[Go-essp-tech] What is the risk that science is done using 'deprecated' data?
Estanislao Gonzalez
gonzalez at dkrz.de
Fri Mar 16 07:54:44 MDT 2012
Hi,
Am 16.03.2012 14:29, schrieb stephen.pascoe at stfc.ac.uk:
>
> Estani,
>
> > Well... we are doing that. That's part of the script (of course, not
> all sites are publishing the same script, but that's yet another
> issue...).
> We are doing it on download, is there a way of doing it after they've
> downloaded?
>
I think I understand now what you mean. They can always perform a
checksum, and the information at the download time is stored in the wget
script. But I see you mean about a notification system.
Well that's something completely different to a checksum, which is what
Gavin was talking about and what Jamie continued on.
Checksums are not meant to notify anything, it's just a simply procedure
to extract a fairly good representation of data in a very brief form.
Indeed it's a good means for basing any comparison as you don't have to
move much data across the wire, but if anything it can be just a brick
for building such a system.
We could start a discussion on this, I just don't think it's so closely
related to checksums.
> > The problem is again, what to do with those sites not publishing
> them or publishing the wrong one.
>
> And also how do we know whether they've change them without updating
> the version.
>
In the worst case, we just don't. If you change BADC files, or remove
them, or change the read permits :-) then you'll realize just when
someone downloads the file and either can't, finds always the wrong
checksum, etc. Not before. And downloading the 1PB archive to see if
something was changed is not feasible.
My 2c,
Estani
>
> S.
>
> ---
>
> Stephen Pascoe +44 (0)1235 445980
>
> Centre of Environmental Data Archival
>
> STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
>
> *From:*Estanislao Gonzalez [mailto:gonzalez at dkrz.de]
> *Sent:* 16 March 2012 13:27
> *To:* Pascoe, Stephen (STFC,RAL,RALSP)
> *Cc:* go-essp-tech at ucar.edu
> *Subject:* Re: [Go-essp-tech] What is the risk that science is done
> using 'deprecated' data?
>
> Well... we are doing that. That's part of the script (of course, not
> all sites are publishing the same script, but that's yet another
> issue...).
> The problem is again, what to do with those sites not publishing them
> or publishing the wrong one.
>
> But I might not be getting the point, you are right.
>
> Thanks for putting the agenda together.
>
> Cheers,
> Estani
>
> Am 16.03.2012 14:22, schrieb stephen.pascoe at stfc.ac.uk:
> <mailto:stephen.pascoe at stfc.ac.uk:>
>
> Estani,
>
> I think the issue is wider than just publishing of checksums. We
> could do a lot more to help users verify they have the right data,
> e.g. automatically comparing checksums to the published ones after
> download.
>
> A new thread on Tuesday's agenda is coming ...
>
> S.
>
> ---
>
> Stephen Pascoe +44 (0)1235 445980
>
> Centre of Environmental Data Archival
>
> STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
>
> *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 *Estanislao Gonzalez
> *Sent:* 16 March 2012 13:15
> *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,
>
> IMHO there is not much to discuss at all.
> We could spare some Minutes to hear if someone has arguments against
> publishing the checksums and/or decide what to do with those cites
> breaking this rule, even partially.
>
> That shouldn't take more than 5'...
> In preparation to that, I'd say that people not wishing to comply with
> this request (providing valid and current checksums *as well* as
> publishing new data *always* under a new version) should start a new
> thread to discuss it (this one is too long and have already changed
> subjects a couple of times).
>
> My 2c,
> Estani
>
> Am 16.03.2012 14:01, schrieb stephen.pascoe at stfc.ac.uk:
> <mailto:stephen.pascoe at stfc.ac.uk:>
>
> Jamie,
>
> There will be a telco at 16:00GMT on Tuesday. We have several
> candidate topics for discussion at the moment (See
> http://esgf.org/wiki/Esgf/Cmip5Meetings) but checksums is not one of
> them. Let me coordinate a realistic agenda and I'll try and ensure
> there is some time to discuss this.
>
> Cheers,
>
> Stephen.
>
> ---
>
> Stephen Pascoe +44 (0)1235 445980
>
> Centre of Environmental Data Archival
>
> STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
>
> *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 *Kettleborough, Jamie
> *Sent:* 16 March 2012 10:27
> *To:* Gavin M. Bell; Barron Jr, Tom O.
> *Cc:* 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?
>
> Hello,
>
> when is the next telco, and is this issue on the agenda?
>
> Thanks,
>
> 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 *Gavin M. Bell
> *Sent:* 12 March 2012 22:21
> *To:* Barron Jr, Tom O.
> *Cc:* 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 Tom,
>
> I don't envy your (ORNL's .et al) position, but this is what must
> be done. This is why Balaji was so adamant about making checksums
> *required* from the very beginning of this endeavor. He was
> right. Though, to be honest it was always something that was
> known... this is not a surprise to anyone. I think that having it
> be "optional" in the publisher was the sticky point. Putting it
> in the publisher is, IMHO, or should be the checksum of last
> resort. Folks should have schemes to calculate these things out
> of band and integrating them back into the publisher... a feature
> that made it's way into the publisher albeit a bit after the
> bell. It is no one's fault just a comedy of errors but... now we
> are all enlightened and know *why* we need checksums (hashes) in a
> distributed system that requires integrity assertions made about
> said data.
>
> Oh well :-(...
>
> At least we are relatively early in the game... if that is any
> consolation :-\
>
> checksums or bust.
>
> P.S.
> Regarding the catalogs, the topic Stephen has been shepherding,
> there are cool things we can do with having the constituent files'
> checksums. Mmmwwaaahhh aahhh aahhhh.... (evil laugh).
>
>
> On 3/12/12 9:46 AM, Barron Jr, Tom O. 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 <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 annotatio!
>
> !
>
> n on x t
>
> hat 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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> Sébastien Denvil
>
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>
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>
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>
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>
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>
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>
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>
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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
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> Gavin M. Bell
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> Gavin M. Bell
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>
> "Never mistake a clear view for a short distance."
>
> -Paul Saffo
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>
> Lawrence Livermore National Labs
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>
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>
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> Estanislao Gonzalez
>
> Max-Planck-Institut für Meteorologie (MPI-M)
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> Room 108 - Bundesstrasse 45a, D-20146 Hamburg, Germany
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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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