[Go-essp-tech] What is the risk that science is done using 'deprecated' data?

stephen.pascoe at stfc.ac.uk stephen.pascoe at stfc.ac.uk
Fri Mar 9 02:48:55 MST 2012 

Hi Estani,

CMIP6+: +1

I'm delighted that this is your experience because it's exactly how DRS atomic datasets were originally designed.  We changed published datasets to be larger aggregations because we thought the software wouldn't cope with so many THREDDS catalogs.  It's a pity that another part of the DRS design -- realms -- haven't proved a good fit with the CMIP5 experiment design or how models are really run.  mip-table =~ realm but not quite and not always.  So publication units usually don't match what changes.

If the technology can cope we should move the publication level to variables.  I wonder whether the new TDS would cope with that many catalogs? ExArch could test this.

S.

On 9 Mar 2012, at 09:02, Estanislao Gonzalez wrote:

> Hi,
> 
> if we start this discussion again (which I'd love to :-)) we should be 
> clear that we are talking about cmip6+ IMHO. Just to avoid mixing what 
> we can and should do now, from what we just can't.
> That being said, we could start discussing what exactly needs to be 
> versioned and why.
> Making a hash that uniquely identifies all the information, like the one 
> you've proposed Stephen, is certainly appealing. Though we will have a 
> lot of hashes, most of them pointing to the same data from the user 
> perspective. For instance, the user download a variable and from that 
> point onwards, other variables got add and changed, catalogs get 
> republished unintentionally or moved to other machines, errors at all 
> stages get corrected, new access to the data get inserted to the 
> catalogs, etc (They do happen, I've done them all). I'd expect about 20 
> different hashes from it, none of them would be interesting to the user.
> IMHO we need to find proper versioning units; the publication unit 
> (realm dataset) as we now use might not be the best option.
> AFAICT everything moves in variable units (atomic datasets). My 
> publication tasks are very different, but it never matches the 
> publication unit we use.... hardly ever.
> 
> For example this is how publication looks from my perspective:
> Normally I get information about a complete ensemble that was created 
> anew. No information on what was changed or not. Just the data (and the 
> computed checksums). I have to find out which datasets are there and how 
> they relate to the ones I've already published (i.e. I have to 
> distinguish between new, changed and deleted).
> Then the other common tasks are, e.g., when a variable was wrongly 
> computed. So I get something like, "umo,vmo from 1pctCO2 are wrong and 
> will be recalculated". This requires me to extract the variables from 
> the datasets (finding out which), publish a new version without them and 
> when they are corrected, generated yet another new version to include 
> the corrected variables.
> This generates 2 Versions without any meaning for those users interested 
> in other variables.
> All the data I get is not related at all with the "realm" datasets (or 
> publication units). And this makes the data management more difficult.
> 
> I just think we might want to review what we need and distinguish the 
> bes units from three different perspectives: the producer (cmor), the 
> data manager (esg) and the user.
> Once we know that for sure (and I doubt it will be the same unit for 
> all), then we can think about unique ids and a hashing procedure, which 
> I strongly support.
> 
> My 2c,
> Estani
> 
> Am 09.03.2012 08:26, schrieb stephen.pascoe at stfc.ac.uk:
>> Hi Gavin,
>> 
>> That would definitely help but I don't think it's sufficient.  How many of us would notice if a centre republished the same dataset (same dataset_id and facet metadata) with different checksums?  Estani would I expect :-) but the system itself wouldn't.
>> 
>> I would like to see a hash of invariants of each dataset used as identifiers.  For that we'd need to strip-out all the information from a THREDDS catalog which might legitimately change without changing the data: URL paths, service endpoints, last-modified, etc., but keeping filenames, checksums and some properties.  Canonicalise a serialisiation then generate a hash.
