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NaturalHistoryMuseum / scratchpads2

Scratchpads 2.0
http://scratchpads.org
GNU General Public License v2.0
199 stars 83 forks source link

Exporting bibliography (format: BibTeX) problem #6631

Closed Morjens123 closed 1 year ago

Morjens123 commented 1 year ago

I tried to export bibliography from https://pistiaistyoryhma.myspecies.info/biblio

The downloaded bib file does not contain all the bibliography entries but contains multiple copies of same references for some reason (see attached image). Am I doing something wrong or what is the problem? Bibliography error

Archilegt commented 1 year ago

The RIS and BibTex export problem has been documented in the BioStor GitHub under Making Myriatrix work for BioStor #100. This is indeed a major problem, as it affects key missions of Scratchpads: to foster data interoperability and to avoid duplication of effort. I cannot help BioStor with Myriapoda and Onychophora bibliographic references until this export issue is solved.

Related RIS issues: Please add RIS field identifier DO #6160 Pagination missing in RIS export files #6502

@therobyouknow, how far are we from migrating to a new Drupal version and implementing the BibCite Module? Literature-wise, it seems that we may have a lot to win from not investing in fixing the old problems and from migrating the references to a new Drupal and module.

benscott commented 1 year ago

The biblio export was always appending records to the export file, rather than creating a new file at the start of the export batch and then appending. So if the export had run previously, all records would be duplicated. Fixed in https://github.com/NaturalHistoryMuseum/scratchpads2/pull/6637, and tested imports are duplicate free when re-imported into Zotero.

Morjens123 commented 1 year ago

Thank you! I tried to export BibTex from here... https://pistiaistyoryhma.myspecies.info/biblio ...and it only exports 50 entries from the bibilography, even though we have over 2000 entries in our database? 50 entries seem to be the number of entries shown per page. How can I download the whole literature database (2445 entries)?

benscott commented 1 year ago

Hi @Morjens123 - thank you very much for checking & sorry that didn't fix it properly! I have just released another fix, and it looks to be working correctly now - 2445 items in the BibTex export and imported into Zotero. How's that looking for you?

Morjens123 commented 1 year ago

It works. Much praise to you sir! Altough I feel bad now, as we have not been very active in updating our website or bibliobraphy. We also sadly are not using many useful features (taxonomy e.g.). I hope in future we will be more active with the website...

benscott commented 1 year ago

Great, glad its now working properly & thanks very much for testing it!

Archilegt commented 1 year ago

Hi, @benscott This is still not working properly for Myriatrix. I took the opportunity that 1500 references were reached and made a RIS export. A quick inspection reveals a 30-plication, so we are back to the problem of the software apparently reading the total number of references, exporting 50, and then replicating those 50 as many times as needed to reach the previously read total number of references. Could you please check this issue again and see if the fix has to be rolled specifically in Myriatrix?

benscott commented 1 year ago

@Archilegt - that should be working on your site as well now?