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[EP-tech] Antwort: RE: Hyperauthorship



Hi Chris,

>From a repository admin's point of view I can see this being the
easiest and probably most obvious way of stating it should not be
cached.  I am just not sure how much of an impact there would be having
to load the citation file each time before making a decision.  Maybe
there is something that caches this periodically (i.e. at the start of
when generate_views runs and when EPrints is reloaded in Apache).

Regards

David Newman

On Fri, 2019-05-31 at 13:46 +0100, Christ?pher Gutteridge wrote:
> I would suggest that the exception should be added to the citation
> file.
> The issue.xml citation is part of /lib/ so can easily be modified in
> an
> upgrade, which was why that was designed that way.
>
> On 31/05/2019 13:02, Newman D.R. wrote:
> >
> > Hi Chris,
> >
> > Thanks for the info.  I will look into it.  I was certainly
> > thinking
> > that citation.pl should probably be called citation_caching.pl.
> >
> > Contextual citations may be an interesting edge case to deal with.
> >  Is
> > this something that is likely will be present for all modern
> > repositories or just the odd few?  I can add an exceptions list
> > based
> > on DataObj type and citation name (e.g. user, eprint, etc. and
> > default,
> > brief, etc.).
> >
> > Regards
> >
> > David Newman
> >
> > On Fri, 2019-05-31 at 12:08 +0100, Christ?pher Gutteridge wrote:
> > >
> > > I would suggest maybe calling it CitationCache to make it less
> > > confusing
> > > as much of the documentation uses "citation" to refer to the
> > > citation
> > > configuration files.
> > >
> > > I seem to recall from when I  looked into this years ago that
> > > there's
> > > a
> > > few citations that should not be cached as they have contextual
> > > information. eg.
> > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2
> > > Fgit
> > > hub.com%2Feprints%2Feprints%2Fblob%2F3.3%2Flib%2Fcitations%2Fepri
> > > nt%2
> > > Fissue.xml&data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450
> > > f41b
> > > 7810a08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdat
> > > a=Ve
> > > hZmkq%2BhGtlV2BoXyoF3Y9hn2zyBc0ki%2FcLJVyYCsA%3D&reserved=0
> > >
> > > On 31/05/2019 12:01, Newman D.R. wrote:
> > > >
> > > > Hi all,
> > > >
> > > > As promised here is the code that I wrote for citation caching:
> > > >
> > > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F
> > > > %2Fg
> > > > ithub.com%2Feprints%2Feprints3.4%2Fcommit%2F6aedd1c2b1ba4ce68fc
> > > > eb5c
> > > > da5&data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f41b7
> > > > 810a
> > > > 08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=d
> > > > IoNV
> > > > ArFilGXLssfRvSqnwCLQcA7Jfc43o9I98shzGw%3D&reserved=0
> > > > c16545a72b9d53
> > > >
> > > > You need to copy default_zero/cfg.d/citations.pl to your local
> > > > archive
> > > > and set enabled to 1.  You then need to run epadmin update to
> > > > create
> > > > the Citation dataset.
> > > >
> > > > I have found that on large browse view listing (e.g. 400-500)
> > > > if
> > > > the
> > > > citations are already cached I get an improvement from a 6
> > > > second
> > > > load
> > > > time to 2 seconds.  However, if the citations need caching
> > > > before
> > > > the
> > > > browse view can be generated then the first load time is 10
> > > > seconds.
> > > >    However, this will be a one off unless you run the
> > > > refresh_citations
> > > > epadmin command that works like refresh_abstracts but for
> > > > citations.
> > > >
> > > > Please feel free to try out and ask any questions.   I have
> > > > done
> > > > some
> > > > basic testing on it but I think it is a little way of deploying
> > > > in
> > > > a
> > > > production environment.  I would want to be confident that
> > > > citations
> > > > are always cleared when an EPrints is modified, which should
> > > > always
> > > > be
> > > > the case but might be susceptible to race conditions where the
> > > > cache is
> > > > not cleared in time and the old cached citation is used rather
> > > > than
> > > > generating a new one.