>> 
>> We'd also need to really keep track of these hashes.  We have checksums and tracking_ids right now and are under-utilising them.
>> 
>> Cheers,
>> Stephen.
>> 
>> On 9 Mar 2012, at 05:05, Gavin M. Bell wrote:
>> 
>> Hello,
>> 
>> If we enforced checksums to be done as a part of publication, then this would address this issue, right?
>> 
>> 
>> On 3/8/12 8:39 AM, stephen.pascoe at stfc.ac.uk<mailto:stephen.pascoe at stfc.ac.uk>  wrote:
>> 
>> Tobias, sorry I miss-typed your name :-)
>> S.
>> 
>> On 8 Mar 2012, at 16:00,<stephen.pascoe at stfc.ac.uk><mailto:stephen.pascoe at stfc.ac.uk>
>>  wrote:
>> 
>> 
>> 
>> Hi Thomas,
>> 
>> As you say, it's too late to do much re-engineering of the system now -- we've attempted to put in place various identifier systems and none of them are working particularly well -- however I think there is another perspective to your proposal:
>> 
>> 1. ESG/CMIP5 is deployed globally across multiple administrative domains and each domain has the ability to cut corners to get things done, e.g. replacing files silently without changing identifiers.
>> 
>> 2. ESG/CMIP5 system is so complex that who'd blame a sys-admin for doing #1 to get the data to scientists when they need it.  Any system that makes it impossible, or even only difficult, to change the underlying data is going to be more complex and difficult to administer than a system that doesn't, unless that system was very rigorously designed, implemented and tested.
>> 
>> Because of #1 I'm convinced that a fit-for-purpose identifier system wouldn't use randomly generated UUIDs but would take the GIT approach of hashing invariants of the dataset so that any changes behind the scenes can be detected.
>> 
>> Because of #2 I'm convinced that now is not the time to start building more software to do this.  We have to stabilise the system and learn the lessons of CMIP5 first.
>> 
>> Cheers,
>> Stephen.
>> 
>> 
>> On 8 Mar 2012, at 15:32, Tobias Weigel wrote:
>> 
>> 
>> 
>> Jamie/All,
>> 
>> these are important questions I have been wondering about as well; we just had a small internal meeting yesterday with Estani and Martina, so I'll try to sum some points up here. I am not too familiar with the ESG publishing process, so I can only guess that Stephen's #1 has something to do with the bending of policies that are for pragmatic reasons not enforced in the CMIP5 process. (My intuition is that *ideally* it should be impossible to make data available without going through the whole publication process. Please correct me if I am misunderstanding this.)
>> 
>> Most of what I have been thinking about however concerns point #2. I'd claim that the risk here should not be underestimated; data consumers being unable to find the data they need is bad ("the advanced search issue"), but users relying on deprecated data - most likely without being aware of it - is certainly dangerous for scientific credibility.
>> My suggestion to address this problem is to use globally persistent identifiers (PIDs) that are automatically assigned to data objects (and metadata etc.) on ESG-publication; data should ideally not be known by its file name or system-internal ID, but via a global identifier that never changes after it has been published. Of course, this sounds like the DOIs, but these are extremely coarse grained and very static. The idea is to attach identifiers to the low-level entities and provide solutions to build up a hierarchical ID system (virtual collections) to account for the various layers used in our data. Such persistent identifiers should then be placed prominently in any user interface dealing with managed data. The important thing is: If data is updated, we don't update the data behind identifier x, but assign a new identifier y and create a typed link between these two (which may be the most challenging part) and perhaps put a small annotation on x that this data is depreca
>> ted. A clever user interface should then redirect a user consistently to the latest version of a dataset if a user accesses the old identifier.
>> This does not make it impossible to use deprecated data, but at least it raises the consumer's awareness of the issue and lowers the barrier to re-retrieve valid data.
