2114977103 cannot download data from pubmed

mdossett
Last week my zotero updated to 5.0.34. I was able to download references from pubmed that day using the google chrome connector as I usually do, but they appeared strangely in my zotero desktop application and when I created a citation page in ms word 2016. Today I opened zotero again and now I cannot download any citations from pubmed. I checked and there are no additional updates to download. How can I get my citation software working properly again? Many thanks,
  • mdossett
    Update, actually Zotero is downloading the reference, but only as a webpage and lists the creator as "al". This is the same funky citation that I was seeing last week.
  • DWL-SDCA
    Please provide the title of the PubMed record or better, the PubMed ID number of the record that you cannot download. In general I've had no problems today with PubMed.

    That said, beginning January 12th PubMed has had a known intermittent problem where the database will not respond to a request using the PMID with item metadata. Tagged data file is empty and the xml export contains nothing below the first <PubmedArticle> tag. I, personally, haven't encountered this for at least 5 days.
  • mdossett
    PMID: 28501229 and PMID: 21691341.
    It actually downloads these citations as webpages rather than downloading the actual citation and it messes up the author names in the process. Could the chrome connector have become messed up in some way?
  • adamsmith
    And you're importing them from https://www.ncbi.nlm.nih.gov/pubmed/21691341 and https://www.ncbi.nlm.nih.gov/pubmed/28501229 respectively, yes? That works for me.
    Is this an ongoing problem for you? When you hover over the Save to Zotero icon, what does it say?

    If this is a recurring issue, worthwhile to go through: https://www.zotero.org/support/troubleshooting_translator_issues
  • mdossett
    Yup, that's where I tried to download them from.
    When I hover over the Zotero icon in chrome it says "Save to Zotero (PubMed)"
    When I select it, I get the following error message in the right lower corner of the screen:
    Saving to My Library…
    An error occurred while saving with PubMed. Attempting to save using Embedded Metadata.
    Mindfulness training reduces the severity of irritable bowel syndrome in women: results of a randomized controlled trial. - PubMed - NCBI
    Snapshot

    This problem started last week when my Zotero auto updated.
  • adamsmith
    Yes, run through the above. This isn't a general problem -- works fine for me.
  • mdossett
    Thanks for sending the link to translator issues. I'm updating my google chrome software to see if that fixes the problem.
  • mdossett
    I updated my google chrome software. The connector is the latest version (5.0.34). I'm still having the same problem.

    I tried resetting the translators in both my desktop zotero software and the connector. When I went to the advanced pane under report errors at the top it says:
    [JavaScript Error: "No Pubmed Data found - Most likely eutils is temporarily down"]

    Still having the same problem. What do you recommend?
  • adamsmith
    How about when you just paste the PMID into the "Add by Identifier" (Magic wand) tool in Zotero. Does that work?
  • mdossett
    The magic wand tool does work in Zotero, thank you. But why after the last update have I been unable to download directly from the pubmed website in Chrome? It would be nice to be able to do this, especially to get the pdf files.
  • adamsmith
    You'd never get PDFs on pubmed -- is this failing on other pages, too?

    The only other things I can think of are a) privacy settings (see 9.) and b) other extensions interfering with Zotero (10.) Have you checked on both?
  • mdossett
    Actually, I have downloaded pdf files of articles from pubmed in the past.

    Privacy settings is not the issue and I disabled the other extensions and that didn't fix it either. Should I try uninstalling and reinstalling Zotero?
  • adamsmith
    You most definitely have not downloaded PDFs from Pubmed using Zotero. I maintain the code and it's not able (or even trying) to do that -- likely you were using Pubmed Central.

    No, don't re-install. Could we get a debug ID from the connector for trying to import from Pubmed? https://www.zotero.org/support/debug_output#zotero_connectors_firefox_chrome_and_safari
  • mdossett
    968529182. Thank you.
  • adamsmith
    @dstillman could you take a look, please?
  • dstillman
    @mdossett: That's a Report ID. We'd want a Debug ID.
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