> > > >
> > > > Regards
> > > >
> > > > David Newman
> > > >
> > > > On Thu, 2019-05-16 at 14:35 +0000, Newman D.R. via Eprints-tech
> > > > wrote:
> > > > >
> > > > > Hi Chris,
> > > > >
> > > > > I have implemented this but it is still under testing to see
> > > > > how
> > > > > much
> > > > > it speeds things up.  I will see if I can make this available
> > > > > as
> > > > > a
> > > > > branch on GitHub at some point.  However, I seem to be
> > > > > already
> > > > > being
> > > > > two jobs at the moment.  So doing interesting EPrints
> > > > > development
> > > > > rather than basic additional functionality and bug fixing is
> > > > > a
> > > > > bit of
> > > > > a
> > > > > luxury time does not afford.
> > > > >
> > > > > Regards
> > > > >
> > > > > David Newman
> > > > >
> > > > > On Thu, 2019-05-16 at 14:25 +0000, Christ?pher Gutteridge via
> > > > > Eprints-
> > > > > tech wrote:
> > > > > >
> > > > > > We should have made something long ago which can cache the
> > > > > > rendered
> > > > > > versions of citations and Export plugins for single items,
> > > > > > and
> > > > > > invalidated the cache when records are altered or the
> > > > > > config is
> > > > > > changed... would speed up everything a load.
> > > > > > (Sorry, I sketched the idea years ago and never implemented
> > > > > > it)
> > > > > > On 16/05/2019 15:08, John Salter via Eprints-tech wrote:
> > > > > > >
> > > > > > > The database takes a big hit for OAI-PMH requests that
> > > > > > > include
> > > > > > > hyper-authored papers.
> > > > > > > We have a block of 100 records that contains ~10 ATLAS
> > > > > > > research
> > > > > > > papers - each with 3,000+ authors.
> > > > > > > This takes a while to generate the XML response (there's
> > > > > > > *a
> > > > > > > lot*
> > > > > > > of
> > > > > > > nodes that get created).
> > > > > > >
> > > > > > > I've got this EPScript addition to limit the authors in a
> > > > > > > citation
> > > > > > > (it's not perfect - I should have used a couple of
> > > > > > > phrases in
> > > > > > > there
> > > > > > > - if I was going to share it formally).
> > > > > > > https://eur03.safelinks.protection.outlook.com/?url=https
> > > > > > > %3A%
> > > > > > > 2F%2
> > > > > > > Fgist.github.com%2Fjesusbagpuss%2Ffbec13d9986fba8e93b56ae
> > > > > > > 5ba3
> > > > > > > 4c1&
> > > > > > > amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c5698f246
> > > > > > > 85c2
> > > > > > > b408
> > > > > > > d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sda
> > > > > > > ta=l
> > > > > > > 7wL8
> > > > > > > BnRgf8EA7E3SxuGBraA1Y%2BjALC8VfrCLI2H4Mc%3D&reserved=
> > > > > > > 0
> > > > > > > 64
> > > > > > >
> > > > > > > On our summary page we also have the full author list
> > > > > > > displayed.
> > > > > > > For us, the issue we're concerned about is that when we
> > > > > > > have
> > > > > > > a
> > > > > > > paper with loads of authors, if someone editing the item
> > > > > > > visits a
> > > > > > > workflow stage with the authors on it, it takes *ages* to
> > > > > > > do
> > > > > > > anything.
> > > > > > >
> > > > > > > Our repo staff want to retain the complete author list -
> > > > > > > so
> > > > > > > I'll
> > > > > > > continue looking down the 'improved input methods' path
> > > > > > > rather
> > > > > > > than
> > > > > > > 'truncate from source' option.
> > > > > > >
> > > > > > > Cheers,
> > > > > > > John
> > > > > > >
> > > > > > > From: eprints-tech-bounces at ecs.soton.ac.uk
> > > > > > > [mailto:eprints-
> > > > > > > tech-
> > > > > > > bou
> > > > > > > nces at ecs.soton.ac.uk] On Behalf Of martin.braendle--- via
> > > > > > > Eprints-
> > > > > > > tech
> > > > > > > Sent: 16 May 2019 14:36
> > > > > > > To: John Salter <J.Salter at leeds.ac.uk>
> > > > > > > Cc: eprints-tech at ecs.soton.ac.uk
> > > > > > > Subject: [EP-tech] Antwort: RE: Hyperauthorship
> > > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > we thought of limiting the rendering, too. However, in
> > > > > > > that
> > > > > > > case,
> > > > > > > the database has to deliver the author records before the
> > > > > > > limit
> > > > > > > is
> > > > > > > applied, which involves a performance penalty. Anyone who
> > > > > > > had
> > > > > > > to
> > > > > > > deal with a 2000 author item in EPrints can tell what
> > > > > > > this is
> > > > > > > like.
