OSA Optics Infobase translator not working again

jtravs
Hi all,

Thanks for your help previously (last year) for fixing the Optics Infobase translator.

However, it seems that since their new site design (a few months) the translator is not working again. An example link is:

http://www.opticsinfobase.org/ol/abstract.cfm?uri=ol-37-13-2769

Thanks for any help!
John
  • adamsmith
    works for me. Run through 5,6,10,11 here:
    http://www.zotero.org/support/troubleshooting_translator_issues
    if 5,6,10 don't help we need a report ID as described in 11.
  • jtravs
    Thanks for your response.

    Nothing on that page seems to be wrong though. I got a report ID: 1489752996, though as far as I can tell those errors are unrelated (but what do I know).

    Here is a better description of the problem: at the above noted page, if I click on the zotero icon in the address bar the white box appears in the bottom right hand corener of firefox, as usual, but nothing is subsequently saved in my database. Additionally, usually while zotero is saving the white box changes to contain some details of the paper being saved, whereas in this case it just stays empty, then disappears. My zotero is working fine on many other journal websites.

    Thanks again for any help!

    John
  • jtravs
    OK, so it works on my version of firefox+zotero on Windows XP. The version which doesn't work is on linux:

    Ubuntu: 12.04
    Firefox: 13.0.1
    Zotero: 3.0.8

    Thanks,
    J
  • adamsmith
    I have it working on exactly that set-up. Any add-ons that you could try disabling? You're using the FF version of Zotero, correct?

    Do you have full-text access to the item - i.e. are you on your university network?
    Or are you using a proxy (in that case - what's the full URL?).
  • fung
    I have the same issue, exactly as John describes it, on Ubuntu 11.10, Firefox 13.0.1, and Zotero 3.0.8. I've tried both enabling and disabling proxies. I have also gone through the troubleshooting suggestions and have checked for incompatible add-ons.
  • adamsmith
    when you say you have checked for incompatible add-ons - that means you have disable _all_ add-ons except Zotero and the Libre Office plugin?
    Also, I'd like another URL and an error report ID - if you look at the report before sending it and post anything that contains "Optical Society of America" here that'd be great (the latter isn't necessary, it just speeds things up - I can't see the error reports, so I have to wait until Dan or Simon posts the content).
  • fung
    All add-ons other than Zotero (I have not installed the Libre Office plugin) have been disabled, but I still get the problem. I submitted error report 1401387347, but the report contained nothing OSA or Optical Society of America related. The URL www.opticsinfobase.org/ol/abstract.cfm?uri=ol-37-14-2772 doesn't work either.
  • adamsmith
    odd, that one, too, works for me. Could you try this again, but this time submit a debug id after trying?
    http://www.zotero.org/support/debug_output
    Also, it looks like it takes a while for the citation to download - so make sure it actually doesn't import in Zotero and the problem isn't just that the box disappears without showing any text.
  • fung
    I've tried a different article and waited for several minutes, but importing from Optics InfoBase still gives the same result. I tried importing this article:

    http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-19-9-8051

    with debug ID D759190982. It also doesn't seem to matter whether I'm trying to import into my personal library, or into a group library (as I was trying to do when the debug report was logged).
  • adamsmith
    Dan, Simon, could you have a look at the debug?
  • dstillman
    (3)(+0000000): Translate: Beginning translation with Optical Society of America

    (3)(+0000000): Translate: Unable to retrieve text for XPath: //meta[@name="citation_conference"]/@content

    (3)(+0000000): Translate: Unable to retrieve text for XPath: //meta[@name="citation_journal_title"]/@content

    (3)(+0000000): Translate: Attempted to load the current document using processDocuments; using loaded document instead

    (3)(+0000000): HTTP GET http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-19-9-8051

    (3)(+0000004): created hidden browser (1)

    (3)(+0001024): HTTP POST articles=211751&ArticleAction=save_endnote2&actions229273=save_endnote2 to http://www.opticsinfobase.org/custom_tags/IB_Download_Citations.cfm

    (3)(+0000136): Translate: Creating translate instance of type import in sandbox

    (4)(+0000001): Translate: Binding sandbox to http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-19-9-8051

    (4)(+0000005): Translate: Parsing code for RIS

    (3)(+0000004): Translate: Beginning translation with RIS

    (5)(+0000003): Translate: Running handler 0 for itemDone

    (3)(+0000000): Translate: Translation successful

    (5)(+0000000): Translate: Running handler 0 for done

    (3)(+0000000): Translate: Translation successful

    (5)(+0000000): Translate: Running handler 0 for done

    (5)(+0000000): Translate: Running handler 1 for done

    (3)(+0000001): deleted hidden browser
  • adamsmith
    sorry, we'll need to run through a couple more rounds of this - it looks like you somehow have a different version of the pages than I'm looking at. Out of curiousity - what's the symbol you see in the URL bar? A book or the article icon (white page with lines?)

    Then, step 2, could you just save the abstract page you're looking at in Firefox (ctrl+s) and make that available to me?

    Finally, step 3, could you download this translator:
    https://gist.github.com/raw/3125235/5b1dd4cc4552b5f793e112c3d0c6d70b10f1cb7f/Optical%20Society%20of%20America.js
    place it into the translator folder of your Zotero data directory
    http://www.zotero.org/support/zotero_data, overwriting the existing file, reload the page and create another round of debug?

