Zotero Connector error with PubMed

estredny

I get the following error while attempting to use Zotero Connector: "An error occurred saving with PubMed. Attempting to save using Embedded Metadata instead." I have gotten this error using both the extensions for Firefox and Google Chrome. It results in the incorrect author data being imported (last name shows up in the first name location and only the first initial of the first name shows up in the last name location) requiring it to be mannually fixed.

dstillman

Example URL?

estredny

Currently every PubMed URL I've tried today. But here is one specific one:

https://pubmed.ncbi.nlm.nih.gov/10601678/

dstillman

Works for me. See Troubleshooting Problems Saving to Zotero.

bgoeckner

I too started having a problem with pub med - was working fine before noon, then around 2pm it would not longer allow me to correctly save files to Zotero (using Safari).
Message for https://pubmed.ncbi.nlm.nih.gov/35776892/ is: "An error occurred saving with PubMed. Attempting to save using Embedded Metadata instead." and it will then load some but not all correct data.
Also no longer able to import lists of articles, when I usually could select several articles to import from search results.

dstillman

Can you provide a Debug ID from the Zotero Connector for reloading the page and trying to save?

bgoeckner

Went in to try to reproduce the errors I was getting and it seems to be resolved now

dstillman

Probably just a temporary problem with the PubMed metadata service

Rintze

I'm seeing PubMed translator (silent) failures with any recent article today. It looks like their metadata service is not returning results for new content:

Old article:
https://pubmed.ncbi.nlm.nih.gov/17284678/
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=PubMed&tool=Zotero&retmode=xml&rettype=citation&id=17284678
(returns full XML object)

New article:
https://pubmed.ncbi.nlm.nih.gov/36107469/
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=PubMed&tool=Zotero&retmode=xml&rettype=citation&id=36107469
(returns empty <PubmedArticleSet/>)

Rintze

And while I was troubleshooting this, it seems that the automated translator test reports at https://zotero-translator-tests.s3.amazonaws.com/index.html haven't been working for at least the past week (this URL is referenced at https://www.zotero.org/support/dev/translators and https://www.zotero.org/support/dev/translators/testing#running_tests).

Rintze

(I have reported the issue with EFetch to NCBI)

adamsmith

yeah, this has come up before -- the API is unfortunately something like 24-48hs behind the website (I believe this is new as of the new catalog), even thought the metadata suggests it should be in the API earlier:

PHST- 2022/09/13 00:00 [accepted]
PHST- 2022/09/15 11:52 [entrez]
PHST- 2022/09/16 06:00 [pubmed]
PHST- 2022/09/16 06:00 [medline]

Not quite sure what to do about that.

Rintze

Ah, thanks.

Rintze

@adamsmith, NCBI only wrote back today that they couldn't reproduce the issue (the URL now also works for me), but they mentioned an upcoming small update to EFetch:

"Please refer to the following link for more details on pending change in PubMed API:
https://ncbiinsights.ncbi.nlm.nih.gov/2022/03/24/test-server-pubmed-api/
https://www.nlm.nih.gov/pubs/techbull/so22/so22_updated_pubmed_e_utilities.html "

Looks like that won't require changes to the translator.

seshonka

I am having this problem now. I went through all the troubleshooting steps for zotero connector and that did not resolve my issue. Here is my debug ID: D1335955665

seshonka

It's working this morning. Looks like Pubmed was doing some updating last night that was affecting this.