Find PDF

imf1956
edited March 20, 2022
Hello. Zotero does often automatically download the PDFs for me, which is great.
But why does Zotero sometimes fail to automatically download PDFs but it will download them if I right click on the reference and click Find Available PDFs? What is happening in those cases and any way to fix?
Thanks for Zotero.
Best
IMF
  • dstillman
    Can you provide steps to reproduce?
  • imf1956
    OK, will try to do better.
    Have Chrome open to PubMed in Windows 10, Zotero application also open
    Use Chrome Zotero importer module to import multiple selected PubMed references by clicking on folder-shaped icon in the toolbar
    All references are imported into the folder open in Zotero; some automatically come with PDF and some don't.
    I right click on reference without a PDF in Zotero and select Find Available PDF (I usually did one ref at a time, but now see I can select multiple refs)
    Sometimes it will find a PDF and download it. I would say it is less than half the time, maybe a quarter of the time it will find one.
    So, don't understand why it doesn't find it the first time through but will with the right-click and try again.
    Hope that helps, thanks. Feel free to ask questions.
    Best
    IMF
  • dstillman
    We need specific examples. Just saying you're importing "multiple selected PubMed references" doesn't let us reproduce it.
  • imf1956
    OK. I will sent PMIDs when I next encounter or run more tests.
    Will anything else be needed?
    Thank you.
    IMF
  • dstillman
    edited March 20, 2022
    We really just need the exact steps to reproduce. That means, literally, what you're typing into the search box and clicking on on-screen to reproduce the problem. That's all we need.
  • imf1956
    Hi. I did a search previously on "heart crypts" previously and downloaded 32 items into a new Zotero folder. I just went into there and stepped through all the references that didn't have PDFs and right clicked on each one and said Find Available PDFs.
    The following four found PDFs listed below. Hopefully between this and my previous detailed explanation it can be worked out. Please ask if questions.
    Thanks, best,
    IMF
    PMID: 30838504
    PMID: 27111322
    PMID: 22277119
    PMID: 22355041
  • dstillman
    edited March 20, 2022
    Ah, OK. So, PubMed is actually a bit of a special case.

    When saving from the connector and a PDF isn't available, we always look for open-access versions of the PDF, the same as Find Available PDF. We don't, however, follow the DOI/URL to look for the PDF there, because in the vast majority of cases people will already be on the publisher site and it would just be a redundant request. But PubMed is different — that will never be the canonical URL.

    We have an open ticket to add special handling for PubMed and a few similar sites to better deal with this. For now, you can either click the DOI link and save from there to save the item and PDF or use Find Available PDF like you're doing as long as you have direct or VPN-based access to gated PDFs. (People with web-based proxies will need to do the former, since Find Available PDF from Zotero won't work via web-based proxies.)
  • imf1956
    I guess I am not part of that vast majority. (Has that actually been polled?) I prefer to stay in PubMed and Zotero, reading the PDFs in Zotero, browsing the literature abstracts and citations in PubMed, and rarely go to the publisher page unless needed to get the PDF or want to download prepared PowerPoint slides.
  • dstillman
    edited March 21, 2022
    You seem to be misunderstanding. I'm talking about literally every publisher site on the internet vs. one field-specific site, PubMed. Zotero supports saving from thousands of publisher sites for countless fields of study, so we can't design it by default so that it makes a duplicate page load every time someone saves to Zotero just because PubMed indexes publications without a direct link to gated PDFs.

    Most people also use web-based proxies rather than direct or VPN-based access, in which case Find Available PDF (either at save time or later) only works for open-access PDFs, making this a fairly low priority. It just wouldn't help very many people.

    But as I say, we have an open ticket to try to improve the PubMed case for people with direct/VPN access.
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