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Bibutils export problem

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Michał L.
2011-05-18
2013-05-28
  • Michał L.
    Michał L.
    2011-05-18

    Hi

    I always get empty file when exporting to bibtex. Export to other formats (Atom XML, MODS XML) seem to work fine.

    - Refbase is installed in home dir in /home/user/public_html/refbase

    - Bibutils installation is in /home/user/public_html/refbase/bibutils (compiled and installed from source version 3.40) and seems to work fine from commandline.

    - Apache has read and execute rights for all files in /home/user/public_html/refbase (including bibutils dir - actually everything has 0755 rights).

    - I tested that PHP can run other programs from /home/user/public_html/refbase/bibutils directory by invoking exec function

    - safe_mode for apache is set to "Off".

    - PHP session directory is located somewhere in /var and obviously is writable by Apache (I guess many other things wouldn't work if it wasn't?).

    - the server runs Red Hat Linux 64bit

    - all values in database seem to be set correctly:

    mysql> SELECT * FROM depends;                              
    +--------+------------+-----------+------------------------------+
    | depends_id | depends_external | depends_enabled | depends_path                                |
    +--------+------------+-----------+------------------------------+
    |          1 | refbase          | true            | NULL                                        |
    |          2 | bibutils         | true            | /home/user/public_html/refbase/bibutils/ |
    |          3 | pdftotext        | true            | NULL                                        |
    +--------+------------+-----------+------------------------------+

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

    What else am I missing?

     
  • What does your error log tell you?  Can you export to any other bibutils formats?  Can you import from formats that require bibutils?

     
  • Michał L.
    Michał L.
    2011-05-18

    There is nothing in php.log. log_errors option in php.ini is "On".
    Maybe the permissions are set incorrectly (only root can write to php.log)? I'm not the admin, but I can ask him to fix it…

    I tried to import this http://beta.refbase.net/show.php?record=11442&exportType=file&submit=Export&exportFormat=BibTeX and failed with:
    "There were validation errors regarding the data you entered:"

     
  • It varies from system to system, but errors are often in apache's error log (e.g. '/var/log/httpd-error.log' on FreeBSD).  Further, you need to make sure you're logging all warnings/notices/errors.

    "There were validation errors regarding the data you entered:"

    That's very different than failing with a blank screen.  You should get an additional error message near the records box that tells you what is wrong….

     
  • Michał L.
    Michał L.
    2011-05-18

    Yeah, I got logs (knew were it was but permissions were wrong) - there is only one message for each failed bibtex export attempt:

    PHP Warning:  htmlspecialchars() : Invalid multibyte sequence in argument in /home/mlenart/public_html/refbase/includes/include.inc.php on line 5442

    "There were validation errors regarding the data you entered:"
    That's very different than failing with a blank screen.  You should get an additional error message near the records box that tells you what is wrong….

    That's all I've got: http://chopin.ipipan.waw.pl/~mlenart/screen.png
    Nothing corresponding to this error in php.log.

     
  • Michał L.
    Michał L.
    2011-05-19

    And by the way - I use SVN (trunk) version of refbase with UTF-8 database and html encoding.

     
  • Michał L.
    Michał L.
    2011-05-25

    Ok, it works now. It appears that refbase couldn't write temp files to /var/lib/php/session (however permissions were ok. Maybe some evil SELinux settings?). I edited execute.inc.php to write these files to "/tmp" instead (maybe it could be configurable option?).

    Thanks anyway.

     
  • session.save_path is taken for granted by a lot of webapps & so I don't know if another option is really the right thing to do.  You might be able to work around this on your system by using an .htaccess file with:

    php_value session.save_path '/tmp'