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bibutils problem

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QL Studio
2012-11-29
2013-05-28
  • QL Studio
    QL Studio
    2012-11-29

    Hi,

    I'm setting refbase up for a client - and have most things working well - however I can't get the exports dependant on bibutils to work.

    I've read all the documentation and many forums topics here which are close, but offer no final solution.

    You can see my phpinfo here: http://refbase-ing.dreamhosters.com/phpinfo.php

    bibutils is installed in a subdirectory insie refbase and the correct reference is in the "depends" table - with a trailing slash.

    I guess from the phpinfo() that I don't need to worry about the location of bibutils in terms of executing code - but I think the problem lies in how this library was installed and perhaps the permissions of the directory and files.

    I read the README in bibutils and executed the required commands in the suggested order to configure, make and install the program - this seemed to complete with error.

    So - could someone please indicate clearly what permissions and under which user the bibutils directory and contained files should have?

    All other export options work - which do not require bibutils - hence my confidence that this is where the problem lies.

    Thanks in advance

    Ray.

     
  • Which version of bibutils are you running?  Have you run other executables on your webhost?  Does import work?  Are you able to look in your logs and your temp directory for any messages and the exported MODS file and any attempted conversions?  By

    configure, make and install the program - this seemed to complete with error.

    did you mean "without" error?  Note that bibutils is downloadable/installable as an executable or a package for most common systems.

    bibutils is typically executed by the webserver user.  So, the directory and utilities must be accessible by that user.  Ditto for the designated temp directory.

    What is the value of the depends_path in the depends table?

     
  • Also note that there could be other access restrictions in place in your host that may prevent executables from running under the web user or prevent access to some of the directories refbase needs.  After you get the problem diagnosed more completely, you may still need to contact your webhosting provider.

     
  • Hi Ray,

    _

    Sorry to hear you're facing so much trouble with the bibutils integration. Just to make sure, I guess import of formats that depend on bibutils (e.g. BibTeX, see http://bibutils.refbase.net/ ) isn't working either?

    Which version of Bibutils are you using? If you're currently using Bibutils v4.x, could you please try Bibutils 3.4 which is still available here:

    http://bibutils.refbase.org/

    and see if this works better.

    I guess you've seen this already, but this troubleshooting advice sums up typical issues related to Bibutils:

    http://www.refbase.net/index.php/Installation-Troubleshooting#Export_of_records_results_in_a_blank_page

    From your description, it sounds as if you've got the bibutils setup in table 'depends' right. However, may I still ask you to post the current contents of your table 'depends', i.e., issue this MySQL command:

    SELECT * FROM depends;

    from within your MySQL command line interpreter, or a web-based MySQL tool such as phpMyAdmin (you may send this information via private mail if you prefer so). See also this forum thread:

    https://sourceforge.net/projects/refbase/forums/forum/218758/topic/3562872

    What is the PHP temp/session directory on your server? Is this accessible and writable by Apache/PHP/Bibutils?

    If you have shell access to the server, can you execute your bibutils tools directly and do they execute successfully? If not, what is the error message on STDOUT?

    W.r.t. permissions for Bibutils: Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x--), and the Bibutils programs should have permissions 755 (rwxr-xr-x). See http://bibutils.refbase.net/

    Matthias
    _

     
  • Knut Krüger
    Knut Krüger
    2012-11-30

    I do not know what the disadvantage (if you have root privileges) from installing bibutlis with  apt-get install bibutils (debian) but is its working without any problem just putting the path (dpkg -L bibutils) with the sql command

    UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";
    

    into the database and enable bibutils wiht

    UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";
    

    and everything is working fine.

    Maybe Matthias or Richard can tell us more why it is better to install it local.

    Knut

     
  • Yes: in general, system-wide installs of bibutils work well.  They actually get around some security packages that limit the directories that executables can be installed to. However, (i) many people don't have root access & can't make system-wide installs and (ii) oftentimes, this won't put executables in a safe_mode_exec directory.