PubMed import doesn't work
Hi,
Importing a PubMed citation no longer works.
Here is an example:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=14283058
Zotero pops up a message:
"Could Not Save Item.
An error occurred while saving this item.
Please try again. If this error persists,
contact the translator author."
Importing from other sites does work, e.g. scholar.google.com
I'm using Firefox 2.0 and Zotero 1.0.0b2.r2
It's very frustrating as I predominately use PubMed and HubMed (which also doesn't work) to gather citations.
Thank you for any help,
Sam
Importing a PubMed citation no longer works.
Here is an example:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=14283058
Zotero pops up a message:
"Could Not Save Item.
An error occurred while saving this item.
Please try again. If this error persists,
contact the translator author."
Importing from other sites does work, e.g. scholar.google.com
I'm using Firefox 2.0 and Zotero 1.0.0b2.r2
It's very frustrating as I predominately use PubMed and HubMed (which also doesn't work) to gather citations.
Thank you for any help,
Sam
This discussion has been closed.
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.?
Thanks for the quick response.
I am not logged in to My NCBI.
I disabled all other extensions and the same error appears.
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.
The error, if we've done our math right, corresponds to an XPath line (doc.evaluate()) in the PubMed scraper's doWeb() method, which seems to suggest that there's something weird going on with parsing of the DOM—or the DOM itself that some people are receiving. (If someone experiencing the problem wants to (g)zip the HTML of an article page that fails and send it to support@zot....org, we can see if it's somehow different from what we're getting.) Simon, who wrote the scraper, is also going to try to rework it to avoid using the DOM this way, which may fix the problem. Otherwise, anyone seeing this error who wants to get their hands dirty can take a look and see if they can figure out what's going on—we'd appreciate any help.
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.
Thanks it works now!
Best,
-Sam
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?
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17494702&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
all the other ones i tried work fine?? Odd that this single citation wont save....
Regards
Andy
Also worked for me just now.. so sorry about that!
regards
Andy
I am trying to import the citation data from http://www.ncbi.nlm.nih.gov/pubmed/10834981; http://www.ncbi.nlm.nih.gov/pubmed/15753260; http://www.ncbi.nlm.nih.gov/pubmed/8779555 by clicking either in the "folder" icon of the previous pubmed search page or for each abstract in the "page" icon at the right of the URL. It used to work fine for any article but now it gives me "an error occurred while saving this article" and some info about translator issues. I went to the translator issues page and verified my mozilla version (3.6), and performed the database integrity check (passed). What should I do?
I had 4 tabs more open while doing my pubmed search. They corresponded to sites of the journals from which I was downloading the articles. When I closed all tabs, reinitiated firefox and tried import it worked. Hope it helps to fix it. Best, Theolis
Is this because the citation is new?
update Zotero (current version is 2.1.10). See if the problem persists, then start a new thread.