>> 
>> As for the point in time; I'd be certain that it is too late now, but it is always a good idea to have plans for future improvement.. :)
>> 
>> Best, Tobias
>> 
>> Am 08.03.2012 13:06, schrieb Kettleborough, Jamie:
>> 
>> 
>> Thanks for the replies on this - any other replies are still very welcome.
>> 
>> Stephen - being selfish - we aren't too worried about 2 as its less of an issue for us (we do a daily trawl of thredds catalogues for new datasets), but I agree it is a problem more generally.  I don't have a feel for which of the problems 1-3 would minimise the risk most if you solved it.  I think making sure new data has a new version is a foundation though.
>> 
>> Part of me wonders though whether its already too late to really do anything with versioning in its current form.  *But* I may be overestimating the size of the problem of new datasets appearing without versions being updated.
>> 
>> Jamie
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> 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 Sébastien Denvil
>> Sent: 08 March 2012 10:41
>> To: go-essp-tech at ucar.edu<mailto:go-essp-tech at ucar.edu>
>> Subject: Re: [Go-essp-tech] What is the risk that science is
>> done using 'deprecated' data?
>> 
>> Hi Stephen, let me add a third point:
>> 
>> 3. Users are aware of a new versions but can't download files
>> so as to have a coherent set of files.
>> 
>> With respect to that point the p2p transition (especially the
>> attribut caching on the node) will be a major step forward.
>> GFDL just upgrad and we have an amazing success rate of 98%.
>> 
>> And I agree with Ashish.
>> 
>> Regards.
>> Sébastien
>> 
>> Le 08/03/2012 11:34, stephen.pascoe at stfc.ac.uk<mailto:stephen.pascoe at stfc.ac.uk>  a écrit :
>> 
>> 
>> Hi Jamie,
>> 
>> I can imagine there is a risk of papers being written on
>> 
>> 
>> deprecated data in two scenarios:
>> 
>> 
>>  1. Data is being updated at datanodes without creating a
>> 
>> 
>> new version
>> 
>> 
>>  2. Users are unaware of new versions available and
>> 
>> 
>> therefore using
>> 
>> 
>> deprecated data
>> 
>> Are you concerned about both of these scenarios?  Your
>> 
>> 
>> email seems to mainly address #1.
>> 
>> 
>> Thanks,
>> Stephen.
>> 
>> On 8 Mar 2012, at 10:21, Kettleborough, Jamie wrote:
>> 
>> 
>> 
>> Hello,
>> 
>> Does anyone have a feel for the current level of risk that
>> 
>> 
>> analysists
>> 
>> 
>> are doing work (with the intention to publish) on data
>> 
>> 
>> that has been
>> 
>> 
>> found to be wrong by the data providers and so deprecated (in some
>> sense)?
>> 
>> My feeling is that versioning isn't working (that may be
>> 
>> 
>> putting it a
>> 
>> 
>> bit strongly.  It is too easy for data providers - in their
>> understandable drive to get their data out - to have
>> 
>> 
>> updated files on
>> 
>> 
>> disk without publishing a new version.   How big a deal does anyone
>> think this is?
>> 
>> If the risk that papers are being written based on
>> 
>> 
>> deprecated data is
>> 
>> 
>> sufficiently large then is there an agreed strategy for
>> 
>> 
>> coping with
>> 
>> 
>> this?  Does it have implications for the requirements of the data
>> publishing/delivery system?
>> 
>> Thanks,
>> 
>> Jamie
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>> --
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>> 
>> --
>> Tobias Weigel
>> 
>> Department of Data Management
>> Deutsches Klimarechenzentrum GmbH (German Climate Computing Center)
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>> 20146 Hamburg
>> Germany
>> 
>> Tel.: +49 40 460094 104
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>> 
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>> 
>> --
>> Gavin M. Bell
>> --
>> 
>>  "Never mistake a clear view for a short distance."
>>                -Paul Saffo
>> 
>> 
>> 
> 
> 
> -- 
> Estanislao Gonzalez
> 
> Max-Planck-Institut für Meteorologie (MPI-M)
> Deutsches Klimarechenzentrum (DKRZ) - German Climate Computing Centre
> Room 108 - Bundesstrasse 45a, D-20146 Hamburg, Germany
> 
> Phone:   +49 (40) 46 00 94-126
> E-Mail:  gonzalez at dkrz.de
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