don't understand the 'avg'
> example, or if I do I don't know if its right (but the point is
> relatively minor). I think the example you quote as one 6 month mean
> field in it. This is based on 1 day means. I think its a little
> anomalous to keep the frequency as 'day' in this case. That's not
> quite consistent with the definition (and I think all other uses) of
> frequency. Strictly speaking frequency should be 6mon no? (I may
> have misunderstood).
>
> I think you're right. I'm not sure why I thought this was the right
> way to do it. I've changed the example,
>
> 5. section 3.5. Does this need clarifying? I think the current
> wording is potentially confusing, I think it should say something like:
>
> 'URLs referencing the data files will have a site dependent prefix
> (that may change due to site-specific data management tasks) followed
> by the directory structure. This directory structure should (but may
> not) follow the recommendations of section 3.3'
>
> I've modified the text as suggested.
>
> 6. I've noticed that the thredds catalogs also expose a thing called
> the file_id, e.g
>
> <property name="file_id"
> value="cmip5.output1.CNRM-CERFACS.CNRM-CM5.rcp45.mon.ocean.Omon.r1i1p1.vo_Omon_CNRM-CM5_rcp45_r1i1p1_203601-204512.nc"/>
>
> I don't know if they need a mention as being anything important (we
> don't use them as they don't give any version info).
>
> We've already given 5 use cases, which I think is enough. The DRS is
> used in a number of other ways.
>
> Hope this is useful,
>
> Yes thanks very much!
> Karl
>
> Jamie
>
> ------------------------------------------------------------------------
>
> *From:*go-essp-tech-bounces at ucar.edu
> <mailto:go-essp-tech-bounces at ucar.edu>
> [mailto:go-essp-tech-bounces at ucar.edu] *On Behalf Of *Karl Taylor
> *Sent:* 10 February 2012 01:32
> *To:* V. Balaji; Steve Hankin; Martin Juckes; Bryan Lawrence;
> Stephen Pascoe; go-essp-tech at ucar.edu <mailto:go-essp-tech at ucar.edu>
> *Subject:* [Go-essp-tech] DRS corrections and extensions
>
> Dear all,
>
> Attached is my attempt to make the DRS consistent with CMIP5 (in
> describing the precision of "time instants"), but primarily to
> extend it to a more complete treatment of spatio-temporal subsets
> or means. I've also corrected a few typos.
>
> Comments most welcome. In particular could someone recheck
> sections 3.3-3.5 (which haven't been changed by me) to see if they
> remain consistent with CMIP5?
>
> thanks and best regards,
> Karl
>
>
> --
> Scanned by iCritical.
>
>
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