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

Fri Mar 16 08:28:53 MDT 2012

>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.

I wasn't really thinking of notification (although we said we'd do that too ;-) ).  Presently the user can check their local files against the checksums in their wget script, assuming they take the precaution of keeping the script.  But they can't check the checksums against what they would download if they reran the script, or what they'd download if they repeated the query to potentially get different versions of files.

This information is available in the THREDDS catalogs and soon through P2P but there's no tool a user can run to compare what they have and what's available.

I believe we should really have a record of these checksums independent of the THREDDS catalogs under the control of the data nodes, so that it can be demonstrated whether a dataset has been republished with different data.  This independent location could be Gateways/P2P-index-nodes if we did real version control.  I.e. once a dataset is published the record of files & checksums never gets overwritten, only new versions appended.

Then it's a tools issue of making it easy to compare local files against the record of published files.

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 13:55
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?

Hi,

Am 16.03.2012 14:29, schrieb stephen.pascoe at stfc.ac.uk:<mailto: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<mailto: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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