> > > > > > > That's why we decided to limit on input already.
> > > > > > >
> > > > > > > Cheers,
> > > > > > >
> > > > > > > Martin
> > > > > > >
> > > > > > > "John Salter" ---16.05.2019 14:36:13---Hi Martin,
> > > > > > > Interesting
> > > > > > > approach. The records I'm, looking at all come via
> > > > > > > Symplectic
> > > > > > > or
> > > > > > > Pure - and w
> > > > > > >
> > > > > > > Von: "John Salter" <J.Salter at leeds.ac.uk>
> > > > > > > An: "martin.braendle at id.uzh.ch" <martin.braendle at id.uzh.c
> > > > > > > h>,
> > > > > > > "eprin
> > > > > > > ts-tech at ecs.soton.ac.uk" <eprints-tech at ecs.soton.ac.uk>
> > > > > > > Datum: 16.05.2019 14:36
> > > > > > > Betreff: RE: [EP-tech] Hyperauthorship
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Hi Martin,
> > > > > > > Interesting approach. The records I'm, looking at all
> > > > > > > come
> > > > > > > via
> > > > > > > Symplectic or Pure - and we could implement some form of
> > > > > > > limit to
> > > > > > > the number of authors - and retain any that are
> > > > > > > 'resolved'
> > > > > > > (local)
> > > > > > > authors.
> > > > > > >
> > > > > > > I was thinking of changing the default input rendering
> > > > > > > for
> > > > > > > the
> > > > > > > creator field along these lines:
> > > > > > > If there are < LIMIT authors, render input as currently
> > > > > > > exists
> > > > > > > If there are > LIMIT authors, render a static list of
> > > > > > > them,
> > > > > > > and
> > > > > > > enhance with javascript to allow editing of specific
> > > > > > > entries
> > > > > > > /
> > > > > > > re-
> > > > > > > ordering / searching filtering the list.
> > > > > > >
> > > > > > > This could even be deployed as a separate workflow stage
> > > > > > > (which
> > > > > > > only appears when there are > LIMIT authors).
> > > > > > >
> > > > > > > I'll have to see what people here think about limiting
> > > > > > > the
> > > > > > > author
> > > > > > > list on the way in to EPrints - that sounds like a better
> > > > > > > place
> > > > > > > to
> > > > > > > be?
> > > > > > >
> > > > > > > Cheers,
> > > > > > > John
> > > > > > >
> > > > > > >
> > > > > > > From: martin.braendle at id.uzh.ch [mailto:martin.braendle at i
> > > > > > > d.uz
> > > > > > > h.ch
> > > > > > > ]
> > > > > > > Sent: 16 May 2019 13:22
> > > > > > > To: eprints-tech at ecs.soton.ac.uk; John Salter <J.Salter at l
> > > > > > > eeds
> > > > > > > .ac.
> > > > > > > uk
> > > > > > > >
> > > > > > > >
> > > > > > > Subject: Re: [EP-tech] Hyperauthorship
> > > > > > >
> > > > > > > Hi John,
> > > > > > >
> > > > > > > we have a lot of high energy physics or biomedical
> > > > > > > articles
> > > > > > > with
> > > > > > > hundreds or thousands of authors. Usually, those are
> > > > > > > submitted
> > > > > > > via
> > > > > > > CrossRef or PubMed import.
> > > > > > >
> > > > > > > We have adapted the corresponding import plugins to limit
> > > > > > > the
> > > > > > > number of authors by a configurable limit (in our case
> > > > > > > 30).
> > > > > > > If
> > > > > > > the
> > > > > > > limit is exceeded, "et al" is added as the  ($limit+1)th
> > > > > > > author,
> > > > > > > the remaining authors are not imported and a warning
> > > > > > > message
> > > > > > > is
> > > > > > > issued. Submitters are then still free to add the
> > > > > > > remaining
> > > > > > > UZH
> > > > > > > authors manually and use et al for authors outside of
> > > > > > > UZH.
