Trouble with NCBI Pubmed translator

2
  • anders_royce
    Thanks ajlyon. It works great.
  • wspi01
    Thanks for resolving this annoying issue! Using Update Now in the General tab of the Preferences resolved the issue in my case. Don't forget to restart Firefox!
  • janphil
    Sorry, I still have the problem even though I installed the .js-file and updated the translator. (also restarted firefox and the computer.) Same problem as the first poster. The workaround suggested by vijumoses (list import) works...
  • ajlyon
    janphil: Have you tried various URLs and it doesn't work for any of them? Are you using Zotero 2.0?
  • jthetzel
    I am also experiencing problems with PubMed that zekeb describes at the top of this thread.

    I first noticed it yesterday morning, and later manually updated the translator using ajlyon's updated javascript above. This fixed it, and the PubMed translator was fully functional.

    I last successfully saved a PubMed citation at 11:54 am today, EST. At some point after that, the translator again broke, with the exact same behavior as before. I have 'updated now' via preferences and re-updated manually using ajlyon's javascript as before, resetting as necessary. Neither approach works today.

    Batch saves still work, as does the PMID magic-wand. Are others experiencing more PubMed issues today, or is this limited to my computer?

    Thanks, especially to ajlyon's previous quick fix.
  • jthetzel
    I should add, I am using Zotero 2.02 with Firefox 3.6.3 on Windows 7 64 bit.
  • ajlyon
    Does the article at http://www.ncbi.nlm.nih.gov/pubmed/9566477 save for you? It still works for me. There's a real chance that my fix does not work for all PubMed pages, in which case I'll look into a more general solution.

    Another possibility is that proxies could be interfering with the META tags, perhaps?
  • spstromberg
    Hi,
    I still have a problem. It seems that if you find an article as the only paper returned with a search the translator doesn't work but if you then go to that articles page (which looks almost the same) the translator works. For example it doesn't work for me here:

    http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=Measuring+two-dimensional+receptor-ligand+binding+kinetics+by+micropipette.

    But it does work here:
    http://www.ncbi.nlm.nih.gov/pubmed/9726957

    Don't understand why. Note that I did update the translator to the one posted on this page.
  • ajlyon
    I've uploaded an updated translator that works for the single result case that you mention. Thanks for the reporting it. You can download the translator from http://groups.google.com/group/zotero-dev/web/NCBI PubMed.js, and install as described above. Please let me know if it works for you, and I will ask to have it pushed to clients.

    Are there still people who can't save anything except search results? Or are there specific pages that won't save?
  • mikke9
    ajlyon, thanks. I created a new file "NCBI PubMed.js", replaced the old one in the translators folder, and it seems to take care of the problem.
    Interestingly enough, with the old translator the problem for me was not with any particular page, but how I arrived to that page. For example, if I searched in PubMed search bar using words, the resulting page could be saved. If instead I searched in PubMed search bar using PMID#, then the resulting page could not be saved. Once the the PMID# method was used, the problem continued for all search methods until Firefox was restarted.
    The other method suggested above: using PMID# in "Identifier" window worked all the time.
  • ajlyon
    edited April 11, 2010
    Just to confirm, you're saying that the updated translator works all the time now?

    In the most recent update, I fixed an issue where, if there was only one hit for a search result (as for a PMID, which will have only one hit by its nature), then the item couldn't be saved.
  • spstromberg
    Hi Ajlyon,
    Thank you so much for fixing that so quickly. I'm very sorry I didn't get to test it sooner I wasn't at my computer over the weekend. I checked and your fix solved my problem. Thank you so much. I think you should ask to have it pushed through to clients.

    Thank you!
    Spstromberg
  • ajlyon
    I've asked that it be pushed to clients. In the meantime, people can continue to update the translator from the address above manually.
  • jthetzel
    Thanks, ajlyon. I just auto-updated, and the PubMed translator is working again.
  • dstillman
    Yes, we've pushed the second revision. Thanks again to ajlyon.
  • janphil
    Thank you all - updating to Zotero 2.0.2 did the trick for me - it works now!
  • Sadie Richards
    After nearly two months of smooth sailing I seem to be experiencing trouble with the PubMed translator once again. It worked fine this morning, but for the past several hours I have not been able to add items by any means tried (neither clicking the icon in the url/address bar nor inserting the PMID via the wand works). I tried restarting FireFox, then restarting my computer without success.

    Adding items from different sites works without issue, but I rely on PubMed entries for posting info (abstracts, pdfs, etc) to a Zotero Group that I facilitate.

    Thanks for your continued help on this!
  • laure bougarel
    Sorry I've tried the two links and updated the translator each time, still can't save any page.
  • techneaux
    edited June 4, 2010
    Same here.. as of this morning, I can no longer add pubmed articles to Zotero. Worked great yesterday. Clicking the icon in the address bar results in an empty red box on the lower left of the screen (instead of being filled with details of the article)... and then nothing is added to Zotero.

    (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20519957)
  • andrew_bohm
    Yup. Same here. Fortunately, clicking the magic wand icon and then inputting the pmid manually as discussed in the earlier posts works. Hopefully this will be a very high priority fix. There are a lot of people working on NIH grants right now, and getting refs from pub med is critical.
  • rwielage
    A couple days ago I noticed the icon stopped working for an individual article. However, the folder icon for a list of articles still worked. Today the folder icon doesn't even display.

    Ovid continues to work.
  • ajlyon
    I'll see what I can do. No promises, but I'll try to finish this in the next 24-48 hours.
  • ajlyon
    Please go to http://github.com/ajlyon/zotero-bits/raw/master/NCBI PubMed.js and save the file to the translators directory of your Zotero data directory (http://www.zotero.org/support/zotero_data).

    It should start working again. If this works for you, please post here so that I can submit this change to be pushed to all users.
  • RACstaff
    Sorry for my ignorance but when you say "save the file" to the data directory do you mean "save page as" or do I somehow copy and paste the coding, or ?

    Thanks for breaking it down for this relatively inexperienced user ;)
  • ajlyon
    Save page as should do the trick.
  • gangadhar
    I had the same problem and am following the discussion when i made to save the page to translators directory it is giving a message as the file already exists can replace the old file with new one.. (i have posted my probelm in trouble shoot and was directed to follw this discussion)
    Thank you
  • ajlyon
    Yes, you need to replace the old file with the new one. You will then need to restart Firefox for it to work on search pages, but it should start working on PubMed article pages immediately.
  • gangadhar
    Oh , thank you verymuch...it started working for PUBMED individual journal articles BUT still the folder option which was giving an option for saving all the references in a web page still not appearing.. we can wait for this option no problem .

    Thank you for solving the problem so quickley.. we can work on the weekend
  • Sadie Richards
    Hooray!!! Hearty thank yous from myself and RACstaff, ajlyon!
  • rwielage
    The folder icon has reappeared, the article icon works, a single item from the folder works, and I'm trying an import of a 200 item search right now. I've never brought in such a large search result set before and it's taking a surprisingly long time.

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