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[EP-tech] Antwort: RE: Hyperauthorship



Hi Chris,

I have made the changes you suggested and they seem to be working will push back to GitHub once I have had a chance to fully review them.  I have added something to perl_lib/EPrints/Citation/EPC.pm that looks out for the start of a citation that looks like this:

<cite:citation xmlns:xhtml="http://www.w3.org/1999/xhtml<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.w3.org%2F1999%2Fxhtml&data=01%7C01%7C%7C5438f7c1042c4025b2c908d6f6667b27%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=Hy%2B2t25AgTZbyVqNp22nXxEHnyDFzsNYv1GqriFGCQk%3D&reserved=0>" xmlns="http://eprints.org/ep3/control"; xmlns:cite="http://eprints.org/ep3/citation"; cite:disable-caching="yes">

This is very much like the code already present that looks for trim-whitespace.

Regards

David Newman

On Wed, 2019-06-05 at 10:20 +0000, Newman D.R. via Eprints-tech wrote:
Hi Chris,

If it is preloaded this is less of an issue, I will have a look to see
how such a variable could be stored as part of this preload.

Regards

David Newman

On Wed, 2019-06-05 at 10:44 +0100, Christ?pher Gutteridge wrote:

Citation XML files are loaded in advance, so that's not an issue:

https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit
hub.com%2Feprints%2Feprints%2Fblob%2F3.3%2Fperl_lib%2FEPrints%2FRepos
itory.pm%23L260&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C47cbfa6d63
684db04f2f08d6e99a710b%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&amp;sda
ta=hDezkbYKSdim%2FgKrTv%2BUtxByE%2BX9OWaIKBDde9t9Cr4%3D&amp;reserved=
0

You'd need to detect the flag in
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit
hub.com%2Feprints%2Feprints%2Fblob%2F3.3%2Fperl_lib%2FEPrints%2FRepos
itory.pm%23L1001&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C47cbfa6d6
3684db04f2f08d6e99a710b%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&amp;sd
ata=5rTcT9srOgaFIypGq1GUj1Y6yja0MxQ6dfckenju7ww%3D&amp;reserved=0
somehow.

I know it feels easier to put the "no cache" config elsewhere but it
really should be part of the citation file itself.


On 05/06/2019 10:21, Newman D.R. wrote:


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%2F
epri
nt%2
Fissue.xml&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f6
6450
f41b
7810a08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&amp;
sdat
a=Ve
hZmkq%2BhGtlV2BoXyoF3Y9hn2zyBc0ki%2FcLJVyYCsA%3D&amp;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%3
A%2F
%2Fg
ithub.com%2Feprints%2Feprints3.4%2Fcommit%2F6aedd1c2b1ba4ce
68fc
eb5c
da5&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f
41b7
810a
08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&amp;sda
ta=d
IoNV
ArFilGXLssfRvSqnwCLQcA7Jfc43o9I98shzGw%3D&amp;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=h
ttps
%3A%
2F%2
Fgist.github.com%2Fjesusbagpuss%2Ffbec13d9986fba8e93b
56ae
5ba3
4c1&
amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c5698
f246
85c2
b408
d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&amp
;sda
ta=l
7wL8
BnRgf8EA7E3SxuGBraA1Y%2BjALC8VfrCLI2H4Mc%3D&amp;reser
ved=
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-bounces at ecs.soton.ac.uk>
[mailto:eprints-
tech-
bou
nces at ecs.soton.ac.uk<mailto: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<mailto:J.Salter at leeds.ac.uk>>
Cc: eprints-tech at ecs.soton.ac.uk<mailto: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<mailto:J.Salter at leeds.ac.uk>>
An: "martin.braendle at id.uzh.ch<mailto:martin.braendle at id.uzh.ch>" <martin.braendle at id.u
zh.c
h>,
"eprin
ts-tech at ecs.soton.ac.uk<mailto:ts-tech at ecs.soton.ac.uk>" <eprints-tech at ecs.soton.ac.u
k>
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 id.uzh.ch> [mailto:martin.braend
le at i<mailto:le at i>
d.uz
h.ch
]
Sent: 16 May 2019 13:22
To: eprints-tech at ecs.soton.ac.uk<mailto:eprints-tech at ecs.soton.ac.uk>; John Salter <J.Salt
er at l<mailto:er 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=h
ttps
%3A%
2F%2
Forcid.org%2F0000-0002-7752-
6567&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35
c569
8f24
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0&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<mailto:'eprints-tech at ecs.soton.ac.uk>'" <eprints-tech at ec
s.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<mailto: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=h
ttp%
3A%2
F%2F
orcid.org%2F0000-0002-8611-
8266&amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35
c569
8f24
685c
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0&am
p;sd
ata=
kjC4zZaCbC3FpYg53MlgUmfkiuWdpysY7o4wYMO7noU%3D&amp;re
serv
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

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