JabRef to Zotero!

sandhya.sekar
I started with the same problem faced with a lot of people who have already posted on this forum, but inspite of employing the troubleshooting suggested, I am unable to resolve the issue - if I export a library from JabRef to Zotero, the pdf and external files are lost; moreover, the sub-groups I have made in JabRef are not getting transferred.

I am not a programmer, so you can understand if I say I have spent too much time to understand even the basic stuff. I am really eager to migrate to zotero, so please try and help.

I have the latest versions of both.
I have tried the following fixes:

http://forums.zotero.org/discussion/6426/smooth-migration-from-jabref-to-zotero/

and some more that are already present on your forum (I found this fix the asiest to follow!).
In this fix, noksagt recommends using a patch given in https://www.zotero.org/trac/ticket/1514
I dont know how to use the .diff file presented!

So is there any way for a 'really smooth' migration from JabRef to Zotero? Can someone please lay it out stepwise for me?

Thanks a ton

Sandhya
  • noksagt
    if I export a library from JabRef to Zotero, the pdf and external files are lost;
    This should work. Can you provide an example of a single record that this fails on?
    moreover, the sub-groups I have made in JabRef are not getting transferred.
    Zotero does not import group information from BibTeX. AFAIK, this is peculiar to JabRef. If you have a limited number of groups, you can work around this by exporting each group and importing it into zotero individually.
    In this fix, noksagt recommends using a patch given in https://www.zotero.org/trac/ticket/1514
    This has already been applied to the translator (more than a year ago).
  • sandhya.sekar
    edited August 30, 2010
    Got it with the groups idea - I was thinking the same, I just thought there may be a neater way of doing the same.
    So I have tried a RIS import and importing via the zotero.layout method suggested in the link I gave above. Here they are:
    Note: I have not mentioned the abstract in full in all cases.

    RIS:
    With RIS, I get the following error:
    "Could not save item: A Zotero operation is currently in progress. Please wait until it has finished and try again."
    After which, Firefox hangs and has to be re-started. After re-starting, there is a folder in zotero under My Library titled "Imported <day, date, time>" but the folder is empty.

    TY - JOUR
    AU - Aegisdottir, Hafdis Hanna
    AU - Kuss, Patrick
    AU - Stocklin, Jurg
    T1 - Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation
    JO - Ann Bot
    Y1 - 2009/12
    VL - 104
    IS - 7
    SP - 1313
    EP - 1322
    UR - http://aob.oxfordjournals.org/cgi/content/abstract/104/7/1313
    L1 - D:\PDFs\butterflies general\Aegisdottir2009.pdf
    N1 - Owner: Sandy
    N1 - Added to JabRef: 2010.03.05
    N2 - <abstract>

    zotero.layout:
    So when I try with the zotero.layout export filter, I get the following error.
    "An error occurred while trying to import the selected file. Please ensure that the file is valid and try again."
    Strangely enough, the first entry is imported (without a pdf, or any external link, or notes attached though). So, I have pasted the first two entries, just to make things clear.

    =========Filter Content============
    @Article{Aegisdottir2009,
    author = {Aegisdottir, Hafdis Hanna and Kuss, Patrick and Stocklin, Jurg},
    title = {Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation},
    journal = {Ann Bot},
    year = {2009},
    volume = {104},
    pages = {1313--1322},
    number = {7},
    url = {http://aob.oxfordjournals.org/cgi/content/abstract/104/7/1313},
    pdf = { PDFsbutterflies general009.pdf },
    owner = {Sandy},
    abstract = {---}
    }=========Filter Content============
    @Article{Althoff2007,
    author = {Althoff, DM},
    title = {The utility of Amplified Fragment Length Polymorphisms in phylogenetics: a comparison of homology within and between genomes},
    journal = {Systematic Biology},
    year = {2007},
    volume = {56},
    pages = {477--484},
    number = {3},
    pdf = { PDFsbutterflies general007.pdf },
    publisher = {Taylor \& Francis},
    owner = {Sandy},
    abstract = {--},

    Thanks again
    Sandhya
  • noksagt
    So I have tried a RIS import and importing via the zotero.layout method suggested in the link I gave above.
    What about the standard BibTeX produced by JabRef? That being said, the RIS imports for me. I didn't check that an attached file is imported (not on windows at the moment), but it looks fine. Both BibTeX entries also import for me, but note that the pdf line does not have a full path to the files & so Zotero would have no way to know where those files are.
  • sandhya.sekar
    The standard BibTex produced by JabRef (BibTeXML) is not recognized by zotero. I dont know if there is something wrong that I am doing here. Again, one entry gets imported inspite of the error message.
    I tried the zotero.layout I explained earlier after I re-installed zotero; but the problem persists.
    The RIS is still making firefox hang.

    I dont know what else I can try!

    Thanks for your time anyway.

    Sandhya
  • adamsmith
    for whatever reason ris import sometimes gets hung up on the file extension.
    Try renaming the file extension from .ris to .txt and try again.
    Don't ask me why, but that has worked for some people.
  • noksagt
    BibTeXML is not the same as BibTeX. Use the 'save' feature of jabref to produce a .bib file.
  • sandhya.sekar
    @ adamsmith: Tried that! Imports only one entry. Without the pdf attached.

    @ noksagt: I tried that as well. Error message:
    An error occurred while trying to import the selected file. Please ensure that the file is valid and try again.

    And, it imports one entry after that without the pdf attached.
  • nerdgirl
    edited September 2, 2010
    I'm also new to Zotero, and trying to do the exact same thing -- import not only the references in my JabRef library, but also import the links to the files. I've got over 300 PDFs in my library so far, and I'm sure it's going to grow considerably more. Therefore, linking the files to their respective entries promises to be a real pain.

