Cannot import from Biomed Central - Genome Biology

sfyoung
The translator doesn't work for citations from Genome Biology at

http://genomebiology.com/2009/10/3/R25
  • adamsmith
    http://www.zotero.org/support/troubleshooting_translator_issues?s[]=translator
    note the instructions at the bottom wtr to report ID and also check #5
  • sfyoung
    I tried again to download the citation from Genome Biology at the URL,
    http://genomebiology.com/2009/10/3/R25. The tooltip said the translator should be "BioMed Central and more". I submitted my error log and got the Report ID 1565072607. I have not found any other reference to problems with that translator in the Zotero Forum. I am running Ubuntu Linux, Firefox 3.6.16 and I just installed the updated Zotero add-on, 2.1.15 I think.
  • ajlyon
    It looks like BMC has switched to a new format on some sites, and not on others. I managed to get it working on Genome Biology, but that broke it for some other sites... This will take some more work.
  • lparsons
    This still appears to be an issue, any suggestions on a workaround or even how to start working on a fix?
  • ajlyon
    I think I have a fix for this-- part of it I already committed to the repository, so first hit "Update Translators" in the Zotero prefs. Then, go to http://github.com/ajlyon/translators/raw/master/BioMed Central and More.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 it chokes on some BMC pages, let me know the URLs. It doesn't yet do full text, but I'll add that once I can confirm that the basic approach is working.
  • ajlyon
    This has been refined somewhat and is now in the main repository, including support for more metadata (pages, DOIs, ISSNs), as well as PDFs. Update translators from the Zotero prefs or wait 24 hours to receive the new version automatically.
  • VHaring
    Just installed Zotero (v3.0b2) on FF v 7.0.1 and can't import the following refrence from Biomed Central: http://www.biomedcentral.com/1471-2105/9/386
    Other papers from the same journal give the same error, but import from other journals work fine.
    The error reports says:
    [JavaScript Error: "cyclic object value" {file: "chrome://zotero/content/xpcom/translation/translate.js" line: 233}]
    and was reported with report ID 1791371420.
  • adamsmith
    edited November 2, 2011
    just to clarify - you're using the Firefox version of Zotero, correct?

    This should work, but for me this one actually completely crashes Firefox. crashes Zotero (an error has occured, please restart Firefox...).
  • VHaring
    Yes, it is the Firefox version and not the stand-alone.

    Luckily for me it does not crash my Firefox, just gives me the "Could not save item" message.
  • ajlyon
    That's not supposed to be possible, but I get the same error as adamsmith. This will be looked into ASAP.

    Error (Zotero 3.0b2, Firefox 7, Ubuntu 11.10):
    [JavaScript Error: "[Exception... "Component returned failure code: 0x80630003 (NS_ERROR_STORAGE_CONSTRAINT) [mozIStorageStatement.execute]" nsresult: "0x80630003 (NS_ERROR_STORAGE_CONSTRAINT)" location: "JS frame :: chrome://zotero/content/xpcom/db.js :: <TOP_LEVEL> :: line 139" data: no] [QUERY: INSERT OR IGNORE INTO collectionItems VALUES (?,?,?)] [ERROR: insert on table "collectionItems" violates foreign key constraint "fki_collectionItems_itemID_items_itemID"]"]

    [JavaScript Error: "uncaught exception: [Exception... "Component returned failure code: 0x80630003 (NS_ERROR_STORAGE_CONSTRAINT) [mozIStorageStatement.execute]" nsresult: "0x80630003 (NS_ERROR_STORAGE_CONSTRAINT)" location: "JS frame :: chrome://zotero/content/xpcom/db.js :: <TOP_LEVEL> :: line 139" data: no] [QUERY: INSERT INTO itemAttachments (itemID, sourceItemID, linkMode, mimeType, charsetID, path, syncState) VALUES (?,?,?,?,?,?,?)] [ERROR: insert on table "itemAttachments" violates foreign key constraint "fki_itemAttachments_sourceItemID_items_sourceItemID"]"]

    [JavaScript Error: "uncaught exception: [Exception... "Component returned failure code: 0x80630003 (NS_ERROR_STORAGE_CONSTRAINT) [mozIStorageStatement.execute]" nsresult: "0x80630003 (NS_ERROR_STORAGE_CONSTRAINT)" location: "JS frame :: chrome://zotero/content/xpcom/db.js :: <TOP_LEVEL> :: line 139" data: no] [QUERY: INSERT INTO itemAttachments (itemID, sourceItemID, linkMode, mimeType, charsetID, path, syncState) VALUES (?,?,?,?,?,?,?)] [ERROR: insert on table "itemAttachments" violates foreign key constraint "fki_itemAttachments_sourceItemID_items_sourceItemID"]"]
  • adamsmith
    (same error message, also FF 7, in may case Ubuntu 11.04
  • ajlyon
    I think I know what's happening here-- it has to do with the change to the Embedded RDF translator, which Biomed was using. Now we're getting a bogus attachment that's causing issues when it saves. Workaround forthcoming, but this should probably be debugged more deeply, since translators shouldn't be able to trigger (non-destructive, yet annoying) errors like this.
  • VHaring
    My reported error message was from my work computer running Windows XP. As this report looks different to yours on Ubuntu, I gave it another shot at home using Fedora 14 and FF 3.6.23. Again a slightly different error message, but no crash:

    [JavaScript Error: "Component is not available" {file: "chrome://zotero/content/xpcom/translation/translate.js" line: 233}]

    If I read the error messages right, in both OSs I tested, the error points to the same line in the same script (chrome://zotero/content/xpcom/translation/translate.js), whereas for you, the error points to a different script (chrome://zotero/content/xpcom/db.js). Unfortunately, I'm not a "coding nut" who could make sense out of these observations, but it might help someone else to find an answer.

    Another observation, when I first installed the "current" version (2.1.10) on Fedora and tried to import that reference, not much happened: an empty red box appeared in the lower left corner - the nothing. No imported reference, no error message. Only after upgrading to the beta version, the error message appeared.
  • viktiglemma
    I cannot store this genome biology paper:
    http://genomebiology.com/2003/4/7/223/abstract

    The workaround is to go to a linking site, but then no pdf will be saved.
  • adamsmith
    we currently don't have a working translator that would get a pdf for that - so the best you'll get is the data without the pdf. If you're using Zotero for FF you can also get that by right-clicking on the icon in the URL bar and selecting "Save to Zotero using Embedded Metadata".
  • aurimas
    I updated the Springer Science+Business Media translator to recognize that site and fixed the PDF import. It will update on your machine automatically within 24 hours or you can update manually from Zotero preferences.

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