> > > > > > >
> > > > > > > Instead of the DOI plugin, we have developed a CrossRef
> > > > > > > plugin
> > > > > > > that
> > > > > > > uses the CrossRef REST API . It implements the author
> > > > > > > limitation
> > > > > > > as
> > > > > > > well. We decided to go with the CrossRef REST API because
> > > > > > > funder
> > > > > > > information can be imported from there.
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > Martin
> > > > > > >
> > > > > > > --
> > > > > > > Dr. Martin Br?ndle
> > > > > > > https://eur03.safelinks.protection.outlook.com/?url=https
> > > > > > > %3A%
> > > > > > > 2F%2
> > > > > > > Forcid.org%2F0000-0002-7752-
> > > > > > > 6567&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c569
> > > > > > > 8f24
> > > > > > > 685c
> > > > > > > 2b408d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&am
> > > > > > > p;sd
> > > > > > > ata=
> > > > > > > VC8Bwg2BLpo%2BybPatYVIyBvALgwZhIZ4Az4bBUkKXFY%3D&amp;rese
> > > > > > > rved
> > > > > > > =0
> > > > > > > Zentrale Informatik
> > > > > > > Universit?t Z?rich
> > > > > > > Stampfenbachstr. 73
> > > > > > > CH-8006 Z?rich
> > > > > > >
> > > > > > > "John Salter via Eprints-tech" ---16.05.2019 14:00:41---
> > > > > > > Hi,
> > > > > > > Has
> > > > > > > anyone done any work on making the EPrints workflow a bit
> > > > > > > more
> > > > > > > sensible when a paper has man
> > > > > > >
> > > > > > > Von: "John Salter via Eprints-tech" <eprints-tech at ecs.sot
> > > > > > > on.a
> > > > > > > c.uk
> > > > > > > An: "'eprints-tech at ecs.soton.ac.uk'" <eprints-tech at ecs.so
> > > > > > > ton.
> > > > > > > ac.u
> > > > > > > k>
> > > > > > > Datum: 16.05.2019 14:00
> > > > > > > Betreff: [EP-tech] Hyperauthorship
> > > > > > > Gesendet von: <eprints-tech-bounces at ecs.soton.ac.uk>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Hi,
> > > > > > > Has anyone done any work on making the EPrints workflow a
> > > > > > > bit
> > > > > > > more
> > > > > > > sensible when a paper has many authors (hundreds or
> > > > > > > thousands)?
> > > > > > >
> > > > > > > Cheers,
> > > > > > > John
> > > > > > >
> > > > > > >
> > > > > > > John Salter
> > > > > > > https://eur03.safelinks.protection.outlook.com/?url=http%
> > > > > > > 3A%2
> > > > > > > F%2F
> > > > > > > orcid.org%2F0000-0002-8611-
> > > > > > > 8266&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c569
> > > > > > > 8f24
> > > > > > > 685c
> > > > > > > 2b408d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&am
> > > > > > > p;sd
> > > > > > > ata=
> > > > > > > kjC4zZaCbC3FpYg53MlgUmfkiuWdpysY7o4wYMO7noU%3D&amp;reserv
> > > > > > > ed=0
> > > > > > >
> > > > > > > White Rose Libraries Technical Officer
> > > > > > > IT - Application Support (Research)
> > > > > > > 10.23B, IT Services Building
> > > > > > > University of Leeds
> > > > > > > Leeds
> > > > > > > LS2 9JT
> > > > > > > 0113 34 37385
> > > > > > >
> > > > > > > Online: https://eur03.safelinks.protection.outlook.com/?u
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> > > > > > > C4a5
> > > > > > > 378f
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> > > > > > > 7Xrl
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> > > > > > > u&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f
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> > > > > > > 01%7
> > > > > > > C01%
> > > > > > > 7Cdrn%40ecs.soton.ac.uk%7C17a35c5698f24685c2b408d6da0bc70
> > > > > > > f%7C
> > > > > > > 4a53
> > > > > > > 78f929f44d3ebe89669d03ada9d8%7C0&amp;sdata=bAAmMyyLM3BKMy
> > > > > > > aJKV
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