    Sorry for the trouble, but I'm working completely blind.
  • fung
    I see the book icon (blue) in the URL bar.

    I have saved the raw HTML of the journal webpage here:

    http://www.physics.harvard.edu/~fung/abstract.cfm.html

    Accompanying files may be found here:

    http://www.physics.harvard.edu/~fung/abstract.cfm_files/

    I've downloaded the OSA translator you put on Github, overwritten the translator previously in the translator directory, and tried importing the same article again, generating debug ID D2099960942.

    Thank you for your help. Is there anything else I should try, or any other tests that I should run?
  • adamsmith
    thanks - Dan, could I get the debug one more time?

    But generally this is baffling.
    The site is exactly what I have, yet for for some reason Zotero doesn't read everything that's on the page - if you look at the debug above:
    "Unable to retrieve text for XPath: //meta[@name="citation_journal_title"]/@content"
    that xpath is right at the top of the page in the metadata.

    Could you try two more things?
    1. Try again with this version of the translator (no new debug needed, just see if it works)
    https://gist.github.com/raw/3125235/b51d6bdc167205dece1b63866718ee332dc8c147/Optical%20Society%20of%20America.js

    If it doesn't - and it probably won't:
    2.
    In both the actual page:
    http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-19-9-8051
    and the page as it comes up from your website:
    http://www.physics.harvard.edu/~fung/abstract.cfm.html

    could you right-click on the icon in the URL bar (i.e. the blue book ath opticsinfobase and what I guess will be an article icon on your site) and see if you can select "Save to Zotero using Embedded Metadata" and if you can try to do that in both cases and see what you get?
  • Simon
    (3)(+0000002): Translate: Beginning translation with Optical Society of America

    (3)(+0000001): Translate: Unable to retrieve text for XPath: //meta[@name="citation_conference"]/@content

    (3)(+0000000): Translate: Unable to retrieve text for XPath: //meta[@name="citation_journal_title"]/@content

    (3)(+0000001): Translate: Attempted to load the current document using processDocuments; using loaded document instead

    (3)(+0000000): HTTP GET http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-19-9-8051

    (3)(+0000004): created hidden browser (1)

    (3)(+0000988): Translate: get: http://www.opticsinfobase.org/custom_tags/IB_Download_Citations.cfm

    (3)(+0000000): Translate: post: articles=211751&ArticleAction=save_endnote2&actions304666=save_endnote2

    (3)(+0000000): HTTP POST articles=211751&ArticleAction=save_endnote2&actions304666=save_endnote2 to http://www.opticsinfobase.org/custom_tags/IB_Download_Citations.cfm

    (3)(+0000121): Translate: RIS: TY - JOUR
    TI - Measuring translational, rotational, and vibrational dynamics in colloids with digital holographic microscopy
    AB - We discuss a new method for simultaneously probing translational, rotational, and vibrational dynamics in dilute colloidal suspensions using digital holographic microscopy (DHM). We record digital holograms of clusters of 1-?m-diameter colloidal spheres interacting through short-range attractions, and we fit the holograms to an exact model of the scattering from multiple spheres. The model, based on the T-matrix formulation, accounts for multiple scattering and near-field coupling. We also explicitly account for the non-asymptotic radial decay of the scattered fields, allowing us to accurately fit holograms recorded with the focal plane located as little as 15 ?m from the particle. Applying the fitting technique to a time-series of holograms of Brownian dimers allows simultaneous measurement of six dynamical modes ? three translational, two rotational, and one vibrational ? on timescales ranging from 10?3 to 1 s. We measure the translational and rotational diffusion constants to a precision of 0.6%, and we use the vibrational data to measure the interaction potential between the spheres to a precision of ?50 nm in separation distance. Finally, we show that the fitting technique can be used to measure dynamics of clusters containing three or more spheres.
    AU - Fung, Jerome
    AU - Martin, K. Eric
    AU - Perry, Rebecca W.
    AU - Kaz, David M.
    AU - McGorty, Ryan
    AU - Manoharan, Vinothan N.
    PB - OSA
    PY - 2011/04/25
    JO - Opt. Express
    JF - Optics Express
    JA - Opt. Express
    VL - 19
    IS - 9
    SP - 8051
    EP - 8065
    KW - Scattering measurements
    KW - Three-dimensional microscopy
    KW - Digital holography
    UR - http://www.opticsexpress.org/abstract.cfm?URI=oe-19-9-8051
    ER -




    (3)(+0000001): Translate: Creating translate instance of type import in sandbox

    (4)(+0000000): Translate: Binding sandbox to http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-19-9-8051

    (4)(+0000005): Translate: Parsing code for RIS

    (3)(+0000007): Translate: Beginning translation with RIS

    (5)(+0000004): Translate: Running handler 0 for itemDone

    (3)(+0000000): Translate: Translation successful

    (5)(+0000000): Translate: Running handler 0 for done

    (3)(+0000000): Translate: Translation successful

    (5)(+0000000): Translate: Running handler 0 for done

    (5)(+0000000): Translate: Running handler 1 for done
  • adamsmith
    Simon - can you see any reason why this would not translate after getting the RIS? This all makes very little sense to me.
  • Simon
    This should now be fixed. Zotero should automatically pull the updated translator within 24 hours. Alternatively, you can click the "Update now" button in the General pane of the` Zotero preferences, and then restart your browser.
  • fung
    It works now -- thank you all very much for your help.
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