Help migrating database

  • Fede

    Fede - 2010-02-20

    I installed manually refbase and its working fine. Even though I can´t install bibutils in my server. This is the error I got:
    Warning: exec() has been disabled for security reasons in /nfs/raven/u1/c/cernuscf/public_html/includes/ on line 131

    This is the answer from our IT guy:
    is referring to the PHP function call exec(), not a filesystem permission. exec() is used to run arbitrary command-line programs from PHP. Due to the security risks, exec() is disabled on the web servers.
    If exec() is required for this software to work, then it won't be possible to run it on his ONID website.

    As far as I understand I will be able to run refbase normally but this will only be a problem to import my preexisting database.

    That data base was build with bibloexpress and I exported into a endnote sitle txt, like this one:

    %A Pérez, A.
    %A Decoud, P.
    %A Carbajal, A.
    %A Rocha, L.
    %T Comportamiento del Acuífero Guaraní en la ciudad de Artigas, Uruguay
    %J I Congreso Mundial Integrado de Aguas Subterráneas. ABAS-ALHSUD
    %D 2000
    %0 Conference Proceedings
    %C Fortaleza, Brasil
    %O Date of Input: 10/02/2006
    %O Priority: Normal

    Is there anyway to import this data base and use refbase as it is now without bibutils?
    It will be a one time import only , then we will add the new references directly into refbase

    thank you


  • Florian

    Florian - 2010-02-22

    I'm a RefBase-User, not a developer, but I think the exec() problem results from the fact that your servers are running a PHP-version greater than 5.2; Ask if its possible to install PHP 5.2 on the server which is running RefBase, and the exec()-Error should go away. If I'm not mistaken there should be another workaround for this problem, which is basically just disabeling the error-messages for this type of error. Try searching this forum - it should be there somewhere…

    For the batch-import thing: did you try the test-database on the refbase homepage and import 10 or so entries with your endnote txt and check if the import-function works?

  • Fede

    Fede - 2010-02-22

    I will try that

  • Richard Karnesky

    The refer/bibix/endnote format cannot be imported into refbase without bibutils.  Have you tried using RIS instead?

  • Fede

    Fede - 2010-02-22

    Didn't tried that yet. I will check.
    But I will probably do is just install refbase in another server that allows me to use bibutils

  • Matthias Steffens

    Hi Fede,

    as Rick noted, it would probably help if you can export to RIS format instead, and import that file.

    Also, as Florian suggested, importing your Endnote data into one of the refbase demo databases (e.g. ), and exporting the data again (in RIS format) might be another option.

    Alternatively, here's another idea: On my local development machine, I have a native function that converts records from Endnote tagged (Endnote Refer) format to refbase. This function may require some further testing before it's ready for a release, but it may actually work well enough with your data. So, if you like, feel free to send me your Endnote data privately (e.g. mail them as a zipped attachment to msteffens -at- refbase -dot- net), and I'll see what I can do.

    HTH, Matthias


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