This is a known problem (mentioned in other threads and on the Known Issues page), though one without a known solution.

To be honest, we're not sure what's going on with this one, as we can't reproduce it and the error messages being produced are less than clear. We may try to rewrite the section of the PubMed scraper that seems to be causing problems, but it's hard to do without being able to see the problem ourselves.

A couple questions for people experiencing this:

1) Are you logged in to My NCBI when the scraping fails?

2) Are you using any other extensions that might affect parsing of the page? Greasemonkey, etc.?

A lot of people are reporting this error with PubMed/HubMed. I decided to run Firefox from a command line and capture the error messages generated by a PubMed page. I hope this is useful to you for debugging.

Here are the messages generated when you go to the NCBI PubMed start page:

zotero(3): binding sandbox to http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed

zotero(3): searching for translators for http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed

zotero(5): SELECT detectCode FROM translators WHERE translatorID = ?

zotero(5): Binding parameter 1 of type string: "fcf41bed-0cbc-3704-85c7-8062a0068a7a"

zotero(3): executed detectCode for PubMed

zotero(3): executed detectCode for COinS

zotero(3): executed detectCode for Embedded RDF


If I do a search and click on a particular article, the abstract icon appears in the address bar. If I click on that icon, I get these messages:

zotero(5): SELECT * FROM translators WHERE translatorID = ? AND translatorType IN (4,5,6,7,12,13,14,15)

zotero(5): Binding parameter 1 of type string: "fcf41bed-0cbc-3704-85c7-8062a0068a7a"

zotero(3): translate called

zotero(3): binding sandbox to http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16944959&query_hl=1&itool=pubmed_docsum

zotero(3): parsing code for PubMed

zotero(3): SyntaxError: missing ) after argument list in parsing code for PubMed
zotero(3): running handler 0 for done

zotero(3): translation using PubMed failed:
message => missing ) after argument list
fileName =>
lineNumber => 108
stack => doWeb()@:0
@:0
@:0

name => SyntaxError
url => http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16944959&query_hl=1&itool=pubmed_docsum
extensions.zotero.cacheTranslatorData => true
extensions.zotero.automaticSnapshots => true

zotero(3): HTTP POST ids[]=fcf41bed-0cbc-3704-85c7-8062a0068a7a&lastUpdated=2006-10-23%2000%3A23%3A00&extVersion=1.0.0b2.r2&errorData=message%20%3D%3E%20missing%20%29%20after%20argument%20list%0AfileName%20%3D%3E%20%0AlineNumber%20%3D%3E%20108%0Astack%20%3D%3E%20doWeb%28%29@%3A0%0A@%3A0%0A@%3A0%0A%0Aname%20%3D%3E%20SyntaxError%0Aurl%20%3D%3E%20http%3A//www.ncbi.nlm.nih.gov/entrez/query.fcgi%3Fdb%3Dpubmed%26cmd%3DRetrieve%26dopt%3DAbstractPlus%26list_uids%3D16944959%26query_hl%3D1%26itool%3Dpubmed_docsum%0Aextensions.zotero.cacheTranslatorData%20%3D%3E%20true%0Aextensions.zotero.automaticSnapshots%20%3D%3E%20true to http://www.zotero.org/repo/report



Hopefully somebody can interpret that and address the issue.

OK, we've solved the PubMed mystery.

It turns out the problem was due to a Firefox bug that causes DOM nodeValues longer than 4K characters to be split into multiple nodes. Any translators that had been updated via the repository with 'code' fields longer than 4K were getting truncated. We didn't notice this bug during testing of the repository update mechanism because most translators aren't that long.

I've put in a workaround for this in the code in the next release. In the meantime, I've managed to shrink the recently updated scrapers to less than the cutoff limit, so your copy of Zotero should auto-repair within the next 24 hours. (We'll have a manual update button in the next release. If you're particularly impatient you can close Firefox, run "DELETE FROM version WHERE schema='lastcheck'" in zotero.sqlite, and restart.)

Let us know if you continue to have problems after 1 a.m. EST Saturday.

Great work guys - the "could not save" problem is now fixed for me.

So the next problem ;)

Has been posted in another thread, but was perhaps lost in the discussion of general PubMed problems. Zotero now saves from PubMed, but I don't get any page numbers in the citation.

Any thoughts?

Page numbers from PubMed now working for me. Thanks guys - this is well on the way to becoming a must-have app.

Works fine for me.

A year later on Zotero 1, firefox 2, vista, I'm finding erratic ability to import a batch of citations from pubmed. Single ones work but several sometimes works and sometimes fails. Right now I searched on samaderine and got 4 hits and they wouldn't import.

I can't get anything to work on pubmed! the little page icon doesn't show up on any of the article i pull up and I can't import from a text file either. I thought this program was going to be helpful, but all I've had is compatibility issues with everything!