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Re: [EP-tech] Antwort: RE: Hyperauthorship
- To: "Newman D.R." <drn@ecs.soton.ac.uk>, "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>, John Salter <J.Salter@leeds.ac.uk>, "martin.braendle@id.uzh.ch" <martin.braendle@id.uzh.ch>
- Subject: Re: [EP-tech] Antwort: RE: Hyperauthorship
- From: Christöpher Gutteridge <totl@soton.ac.uk>
- Date: Fri, 31 May 2019 12:46:29 +0000
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, Christöpher 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%2Fgit >> hub.com%2Feprints%2Feprints%2Fblob%2F3.3%2Flib%2Fcitations%2Feprint%2 >> Fissue.xml&data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f41b >> 7810a08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=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%2F6aedd1c2b1ba4ce68fceb5c >>> da5&data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f41b7810a >>> 08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=dIoNV >>> 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, Christöpher 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%2Ffbec13d9986fba8e93b56ae5ba3 >>>>>> 4c1& >>>>>> amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c5698f24685c2 >>>>>> b408 >>>>>> d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=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@ecs.soton.ac.uk [mailto:eprints- >>>>>> tech- >>>>>> bou >>>>>> nces@ecs.soton.ac.uk] On Behalf Of martin.braendle--- via >>>>>> Eprints- >>>>>> tech >>>>>> Sent: 16 May 2019 14:36 >>>>>> To: John Salter <J.Salter@leeds.ac.uk> >>>>>> Cc: eprints-tech@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@leeds.ac.uk> >>>>>> An: "martin.braendle@id.uzh.ch" <martin.braendle@id.uzh.ch>, >>>>>> "eprin >>>>>> ts-tech@ecs.soton.ac.uk" <eprints-tech@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@id.uzh.ch [mailto:martin.braendle@id.uz >>>>>> h.ch >>>>>> ] >>>>>> Sent: 16 May 2019 13:22 >>>>>> To: eprints-tech@ecs.soton.ac.uk; John Salter <J.Salter@leeds >>>>>> .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 Brändle >>>>>> https://eur03.safelinks.protection.outlook.com/?url=https%3A% >>>>>> 2F%2 >>>>>> Forcid.org%2F0000-0002-7752- >>>>>> 6567&data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c5698f24 >>>>>> 685c >>>>>> 2b408d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sd >>>>>> ata= >>>>>> VC8Bwg2BLpo%2BybPatYVIyBvALgwZhIZ4Az4bBUkKXFY%3D&reserved >>>>>> =0 >>>>>> Zentrale Informatik >>>>>> Universität Zürich >>>>>> Stampfenbachstr. 73 >>>>>> CH-8006 Zürich >>>>>> >>>>>> "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@ecs.soton.a >>>>>> c.uk >>>>>> An: "'eprints-tech@ecs.soton.ac.uk'" <eprints-tech@ecs.soton. >>>>>> ac.u >>>>>> k> >>>>>> Datum: 16.05.2019 14:00 >>>>>> Betreff: [EP-tech] Hyperauthorship >>>>>> Gesendet von: <eprints-tech-bounces@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&data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7C17a35c5698f24 >>>>>> 685c >>>>>> 2b408d6da0bc70f%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sd >>>>>> ata= >>>>>> kjC4zZaCbC3FpYg53MlgUmfkiuWdpysY7o4wYMO7noU%3D&reserved=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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u8NjmmoI0nGkhe3Nf9HtX%2FjcbJv704p30RbHNn4%2FnE%3D&reserved= >>>>> 