    Is there a good way to speed or automate this process, or to get my old reference manager to include a full path to the linked file that Zotero can use?

    I'm using Ubuntu Linux 10.04, Firefox (obviously) 3.6.8, and plan to link Zotero to OpenOffice 3.2.0.10 (IIRC), and JabRef 2.5, once I get this whole thing working. (The reason I'm trying to switch from JabRef in the first place is that it's disrupting my Autocorrect settings, so it's do my bibliography by hand, type out species and strain names with correct italicization and greek letters a million times by hand, or find something that actually works.)
    ETA: The link in the first post allows me to import 5 entries, then throws an error and imports the sixth without the PDF link.
  • noksagt
    @sandhya.sekar
    An error occurred while trying to import the selected file. Please ensure that the file is valid and try again.
    Had you been getting this before? You do not describe it in your original message. See http://www.zotero.org/support/troubleshooting_translator_issues and also try to import a subset of your database to confirm that the BibTeX translator is working for you and to isolate any individual records that might cause it to fail.

    @nerdgirl
    The link in the first post allows me to import 5 entries, then throws an error and imports the sixth without the PDF link.
    I don't see why the link in the first post should be necessary. The current version of the Zotero importer can import the file links generated by the current version of JabRef. What do the file links in your JabRef-managed BibTeX file look like? What error is thrown?
    Is there a good way to...get my old reference manager to include a full path to the linked file that Zotero can use?
    Feel free to show what your file looks like now, but issues concerning JabRef export are better answered by JabRef support.
  • pobrien86
    I get an error as well. Case 1: bibtex file with single entry from jabref, freshly created in Jabref 2.6, with both url and pdf (file field) links.

    report ID: 1706356244

    [JavaScript Error: "Error getting file from attachment path: file://D\" {file: "chrome://zotero/content/xpcom/translate.js" line: 1414}]

    [JavaScript Error: "[Exception... "Component returned failure code: 0x80004005 (NS_ERROR_FAILURE) [nsIFileURL.file]" nsresult: "0x80004005 (NS_ERROR_FAILURE)" location: "JS frame :: chrome://zotero/content/xpcom/translate.js :: anonymous :: line 1405" data: no]" {file: "file:///D:/Documents/Zotero/translators/BibTeX.js" line: 0}]

    [JavaScript Error: "Collection 2 not found" {file: "chrome://zotero/content/xpcom/search.js" line: 432}]

    HERE is the bibtex:
    % This file was created with JabRef 2.6.
    % Encoding: Cp1252

    @ARTICLE{ni2007graphene,
    author = {Ni, ZH and Wang, HM and Kasim, J. and Fan, HM and Yu, T. and Wu,
    YH and Feng, YP and Shen, ZX},
    title = {Graphene thickness determination using reflection and contrast spectroscopy},
    journal = {Nano Lett},
    year = {2007},
    volume = {7},
    pages = {2758--2763},
    number = {9},
    doi = {10.1021/nl071254m},
    file = {:D\:\\nl071254m.pdf:PDF},
    owner = {Peter},
    publisher = {ACS Publications},
    timestamp = {2010.10.21},
    url = {http://pubs.acs.org/doi/abs/10.1021/nl071254m}
    }

    @comment{jabref-meta: selector_publisher:}

    @comment{jabref-meta: selector_author:}

    @comment{jabref-meta: selector_journal:}

    @comment{jabref-meta: selector_keywords:}


    CASE 2: export a single file to bibtex from Mendeley, with pdf link.

    Report ID 1029717620

    nearly identical result. Both .bib files use the exact same file field format. From a little reading this is a well known issue and it appeared to have been 'fixed' and yet the translate.js file hasn't been updated in 15 months and people are still having issues?
  • noksagt
    edited October 21, 2010
    I'm responsible for adding the ability to import the different styles of links & I'm on Linux. I had not encountered a windows-formatted file link as in your file or the specific error that you encountered (and you seem to be the first one in this thread to post either). Thanks for your report. I believe the error is probably in parsing\:used to denote the drive letter. An easy fix would to replace that with:|
  • eichler
    I tried your recommendation but it does not work. The following file (using windows and zotero 2.0.9) works if I remove the file entry:

    % This file was created with JabRef 2.6.
    % Encoding: UTF8

    @TECHREPORT{Dimkov2009Portunes:,
    author = {T. Dimkov and W. Pieters and P. H. Hartel},
    title = {Portunes: generating attack scenarios by finding inconsistencies
    between security policies in the physical, digital and social domain},
    year = {2009},
    type = {Technical Report},
    number = {TR-CTIT-09-15},
    address = {Enschede},
    month = {April},
    crossref = {Dimkov2008},
    eprintid = {15308},
    file = {:Ablage\\Dimkov et al (2009) - Portunes - generating attac scenarios by finding inconsistencies.pdf:PDF},
    howpublished = {http://eprints.eemcs.utwente.nl/15308/},
    issn = {1381-3625},
    keywords = {insider threat, physical security, security awareness, security model},
    num_pages = {17},
    publisher = {Centre for Telematics and Information Technology, University of Twente},
    research_groups = {EWI-DIES: Distributed and Embedded Security, EWI-IS: Information Systems},
    research_programs = {CTIT-ISTRICE: Integrated Security and Privacy in a Networked World},
    research_projects = {VISPER: The VIrtual Security PERimeter for digital, physical, and
    organisational security}
    }
  • noksagt
    Relative paths are not yet supported.
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