PubMed XML Import Error
Report ID: 948161501
I have been receiving the following error message when trying to import an XML file of a PubMed Search (with 1784 references) into Zotero:
"an error occurred while trying to import the selected file. Please ensure that the file is valid and try again."
I have tried downloading the XML from three different browsers (Chrome, Safari, and Firefox), have updated and restarted Zotero, have cleared my browser cache, have ensured I have ample storage available in Zotero, and still receive the exact same message.
Please help!
I have been receiving the following error message when trying to import an XML file of a PubMed Search (with 1784 references) into Zotero:
"an error occurred while trying to import the selected file. Please ensure that the file is valid and try again."
I have tried downloading the XML from three different browsers (Chrome, Safari, and Firefox), have updated and restarted Zotero, have cleared my browser cache, have ensured I have ample storage available in Zotero, and still receive the exact same message.
Please help!
Thank you for your quick reply!
Other thoughts for what might be causing the error?
Search (((((((Food preferences[mesh] OR health knowledge, attitudes, practice[MeSH Terms] OR knowledge[tiab] OR "well-being"[tiab] OR "well being"[tiab] OR (food and (habits[tiab] OR habit[tiab] OR choice[tiab] OR choices[tiab] OR behavior[tiab] OR behaviors[tiab] OR preferences[tiab] OR preference[tiab] OR attitudes[tiab] OR attitude[tiab])) OR outcome[tiab] OR outcomes[tiab] OR measure[tiab] OR measures[tiab] OR outcome assessment health care[MeSH Terms])) AND (cooking[MeSH Terms] OR culinary[Title/Abstract] OR cooking[Title/Abstract] OR cook[Title/Abstract] OR “food preparation”[Title/Abstract] OR “meal preparation”[tiab])))) AND (schools[Title/Abstract] OR school[Title/Abstract] OR schools[mesh] OR elementary[tiab] OR “high-school”[tiab] OR “high school”[tiab] OR youth[Title/Abstract] OR teenager[Title/Abstract] OR teen[Title/Abstract] OR teens[Title/Abstract] OR adolescent[Title/Abstract] OR adolescents[Title/Abstract] OR adolescence[tiab] OR pupil[Title/Abstract] OR pupils[Title/Abstract] OR student[Title/Abstract] OR students[Title/Abstract] OR child[Title/Abstract] OR children[Title/Abstract] OR youth[MeSH Terms] OR adolescent[MeSH Terms] OR child[MeSH Terms] OR minor[tiab] OR minors[tiab] OR minor[mesh])) AND ( "1980/01/01"[PDat] : "2017/11/31"[PDat] )) AND ( "1980/01/01"[PDat] : "2017/11/31"[PDat] )) Sort by: Title Filters: Publication date from 1980/01/01 to 2017/11/31
(((((((Food preferences[mesh] OR health knowledge, attitudes, practice[MeSH Terms] OR knowledge[tiab] OR "well-being"[tiab] OR "well being"[tiab] OR (food and (habits[tiab] OR habit[tiab] OR choice[tiab] OR choices[tiab] OR behavior[tiab] OR behaviors[tiab] OR preferences[tiab] OR preference[tiab] OR attitudes[tiab] OR attitude[tiab])) OR outcome[tiab] OR outcomes[tiab] OR measure[tiab] OR measures[tiab] OR outcome assessment health care[MeSH Terms])) AND (cooking[MeSH Terms] OR culinary[Title/Abstract] OR cooking[Title/Abstract] OR cook[Title/Abstract] OR “food preparation”[Title/Abstract] OR “meal preparation”[tiab])))) AND (schools[Title/Abstract] OR school[Title/Abstract] OR schools[mesh] OR elementary[tiab] OR “high-school”[tiab] OR “high school”[tiab] OR youth[Title/Abstract] OR teenager[Title/Abstract] OR teen[Title/Abstract] OR teens[Title/Abstract] OR adolescent[Title/Abstract] OR adolescents[Title/Abstract] OR adolescence[tiab] OR pupil[Title/Abstract] OR pupils[Title/Abstract] OR student[Title/Abstract] OR students[Title/Abstract] OR child[Title/Abstract] OR children[Title/Abstract] OR youth[MeSH Terms] OR adolescent[MeSH Terms] OR child[MeSH Terms] OR minor[tiab] OR minors[tiab] OR minor[mesh])) AND ( "1980/01/01"[PDat] : "2017/11/31"[PDat] )) AND ( "1980/01/01"[PDat] : "2017/11/31"[PDat] ))
into the search constructor on https://www.ncbi.nlm.nih.gov/pubmed/advanced only gets my 1531 hits. If then do Send to --> File and select XML, they all import fine for me.
I will try it without that sort option, but imagine I will still get the same error...
Still no idea why the XML route is not working for me -- perhaps a flash memory issue with my laptop?
I re-ordered the items by title and examined the first and last pages - no missing titles.
I set "English only" as a pubmed filter before I exported the articles. (And I'm most of the way through screening them and haven't yet come across one where the title is in another language or screwed up in any other way.)
I tried displaying 200 citations in pubmed on a webpage and tried the browser capture function. I select and the little red box appears and the list appears in it as one would expect. Then at the bottom of the list is the same error message and it doesn't import. That happens regardless of whether it's 1 item or 200 items selected. And there's nothing wrong with the titles, and all in English. (Trying the same thing with googlescholar DOES work). If I have a complete citation on the page rather than the list, Zotero DOES capture it, though not entirely faithfully.
I'm using Zotero on a Mac, but that shouldn't matter. It updated within the last 24 hours or so. And I've restarted both the machine & Zotero.
If so, could we get debug output from Zotero for a failed attempt to import an XML file that is as small as possible?
For example:
1. Search for test
2. Choose to only show five search results
3. Select Format --> XML
4. Select all + copy
5. Turn on debug ouput in Zotero (note we want this from Zotero, not the connector)
6. Import from clipboard
--> assuming this fails
7. Submit Debug
8. Post debug ID here
The debug code is D1197405201.
I haven't looked into this yet, but it's still on my list.