Problems with PubMed Site Translators

vincehay
Yesterday when trialing Zotero 1.5 Sync. I was able to (down)load both single files and Folders into Zotero 1.5 from PubMed. However today (22Nov) when I click the folders download option in a PubMed search I keep getting a "Could not save item ... check know translator issues' I went through the translator issues, and checked and changed the points as detailed, but these did not resolve this issue.
the URL is
http://www.ncbi.nlm.nih.gov/sites/entrez
Any suggestions
  • pesho
    Same here. Downloading multiple items doesn't work anymore.
  • Tanja
    Same here. It still worked on Friday (21Nov) but no longer today. I updated Firefox this morning, does it have to do with it?
  • bwheeler
    Me too, I am hoping a translator change will be out soon, as I've got a lot of parsing to do!
  • delenca
    Here too. For the developers, here's the error information:
    To reproduce:
    Just go pubmed and try to "save to zotero" - Zotero will complain of a translator error.
    http://www.ncbi.nlm.nih.gov/sites/entrez

    Report Id: 252415006
    [JavaScript Error: "Cannot add invalid tag 2 in Zotero.Item.addTagByID()" {file: "file:///C:/Documents%20and%20Settings/delenca/Application%20Data/Mozilla/Firefox/Profiles/cnhzfpsj.default/zotero/translators/NCBI%20PubMed.js" line: 0}]
  • Tjowens
    Confirmed, ticket created. https://www.zotero.org/trac/ticket/1225
  • mcburton
    We have fixed this translator issue. Your copy of Zotero should auto-update within 24 hours, or you can update manually by clicking "Update Now" in the General pane of the Zotero preferences.
  • delenca
    The pubmed translator is broken again. Exact same error (or at least description - "can't add invalid tag 2""

    Report ID: 1777493063
    [JavaScript Error: "Cannot add invalid tag 2 in Zotero.Item.addTagByID()" {file: "file:///C:/Documents%20and%20Settings/delenca/Application%20Data/Mozilla/Firefox/Profiles/hdaopzub.default/zotero/translators/NCBI%20PubMed.js" line: 0}]

    To reproduce:
    Just go pubmed and try to "save to zotero" - Zotero will complain of a translator error.
    http://www.ncbi.nlm.nih.gov/sites/entrez
  • dstillman
    delenca: That's an issue specific to the Sync Preview—the PubMed translator itself is working fine. While we work on a fix, restarting Firefox when you run into this error might allow you to save.
  • delenca
    Hi Dan,

    Thanks, I had missed that. I believe it got fixed at some point in my Sync Preview edition. And, as an FYI, the problem is not getting fixed by restarting firefox.

    Thanks,
    -Alex
  • jheadrick
    At some point over the past week or two, PubMed's ability to import into Zotero has changed. Prior, I had a file icon in the address bar that allowed me to pull up all the articles that were being viewed on the page and check those I wanted for my library. Now a single paper icon is present, and when clicked, only the first article of the page is imported. Is this a PubMed translator issue?
  • KR
    Same problem here. I tried both 1.0.9 and 1.5 beta. Please advise.
  • judyblue
    I have noticed the same problem. I am using 1.5b2, and restarting Zotero or Firefox does not fix the problem.
  • RintzeRintze
    edited April 23, 2009
    Patch
  • dstillman
    The updated translator has been pushed to the repo. Your copy of Zotero should auto-update within 24 hours, or you can update manually by clicking Update Now in the General pane of the Zotero prefs.

    Thanks to Rintze for the patch.
  • KR
    Thanks for the patch. However, when trying to import a list of (100) entries from PubMed, Zotero imports the first entry once and appears to crash on the second, importing it for an indefinite number of times without proceeding to the third and subseuqent entries. Same problem for both version 1.0.9 and 1.5beta. Please advise.
  • RintzeRintze
    edited April 28, 2009
    (blushing) I narrowed it down to the pagination patch I submitted earlier. I think I know what's the problem:
    for (var j in pageRange) {
    var pageRangeStart = pageRange[j].match(/^\d+/)[0];
    var pageRangeEnd = pageRange[j].match(/\d+$/)[0];
    if (pageRangeStart.length > pageRangeEnd.length) {
    pageRangeEnd = pageRangeStart.substring(0,pageRangeStart.length-pageRangeEnd.length) + pageRangeEnd;
    fullPageRange = fullPageRange.replace(pageRange[j],pageRangeStart+"-"+pageRangeEnd); }
    }
    This piece of code originally uses the variable "i" which has been declared earlier to keep track of the different XML entries. In most cases the page range will be continuous. This results in variable pageRange having only a single property, which resets i to 1, hence the infinite looping. Using "j" solves the problem.
  • RintzeRintze
    Patch:
    http://zotero-dev.googlegroups.com/web/NCBI PubMed mea culpa.patch
  • dstillman
    Pushed to repo.
  • jhmorneau
    Same as KR explained above. I was doing a 1 hour course to teach students how to use Zotero with Pubmed and it crashed when I tried to import a list of entries !

    Oooops ! ;-)

    Nevertheless, I carried on, importing entries one by one, and at the end of the course, the students said they were quite impressed by Zotero :-)

    PS : will the fix for this bug be available for download later this week?

    Best regards,
    JHM
  • RintzeRintze
    edited April 28, 2009
    jhmorneau, my apologies for messing up your course. According to the log Dan made the fixed translator available about 4 hours ago. On how to get the update, see the post above by mcburton:
    "We have fixed this translator issue. Your copy of Zotero should auto-update within 24 hours, or you can update manually by clicking "Update Now" in the General pane of the Zotero preferences."
  • KR
    edited April 29, 2009
    Rintze, thanks a lot for the fixes.
  • jhmorneau
    Thank you so much for the fix !
    I appreciate that !
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