0 >>>>> ook.com/?url=http%3A%2F%2Fwiki.eprints.org%2F&data=01%7C01% >>>>> 7Cdr >>>>> n%40ecs.soton.ac.uk%7C17a35c5698f24685c2b408d6da0bc70f%7C4a5378 >>>>> f929 >>>>> f44d3ebe89669d03ada9d8%7C0&sdata=bAAmMyyLM3BKMyaJKV0%2BlVkj >>>>> LTLh >>>>> eWtP7AMKx2OXs14%3D&reserved=0 >>>>> *** EPrints developers Forum: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Feur03.safelinks.protectio&data=01%7C01%7C%7C08e594b094b446d7c72e08d6e5c5fff2%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=VS%2F8isUgEIkmHz238xzP7fThAJMZqoLP7Aq7KzOR%2FSc%3D&reserved=0 >>>>> n.outlook.com/?url=https%3A%2F%2Feur03.safelinks.protection.ou& >>>>> amp;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f41b7810a >>>>> 08d6e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=Q >>>>> 1OD0nvtS8fKBXdR0pTR0GRUwFFsNQOofpClgDPPkBE%3D&reserved=0 >>>>> tlook.com/?url=http%3A%2F%2Fforum.eprints.org%2F&data=01%7C >>>>> 01%7 >>>>> Cdrn%40ecs.soton.ac.uk%7C17a35c5698f24685c2b408d6da0bc70f%7C4a5 >>>>> 378f >>>>> 929f44d3ebe89669d03ada9d8%7C0&sdata=x1u8ms27jNFOjBeMVmcvFZ6 >>>>> gli% >>>>> 2BMlgw3bd%2Bd7PMyATg%3D&reserved=0 >>>> *** Options: http://mailman.ecs.soton.ac.uk/mailman/listinfo/epri >>>> nts- >>>> tech >>>> *** Archive: https://eur03.safelinks.protection.outlook.com/?url= >>>> http >>>> %3A%2F%2Fwww.eprints.org%2Ftech.php%2F&data=01%7C01%7Cdrn%40e >>>> cs.s >>>> oton.ac.uk%7C17a35c5698f24685c2b408d6da0bc70f%7C4a5378f929f44d3eb >>>> e896 >>>> 69d03ada9d8%7C0&sdata=3dwAZ3WMVCcJQSfKyX%2FCHM%2BAREOusIkcEIj >>>> kf96 >>>> 9tzk%3D&reserved=0 >>>> *** EPrints community wiki: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Feur03.safelinks.protection.ou&data=01%7C01%7C%7C08e594b094b446d7c72e08d6e5c5fff2%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=iNpyaiU0u8G%2Fi9nIv%2B4pNlkuJ4eJPYtO2%2B7db3QykrM%3D&reserved=0 >>>> tlook.com/?url=https%3A%2F%2Feur03.safelinks.protection.outloo&am >>>> p;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f41b7810a08d6 >>>> e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=IyDVijH >>>> sZSMIIWtFVZa%2FisKla8z8DYwclqSJIc3yyRY%3D&reserved=0 >>>> k.com/?url=http%3A%2F%2Fwiki.eprints.org%2F&data=01%7C01%7Cdr >>>> n%40 >>>> ecs.soton.ac.uk%7C17a35c5698f24685c2b408d6da0bc70f%7C4a5378f929f4 >>>> 4d3e >>>> be89669d03ada9d8%7C0&sdata=bAAmMyyLM3BKMyaJKV0%2BlVkjLTLheWtP >>>> 7AMK >>>> x2OXs14%3D&reserved=0 >>>> *** EPrints developers Forum: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Feur03.safelinks.protection&data=01%7C01%7C%7C08e594b094b446d7c72e08d6e5c5fff2%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=hQTVctnAXVBm%2FVsBkm2WMEqmSXuPIHu%2FURxykT1hSyY%3D&reserved=0. >>>> outlook.com/?url=https%3A%2F%2Feur03.safelinks.protection.outl&am >>>> p;data=01%7C01%7Cdrn%40ecs.soton.ac.uk%7Cdcea7f66450f41b7810a08d6 >>>> e5b85b53%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=Tu8Njmm >>>> oI0nGkhe3Nf9HtX%2FjcbJv704p30RbHNn4%2FnE%3D&reserved=0 >>>> ook.com/?url=http%3A%2F%2Fforum.eprints.org%2F&data=01%7C01%7 >>>> Cdrn >>>> %40ecs.soton.ac.uk%7C17a35c5698f24685c2b408d6da0bc70f%7C4a5378f92 >>>> 9f44 >>>> d3ebe89669d03ada9d8%7C0&sdata=x1u8ms27jNFOjBeMVmcvFZ6gli%2BMl >>>> gw3b >>>> d%2Bd7PMyATg%3D&reserved=0
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