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retorquere / zotero-pmcid-fetcher

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Zotero - PMID/PMCID #6

Closed vicdsim closed 1 year ago

vicdsim commented 1 year ago

I'm submitted this on recommendation of Zotero forum. Migrating articles from another library into Zotero, tags are missing. I've completed the following operation numerous times with no results. See screenshots attached.

Slide 1 - shows no tags present. Slide 2 - select all items in folder, right click, select Fetch PMCID keys. Note - nothing visibly/audibly happens. No tags appear in Zotero library. Slide 3 - right click and select Export items.
Slide 4 - Export items to CSV. Slide 5 - CSV does not contain PMID/PMCID numbers (zero hits on search results).

Thank you.

2023-04-26 github fetcher bug.pptx

retorquere commented 1 year ago

Do all of these items have a DOI?

vicdsim commented 1 year ago

Most do have DOI. See attached. 2023-04-26 DOI numbers.pptx

retorquere commented 1 year ago

Can you select a few of those, export as Zotero RDF, and attach that here (not a screenshot, the RDF file).

vicdsim commented 1 year ago

export notes or export files?

retorquere commented 1 year ago

Neither

vicdsim commented 1 year ago

see attached

retorquere commented 1 year ago

Nothing is attached.

vicdsim commented 1 year ago

file type not supported.

retorquere commented 1 year ago

Zip it, then attach.

vicdsim commented 1 year ago

Exported Items.zip

retorquere commented 1 year ago

Please update to 0.0.18 and try again

retorquere commented 1 year ago

Does that work?

vicdsim commented 1 year ago

Updated to 0.0.18 with some success. See error messages in slide 1 of attached. Slides 2-5 are examples of failure to import tags. Slide 2 specifically is an item with doi, pmid and pmcid which failed. 2023-05-01 PMCID Error.pptx

retorquere commented 1 year ago

Please always attach an zotero RDF export of problematic entries.

vicdsim commented 1 year ago

2023-05-01 Exported Items.zip

retorquere commented 1 year ago

You hit a transient error on the NCBI API. Most items should resolve now. I have put up a new version that will have more readable error messages, you can upgrade in the addons screen.

vicdsim commented 1 year ago

I continue to get errors. Approx 1/3 of the items don't return tags, at least some of which include DOI/PMID/PMCID. Please see attached. 2023-05-02 errors.pptx Exported Items (2).zip

retorquere commented 1 year ago

New version is up, please upgrade. The NCBI API only allows 3 requests per second, so I've spaced them out that way, but one item among the ones in your last post will not resolve because NCBI doesn't know what to do with it: try DOI 10.3109/s10165-008-0045-0 on https://www.ncbi.nlm.nih.gov/pmc/tools/idconv/.

retorquere commented 1 year ago

Good?

vicdsim commented 1 year ago

Sorry for the delay, I'm back on this project. Please see attached two DOI errors. Exported Items2.zip

retorquere commented 1 year ago
vicdsim commented 1 year ago

I'm just a user with no technical or medical library expertise. Would you kindly explain the ID Converter? If I understand what you've inferred, if the converter doesn't get a hit on the DOI, then there is nothing further to be done. What if I get something other than an error message? In that case I should report to you?

retorquere commented 1 year ago

Correct -- if the plugin message says "phrases not found", that's NCBIs way of saying "I don't know this DOI". I'll see if I can make this message more clear.

There's no need to pre-test every DOI, but if you see "phrases not found" (or the better message I may be able to show), you can either trust that or verify at https://www.ncbi.nlm.nih.gov/pmc/tools/idconv/ to see whether that's the case. Any other error you can report here.

vicdsim commented 1 year ago

Thanks. Please see screenshots attached. When I put the DOI into the converter, it is recognized and associated with PMID/PMCID, but Zotero PMCID Fetcher has not captured tags. Are these items that you would troubleshoot? If so, I will continue looking for similar issues and send an RDF export.

2023-06-07 no tags, no ID converter error.pptx

retorquere commented 1 year ago

Please attach an RDF export of that item -- if I fetch 10.1016/j.jdin.2022.07.006 through the fetcher plugin I get

PMID: 36089937
PMCID: PMC9449733

as expected.

fjavier10 commented 1 year ago

Cannot download/install zotero-pmcid-fetcher-0.0.23.xpi, using Firefox 116.0.3 (64-bit) Windows 10 64b education. As I click the link a message appears: "github.com. The add-on downloaded from this site could not be installed because it appears to be corrupt". Please, advice. Javier

retorquere commented 1 year ago

Download it by right-clicking and choose save-as, not left-clicking.