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

Bryan Lawrence bryan.lawrence at ncas.ac.uk
Mon Mar 12 13:09:32 MDT 2012 

Hi Folks

I totally agree with Balaji.

But I don't understand in any case what data has been *published* at ORNL as the primary data node that's not online on disk somewhere?

Thanks
Bryan

> Sorry, I don't see how checksumming can be optional even if the costs
> are as high as you describe. How is a user to know whether the bits
> they downloaded are good or not? What is the recourse if papers are
> written using the wrong bits, and later, an independent analysis of
> the same data do not reproduce the same result?
> 
> PS. There are already FOIA requests out for CMIP5 models and data.
> It's a jungle out there... be sure that hostile eyes will be going
> over every result and finding...
> 
> On Mon, Mar 12, 2012 at 12:46 PM, Barron Jr, Tom O. <tbarron at ornl.gov> wrote:
> > Thanks for the reply, Gavin. I understand what you say.
> >
> > I just wanted to highlight that a significant amount of data has been published without checksums at ORNL on the ESG2 gateway. Extracting it all from the HPSS archive for checksumming in preparation for republishing on the ESGF portal will take significant time. I'm not saying we shouldn't do it. Just that we shouldn't expect to get it done quickly.
> >
> > Tom
> >
> > On 2012.0309, at 17:24, Gavin M. Bell wrote:
> >
> >> Hi Tom,
> >>
> >> In the simplest form of the assertions we have made about checksums... If you can't get the checksums then it shouldn't / can't be published, period.  So access must be gotten and checksums computed.  Otherwise you simply can't *trust* the data is "who it says it is".
> >>
> >> On 3/9/12 11:10 AM, Barron Jr, Tom O. wrote:
> >>> How will a requirement for checksums affect the ability to publish offline datasets that are not immediately accessible for computing a checksum?
> >>>
> >>> On 2012.0309, at 03:47, Gavin M. Bell wrote:
> >>>
> >>>
> >>>> With checksums, we can put in client-side sanity checking tools to give users peace of mind.  The other side benefit would be alerting offending sites that something is wrong.  I agree with you, Bryan, checksums are a must.  We can enforce it mechanically in the publisher.  This is worth bringing up at the next call - without spending too much time on it.
> >>>>
> >>>> On 3/9/12 12:20 AM, Bryan Lawrence wrote:
> >>>>
> >>>>> Karl has written to modellng centres requiring them to do this, and I think we should start enforcing it.
> >>>>> Bryan
> >>>>>
> >>>>>
> >>>>>
> >>>>>> 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
> >>>>>>
> >>>>>>  wrote:
> >>>>>>
> >>>>>>
> >>>>>>> Tobias, sorry I miss-typed your name :-)
> >>>>>>> S.
> >>>>>>>
> >>>>>>> On 8 Mar 2012, at 16:00,
> >>>>>>>
> >>>>>>> <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
> >>>>>>>>>>>
> >>>>>>>>>>> ] On Behalf Of Sébastien Denvil
> >>>>>>>>>>> Sent: 08 March 2012 10:41
> >>>>>>>>>>> To:
> >>>>>>>>>>>
> >>>>>>>>>>> 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
> >>>>>>>>>>>
> >>>>>>>>>>>  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
> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> GO-ESSP-TECH mailing list
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> GO-ESSP-TECH at ucar.edu
> >>>>>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/go-essp-tech
> >>>>>>>>>>> --
> >>>>>>>>>>> Sébastien Denvil
> >>>>>>>>>>> IPSL, Pôle de modélisation du climat
> >>>>>>>>>>> UPMC, Case 101, 4 place Jussieu,
> >>>>>>>>>>> 75252 Paris Cedex 5
> >>>>>>>>>>>
> >>>>>>>>>>> Tour 45-55 2ème étage Bureau 209
> >>>>>>>>>>> Tel: 33 1 44 27 21 10
> >>>>>>>>>>> Fax: 33 1 44 27 39 02
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>> _______________________________________________
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> >>>>>>>>>>
> >>>>>>>>>>
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> >>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/go-essp-tech
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> Department of Data Management
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> >>>>> --
> >>>>> Bryan Lawrence
> >>>>> University of Reading:  Professor of Weather and Climate Computing.
> >>>>> National Centre for Atmospheric Science: Director of Models and Data.
> >>>>> STFC: Director of the Centre for Environmental Data Archival.
> >>>>> Ph: +44 118 3786507 or 1235 445012; Web:home.badc.rl.ac.uk/lawrence
> >>>>>
> >>>>>
> >>>> --
> >>>> Gavin M. Bell
> >>>> --
> >>>>
> >>>>  "Never mistake a clear view for a short distance."
> >>>>                      -Paul Saffo
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> GO-ESSP-TECH mailing list
> >>>>
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> >>>> http://mailman.ucar.edu/mailman/listinfo/go-essp-tech
> >>> _______________________________________________
> >>> GO-ESSP-TECH mailing list
> >>>
> >>> GO-ESSP-TECH at ucar.edu
> >>> http://mailman.ucar.edu/mailman/listinfo/go-essp-tech
> >>
> >> --
> >> Gavin M. Bell
> >> --
> >>
> >>  "Never mistake a clear view for a short distance."
> >>                      -Paul Saffo
> >>
> >>
> >
> > _______________________________________________
> > GO-ESSP-TECH mailing list
> > GO-ESSP-TECH at ucar.edu
> > http://mailman.ucar.edu/mailman/listinfo/go-essp-tech
> 
> 
> 
> 

--
Bryan Lawrence
University of Reading:  Professor of Weather and Climate Computing.
National Centre for Atmospheric Science: Director of Models and Data. 
STFC: Director of the Centre for Environmental Data Archival.
Ph: +44 118 3786507 or 1235 445012; Web:home.badc.rl.ac.uk/lawrence

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